From af8f245f489de21bce9fb08f0fd8fd7a55efd9d5 Mon Sep 17 00:00:00 2001 From: Sinan Date: Fri, 20 Sep 2019 17:52:11 -0700 Subject: [PATCH 001/499] py-protobuf package: fix import error for Python 2.x (#12873) --- var/spack/repos/builtin/packages/py-protobuf/package.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py index 8730b265f7c..c23029faa11 100644 --- a/var/spack/repos/builtin/packages/py-protobuf/package.py +++ b/var/spack/repos/builtin/packages/py-protobuf/package.py @@ -42,3 +42,11 @@ def build_args(self, spec, prefix): def install_args(self, spec, prefix): args = super(PyProtobuf, self).install_args(spec, prefix) return args + ['--cpp_implementation'] + + @run_after('install') + def fix_import_error(self): + if str(self.spec['python'].version.up_to(1)) == '2': + touch = which('touch') + touch(self.prefix + '/' + + self.spec['python'].package.site_packages_dir + + '/google/__init__.py') From e26b23e9806f02f8f0d1c32f7f669bf35235dff3 Mon Sep 17 00:00:00 2001 From: t-karatsu Date: Fri, 20 Sep 2019 15:58:07 +0900 Subject: [PATCH 002/499] intel-tbb: fix typo. --- var/spack/repos/builtin/packages/intel-tbb/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py index c69ac29eb96..7c3eb7d937f 100644 --- a/var/spack/repos/builtin/packages/intel-tbb/package.py +++ b/var/spack/repos/builtin/packages/intel-tbb/package.py @@ -124,7 +124,7 @@ def coerce_to_spack(self, tbb_build_subdir): if l.strip().startswith("CPLUS ="): of.write("# coerced to spack\n") of.write("CPLUS = $(CXX)\n") - elif l.strip().startswith("CPLUS ="): + elif l.strip().startswith("CONLY ="): of.write("# coerced to spack\n") of.write("CONLY = $(CC)\n") else: From 326c2718d5bd5cd954e4512e0e476141705e3f1b Mon Sep 17 00:00:00 2001 From: Sinan Date: Fri, 20 Sep 2019 17:59:50 -0700 Subject: [PATCH 003/499] New package: py-gast (#12874) --- .../repos/builtin/packages/py-gast/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-gast/package.py diff --git a/var/spack/repos/builtin/packages/py-gast/package.py b/var/spack/repos/builtin/packages/py-gast/package.py new file mode 100644 index 00000000000..086bb7af8bf --- /dev/null +++ b/var/spack/repos/builtin/packages/py-gast/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyGast(PythonPackage): + """Python AST that abstracts the underlying Python version""" + + homepage = "https://github.com/serge-sans-paille/gast" + url = "https://pypi.io/packages/source/g/gast/gast-0.3.2.tar.gz" + + version('0.3.2', sha256='5c7617f1f6c8b8b426819642b16b9016727ddaecd16af9a07753e537eba8a3a5') + + depends_on('py-setuptools', type='build') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) From d9c22e3f9c26fb989c18062f84eaa69d7809a059 Mon Sep 17 00:00:00 2001 From: Jordan Ogas Date: Fri, 20 Sep 2019 19:01:40 -0600 Subject: [PATCH 004/499] charliecloud package: add version 0.11 and test dependency (#12861) --- var/spack/repos/builtin/packages/charliecloud/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py index 5964333bf3c..3f91686f86f 100644 --- a/var/spack/repos/builtin/packages/charliecloud/package.py +++ b/var/spack/repos/builtin/packages/charliecloud/package.py @@ -14,6 +14,7 @@ class Charliecloud(MakefilePackage): git = "https://github.com/hpc/charliecloud.git" version('master', branch='master') + version('0.11', sha256='942d3c7a74c978fd7420cb2b255e618f4f0acaafb6025160bc3a4deeb687ef3c') version('0.10', sha256='5cf00b170e7568750ca0b828c43c0857c39674860b480d757057450d69f1a21e') version('0.9.10', sha256='44e821b62f9c447749d3ed0d2b2e44d374153058814704a5543e83f42db2a45a') version('0.9.9', sha256='2624c5a0b19a01c9bca0acf873ceeaec401b9185a23e9108fadbcee0b9d74736') @@ -40,6 +41,9 @@ class Charliecloud(MakefilePackage): depends_on('py-sphinx', type='build', when='+docs') depends_on('py-sphinx-rtd-theme', type='build', when='+docs') + # bash automated testing harness (bats) + depends_on('bats@0.4.0', type='test') + def url_for_version(self, version): if version >= Version('0.9.8'): url = "https://github.com/hpc/charliecloud/releases/download/v{0}/charliecloud-{0}.tar.gz" From ef652ee42ad425c58c711a848d8c3af946281565 Mon Sep 17 00:00:00 2001 From: Paul Date: Fri, 20 Sep 2019 19:14:41 -0600 Subject: [PATCH 005/499] czmq package: add autoreconf stage (#12846) --- var/spack/repos/builtin/packages/czmq/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index 88ab33005a7..8070b891ba5 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -22,6 +22,10 @@ class Czmq(AutotoolsPackage): depends_on("libuuid") depends_on('zeromq') + def autoreconf(self, spec, prefix): + autogen = Executable('./autogen.sh') + autogen() + def configure_args(self): config_args = [] if 'clang' in self.compiler.name: From 7a1dd517b8470ac3e01ff41075a076ef8aad5e44 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 21 Sep 2019 15:47:34 -0700 Subject: [PATCH 006/499] externals: avoid importing requests in jsonschema Spack doesn't need `requests`, and neither does `jsonschema`, but `jsonschema` tries to import it, and it'll succeed if `requests` is on your machine (which is likely, given how popular it is). This commit removes the import to improve Spack's startup time a bit. On a mac with SSD, the import of requests is ~28% of Spack's startup time when run as `spack --print-shell-vars sh,modules` (.069 / .25 seconds), which is what `setup-env.sh` runs. On a Linux cluster where Python is mounted from NFS, this reduces `setup-env.sh` source time from ~1s to .75s. Note: This issue will be eliminated if we upgrade to a newer `jsonschema` (we'd need to drop Python 2.6 for that). See https://github.com/Julian/jsonschema/pull/388. --- lib/spack/external/jsonschema/validators.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/lib/spack/external/jsonschema/validators.py b/lib/spack/external/jsonschema/validators.py index 3e326844f4c..30c35153980 100644 --- a/lib/spack/external/jsonschema/validators.py +++ b/lib/spack/external/jsonschema/validators.py @@ -4,10 +4,7 @@ import json import numbers -try: - import requests -except ImportError: - requests = None +requests = None from jsonschema import _utils, _validators from jsonschema.compat import ( From 53ab298e88f80454f7f7c20ef200a3dbd0870473 Mon Sep 17 00:00:00 2001 From: Xavier Delaruelle Date: Sun, 22 Sep 2019 04:32:27 +0200 Subject: [PATCH 007/499] environment-modules: add version 4.3.1 (#12893) --- .../repos/builtin/packages/environment-modules/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py index af46a326cfd..3f47fa8c2b1 100644 --- a/var/spack/repos/builtin/packages/environment-modules/package.py +++ b/var/spack/repos/builtin/packages/environment-modules/package.py @@ -12,10 +12,11 @@ class EnvironmentModules(Package): """ homepage = 'https://cea-hpc.github.io/modules/' - url = 'https://github.com/cea-hpc/modules/releases/download/v4.3.0/modules-4.3.0.tar.gz' + url = 'https://github.com/cea-hpc/modules/releases/download/v4.3.1/modules-4.3.1.tar.gz' maintainers = ['xdelaruelle'] + version('4.3.1', sha256='979efb5b3d3c8df2c3c364aaba61f97a459456fc5bbc092dfc02677da63e5654') version('4.3.0', sha256='231f059c4109a2d3028c771f483f6c92f1f3689eb0033648ce00060dad00e103') version('4.2.5', sha256='3375b454568e7bbec7748cd6173516ef9f30a3d8e13c3e99c02794a6a3bc3c8c') version('4.2.4', sha256='416dda94141e4778356e2aa9ba8687e6522a1eb197b3caf00a82e5fa2707709a') From b4e148b5623e8b6506a390a42c70c538a7d840d5 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sun, 22 Sep 2019 07:43:57 -0700 Subject: [PATCH 008/499] externals: add note to jsonschema about modifications (#12895) --- lib/spack/external/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/spack/external/__init__.py b/lib/spack/external/__init__.py index e7d1baaf195..f791bc3067c 100644 --- a/lib/spack/external/__init__.py +++ b/lib/spack/external/__init__.py @@ -55,7 +55,9 @@ * Usage: An implementation of JSON Schema for Python. * Version: 2.4.0 (last version before functools32 dependency was added) * Note: functools32 doesn't support Python 2.6 or 3.0, so jsonschema - cannot be upgraded any further + cannot be upgraded any further until we drop 2.6. + Also, jsonschema/validators.py has been modified NOT to try to import + requests (see 7a1dd517b8). markupsafe ---------- From 27d4e9a1d1e869bf6567deef56bda4fb70e46e5e Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Mon, 23 Sep 2019 13:04:29 -0400 Subject: [PATCH 009/499] QT package: only enable fontconfig when freetype is enabled (#12574) The 'fontconfig' option is only valid when freetype is enabled. --- var/spack/repos/builtin/packages/qt/package.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 8b192de89fe..c67b6a76af5 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -149,7 +149,7 @@ class Qt(Package): # Non-macOS dependencies and special macOS constraints if MACOS_VERSION is None: - depends_on("fontconfig") + depends_on("fontconfig", when='freetype=spack') depends_on("libx11") depends_on("libxcb") depends_on("libxkbcommon") @@ -318,6 +318,9 @@ def common_config_args(self): '-system-freetype', '-I{0}/freetype2'.format(self.spec['freetype'].prefix.include) ]) + if not MACOS_VERSION: + config_args.append('-fontconfig') + elif self.spec.variants['freetype'].value == 'qt': config_args.append('-qt-freetype') else: @@ -347,9 +350,6 @@ def common_config_args(self): if self.spec.satisfies('@5.7:'): config_args.append('-system-doubleconversion') - if not MACOS_VERSION: - config_args.append('-fontconfig') - if '@:5.7.1' in self.spec: config_args.append('-no-openvg') else: From 08e77e1b41738abda7613247c7fcf64734c70039 Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Mon, 23 Sep 2019 10:18:50 -0700 Subject: [PATCH 010/499] tests: more template creation tests (#12882) Addresses #12804 This PR adds the creation of the remaining (16) templates to ensure we can create them with expected content. The goal is to facilitate catching during testing. --- lib/spack/spack/test/cmd/create.py | 58 +++++++++++++++++++++++++----- 1 file changed, 50 insertions(+), 8 deletions(-) diff --git a/lib/spack/spack/test/cmd/create.py b/lib/spack/spack/test/cmd/create.py index 030140c74e1..27d2b252bb1 100644 --- a/lib/spack/spack/test/cmd/create.py +++ b/lib/spack/spack/test/cmd/create.py @@ -24,23 +24,65 @@ def parser(): return prs -@pytest.mark.parametrize('args,name_index,expected', [ - (['test-package'], 0, [r'TestPackage(Package)', r'def install(self']), - (['-n', 'test-named-package', 'file://example.tar.gz'], 1, +@pytest.mark.parametrize('args,name,expected', [ + # Basic package cases + (['test-package'], 'test-package', + [r'TestPackage(Package)', r'def install(self']), + (['-n', 'test-named-package', 'file://example.tar.gz'], + 'test-named-package', [r'TestNamedPackage(Package)', r'def install(self']), - (['file://example.tar.gz'], -1, + (['file://example.tar.gz'], 'example', [r'Example(Package)', r'def install(self']), - (['-t', 'bundle', 'test-bundle'], 2, [r'TestBundle(BundlePackage)']) + + # Template-specific cases + (['-t', 'autoreconf', 'test-autoreconf'], 'test-autoreconf', + [r'TestAutoreconf(AutotoolsPackage)', r"depends_on('autoconf", + r'def autoreconf(self', r'def configure_args(self']), + (['-t', 'autotools', 'test-autotools'], 'test-autotools', + [r'TestAutotools(AutotoolsPackage)', r'def configure_args(self']), + (['-t', 'bazel', 'test-bazel'], 'test-bazel', + [r'TestBazel(Package)', r"depends_on('bazel", r'bazel()']), + (['-t', 'bundle', 'test-bundle'], 'test-bundle', + [r'TestBundle(BundlePackage)']), + (['-t', 'cmake', 'test-cmake'], 'test-cmake', + [r'TestCmake(CMakePackage)', r'def cmake_args(self']), + (['-t', 'intel', 'test-intel'], 'test-intel', + [r'TestIntel(IntelPackage)', r'setup_environment']), + (['-t', 'makefile', 'test-makefile'], 'test-makefile', + [r'TestMakefile(MakefilePackage)', r'def edit(self', r'makefile']), + (['-t', 'meson', 'test-meson'], 'test-meson', + [r'TestMeson(MesonPackage)', r'def meson_args(self']), + (['-t', 'octave', 'test-octave'], 'octave-test-octave', + [r'OctaveTestOctave(OctavePackage)', r"extends('octave", + r"depends_on('octave"]), + (['-t', 'perlbuild', 'test-perlbuild'], 'perl-test-perlbuild', + [r'PerlTestPerlbuild(PerlPackage)', r"depends_on('perl-module-build", + r'def configure_args(self']), + (['-t', 'perlmake', 'test-perlmake'], 'perl-test-perlmake', + [r'PerlTestPerlmake(PerlPackage)', r"depends_on('perl-", + r'def configure_args(self']), + (['-t', 'python', 'test-python'], 'py-test-python', + [r'PyTestPython(PythonPackage)', r"depends_on('py-", + r'def build_args(self']), + (['-t', 'qmake', 'test-qmake'], 'test-qmake', + [r'TestQmake(QMakePackage)', r'def qmake_args(self']), + (['-t', 'r', 'test-r'], 'r-test-r', + [r'RTestR(RPackage)', r"depends_on('r-", r'def configure_args(self']), + (['-t', 'scons', 'test-scons'], 'test-scons', + [r'TestScons(SConsPackage)', r'def build_args(self']), + (['-t', 'sip', 'test-sip'], 'py-test-sip', + [r'PyTestSip(SIPPackage)', r'def configure_args(self']), + (['-t', 'waf', 'test-waf'], 'test-waf', + [r'TestWaf(WafPackage)', r'configure_args()']) ]) -def test_create_template(parser, mock_test_repo, args, name_index, expected): +def test_create_template(parser, mock_test_repo, args, name, expected): """Test template creation.""" repo, repodir = mock_test_repo constr_args = parser.parse_args(['--skip-editor'] + args) spack.cmd.create.create(parser, constr_args) - pkg_name = args[name_index] if name_index > -1 else 'example' - filename = repo.filename_for_package_name(pkg_name) + filename = repo.filename_for_package_name(name) assert os.path.exists(filename) with open(filename, 'r') as package_file: From 958b81a5649c0bef525ef7cd55f405606ff66c17 Mon Sep 17 00:00:00 2001 From: Jed Brown Date: Mon, 23 Sep 2019 11:38:44 -0600 Subject: [PATCH 011/499] libceed package: add version 0.5 (#12875) Also enable vectorization via -O3 for gcc/clang --- var/spack/repos/builtin/packages/libceed/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/libceed/package.py b/var/spack/repos/builtin/packages/libceed/package.py index ecce991e8fc..5eb11a6ef8d 100644 --- a/var/spack/repos/builtin/packages/libceed/package.py +++ b/var/spack/repos/builtin/packages/libceed/package.py @@ -13,6 +13,7 @@ class Libceed(Package): git = "https://github.com/CEED/libCEED.git" version('develop', branch='master') + version('0.5', tag='v0.5') version('0.4', tag='v0.4') version('0.2', tag='v0.2') version('0.1', tag='v0.1') @@ -60,7 +61,7 @@ def common_make_opts(self): if '+debug' in spec: opt = '-g' elif compiler.name == 'gcc': - opt = '-O -g -ffp-contract=fast' + opt = '-O3 -g -ffp-contract=fast' if compiler.target in ['x86_64']: opt += ' -march=native' elif compiler.target in ['ppc64le']: @@ -68,7 +69,7 @@ def common_make_opts(self): if compiler.version >= ver(4.9): opt += ' -fopenmp-simd' elif compiler.name == 'clang': - opt = '-O -g -march=native -ffp-contract=fast' + opt = '-O3 -g -march=native -ffp-contract=fast' if compiler.version.string.endswith('-apple'): if compiler.version >= ver(10): opt += ' -fopenmp-simd' From d6555f64b0e352cf42709d46e5e9a8201a9966e8 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 23 Sep 2019 17:25:33 -0500 Subject: [PATCH 012/499] Fix detection of Apple Clang 11.0.0 (#12912) --- lib/spack/spack/compilers/clang.py | 2 +- lib/spack/spack/test/compilers.py | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py index 209759e7be1..ea4ddaf4015 100644 --- a/lib/spack/spack/compilers/clang.py +++ b/lib/spack/spack/compilers/clang.py @@ -205,7 +205,7 @@ def extract_version_from_output(cls, output): ver = 'unknown' match = re.search( # Apple's LLVM compiler has its own versions, so suffix them. - r'^Apple LLVM version ([^ )]+)|' + r'^Apple (?:LLVM|clang) version ([^ )]+)|' # Normal clang compiler versions are left as-is r'clang version ([^ )]+)-svn[~.\w\d-]*|' r'clang version ([^ )]+)-[~.\w\d-]*|' diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py index 171d390de66..dc104225f12 100644 --- a/lib/spack/spack/test/compilers.py +++ b/lib/spack/spack/test/compilers.py @@ -329,6 +329,11 @@ def test_fj_flags(): @pytest.mark.regression('10191') @pytest.mark.parametrize('version_str,expected_version', [ # macOS clang + ('Apple clang version 11.0.0 (clang-1100.0.33.8)\n' + 'Target: x86_64-apple-darwin18.7.0\n' + 'Thread model: posix\n' + 'InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin\n', # noqa + '11.0.0-apple'), ('Apple LLVM version 7.0.2 (clang-700.1.81)\n' 'Target: x86_64-apple-darwin15.2.0\n' 'Thread model: posix\n', '7.0.2-apple'), From 53db1eafb9e6c59efba10383d917afdcaf26f718 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 23 Sep 2019 18:54:47 -0500 Subject: [PATCH 013/499] Fix installation permissions on BLIS and libflame libs (#12919) * Fix installation permissions on BLIS and libflame libs * Fix undefined symbols --- .../packages/blis/Makefile_0.6.0.patch | 31 +++++++++++++++++++ .../repos/builtin/packages/blis/package.py | 4 +++ .../packages/libflame/Makefile_5.2.0.patch | 31 +++++++++++++++++++ .../builtin/packages/libflame/package.py | 17 ++++++++-- 4 files changed, 80 insertions(+), 3 deletions(-) create mode 100644 var/spack/repos/builtin/packages/blis/Makefile_0.6.0.patch create mode 100644 var/spack/repos/builtin/packages/libflame/Makefile_5.2.0.patch diff --git a/var/spack/repos/builtin/packages/blis/Makefile_0.6.0.patch b/var/spack/repos/builtin/packages/blis/Makefile_0.6.0.patch new file mode 100644 index 00000000000..e25ef4a7f48 --- /dev/null +++ b/var/spack/repos/builtin/packages/blis/Makefile_0.6.0.patch @@ -0,0 +1,31 @@ +From bc16ec7d1e2a30ce4a751255b70c9cbe87409e4f Mon Sep 17 00:00:00 2001 +From: "Field G. Van Zee" +Date: Mon, 23 Sep 2019 15:37:33 -0500 +Subject: [PATCH] Set execute bits of shared library at install-time. + +Details: +- Modified the 0644 octal code used during installation of shared + libraries to 0755 (for Linux/OSX only). Thanks to Adam J. Stewart + for reporting this issue via #343. +--- + Makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/Makefile b/Makefile +index 9cc81c9d..3c0e27f3 100644 +--- a/Makefile ++++ b/Makefile +@@ -953,11 +953,11 @@ ifeq ($(IS_WIN),no) + $(INSTALL_LIBDIR)/%.$(LIBBLIS_SO_MMB_EXT): $(BASE_LIB_PATH)/%.$(SHLIB_EXT) $(CONFIG_MK_FILE) + ifeq ($(ENABLE_VERBOSE),yes) + $(MKDIR) $(@D) +- $(INSTALL) -m 0644 $< $@ ++ $(INSTALL) -m 0755 $< $@ + else + @echo "Installing $(@F) into $(INSTALL_LIBDIR)/" + @$(MKDIR) $(@D) +- @$(INSTALL) -m 0644 $< $@ ++ @$(INSTALL) -m 0755 $< $@ + endif + + else # ifeq ($(IS_WIN),yes) diff --git a/var/spack/repos/builtin/packages/blis/package.py b/var/spack/repos/builtin/packages/blis/package.py index 9bc167b2f74..45f81689d83 100644 --- a/var/spack/repos/builtin/packages/blis/package.py +++ b/var/spack/repos/builtin/packages/blis/package.py @@ -73,6 +73,10 @@ class Blis(Package): provides('blas', when="+blas") provides('blas', when="+cblas") + # Problems with permissions on installed libraries: + # https://github.com/flame/blis/issues/343 + patch('Makefile_0.6.0.patch', when='@0.4.0:0.6.0') + phases = ['configure', 'build', 'install'] def configure(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/libflame/Makefile_5.2.0.patch b/var/spack/repos/builtin/packages/libflame/Makefile_5.2.0.patch new file mode 100644 index 00000000000..3cd7510f3de --- /dev/null +++ b/var/spack/repos/builtin/packages/libflame/Makefile_5.2.0.patch @@ -0,0 +1,31 @@ +From 4356779fe843fb30b3728f5fdab049c7291d89c6 Mon Sep 17 00:00:00 2001 +From: "Field G. Van Zee" +Date: Mon, 23 Sep 2019 15:15:15 -0500 +Subject: [PATCH] Set execute bits of shared library at install-time. + +Details: +- Modified the 0644 octal code used during installation of shared + libraries to 0755. Thanks to Adam J. Stewart for reporting this + issue in #24. +--- + Makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/Makefile b/Makefile +index d856af4c..6bd8bdce 100644 +--- a/Makefile ++++ b/Makefile +@@ -643,11 +643,11 @@ endif + $(INSTALL_LIBDIR)/%.$(LIBFLAME_SO_MMB_EXT): $(BASE_LIB_PATH)/%.$(SHLIB_EXT) $(CONFIG_MK_FILE) + ifeq ($(ENABLE_VERBOSE),yes) + $(MKDIR) $(@D) +- $(INSTALL) -m 0644 $< $@ ++ $(INSTALL) -m 0755 $< $@ + else + @echo "Installing $(@F) into $(INSTALL_LIBDIR)/" + @$(MKDIR) $(@D) +- @$(INSTALL) -m 0644 $< $@ ++ @$(INSTALL) -m 0755 $< $@ + endif + + diff --git a/var/spack/repos/builtin/packages/libflame/package.py b/var/spack/repos/builtin/packages/libflame/package.py index 7a735be7b67..7c5beda2f88 100644 --- a/var/spack/repos/builtin/packages/libflame/package.py +++ b/var/spack/repos/builtin/packages/libflame/package.py @@ -46,12 +46,20 @@ class Libflame(AutotoolsPackage): # TODO: Libflame prefers to defer to an external # LAPACK library for small problems. Is this to be - # implemented in spack ? + # implemented in spack? - # There is a known issue with the makefile : + # Libflame has a secondary dependency on BLAS: + # https://github.com/flame/libflame/issues/24 + depends_on('blas') + + # There is a known issue with the makefile: # https://groups.google.com/forum/#!topic/libflame-discuss/lQKEfjyudOY patch('Makefile_5.1.0.patch', when='@5.1.0') + # Problems with permissions on installed libraries: + # https://github.com/flame/libflame/issues/24 + patch('Makefile_5.2.0.patch', when='@5.2.0') + def flag_handler(self, name, flags): # -std=gnu99 at least required, old versions of GCC default to -std=c90 if self.spec.satisfies('%gcc@:5.1') and name == 'cflags': @@ -59,7 +67,10 @@ def flag_handler(self, name, flags): return (flags, None, None) def configure_args(self): - config_args = [] + # Libflame has a secondary dependency on BLAS, + # but doesn't know which library name to expect: + # https://github.com/flame/libflame/issues/24 + config_args = ['LIBS=' + self.spec['blas'].libs.link_flags] if '+lapack2flame' in self.spec: config_args.append("--enable-lapack2flame") From 2468ccee586026ab075f3b5ae60a0d1d64221b96 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 24 Sep 2019 06:54:13 +0200 Subject: [PATCH 014/499] AMD: fix architecture hierarchy (zen) (#12913) * microarchitectures: zen starts from x86_64, not from excavator * Unit tests: fixed a test that is wrong with the new modeling * microarchitectures: fixed features and inheritance for 15h family bulldozer doesn't inherit from barcelona (10h) + added xop, lwp and tbm instruction sets to the 15h family (it distinguish the family from 17h) --- .../llnl/util/cpu/microarchitectures.json | 30 +++++++++---------- .../test/data/targets/linux-rhel6-piledriver | 29 ++++++++++++++++++ lib/spack/spack/test/llnl/util/cpu.py | 3 +- 3 files changed, 45 insertions(+), 17 deletions(-) create mode 100644 lib/spack/spack/test/data/targets/linux-rhel6-piledriver diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index d540d111947..1ee782b408a 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -514,19 +514,8 @@ } } }, - "barcelona": { - "from": "x86_64", - "vendor": "AuthenticAMD", - "features": [ - "mmx", - "sse", - "sse2", - "sse4a", - "abm" - ] - }, "bulldozer": { - "from": "barcelona", + "from": "x86_64", "vendor": "AuthenticAMD", "features": [ "mmx", @@ -562,6 +551,8 @@ "sse4a", "abm", "avx", + "xop", + "lwp", "aes", "pclmulqdq", "cx16", @@ -570,7 +561,8 @@ "sse4_2", "bmi1", "f16c", - "fma" + "fma", + "tbm" ], "compilers": { "gcc": { @@ -590,6 +582,8 @@ "sse4a", "abm", "avx", + "xop", + "lwp", "aes", "pclmulqdq", "cx16", @@ -599,7 +593,8 @@ "bmi1", "f16c", "fma", - "fsgsbase" + "fsgsbase", + "tbm" ], "compilers": { "gcc": { @@ -619,6 +614,8 @@ "sse4a", "abm", "avx", + "xop", + "lwp", "aes", "pclmulqdq", "cx16", @@ -631,7 +628,8 @@ "fsgsbase", "bmi2", "avx2", - "movbe" + "movbe", + "tbm" ], "compilers": { "gcc": { @@ -642,7 +640,7 @@ } }, "zen": { - "from": "excavator", + "from": "x86_64", "vendor": "AuthenticAMD", "features": [ "bmi1", diff --git a/lib/spack/spack/test/data/targets/linux-rhel6-piledriver b/lib/spack/spack/test/data/targets/linux-rhel6-piledriver new file mode 100644 index 00000000000..599d0c6fe7a --- /dev/null +++ b/lib/spack/spack/test/data/targets/linux-rhel6-piledriver @@ -0,0 +1,29 @@ +processor : 0 +vendor_id : AuthenticAMD +cpu family : 21 +model : 2 +model name : AMD FX(tm)-8350 Eight-Core Processor +stepping : 0 +microcode : 0x6000832 +cpu MHz : 4013.832 +cache size : 2048 KB +physical id : 0 +siblings : 8 +core id : 0 +cpu cores : 4 +apicid : 16 +initial apicid : 0 +fpu : yes +fpu_exception : yes +cpuid level : 13 +wp : yes +flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 popcnt aes xsave avx f16c lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 tce nodeid_msr tbm topoext perfctr_core perfctr_nb arat cpb hw_pstate npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold vmmcall bmi1 +bugs : fxsave_leak sysret_ss_attrs +bogomips : 8030.15 +TLB size : 1536 4K pages +clflush size : 64 +cache_alignment : 64 +address sizes : 48 bits physical, 48 bits virtual +power management: ts ttp tm 100mhzsteps hwpstate cpb eff_freq_ro + +# /proc/cpuinfo taken from https://www.redhat.com/archives/vfio-users/2015-August/msg00111.html \ No newline at end of file diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 6f6b9fec4d5..836514cc3c7 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -26,6 +26,7 @@ 'linux-rhel7-ivybridge', 'linux-rhel7-haswell', 'linux-rhel7-zen', + 'linux-rhel6-piledriver', 'linux-centos7-power8le', 'darwin-mojave-ivybridge', 'darwin-mojave-broadwell', @@ -112,7 +113,7 @@ def test_equality(supported_target): # Test microarchitectures that are ordered with respect to each other ('x86_64 < skylake', True), ('icelake > skylake', True), - ('piledriver <= zen', True), + ('piledriver <= steamroller', True), ('zen2 >= zen', True), ('zen >= zen', True), # Test unrelated microarchitectures From 18d63a239f901c36e889b604ee7dd284d7d976f0 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 24 Sep 2019 01:18:48 -0700 Subject: [PATCH 015/499] bugfix: use string keys to set preferred targets (#12921) Preferred targets were failing because we were looking them up by Microarchitecture object, not by string. - [x] Add a call to `str()` to fix target lookup. - [x] Add a test to exercise this part of concretization. - [x] Add documentation for setting `target` in `packages.yaml` --- lib/spack/docs/basic_usage.rst | 8 +++++--- lib/spack/docs/build_settings.rst | 11 +++++----- lib/spack/spack/concretize.py | 2 +- .../spack/test/concretize_preferences.py | 20 +++++++++++++++++++ 4 files changed, 32 insertions(+), 9 deletions(-) diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index 8d81db4cb4f..1c61a388995 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -865,9 +865,11 @@ or together by using the reserved keyword ``arch``: $ spack install libelf arch=cray-CNL10-haswell -Normally users don't have to bother specifying the architecture -if they are installing software for their current host as in that case the -values will be detected automatically. +Normally users don't have to bother specifying the architecture if they +are installing software for their current host, as in that case the +values will be detected automatically. If you need fine-grained control +over which packages use which targets (or over *all* packages' default +target), see :ref:`concretization-preferences`. .. admonition:: Cray machines diff --git a/lib/spack/docs/build_settings.rst b/lib/spack/docs/build_settings.rst index 1b6912a2e67..fbd73d7a522 100644 --- a/lib/spack/docs/build_settings.rst +++ b/lib/spack/docs/build_settings.rst @@ -149,6 +149,7 @@ Here's an example ``packages.yaml`` file that sets preferred packages: version: [2.2, 2.4, 2.3] all: compiler: [gcc@4.4.7, 'gcc@4.6:', intel, clang, pgi] + target: [sandybridge] providers: mpi: [mvapich2, mpich, openmpi] @@ -162,11 +163,11 @@ on the command line if explicitly requested. Each ``packages.yaml`` file begins with the string ``packages:`` and package names are specified on the next level. The special string ``all`` -applies settings to each package. Underneath each package name is -one or more components: ``compiler``, ``variants``, ``version``, -or ``providers``. Each component has an ordered list of spec -``constraints``, with earlier entries in the list being preferred over -later entries. +applies settings to *all* packages. Underneath each package name is one +or more components: ``compiler``, ``variants``, ``version``, +``providers``, and ``target``. Each component has an ordered list of +spec ``constraints``, with earlier entries in the list being preferred +over later entries. Sometimes a package installation may have constraints that forbid the first concretization rule, in which case Spack will use the first diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py index ed8f6ac2e75..a31529e0ea8 100644 --- a/lib/spack/spack/concretize.py +++ b/lib/spack/spack/concretize.py @@ -291,7 +291,7 @@ def tspec_filter(s): # we only consider x86_64 targets when on an # x86_64 machine, etc. This may need to change to # enable setting cross compiling as a default - target = cpu.targets[s.architecture.target] + target = cpu.targets[str(s.architecture.target)] arch_family_name = target.family.name return arch_family_name == platform.machine() diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py index e7c8727371a..5563bad75b0 100644 --- a/lib/spack/spack/test/concretize_preferences.py +++ b/lib/spack/spack/test/concretize_preferences.py @@ -96,6 +96,26 @@ def test_preferred_compilers(self, mutable_mock_packages): spec = concretize('mpileaks') assert spec.compiler == spack.spec.CompilerSpec('gcc@4.5.0') + def test_preferred_target(self, mutable_mock_packages): + """Test preferred compilers are applied correctly + """ + spec = concretize('mpich') + default = str(spec.target) + preferred = str(spec.target.family) + + update_packages('mpich', 'target', [preferred]) + spec = concretize('mpich') + assert str(spec.target) == preferred + + spec = concretize('mpileaks') + assert str(spec['mpileaks'].target) == default + assert str(spec['mpich'].target) == preferred + + update_packages('mpileaks', 'target', [preferred]) + spec = concretize('mpileaks') + assert str(spec['mpich'].target) == preferred + assert str(spec['mpich'].target) == preferred + def test_preferred_versions(self): """Test preferred package versions are applied correctly """ From 9aca0a17f48018b672e74507e9fb4b01c937be25 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Tue, 24 Sep 2019 18:17:29 +0900 Subject: [PATCH 016/499] Fujitsu compilers: added 'verbose_flag' method (#12922) --- lib/spack/spack/compilers/fj.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/spack/spack/compilers/fj.py b/lib/spack/spack/compilers/fj.py index d0527790725..1ddffd91af7 100644 --- a/lib/spack/spack/compilers/fj.py +++ b/lib/spack/spack/compilers/fj.py @@ -28,6 +28,10 @@ class Fj(spack.compiler.Compiler): version_argument = '--version' version_regex = r'\((?:FCC|FRT)\) ([\d.]+)' + @classmethod + def verbose_flag(cls): + return "-v" + @property def openmp_flag(self): return "-Kopenmp" From 1d316c4eb3b6f19b440e58c78b496a664c9d250c Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 24 Sep 2019 03:19:19 -0700 Subject: [PATCH 017/499] spdlog: added version 1.4.1 (#12917) Add newest release with ability to pre-build as shared or static library. --- .../repos/builtin/packages/spdlog/package.py | 24 ++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/spdlog/package.py b/var/spack/repos/builtin/packages/spdlog/package.py index e621ad431b2..2bf342f38b2 100644 --- a/var/spack/repos/builtin/packages/spdlog/package.py +++ b/var/spack/repos/builtin/packages/spdlog/package.py @@ -12,6 +12,7 @@ class Spdlog(CMakePackage): homepage = "https://github.com/gabime/spdlog" url = "https://github.com/gabime/spdlog/archive/v0.9.0.tar.gz" + version('1.4.1', sha256='3291958eb54ed942d1bd3aef1b4f8ccf70566cbc04d34296ec61eb96ceb73cff') version('1.2.1', sha256='867a4b7cedf9805e6f76d3ca41889679054f7e5a3b67722fe6d0eae41852a767') version('1.2.0', sha256='0ba31b9e7f8e43a7be328ab0236d57810e5d4fc8a1a7842df665ae22d5cbd128') version('1.1.0', sha256='3dbcbfd8c07e25f5e0d662b194d3a7772ef214358c49ada23c044c4747ce8b19') @@ -28,4 +29,25 @@ class Spdlog(CMakePackage): version('0.10.0', '57b471ef97a23cc29c38b62e00e89a411a87ea7f') version('0.9.0', 'dda741ef8e12d57d91f778d85e95a27d84a82ac4') - depends_on('cmake@3.1:', type='build') + variant('shared', default=True, + description='Build shared libraries (v1.4.0+)') + + depends_on('cmake@3.2:', type='build') + + def cmake_args(self): + spec = self.spec + + args = [] + + if self.spec.version >= Version('1.4.0'): + args.extend([ + '-DSPDLOG_BUILD_SHARED:BOOL={0}'.format( + 'ON' if '+shared' in spec else 'OFF'), + # tests and examples + '-DSPDLOG_BUILD_TESTS:BOOL={0}'.format( + 'ON' if self.run_tests else 'OFF'), + '-DSPDLOG_BUILD_EXAMPLE:BOOL={0}'.format( + 'ON' if self.run_tests else 'OFF') + ]) + + return args From ca11ce06b894857c3bcf060513aadb12bc743114 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 24 Sep 2019 05:44:28 -0500 Subject: [PATCH 018/499] Add missing dependencies to perl-http-daemon (#12898) Added the following dependencies: + depends_on('perl-http-date', type=('build', 'run')) + depends_on('perl-module-build-tiny', type='build') --- var/spack/repos/builtin/packages/perl-http-daemon/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/perl-http-daemon/package.py b/var/spack/repos/builtin/packages/perl-http-daemon/package.py index 01159493267..5bebdb4ec57 100644 --- a/var/spack/repos/builtin/packages/perl-http-daemon/package.py +++ b/var/spack/repos/builtin/packages/perl-http-daemon/package.py @@ -16,3 +16,5 @@ class PerlHttpDaemon(PerlPackage): depends_on('perl-lwp-mediatypes', type=('build', 'run')) depends_on('perl-http-message', type=('build', 'run')) + depends_on('perl-http-date', type=('build', 'run')) + depends_on('perl-module-build-tiny', type='build') From b508eaa8067efc1861e85c86feb0287b838e3fb5 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 24 Sep 2019 05:45:02 -0500 Subject: [PATCH 019/499] Added depencies to perl-libwww-perl (#12899) The following dependencies are needed for perl-libwww-perl according to https://metacpan.org: + depends_on('perl-encode-locale', type=('build', 'run')) + depends_on('perl-file-listing', type=('build', 'run')) + depends_on('perl-html-parser', type=('build', 'run')) + depends_on('perl-http-cookies', type=('build', 'run')) + depends_on('perl-http-daemon', type=('build', 'run')) + depends_on('perl-http-date', type=('build', 'run')) + depends_on('perl-http-message', type=('build', 'run')) + depends_on('perl-http-negotiate', type=('build', 'run')) + depends_on('perl-lwp-mediatypes', type=('build', 'run')) + depends_on('perl-net-http', type=('build', 'run')) + depends_on('perl-try-tiny', type=('build', 'run')) + depends_on('perl-uri', type=('build', 'run')) + depends_on('perl-www-robotrules', type=('build', 'run')) --- .../builtin/packages/perl-libwww-perl/package.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py index 795446cba04..ea2ef1f6f48 100644 --- a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py @@ -16,3 +16,17 @@ class PerlLibwwwPerl(PerlPackage): url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz" version('6.33', '2e15c1c789ac9036c99d094e47e3da23') + + depends_on('perl-encode-locale', type=('build', 'run')) + depends_on('perl-file-listing', type=('build', 'run')) + depends_on('perl-html-parser', type=('build', 'run')) + depends_on('perl-http-cookies', type=('build', 'run')) + depends_on('perl-http-daemon', type=('build', 'run')) + depends_on('perl-http-date', type=('build', 'run')) + depends_on('perl-http-message', type=('build', 'run')) + depends_on('perl-http-negotiate', type=('build', 'run')) + depends_on('perl-lwp-mediatypes', type=('build', 'run')) + depends_on('perl-net-http', type=('build', 'run')) + depends_on('perl-try-tiny', type=('build', 'run')) + depends_on('perl-uri', type=('build', 'run')) + depends_on('perl-www-robotrules', type=('build', 'run')) From fa5a9cd87824e8ff370d41a50542819c73b11a76 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 24 Sep 2019 05:45:39 -0500 Subject: [PATCH 020/499] Added missing dependencies for perl-list-moreutils (#12900) The following dependencies were added: + depends_on('perl-exporter-tiny', type=('build', 'run')) + depends_on('perl-list-moreutils-xs', type=('build', 'run')) --- .../repos/builtin/packages/perl-list-moreutils/package.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py index 81b6492aa1b..fd60e656681 100644 --- a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py +++ b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py @@ -13,3 +13,6 @@ class PerlListMoreutils(PerlPackage): url = "http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/List-MoreUtils-0.428.tar.gz" version('0.428', '493032a211cdff1fcf45f59ebd680407') + + depends_on('perl-exporter-tiny', type=('build', 'run')) + depends_on('perl-list-moreutils-xs', type=('build', 'run')) From 10d5e90e65e792d0fae3879dd5f512bdc7b95da6 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 24 Sep 2019 05:51:55 -0500 Subject: [PATCH 021/499] Add missing dependency to perl-xml-parser (#12903) This PR adds the following dependency: + depends_on('perl-libwww-perl', type=('build', 'run')) --- var/spack/repos/builtin/packages/perl-xml-parser/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/perl-xml-parser/package.py b/var/spack/repos/builtin/packages/perl-xml-parser/package.py index ed8af41a346..b1407fe9a80 100644 --- a/var/spack/repos/builtin/packages/perl-xml-parser/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-parser/package.py @@ -16,6 +16,7 @@ class PerlXmlParser(PerlPackage): version('2.44', 'af4813fe3952362451201ced6fbce379') depends_on('expat') + depends_on('perl-libwww-perl', type=('build', 'run')) def configure_args(self): args = [] From 6dd9dbc07177b6ca424bd755b5f6a1030f7aedae Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Tue, 24 Sep 2019 08:38:19 -0500 Subject: [PATCH 022/499] Change get_patchelf to immediately return patchelf path if found (#12925) --- lib/spack/spack/relocate.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index 01fc913a0ef..8873d1d725d 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -66,20 +66,20 @@ def get_patchelf(): Returns the full patchelf binary path. """ # as we may need patchelf, find out where it is - if str(spack.architecture.platform()) == 'test': - return None - if str(spack.architecture.platform()) == 'darwin': - return None patchelf = spack.util.executable.which('patchelf') - if patchelf is None: + if patchelf is not None: + return patchelf.path + else: + if str(spack.architecture.platform()) == 'test': + return None + if str(spack.architecture.platform()) == 'darwin': + return None patchelf_spec = spack.cmd.parse_specs("patchelf", concretize=True)[0] patchelf = spack.repo.get(patchelf_spec) if not patchelf.installed: patchelf.do_install(use_cache=False) patchelf_executable = os.path.join(patchelf.prefix.bin, "patchelf") return patchelf_executable - else: - return patchelf.path def get_existing_elf_rpaths(path_name): From 6cd5edacca8e4cacbcaf104b3c241097fc83568f Mon Sep 17 00:00:00 2001 From: Simo Tuomisto Date: Tue, 24 Sep 2019 16:54:23 +0300 Subject: [PATCH 023/499] heaptrack: added new package at version 1.1.0 (#12844) --- .../builtin/packages/heaptrack/package.py | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 var/spack/repos/builtin/packages/heaptrack/package.py diff --git a/var/spack/repos/builtin/packages/heaptrack/package.py b/var/spack/repos/builtin/packages/heaptrack/package.py new file mode 100644 index 00000000000..7c0b254f009 --- /dev/null +++ b/var/spack/repos/builtin/packages/heaptrack/package.py @@ -0,0 +1,36 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Heaptrack(CMakePackage): + """Heaptrack is a heap memory profiler that traces all memory allocations + and annotates these events with stack traces. + """ + + homepage = "https://github.com/KDE/heaptrack" + url = "https://github.com/KDE/heaptrack/archive/v1.1.0.tar.gz" + + version('1.1.0', sha256='bd247ac67d1ecf023ec7e2a2888764bfc03e2f8b24876928ca6aa0cdb3a07309') + + depends_on('boost@1.41:') + depends_on('cmake@2.8.9:') + depends_on('elfutils') + depends_on('libunwind') + depends_on('zlib') + depends_on('zstd') + + def cmake_args(self): + + spec = self.spec + + cmake_args = [ + "-DBOOST_ROOT={0}".format(spec['boost'].prefix), + "-DBOOST_LIBRARY_DIR={0}".format(spec['boost'].prefix.lib), + "-DBOOST_INCLUDE_DIR={0}".format(spec['boost'].prefix.include), + "-DBOOST_NO_SYSTEM_PATHS:BOOL=ON", + "-DBoost_NO_BOOST_CMAKE:BOOL=ON", + ] + return cmake_args From 065cbe89fed448fcc64593f679867a7a7ad3cbd1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 24 Sep 2019 11:47:54 -0500 Subject: [PATCH 024/499] Fix "specific target" detection in Python 3 (#12906) The output of subprocess.check_output is a byte string in Python 3. This causes dictionary lookup to fail later on. A try-except around this function prevented this error from being noticed. Removed this so that more errors can propagate out. --- lib/spack/llnl/util/cpu/detect.py | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/lib/spack/llnl/util/cpu/detect.py b/lib/spack/llnl/util/cpu/detect.py index 40a427a5dab..7744d5acd23 100644 --- a/lib/spack/llnl/util/cpu/detect.py +++ b/lib/spack/llnl/util/cpu/detect.py @@ -7,7 +7,7 @@ import platform import re import subprocess -import sys +import warnings import six @@ -76,11 +76,8 @@ def proc_cpuinfo(): def check_output(args): - if sys.version_info[:2] == (2, 6): - return subprocess.run( - args, check=True, stdout=subprocess.PIPE).stdout # nopyqver - else: - return subprocess.check_output(args) # nopyqver + output = subprocess.Popen(args, stdout=subprocess.PIPE).communicate()[0] + return six.text_type(output.decode('utf-8')) @info_dict(operating_system='Darwin') @@ -126,8 +123,8 @@ def raw_info_dictionary(): for factory in info_factory[platform.system()]: try: info = factory() - except Exception: - pass + except Exception as e: + warnings.warn(str(e)) if info: break From 7a11a2ccdb2a6a698c8df81beb230a4d210c3ff5 Mon Sep 17 00:00:00 2001 From: Mathias Jacquelin Date: Tue, 24 Sep 2019 13:25:06 -0700 Subject: [PATCH 025/499] Upcxx package: remove warning, add version 2019.9.0 (#12880) A function added to this package ran as part of importing it and printed a warning for most Spack invocations, this removes the warning message. Also: * Use compilers directly instead of Spack compiler wrappers (since references to the compiler are embedded in text and binary files of the installation) * Add 'cross' variant for setting CROSS environment variable for build * Set UPCXX_INSTALL for generated module files * Set UPCXX_GASNET_CONDUIT/UPCXX_NETWORK in generated module files on Cray systems * Also set UPCXX_NETWORK in build environment for Cray systems --- .../repos/builtin/packages/upcxx/package.py | 62 ++++++++----------- 1 file changed, 26 insertions(+), 36 deletions(-) diff --git a/var/spack/repos/builtin/packages/upcxx/package.py b/var/spack/repos/builtin/packages/upcxx/package.py index fa0874ed7ed..bf78c3d27b7 100644 --- a/var/spack/repos/builtin/packages/upcxx/package.py +++ b/var/spack/repos/builtin/packages/upcxx/package.py @@ -4,31 +4,15 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import llnl.util.tty as tty -import os -def detect_scheduler(): - if (os.environ.get('CROSS') is None): - srunbin = which('srun') - if srunbin is None: - aprunbin = which('aprun') - if aprunbin is None: - tty.warn("CROSS has not been set, however " - "cannot detect scheduler.") - return 'none' - else: - tty.warn("CROSS has not been set, however " - "aprun has been found, assuming alps scheduler.") - return 'alps' - else: - tty.warn("CROSS has not been set, however " - "srun has been found, assuming slurm scheduler.") - return 'slurm' - else: - tty.warn("CROSS has been set to %s by the user." - % os.environ.get('CROSS')) - return 'user' +def cross_detect(): + if spack.architecture.platform().name == 'cray': + if which('srun'): + return 'cray-aries-slurm' + if which('alps'): + return 'cray-aries-alps' + return 'none' class Upcxx(Package): @@ -40,15 +24,16 @@ class Upcxx(Package): homepage = "https://upcxx.lbl.gov" + version('2019.9.0', '7642877e05300e38f6fa0afbc6062788') version('2019.3.2', '844722cb0e8c0bc649017fce86469457') variant('cuda', default=False, description='Builds a CUDA-enabled version of UPC++') - variant('scheduler', values=('slurm', 'alps', 'user', 'none'), - default=detect_scheduler(), - description="Resource manager to use") - conflicts('scheduler=none', when='platform=cray', + variant('cross', default=cross_detect(), + description="UPC++ cross-compile target (autodetect by default)") + + conflicts('cross=none', when='platform=cray', msg='None is unacceptable on Cray.') depends_on('cuda', when='+cuda') @@ -63,18 +48,20 @@ def url_for_version(self, version): def setup_environment(self, spack_env, run_env): if 'platform=cray' in self.spec: spack_env.set('GASNET_CONFIGURE_ARGS', '--enable-mpi=probe') - if "scheduler=slurm" in self.spec: - tty.warn("CROSS has been automatically set to %s." - % 'cray-aries-slurm') - spack_env.set('CROSS', 'cray-aries-slurm') - elif "scheduler=alps" in self.spec: - tty.warn("CROSS has been automatically set to %s." - % 'cray-aries-alps') - spack_env.set('CROSS', 'cray-aries-alps') + + if 'cross=none' not in self.spec: + spack_env.set('CROSS', self.spec.variants['cross'].value) + if '+cuda' in self.spec: spack_env.set('UPCXX_CUDA', '1') spack_env.set('UPCXX_CUDA_NVCC', self.spec['cuda'].prefix.bin.nvcc) + run_env.set('UPCXX_INSTALL', self.prefix) + run_env.set('UPCXX', self.prefix.bin.upcxx) + if 'platform=cray' in self.spec: + run_env.set('UPCXX_GASNET_CONDUIT', 'aries') + run_env.set('UPCXX_NETWORK', 'aries') + def setup_dependent_package(self, module, dep_spec): dep_spec.upcxx = self.prefix.bin.upcxx @@ -83,7 +70,10 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec): spack_env.set('UPCXX', self.prefix.bin.upcxx) if 'platform=cray' in self.spec: spack_env.set('UPCXX_GASNET_CONDUIT', 'aries') + spack_env.set('UPCXX_NETWORK', 'aries') def install(self, spec, prefix): - installsh = Executable('./install') + env['CC'] = self.compiler.cc + env['CXX'] = self.compiler.cxx + installsh = Executable("./install") installsh(prefix) From e123058721952dcc552105e63315f64e3b189b1f Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 25 Sep 2019 09:00:01 -0600 Subject: [PATCH 026/499] kokkos-kernels: initial commit (#12934) --- .../packages/kokkos-kernels/makefile.patch | 53 +++++++++++++++++++ .../packages/kokkos-kernels/package.py | 53 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 var/spack/repos/builtin/packages/kokkos-kernels/makefile.patch create mode 100644 var/spack/repos/builtin/packages/kokkos-kernels/package.py diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/makefile.patch b/var/spack/repos/builtin/packages/kokkos-kernels/makefile.patch new file mode 100644 index 00000000000..639bfd4d581 --- /dev/null +++ b/var/spack/repos/builtin/packages/kokkos-kernels/makefile.patch @@ -0,0 +1,53 @@ +--- ./src/Makefile 2018-11-05 13:28:12.000000000 -0700 ++++ ./src/Makefile 2018-11-08 16:01:05.000000000 -0700 +@@ -1,37 +1,24 @@ ++include $(KOKKOS_PATH)/Makefile.kokkos + #======================================================================= + #=================== Settings ========================================== + #======================================================================= + +-ifndef KOKKOSKERNELS_PATH +- MAKEFILE_PATH := $(abspath $(lastword $(MAKEFILE_LIST))) +- KOKKOSKERNELS_PATH = $(subst Makefile.minimal,,$(MAKEFILE_PATH)).. +-endif +- +-KOKKOS_PATH = ${KOKKOSKERNELS_PATH}/../kokkos +- +- +-KOKKOS_DEVICES=OpenMP +- +-KOKKOSKERNELS_SCALARS="'double,complex'" ++KOKKOSKERNELS_SCALARS="'double'" + KOKKOSKERNELS_OPTIONS=eti-only + +-ifndef PREFIX +- PREFIX = ${CURDIR}/install +-endif +-KOKKOSKERNELS_INSTALL_PATH = ${PREFIX} + + default: build + + CXX = g++ + +-CXXFLAGS = -O3 -g ++CXXFLAGS = -O3 + LINK = ${CXX} +-LINKFLAGS = ++LINKFLAGS = $(KOKKOS_LINK_FLAGS) + + DEPFLAGS = -M + + OBJ = +-LIB = -lpthread ++LIB = $(KOKKOS_LIBS) + + + #======================================================================= +@@ -91,5 +78,4 @@ + + build: kokkoskernels-build-lib + +-install: kokkoskernels-install +- ++install: kokkoskernels-install +\ No newline at end of file diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/package.py b/var/spack/repos/builtin/packages/kokkos-kernels/package.py new file mode 100644 index 00000000000..6694cc02d4e --- /dev/null +++ b/var/spack/repos/builtin/packages/kokkos-kernels/package.py @@ -0,0 +1,53 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class KokkosKernels(MakefilePackage): + """Kokkos C++ Performance Portability Programming EcoSystem: Math Kernels - + Provides BLAS, Sparse BLAS and Graph Kernels.""" + + homepage = "https://github.com/kokkos/kokkos-kernels" + url = "https://github.com/kokkos/kokkos-kernels/archive/2.7.00.tar.gz" + + version('2.7.00', 'dfb21f26da9f1f976d84826a1510d91e') + version('2.6.00', 'ef8ba7509d82417dbc82a2f021886949') + version('2.5.00', '94f4bd78b36b9c53c18df3ccfd552041') + version('develop', git='https://github.com/kokkos/kokkos-kernels', + branch='develop') + + # make sure kokkos kernels version matches kokkos + depends_on('kokkos@2.5.00', when='@2.5.00') + depends_on('kokkos@2.6.00', when='@2.6.00') + depends_on('kokkos@2.7.00', when='@2.7.00') + depends_on('kokkos@develop', when='@develop') + + patch('makefile.patch') + + def edit(self, spec, prefix): + makefile = FileFilter("src/Makefile") + makefile.filter('CXX = .*', 'CXX = ' + env['CXX']) + + def build(self, spec, prefix): + with working_dir('build', create=True): + makefile_path = '%s%s' % (self.stage.source_path, '/src/Makefile') + copy(makefile_path, 'Makefile') + make_args = [ + 'KOKKOSKERNELS_INSTALL_PATH=%s' % prefix, + 'KOKKOSKERNELS_PATH=%s' % self.stage.source_path, + 'KOKKOS_PATH=%s' % spec['kokkos'].prefix + ] + + make('build', *make_args) + + def install(self, spec, prefix): + with working_dir('build', create=False): + make_args = [ + 'KOKKOSKERNELS_INSTALL_PATH=%s' % prefix, + 'KOKKOSKERNELS_PATH=%s' % self.stage.source_path, + 'KOKKOS_PATH=%s' % spec['kokkos'].prefix + ] + make('install', *make_args) From ccfe8aaf76f8fc294ea1bf0a9a1cd829c4166c5f Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 25 Sep 2019 11:29:43 -0600 Subject: [PATCH 027/499] portage: fix RelWithDebInfo build (#12944) --- .../repos/builtin/packages/portage/package.py | 3 +++ .../packages/portage/rel-with-deb-info.patch | 16 ++++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/portage/rel-with-deb-info.patch diff --git a/var/spack/repos/builtin/packages/portage/package.py b/var/spack/repos/builtin/packages/portage/package.py index de77330983f..91fc5fa4dc5 100644 --- a/var/spack/repos/builtin/packages/portage/package.py +++ b/var/spack/repos/builtin/packages/portage/package.py @@ -27,6 +27,9 @@ class Portage(CMakePackage): # part of https://github.com/laristra/cinch/commit/f87f848269fac25aa5b8d0bd5d9c9b2d2d6fb0ad # fixed in version above 1.2.2 patch('p_lapacke_config.patch', when='@1.2.2') + # don't enable debug prints in RelWithDebInfo build + # fixed in version above 1.2.2 + patch('rel-with-deb-info.patch', when='@1.2.2') variant('mpi', default=True, description='Support MPI') diff --git a/var/spack/repos/builtin/packages/portage/rel-with-deb-info.patch b/var/spack/repos/builtin/packages/portage/rel-with-deb-info.patch new file mode 100644 index 00000000000..ca040cee3b9 --- /dev/null +++ b/var/spack/repos/builtin/packages/portage/rel-with-deb-info.patch @@ -0,0 +1,16 @@ +--- portage/cinch/cmake/globals.cmake.orig 2018-07-16 13:42:23.000000000 -0600 ++++ portage/cinch/cmake/globals.cmake 2019-07-09 16:27:56.021566000 -0600 +@@ -22,11 +22,9 @@ + "CMake build type " FORCE) + endif(NOT CMAKE_BUILD_TYPE) + +-if("${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR +- "${CMAKE_BUILD_TYPE}" STREQUAL "RelWithDebInfo") ++if("${CMAKE_BUILD_TYPE}" STREQUAL "Debug") + add_definitions(-DDEBUG) +-endif("${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR +- "${CMAKE_BUILD_TYPE}" STREQUAL "RelWithDebInfo") ++endif("${CMAKE_BUILD_TYPE}" STREQUAL "Debug") + + #------------------------------------------------------------------------------# + # Print useful information From 71cc29691b537e55120e92ab8081ace66de4a00f Mon Sep 17 00:00:00 2001 From: Matthieu Dorier Date: Wed, 25 Sep 2019 15:15:23 -0500 Subject: [PATCH 028/499] openblas: fixed a query to target family (#12910) --- var/spack/repos/builtin/packages/openblas/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 980585c58c9..7dfa98efd88 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -201,7 +201,7 @@ def make_defs(self): if '+ilp64' in self.spec: make_defs += ['INTERFACE64=1'] - if 'x86' in self.spec.architecture.target.lower(): + if self.spec.target.family == 'x86_64': if '~avx2' in self.spec: make_defs += ['NO_AVX2=1'] if '~avx512' in self.spec: From 4e858e24b0ffccd8962e376f9ffc6cd93ad5c0dd Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 25 Sep 2019 18:37:33 -0500 Subject: [PATCH 029/499] libflame: fix macOS build (#12950) --- .../libflame/Makefile_5.2.0_darwin.patch | 231 ++++++++++++++++++ .../builtin/packages/libflame/package.py | 10 + 2 files changed, 241 insertions(+) create mode 100644 var/spack/repos/builtin/packages/libflame/Makefile_5.2.0_darwin.patch diff --git a/var/spack/repos/builtin/packages/libflame/Makefile_5.2.0_darwin.patch b/var/spack/repos/builtin/packages/libflame/Makefile_5.2.0_darwin.patch new file mode 100644 index 00000000000..44646cbc555 --- /dev/null +++ b/var/spack/repos/builtin/packages/libflame/Makefile_5.2.0_darwin.patch @@ -0,0 +1,231 @@ +From 6dd3c19978a0b805b0e294271ce8f5ef2f421425 Mon Sep 17 00:00:00 2001 +From: "Field G. Van Zee" +Date: Wed, 25 Sep 2019 12:46:23 -0500 +Subject: [PATCH] Use OSX-specific SOFLAGS when building shared lib. + +Details: +- Use linker flags and shared library suffix specific to OSX/Darwin when + the user appears to be building in OSX/Darwin. The OS is queried using + 'uname -s'. Thanks to Adam J. Stewart for reporting this issue in #23. +- Substitute os_name from configure into config.mk (and echo in + post-configure.sh). +- Substitute CC_VENDOR from configure into config.mk (and echo in + post-configure.sh). This variable isn't needed yet, but may be in the + future. +- Autoconf update to configure. +- Whitespace changes. +--- + Makefile | 22 +++++++++++++++++++++- + build/ac-macros/fla_observe_os_name.m4 | 11 +++++++++++ + build/ac-macros/fla_require_cc.m4 | 8 ++++++-- + build/config.mk.in | 5 +++++ + build/post-configure.sh.in | 5 +++++ + configure | 15 +++++++++++++++ + configure.ac | 3 +++ + 7 files changed, 66 insertions(+), 3 deletions(-) + create mode 100644 build/ac-macros/fla_observe_os_name.m4 + +diff --git a/Makefile b/Makefile +index 6bd8bdce..f9681439 100644 +--- a/Makefile ++++ b/Makefile +@@ -92,7 +92,12 @@ endif + + # --- Shared library extension --- + +-SHLIB_EXT := so ++# The shared (dynamic) library file suffix is different for Linux and OS X. ++ifeq ($(OS_NAME),Darwin) ++SHLIB_EXT := dylib ++else ++SHLIB_EXT := so ++endif + + # --- Library names --- + +@@ -107,8 +112,15 @@ LIBFLAME_SO := $(LIBFLAME).$(SHLIB_EXT) + LIBFLAME_A_PATH := $(BASE_LIB_PATH)/$(LIBFLAME_A) + LIBFLAME_SO_PATH := $(BASE_LIB_PATH)/$(LIBFLAME_SO) + ++ifeq ($(OS_NAME),Darwin) ++# OS X shared library extensions. ++LIBFLAME_SO_MAJ_EXT := $(SO_MAJOR).$(SHLIB_EXT) ++LIBFLAME_SO_MMB_EXT := $(SO_MMB).$(SHLIB_EXT) ++else ++# Linux shared library extensions. + LIBFLAME_SO_MAJ_EXT := $(SHLIB_EXT).$(SO_MAJOR) + LIBFLAME_SO_MMB_EXT := $(SHLIB_EXT).$(SO_MMB) ++endif + + LIBFLAME_SONAME := $(LIBFLAME).$(LIBFLAME_SO_MAJ_EXT) + LIBFLAME_SO_MAJ_PATH := $(BASE_LIB_PATH)/$(LIBFLAME_SONAME) +@@ -124,8 +136,15 @@ LIBFLAME_SO_OUTPUT_NAME := $(LIBFLAME_SO_PATH) + + # Specify the shared library's 'soname' field. + # NOTE: The flag for creating shared objects is different for Linux and OS X. ++ifeq ($(OS_NAME),Darwin) ++# OS X shared library link flags. ++SOFLAGS := -dynamiclib ++SOFLAGS += -Wl,-install_name,$(LIBFLAME_SONAME) ++else + SOFLAGS := -shared ++# Linux shared library link flags. + SOFLAGS += -Wl,-soname,$(LIBFLAME_SONAME) ++endif + + + +diff --git a/build/ac-macros/fla_observe_os_name.m4 b/build/ac-macros/fla_observe_os_name.m4 +new file mode 100644 +index 00000000..d3dbbf99 +--- /dev/null ++++ b/build/ac-macros/fla_observe_os_name.m4 +@@ -0,0 +1,11 @@ ++AC_DEFUN([FLA_OBSERVE_OS_NAME], ++[ ++ os_name=$(uname -s) ++ os_vers=$(uname -r) ++ ++ dnl os_name_esc=$(echo "${os_name}" | sed 's/\//\\\//g') ++ ++ dnl Substitute the OS name and version into autoconf output files ++ AC_SUBST(os_name) ++ AC_SUBST(os_vers) ++]) +diff --git a/build/ac-macros/fla_require_cc.m4 b/build/ac-macros/fla_require_cc.m4 +index 7f8131d8..5dd7cd38 100644 +--- a/build/ac-macros/fla_require_cc.m4 ++++ b/build/ac-macros/fla_require_cc.m4 +@@ -6,19 +6,23 @@ AC_DEFUN([FLA_REQUIRE_CC], + dnl whether the user provided his own definition of CFLAGS. + fla_userdef_cflags=$CFLAGS + +- dnl Find a C compiler. ++ dnl Find a C compiler. + dnl If the CC environment variable is not already set, search for the + dnl compiler defined by fla_requested_cc (which may be empty) and then + dnl continue searching for the compilers in $fla_c_compiler_list, if + dnl necessary. Also, if the C compiler found is not in ANSI mode, then + dnl try to add an option to make it so. If the GNU gcc was found, then +- dnl GCC shell variable is set to `yes'. ++ dnl GCC shell variable is set to `yes'. + AC_PROG_CC([$fla_requested_cc $fla_c_compiler_list]) + + if test "$CC" = "" ; then + AC_MSG_ERROR([Could not locate any of the following C compilers: $CC $fla_requested_cc $fla_c_compiler_list. Cannot continue without a C compiler.],[1]) + fi ++ ++ dnl Ascertain the compiler "vendor". ++ CC_VENDOR=$(echo "$CC" | egrep -o 'icc|gcc|clang|emcc|pnacl|IBM' | { read first rest ; echo $first ; }) + + dnl Substitute the user-defined CFLAGS into the autoconf output files. + AC_SUBST(fla_userdef_cflags) ++ AC_SUBST(CC_VENDOR) + ]) +diff --git a/build/config.mk.in b/build/config.mk.in +index c4679b51..37cedb96 100644 +--- a/build/config.mk.in ++++ b/build/config.mk.in +@@ -28,6 +28,10 @@ SO_MMB := $(SO_MAJOR).$(SO_MINORB) + # library name. + ARCH := @fla_host_cpu@ + ++# This variable identifies the operating system / kernel. It is the result of ++# 'uname -s'. ++OS_NAME := @os_name@ ++ + # We have to set these particular variables because some of the @anchors@ + # that are substituted in via configure may be defined *in terms of* these + # variables. For example, @libdir@ may be replaced with '${exec_prefix}/lib', +@@ -101,6 +105,7 @@ EMPTY_FILE := /dev/null + + # --- Determine the C compiler and related flags --- + CC := @CC@ ++CC_VENDOR := @CC_VENDOR@ + CPPROCFLAGS := -D_POSIX_C_SOURCE=200809L @DEFS@ @fla_blis_flags@ + CMISCFLAGS := @fla_c_lang_flags@ @fla_c_openmp_flags@ @fla_c_prof_flags@ + CDBGFLAGS := @fla_c_debug_flags@ +diff --git a/build/post-configure.sh.in b/build/post-configure.sh.in +index 26f9110d..61d59bca 100755 +--- a/build/post-configure.sh.in ++++ b/build/post-configure.sh.in +@@ -17,6 +17,10 @@ echo "" + echo "build system type............................... : @build@" + echo "host system type................................ : @host@" + ++echo "" ++echo "OS name......................................... : @os_name@" ++echo "OS version...................................... : @os_vers@" ++ + echo "" + echo "Enable verbose make output...................... : @fla_enable_verbose_make_output@" + +@@ -25,6 +29,7 @@ echo "Enable maximum argument list hack............... : @fla_enable_max_arg_lis + + echo "" + echo "C compiler...................................... : @CC@" ++echo "C compiler vendor............................... : @CC_VENDOR@" + echo "Library archiver................................ : @AR@" + echo "Library archive indexer......................... : @RANLIB@" + +diff --git a/configure b/configure +index c3d19bbc..1e24f9a5 100755 +--- a/configure ++++ b/configure +@@ -698,6 +698,7 @@ INSTALL_SCRIPT + INSTALL_PROGRAM + RANLIB + AR ++CC_VENDOR + fla_userdef_cflags + OBJEXT + EXEEXT +@@ -707,6 +708,8 @@ LDFLAGS + CFLAGS + CC + fla_gnu_make_found ++os_vers ++os_name + fla_host_cpu + host_os + host_vendor +@@ -2738,6 +2741,15 @@ case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac + + + ++ os_name=$(uname -s) ++ os_vers=$(uname -r) ++ ++ ++ ++ ++ ++ ++ + + + +@@ -3462,6 +3474,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu + as_fn_error 1 "Could not locate any of the following C compilers: $CC $fla_requested_cc $fla_c_compiler_list. Cannot continue without a C compiler." "$LINENO" 5 + fi + ++ CC_VENDOR=$(echo "$CC" | egrep -o 'icc|gcc|clang|emcc|pnacl|IBM' | { read first rest ; echo $first ; }) ++ ++ + + + +diff --git a/configure.ac b/configure.ac +index 790ac90e..d8b0e6b0 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -227,6 +227,9 @@ dnl AC_PROG_CC and AC_PROG_F77 marcos in the variables fla_c_compiler_list and + dnl fla_f77_compiler_list, respectively. + FLA_OBSERVE_HOST_CPU_TYPE + ++dnl Set the @os_name@ output variable to the output of 'uname -s'. ++FLA_OBSERVE_OS_NAME ++ + dnl Set the default value of the $prefix value, normally set by the --prefix + dnl option to configure. + dnl AC_PREFIX_DEFAULT([$HOME/flame]) diff --git a/var/spack/repos/builtin/packages/libflame/package.py b/var/spack/repos/builtin/packages/libflame/package.py index 7c5beda2f88..9ed5baec597 100644 --- a/var/spack/repos/builtin/packages/libflame/package.py +++ b/var/spack/repos/builtin/packages/libflame/package.py @@ -60,6 +60,10 @@ class Libflame(AutotoolsPackage): # https://github.com/flame/libflame/issues/24 patch('Makefile_5.2.0.patch', when='@5.2.0') + # Problems building on macOS: + # https://github.com/flame/libflame/issues/23 + patch('Makefile_5.2.0_darwin.patch', when='@5.2.0') + def flag_handler(self, name, flags): # -std=gnu99 at least required, old versions of GCC default to -std=c90 if self.spec.satisfies('%gcc@:5.1') and name == 'cflags': @@ -104,3 +108,9 @@ def configure_args(self): config_args.append("--enable-max-arg-list-hack") return config_args + + @run_after('install') + def darwin_fix(self): + # The shared library is not installed correctly on Darwin; fix this + if self.spec.satisfies('platform=darwin'): + fix_darwin_install_name(self.prefix.lib) From e6cae978b8018f87d1129cbb7a33f0f27d9c497b Mon Sep 17 00:00:00 2001 From: Matthieu Dorier Date: Wed, 25 Sep 2019 18:41:02 -0500 Subject: [PATCH 030/499] llvm, mesa: update target comparison semantics (#12914) * llvm: fixed issues with syntax and formatting * use spec.architecture.target.family * use spec.target instead of spec.architecture.target * mesa: use == instead of __contains__ --- var/spack/repos/builtin/packages/llvm/package.py | 15 +++++++++------ var/spack/repos/builtin/packages/mesa/package.py | 2 +- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 407898d5f09..5946d6c784f 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -683,16 +683,19 @@ def cmake_args(self): # hence the test to see if the version starts with "flang". targets.append('CppBackend') - if 'x86' in spec.architecture.target.lower(): + if spec.target.family == 'x86' or spec.target.family == 'x86_64': targets.append('X86') - elif 'arm' in spec.architecture.target.lower(): + elif spec.target.family == 'arm': targets.append('ARM') - elif 'aarch64' in spec.architecture.target.lower(): + elif spec.target.family == 'aarch64': targets.append('AArch64') - elif 'sparc' in spec.architecture.target.lower(): + elif (spec.target.family == 'sparc' or + spec.target.family == 'sparc64'): targets.append('Sparc') - elif ('ppc' in spec.architecture.target.lower() or - 'power' in spec.architecture.target.lower()): + elif (spec.target.family == 'ppc64' or + spec.target.family == 'ppc64le' or + spec.target.family == 'ppc' or + spec.target.family == 'ppcle'): targets.append('PowerPC') cmake_args.append( diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py index dba6c5d982d..918ae841d08 100644 --- a/var/spack/repos/builtin/packages/mesa/package.py +++ b/var/spack/repos/builtin/packages/mesa/package.py @@ -101,7 +101,7 @@ def configure_args(self): args_gallium_drivers = ['swrast'] args_dri_drivers = [] - if 'arm' in spec.architecture.target.lower(): + if spec.target.family == 'arm': args.append('--disable-libunwind') num_frontends = 0 From 507b28de1888b2f0948f11843973d278f0886573 Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 25 Sep 2019 18:44:57 -0700 Subject: [PATCH 031/499] py-imageio package: add versions 2.4.1 and 2.5.0 (#12884) --- var/spack/repos/builtin/packages/py-imageio/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/py-imageio/package.py b/var/spack/repos/builtin/packages/py-imageio/package.py index 6496ec61795..6fec54c19c4 100644 --- a/var/spack/repos/builtin/packages/py-imageio/package.py +++ b/var/spack/repos/builtin/packages/py-imageio/package.py @@ -15,6 +15,8 @@ class PyImageio(PythonPackage): homepage = "http://imageio.github.io/" url = "https://pypi.io/packages/source/i/imageio/imageio-2.3.0.tar.gz" + version('2.5.0', sha256='42e65aadfc3d57a1043615c92bdf6319b67589e49a0aae2b985b82144aceacad') + version('2.4.1', sha256='16b8077bc8a5fa7a58b3e744f7ecbb156d8c088132df31e0f4f546c98de3514a') version('2.3.0', '4722c4e1c366748abcb18729881cffb8') # TODO: Add variants for plugins, and optional dependencies From c5860d89b7aaca7891d76a1b8fec10321c756136 Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 25 Sep 2019 18:48:48 -0700 Subject: [PATCH 032/499] libspatialite package: add version 3.0.1 and missing dependencies (#12843) --- .../repos/builtin/packages/libspatialite/package.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/libspatialite/package.py b/var/spack/repos/builtin/packages/libspatialite/package.py index e8113894362..abf40719fa2 100644 --- a/var/spack/repos/builtin/packages/libspatialite/package.py +++ b/var/spack/repos/builtin/packages/libspatialite/package.py @@ -11,11 +11,15 @@ class Libspatialite(AutotoolsPackage): SQLite core to support fully fledged Spatial SQL capabilities.""" homepage = "http://www.gaia-gis.it" - url = "http://www.gaia-gis.it/gaia-sins/libspatialite-4.3.0a.tar.gz" + url = "http://www.gaia-gis.it/gaia-sins/libspatialite-sources/libspatialite-4.3.0a.tar.gz" - version('4.3.0a', '6b380b332c00da6f76f432b10a1a338c') + version('4.3.0a', sha256='88900030a4762904a7880273f292e5e8ca6b15b7c6c3fb88ffa9e67ee8a5a499') + version('3.0.1', sha256='4983d6584069fd5ff0cfcccccee1015088dab2db177c0dc7050ce8306b68f8e6') - depends_on('sqlite') + depends_on('pkg-config', type='build') + depends_on('sqlite+rtree') depends_on('proj@:5') depends_on('geos') depends_on('freexl') + depends_on('libiconv') + depends_on('libxml2') From dd626a0f07e356e2f4c986125ded86ea1c83b072 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 25 Sep 2019 21:04:57 -0500 Subject: [PATCH 033/499] interproscan package: add version 4.8, patch for version 5 (#12897) This PR adds interproscan-4.8, which has a completely different build system than version 5. Note that this builds for running on a host as opposed to a queue system. I am fairly certain that a queue system can be configured later. This PR also adds a patch for intrproscan-5 to build when the user building the packages has a large GID by setting posix mode for tar. --- .../packages/interproscan/large-gid.patch | 22 +++ .../interproscan/non-interactive.patch | 165 ++++++++++++++++++ .../builtin/packages/interproscan/package.py | 38 +++- 3 files changed, 222 insertions(+), 3 deletions(-) create mode 100644 var/spack/repos/builtin/packages/interproscan/large-gid.patch create mode 100644 var/spack/repos/builtin/packages/interproscan/non-interactive.patch diff --git a/var/spack/repos/builtin/packages/interproscan/large-gid.patch b/var/spack/repos/builtin/packages/interproscan/large-gid.patch new file mode 100644 index 00000000000..7e06b694f89 --- /dev/null +++ b/var/spack/repos/builtin/packages/interproscan/large-gid.patch @@ -0,0 +1,22 @@ +diff -ruN a/core/jms-implementation/pom.xml b/core/jms-implementation/pom.xml +--- a/core/jms-implementation/pom.xml 2019-07-03 04:17:42.000000000 -0500 ++++ b/core/jms-implementation/pom.xml 2019-09-21 10:20:42.710868269 -0500 +@@ -275,6 +275,7 @@ + + assembly.xml + ++ posix + interproscan-5 + + +diff -ruN a/core/precalcmatches/berkeley/pom.xml b/core/precalcmatches/berkeley/pom.xml +--- a/core/precalcmatches/berkeley/pom.xml 2019-07-03 04:17:42.000000000 -0500 ++++ b/core/precalcmatches/berkeley/pom.xml 2019-09-21 10:21:16.874804845 -0500 +@@ -41,6 +41,7 @@ + + assembly.xml + ++ posix + berkeley-db-builder + + diff --git a/var/spack/repos/builtin/packages/interproscan/non-interactive.patch b/var/spack/repos/builtin/packages/interproscan/non-interactive.patch new file mode 100644 index 00000000000..a658c7c53d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/interproscan/non-interactive.patch @@ -0,0 +1,165 @@ +--- a/Config.pl 2019-09-21 20:28:01.980128054 -0500 ++++ b/Config.pl 2019-09-21 21:45:50.926522289 -0500 +@@ -75,11 +75,12 @@ + close INS; + } + +-$insDone = get_user_prompt('Reconfigure everything? (first time install)', $insDone, '(y|n)'); ++$insDone = 'y'; + + $Tip = "!\n! InterProScan needs to know where it is installed and where perl is installed\n!"; + + undef($set_path); ++$set_path = 'y'; + + while(!defined($set_path)){ + $set_path = get_user_prompt('Do you want to set paths to perl and the installation directory?', $insDone, 'y|n', $Tip); +@@ -106,7 +107,7 @@ + $suggest_path = $HOME if($HOME ne ""); + chomp($suggest_path); + +- $install_path = get_user_prompt('Please enter the full path for the InterProScan installation', $suggest_path, '.+', $Tip); ++ $install_path = $suggest_path; + + unless ( -d $install_path ) + { +@@ -121,7 +122,7 @@ + #Setting the iprscan home installation path + for(@homechange){ + my $file = $install_path . $ARG; +- patch_file($file, "\\\$ENV{IPRSCAN_HOME}", "$install_path"); ++ patch_file($file, "\\\$ENV\\\{IPRSCAN_HOME\\\}", "$install_path"); + patch_file($file, "IPRSCAN_HOME", "$install_path", 1); + } + +@@ -133,7 +134,7 @@ + undef($res); + + while(!defined($res)){ +- $res = get_user_prompt("Do you want to set another Perl command in place of [$PERL_CMD]?", 'n' , 'y|n'); ++ $res = $PERL_CMD; + unless(defined($res)){ + print STDOUT "WARNING: The input is not valid must be \'y\' or \'n\', try again\n"; + undef($res); +@@ -174,7 +175,7 @@ + unless(open(MOD, ">$PWD/test.pl")){ + die "FATAL: Could not open $PWD/test.pl in writing mode to test for presence of modules :$!\n"; + } +- print MOD "#!$PERL_CMD\n"; ++ print MOD "#!/usr/bin/env perl\n"; + print MOD "use $ARG;\n"; + print MOD "1;\n"; + close MOD; +@@ -203,7 +204,7 @@ + $Tip = "!\n! To cope with bulk jobs and to enable efficient parallelization, InterProScan splits input files\n" + ."! with FASTA formatted sequences into smaller parts (chunks). Default size is \"100\" sequences per chunk\n!"; + +-$setcnk = get_user_prompt('Do you want to setup chunk size', $insDone, '(y|n)', $Tip); ++$setcnk = 'y'; + my $chunkz; + + if ($setcnk eq "y") +@@ -211,7 +212,7 @@ + $Tip = "!\n! Here you should specify the maximum number of sequences allowed in each part (chunk). Please note\n" + ."! it is not recommended to have more then 3000 chunks.\n!"; + +- $chunkz = get_user_prompt('Enter chunk size', '100', '[0-9]+', $Tip); ++ $chunkz = '100'; + } + print STDOUT "\n"; + +@@ -225,7 +226,7 @@ + + my($maxinaa, $maxinnt, $maxlennt, $minlenaa, $minorflen, $cdntable) = (undef, undef, undef, undef, undef, undef); + +-my $setseq = get_user_prompt('Do you want to configure this?', $insDone, '(y|n)', $Tip); ++my $setseq = 'y'; + + if($setseq eq 'y'){ + $maxinaa = '1000'; +@@ -234,13 +235,6 @@ + $minlenaa = '5'; + $minorflen = '50'; + $cdntable = '0'; +- +- $maxinaa = get_user_prompt('Enter the maximum number of input protein sequences allowed', $maxinaa, '\d+'); +- $maxinnt = get_user_prompt('Enter the maximum number of input nucleic sequences allowed', $maxinnt, '\d+'); +- $maxlennt = get_user_prompt('Enter the maximum length (in nucleic acids) for a nucleotide sequence', $maxlennt, '\d+'); +- $minlenaa = get_user_prompt('Enter the minimum length (in amino acids) for a protein sequence', $minlenaa, '\d+'); +- $minorflen = get_user_prompt('Enter the minimum allowed length of a translated orf', $minorflen, '\d+'); +- $cdntable = get_user_prompt('Enter the default codon table value to use to translate dna/rna in six frames', $cdntable, '\d+'); + } + print STDOUT "\n"; + +@@ -249,7 +243,7 @@ + ."! set up a particular search tool against a database and how exactly that application will be configured to run\n" + ."! in this next section. You will configure the queue systems (if any) you will use, first\n!"; + +-$applset = get_user_prompt('Do you want to setup applications (if you don\'t, no applications will be included in InterProScan by default)?', $insDone, '(y|n)', $Tip); ++$applset = 'y'; + my @setAppl = (); + + if($applset eq "y"){ +@@ -258,7 +252,7 @@ + ."! Currently, we mainly support LSF (which is used at EBI) however, we also provide configuration files for other systems\n" + ."! which are listed in the documentation\n!"; + +- $UseQ = get_user_prompt('Do you wish to use a queue system?', 'n', '(y|n)', $Tip); ++ $UseQ = 'n'; + $Qsys = undef; + + my $cluster = 'foo'; +@@ -395,7 +389,7 @@ + + #Defining local host name and arch + my $supported_arch = 'OSF1|IRIX64|Linux|SunOS|Darwin|AIX'; +- ($local_server = `hostname`); ++ ($local_server = 'localhost'); + ($local_arch = `uname`); + ($serv = $local_server); + $local_server =~ s/\n//g; +@@ -416,7 +410,7 @@ + + my $rep = ($ARG eq "tmhmm" || $ARG eq "signalp" ? 'n' : 'y'); + $Tip = "! ".ucfirst($ARG) . " " . $appldesc->{$ARG}; +- my $useappl = get_user_prompt("Do you want to use $ARG ?", $rep, '(y|n)', $Tip); ++ my $useappl = 'y'; + my $linkdone = "$HOME/bin/binaries"; + my $arch = `uname`; + $arch =~ s/\n//g; +@@ -502,7 +496,7 @@ + + SERVER : while(!defined($res_server)){ + +- $res_server = get_user_prompt("\nPlease enter the execution host name of $ARG (or if you want to run locally, enter \'localhost\')", $serv, '\S+'); ++ $res_server = 'localhost'; + chomp($res_server); + if($local_server ne $res_server){ + # rsh command has different behavior depending on the shell type. +@@ -658,7 +652,7 @@ + $Tip = "!\n! You can specify an email address for the administrator. By default it will be you ($ENV{USER})\n" + ."! Administrators receive an email when a problem occurs in InterProScan.\n!"; + +- $user = get_user_prompt("Do you want to set an administrator email address?", 'y', 'y|n', $Tip); ++ $user = 'n'; + if($user eq 'y'){ + $user = get_user_prompt("Please enter the email address of the administrator:", '', '[\w\.\-]+\@[\w\.\-]+'); + }else{ +@@ -735,7 +729,7 @@ + + $Tip = "!\n! InterProScan can be launched through a web interface. It can also be launched through secure HTTP (https)\n!"; + +-my $useWeb = get_user_prompt("Do you want to run InterProScan using a web interface?", 'n', 'y|n', $Tip); ++my $useWeb = 'n'; + my $HTTPProto; + if($useWeb eq 'y'){ + +@@ -816,7 +810,7 @@ + $Tip = "!\n! We would appreciate it if you would register your installation of InterProScan. This will allow us to notify you\n" + ."! of bug fixes and new releases of the software. We will not use your email address for any other purpose.\n!"; + +-my $register = get_user_prompt("Would you like to register InterProScan?", $insDone, '(y|n)', $Tip); ++my $register = 'n'; + if ($register eq "y") + { + my $org_name = get_user_prompt("What is the name of your organization?", '', '\S+'); diff --git a/var/spack/repos/builtin/packages/interproscan/package.py b/var/spack/repos/builtin/packages/interproscan/package.py index 85af451423c..dcd09fa54a4 100644 --- a/var/spack/repos/builtin/packages/interproscan/package.py +++ b/var/spack/repos/builtin/packages/interproscan/package.py @@ -16,11 +16,30 @@ class Interproscan(Package): url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz" version('5.36-75.0', sha256='383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb') + version('4.8', + sha256='f1cb0ae1218eb05ed59ad7f94883f474eb9a6185a56ad3a93a364acb73506a3f', + url='ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/4/RELEASE/4.8/iprscan_v4.8.tar.gz') - depends_on('java@8.0:8.9', type=('build', 'run')) - depends_on('maven', type='build') + resource( + when='@:4.8', + name='binaries', + url="http://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/BIN/4.x/iprscan_bin4.x_Linux64.tar.gz", + sha256='551610a4682b112522f3ded5268f76ba9a47399a72e726fafb17cc938a50e7ee', + ) + + depends_on('java@8.0:8.9', when='@5:', type=('build', 'run')) + depends_on('maven', when='@5:', type='build') + depends_on('python@3:', when='@5:', type=('build', 'run')) depends_on('perl@5:', type=('build', 'run')) - depends_on('python@3:', type=('build', 'run')) + depends_on('perl-cgi', when='@:4.8', type=('build', 'run')) + depends_on('perl-mailtools', when='@:4.8', type=('build', 'run')) + depends_on('perl-xml-quote', when='@:4.8', type=('build', 'run')) + depends_on('perl-xml-parser', when='@:4.8', type=('build', 'run')) + depends_on('perl-io-string', when='@:4.8', type=('build', 'run')) + depends_on('perl-io-stringy', when='@:4.8', type=('build', 'run')) + + patch('large-gid.patch', when='@5:') + patch('non-interactive.patch', when='@:4.8') def install(self, spec, prefix): with working_dir('core'): @@ -31,3 +50,16 @@ def install(self, spec, prefix): # link the main shell script into the PATH ips_bin_suffix = 'core/jms-implementation/target/interproscan-5-dist' symlink(join_path(prefix, ips_bin_suffix), prefix.bin) + + @when('@:4.8') + def install(self, spec, prefix): + perl = which('perl') + + src = join_path(self.stage.source_path, 'iprscan', 'bin', 'Linux') + dst = join_path(self.stage.source_path, 'bin', 'binaries') + force_symlink(src, dst) + + install_tree('.', prefix) + + with working_dir(prefix): + perl('Config.pl') From b384504218b47facd885bad3e9933e945a7de6a4 Mon Sep 17 00:00:00 2001 From: liuyangzhuan Date: Wed, 25 Sep 2019 19:16:47 -0700 Subject: [PATCH 034/499] butterflypack package: add version 1.0.3 (#12927) --- var/spack/repos/builtin/packages/butterflypack/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/butterflypack/package.py b/var/spack/repos/builtin/packages/butterflypack/package.py index 2b61d69c230..fee827e0648 100644 --- a/var/spack/repos/builtin/packages/butterflypack/package.py +++ b/var/spack/repos/builtin/packages/butterflypack/package.py @@ -22,12 +22,13 @@ class Butterflypack(CMakePackage): homepage = "https://github.com/liuyangzhuan/ButterflyPACK" git = "https://github.com/liuyangzhuan/ButterflyPACK.git" - url = "https://github.com/liuyangzhuan/ButterflyPACK/archive/v1.0.0.tar.gz" + url = "https://github.com/liuyangzhuan/ButterflyPACK/archive/v1.0.3.tar.gz" maintainers = ['liuyangzhuan'] version('master', branch='master') version('1.0.0', sha256='86c5eb09a18522367d63ce2bacf67ca1c9813ef351a1443baaab3c53f0d77232') version('1.0.1', sha256='e8ada37466a19f49e13456b150700d4c3afaad2ddbe3678f4e933f9d556a24a5') + version('1.0.3', sha256='acf9bc98dd7fea31ab73756b68b3333228b53ab0e85400a8250fcc749a1a6656') variant('shared', default=True, description='Build shared libraries') From f2967b6c16effd26ce007cf86cadbb645c574f50 Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Wed, 25 Sep 2019 22:25:24 -0400 Subject: [PATCH 035/499] New package: flibcpp (Fortran bindings to C++ standard library) (#12926) --- .../repos/builtin/packages/flibcpp/package.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/flibcpp/package.py diff --git a/var/spack/repos/builtin/packages/flibcpp/package.py b/var/spack/repos/builtin/packages/flibcpp/package.py new file mode 100644 index 00000000000..b03fa79cbb4 --- /dev/null +++ b/var/spack/repos/builtin/packages/flibcpp/package.py @@ -0,0 +1,44 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Flibcpp(CMakePackage): + """Fortran bindings to the C++ Standard Library. + """ + + homepage = "https://flibcpp.readthedocs.io/en/latest" + git = "https://github.com/swig-fortran/flibcpp.git" + url = "https://github.com/swig-fortran/flibcpp/archive/v0.3.0.tar.gz" + + version('master', branch='master') + version('0.3.1', sha256='871570124122c18018478275d5040b4b787d1966e50ee95b634b0b5e0cd27e91') + + variant('doc', default=False, description='Build and install documentation') + variant('shared', default=True, description='Build shared libraries') + variant('swig', default=False, + description='Regenerate source files using SWIG') + variant('fstd', default='03', values=('none', '03', '08', '15', '18'), + multi=False, description='Build with this Fortran standard') + + depends_on('swig@fortran', type='build', when="+swig") + depends_on('py-sphinx', type='build', when="+doc") + + def cmake_args(self): + spec = self.spec + + def hasopt(key): + return "ON" if ("+" + key) in spec else "OFF" + + testopt = "ON" if self.run_tests else "OFF" + opts = [('BUILD_SHARED_LIBS', hasopt('shared')), + ('BUILD_TESTING', testopt), + ('FLIBCPP_BUILD_DOCS', hasopt('doc')), + ('FLIBCPP_BUILD_EXAMPLES', testopt)] + fstd = spec.variants['fstd'].value + opts.append(('FLIBCPP_FORTRAN_STD', fstd)) + + return ['-D{0}={1}'.format(k, v) for (k, v) in opts] From 78d051b5343af1d5d5125bbdd86a014b469f9efb Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 26 Sep 2019 09:33:18 +0200 Subject: [PATCH 036/499] parsimonator: simplified recipe by removing SIMD variants (#12949) Now the support for SSE3 or AVX is tested on the selected target --- .../builtin/packages/parsimonator/package.py | 60 ++++--------------- 1 file changed, 11 insertions(+), 49 deletions(-) diff --git a/var/spack/repos/builtin/packages/parsimonator/package.py b/var/spack/repos/builtin/packages/parsimonator/package.py index b72525d94de..4ebbac8498b 100644 --- a/var/spack/repos/builtin/packages/parsimonator/package.py +++ b/var/spack/repos/builtin/packages/parsimonator/package.py @@ -3,66 +3,30 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * -from spack.spec import ConflictsInSpecError - class Parsimonator(MakefilePackage): """Parsimonator is a no-frills light-weight implementation for building - starting trees under parsimony for RAxML""" + starting trees under parsimony for RAxML. + """ homepage = "http://www.exelixis-lab.org/" git = "https://github.com/stamatak/Parsimonator-1.0.2.git" version('1.0.2', commit='78368c6ab1e9adc7e9c6ec9256dd7ff2a5bb1b0a') - variant('sse', default=False, description='Enable SSE in order to substantially speed up execution') - variant('avx', default=False, description='Enable AVX in order to substantially speed up execution') - - conflicts('+avx', when='+sse') - patch('nox86.patch') - def flag_handler(self, name, flags): - arch = '' - spec = self.spec - if spec.satisfies("platform=cray"): - # FIXME; It is assumed that cray is x86_64. - # If you support arm on cray, you need to fix it. - arch = 'x86_64' - if arch != 'x86_64' and spec.target.family != 'x86_64': - if spec.satisfies("+sse"): - raise ConflictsInSpecError( - spec, - [( - spec, - spec.architecture.target, - spec.variants['sse'], - '+sse is valid only on x86_64' - )] - ) - if spec.satisfies("+avx"): - raise ConflictsInSpecError( - spec, - [( - spec, - spec.architecture.target, - spec.variants['avx'], - '+avx is valid only on x86_64' - )] - ) - return (flags, None, None) - @property def makefile_file(self): if self.spec.target.family != 'x86_64': return 'Makefile.nosse' - elif '+sse' in self.spec: - return 'Makefile.SSE3.gcc' - elif '+avx' in self.spec: + + if 'avx' in self.spec.target: return 'Makefile.AVX.gcc' - else: - return 'Makefile.gcc' + elif 'sse3' in self.spec.target: + return 'Makefile.SSE3.gcc' + + return 'Makefile.gcc' def edit(self, spec, prefix): makefile = FileFilter(self.makefile_file) @@ -73,11 +37,9 @@ def build(self, spec, prefix): def install(self, spec, prefix): mkdirp(prefix.bin) - if self.spec.target.family != 'x86_64': - install('parsimonator', prefix.bin) - elif '+sse' in spec: - install('parsimonator-SSE3', prefix.bin) - elif '+avx' in spec: + if 'avx' in self.spec.target: install('parsimonator-AVX', prefix.bin) + elif 'sse3' in self.spec.target: + install('parsimonator-SSE3', prefix.bin) else: install('parsimonator', prefix.bin) From 31e5318c240e12d59b01972cbaf92680ef4be6bd Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 26 Sep 2019 10:02:08 +0200 Subject: [PATCH 037/499] Removed references to '(-march|-mtune|-mcpu)=native' (#12948) Now that Spack injects microarchitecture specific optimizations for the selected target, packages should avoid adding flags that could step over those. --- var/spack/repos/builtin/packages/cp2k/package.py | 1 - var/spack/repos/builtin/packages/dealii/package.py | 3 --- var/spack/repos/builtin/packages/elpa/package.py | 4 ++-- var/spack/repos/builtin/packages/hpgmg/package.py | 5 ----- var/spack/repos/builtin/packages/krims/package.py | 2 -- var/spack/repos/builtin/packages/lazyten/package.py | 2 -- var/spack/repos/builtin/packages/libceed/package.py | 4 ---- var/spack/repos/builtin/packages/nanoflann/package.py | 4 +--- var/spack/repos/builtin/packages/rocksdb/package.py | 10 ++++------ var/spack/repos/builtin/packages/tealeaf/package.py | 5 +---- var/spack/repos/tutorial/packages/elpa/package.py | 7 ++----- 11 files changed, 10 insertions(+), 37 deletions(-) diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index 3674ac9c1cf..23edfd10b21 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -160,7 +160,6 @@ def edit(self, spec, prefix): optimization_flags = { 'gcc': [ '-O2', - '-mtune=native', '-funroll-loops', '-ftree-vectorize', ], diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index eac2fc4892e..109b67da2da 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -277,13 +277,10 @@ def cmake_args(self): # https://groups.google.com/forum/?fromgroups#!topic/dealii/3Yjy8CBIrgU if spec.satisfies('%gcc'): cxx_flags_release.extend(['-O3']) - cxx_flags.extend(['-march=native']) elif spec.satisfies('%intel'): cxx_flags_release.extend(['-O3']) - cxx_flags.extend(['-march=native']) elif spec.satisfies('%clang'): cxx_flags_release.extend(['-O3', '-ffp-contract=fast']) - cxx_flags.extend(['-march=native']) # Python bindings if spec.satisfies('@8.5.0:'): diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py index d73371e93c5..cc3f75a4c0c 100644 --- a/var/spack/repos/builtin/packages/elpa/package.py +++ b/var/spack/repos/builtin/packages/elpa/package.py @@ -84,8 +84,8 @@ def configure_args(self): # adjust the C compiler or CFLAGS if '+optflags' in self.spec: options.extend([ - 'FCFLAGS=-O2 -march=native -ffree-line-length-none', - 'CFLAGS=-O2 -march=native' + 'FCFLAGS=-O2 -ffree-line-length-none', + 'CFLAGS=-O2' ]) if '+openmp' in self.spec: options.append('--enable-openmp') diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py index 6807b79ae5e..64d9fafa048 100644 --- a/var/spack/repos/builtin/packages/hpgmg/package.py +++ b/var/spack/repos/builtin/packages/hpgmg/package.py @@ -66,11 +66,6 @@ def configure_args(self): cflags.append('-g') elif any(map(self.spec.satisfies, ['%gcc', '%clang', '%intel'])): cflags.append('-O3') - if self.compiler.target in ['x86_64']: - cflags.append('-march=native') - elif not self.spec.satisfies('target=aarch64: %gcc@:5.9'): - cflags.append('-mcpu=native') - cflags.append('-mtune=native') else: cflags.append('-O3') diff --git a/var/spack/repos/builtin/packages/krims/package.py b/var/spack/repos/builtin/packages/krims/package.py index 640c2e82da0..3a08b61820a 100644 --- a/var/spack/repos/builtin/packages/krims/package.py +++ b/var/spack/repos/builtin/packages/krims/package.py @@ -58,8 +58,6 @@ def cmake_args(self): "-DAUTOCHECKOUT_MISSING_REPOS=OFF", # "-DBUILD_SHARED_LIBS=" + str("+shared" in spec), - "-DDRB_MACHINE_SPECIFIC_OPTIM_Release=ON", # Adds -march=native - # # TODO Hard-disable tests for now, since rapidcheck not in Spack "-DKRIMS_ENABLE_TESTS=OFF", "-DKRIMS_ENABLE_EXAMPLES=" + str("+examples" in spec), diff --git a/var/spack/repos/builtin/packages/lazyten/package.py b/var/spack/repos/builtin/packages/lazyten/package.py index 3ae9f2c88ca..7a0061a656a 100644 --- a/var/spack/repos/builtin/packages/lazyten/package.py +++ b/var/spack/repos/builtin/packages/lazyten/package.py @@ -71,8 +71,6 @@ def cmake_args(self): "-DAUTOCHECKOUT_MISSING_REPOS=OFF", # "-DBUILD_SHARED_LIBS=" + str("+shared" in spec), - "-DDRB_MACHINE_SPECIFIC_OPTIM_Release=ON", # Adds -march=native - # # TODO Hard-disable tests for now, since rapidcheck not in Spack "-DLAZYTEN_ENABLE_TESTS=OFF", "-DLAZYTEN_ENABLE_EXAMPLES=" + str("+examples" in spec), diff --git a/var/spack/repos/builtin/packages/libceed/package.py b/var/spack/repos/builtin/packages/libceed/package.py index 5eb11a6ef8d..2991b5bc8b4 100644 --- a/var/spack/repos/builtin/packages/libceed/package.py +++ b/var/spack/repos/builtin/packages/libceed/package.py @@ -62,10 +62,6 @@ def common_make_opts(self): opt = '-g' elif compiler.name == 'gcc': opt = '-O3 -g -ffp-contract=fast' - if compiler.target in ['x86_64']: - opt += ' -march=native' - elif compiler.target in ['ppc64le']: - opt += ' -mcpu=native -mtune=native' if compiler.version >= ver(4.9): opt += ' -fopenmp-simd' elif compiler.name == 'clang': diff --git a/var/spack/repos/builtin/packages/nanoflann/package.py b/var/spack/repos/builtin/packages/nanoflann/package.py index 2e5a2594696..d2fe6f642b8 100644 --- a/var/spack/repos/builtin/packages/nanoflann/package.py +++ b/var/spack/repos/builtin/packages/nanoflann/package.py @@ -16,9 +16,7 @@ class Nanoflann(CMakePackage): version('1.2.3', '92a0f44a631c41aa06f9716c51dcdb11') def patch(self): - if self.spec.target.family == 'aarch64' and \ - self.spec.satisfies('%gcc@:5.9'): - filter_file('-mtune=native', '', 'CMakeLists.txt') + filter_file('-mtune=native', '', 'CMakeLists.txt') def cmake_args(self): args = ['-DBUILD_SHARED_LIBS=ON'] diff --git a/var/spack/repos/builtin/packages/rocksdb/package.py b/var/spack/repos/builtin/packages/rocksdb/package.py index 4d13393dde0..e002c5b14e8 100644 --- a/var/spack/repos/builtin/packages/rocksdb/package.py +++ b/var/spack/repos/builtin/packages/rocksdb/package.py @@ -35,12 +35,10 @@ class Rocksdb(MakefilePackage): phases = ['install'] def patch(self): - if (self.spec.target.family == 'aarch64' and - self.spec.satisfies('%gcc@:5.9')): - filter_file( - '-march=native', '', - join_path('build_tools', 'build_detect_platform') - ) + filter_file( + '-march=native', '', + join_path('build_tools', 'build_detect_platform') + ) def install(self, spec, prefix): cflags = [] diff --git a/var/spack/repos/builtin/packages/tealeaf/package.py b/var/spack/repos/builtin/packages/tealeaf/package.py index 49b13251afc..4a720fa115e 100644 --- a/var/spack/repos/builtin/packages/tealeaf/package.py +++ b/var/spack/repos/builtin/packages/tealeaf/package.py @@ -25,10 +25,7 @@ class Tealeaf(MakefilePackage): depends_on('mpi') def edit(self, spec, prefix): - if spec.target.family == 'aarch64' and spec.satisfies('%gcc@:5.9'): - filter_file( - '-march=native', '', join_path('TeaLeaf_ref', 'Makefile') - ) + filter_file('-march=native', '', join_path('TeaLeaf_ref', 'Makefile')) @property def build_targets(self): diff --git a/var/spack/repos/tutorial/packages/elpa/package.py b/var/spack/repos/tutorial/packages/elpa/package.py index 9ddae2b8b77..f8c4ca78731 100644 --- a/var/spack/repos/tutorial/packages/elpa/package.py +++ b/var/spack/repos/tutorial/packages/elpa/package.py @@ -65,13 +65,10 @@ def configure_args(self): # https://src.fedoraproject.org/cgit/rpms/elpa.git/ # https://packages.qa.debian.org/e/elpa.html options = [] - # without -march=native there is configure error for 2017.05.02 - # Could not compile test program, try with --disable-sse, or - # adjust the C compiler or CFLAGS if '+optflags' in self.spec: options.extend([ - 'FCFLAGS=-O2 -march=native -ffree-line-length-none', - 'CFLAGS=-O2 -march=native' + 'FCFLAGS=-O2 -ffree-line-length-none', + 'CFLAGS=-O2' ]) if '+openmp' in self.spec: options.append('--enable-openmp') From 90236bc9f54a0fccbf0e133d09ce258b379e5ae3 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 26 Sep 2019 10:25:12 +0200 Subject: [PATCH 038/499] Update target comparison semantic for a few packages (#12947) Use spec.target.family instead of spec.architecture.target --- .../repos/builtin/packages/blast-plus/package.py | 2 +- .../repos/builtin/packages/catalyst/package.py | 3 +-- .../repos/builtin/packages/hpctoolkit/package.py | 3 +-- .../repos/builtin/packages/openfoam/package.py | 4 ++-- var/spack/repos/builtin/packages/ross/package.py | 2 +- .../repos/builtin/packages/templight/package.py | 14 ++++++++------ 6 files changed, 14 insertions(+), 14 deletions(-) diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py index c02d0107762..7722e1b2a4e 100644 --- a/var/spack/repos/builtin/packages/blast-plus/package.py +++ b/var/spack/repos/builtin/packages/blast-plus/package.py @@ -105,7 +105,7 @@ def configure_args(self): '--without-boost', ] - if 'aarch64' not in spec.architecture.target.lower(): + if spec.target.family != 'aarch64': config_args.append('--with-64') if '+static' in spec: config_args.append('--with-static') diff --git a/var/spack/repos/builtin/packages/catalyst/package.py b/var/spack/repos/builtin/packages/catalyst/package.py index 6c62aa0039f..1289ace5241 100644 --- a/var/spack/repos/builtin/packages/catalyst/package.py +++ b/var/spack/repos/builtin/packages/catalyst/package.py @@ -225,8 +225,7 @@ def nvariant_bool(feature): else: cmake_args.append('-DPARAVIEW_ENABLE_PYTHON:BOOL=OFF') - arch = spec.architecture - if(arch.platform == 'linux' and arch.target == 'aarch64'): + if spec.platform == 'linux' and spec.target == 'aarch64': cmake_args.append('-DCMAKE_CXX_FLAGS=-DPNG_ARM_NEON_OPT=0') cmake_args.append('-DCMAKE_C_FLAGS=-DPNG_ARM_NEON_OPT=0') diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py index f149537a511..e10b447dca9 100644 --- a/var/spack/repos/builtin/packages/hpctoolkit/package.py +++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py @@ -90,7 +90,6 @@ class Hpctoolkit(AutotoolsPackage): def configure_args(self): spec = self.spec - target = spec.architecture.target args = [ '--with-binutils=%s' % spec['binutils'].prefix, @@ -117,7 +116,7 @@ def configure_args(self): if spec.satisfies('@gpu'): args.append('--with-mbedtls=%s' % spec['mbedtls'].prefix) - if target == 'x86_64': + if spec.target.family == 'x86_64': args.append('--with-xed=%s' % spec['intel-xed'].prefix) if '+papi' in spec: diff --git a/var/spack/repos/builtin/packages/openfoam/package.py b/var/spack/repos/builtin/packages/openfoam/package.py index 5ee8bcf0bbf..2a1bdb6e0e2 100644 --- a/var/spack/repos/builtin/packages/openfoam/package.py +++ b/var/spack/repos/builtin/packages/openfoam/package.py @@ -788,8 +788,8 @@ def __init__(self, spec, **kwargs): # spec.architecture.platform is like `uname -s`, but lower-case platform = spec.architecture.platform - # spec.architecture.target is like `uname -m` - target = spec.architecture.target + # spec.target.family is like `uname -m` + target = spec.target.family if platform == 'linux': if target == 'x86_64': diff --git a/var/spack/repos/builtin/packages/ross/package.py b/var/spack/repos/builtin/packages/ross/package.py index 13a2624ec24..62d65cc0957 100644 --- a/var/spack/repos/builtin/packages/ross/package.py +++ b/var/spack/repos/builtin/packages/ross/package.py @@ -26,7 +26,7 @@ def cmake_args(self): args = [] args.append("-DBUILD_SHARED_LIBS=ON") - args.append("-DARCH=%s" % self.spec.architecture.target) + args.append("-DARCH=%s" % self.spec.target) args.append("-DCMAKE_C_COMPILER=%s" % self.spec['mpi'].mpicc) args.append("-DCMAKE_CXX_COMPILER=%s" % self.spec['mpi'].mpicxx) diff --git a/var/spack/repos/builtin/packages/templight/package.py b/var/spack/repos/builtin/packages/templight/package.py index 1a492bc82c5..34f75964e10 100644 --- a/var/spack/repos/builtin/packages/templight/package.py +++ b/var/spack/repos/builtin/packages/templight/package.py @@ -135,16 +135,18 @@ def cmake_args(self): targets = ['NVPTX', 'AMDGPU'] - if 'x86' in spec.architecture.target.lower(): + if spec.target.family == 'x86' or spec.target.family == 'x86_64': targets.append('X86') - elif 'arm' in spec.architecture.target.lower(): + elif spec.target.family == 'arm': targets.append('ARM') - elif 'aarch64' in spec.architecture.target.lower(): + elif spec.target.family == 'aarch64': targets.append('AArch64') - elif 'sparc' in spec.architecture.target.lower(): + elif spec.target.family == 'sparc' or spec.target.family == 'sparc64': targets.append('Sparc') - elif ('ppc' in spec.architecture.target.lower() or - 'power' in spec.architecture.target.lower()): + elif (spec.target.family == 'ppc64' or + spec.target.family == 'ppc64le' or + spec.target.family == 'ppc' or + spec.target.family == 'ppcle'): targets.append('PowerPC') cmake_args.append( From 321e956fa94d3e5faf9c96c249f25275c7aa60ca Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Thu, 26 Sep 2019 11:48:22 -0500 Subject: [PATCH 039/499] External: add macholib and altgraph needed to relocate Mach-o binaries on Linux (#12909) --- COPYRIGHT | 8 + lib/spack/external/__init__.py | 14 + lib/spack/external/altgraph/Dot.py | 309 +++ lib/spack/external/altgraph/Graph.py | 680 +++++++ lib/spack/external/altgraph/GraphAlgo.py | 166 ++ lib/spack/external/altgraph/GraphStat.py | 73 + lib/spack/external/altgraph/GraphUtil.py | 144 ++ lib/spack/external/altgraph/ObjectGraph.py | 212 +++ lib/spack/external/altgraph/__init__.py | 147 ++ lib/spack/external/macholib/MachO.py | 435 +++++ lib/spack/external/macholib/MachOGraph.py | 138 ++ .../external/macholib/MachOStandalone.py | 169 ++ lib/spack/external/macholib/SymbolTable.py | 86 + lib/spack/external/macholib/__init__.py | 8 + lib/spack/external/macholib/__main__.py | 83 + lib/spack/external/macholib/_cmdline.py | 48 + lib/spack/external/macholib/dyld.py | 190 ++ lib/spack/external/macholib/dylib.py | 43 + lib/spack/external/macholib/framework.py | 43 + .../external/macholib/itergraphreport.py | 73 + lib/spack/external/macholib/mach_o.py | 1665 +++++++++++++++++ lib/spack/external/macholib/macho_dump.py | 58 + lib/spack/external/macholib/macho_find.py | 21 + .../external/macholib/macho_standalone.py | 31 + lib/spack/external/macholib/ptypes.py | 331 ++++ lib/spack/external/macholib/util.py | 258 +++ 26 files changed, 5433 insertions(+) create mode 100644 lib/spack/external/altgraph/Dot.py create mode 100644 lib/spack/external/altgraph/Graph.py create mode 100644 lib/spack/external/altgraph/GraphAlgo.py create mode 100644 lib/spack/external/altgraph/GraphStat.py create mode 100644 lib/spack/external/altgraph/GraphUtil.py create mode 100644 lib/spack/external/altgraph/ObjectGraph.py create mode 100644 lib/spack/external/altgraph/__init__.py create mode 100644 lib/spack/external/macholib/MachO.py create mode 100644 lib/spack/external/macholib/MachOGraph.py create mode 100644 lib/spack/external/macholib/MachOStandalone.py create mode 100644 lib/spack/external/macholib/SymbolTable.py create mode 100644 lib/spack/external/macholib/__init__.py create mode 100644 lib/spack/external/macholib/__main__.py create mode 100644 lib/spack/external/macholib/_cmdline.py create mode 100644 lib/spack/external/macholib/dyld.py create mode 100644 lib/spack/external/macholib/dylib.py create mode 100644 lib/spack/external/macholib/framework.py create mode 100644 lib/spack/external/macholib/itergraphreport.py create mode 100644 lib/spack/external/macholib/mach_o.py create mode 100644 lib/spack/external/macholib/macho_dump.py create mode 100644 lib/spack/external/macholib/macho_find.py create mode 100644 lib/spack/external/macholib/macho_standalone.py create mode 100644 lib/spack/external/macholib/ptypes.py create mode 100644 lib/spack/external/macholib/util.py diff --git a/COPYRIGHT b/COPYRIGHT index d2cdb2a0f40..ba792d2a9f2 100644 --- a/COPYRIGHT +++ b/COPYRIGHT @@ -83,3 +83,11 @@ PackageLicenseDeclared: MIT PackageName: six PackageHomePage: https://pypi.python.org/pypi/six PackageLicenseDeclared: MIT + +PackageName: macholib +PackageHomePage: https://macholib.readthedocs.io/en/latest/index.html +PackageLicenseDeclared: MIT + +PackageName: altgraph +PackageHomePage: https://altgraph.readthedocs.io/en/latest/index.html +PackageLicenseDeclared: MIT diff --git a/lib/spack/external/__init__.py b/lib/spack/external/__init__.py index f791bc3067c..1001ff5ffff 100644 --- a/lib/spack/external/__init__.py +++ b/lib/spack/external/__init__.py @@ -119,4 +119,18 @@ * Homepage: https://pypi.python.org/pypi/six * Usage: Python 2 and 3 compatibility utilities. * Version: 1.11.0 + +macholib +-------- + +* Homepage: https://macholib.readthedocs.io/en/latest/index.html# +* Usage: Manipulation of Mach-o binaries for relocating macOS buildcaches on Linux +* Version: 1.12 + +altgraph +-------- + +* Homepage: https://altgraph.readthedocs.io/en/latest/index.html +* Usage: dependency of macholib +* Version: 0.16.1 """ diff --git a/lib/spack/external/altgraph/Dot.py b/lib/spack/external/altgraph/Dot.py new file mode 100644 index 00000000000..3ef04d4c5b8 --- /dev/null +++ b/lib/spack/external/altgraph/Dot.py @@ -0,0 +1,309 @@ +''' +altgraph.Dot - Interface to the dot language +============================================ + +The :py:mod:`~altgraph.Dot` module provides a simple interface to the +file format used in the +`graphviz `_ +program. The module is intended to offload the most tedious part of the process +(the **dot** file generation) while transparently exposing most of its +features. + +To display the graphs or to generate image files the +`graphviz `_ +package needs to be installed on the system, moreover the :command:`dot` and +:command:`dotty` programs must be accesible in the program path so that they +can be ran from processes spawned within the module. + +Example usage +------------- + +Here is a typical usage:: + + from altgraph import Graph, Dot + + # create a graph + edges = [ (1,2), (1,3), (3,4), (3,5), (4,5), (5,4) ] + graph = Graph.Graph(edges) + + # create a dot representation of the graph + dot = Dot.Dot(graph) + + # display the graph + dot.display() + + # save the dot representation into the mydot.dot file + dot.save_dot(file_name='mydot.dot') + + # save dot file as gif image into the graph.gif file + dot.save_img(file_name='graph', file_type='gif') + +Directed graph and non-directed graph +------------------------------------- + +Dot class can use for both directed graph and non-directed graph +by passing ``graphtype`` parameter. + +Example:: + + # create directed graph(default) + dot = Dot.Dot(graph, graphtype="digraph") + + # create non-directed graph + dot = Dot.Dot(graph, graphtype="graph") + +Customizing the output +---------------------- + +The graph drawing process may be customized by passing +valid :command:`dot` parameters for the nodes and edges. For a list of all +parameters see the `graphviz `_ +documentation. + +Example:: + + # customizing the way the overall graph is drawn + dot.style(size='10,10', rankdir='RL', page='5, 5' , ranksep=0.75) + + # customizing node drawing + dot.node_style(1, label='BASE_NODE',shape='box', color='blue' ) + dot.node_style(2, style='filled', fillcolor='red') + + # customizing edge drawing + dot.edge_style(1, 2, style='dotted') + dot.edge_style(3, 5, arrowhead='dot', label='binds', labelangle='90') + dot.edge_style(4, 5, arrowsize=2, style='bold') + + +.. note:: + + dotty (invoked via :py:func:`~altgraph.Dot.display`) may not be able to + display all graphics styles. To verify the output save it to an image file + and look at it that way. + +Valid attributes +---------------- + + - dot styles, passed via the :py:meth:`Dot.style` method:: + + rankdir = 'LR' (draws the graph horizontally, left to right) + ranksep = number (rank separation in inches) + + - node attributes, passed via the :py:meth:`Dot.node_style` method:: + + style = 'filled' | 'invisible' | 'diagonals' | 'rounded' + shape = 'box' | 'ellipse' | 'circle' | 'point' | 'triangle' + + - edge attributes, passed via the :py:meth:`Dot.edge_style` method:: + + style = 'dashed' | 'dotted' | 'solid' | 'invis' | 'bold' + arrowhead = 'box' | 'crow' | 'diamond' | 'dot' | 'inv' | 'none' + | 'tee' | 'vee' + weight = number (the larger the number the closer the nodes will be) + + - valid `graphviz colors + `_ + + - for more details on how to control the graph drawing process see the + `graphviz reference + `_. +''' +import os +import warnings + +from altgraph import GraphError + + +class Dot(object): + ''' + A class providing a **graphviz** (dot language) representation + allowing a fine grained control over how the graph is being + displayed. + + If the :command:`dot` and :command:`dotty` programs are not in the current + system path their location needs to be specified in the contructor. + ''' + + def __init__( + self, graph=None, nodes=None, edgefn=None, nodevisitor=None, + edgevisitor=None, name="G", dot='dot', dotty='dotty', + neato='neato', graphtype="digraph"): + ''' + Initialization. + ''' + self.name, self.attr = name, {} + + assert graphtype in ['graph', 'digraph'] + self.type = graphtype + + self.temp_dot = "tmp_dot.dot" + self.temp_neo = "tmp_neo.dot" + + self.dot, self.dotty, self.neato = dot, dotty, neato + + # self.nodes: node styles + # self.edges: edge styles + self.nodes, self.edges = {}, {} + + if graph is not None and nodes is None: + nodes = graph + if graph is not None and edgefn is None: + def edgefn(node, graph=graph): + return graph.out_nbrs(node) + if nodes is None: + nodes = () + + seen = set() + for node in nodes: + if nodevisitor is None: + style = {} + else: + style = nodevisitor(node) + if style is not None: + self.nodes[node] = {} + self.node_style(node, **style) + seen.add(node) + if edgefn is not None: + for head in seen: + for tail in (n for n in edgefn(head) if n in seen): + if edgevisitor is None: + edgestyle = {} + else: + edgestyle = edgevisitor(head, tail) + if edgestyle is not None: + if head not in self.edges: + self.edges[head] = {} + self.edges[head][tail] = {} + self.edge_style(head, tail, **edgestyle) + + def style(self, **attr): + ''' + Changes the overall style + ''' + self.attr = attr + + def display(self, mode='dot'): + ''' + Displays the current graph via dotty + ''' + + if mode == 'neato': + self.save_dot(self.temp_neo) + neato_cmd = "%s -o %s %s" % ( + self.neato, self.temp_dot, self.temp_neo) + os.system(neato_cmd) + else: + self.save_dot(self.temp_dot) + + plot_cmd = "%s %s" % (self.dotty, self.temp_dot) + os.system(plot_cmd) + + def node_style(self, node, **kwargs): + ''' + Modifies a node style to the dot representation. + ''' + if node not in self.edges: + self.edges[node] = {} + self.nodes[node] = kwargs + + def all_node_style(self, **kwargs): + ''' + Modifies all node styles + ''' + for node in self.nodes: + self.node_style(node, **kwargs) + + def edge_style(self, head, tail, **kwargs): + ''' + Modifies an edge style to the dot representation. + ''' + if tail not in self.nodes: + raise GraphError("invalid node %s" % (tail,)) + + try: + if tail not in self.edges[head]: + self.edges[head][tail] = {} + self.edges[head][tail] = kwargs + except KeyError: + raise GraphError("invalid edge %s -> %s " % (head, tail)) + + def iterdot(self): + # write graph title + if self.type == 'digraph': + yield 'digraph %s {\n' % (self.name,) + elif self.type == 'graph': + yield 'graph %s {\n' % (self.name,) + + else: + raise GraphError("unsupported graphtype %s" % (self.type,)) + + # write overall graph attributes + for attr_name, attr_value in sorted(self.attr.items()): + yield '%s="%s";' % (attr_name, attr_value) + yield '\n' + + # some reusable patterns + cpatt = '%s="%s",' # to separate attributes + epatt = '];\n' # to end attributes + + # write node attributes + for node_name, node_attr in sorted(self.nodes.items()): + yield '\t"%s" [' % (node_name,) + for attr_name, attr_value in sorted(node_attr.items()): + yield cpatt % (attr_name, attr_value) + yield epatt + + # write edge attributes + for head in sorted(self.edges): + for tail in sorted(self.edges[head]): + if self.type == 'digraph': + yield '\t"%s" -> "%s" [' % (head, tail) + else: + yield '\t"%s" -- "%s" [' % (head, tail) + for attr_name, attr_value in \ + sorted(self.edges[head][tail].items()): + yield cpatt % (attr_name, attr_value) + yield epatt + + # finish file + yield '}\n' + + def __iter__(self): + return self.iterdot() + + def save_dot(self, file_name=None): + ''' + Saves the current graph representation into a file + ''' + + if not file_name: + warnings.warn(DeprecationWarning, "always pass a file_name") + file_name = self.temp_dot + + with open(file_name, "w") as fp: + for chunk in self.iterdot(): + fp.write(chunk) + + def save_img(self, file_name=None, file_type="gif", mode='dot'): + ''' + Saves the dot file as an image file + ''' + + if not file_name: + warnings.warn(DeprecationWarning, "always pass a file_name") + file_name = "out" + + if mode == 'neato': + self.save_dot(self.temp_neo) + neato_cmd = "%s -o %s %s" % ( + self.neato, self.temp_dot, self.temp_neo) + os.system(neato_cmd) + plot_cmd = self.dot + else: + self.save_dot(self.temp_dot) + plot_cmd = self.dot + + file_name = "%s.%s" % (file_name, file_type) + create_cmd = "%s -T%s %s -o %s" % ( + plot_cmd, file_type, self.temp_dot, file_name) + os.system(create_cmd) diff --git a/lib/spack/external/altgraph/Graph.py b/lib/spack/external/altgraph/Graph.py new file mode 100644 index 00000000000..fc4f7e97435 --- /dev/null +++ b/lib/spack/external/altgraph/Graph.py @@ -0,0 +1,680 @@ +""" +altgraph.Graph - Base Graph class +================================= + +.. + #--Version 2.1 + #--Bob Ippolito October, 2004 + + #--Version 2.0 + #--Istvan Albert June, 2004 + + #--Version 1.0 + #--Nathan Denny, May 27, 1999 +""" + +from altgraph import GraphError +from collections import deque + + +class Graph(object): + """ + The Graph class represents a directed graph with *N* nodes and *E* edges. + + Naming conventions: + + - the prefixes such as *out*, *inc* and *all* will refer to methods + that operate on the outgoing, incoming or all edges of that node. + + For example: :py:meth:`inc_degree` will refer to the degree of the node + computed over the incoming edges (the number of neighbours linking to + the node). + + - the prefixes such as *forw* and *back* will refer to the + orientation of the edges used in the method with respect to the node. + + For example: :py:meth:`forw_bfs` will start at the node then use the + outgoing edges to traverse the graph (goes forward). + """ + + def __init__(self, edges=None): + """ + Initialization + """ + + self.next_edge = 0 + self.nodes, self.edges = {}, {} + self.hidden_edges, self.hidden_nodes = {}, {} + + if edges is not None: + for item in edges: + if len(item) == 2: + head, tail = item + self.add_edge(head, tail) + elif len(item) == 3: + head, tail, data = item + self.add_edge(head, tail, data) + else: + raise GraphError("Cannot create edge from %s" % (item,)) + + def __repr__(self): + return '' % ( + self.number_of_nodes(), self.number_of_edges()) + + def add_node(self, node, node_data=None): + """ + Adds a new node to the graph. Arbitrary data can be attached to the + node via the node_data parameter. Adding the same node twice will be + silently ignored. + + The node must be a hashable value. + """ + # + # the nodes will contain tuples that will store incoming edges, + # outgoing edges and data + # + # index 0 -> incoming edges + # index 1 -> outgoing edges + + if node in self.hidden_nodes: + # Node is present, but hidden + return + + if node not in self.nodes: + self.nodes[node] = ([], [], node_data) + + def add_edge(self, head_id, tail_id, edge_data=1, create_nodes=True): + """ + Adds a directed edge going from head_id to tail_id. + Arbitrary data can be attached to the edge via edge_data. + It may create the nodes if adding edges between nonexisting ones. + + :param head_id: head node + :param tail_id: tail node + :param edge_data: (optional) data attached to the edge + :param create_nodes: (optional) creates the head_id or tail_id + node in case they did not exist + """ + # shorcut + edge = self.next_edge + + # add nodes if on automatic node creation + if create_nodes: + self.add_node(head_id) + self.add_node(tail_id) + + # update the corresponding incoming and outgoing lists in the nodes + # index 0 -> incoming edges + # index 1 -> outgoing edges + + try: + self.nodes[tail_id][0].append(edge) + self.nodes[head_id][1].append(edge) + except KeyError: + raise GraphError('Invalid nodes %s -> %s' % (head_id, tail_id)) + + # store edge information + self.edges[edge] = (head_id, tail_id, edge_data) + + self.next_edge += 1 + + def hide_edge(self, edge): + """ + Hides an edge from the graph. The edge may be unhidden at some later + time. + """ + try: + head_id, tail_id, edge_data = \ + self.hidden_edges[edge] = self.edges[edge] + self.nodes[tail_id][0].remove(edge) + self.nodes[head_id][1].remove(edge) + del self.edges[edge] + except KeyError: + raise GraphError('Invalid edge %s' % edge) + + def hide_node(self, node): + """ + Hides a node from the graph. The incoming and outgoing edges of the + node will also be hidden. The node may be unhidden at some later time. + """ + try: + all_edges = self.all_edges(node) + self.hidden_nodes[node] = (self.nodes[node], all_edges) + for edge in all_edges: + self.hide_edge(edge) + del self.nodes[node] + except KeyError: + raise GraphError('Invalid node %s' % node) + + def restore_node(self, node): + """ + Restores a previously hidden node back into the graph and restores + all of its incoming and outgoing edges. + """ + try: + self.nodes[node], all_edges = self.hidden_nodes[node] + for edge in all_edges: + self.restore_edge(edge) + del self.hidden_nodes[node] + except KeyError: + raise GraphError('Invalid node %s' % node) + + def restore_edge(self, edge): + """ + Restores a previously hidden edge back into the graph. + """ + try: + head_id, tail_id, data = self.hidden_edges[edge] + self.nodes[tail_id][0].append(edge) + self.nodes[head_id][1].append(edge) + self.edges[edge] = head_id, tail_id, data + del self.hidden_edges[edge] + except KeyError: + raise GraphError('Invalid edge %s' % edge) + + def restore_all_edges(self): + """ + Restores all hidden edges. + """ + for edge in list(self.hidden_edges.keys()): + try: + self.restore_edge(edge) + except GraphError: + pass + + def restore_all_nodes(self): + """ + Restores all hidden nodes. + """ + for node in list(self.hidden_nodes.keys()): + self.restore_node(node) + + def __contains__(self, node): + """ + Test whether a node is in the graph + """ + return node in self.nodes + + def edge_by_id(self, edge): + """ + Returns the edge that connects the head_id and tail_id nodes + """ + try: + head, tail, data = self.edges[edge] + except KeyError: + head, tail = None, None + raise GraphError('Invalid edge %s' % edge) + + return (head, tail) + + def edge_by_node(self, head, tail): + """ + Returns the edge that connects the head_id and tail_id nodes + """ + for edge in self.out_edges(head): + if self.tail(edge) == tail: + return edge + return None + + def number_of_nodes(self): + """ + Returns the number of nodes + """ + return len(self.nodes) + + def number_of_edges(self): + """ + Returns the number of edges + """ + return len(self.edges) + + def __iter__(self): + """ + Iterates over all nodes in the graph + """ + return iter(self.nodes) + + def node_list(self): + """ + Return a list of the node ids for all visible nodes in the graph. + """ + return list(self.nodes.keys()) + + def edge_list(self): + """ + Returns an iterator for all visible nodes in the graph. + """ + return list(self.edges.keys()) + + def number_of_hidden_edges(self): + """ + Returns the number of hidden edges + """ + return len(self.hidden_edges) + + def number_of_hidden_nodes(self): + """ + Returns the number of hidden nodes + """ + return len(self.hidden_nodes) + + def hidden_node_list(self): + """ + Returns the list with the hidden nodes + """ + return list(self.hidden_nodes.keys()) + + def hidden_edge_list(self): + """ + Returns a list with the hidden edges + """ + return list(self.hidden_edges.keys()) + + def describe_node(self, node): + """ + return node, node data, outgoing edges, incoming edges for node + """ + incoming, outgoing, data = self.nodes[node] + return node, data, outgoing, incoming + + def describe_edge(self, edge): + """ + return edge, edge data, head, tail for edge + """ + head, tail, data = self.edges[edge] + return edge, data, head, tail + + def node_data(self, node): + """ + Returns the data associated with a node + """ + return self.nodes[node][2] + + def edge_data(self, edge): + """ + Returns the data associated with an edge + """ + return self.edges[edge][2] + + def update_edge_data(self, edge, edge_data): + """ + Replace the edge data for a specific edge + """ + self.edges[edge] = self.edges[edge][0:2] + (edge_data,) + + def head(self, edge): + """ + Returns the node of the head of the edge. + """ + return self.edges[edge][0] + + def tail(self, edge): + """ + Returns node of the tail of the edge. + """ + return self.edges[edge][1] + + def out_nbrs(self, node): + """ + List of nodes connected by outgoing edges + """ + return [self.tail(n) for n in self.out_edges(node)] + + def inc_nbrs(self, node): + """ + List of nodes connected by incoming edges + """ + return [self.head(n) for n in self.inc_edges(node)] + + def all_nbrs(self, node): + """ + List of nodes connected by incoming and outgoing edges + """ + return list(dict.fromkeys(self.inc_nbrs(node) + self.out_nbrs(node))) + + def out_edges(self, node): + """ + Returns a list of the outgoing edges + """ + try: + return list(self.nodes[node][1]) + except KeyError: + raise GraphError('Invalid node %s' % node) + + def inc_edges(self, node): + """ + Returns a list of the incoming edges + """ + try: + return list(self.nodes[node][0]) + except KeyError: + raise GraphError('Invalid node %s' % node) + + def all_edges(self, node): + """ + Returns a list of incoming and outging edges. + """ + return set(self.inc_edges(node) + self.out_edges(node)) + + def out_degree(self, node): + """ + Returns the number of outgoing edges + """ + return len(self.out_edges(node)) + + def inc_degree(self, node): + """ + Returns the number of incoming edges + """ + return len(self.inc_edges(node)) + + def all_degree(self, node): + """ + The total degree of a node + """ + return self.inc_degree(node) + self.out_degree(node) + + def _topo_sort(self, forward=True): + """ + Topological sort. + + Returns a list of nodes where the successors (based on outgoing and + incoming edges selected by the forward parameter) of any given node + appear in the sequence after that node. + """ + topo_list = [] + queue = deque() + indeg = {} + + # select the operation that will be performed + if forward: + get_edges = self.out_edges + get_degree = self.inc_degree + get_next = self.tail + else: + get_edges = self.inc_edges + get_degree = self.out_degree + get_next = self.head + + for node in self.node_list(): + degree = get_degree(node) + if degree: + indeg[node] = degree + else: + queue.append(node) + + while queue: + curr_node = queue.popleft() + topo_list.append(curr_node) + for edge in get_edges(curr_node): + tail_id = get_next(edge) + if tail_id in indeg: + indeg[tail_id] -= 1 + if indeg[tail_id] == 0: + queue.append(tail_id) + + if len(topo_list) == len(self.node_list()): + valid = True + else: + # the graph has cycles, invalid topological sort + valid = False + + return (valid, topo_list) + + def forw_topo_sort(self): + """ + Topological sort. + + Returns a list of nodes where the successors (based on outgoing edges) + of any given node appear in the sequence after that node. + """ + return self._topo_sort(forward=True) + + def back_topo_sort(self): + """ + Reverse topological sort. + + Returns a list of nodes where the successors (based on incoming edges) + of any given node appear in the sequence after that node. + """ + return self._topo_sort(forward=False) + + def _bfs_subgraph(self, start_id, forward=True): + """ + Private method creates a subgraph in a bfs order. + + The forward parameter specifies whether it is a forward or backward + traversal. + """ + if forward: + get_bfs = self.forw_bfs + get_nbrs = self.out_nbrs + else: + get_bfs = self.back_bfs + get_nbrs = self.inc_nbrs + + g = Graph() + bfs_list = get_bfs(start_id) + for node in bfs_list: + g.add_node(node) + + for node in bfs_list: + for nbr_id in get_nbrs(node): + if forward: + g.add_edge(node, nbr_id) + else: + g.add_edge(nbr_id, node) + + return g + + def forw_bfs_subgraph(self, start_id): + """ + Creates and returns a subgraph consisting of the breadth first + reachable nodes based on their outgoing edges. + """ + return self._bfs_subgraph(start_id, forward=True) + + def back_bfs_subgraph(self, start_id): + """ + Creates and returns a subgraph consisting of the breadth first + reachable nodes based on the incoming edges. + """ + return self._bfs_subgraph(start_id, forward=False) + + def iterdfs(self, start, end=None, forward=True): + """ + Collecting nodes in some depth first traversal. + + The forward parameter specifies whether it is a forward or backward + traversal. + """ + visited, stack = set([start]), deque([start]) + + if forward: + get_edges = self.out_edges + get_next = self.tail + else: + get_edges = self.inc_edges + get_next = self.head + + while stack: + curr_node = stack.pop() + yield curr_node + if curr_node == end: + break + for edge in sorted(get_edges(curr_node)): + tail = get_next(edge) + if tail not in visited: + visited.add(tail) + stack.append(tail) + + def iterdata(self, start, end=None, forward=True, condition=None): + """ + Perform a depth-first walk of the graph (as ``iterdfs``) + and yield the item data of every node where condition matches. The + condition callback is only called when node_data is not None. + """ + + visited, stack = set([start]), deque([start]) + + if forward: + get_edges = self.out_edges + get_next = self.tail + else: + get_edges = self.inc_edges + get_next = self.head + + get_data = self.node_data + + while stack: + curr_node = stack.pop() + curr_data = get_data(curr_node) + if curr_data is not None: + if condition is not None and not condition(curr_data): + continue + yield curr_data + if curr_node == end: + break + for edge in get_edges(curr_node): + tail = get_next(edge) + if tail not in visited: + visited.add(tail) + stack.append(tail) + + def _iterbfs(self, start, end=None, forward=True): + """ + The forward parameter specifies whether it is a forward or backward + traversal. Returns a list of tuples where the first value is the hop + value the second value is the node id. + """ + queue, visited = deque([(start, 0)]), set([start]) + + # the direction of the bfs depends on the edges that are sampled + if forward: + get_edges = self.out_edges + get_next = self.tail + else: + get_edges = self.inc_edges + get_next = self.head + + while queue: + curr_node, curr_step = queue.popleft() + yield (curr_node, curr_step) + if curr_node == end: + break + for edge in get_edges(curr_node): + tail = get_next(edge) + if tail not in visited: + visited.add(tail) + queue.append((tail, curr_step + 1)) + + def forw_bfs(self, start, end=None): + """ + Returns a list of nodes in some forward BFS order. + + Starting from the start node the breadth first search proceeds along + outgoing edges. + """ + return [node for node, step in self._iterbfs(start, end, forward=True)] + + def back_bfs(self, start, end=None): + """ + Returns a list of nodes in some backward BFS order. + + Starting from the start node the breadth first search proceeds along + incoming edges. + """ + return [node for node, _ in self._iterbfs(start, end, forward=False)] + + def forw_dfs(self, start, end=None): + """ + Returns a list of nodes in some forward DFS order. + + Starting with the start node the depth first search proceeds along + outgoing edges. + """ + return list(self.iterdfs(start, end, forward=True)) + + def back_dfs(self, start, end=None): + """ + Returns a list of nodes in some backward DFS order. + + Starting from the start node the depth first search proceeds along + incoming edges. + """ + return list(self.iterdfs(start, end, forward=False)) + + def connected(self): + """ + Returns :py:data:`True` if the graph's every node can be reached from + every other node. + """ + node_list = self.node_list() + for node in node_list: + bfs_list = self.forw_bfs(node) + if len(bfs_list) != len(node_list): + return False + return True + + def clust_coef(self, node): + """ + Computes and returns the local clustering coefficient of node. + + The local cluster coefficient is proportion of the actual number of + edges between neighbours of node and the maximum number of edges + between those neighbours. + + See "Local Clustering Coefficient" on + + for a formal definition. + """ + num = 0 + nbr_set = set(self.out_nbrs(node)) + + if node in nbr_set: + nbr_set.remove(node) # loop defense + + for nbr in nbr_set: + sec_set = set(self.out_nbrs(nbr)) + if nbr in sec_set: + sec_set.remove(nbr) # loop defense + num += len(nbr_set & sec_set) + + nbr_num = len(nbr_set) + if nbr_num: + clust_coef = float(num) / (nbr_num * (nbr_num - 1)) + else: + clust_coef = 0.0 + return clust_coef + + def get_hops(self, start, end=None, forward=True): + """ + Computes the hop distance to all nodes centered around a node. + + First order neighbours are at hop 1, their neigbours are at hop 2 etc. + Uses :py:meth:`forw_bfs` or :py:meth:`back_bfs` depending on the value + of the forward parameter. If the distance between all neighbouring + nodes is 1 the hop number corresponds to the shortest distance between + the nodes. + + :param start: the starting node + :param end: ending node (optional). When not specified will search the + whole graph. + :param forward: directionality parameter (optional). + If C{True} (default) it uses L{forw_bfs} otherwise L{back_bfs}. + :return: returns a list of tuples where each tuple contains the + node and the hop. + + Typical usage:: + + >>> print (graph.get_hops(1, 8)) + >>> [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)] + # node 1 is at 0 hops + # node 2 is at 1 hop + # ... + # node 8 is at 5 hops + """ + if forward: + return list(self._iterbfs(start=start, end=end, forward=True)) + else: + return list(self._iterbfs(start=start, end=end, forward=False)) diff --git a/lib/spack/external/altgraph/GraphAlgo.py b/lib/spack/external/altgraph/GraphAlgo.py new file mode 100644 index 00000000000..b51e536314e --- /dev/null +++ b/lib/spack/external/altgraph/GraphAlgo.py @@ -0,0 +1,166 @@ +''' +altgraph.GraphAlgo - Graph algorithms +===================================== +''' +from altgraph import GraphError + + +def dijkstra(graph, start, end=None): + """ + Dijkstra's algorithm for shortest paths + + `David Eppstein, UC Irvine, 4 April 2002 + `_ + + `Python Cookbook Recipe + `_ + + Find shortest paths from the start node to all nodes nearer than or + equal to the end node. + + Dijkstra's algorithm is only guaranteed to work correctly when all edge + lengths are positive. This code does not verify this property for all + edges (only the edges examined until the end vertex is reached), but will + correctly compute shortest paths even for some graphs with negative edges, + and will raise an exception if it discovers that a negative edge has + caused it to make a mistake. + + Adapted to altgraph by Istvan Albert, Pennsylvania State University - + June, 9 2004 + """ + D = {} # dictionary of final distances + P = {} # dictionary of predecessors + Q = _priorityDictionary() # estimated distances of non-final vertices + Q[start] = 0 + + for v in Q: + D[v] = Q[v] + if v == end: + break + + for w in graph.out_nbrs(v): + edge_id = graph.edge_by_node(v, w) + vwLength = D[v] + graph.edge_data(edge_id) + if w in D: + if vwLength < D[w]: + raise GraphError( + "Dijkstra: found better path to already-final vertex") + elif w not in Q or vwLength < Q[w]: + Q[w] = vwLength + P[w] = v + + return (D, P) + + +def shortest_path(graph, start, end): + """ + Find a single shortest path from the *start* node to the *end* node. + The input has the same conventions as dijkstra(). The output is a list of + the nodes in order along the shortest path. + + **Note that the distances must be stored in the edge data as numeric data** + """ + + D, P = dijkstra(graph, start, end) + Path = [] + while 1: + Path.append(end) + if end == start: + break + end = P[end] + Path.reverse() + return Path + + +# +# Utility classes and functions +# +class _priorityDictionary(dict): + ''' + Priority dictionary using binary heaps (internal use only) + + David Eppstein, UC Irvine, 8 Mar 2002 + + Implements a data structure that acts almost like a dictionary, with + two modifications: + + 1. D.smallest() returns the value x minimizing D[x]. For this to + work correctly, all values D[x] stored in the dictionary must be + comparable. + + 2. iterating "for x in D" finds and removes the items from D in sorted + order. Each item is not removed until the next item is requested, + so D[x] will still return a useful value until the next iteration + of the for-loop. Each operation takes logarithmic amortized time. + ''' + + def __init__(self): + ''' + Initialize priorityDictionary by creating binary heap of pairs + (value,key). Note that changing or removing a dict entry will not + remove the old pair from the heap until it is found by smallest() + or until the heap is rebuilt. + ''' + self.__heap = [] + dict.__init__(self) + + def smallest(self): + ''' + Find smallest item after removing deleted items from front of heap. + ''' + if len(self) == 0: + raise IndexError("smallest of empty priorityDictionary") + heap = self.__heap + while heap[0][1] not in self or self[heap[0][1]] != heap[0][0]: + lastItem = heap.pop() + insertionPoint = 0 + while 1: + smallChild = 2*insertionPoint+1 + if smallChild+1 < len(heap) and \ + heap[smallChild] > heap[smallChild+1]: + smallChild += 1 + if smallChild >= len(heap) or lastItem <= heap[smallChild]: + heap[insertionPoint] = lastItem + break + heap[insertionPoint] = heap[smallChild] + insertionPoint = smallChild + return heap[0][1] + + def __iter__(self): + ''' + Create destructive sorted iterator of priorityDictionary. + ''' + def iterfn(): + while len(self) > 0: + x = self.smallest() + yield x + del self[x] + return iterfn() + + def __setitem__(self, key, val): + ''' + Change value stored in dictionary and add corresponding pair to heap. + Rebuilds the heap if the number of deleted items gets large, to avoid + memory leakage. + ''' + dict.__setitem__(self, key, val) + heap = self.__heap + if len(heap) > 2 * len(self): + self.__heap = [(v, k) for k, v in self.items()] + self.__heap.sort() + else: + newPair = (val, key) + insertionPoint = len(heap) + heap.append(None) + while insertionPoint > 0 and newPair < heap[(insertionPoint-1)//2]: + heap[insertionPoint] = heap[(insertionPoint-1)//2] + insertionPoint = (insertionPoint-1)//2 + heap[insertionPoint] = newPair + + def setdefault(self, key, val): + ''' + Reimplement setdefault to pass through our customized __setitem__. + ''' + if key not in self: + self[key] = val + return self[key] diff --git a/lib/spack/external/altgraph/GraphStat.py b/lib/spack/external/altgraph/GraphStat.py new file mode 100644 index 00000000000..003b7167e7f --- /dev/null +++ b/lib/spack/external/altgraph/GraphStat.py @@ -0,0 +1,73 @@ +''' +altgraph.GraphStat - Functions providing various graph statistics +================================================================= +''' + + +def degree_dist(graph, limits=(0, 0), bin_num=10, mode='out'): + ''' + Computes the degree distribution for a graph. + + Returns a list of tuples where the first element of the tuple is the + center of the bin representing a range of degrees and the second element + of the tuple are the number of nodes with the degree falling in the range. + + Example:: + + .... + ''' + + deg = [] + if mode == 'inc': + get_deg = graph.inc_degree + else: + get_deg = graph.out_degree + + for node in graph: + deg.append(get_deg(node)) + + if not deg: + return [] + + results = _binning(values=deg, limits=limits, bin_num=bin_num) + + return results + + +_EPS = 1.0/(2.0**32) + + +def _binning(values, limits=(0, 0), bin_num=10): + ''' + Bins data that falls between certain limits, if the limits are (0, 0) the + minimum and maximum values are used. + + Returns a list of tuples where the first element of the tuple is the + center of the bin and the second element of the tuple are the counts. + ''' + if limits == (0, 0): + min_val, max_val = min(values) - _EPS, max(values) + _EPS + else: + min_val, max_val = limits + + # get bin size + bin_size = (max_val - min_val)/float(bin_num) + bins = [0] * (bin_num) + + # will ignore these outliers for now + for value in values: + try: + if (value - min_val) >= 0: + index = int((value - min_val)/float(bin_size)) + bins[index] += 1 + except IndexError: + pass + + # make it ready for an x,y plot + result = [] + center = (bin_size/2) + min_val + for i, y in enumerate(bins): + x = center + bin_size * i + result.append((x, y)) + + return result diff --git a/lib/spack/external/altgraph/GraphUtil.py b/lib/spack/external/altgraph/GraphUtil.py new file mode 100644 index 00000000000..500a74b9f7c --- /dev/null +++ b/lib/spack/external/altgraph/GraphUtil.py @@ -0,0 +1,144 @@ +''' +altgraph.GraphUtil - Utility classes and functions +================================================== +''' + +import random +from collections import deque +from altgraph import Graph +from altgraph import GraphError + + +def generate_random_graph( + node_num, edge_num, self_loops=False, multi_edges=False): + ''' + Generates and returns a :py:class:`~altgraph.Graph.Graph` instance with + *node_num* nodes randomly connected by *edge_num* edges. + ''' + g = Graph.Graph() + + if not multi_edges: + if self_loops: + max_edges = node_num * node_num + else: + max_edges = node_num * (node_num-1) + + if edge_num > max_edges: + raise GraphError( + "inconsistent arguments to 'generate_random_graph'") + + nodes = range(node_num) + + for node in nodes: + g.add_node(node) + + while 1: + head = random.choice(nodes) + tail = random.choice(nodes) + + # loop defense + if head == tail and not self_loops: + continue + + # multiple edge defense + if g.edge_by_node(head, tail) is not None and not multi_edges: + continue + + # add the edge + g.add_edge(head, tail) + if g.number_of_edges() >= edge_num: + break + + return g + + +def generate_scale_free_graph( + steps, growth_num, self_loops=False, multi_edges=False): + ''' + Generates and returns a :py:class:`~altgraph.Graph.Graph` instance that + will have *steps* \* *growth_num* nodes and a scale free (powerlaw) + connectivity. Starting with a fully connected graph with *growth_num* + nodes at every step *growth_num* nodes are added to the graph and are + connected to existing nodes with a probability proportional to the degree + of these existing nodes. + ''' + # FIXME: The code doesn't seem to do what the documentation claims. + graph = Graph.Graph() + + # initialize the graph + store = [] + for i in range(growth_num): + for j in range(i + 1, growth_num): + store.append(i) + store.append(j) + graph.add_edge(i, j) + + # generate + for node in range(growth_num, steps * growth_num): + graph.add_node(node) + while graph.out_degree(node) < growth_num: + nbr = random.choice(store) + + # loop defense + if node == nbr and not self_loops: + continue + + # multi edge defense + if graph.edge_by_node(node, nbr) and not multi_edges: + continue + + graph.add_edge(node, nbr) + + for nbr in graph.out_nbrs(node): + store.append(node) + store.append(nbr) + + return graph + + +def filter_stack(graph, head, filters): + """ + Perform a walk in a depth-first order starting + at *head*. + + Returns (visited, removes, orphans). + + * visited: the set of visited nodes + * removes: the list of nodes where the node + data does not all *filters* + * orphans: tuples of (last_good, node), + where node is not in removes, is directly + reachable from a node in *removes* and + *last_good* is the closest upstream node that is not + in *removes*. + """ + + visited, removes, orphans = set([head]), set(), set() + stack = deque([(head, head)]) + get_data = graph.node_data + get_edges = graph.out_edges + get_tail = graph.tail + + while stack: + last_good, node = stack.pop() + data = get_data(node) + if data is not None: + for filtfunc in filters: + if not filtfunc(data): + removes.add(node) + break + else: + last_good = node + for edge in get_edges(node): + tail = get_tail(edge) + if last_good is not node: + orphans.add((last_good, tail)) + if tail not in visited: + visited.add(tail) + stack.append((last_good, tail)) + + orphans = [ + (lg, tl) + for (lg, tl) in orphans if tl not in removes] + + return visited, removes, orphans diff --git a/lib/spack/external/altgraph/ObjectGraph.py b/lib/spack/external/altgraph/ObjectGraph.py new file mode 100644 index 00000000000..f3d6fa187b0 --- /dev/null +++ b/lib/spack/external/altgraph/ObjectGraph.py @@ -0,0 +1,212 @@ +""" +altgraph.ObjectGraph - Graph of objects with an identifier +========================================================== + +A graph of objects that have a "graphident" attribute. +graphident is the key for the object in the graph +""" + +from altgraph import GraphError +from altgraph.Graph import Graph +from altgraph.GraphUtil import filter_stack + + +class ObjectGraph(object): + """ + A graph of objects that have a "graphident" attribute. + graphident is the key for the object in the graph + """ + + def __init__(self, graph=None, debug=0): + if graph is None: + graph = Graph() + self.graphident = self + self.graph = graph + self.debug = debug + self.indent = 0 + graph.add_node(self, None) + + def __repr__(self): + return '<%s>' % (type(self).__name__,) + + def flatten(self, condition=None, start=None): + """ + Iterate over the subgraph that is entirely reachable by condition + starting from the given start node or the ObjectGraph root + """ + if start is None: + start = self + start = self.getRawIdent(start) + return self.graph.iterdata(start=start, condition=condition) + + def nodes(self): + for ident in self.graph: + node = self.graph.node_data(ident) + if node is not None: + yield self.graph.node_data(ident) + + def get_edges(self, node): + if node is None: + node = self + start = self.getRawIdent(node) + _, _, outraw, incraw = self.graph.describe_node(start) + + def iter_edges(lst, n): + seen = set() + for tpl in (self.graph.describe_edge(e) for e in lst): + ident = tpl[n] + if ident not in seen: + yield self.findNode(ident) + seen.add(ident) + return iter_edges(outraw, 3), iter_edges(incraw, 2) + + def edgeData(self, fromNode, toNode): + if fromNode is None: + fromNode = self + start = self.getRawIdent(fromNode) + stop = self.getRawIdent(toNode) + edge = self.graph.edge_by_node(start, stop) + return self.graph.edge_data(edge) + + def updateEdgeData(self, fromNode, toNode, edgeData): + if fromNode is None: + fromNode = self + start = self.getRawIdent(fromNode) + stop = self.getRawIdent(toNode) + edge = self.graph.edge_by_node(start, stop) + self.graph.update_edge_data(edge, edgeData) + + def filterStack(self, filters): + """ + Filter the ObjectGraph in-place by removing all edges to nodes that + do not match every filter in the given filter list + + Returns a tuple containing the number of: + (nodes_visited, nodes_removed, nodes_orphaned) + """ + visited, removes, orphans = filter_stack(self.graph, self, filters) + + for last_good, tail in orphans: + self.graph.add_edge(last_good, tail, edge_data='orphan') + + for node in removes: + self.graph.hide_node(node) + + return len(visited)-1, len(removes), len(orphans) + + def removeNode(self, node): + """ + Remove the given node from the graph if it exists + """ + ident = self.getIdent(node) + if ident is not None: + self.graph.hide_node(ident) + + def removeReference(self, fromnode, tonode): + """ + Remove all edges from fromnode to tonode + """ + if fromnode is None: + fromnode = self + fromident = self.getIdent(fromnode) + toident = self.getIdent(tonode) + if fromident is not None and toident is not None: + while True: + edge = self.graph.edge_by_node(fromident, toident) + if edge is None: + break + self.graph.hide_edge(edge) + + def getIdent(self, node): + """ + Get the graph identifier for a node + """ + ident = self.getRawIdent(node) + if ident is not None: + return ident + node = self.findNode(node) + if node is None: + return None + return node.graphident + + def getRawIdent(self, node): + """ + Get the identifier for a node object + """ + if node is self: + return node + ident = getattr(node, 'graphident', None) + return ident + + def __contains__(self, node): + return self.findNode(node) is not None + + def findNode(self, node): + """ + Find the node on the graph + """ + ident = self.getRawIdent(node) + if ident is None: + ident = node + try: + return self.graph.node_data(ident) + except KeyError: + return None + + def addNode(self, node): + """ + Add a node to the graph referenced by the root + """ + self.msg(4, "addNode", node) + + try: + self.graph.restore_node(node.graphident) + except GraphError: + self.graph.add_node(node.graphident, node) + + def createReference(self, fromnode, tonode, edge_data=None): + """ + Create a reference from fromnode to tonode + """ + if fromnode is None: + fromnode = self + fromident, toident = self.getIdent(fromnode), self.getIdent(tonode) + if fromident is None or toident is None: + return + self.msg(4, "createReference", fromnode, tonode, edge_data) + self.graph.add_edge(fromident, toident, edge_data=edge_data) + + def createNode(self, cls, name, *args, **kw): + """ + Add a node of type cls to the graph if it does not already exist + by the given name + """ + m = self.findNode(name) + if m is None: + m = cls(name, *args, **kw) + self.addNode(m) + return m + + def msg(self, level, s, *args): + """ + Print a debug message with the given level + """ + if s and level <= self.debug: + print("%s%s %s" % ( + " " * self.indent, s, ' '.join(map(repr, args)))) + + def msgin(self, level, s, *args): + """ + Print a debug message and indent + """ + if level <= self.debug: + self.msg(level, s, *args) + self.indent = self.indent + 1 + + def msgout(self, level, s, *args): + """ + Dedent and print a debug message + """ + if level <= self.debug: + self.indent = self.indent - 1 + self.msg(level, s, *args) diff --git a/lib/spack/external/altgraph/__init__.py b/lib/spack/external/altgraph/__init__.py new file mode 100644 index 00000000000..289c6408d11 --- /dev/null +++ b/lib/spack/external/altgraph/__init__.py @@ -0,0 +1,147 @@ +''' +altgraph - a python graph library +================================= + +altgraph is a fork of `graphlib `_ tailored +to use newer Python 2.3+ features, including additional support used by the +py2app suite (modulegraph and macholib, specifically). + +altgraph is a python based graph (network) representation and manipulation +package. It has started out as an extension to the +`graph_lib module +`_ +written by Nathan Denny it has been significantly optimized and expanded. + +The :class:`altgraph.Graph.Graph` class is loosely modeled after the +`LEDA `_ +(Library of Efficient Datatypes) representation. The library +includes methods for constructing graphs, BFS and DFS traversals, +topological sort, finding connected components, shortest paths as well as a +number graph statistics functions. The library can also visualize graphs +via `graphviz `_. + +The package contains the following modules: + + - the :py:mod:`altgraph.Graph` module contains the + :class:`~altgraph.Graph.Graph` class that stores the graph data + + - the :py:mod:`altgraph.GraphAlgo` module implements graph algorithms + operating on graphs (:py:class:`~altgraph.Graph.Graph`} instances) + + - the :py:mod:`altgraph.GraphStat` module contains functions for + computing statistical measures on graphs + + - the :py:mod:`altgraph.GraphUtil` module contains functions for + generating, reading and saving graphs + + - the :py:mod:`altgraph.Dot` module contains functions for displaying + graphs via `graphviz `_ + + - the :py:mod:`altgraph.ObjectGraph` module implements a graph of + objects with a unique identifier + +Installation +------------ + +Download and unpack the archive then type:: + + python setup.py install + +This will install the library in the default location. For instructions on +how to customize the install procedure read the output of:: + + python setup.py --help install + +To verify that the code works run the test suite:: + + python setup.py test + +Example usage +------------- + +Lets assume that we want to analyze the graph below (links to the full picture) +GRAPH_IMG. Our script then might look the following way:: + + from altgraph import Graph, GraphAlgo, Dot + + # these are the edges + edges = [ (1,2), (2,4), (1,3), (2,4), (3,4), (4,5), (6,5), + (6,14), (14,15), (6, 15), (5,7), (7, 8), (7,13), (12,8), + (8,13), (11,12), (11,9), (13,11), (9,13), (13,10) ] + + # creates the graph + graph = Graph.Graph() + for head, tail in edges: + graph.add_edge(head, tail) + + # do a forward bfs from 1 at most to 20 + print(graph.forw_bfs(1)) + +This will print the nodes in some breadth first order:: + + [1, 2, 3, 4, 5, 7, 8, 13, 11, 10, 12, 9] + +If we wanted to get the hop-distance from node 1 to node 8 +we coud write:: + + print(graph.get_hops(1, 8)) + +This will print the following:: + + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)] + +Node 1 is at 0 hops since it is the starting node, nodes 2,3 are 1 hop away ... +node 8 is 5 hops away. To find the shortest distance between two nodes you +can use:: + + print(GraphAlgo.shortest_path(graph, 1, 12)) + +It will print the nodes on one (if there are more) the shortest paths:: + + [1, 2, 4, 5, 7, 13, 11, 12] + +To display the graph we can use the GraphViz backend:: + + dot = Dot.Dot(graph) + + # display the graph on the monitor + dot.display() + + # save it in an image file + dot.save_img(file_name='graph', file_type='gif') + + + +.. + @author: U{Istvan Albert} + + @license: MIT License + + Copyright (c) 2004 Istvan Albert unless otherwise noted. + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to + deal in the Software without restriction, including without limitation the + rights to use, copy, modify, merge, publish, distribute, sublicense, + and/or sell copies of the Software, and to permit persons to whom the + Software is furnished to do so. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS + IN THE SOFTWARE. + @requires: Python 2.3 or higher + + @newfield contributor: Contributors: + @contributor: U{Reka Albert } + +''' +import pkg_resources +__version__ = pkg_resources.require('altgraph')[0].version + + +class GraphError(ValueError): + pass diff --git a/lib/spack/external/macholib/MachO.py b/lib/spack/external/macholib/MachO.py new file mode 100644 index 00000000000..84b4e4b717a --- /dev/null +++ b/lib/spack/external/macholib/MachO.py @@ -0,0 +1,435 @@ +""" +Utilities for reading and writing Mach-O headers +""" +from __future__ import print_function + +import sys +import struct +import os + +from .mach_o import MH_FILETYPE_SHORTNAMES, LC_DYSYMTAB, LC_SYMTAB +from .mach_o import load_command, S_ZEROFILL, section_64, section +from .mach_o import LC_REGISTRY, LC_ID_DYLIB, LC_SEGMENT, fat_header +from .mach_o import LC_SEGMENT_64, MH_CIGAM_64, MH_MAGIC_64, FAT_MAGIC +from .mach_o import mach_header, fat_arch64, FAT_MAGIC_64, fat_arch +from .mach_o import LC_REEXPORT_DYLIB, LC_PREBOUND_DYLIB, LC_LOAD_WEAK_DYLIB +from .mach_o import LC_LOAD_UPWARD_DYLIB, LC_LOAD_DYLIB, mach_header_64 +from .mach_o import MH_CIGAM, MH_MAGIC +from .ptypes import sizeof + +from macholib.util import fileview +try: + from macholib.compat import bytes +except ImportError: + pass + +try: + unicode +except NameError: + unicode = str + +if sys.version_info[0] == 2: + range = xrange # noqa: F821 + +__all__ = ['MachO'] + +_RELOCATABLE = set(( + # relocatable commands that should be used for dependency walking + LC_LOAD_DYLIB, + LC_LOAD_UPWARD_DYLIB, + LC_LOAD_WEAK_DYLIB, + LC_PREBOUND_DYLIB, + LC_REEXPORT_DYLIB, +)) + +_RELOCATABLE_NAMES = { + LC_LOAD_DYLIB: 'load_dylib', + LC_LOAD_UPWARD_DYLIB: 'load_upward_dylib', + LC_LOAD_WEAK_DYLIB: 'load_weak_dylib', + LC_PREBOUND_DYLIB: 'prebound_dylib', + LC_REEXPORT_DYLIB: 'reexport_dylib', +} + + +def _shouldRelocateCommand(cmd): + """ + Should this command id be investigated for relocation? + """ + return cmd in _RELOCATABLE + + +def lc_str_value(offset, cmd_info): + """ + Fetch the actual value of a field of type "lc_str" + """ + cmd_load, cmd_cmd, cmd_data = cmd_info + + offset -= sizeof(cmd_load) + sizeof(cmd_cmd) + return cmd_data[offset:].strip(b'\x00') + + +class MachO(object): + """ + Provides reading/writing the Mach-O header of a specific existing file + """ + # filename - the original filename of this mach-o + # sizediff - the current deviation from the initial mach-o size + # header - the mach-o header + # commands - a list of (load_command, somecommand, data) + # data is either a str, or a list of segment structures + # total_size - the current mach-o header size (including header) + # low_offset - essentially, the maximum mach-o header size + # id_cmd - the index of my id command, or None + + def __init__(self, filename): + + # supports the ObjectGraph protocol + self.graphident = filename + self.filename = filename + self.loader_path = os.path.dirname(filename) + + # initialized by load + self.fat = None + self.headers = [] + with open(filename, 'rb') as fp: + self.load(fp) + + def __repr__(self): + return "" % (self.filename,) + + def load(self, fh): + assert fh.tell() == 0 + header = struct.unpack('>I', fh.read(4))[0] + fh.seek(0) + if header in (FAT_MAGIC, FAT_MAGIC_64): + self.load_fat(fh) + else: + fh.seek(0, 2) + size = fh.tell() + fh.seek(0) + self.load_header(fh, 0, size) + + def load_fat(self, fh): + self.fat = fat_header.from_fileobj(fh) + if self.fat.magic == FAT_MAGIC: + archs = [fat_arch.from_fileobj(fh) + for i in range(self.fat.nfat_arch)] + elif self.fat.magic == FAT_MAGIC_64: + archs = [fat_arch64.from_fileobj(fh) + for i in range(self.fat.nfat_arch)] + else: + raise ValueError("Unknown fat header magic: %r" % (self.fat.magic)) + + for arch in archs: + self.load_header(fh, arch.offset, arch.size) + + def rewriteLoadCommands(self, *args, **kw): + changed = False + for header in self.headers: + if header.rewriteLoadCommands(*args, **kw): + changed = True + return changed + + def load_header(self, fh, offset, size): + fh.seek(offset) + header = struct.unpack('>I', fh.read(4))[0] + fh.seek(offset) + if header == MH_MAGIC: + magic, hdr, endian = MH_MAGIC, mach_header, '>' + elif header == MH_CIGAM: + magic, hdr, endian = MH_CIGAM, mach_header, '<' + elif header == MH_MAGIC_64: + magic, hdr, endian = MH_MAGIC_64, mach_header_64, '>' + elif header == MH_CIGAM_64: + magic, hdr, endian = MH_CIGAM_64, mach_header_64, '<' + else: + raise ValueError("Unknown Mach-O header: 0x%08x in %r" % ( + header, fh)) + hdr = MachOHeader(self, fh, offset, size, magic, hdr, endian) + self.headers.append(hdr) + + def write(self, f): + for header in self.headers: + header.write(f) + + +class MachOHeader(object): + """ + Provides reading/writing the Mach-O header of a specific existing file + """ + # filename - the original filename of this mach-o + # sizediff - the current deviation from the initial mach-o size + # header - the mach-o header + # commands - a list of (load_command, somecommand, data) + # data is either a str, or a list of segment structures + # total_size - the current mach-o header size (including header) + # low_offset - essentially, the maximum mach-o header size + # id_cmd - the index of my id command, or None + + def __init__(self, parent, fh, offset, size, magic, hdr, endian): + self.MH_MAGIC = magic + self.mach_header = hdr + + # These are all initialized by self.load() + self.parent = parent + self.offset = offset + self.size = size + + self.endian = endian + self.header = None + self.commands = None + self.id_cmd = None + self.sizediff = None + self.total_size = None + self.low_offset = None + self.filetype = None + self.headers = [] + + self.load(fh) + + def __repr__(self): + return "<%s filename=%r offset=%d size=%d endian=%r>" % ( + type(self).__name__, self.parent.filename, self.offset, self.size, + self.endian) + + def load(self, fh): + fh = fileview(fh, self.offset, self.size) + fh.seek(0) + + self.sizediff = 0 + kw = {'_endian_': self.endian} + header = self.mach_header.from_fileobj(fh, **kw) + self.header = header + # if header.magic != self.MH_MAGIC: + # raise ValueError("header has magic %08x, expecting %08x" % ( + # header.magic, self.MH_MAGIC)) + + cmd = self.commands = [] + + self.filetype = self.get_filetype_shortname(header.filetype) + + read_bytes = 0 + low_offset = sys.maxsize + for i in range(header.ncmds): + # read the load command + cmd_load = load_command.from_fileobj(fh, **kw) + + # read the specific command + klass = LC_REGISTRY.get(cmd_load.cmd, None) + if klass is None: + raise ValueError("Unknown load command: %d" % (cmd_load.cmd,)) + cmd_cmd = klass.from_fileobj(fh, **kw) + + if cmd_load.cmd == LC_ID_DYLIB: + # remember where this command was + if self.id_cmd is not None: + raise ValueError("This dylib already has an id") + self.id_cmd = i + + if cmd_load.cmd in (LC_SEGMENT, LC_SEGMENT_64): + # for segment commands, read the list of segments + segs = [] + # assert that the size makes sense + if cmd_load.cmd == LC_SEGMENT: + section_cls = section + else: # LC_SEGMENT_64 + section_cls = section_64 + + expected_size = ( + sizeof(klass) + sizeof(load_command) + + (sizeof(section_cls) * cmd_cmd.nsects) + ) + if cmd_load.cmdsize != expected_size: + raise ValueError("Segment size mismatch") + # this is a zero block or something + # so the beginning is wherever the fileoff of this command is + if cmd_cmd.nsects == 0: + if cmd_cmd.filesize != 0: + low_offset = min(low_offset, cmd_cmd.fileoff) + else: + # this one has multiple segments + for j in range(cmd_cmd.nsects): + # read the segment + seg = section_cls.from_fileobj(fh, **kw) + # if the segment has a size and is not zero filled + # then its beginning is the offset of this segment + not_zerofill = ((seg.flags & S_ZEROFILL) != S_ZEROFILL) + if seg.offset > 0 and seg.size > 0 and not_zerofill: + low_offset = min(low_offset, seg.offset) + if not_zerofill: + c = fh.tell() + fh.seek(seg.offset) + sd = fh.read(seg.size) + seg.add_section_data(sd) + fh.seek(c) + segs.append(seg) + # data is a list of segments + cmd_data = segs + + # XXX: Disabled for now because writing back doesn't work + # elif cmd_load.cmd == LC_CODE_SIGNATURE: + # c = fh.tell() + # fh.seek(cmd_cmd.dataoff) + # cmd_data = fh.read(cmd_cmd.datasize) + # fh.seek(c) + # elif cmd_load.cmd == LC_SYMTAB: + # c = fh.tell() + # fh.seek(cmd_cmd.stroff) + # cmd_data = fh.read(cmd_cmd.strsize) + # fh.seek(c) + + else: + # data is a raw str + data_size = ( + cmd_load.cmdsize - sizeof(klass) - sizeof(load_command) + ) + cmd_data = fh.read(data_size) + cmd.append((cmd_load, cmd_cmd, cmd_data)) + read_bytes += cmd_load.cmdsize + + # make sure the header made sense + if read_bytes != header.sizeofcmds: + raise ValueError("Read %d bytes, header reports %d bytes" % ( + read_bytes, header.sizeofcmds)) + self.total_size = sizeof(self.mach_header) + read_bytes + self.low_offset = low_offset + + def walkRelocatables(self, shouldRelocateCommand=_shouldRelocateCommand): + """ + for all relocatable commands + yield (command_index, command_name, filename) + """ + for (idx, (lc, cmd, data)) in enumerate(self.commands): + if shouldRelocateCommand(lc.cmd): + name = _RELOCATABLE_NAMES[lc.cmd] + ofs = cmd.name - sizeof(lc.__class__) - sizeof(cmd.__class__) + yield idx, name, data[ofs:data.find(b'\x00', ofs)].decode( + sys.getfilesystemencoding()) + + def rewriteInstallNameCommand(self, loadcmd): + """Rewrite the load command of this dylib""" + if self.id_cmd is not None: + self.rewriteDataForCommand(self.id_cmd, loadcmd) + return True + return False + + def changedHeaderSizeBy(self, bytes): + self.sizediff += bytes + if (self.total_size + self.sizediff) > self.low_offset: + print( + "WARNING: Mach-O header in %r may be too large to relocate" % ( + self.parent.filename,)) + + def rewriteLoadCommands(self, changefunc): + """ + Rewrite the load commands based upon a change dictionary + """ + data = changefunc(self.parent.filename) + changed = False + if data is not None: + if self.rewriteInstallNameCommand( + data.encode(sys.getfilesystemencoding())): + changed = True + for idx, name, filename in self.walkRelocatables(): + data = changefunc(filename) + if data is not None: + if self.rewriteDataForCommand(idx, data.encode( + sys.getfilesystemencoding())): + changed = True + return changed + + def rewriteDataForCommand(self, idx, data): + lc, cmd, old_data = self.commands[idx] + hdrsize = sizeof(lc.__class__) + sizeof(cmd.__class__) + align = struct.calcsize('Q') + data = data + (b'\x00' * (align - (len(data) % align))) + newsize = hdrsize + len(data) + self.commands[idx] = (lc, cmd, data) + self.changedHeaderSizeBy(newsize - lc.cmdsize) + lc.cmdsize, cmd.name = newsize, hdrsize + return True + + def synchronize_size(self): + if (self.total_size + self.sizediff) > self.low_offset: + raise ValueError( + ("New Mach-O header is too large to relocate in %r " + "(new size=%r, max size=%r, delta=%r)") % ( + self.parent.filename, self.total_size + self.sizediff, + self.low_offset, self.sizediff)) + self.header.sizeofcmds += self.sizediff + self.total_size = sizeof(self.mach_header) + self.header.sizeofcmds + self.sizediff = 0 + + def write(self, fileobj): + fileobj = fileview(fileobj, self.offset, self.size) + fileobj.seek(0) + + # serialize all the mach-o commands + self.synchronize_size() + + self.header.to_fileobj(fileobj) + for lc, cmd, data in self.commands: + lc.to_fileobj(fileobj) + cmd.to_fileobj(fileobj) + + if sys.version_info[0] == 2: + if isinstance(data, unicode): + fileobj.write(data.encode(sys.getfilesystemencoding())) + + elif isinstance(data, (bytes, str)): + fileobj.write(data) + else: + # segments.. + for obj in data: + obj.to_fileobj(fileobj) + else: + if isinstance(data, str): + fileobj.write(data.encode(sys.getfilesystemencoding())) + + elif isinstance(data, bytes): + fileobj.write(data) + + else: + # segments.. + for obj in data: + obj.to_fileobj(fileobj) + + # zero out the unused space, doubt this is strictly necessary + # and is generally probably already the case + fileobj.write(b'\x00' * (self.low_offset - fileobj.tell())) + + def getSymbolTableCommand(self): + for lc, cmd, data in self.commands: + if lc.cmd == LC_SYMTAB: + return cmd + return None + + def getDynamicSymbolTableCommand(self): + for lc, cmd, data in self.commands: + if lc.cmd == LC_DYSYMTAB: + return cmd + return None + + def get_filetype_shortname(self, filetype): + if filetype in MH_FILETYPE_SHORTNAMES: + return MH_FILETYPE_SHORTNAMES[filetype] + else: + return 'unknown' + + +def main(fn): + m = MachO(fn) + seen = set() + for header in m.headers: + for idx, name, other in header.walkRelocatables(): + if other not in seen: + seen.add(other) + print('\t' + name + ": " + other) + + +if __name__ == '__main__': + import sys + files = sys.argv[1:] or ['/bin/ls'] + for fn in files: + print(fn) + main(fn) diff --git a/lib/spack/external/macholib/MachOGraph.py b/lib/spack/external/macholib/MachOGraph.py new file mode 100644 index 00000000000..5a733c3ed0f --- /dev/null +++ b/lib/spack/external/macholib/MachOGraph.py @@ -0,0 +1,138 @@ +""" +Utilities for reading and writing Mach-O headers +""" + +import os +import sys + +from altgraph.ObjectGraph import ObjectGraph + +from macholib.dyld import dyld_find +from macholib.MachO import MachO +from macholib.itergraphreport import itergraphreport + +__all__ = ['MachOGraph'] + +try: + unicode +except NameError: + unicode = str + + +class MissingMachO(object): + def __init__(self, filename): + self.graphident = filename + self.headers = () + + def __repr__(self): + return '<%s graphident=%r>' % (type(self).__name__, self.graphident) + + +class MachOGraph(ObjectGraph): + """ + Graph data structure of Mach-O dependencies + """ + def __init__(self, debug=0, graph=None, env=None, executable_path=None): + super(MachOGraph, self).__init__(debug=debug, graph=graph) + self.env = env + self.trans_table = {} + self.executable_path = executable_path + + def locate(self, filename, loader=None): + if not isinstance(filename, (str, unicode)): + raise TypeError("%r is not a string" % (filename,)) + if filename.startswith('@loader_path/') and loader is not None: + fn = self.trans_table.get((loader.filename, filename)) + if fn is None: + loader_path = loader.loader_path + + try: + fn = dyld_find( + filename, env=self.env, + executable_path=self.executable_path, + loader_path=loader_path) + self.trans_table[(loader.filename, filename)] = fn + except ValueError: + return None + + else: + fn = self.trans_table.get(filename) + if fn is None: + try: + fn = dyld_find( + filename, env=self.env, + executable_path=self.executable_path) + self.trans_table[filename] = fn + except ValueError: + return None + return fn + + def findNode(self, name, loader=None): + assert isinstance(name, (str, unicode)) + data = super(MachOGraph, self).findNode(name) + if data is not None: + return data + newname = self.locate(name, loader=loader) + if newname is not None and newname != name: + return self.findNode(newname) + return None + + def run_file(self, pathname, caller=None): + assert isinstance(pathname, (str, unicode)) + self.msgin(2, "run_file", pathname) + m = self.findNode(pathname, loader=caller) + if m is None: + if not os.path.exists(pathname): + raise ValueError('%r does not exist' % (pathname,)) + m = self.createNode(MachO, pathname) + self.createReference(caller, m, edge_data='run_file') + self.scan_node(m) + self.msgout(2, '') + return m + + def load_file(self, name, caller=None): + assert isinstance(name, (str, unicode)) + self.msgin(2, "load_file", name, caller) + m = self.findNode(name, loader=caller) + if m is None: + newname = self.locate(name, loader=caller) + if newname is not None and newname != name: + return self.load_file(newname, caller=caller) + if os.path.exists(name): + m = self.createNode(MachO, name) + self.scan_node(m) + else: + m = self.createNode(MissingMachO, name) + self.msgout(2, '') + return m + + def scan_node(self, node): + self.msgin(2, 'scan_node', node) + for header in node.headers: + for idx, name, filename in header.walkRelocatables(): + assert isinstance(name, (str, unicode)) + assert isinstance(filename, (str, unicode)) + m = self.load_file(filename, caller=node) + self.createReference(node, m, edge_data=name) + self.msgout(2, '', node) + + def itergraphreport(self, name='G'): + nodes = map(self.graph.describe_node, self.graph.iterdfs(self)) + describe_edge = self.graph.describe_edge + return itergraphreport(nodes, describe_edge, name=name) + + def graphreport(self, fileobj=None): + if fileobj is None: + fileobj = sys.stdout + fileobj.writelines(self.itergraphreport()) + + +def main(args): + g = MachOGraph() + for arg in args: + g.run_file(arg) + g.graphreport() + + +if __name__ == '__main__': + main(sys.argv[1:] or ['/bin/ls']) diff --git a/lib/spack/external/macholib/MachOStandalone.py b/lib/spack/external/macholib/MachOStandalone.py new file mode 100644 index 00000000000..c4f5b84d19d --- /dev/null +++ b/lib/spack/external/macholib/MachOStandalone.py @@ -0,0 +1,169 @@ +import os + +from macholib.MachOGraph import MachOGraph, MissingMachO +from macholib.util import iter_platform_files, in_system_path, mergecopy, \ + mergetree, flipwritable, has_filename_filter +from macholib.dyld import framework_info +from collections import deque + + +class ExcludedMachO(MissingMachO): + pass + + +class FilteredMachOGraph(MachOGraph): + def __init__(self, delegate, *args, **kwargs): + super(FilteredMachOGraph, self).__init__(*args, **kwargs) + self.delegate = delegate + + def createNode(self, cls, name): + cls = self.delegate.getClass(name, cls) + res = super(FilteredMachOGraph, self).createNode(cls, name) + return self.delegate.update_node(res) + + def locate(self, filename, loader=None): + newname = super(FilteredMachOGraph, self).locate(filename, loader) + print("locate", filename, loader, "->", newname) + if newname is None: + return None + return self.delegate.locate(newname, loader=loader) + + +class MachOStandalone(object): + def __init__( + self, base, dest=None, graph=None, env=None, + executable_path=None): + self.base = os.path.join(os.path.abspath(base), '') + if dest is None: + dest = os.path.join(self.base, 'Contents', 'Frameworks') + self.dest = dest + self.mm = FilteredMachOGraph( + self, graph=graph, env=env, executable_path=executable_path) + self.changemap = {} + self.excludes = [] + self.pending = deque() + + def update_node(self, m): + return m + + def getClass(self, name, cls): + if in_system_path(name): + return ExcludedMachO + for base in self.excludes: + if name.startswith(base): + return ExcludedMachO + return cls + + def locate(self, filename, loader=None): + if in_system_path(filename): + return filename + if filename.startswith(self.base): + return filename + for base in self.excludes: + if filename.startswith(base): + return filename + if filename in self.changemap: + return self.changemap[filename] + info = framework_info(filename) + if info is None: + res = self.copy_dylib(filename) + self.changemap[filename] = res + return res + else: + res = self.copy_framework(info) + self.changemap[filename] = res + return res + + def copy_dylib(self, filename): + # When the filename is a symlink use the basename of the target of + # the link as the name in standalone bundle. This avoids problems + # when two libraries link to the same dylib but using different + # symlinks. + if os.path.islink(filename): + dest = os.path.join( + self.dest, os.path.basename(os.path.realpath(filename))) + else: + dest = os.path.join(self.dest, os.path.basename(filename)) + + if not os.path.exists(dest): + self.mergecopy(filename, dest) + return dest + + def mergecopy(self, src, dest): + return mergecopy(src, dest) + + def mergetree(self, src, dest): + return mergetree(src, dest) + + def copy_framework(self, info): + dest = os.path.join(self.dest, info['shortname'] + '.framework') + destfn = os.path.join(self.dest, info['name']) + src = os.path.join(info['location'], info['shortname'] + '.framework') + if not os.path.exists(dest): + self.mergetree(src, dest) + self.pending.append((destfn, iter_platform_files(dest))) + return destfn + + def run(self, platfiles=None, contents=None): + mm = self.mm + if contents is None: + contents = '@executable_path/..' + if platfiles is None: + platfiles = iter_platform_files(self.base) + + for fn in platfiles: + mm.run_file(fn) + + while self.pending: + fmwk, files = self.pending.popleft() + ref = mm.findNode(fmwk) + for fn in files: + mm.run_file(fn, caller=ref) + + changemap = {} + skipcontents = os.path.join(os.path.dirname(self.dest), '') + machfiles = [] + + for node in mm.flatten(has_filename_filter): + machfiles.append(node) + dest = os.path.join( + contents, os.path.normpath(node.filename[len(skipcontents):])) + changemap[node.filename] = dest + + def changefunc(path): + if path.startswith('@loader_path/'): + # XXX: This is a quick hack for py2app: In that + # usecase paths like this are found in the load + # commands of relocatable wheels. Those don't + # need rewriting. + return path + + res = mm.locate(path) + rv = changemap.get(res) + if rv is None and path.startswith('@loader_path/'): + rv = changemap.get(mm.locate(mm.trans_table.get( + (node.filename, path)))) + return rv + + for node in machfiles: + fn = mm.locate(node.filename) + if fn is None: + continue + rewroteAny = False + for header in node.headers: + if node.rewriteLoadCommands(changefunc): + rewroteAny = True + if rewroteAny: + old_mode = flipwritable(fn) + try: + with open(fn, 'rb+') as f: + for header in node.headers: + f.seek(0) + node.write(f) + f.seek(0, 2) + f.flush() + finally: + flipwritable(fn, old_mode) + + allfiles = [mm.locate(node.filename) for node in machfiles] + return set(filter(None, allfiles)) diff --git a/lib/spack/external/macholib/SymbolTable.py b/lib/spack/external/macholib/SymbolTable.py new file mode 100644 index 00000000000..bf4d383ab70 --- /dev/null +++ b/lib/spack/external/macholib/SymbolTable.py @@ -0,0 +1,86 @@ +""" +Class to read the symbol table from a Mach-O header +""" +from __future__ import with_statement + +from macholib.mach_o import relocation_info, dylib_reference, dylib_module +from macholib.mach_o import dylib_table_of_contents, nlist, nlist_64 +from macholib.mach_o import MH_CIGAM_64, MH_MAGIC_64 +import sys + +__all__ = ['SymbolTable'] + +if sys.version_info[0] == 2: + range = xrange # noqa: F821 + + +class SymbolTable(object): + def __init__(self, macho, header=None, openfile=None): + if openfile is None: + openfile = open + if header is None: + header = macho.headers[0] + self.macho_header = header + with openfile(macho.filename, 'rb') as fh: + self.symtab = header.getSymbolTableCommand() + self.dysymtab = header.getDynamicSymbolTableCommand() + + if self.symtab is not None: + self.nlists = self.readSymbolTable(fh) + + if self.dysymtab is not None: + self.readDynamicSymbolTable(fh) + + def readSymbolTable(self, fh): + cmd = self.symtab + fh.seek(self.macho_header.offset + cmd.stroff) + strtab = fh.read(cmd.strsize) + fh.seek(self.macho_header.offset + cmd.symoff) + nlists = [] + + if self.macho_header.MH_MAGIC in [MH_MAGIC_64, MH_CIGAM_64]: + cls = nlist_64 + else: + cls = nlist + + for i in range(cmd.nsyms): + cmd = cls.from_fileobj(fh, _endian_=self.macho_header.endian) + if cmd.n_un == 0: + nlists.append((cmd, '')) + else: + nlists.append( + (cmd, strtab[cmd.n_un:strtab.find(b'\x00', cmd.n_un)])) + return nlists + + def readDynamicSymbolTable(self, fh): + cmd = self.dysymtab + nlists = self.nlists + + self.localsyms = nlists[cmd.ilocalsym:cmd.ilocalsym+cmd.nlocalsym] + self.extdefsyms = nlists[cmd.iextdefsym:cmd.iextdefsym+cmd.nextdefsym] + self.undefsyms = nlists[cmd.iundefsym:cmd.iundefsym+cmd.nundefsym] + if cmd.tocoff == 0: + self.toc = None + else: + self.toc = self.readtoc(fh, cmd.tocoff, cmd.ntoc) + + def readtoc(self, fh, off, n): + fh.seek(self.macho_header.offset + off) + return [dylib_table_of_contents.from_fileobj(fh) for i in range(n)] + + def readmodtab(self, fh, off, n): + fh.seek(self.macho_header.offset + off) + return [dylib_module.from_fileobj(fh) for i in range(n)] + + def readsym(self, fh, off, n): + fh.seek(self.macho_header.offset + off) + refs = [] + for i in range(n): + ref = dylib_reference.from_fileobj(fh) + isym, flags = divmod(ref.isym_flags, 256) + refs.append((self.nlists[isym], flags)) + return refs + + def readrel(self, fh, off, n): + fh.seek(self.macho_header.offset + off) + return [relocation_info.from_fileobj(fh) for i in range(n)] diff --git a/lib/spack/external/macholib/__init__.py b/lib/spack/external/macholib/__init__.py new file mode 100644 index 00000000000..f77c79492bc --- /dev/null +++ b/lib/spack/external/macholib/__init__.py @@ -0,0 +1,8 @@ +""" +Enough Mach-O to make your head spin. + +See the relevant header files in /usr/include/mach-o + +And also Apple's documentation. +""" +__version__ = '1.10' diff --git a/lib/spack/external/macholib/__main__.py b/lib/spack/external/macholib/__main__.py new file mode 100644 index 00000000000..66eaad865cf --- /dev/null +++ b/lib/spack/external/macholib/__main__.py @@ -0,0 +1,83 @@ +from __future__ import print_function, absolute_import +import os +import sys + +from macholib.util import is_platform_file +from macholib import macho_dump +from macholib import macho_standalone + +gCommand = None + + +def check_file(fp, path, callback): + if not os.path.exists(path): + print( + '%s: %s: No such file or directory' % (gCommand, path), + file=sys.stderr) + return 1 + + try: + is_plat = is_platform_file(path) + + except IOError as msg: + print('%s: %s: %s' % (gCommand, path, msg), file=sys.stderr) + return 1 + + else: + if is_plat: + callback(fp, path) + return 0 + + +def walk_tree(callback, paths): + err = 0 + + for base in paths: + if os.path.isdir(base): + for root, dirs, files in os.walk(base): + for fn in files: + err |= check_file( + sys.stdout, os.path.join(root, fn), callback) + else: + err |= check_file(sys.stdout, base, callback) + + return err + + +def print_usage(fp): + print("Usage:", file=fp) + print(" python -mmacholib [help|--help]", file=fp) + print(" python -mmacholib dump FILE ...", file=fp) + print(" python -mmacholib find DIR ...", file=fp) + print(" python -mmacholib standalone DIR ...", file=fp) + + +def main(): + global gCommand + if len(sys.argv) < 3: + print_usage(sys.stderr) + sys.exit(1) + + gCommand = sys.argv[1] + + if gCommand == 'dump': + walk_tree(macho_dump.print_file, sys.argv[2:]) + + elif gCommand == 'find': + walk_tree(lambda fp, path: print(path, file=fp), sys.argv[2:]) + + elif gCommand == 'standalone': + for dn in sys.argv[2:]: + macho_standalone.standaloneApp(dn) + + elif gCommand in ('help', '--help'): + print_usage(sys.stdout) + sys.exit(0) + + else: + print_usage(sys.stderr) + sys.exit(1) + + +if __name__ == "__main__": + main() diff --git a/lib/spack/external/macholib/_cmdline.py b/lib/spack/external/macholib/_cmdline.py new file mode 100644 index 00000000000..c6227334a1a --- /dev/null +++ b/lib/spack/external/macholib/_cmdline.py @@ -0,0 +1,48 @@ +""" +Internal helpers for basic commandline tools +""" +from __future__ import print_function, absolute_import +import os +import sys + +from macholib.util import is_platform_file + + +def check_file(fp, path, callback): + if not os.path.exists(path): + print('%s: %s: No such file or directory' % ( + sys.argv[0], path), file=sys.stderr) + return 1 + + try: + is_plat = is_platform_file(path) + + except IOError as msg: + print('%s: %s: %s' % (sys.argv[0], path, msg), file=sys.stderr) + return 1 + + else: + if is_plat: + callback(fp, path) + return 0 + + +def main(callback): + args = sys.argv[1:] + name = os.path.basename(sys.argv[0]) + err = 0 + + if not args: + print("Usage: %s filename..." % (name,), file=sys.stderr) + return 1 + + for base in args: + if os.path.isdir(base): + for root, dirs, files in os.walk(base): + for fn in files: + err |= check_file( + sys.stdout, os.path.join(root, fn), callback) + else: + err |= check_file(sys.stdout, base, callback) + + return err diff --git a/lib/spack/external/macholib/dyld.py b/lib/spack/external/macholib/dyld.py new file mode 100644 index 00000000000..1157ebf0078 --- /dev/null +++ b/lib/spack/external/macholib/dyld.py @@ -0,0 +1,190 @@ +""" +dyld emulation +""" + +from itertools import chain + +import os +import sys + +from macholib.framework import framework_info +from macholib.dylib import dylib_info + +__all__ = [ + 'dyld_find', 'framework_find', + 'framework_info', 'dylib_info', +] + +# These are the defaults as per man dyld(1) +# +_DEFAULT_FRAMEWORK_FALLBACK = [ + os.path.expanduser("~/Library/Frameworks"), + "/Library/Frameworks", + "/Network/Library/Frameworks", + "/System/Library/Frameworks", +] + +_DEFAULT_LIBRARY_FALLBACK = [ + os.path.expanduser("~/lib"), + "/usr/local/lib", + "/lib", + "/usr/lib", +] + +# XXX: Is this function still needed? +if sys.version_info[0] == 2: + def _ensure_utf8(s): + if isinstance(s, unicode): # noqa: F821 + return s.encode('utf8') + return s +else: + def _ensure_utf8(s): + if s is not None and not isinstance(s, str): + raise ValueError(s) + return s + + +def _dyld_env(env, var): + if env is None: + env = os.environ + rval = env.get(var) + if rval is None or rval == '': + return [] + return rval.split(':') + + +def dyld_image_suffix(env=None): + if env is None: + env = os.environ + return env.get('DYLD_IMAGE_SUFFIX') + + +def dyld_framework_path(env=None): + return _dyld_env(env, 'DYLD_FRAMEWORK_PATH') + + +def dyld_library_path(env=None): + return _dyld_env(env, 'DYLD_LIBRARY_PATH') + + +def dyld_fallback_framework_path(env=None): + return _dyld_env(env, 'DYLD_FALLBACK_FRAMEWORK_PATH') + + +def dyld_fallback_library_path(env=None): + return _dyld_env(env, 'DYLD_FALLBACK_LIBRARY_PATH') + + +def dyld_image_suffix_search(iterator, env=None): + """For a potential path iterator, add DYLD_IMAGE_SUFFIX semantics""" + suffix = dyld_image_suffix(env) + if suffix is None: + return iterator + + def _inject(iterator=iterator, suffix=suffix): + for path in iterator: + if path.endswith('.dylib'): + yield path[:-len('.dylib')] + suffix + '.dylib' + else: + yield path + suffix + yield path + + return _inject() + + +def dyld_override_search(name, env=None): + # If DYLD_FRAMEWORK_PATH is set and this dylib_name is a + # framework name, use the first file that exists in the framework + # path if any. If there is none go on to search the DYLD_LIBRARY_PATH + # if any. + + framework = framework_info(name) + + if framework is not None: + for path in dyld_framework_path(env): + yield os.path.join(path, framework['name']) + + # If DYLD_LIBRARY_PATH is set then use the first file that exists + # in the path. If none use the original name. + for path in dyld_library_path(env): + yield os.path.join(path, os.path.basename(name)) + + +def dyld_executable_path_search(name, executable_path=None): + # If we haven't done any searching and found a library and the + # dylib_name starts with "@executable_path/" then construct the + # library name. + if name.startswith('@executable_path/') and executable_path is not None: + yield os.path.join(executable_path, name[len('@executable_path/'):]) + + +def dyld_loader_search(name, loader_path=None): + # If we haven't done any searching and found a library and the + # dylib_name starts with "@loader_path/" then construct the + # library name. + if name.startswith('@loader_path/') and loader_path is not None: + yield os.path.join(loader_path, name[len('@loader_path/'):]) + + +def dyld_default_search(name, env=None): + yield name + + framework = framework_info(name) + + if framework is not None: + fallback_framework_path = dyld_fallback_framework_path(env) + + if fallback_framework_path: + for path in fallback_framework_path: + yield os.path.join(path, framework['name']) + + else: + for path in _DEFAULT_FRAMEWORK_FALLBACK: + yield os.path.join(path, framework['name']) + + fallback_library_path = dyld_fallback_library_path(env) + if fallback_library_path: + for path in fallback_library_path: + yield os.path.join(path, os.path.basename(name)) + + else: + for path in _DEFAULT_LIBRARY_FALLBACK: + yield os.path.join(path, os.path.basename(name)) + + +def dyld_find(name, executable_path=None, env=None, loader_path=None): + """ + Find a library or framework using dyld semantics + """ + name = _ensure_utf8(name) + executable_path = _ensure_utf8(executable_path) + for path in dyld_image_suffix_search(chain( + dyld_override_search(name, env), + dyld_executable_path_search(name, executable_path), + dyld_loader_search(name, loader_path), + dyld_default_search(name, env), + ), env): + if os.path.isfile(path): + return path + raise ValueError("dylib %s could not be found" % (name,)) + + +def framework_find(fn, executable_path=None, env=None): + """ + Find a framework using dyld semantics in a very loose manner. + + Will take input such as: + Python + Python.framework + Python.framework/Versions/Current + """ + try: + return dyld_find(fn, executable_path=executable_path, env=env) + except ValueError: + pass + fmwk_index = fn.rfind('.framework') + if fmwk_index == -1: + fmwk_index = len(fn) + fn += '.framework' + fn = os.path.join(fn, os.path.basename(fn[:fmwk_index])) + return dyld_find(fn, executable_path=executable_path, env=env) diff --git a/lib/spack/external/macholib/dylib.py b/lib/spack/external/macholib/dylib.py new file mode 100644 index 00000000000..5b06b40e13b --- /dev/null +++ b/lib/spack/external/macholib/dylib.py @@ -0,0 +1,43 @@ +""" +Generic dylib path manipulation +""" + +import re + +__all__ = ['dylib_info'] + +_DYLIB_RE = re.compile(r"""(?x) +(?P^.*)(?:^|/) +(?P + (?P\w+?) + (?:\.(?P[^._]+))? + (?:_(?P[^._]+))? + \.dylib$ +) +""") + + +def dylib_info(filename): + """ + A dylib name can take one of the following four forms: + Location/Name.SomeVersion_Suffix.dylib + Location/Name.SomeVersion.dylib + Location/Name_Suffix.dylib + Location/Name.dylib + + returns None if not found or a mapping equivalent to: + dict( + location='Location', + name='Name.SomeVersion_Suffix.dylib', + shortname='Name', + version='SomeVersion', + suffix='Suffix', + ) + + Note that SomeVersion and Suffix are optional and may be None + if not present. + """ + is_dylib = _DYLIB_RE.match(filename) + if not is_dylib: + return None + return is_dylib.groupdict() diff --git a/lib/spack/external/macholib/framework.py b/lib/spack/external/macholib/framework.py new file mode 100644 index 00000000000..8f8632c209c --- /dev/null +++ b/lib/spack/external/macholib/framework.py @@ -0,0 +1,43 @@ +""" +Generic framework path manipulation +""" + +import re + +__all__ = ['framework_info'] + +_STRICT_FRAMEWORK_RE = re.compile(r"""(?x) +(?P^.*)(?:^|/) +(?P + (?P[-_A-Za-z0-9]+).framework/ + (?:Versions/(?P[^/]+)/)? + (?P=shortname) + (?:_(?P[^_]+))? +)$ +""") + + +def framework_info(filename): + """ + A framework name can take one of the following four forms: + Location/Name.framework/Versions/SomeVersion/Name_Suffix + Location/Name.framework/Versions/SomeVersion/Name + Location/Name.framework/Name_Suffix + Location/Name.framework/Name + + returns None if not found, or a mapping equivalent to: + dict( + location='Location', + name='Name.framework/Versions/SomeVersion/Name_Suffix', + shortname='Name', + version='SomeVersion', + suffix='Suffix', + ) + + Note that SomeVersion and Suffix are optional and may be None + if not present + """ + is_framework = _STRICT_FRAMEWORK_RE.match(filename) + if not is_framework: + return None + return is_framework.groupdict() diff --git a/lib/spack/external/macholib/itergraphreport.py b/lib/spack/external/macholib/itergraphreport.py new file mode 100644 index 00000000000..eea3fd69bc9 --- /dev/null +++ b/lib/spack/external/macholib/itergraphreport.py @@ -0,0 +1,73 @@ +""" +Utilities for creating dot output from a MachOGraph + +XXX: need to rewrite this based on altgraph.Dot +""" + +from collections import deque + +try: + from itertools import imap +except ImportError: + imap = map + +__all__ = ['itergraphreport'] + + +def itergraphreport(nodes, describe_edge, name='G'): + edges = deque() + nodetoident = {} + + def nodevisitor(node, data, outgoing, incoming): + return {'label': str(node)} + + def edgevisitor(edge, data, head, tail): + return {} + + yield 'digraph %s {\n' % (name,) + attr = dict(rankdir='LR', concentrate='true') + cpatt = '%s="%s"' + for item in attr.iteritems(): + yield '\t%s;\n' % (cpatt % item,) + + # find all packages (subgraphs) + for (node, data, outgoing, incoming) in nodes: + nodetoident[node] = getattr(data, 'identifier', node) + + # create sets for subgraph, write out descriptions + for (node, data, outgoing, incoming) in nodes: + # update edges + for edge in imap(describe_edge, outgoing): + edges.append(edge) + + # describe node + yield '\t"%s" [%s];\n' % ( + node, + ','.join([ + (cpatt % item) for item in + nodevisitor(node, data, outgoing, incoming).iteritems() + ]), + ) + + graph = [] + + while edges: + edge, data, head, tail = edges.popleft() + if data in ('run_file', 'load_dylib'): + graph.append((edge, data, head, tail)) + + def do_graph(edges, tabs): + edgestr = tabs + '"%s" -> "%s" [%s];\n' + # describe edge + for (edge, data, head, tail) in edges: + attribs = edgevisitor(edge, data, head, tail) + yield edgestr % ( + head, + tail, + ','.join([(cpatt % item) for item in attribs.iteritems()]), + ) + + for s in do_graph(graph, '\t'): + yield s + + yield '}\n' diff --git a/lib/spack/external/macholib/mach_o.py b/lib/spack/external/macholib/mach_o.py new file mode 100644 index 00000000000..7c5803d939b --- /dev/null +++ b/lib/spack/external/macholib/mach_o.py @@ -0,0 +1,1665 @@ +""" +Other than changing the load commands in such a way that they do not +contain the load command itself, this is largely a by-hand conversion +of the C headers. Hopefully everything in here should be at least as +obvious as the C headers, and you should be using the C headers as a real +reference because the documentation didn't come along for the ride. + +Doing much of anything with the symbol tables or segments is really +not covered at this point. + +See /usr/include/mach-o and friends. +""" + +import time + +from macholib.ptypes import p_uint32, p_uint64, Structure, p_long, pypackable +from macholib.ptypes import p_int64, p_short, p_uint8, p_int32, p_ulong + +_CPU_ARCH_ABI64 = 0x01000000 + +CPU_TYPE_NAMES = { + -1: 'ANY', + 1: 'VAX', + 6: 'MC680x0', + 7: 'i386', + _CPU_ARCH_ABI64 | 7: 'x86_64', + 8: 'MIPS', + 10: 'MC98000', + 11: 'HPPA', + 12: 'ARM', + _CPU_ARCH_ABI64 | 12: 'ARM64', + 13: 'MC88000', + 14: 'SPARC', + 15: 'i860', + 16: 'Alpha', + 18: 'PowerPC', + _CPU_ARCH_ABI64 | 18: 'PowerPC64', +} + +INTEL64_SUBTYPE = { + 3: "CPU_SUBTYPE_X86_64_ALL", + 4: "CPU_SUBTYPE_X86_ARCH1", + 8: "CPU_SUBTYPE_X86_64_H", +} + +# define CPU_SUBTYPE_INTEL(f, m) ((cpu_subtype_t) (f) + ((m) << 4)) +INTEL_SUBTYPE = { + 0: "CPU_SUBTYPE_INTEL_MODEL_ALL", + 1: "CPU_THREADTYPE_INTEL_HTT", + 3: "CPU_SUBTYPE_I386_ALL", + 4: "CPU_SUBTYPE_486", + 5: "CPU_SUBTYPE_586", + 8: "CPU_SUBTYPE_PENTIUM_3", + 9: "CPU_SUBTYPE_PENTIUM_M", + 10: "CPU_SUBTYPE_PENTIUM_4", + 11: "CPU_SUBTYPE_ITANIUM", + 12: "CPU_SUBTYPE_XEON", + 34: "CPU_SUBTYPE_XEON_MP", + 42: "CPU_SUBTYPE_PENTIUM_4_M", + 43: "CPU_SUBTYPE_ITANIUM_2", + 38: "CPU_SUBTYPE_PENTPRO", + 40: "CPU_SUBTYPE_PENTIUM_3_M", + 52: "CPU_SUBTYPE_PENTIUM_3_XEON", + 102: "CPU_SUBTYPE_PENTII_M3", + 132: "CPU_SUBTYPE_486SX", + 166: "CPU_SUBTYPE_PENTII_M5", + 199: "CPU_SUBTYPE_CELERON", + 231: "CPU_SUBTYPE_CELERON_MOBILE" +} + +MC680_SUBTYPE = { + 1: "CPU_SUBTYPE_MC680x0_ALL", + 2: "CPU_SUBTYPE_MC68040", + 3: "CPU_SUBTYPE_MC68030_ONLY" +} + +MIPS_SUBTYPE = { + 0: "CPU_SUBTYPE_MIPS_ALL", + 1: "CPU_SUBTYPE_MIPS_R2300", + 2: "CPU_SUBTYPE_MIPS_R2600", + 3: "CPU_SUBTYPE_MIPS_R2800", + 4: "CPU_SUBTYPE_MIPS_R2000a", + 5: "CPU_SUBTYPE_MIPS_R2000", + 6: "CPU_SUBTYPE_MIPS_R3000a", + 7: "CPU_SUBTYPE_MIPS_R3000" +} + +MC98000_SUBTYPE = { + 0: "CPU_SUBTYPE_MC98000_ALL", + 1: "CPU_SUBTYPE_MC98601" +} + +HPPA_SUBTYPE = { + 0: "CPU_SUBTYPE_HPPA_7100", + 1: "CPU_SUBTYPE_HPPA_7100LC" +} + +MC88_SUBTYPE = { + 0: "CPU_SUBTYPE_MC88000_ALL", + 1: "CPU_SUBTYPE_MC88100", + 2: "CPU_SUBTYPE_MC88110" +} + +SPARC_SUBTYPE = { + 0: "CPU_SUBTYPE_SPARC_ALL" +} + +I860_SUBTYPE = { + 0: "CPU_SUBTYPE_I860_ALL", + 1: "CPU_SUBTYPE_I860_860" +} + +POWERPC_SUBTYPE = { + 0: "CPU_SUBTYPE_POWERPC_ALL", + 1: "CPU_SUBTYPE_POWERPC_601", + 2: "CPU_SUBTYPE_POWERPC_602", + 3: "CPU_SUBTYPE_POWERPC_603", + 4: "CPU_SUBTYPE_POWERPC_603e", + 5: "CPU_SUBTYPE_POWERPC_603ev", + 6: "CPU_SUBTYPE_POWERPC_604", + 7: "CPU_SUBTYPE_POWERPC_604e", + 8: "CPU_SUBTYPE_POWERPC_620", + 9: "CPU_SUBTYPE_POWERPC_750", + 10: "CPU_SUBTYPE_POWERPC_7400", + 11: "CPU_SUBTYPE_POWERPC_7450", + 100: "CPU_SUBTYPE_POWERPC_970" +} + +ARM_SUBTYPE = { + 0: "CPU_SUBTYPE_ARM_ALL12", + 5: "CPU_SUBTYPE_ARM_V4T", + 6: "CPU_SUBTYPE_ARM_V6", + 7: "CPU_SUBTYPE_ARM_V5TEJ", + 8: "CPU_SUBTYPE_ARM_XSCALE", + 9: "CPU_SUBTYPE_ARM_V7", + 10: "CPU_SUBTYPE_ARM_V7F", + 11: "CPU_SUBTYPE_ARM_V7S", + 12: "CPU_SUBTYPE_ARM_V7K", + 13: "CPU_SUBTYPE_ARM_V8", + 14: "CPU_SUBTYPE_ARM_V6M", + 15: "CPU_SUBTYPE_ARM_V7M", + 16: "CPU_SUBTYPE_ARM_V7EM", +} + +ARM64_SUBTYPE = { + 0: "CPU_SUBTYPE_ARM64_ALL", + 1: "CPU_SUBTYPE_ARM64_V8", +} + +VAX_SUBTYPE = { + 0: "CPU_SUBTYPE_VAX_ALL", + 1: "CPU_SUBTYPE_VAX780", + 2: "CPU_SUBTYPE_VAX785", + 3: "CPU_SUBTYPE_VAX750", + 4: "CPU_SUBTYPE_VAX730", + 5: "CPU_SUBTYPE_UVAXI", + 6: "CPU_SUBTYPE_UVAXII", + 7: "CPU_SUBTYPE_VAX8200", + 8: "CPU_SUBTYPE_VAX8500", + 9: "CPU_SUBTYPE_VAX8600", + 10: "CPU_SUBTYPE_VAX8650", + 11: "CPU_SUBTYPE_VAX8800", + 12: "CPU_SUBTYPE_UVAXIII", +} + + +def get_cpu_subtype(cpu_type, cpu_subtype): + st = cpu_subtype & 0x0fffffff + + if cpu_type == 1: + subtype = VAX_SUBTYPE.get(st, st) + elif cpu_type == 6: + subtype = MC680_SUBTYPE.get(st, st) + elif cpu_type == 7: + subtype = INTEL_SUBTYPE.get(st, st) + elif cpu_type == 7 | _CPU_ARCH_ABI64: + subtype = INTEL64_SUBTYPE.get(st, st) + elif cpu_type == 8: + subtype = MIPS_SUBTYPE.get(st, st) + elif cpu_type == 10: + subtype = MC98000_SUBTYPE.get(st, st) + elif cpu_type == 11: + subtype = HPPA_SUBTYPE.get(st, st) + elif cpu_type == 12: + subtype = ARM_SUBTYPE.get(st, st) + elif cpu_type == 12 | _CPU_ARCH_ABI64: + subtype = ARM64_SUBTYPE.get(st, st) + elif cpu_type == 13: + subtype = MC88_SUBTYPE.get(st, st) + elif cpu_type == 14: + subtype = SPARC_SUBTYPE.get(st, st) + elif cpu_type == 15: + subtype = I860_SUBTYPE.get(st, st) + elif cpu_type == 16: + subtype = MIPS_SUBTYPE.get(st, st) + elif cpu_type == 18: + subtype = POWERPC_SUBTYPE.get(st, st) + elif cpu_type == 18 | _CPU_ARCH_ABI64: + subtype = POWERPC_SUBTYPE.get(st, st) + else: + subtype = str(st) + + return subtype + + +_MH_EXECUTE_SYM = "__mh_execute_header" +MH_EXECUTE_SYM = "_mh_execute_header" +_MH_BUNDLE_SYM = "__mh_bundle_header" +MH_BUNDLE_SYM = "_mh_bundle_header" +_MH_DYLIB_SYM = "__mh_dylib_header" +MH_DYLIB_SYM = "_mh_dylib_header" +_MH_DYLINKER_SYM = "__mh_dylinker_header" +MH_DYLINKER_SYM = "_mh_dylinker_header" + +( + MH_OBJECT, MH_EXECUTE, MH_FVMLIB, MH_CORE, MH_PRELOAD, MH_DYLIB, + MH_DYLINKER, MH_BUNDLE, MH_DYLIB_STUB, MH_DSYM +) = range(0x1, 0xb) + +( + MH_NOUNDEFS, MH_INCRLINK, MH_DYLDLINK, MH_BINDATLOAD, MH_PREBOUND, + MH_SPLIT_SEGS, MH_LAZY_INIT, MH_TWOLEVEL, MH_FORCE_FLAT, MH_NOMULTIDEFS, + MH_NOFIXPREBINDING, MH_PREBINDABLE, MH_ALLMODSBOUND, + MH_SUBSECTIONS_VIA_SYMBOLS, MH_CANONICAL, MH_WEAK_DEFINES, + MH_BINDS_TO_WEAK, MH_ALLOW_STACK_EXECUTION, + MH_ROOT_SAFE, MH_SETUID_SAFE, MH_NO_REEXPORTED_DYLIBS, MH_PIE, + MH_DEAD_STRIPPABLE_DYLIB, MH_HAS_TLV_DESCRIPTORS, MH_NO_HEAP_EXECUTION, + MH_APP_EXTENSION_SAFE +) = map((1).__lshift__, range(26)) + +MH_MAGIC = 0xfeedface +MH_CIGAM = 0xcefaedfe +MH_MAGIC_64 = 0xfeedfacf +MH_CIGAM_64 = 0xcffaedfe + +integer_t = p_int32 +cpu_type_t = integer_t +cpu_subtype_t = p_uint32 + +MH_FILETYPE_NAMES = { + MH_OBJECT: 'relocatable object', + MH_EXECUTE: 'demand paged executable', + MH_FVMLIB: 'fixed vm shared library', + MH_CORE: 'core', + MH_PRELOAD: 'preloaded executable', + MH_DYLIB: 'dynamically bound shared library', + MH_DYLINKER: 'dynamic link editor', + MH_BUNDLE: 'dynamically bound bundle', + MH_DYLIB_STUB: 'shared library stub for static linking', + MH_DSYM: 'symbol information', +} + +MH_FILETYPE_SHORTNAMES = { + MH_OBJECT: 'object', + MH_EXECUTE: 'execute', + MH_FVMLIB: 'fvmlib', + MH_CORE: 'core', + MH_PRELOAD: 'preload', + MH_DYLIB: 'dylib', + MH_DYLINKER: 'dylinker', + MH_BUNDLE: 'bundle', + MH_DYLIB_STUB: 'dylib_stub', + MH_DSYM: 'dsym', +} + +MH_FLAGS_NAMES = { + MH_NOUNDEFS: 'MH_NOUNDEFS', + MH_INCRLINK: 'MH_INCRLINK', + MH_DYLDLINK: 'MH_DYLDLINK', + MH_BINDATLOAD: 'MH_BINDATLOAD', + MH_PREBOUND: 'MH_PREBOUND', + MH_SPLIT_SEGS: 'MH_SPLIT_SEGS', + MH_LAZY_INIT: 'MH_LAZY_INIT', + MH_TWOLEVEL: 'MH_TWOLEVEL', + MH_FORCE_FLAT: 'MH_FORCE_FLAT', + MH_NOMULTIDEFS: 'MH_NOMULTIDEFS', + MH_NOFIXPREBINDING: 'MH_NOFIXPREBINDING', + MH_PREBINDABLE: 'MH_PREBINDABLE', + MH_ALLMODSBOUND: 'MH_ALLMODSBOUND', + MH_SUBSECTIONS_VIA_SYMBOLS: 'MH_SUBSECTIONS_VIA_SYMBOLS', + MH_CANONICAL: 'MH_CANONICAL', + MH_WEAK_DEFINES: 'MH_WEAK_DEFINES', + MH_BINDS_TO_WEAK: 'MH_BINDS_TO_WEAK', + MH_ALLOW_STACK_EXECUTION: 'MH_ALLOW_STACK_EXECUTION', + MH_ROOT_SAFE: 'MH_ROOT_SAFE', + MH_SETUID_SAFE: 'MH_SETUID_SAFE', + MH_NO_REEXPORTED_DYLIBS: 'MH_NO_REEXPORTED_DYLIBS', + MH_PIE: 'MH_PIE', + MH_DEAD_STRIPPABLE_DYLIB: 'MH_DEAD_STRIPPABLE_DYLIB', + MH_HAS_TLV_DESCRIPTORS: 'MH_HAS_TLV_DESCRIPTORS', + MH_NO_HEAP_EXECUTION: 'MH_NO_HEAP_EXECUTION', + MH_APP_EXTENSION_SAFE: 'MH_APP_EXTENSION_SAFE', +} + +MH_FLAGS_DESCRIPTIONS = { + MH_NOUNDEFS: 'no undefined references', + MH_INCRLINK: 'output of an incremental link', + MH_DYLDLINK: 'input for the dynamic linker', + MH_BINDATLOAD: 'undefined references bound dynamically when loaded', + MH_PREBOUND: 'dynamic undefined references prebound', + MH_SPLIT_SEGS: 'split read-only and read-write segments', + MH_LAZY_INIT: '(obsolete)', + MH_TWOLEVEL: 'using two-level name space bindings', + MH_FORCE_FLAT: 'forcing all imagges to use flat name space bindings', + MH_NOMULTIDEFS: 'umbrella guarantees no multiple definitions', + MH_NOFIXPREBINDING: 'do not notify prebinding agent about this executable', + MH_PREBINDABLE: + 'the binary is not prebound but can have its prebinding redone', + MH_ALLMODSBOUND: + 'indicates that this binary binds to all two-level namespace modules ' + 'of its dependent libraries', + MH_SUBSECTIONS_VIA_SYMBOLS: + 'safe to divide up the sections into sub-sections via symbols for ' + 'dead code stripping', + MH_CANONICAL: + 'the binary has been canonicalized via the unprebind operation', + MH_WEAK_DEFINES: 'the final linked image contains external weak symbols', + MH_BINDS_TO_WEAK: 'the final linked image uses weak symbols', + MH_ALLOW_STACK_EXECUTION: + 'all stacks in the task will be given stack execution privilege', + MH_ROOT_SAFE: + 'the binary declares it is safe for use in processes with uid zero', + MH_SETUID_SAFE: + 'the binary declares it is safe for use in processes when issetugid() ' + 'is true', + MH_NO_REEXPORTED_DYLIBS: + 'the static linker does not need to examine dependent dylibs to see ' + 'if any are re-exported', + MH_PIE: 'the OS will load the main executable at a random address', + MH_DEAD_STRIPPABLE_DYLIB: + 'the static linker will automatically not create a LC_LOAD_DYLIB load ' + 'command to the dylib if no symbols are being referenced from the ' + 'dylib', + MH_HAS_TLV_DESCRIPTORS: + 'contains a section of type S_THREAD_LOCAL_VARIABLES', + MH_NO_HEAP_EXECUTION: + 'the OS will run the main executable with a non-executable heap ' + 'even on platforms that don\'t require it', + MH_APP_EXTENSION_SAFE: + 'the code was linked for use in an application extension.', +} + + +class mach_version_helper(Structure): + _fields_ = ( + ('_version', p_uint32), + ) + + @property + def major(self): + return self._version >> 16 & 0xffff + + @major.setter + def major(self, v): + self._version = (self._version & 0xffff) | (v << 16) + + @property + def minor(self): + return self._version >> 8 & 0xff + + @minor.setter + def minor(self, v): + self._version = (self._version & 0xffff00ff) | (v << 8) + + @property + def rev(self): + return self._version & 0xff + + @rev.setter + def rev(self, v): + return (self._version & 0xffffff00) | v + + def __str__(self): + return '%s.%s.%s' % (self.major, self.minor, self.rev) + + +class mach_timestamp_helper(p_uint32): + def __str__(self): + return time.ctime(self) + + +def read_struct(f, s, **kw): + return s.from_fileobj(f, **kw) + + +class mach_header(Structure): + _fields_ = ( + ('magic', p_uint32), + ('cputype', cpu_type_t), + ('cpusubtype', cpu_subtype_t), + ('filetype', p_uint32), + ('ncmds', p_uint32), + ('sizeofcmds', p_uint32), + ('flags', p_uint32), + ) + + def _describe(self): + bit = 1 + flags = self.flags + dflags = [] + while flags and bit < (1 << 32): + if flags & bit: + dflags.append({ + 'name': MH_FLAGS_NAMES.get(bit, str(bit)), + 'description': MH_FLAGS_DESCRIPTIONS.get(bit, str(bit)) + }) + flags = flags ^ bit + bit <<= 1 + return ( + ('magic', int(self.magic)), + ('cputype_string', CPU_TYPE_NAMES.get(self.cputype, self.cputype)), + ('cputype', int(self.cputype)), + ('cpusubtype_string', + get_cpu_subtype(self.cputype, self.cpusubtype)), + ('cpusubtype', int(self.cpusubtype)), + ('filetype_string', + MH_FILETYPE_NAMES.get(self.filetype, self.filetype)), + ('filetype', int(self.filetype)), + ('ncmds', self.ncmds), + ('sizeofcmds', self.sizeofcmds), + ('flags', dflags), + ('raw_flags', int(self.flags)) + ) + + +class mach_header_64(mach_header): + _fields_ = mach_header._fields_ + (('reserved', p_uint32),) + + +class load_command(Structure): + _fields_ = ( + ('cmd', p_uint32), + ('cmdsize', p_uint32), + ) + + def get_cmd_name(self): + return LC_NAMES.get(self.cmd, self.cmd) + + +LC_REQ_DYLD = 0x80000000 + +( + LC_SEGMENT, LC_SYMTAB, LC_SYMSEG, LC_THREAD, LC_UNIXTHREAD, LC_LOADFVMLIB, + LC_IDFVMLIB, LC_IDENT, LC_FVMFILE, LC_PREPAGE, LC_DYSYMTAB, LC_LOAD_DYLIB, + LC_ID_DYLIB, LC_LOAD_DYLINKER, LC_ID_DYLINKER, LC_PREBOUND_DYLIB, + LC_ROUTINES, LC_SUB_FRAMEWORK, LC_SUB_UMBRELLA, LC_SUB_CLIENT, + LC_SUB_LIBRARY, LC_TWOLEVEL_HINTS, LC_PREBIND_CKSUM +) = range(0x1, 0x18) + +LC_LOAD_WEAK_DYLIB = LC_REQ_DYLD | 0x18 + +LC_SEGMENT_64 = 0x19 +LC_ROUTINES_64 = 0x1a +LC_UUID = 0x1b +LC_RPATH = (0x1c | LC_REQ_DYLD) +LC_CODE_SIGNATURE = 0x1d +LC_CODE_SEGMENT_SPLIT_INFO = 0x1e +LC_REEXPORT_DYLIB = 0x1f | LC_REQ_DYLD +LC_LAZY_LOAD_DYLIB = 0x20 +LC_ENCRYPTION_INFO = 0x21 +LC_DYLD_INFO = 0x22 +LC_DYLD_INFO_ONLY = 0x22 | LC_REQ_DYLD +LC_LOAD_UPWARD_DYLIB = 0x23 | LC_REQ_DYLD +LC_VERSION_MIN_MACOSX = 0x24 +LC_VERSION_MIN_IPHONEOS = 0x25 +LC_FUNCTION_STARTS = 0x26 +LC_DYLD_ENVIRONMENT = 0x27 +LC_MAIN = 0x28 | LC_REQ_DYLD +LC_DATA_IN_CODE = 0x29 +LC_SOURCE_VERSION = 0x2a +LC_DYLIB_CODE_SIGN_DRS = 0x2b +LC_ENCRYPTION_INFO_64 = 0x2c +LC_LINKER_OPTION = 0x2d +LC_LINKER_OPTIMIZATION_HINT = 0x2e +LC_VERSION_MIN_TVOS = 0x2f +LC_VERSION_MIN_WATCHOS = 0x30 +LC_NOTE = 0x31 +LC_BUILD_VERSION = 0x32 + + +# this is really a union.. but whatever +class lc_str(p_uint32): + pass + + +p_str16 = pypackable('p_str16', bytes, '16s') + +vm_prot_t = p_int32 + + +class segment_command(Structure): + _fields_ = ( + ('segname', p_str16), + ('vmaddr', p_uint32), + ('vmsize', p_uint32), + ('fileoff', p_uint32), + ('filesize', p_uint32), + ('maxprot', vm_prot_t), + ('initprot', vm_prot_t), + ('nsects', p_uint32), # read the section structures ? + ('flags', p_uint32), + ) + + def describe(self): + s = {} + s['segname'] = self.segname.rstrip('\x00') + s['vmaddr'] = int(self.vmaddr) + s['vmsize'] = int(self.vmsize) + s['fileoff'] = int(self.fileoff) + s['filesize'] = int(self.filesize) + s['initprot'] = self.get_initial_virtual_memory_protections() + s['initprot_raw'] = int(self.initprot) + s['maxprot'] = self.get_max_virtual_memory_protections() + s['maxprot_raw'] = int(self.maxprot) + s['nsects'] = int(self.nsects) + s['flags'] = self.flags + return s + + def get_initial_virtual_memory_protections(self): + vm = [] + if self.initprot == 0: + vm.append("VM_PROT_NONE") + if self.initprot & 1: + vm.append("VM_PROT_READ") + if self.initprot & 2: + vm.append("VM_PROT_WRITE") + if self.initprot & 4: + vm.append("VM_PROT_EXECUTE") + return vm + + def get_max_virtual_memory_protections(self): + vm = [] + if self.maxprot == 0: + vm.append("VM_PROT_NONE") + if self.maxprot & 1: + vm.append("VM_PROT_READ") + if self.maxprot & 2: + vm.append("VM_PROT_WRITE") + if self.maxprot & 4: + vm.append("VM_PROT_EXECUTE") + return vm + + +class segment_command_64(Structure): + _fields_ = ( + ('segname', p_str16), + ('vmaddr', p_uint64), + ('vmsize', p_uint64), + ('fileoff', p_uint64), + ('filesize', p_uint64), + ('maxprot', vm_prot_t), + ('initprot', vm_prot_t), + ('nsects', p_uint32), # read the section structures ? + ('flags', p_uint32), + ) + + def describe(self): + s = {} + s['segname'] = self.segname.rstrip('\x00') + s['vmaddr'] = int(self.vmaddr) + s['vmsize'] = int(self.vmsize) + s['fileoff'] = int(self.fileoff) + s['filesize'] = int(self.filesize) + s['initprot'] = self.get_initial_virtual_memory_protections() + s['initprot_raw'] = int(self.initprot) + s['maxprot'] = self.get_max_virtual_memory_protections() + s['maxprot_raw'] = int(self.maxprot) + s['nsects'] = int(self.nsects) + s['flags'] = self.flags + return s + + def get_initial_virtual_memory_protections(self): + vm = [] + if self.initprot == 0: + vm.append("VM_PROT_NONE") + if self.initprot & 1: + vm.append("VM_PROT_READ") + if self.initprot & 2: + vm.append("VM_PROT_WRITE") + if self.initprot & 4: + vm.append("VM_PROT_EXECUTE") + return vm + + def get_max_virtual_memory_protections(self): + vm = [] + if self.maxprot == 0: + vm.append("VM_PROT_NONE") + if self.maxprot & 1: + vm.append("VM_PROT_READ") + if self.maxprot & 2: + vm.append("VM_PROT_WRITE") + if self.maxprot & 4: + vm.append("VM_PROT_EXECUTE") + return vm + + +SG_HIGHVM = 0x1 +SG_FVMLIB = 0x2 +SG_NORELOC = 0x4 +SG_PROTECTED_VERSION_1 = 0x8 + + +class section(Structure): + _fields_ = ( + ('sectname', p_str16), + ('segname', p_str16), + ('addr', p_uint32), + ('size', p_uint32), + ('offset', p_uint32), + ('align', p_uint32), + ('reloff', p_uint32), + ('nreloc', p_uint32), + ('flags', p_uint32), + ('reserved1', p_uint32), + ('reserved2', p_uint32), + ) + + def describe(self): + s = {} + s['sectname'] = self.sectname.rstrip('\x00') + s['segname'] = self.segname.rstrip('\x00') + s['addr'] = int(self.addr) + s['size'] = int(self.size) + s['offset'] = int(self.offset) + s['align'] = int(self.align) + s['reloff'] = int(self.reloff) + s['nreloc'] = int(self.nreloc) + f = {} + f['type'] = FLAG_SECTION_TYPES[int(self.flags) & 0xff] + f['attributes'] = [] + for k in FLAG_SECTION_ATTRIBUTES: + if k & self.flags: + f['attributes'].append(FLAG_SECTION_ATTRIBUTES[k]) + if not f['attributes']: + del f['attributes'] + s['flags'] = f + s['reserved1'] = int(self.reserved1) + s['reserved2'] = int(self.reserved2) + return s + + def add_section_data(self, data): + self.section_data = data + + +class section_64(Structure): + _fields_ = ( + ('sectname', p_str16), + ('segname', p_str16), + ('addr', p_uint64), + ('size', p_uint64), + ('offset', p_uint32), + ('align', p_uint32), + ('reloff', p_uint32), + ('nreloc', p_uint32), + ('flags', p_uint32), + ('reserved1', p_uint32), + ('reserved2', p_uint32), + ('reserved3', p_uint32), + ) + + def describe(self): + s = {} + s['sectname'] = self.sectname.rstrip('\x00') + s['segname'] = self.segname.rstrip('\x00') + s['addr'] = int(self.addr) + s['size'] = int(self.size) + s['offset'] = int(self.offset) + s['align'] = int(self.align) + s['reloff'] = int(self.reloff) + s['nreloc'] = int(self.nreloc) + f = {} + f['type'] = FLAG_SECTION_TYPES[int(self.flags) & 0xff] + f['attributes'] = [] + for k in FLAG_SECTION_ATTRIBUTES: + if k & self.flags: + f['attributes'].append(FLAG_SECTION_ATTRIBUTES[k]) + if not f['attributes']: + del f['attributes'] + s['flags'] = f + s['reserved1'] = int(self.reserved1) + s['reserved2'] = int(self.reserved2) + s['reserved3'] = int(self.reserved3) + return s + + def add_section_data(self, data): + self.section_data = data + + +SECTION_TYPE = 0xff +SECTION_ATTRIBUTES = 0xffffff00 +S_REGULAR = 0x0 +S_ZEROFILL = 0x1 +S_CSTRING_LITERALS = 0x2 +S_4BYTE_LITERALS = 0x3 +S_8BYTE_LITERALS = 0x4 +S_LITERAL_POINTERS = 0x5 +S_NON_LAZY_SYMBOL_POINTERS = 0x6 +S_LAZY_SYMBOL_POINTERS = 0x7 +S_SYMBOL_STUBS = 0x8 +S_MOD_INIT_FUNC_POINTERS = 0x9 +S_MOD_TERM_FUNC_POINTERS = 0xa +S_COALESCED = 0xb +S_GB_ZEROFILL = 0xc +S_INTERPOSING = 0xd +S_16BYTE_LITERALS = 0xe +S_DTRACE_DOF = 0xf +S_LAZY_DYLIB_SYMBOL_POINTERS = 0x10 +S_THREAD_LOCAL_REGULAR = 0x11 +S_THREAD_LOCAL_ZEROFILL = 0x12 +S_THREAD_LOCAL_VARIABLES = 0x13 +S_THREAD_LOCAL_VARIABLE_POINTERS = 0x14 +S_THREAD_LOCAL_INIT_FUNCTION_POINTERS = 0x15 + +FLAG_SECTION_TYPES = { + S_REGULAR: "S_REGULAR", + S_ZEROFILL: "S_ZEROFILL", + S_CSTRING_LITERALS: "S_CSTRING_LITERALS", + S_4BYTE_LITERALS: "S_4BYTE_LITERALS", + S_8BYTE_LITERALS: "S_8BYTE_LITERALS", + S_LITERAL_POINTERS: "S_LITERAL_POINTERS", + S_NON_LAZY_SYMBOL_POINTERS: "S_NON_LAZY_SYMBOL_POINTERS", + S_LAZY_SYMBOL_POINTERS: "S_LAZY_SYMBOL_POINTERS", + S_SYMBOL_STUBS: "S_SYMBOL_STUBS", + S_MOD_INIT_FUNC_POINTERS: "S_MOD_INIT_FUNC_POINTERS", + S_MOD_TERM_FUNC_POINTERS: "S_MOD_TERM_FUNC_POINTERS", + S_COALESCED: "S_COALESCED", + S_GB_ZEROFILL: "S_GB_ZEROFILL", + S_INTERPOSING: "S_INTERPOSING", + S_16BYTE_LITERALS: "S_16BYTE_LITERALS", + S_DTRACE_DOF: "S_DTRACE_DOF", + S_LAZY_DYLIB_SYMBOL_POINTERS: "S_LAZY_DYLIB_SYMBOL_POINTERS", + S_THREAD_LOCAL_REGULAR: "S_THREAD_LOCAL_REGULAR", + S_THREAD_LOCAL_ZEROFILL: "S_THREAD_LOCAL_ZEROFILL", + S_THREAD_LOCAL_VARIABLES: "S_THREAD_LOCAL_VARIABLES", + S_THREAD_LOCAL_VARIABLE_POINTERS: "S_THREAD_LOCAL_VARIABLE_POINTERS", + S_THREAD_LOCAL_INIT_FUNCTION_POINTERS: + "S_THREAD_LOCAL_INIT_FUNCTION_POINTERS" +} + +SECTION_ATTRIBUTES_USR = 0xff000000 +S_ATTR_PURE_INSTRUCTIONS = 0x80000000 +S_ATTR_NO_TOC = 0x40000000 +S_ATTR_STRIP_STATIC_SYMS = 0x20000000 +S_ATTR_NO_DEAD_STRIP = 0x10000000 +S_ATTR_LIVE_SUPPORT = 0x08000000 +S_ATTR_SELF_MODIFYING_CODE = 0x04000000 +S_ATTR_DEBUG = 0x02000000 + +SECTION_ATTRIBUTES_SYS = 0x00ffff00 +S_ATTR_SOME_INSTRUCTIONS = 0x00000400 +S_ATTR_EXT_RELOC = 0x00000200 +S_ATTR_LOC_RELOC = 0x00000100 + +FLAG_SECTION_ATTRIBUTES = { + S_ATTR_PURE_INSTRUCTIONS: "S_ATTR_PURE_INSTRUCTIONS", + S_ATTR_NO_TOC: "S_ATTR_NO_TOC", + S_ATTR_STRIP_STATIC_SYMS: "S_ATTR_STRIP_STATIC_SYMS", + S_ATTR_NO_DEAD_STRIP: "S_ATTR_NO_DEAD_STRIP", + S_ATTR_LIVE_SUPPORT: "S_ATTR_LIVE_SUPPORT", + S_ATTR_SELF_MODIFYING_CODE: "S_ATTR_SELF_MODIFYING_CODE", + S_ATTR_DEBUG: "S_ATTR_DEBUG", + S_ATTR_SOME_INSTRUCTIONS: "S_ATTR_SOME_INSTRUCTIONS", + S_ATTR_EXT_RELOC: "S_ATTR_EXT_RELOC", + S_ATTR_LOC_RELOC: "S_ATTR_LOC_RELOC" +} + +SEG_PAGEZERO = "__PAGEZERO" +SEG_TEXT = "__TEXT" +SECT_TEXT = "__text" +SECT_FVMLIB_INIT0 = "__fvmlib_init0" +SECT_FVMLIB_INIT1 = "__fvmlib_init1" +SEG_DATA = "__DATA" +SECT_DATA = "__data" +SECT_BSS = "__bss" +SECT_COMMON = "__common" +SEG_OBJC = "__OBJC" +SECT_OBJC_SYMBOLS = "__symbol_table" +SECT_OBJC_MODULES = "__module_info" +SECT_OBJC_STRINGS = "__selector_strs" +SECT_OBJC_REFS = "__selector_refs" +SEG_ICON = "__ICON" +SECT_ICON_HEADER = "__header" +SECT_ICON_TIFF = "__tiff" +SEG_LINKEDIT = "__LINKEDIT" +SEG_UNIXSTACK = "__UNIXSTACK" +SEG_IMPORT = "__IMPORT" + +# +# I really should remove all these _command classes because they +# are no different. I decided to keep the load commands separate, +# so classes like fvmlib and fvmlib_command are equivalent. +# + + +class fvmlib(Structure): + _fields_ = ( + ('name', lc_str), + ('minor_version', mach_version_helper), + ('header_addr', p_uint32), + ) + + +class fvmlib_command(Structure): + _fields_ = fvmlib._fields_ + + def describe(self): + s = {} + s['header_addr'] = int(self.header_addr) + return s + + +class dylib(Structure): + _fields_ = ( + ('name', lc_str), + ('timestamp', mach_timestamp_helper), + ('current_version', mach_version_helper), + ('compatibility_version', mach_version_helper), + ) + + +# merged dylib structure +class dylib_command(Structure): + _fields_ = dylib._fields_ + + def describe(self): + s = {} + s['timestamp'] = str(self.timestamp) + s['current_version'] = str(self.current_version) + s['compatibility_version'] = str(self.compatibility_version) + return s + + +class sub_framework_command(Structure): + _fields_ = ( + ('umbrella', lc_str), + ) + + def describe(self): + return {} + + +class sub_client_command(Structure): + _fields_ = ( + ('client', lc_str), + ) + + def describe(self): + return {} + + +class sub_umbrella_command(Structure): + _fields_ = ( + ('sub_umbrella', lc_str), + ) + + def describe(self): + return {} + + +class sub_library_command(Structure): + _fields_ = ( + ('sub_library', lc_str), + ) + + def describe(self): + return {} + + +class prebound_dylib_command(Structure): + _fields_ = ( + ('name', lc_str), + ('nmodules', p_uint32), + ('linked_modules', lc_str), + ) + + def describe(self): + return {'nmodules': int(self.nmodules)} + + +class dylinker_command(Structure): + _fields_ = ( + ('name', lc_str), + ) + + def describe(self): + return {} + + +class thread_command(Structure): + _fields_ = ( + ('flavor', p_uint32), + ('count', p_uint32) + ) + + def describe(self): + s = {} + s['flavor'] = int(self.flavor) + s['count'] = int(self.count) + return s + + +class entry_point_command(Structure): + _fields_ = ( + ('entryoff', p_uint64), + ('stacksize', p_uint64), + ) + + def describe(self): + s = {} + s['entryoff'] = int(self.entryoff) + s['stacksize'] = int(self.stacksize) + return s + + +class routines_command(Structure): + _fields_ = ( + ('init_address', p_uint32), + ('init_module', p_uint32), + ('reserved1', p_uint32), + ('reserved2', p_uint32), + ('reserved3', p_uint32), + ('reserved4', p_uint32), + ('reserved5', p_uint32), + ('reserved6', p_uint32), + ) + + def describe(self): + s = {} + s['init_address'] = int(self.init_address) + s['init_module'] = int(self.init_module) + s['reserved1'] = int(self.reserved1) + s['reserved2'] = int(self.reserved2) + s['reserved3'] = int(self.reserved3) + s['reserved4'] = int(self.reserved4) + s['reserved5'] = int(self.reserved5) + s['reserved6'] = int(self.reserved6) + return s + + +class routines_command_64(Structure): + _fields_ = ( + ('init_address', p_uint64), + ('init_module', p_uint64), + ('reserved1', p_uint64), + ('reserved2', p_uint64), + ('reserved3', p_uint64), + ('reserved4', p_uint64), + ('reserved5', p_uint64), + ('reserved6', p_uint64), + ) + + def describe(self): + s = {} + s['init_address'] = int(self.init_address) + s['init_module'] = int(self.init_module) + s['reserved1'] = int(self.reserved1) + s['reserved2'] = int(self.reserved2) + s['reserved3'] = int(self.reserved3) + s['reserved4'] = int(self.reserved4) + s['reserved5'] = int(self.reserved5) + s['reserved6'] = int(self.reserved6) + return s + + +class symtab_command(Structure): + _fields_ = ( + ('symoff', p_uint32), + ('nsyms', p_uint32), + ('stroff', p_uint32), + ('strsize', p_uint32), + ) + + def describe(self): + s = {} + s['symoff'] = int(self.symoff) + s['nsyms'] = int(self.nsyms) + s['stroff'] = int(self.stroff) + s['strsize'] = int(self.strsize) + return s + + +class dysymtab_command(Structure): + _fields_ = ( + ('ilocalsym', p_uint32), + ('nlocalsym', p_uint32), + ('iextdefsym', p_uint32), + ('nextdefsym', p_uint32), + ('iundefsym', p_uint32), + ('nundefsym', p_uint32), + ('tocoff', p_uint32), + ('ntoc', p_uint32), + ('modtaboff', p_uint32), + ('nmodtab', p_uint32), + ('extrefsymoff', p_uint32), + ('nextrefsyms', p_uint32), + ('indirectsymoff', p_uint32), + ('nindirectsyms', p_uint32), + ('extreloff', p_uint32), + ('nextrel', p_uint32), + ('locreloff', p_uint32), + ('nlocrel', p_uint32), + ) + + def describe(self): + dys = {} + dys['ilocalsym'] = int(self.ilocalsym) + dys['nlocalsym'] = int(self.nlocalsym) + dys['iextdefsym'] = int(self.iextdefsym) + dys['nextdefsym'] = int(self.nextdefsym) + dys['iundefsym'] = int(self.iundefsym) + dys['nundefsym'] = int(self.nundefsym) + dys['tocoff'] = int(self.tocoff) + dys['ntoc'] = int(self.ntoc) + dys['modtaboff'] = int(self.modtaboff) + dys['nmodtab'] = int(self.nmodtab) + dys['extrefsymoff'] = int(self.extrefsymoff) + dys['nextrefsyms'] = int(self.nextrefsyms) + dys['indirectsymoff'] = int(self.indirectsymoff) + dys['nindirectsyms'] = int(self.nindirectsyms) + dys['extreloff'] = int(self.extreloff) + dys['nextrel'] = int(self.nextrel) + dys['locreloff'] = int(self.locreloff) + dys['nlocrel'] = int(self.nlocrel) + return dys + + +INDIRECT_SYMBOL_LOCAL = 0x80000000 +INDIRECT_SYMBOL_ABS = 0x40000000 + + +class dylib_table_of_contents(Structure): + _fields_ = ( + ('symbol_index', p_uint32), + ('module_index', p_uint32), + ) + + +class dylib_module(Structure): + _fields_ = ( + ('module_name', p_uint32), + ('iextdefsym', p_uint32), + ('nextdefsym', p_uint32), + ('irefsym', p_uint32), + ('nrefsym', p_uint32), + ('ilocalsym', p_uint32), + ('nlocalsym', p_uint32), + ('iextrel', p_uint32), + ('nextrel', p_uint32), + ('iinit_iterm', p_uint32), + ('ninit_nterm', p_uint32), + ('objc_module_info_addr', p_uint32), + ('objc_module_info_size', p_uint32), + ) + + +class dylib_module_64(Structure): + _fields_ = ( + ('module_name', p_uint32), + ('iextdefsym', p_uint32), + ('nextdefsym', p_uint32), + ('irefsym', p_uint32), + ('nrefsym', p_uint32), + ('ilocalsym', p_uint32), + ('nlocalsym', p_uint32), + ('iextrel', p_uint32), + ('nextrel', p_uint32), + ('iinit_iterm', p_uint32), + ('ninit_nterm', p_uint32), + ('objc_module_info_size', p_uint32), + ('objc_module_info_addr', p_uint64), + ) + + +class dylib_reference(Structure): + _fields_ = ( + # XXX - ick, fix + ('isym_flags', p_uint32), + # ('isym', p_uint8 * 3), + # ('flags', p_uint8), + ) + + +class twolevel_hints_command(Structure): + _fields_ = ( + ('offset', p_uint32), + ('nhints', p_uint32), + ) + + def describe(self): + s = {} + s['offset'] = int(self.offset) + s['nhints'] = int(self.nhints) + return s + + +class twolevel_hint(Structure): + _fields_ = ( + # XXX - ick, fix + ('isub_image_itoc', p_uint32), + # ('isub_image', p_uint8), + # ('itoc', p_uint8 * 3), + ) + + +class prebind_cksum_command(Structure): + _fields_ = ( + ('cksum', p_uint32), + ) + + def describe(self): + return {'cksum': int(self.cksum)} + + +class symseg_command(Structure): + _fields_ = ( + ('offset', p_uint32), + ('size', p_uint32), + ) + + def describe(self): + s = {} + s['offset'] = int(self.offset) + s['size'] = int(self.size) + + +class ident_command(Structure): + _fields_ = ( + ) + + def describe(self): + return {} + + +class fvmfile_command(Structure): + _fields_ = ( + ('name', lc_str), + ('header_addr', p_uint32), + ) + + def describe(self): + return {'header_addr': int(self.header_addr)} + + +class uuid_command (Structure): + _fields_ = ( + ('uuid', p_str16), + ) + + def describe(self): + return {'uuid': self.uuid.rstrip('\x00')} + + +class rpath_command (Structure): + _fields_ = ( + ('path', lc_str), + ) + + def describe(self): + return {} + + +class linkedit_data_command (Structure): + _fields_ = ( + ('dataoff', p_uint32), + ('datasize', p_uint32), + ) + + def describe(self): + s = {} + s['dataoff'] = int(self.dataoff) + s['datasize'] = int(self.datasize) + return s + + +class version_min_command (Structure): + _fields_ = ( + ('version', p_uint32), # X.Y.Z is encoded in nibbles xxxx.yy.zz + ('sdk', p_uint32), + ) + + def describe(self): + v = int(self.version) + v3 = v & 0xFF + v = v >> 8 + v2 = v & 0xFF + v = v >> 8 + v1 = v & 0xFFFF + s = int(self.sdk) + s3 = s & 0xFF + s = s >> 8 + s2 = s & 0xFF + s = s >> 8 + s1 = s & 0xFFFF + return { + 'version': str(int(v1)) + "." + str(int(v2)) + "." + str(int(v3)), + 'sdk': str(int(s1)) + "." + str(int(s2)) + "." + str(int(s3)) + } + + +class source_version_command (Structure): + _fields_ = ( + ('version', p_uint64), + ) + + def describe(self): + v = int(self.version) + a = v >> 40 + b = (v >> 30) & 0x3ff + c = (v >> 20) & 0x3ff + d = (v >> 10) & 0x3ff + e = v & 0x3ff + r = str(a)+'.'+str(b)+'.'+str(c)+'.'+str(d)+'.'+str(e) + return {'version': r} + + +class note_command (Structure): + _fields_ = ( + ('data_owner', p_str16), + ('offset', p_uint64), + ('size', p_uint64), + ) + + +class build_version_command (Structure): + _fields_ = ( + ('platform', p_uint32), + ('minos', p_uint32), + ('sdk', p_uint32), + ('ntools', p_uint32), + ) + + # XXX: Add computed field for accessing 'tools' array + + +class build_tool_version (Structure): + _fields_ = ( + ('tool', p_uint32), + ('version', p_uint32), + ) + + +class data_in_code_entry (Structure): + _fields_ = ( + ('offset', p_uint32), + ('length', p_uint32), + ('kind', p_uint32), + ) + + def describe(self): + return { + 'offset': self.offset, 'length': self.length, 'kind': self.kind} + + +DICE_KIND_DATA = 0x0001 +DICE_KIND_JUMP_TABLE8 = 0x0002 +DICE_KIND_JUMP_TABLE16 = 0x0003 +DICE_KIND_JUMP_TABLE32 = 0x0004 +DICE_KIND_ABS_JUMP_TABLE32 = 0x0005 + +DATA_IN_CODE_KINDS = { + DICE_KIND_DATA: 'DICE_KIND_DATA', + DICE_KIND_JUMP_TABLE8: 'DICE_KIND_JUMP_TABLE8', + DICE_KIND_JUMP_TABLE16: 'DICE_KIND_JUMP_TABLE16', + DICE_KIND_JUMP_TABLE32: 'DICE_KIND_JUMP_TABLE32', + DICE_KIND_ABS_JUMP_TABLE32: 'DICE_KIND_ABS_JUMP_TABLE32', +} + + +class tlv_descriptor (Structure): + _fields_ = ( + ('thunk', p_long), # Actually a pointer to a function + ('key', p_ulong), + ('offset', p_ulong), + ) + + def describe(self): + return {'thunk': self.thunk, 'key': self.key, 'offset': self.offset} + + +class encryption_info_command (Structure): + _fields_ = ( + ('cryptoff', p_uint32), + ('cryptsize', p_uint32), + ('cryptid', p_uint32), + ) + + def describe(self): + s = {} + s['cryptoff'] = int(self.cryptoff) + s['cryptsize'] = int(self.cryptsize) + s['cryptid'] = int(self.cryptid) + return s + + +class encryption_info_command_64 (Structure): + _fields_ = ( + ('cryptoff', p_uint32), + ('cryptsize', p_uint32), + ('cryptid', p_uint32), + ('pad', p_uint32), + ) + + def describe(self): + s = {} + s['cryptoff'] = int(self.cryptoff) + s['cryptsize'] = int(self.cryptsize) + s['cryptid'] = int(self.cryptid) + s['pad'] = int(self.pad) + return s + + +class dyld_info_command (Structure): + _fields_ = ( + ('rebase_off', p_uint32), + ('rebase_size', p_uint32), + ('bind_off', p_uint32), + ('bind_size', p_uint32), + ('weak_bind_off', p_uint32), + ('weak_bind_size', p_uint32), + ('lazy_bind_off', p_uint32), + ('lazy_bind_size', p_uint32), + ('export_off', p_uint32), + ('export_size', p_uint32), + ) + + def describe(self): + dyld = {} + dyld['rebase_off'] = int(self.rebase_off) + dyld['rebase_size'] = int(self.rebase_size) + dyld['bind_off'] = int(self.bind_off) + dyld['bind_size'] = int(self.bind_size) + dyld['weak_bind_off'] = int(self.weak_bind_off) + dyld['weak_bind_size'] = int(self.weak_bind_size) + dyld['lazy_bind_off'] = int(self.lazy_bind_off) + dyld['lazy_bind_size'] = int(self.lazy_bind_size) + dyld['export_off'] = int(self.export_off) + dyld['export_size'] = int(self.export_size) + return dyld + + +class linker_option_command (Structure): + _fields_ = ( + ('count', p_uint32), + ) + + def describe(self): + return {'count': int(self.count)} + + +LC_REGISTRY = { + LC_SEGMENT: segment_command, + LC_IDFVMLIB: fvmlib_command, + LC_LOADFVMLIB: fvmlib_command, + LC_ID_DYLIB: dylib_command, + LC_LOAD_DYLIB: dylib_command, + LC_LOAD_WEAK_DYLIB: dylib_command, + LC_SUB_FRAMEWORK: sub_framework_command, + LC_SUB_CLIENT: sub_client_command, + LC_SUB_UMBRELLA: sub_umbrella_command, + LC_SUB_LIBRARY: sub_library_command, + LC_PREBOUND_DYLIB: prebound_dylib_command, + LC_ID_DYLINKER: dylinker_command, + LC_LOAD_DYLINKER: dylinker_command, + LC_THREAD: thread_command, + LC_UNIXTHREAD: thread_command, + LC_ROUTINES: routines_command, + LC_SYMTAB: symtab_command, + LC_DYSYMTAB: dysymtab_command, + LC_TWOLEVEL_HINTS: twolevel_hints_command, + LC_PREBIND_CKSUM: prebind_cksum_command, + LC_SYMSEG: symseg_command, + LC_IDENT: ident_command, + LC_FVMFILE: fvmfile_command, + LC_SEGMENT_64: segment_command_64, + LC_ROUTINES_64: routines_command_64, + LC_UUID: uuid_command, + LC_RPATH: rpath_command, + LC_CODE_SIGNATURE: linkedit_data_command, + LC_CODE_SEGMENT_SPLIT_INFO: linkedit_data_command, + LC_REEXPORT_DYLIB: dylib_command, + LC_LAZY_LOAD_DYLIB: dylib_command, + LC_ENCRYPTION_INFO: encryption_info_command, + LC_DYLD_INFO: dyld_info_command, + LC_DYLD_INFO_ONLY: dyld_info_command, + LC_LOAD_UPWARD_DYLIB: dylib_command, + LC_VERSION_MIN_MACOSX: version_min_command, + LC_VERSION_MIN_IPHONEOS: version_min_command, + LC_FUNCTION_STARTS: linkedit_data_command, + LC_DYLD_ENVIRONMENT: dylinker_command, + LC_MAIN: entry_point_command, + LC_DATA_IN_CODE: linkedit_data_command, + LC_SOURCE_VERSION: source_version_command, + LC_DYLIB_CODE_SIGN_DRS: linkedit_data_command, + LC_ENCRYPTION_INFO_64: encryption_info_command_64, + LC_LINKER_OPTION: linker_option_command, + LC_LINKER_OPTIMIZATION_HINT: linkedit_data_command, + LC_VERSION_MIN_TVOS: version_min_command, + LC_VERSION_MIN_WATCHOS: version_min_command, + LC_NOTE: note_command, + LC_BUILD_VERSION: build_version_command, +} + +LC_NAMES = { + LC_SEGMENT: 'LC_SEGMENT', + LC_IDFVMLIB: 'LC_IDFVMLIB', + LC_LOADFVMLIB: 'LC_LOADFVMLIB', + LC_ID_DYLIB: 'LC_ID_DYLIB', + LC_LOAD_DYLIB: 'LC_LOAD_DYLIB', + LC_LOAD_WEAK_DYLIB: 'LC_LOAD_WEAK_DYLIB', + LC_SUB_FRAMEWORK: 'LC_SUB_FRAMEWORK', + LC_SUB_CLIENT: 'LC_SUB_CLIENT', + LC_SUB_UMBRELLA: 'LC_SUB_UMBRELLA', + LC_SUB_LIBRARY: 'LC_SUB_LIBRARY', + LC_PREBOUND_DYLIB: 'LC_PREBOUND_DYLIB', + LC_ID_DYLINKER: 'LC_ID_DYLINKER', + LC_LOAD_DYLINKER: 'LC_LOAD_DYLINKER', + LC_THREAD: 'LC_THREAD', + LC_UNIXTHREAD: 'LC_UNIXTHREAD', + LC_ROUTINES: 'LC_ROUTINES', + LC_SYMTAB: 'LC_SYMTAB', + LC_DYSYMTAB: 'LC_DYSYMTAB', + LC_TWOLEVEL_HINTS: 'LC_TWOLEVEL_HINTS', + LC_PREBIND_CKSUM: 'LC_PREBIND_CKSUM', + LC_SYMSEG: 'LC_SYMSEG', + LC_IDENT: 'LC_IDENT', + LC_FVMFILE: 'LC_FVMFILE', + LC_SEGMENT_64: 'LC_SEGMENT_64', + LC_ROUTINES_64: 'LC_ROUTINES_64', + LC_UUID: 'LC_UUID', + LC_RPATH: 'LC_RPATH', + LC_CODE_SIGNATURE: 'LC_CODE_SIGNATURE', + LC_CODE_SEGMENT_SPLIT_INFO: 'LC_CODE_SEGMENT_SPLIT_INFO', + LC_REEXPORT_DYLIB: 'LC_REEXPORT_DYLIB', + LC_LAZY_LOAD_DYLIB: 'LC_LAZY_LOAD_DYLIB', + LC_ENCRYPTION_INFO: 'LC_ENCRYPTION_INFO', + LC_DYLD_INFO: 'LC_DYLD_INFO', + LC_DYLD_INFO_ONLY: 'LC_DYLD_INFO_ONLY', + LC_LOAD_UPWARD_DYLIB: 'LC_LOAD_UPWARD_DYLIB', + LC_VERSION_MIN_MACOSX: 'LC_VERSION_MIN_MACOSX', + LC_VERSION_MIN_IPHONEOS: 'LC_VERSION_MIN_IPHONEOS', + LC_FUNCTION_STARTS: 'LC_FUNCTION_STARTS', + LC_DYLD_ENVIRONMENT: 'LC_DYLD_ENVIRONMENT', + LC_MAIN: 'LC_MAIN', + LC_DATA_IN_CODE: 'LC_DATA_IN_CODE', + LC_SOURCE_VERSION: 'LC_SOURCE_VERSION', + LC_DYLIB_CODE_SIGN_DRS: 'LC_DYLIB_CODE_SIGN_DRS', + LC_LINKER_OPTIMIZATION_HINT: 'LC_LINKER_OPTIMIZATION_HINT', + LC_VERSION_MIN_TVOS: 'LC_VERSION_MIN_TVOS', + LC_VERSION_MIN_WATCHOS: 'LC_VERSION_MIN_WATCHOS', + LC_NOTE: 'LC_NOTE', + LC_BUILD_VERSION: 'LC_BUILD_VERSION', +} + + +# this is another union. +class n_un(p_int32): + pass + + +class nlist(Structure): + _fields_ = ( + ('n_un', n_un), + ('n_type', p_uint8), + ('n_sect', p_uint8), + ('n_desc', p_short), + ('n_value', p_uint32), + ) + + +class nlist_64(Structure): + _fields_ = [ + ('n_un', n_un), + ('n_type', p_uint8), + ('n_sect', p_uint8), + ('n_desc', p_short), + ('n_value', p_int64), + ] + + +N_STAB = 0xe0 +N_PEXT = 0x10 +N_TYPE = 0x0e +N_EXT = 0x01 + +N_UNDF = 0x0 +N_ABS = 0x2 +N_SECT = 0xe +N_PBUD = 0xc +N_INDR = 0xa + +NO_SECT = 0 +MAX_SECT = 255 + + +class relocation_info(Structure): + # XXX: Need to add code for decoding the bitfield! + _fields_ = ( + ('r_address', p_uint32), + ('_r_bitfield', p_uint32), + ) + + def _describe(self): + return ( + ('r_address', self.r_address), + ('_r_bitfield', self._r_bitfield), + ) + + +def GET_COMM_ALIGN(n_desc): + return (n_desc >> 8) & 0x0f + + +def SET_COMM_ALIGN(n_desc, align): + return (n_desc & 0xf0ff) | ((align & 0x0f) << 8) + + +REFERENCE_TYPE = 0xf +REFERENCE_FLAG_UNDEFINED_NON_LAZY = 0 +REFERENCE_FLAG_UNDEFINED_LAZY = 1 +REFERENCE_FLAG_DEFINED = 2 +REFERENCE_FLAG_PRIVATE_DEFINED = 3 +REFERENCE_FLAG_PRIVATE_UNDEFINED_NON_LAZY = 4 +REFERENCE_FLAG_PRIVATE_UNDEFINED_LAZY = 5 + +REFERENCED_DYNAMICALLY = 0x0010 + + +def GET_LIBRARY_ORDINAL(n_desc): + return (((n_desc) >> 8) & 0xff) + + +def SET_LIBRARY_ORDINAL(n_desc, ordinal): + return (((n_desc) & 0x00ff) | (((ordinal & 0xff) << 8))) + + +SELF_LIBRARY_ORDINAL = 0x0 +MAX_LIBRARY_ORDINAL = 0xfd +DYNAMIC_LOOKUP_ORDINAL = 0xfe +EXECUTABLE_ORDINAL = 0xff + +N_NO_DEAD_STRIP = 0x0020 +N_DESC_DISCARDED = 0x0020 +N_WEAK_REF = 0x0040 +N_WEAK_DEF = 0x0080 +N_REF_TO_WEAK = 0x0080 +N_ARM_THUMB_DEF = 0x0008 +N_SYMBOL_RESOLVER = 0x0100 +N_ALT_ENTRY = 0x0200 + +# /usr/include/mach-o/fat.h +FAT_MAGIC = 0xcafebabe +FAT_CIGAM = 0xbebafeca +FAT_MAGIC_64 = 0xcafebabf +FAT_CIGAM_64 = 0xbfbafeca + + +class fat_header(Structure): + _fields_ = ( + ('magic', p_uint32), + ('nfat_arch', p_uint32), + ) + + +class fat_arch(Structure): + _fields_ = ( + ('cputype', cpu_type_t), + ('cpusubtype', cpu_subtype_t), + ('offset', p_uint32), + ('size', p_uint32), + ('align', p_uint32), + ) + + +class fat_arch64(Structure): + _fields_ = ( + ('cputype', cpu_type_t), + ('cpusubtype', cpu_subtype_t), + ('offset', p_uint64), + ('size', p_uint64), + ('align', p_uint32), + ('reserved', p_uint32), + ) + + +REBASE_TYPE_POINTER = 1 # noqa: E221 +REBASE_TYPE_TEXT_ABSOLUTE32 = 2 # noqa: E221 +REBASE_TYPE_TEXT_PCREL32 = 3 # noqa: E221 + +REBASE_OPCODE_MASK = 0xF0 # noqa: E221 +REBASE_IMMEDIATE_MASK = 0x0F # noqa: E221 +REBASE_OPCODE_DONE = 0x00 # noqa: E221 +REBASE_OPCODE_SET_TYPE_IMM = 0x10 # noqa: E221 +REBASE_OPCODE_SET_SEGMENT_AND_OFFSET_ULEB = 0x20 # noqa: E221 +REBASE_OPCODE_ADD_ADDR_ULEB = 0x30 # noqa: E221 +REBASE_OPCODE_ADD_ADDR_IMM_SCALED = 0x40 # noqa: E221 +REBASE_OPCODE_DO_REBASE_IMM_TIMES = 0x50 # noqa: E221 +REBASE_OPCODE_DO_REBASE_ULEB_TIMES = 0x60 # noqa: E221 +REBASE_OPCODE_DO_REBASE_ADD_ADDR_ULEB = 0x70 # noqa: E221 +REBASE_OPCODE_DO_REBASE_ULEB_TIMES_SKIPPING_ULEB = 0x80 # noqa: E221 + +BIND_TYPE_POINTER = 1 # noqa: E221 +BIND_TYPE_TEXT_ABSOLUTE32 = 2 # noqa: E221 +BIND_TYPE_TEXT_PCREL32 = 3 # noqa: E221 + +BIND_SPECIAL_DYLIB_SELF = 0 # noqa: E221 +BIND_SPECIAL_DYLIB_MAIN_EXECUTABLE = -1 # noqa: E221 +BIND_SPECIAL_DYLIB_FLAT_LOOKUP = -2 # noqa: E221 + +BIND_SYMBOL_FLAGS_WEAK_IMPORT = 0x1 # noqa: E221 +BIND_SYMBOL_FLAGS_NON_WEAK_DEFINITION = 0x8 # noqa: E221 + +BIND_OPCODE_MASK = 0xF0 # noqa: E221 +BIND_IMMEDIATE_MASK = 0x0F # noqa: E221 +BIND_OPCODE_DONE = 0x00 # noqa: E221 +BIND_OPCODE_SET_DYLIB_ORDINAL_IMM = 0x10 # noqa: E221 +BIND_OPCODE_SET_DYLIB_ORDINAL_ULEB = 0x20 # noqa: E221 +BIND_OPCODE_SET_DYLIB_SPECIAL_IMM = 0x30 # noqa: E221 +BIND_OPCODE_SET_SYMBOL_TRAILING_FLAGS_IMM = 0x40 # noqa: E221 +BIND_OPCODE_SET_TYPE_IMM = 0x50 # noqa: E221 +BIND_OPCODE_SET_ADDEND_SLEB = 0x60 # noqa: E221 +BIND_OPCODE_SET_SEGMENT_AND_OFFSET_ULEB = 0x70 # noqa: E221 +BIND_OPCODE_ADD_ADDR_ULEB = 0x80 # noqa: E221 +BIND_OPCODE_DO_BIND = 0x90 # noqa: E221 +BIND_OPCODE_DO_BIND_ADD_ADDR_ULEB = 0xA0 # noqa: E221 +BIND_OPCODE_DO_BIND_ADD_ADDR_IMM_SCALED = 0xB0 # noqa: E221 +BIND_OPCODE_DO_BIND_ULEB_TIMES_SKIPPING_ULEB = 0xC0 # noqa: E221 + +EXPORT_SYMBOL_FLAGS_KIND_MASK = 0x03 # noqa: E221 +EXPORT_SYMBOL_FLAGS_KIND_REGULAR = 0x00 # noqa: E221 +EXPORT_SYMBOL_FLAGS_KIND_THREAD_LOCAL = 0x01 # noqa: E221 +EXPORT_SYMBOL_FLAGS_WEAK_DEFINITION = 0x04 # noqa: E221 +EXPORT_SYMBOL_FLAGS_REEXPORT = 0x08 # noqa: E221 +EXPORT_SYMBOL_FLAGS_STUB_AND_RESOLVER = 0x10 # noqa: E221 + +PLATFORM_MACOS = 1 +PLATFORM_IOS = 2 +PLATFORM_TVOS = 3 +PLATFORM_WATCHOS = 4 +PLATFORM_BRIDGEOS = 5 +PLATFORM_IOSMAC = 6 +PLATFORM_IOSSIMULATOR = 7 +PLATFORM_TVOSSIMULATOR = 8 +PLATFORM_WATCHOSSIMULATOR = 9 + +PLATFORM_NAMES = { + PLATFORM_MACOS: 'macOS', + PLATFORM_IOS: 'iOS', + PLATFORM_TVOS: 'tvOS', + PLATFORM_WATCHOS: 'watchOS', + PLATFORM_BRIDGEOS: 'bridgeOS', + PLATFORM_IOSMAC: 'ios-on-mac', + PLATFORM_IOSSIMULATOR: 'iOS simulator', + PLATFORM_TVOSSIMULATOR: 'tvOS simulator', + PLATFORM_WATCHOSSIMULATOR: 'watchOS simulator', +} + +TOOL_CLANG = 1 +TOOL_SWIFT = 2 +TOOL_LD = 3 + +TOOL_NAMES = { + TOOL_CLANG: 'clang', + TOOL_SWIFT: 'swift', + TOOL_LD: 'ld', +} diff --git a/lib/spack/external/macholib/macho_dump.py b/lib/spack/external/macholib/macho_dump.py new file mode 100644 index 00000000000..a30c2b92f87 --- /dev/null +++ b/lib/spack/external/macholib/macho_dump.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import sys + +from macholib._cmdline import main as _main +from macholib.MachO import MachO +from macholib.mach_o import get_cpu_subtype, CPU_TYPE_NAMES +from macholib.mach_o import MH_CIGAM_64, MH_MAGIC_64 + +ARCH_MAP = { + ('<', '64-bit'): 'x86_64', + ('<', '32-bit'): 'i386', + ('>', '64-bit'): 'ppc64', + ('>', '32-bit'): 'ppc', +} + + +def print_file(fp, path): + print(path, file=fp) + m = MachO(path) + for header in m.headers: + seen = set() + + if header.MH_MAGIC == MH_MAGIC_64 or header.MH_MAGIC == MH_CIGAM_64: + sz = '64-bit' + else: + sz = '32-bit' + + arch = CPU_TYPE_NAMES.get( + header.header.cputype, header.header.cputype) + + subarch = get_cpu_subtype( + header.header.cputype, header.header.cpusubtype) + + print(' [%s endian=%r size=%r arch=%r subarch=%r]' % ( + header.__class__.__name__, header.endian, sz, arch, subarch), + file=fp) + for idx, name, other in header.walkRelocatables(): + if other not in seen: + seen.add(other) + print('\t' + other, file=fp) + print('', file=fp) + + +def main(): + print( + "WARNING: 'macho_dump' is deprecated, use 'python -mmacholib dump' " + "instead") + _main(print_file) + + +if __name__ == '__main__': + try: + sys.exit(main()) + except KeyboardInterrupt: + pass diff --git a/lib/spack/external/macholib/macho_find.py b/lib/spack/external/macholib/macho_find.py new file mode 100644 index 00000000000..8f8243e6db4 --- /dev/null +++ b/lib/spack/external/macholib/macho_find.py @@ -0,0 +1,21 @@ +#!/usr/bin/env python +from __future__ import print_function +from macholib._cmdline import main as _main + + +def print_file(fp, path): + print(path, file=fp) + + +def main(): + print( + "WARNING: 'macho_find' is deprecated, " + "use 'python -mmacholib dump' instead") + _main(print_file) + + +if __name__ == '__main__': + try: + main() + except KeyboardInterrupt: + pass diff --git a/lib/spack/external/macholib/macho_standalone.py b/lib/spack/external/macholib/macho_standalone.py new file mode 100644 index 00000000000..f9ce91e9bfd --- /dev/null +++ b/lib/spack/external/macholib/macho_standalone.py @@ -0,0 +1,31 @@ +#!/usr/bin/env python + +import os +import sys + +from macholib.MachOStandalone import MachOStandalone +from macholib.util import strip_files + + +def standaloneApp(path): + if not (os.path.isdir(path) and os.path.exists( + os.path.join(path, 'Contents'))): + print( + '%s: %s does not look like an app bundle' % (sys.argv[0], path)) + sys.exit(1) + files = MachOStandalone(path).run() + strip_files(files) + + +def main(): + print( + "WARNING: 'macho_standalone' is deprecated, use " + "'python -mmacholib standalone' instead") + if not sys.argv[1:]: + raise SystemExit('usage: %s [appbundle ...]' % (sys.argv[0],)) + for fn in sys.argv[1:]: + standaloneApp(fn) + + +if __name__ == '__main__': + main() diff --git a/lib/spack/external/macholib/ptypes.py b/lib/spack/external/macholib/ptypes.py new file mode 100644 index 00000000000..a5643696b69 --- /dev/null +++ b/lib/spack/external/macholib/ptypes.py @@ -0,0 +1,331 @@ +""" +This module defines packable types, that is types than can be easily +converted to a binary format as used in MachO headers. +""" +import struct +import sys + +try: + from itertools import izip, imap +except ImportError: + izip, imap = zip, map +from itertools import chain, starmap + +__all__ = """ +sizeof +BasePackable +Structure +pypackable +p_char +p_byte +p_ubyte +p_short +p_ushort +p_int +p_uint +p_long +p_ulong +p_longlong +p_ulonglong +p_int8 +p_uint8 +p_int16 +p_uint16 +p_int32 +p_uint32 +p_int64 +p_uint64 +p_float +p_double +""".split() + + +def sizeof(s): + """ + Return the size of an object when packed + """ + if hasattr(s, '_size_'): + return s._size_ + + elif isinstance(s, bytes): + return len(s) + + raise ValueError(s) + + +class MetaPackable(type): + """ + Fixed size struct.unpack-able types use from_tuple as their designated + initializer + """ + def from_mmap(cls, mm, ptr, **kw): + return cls.from_str(mm[ptr:ptr+cls._size_], **kw) + + def from_fileobj(cls, f, **kw): + return cls.from_str(f.read(cls._size_), **kw) + + def from_str(cls, s, **kw): + endian = kw.get('_endian_', cls._endian_) + return cls.from_tuple(struct.unpack(endian + cls._format_, s), **kw) + + def from_tuple(cls, tpl, **kw): + return cls(tpl[0], **kw) + + +class BasePackable(object): + _endian_ = '>' + + def to_str(self): + raise NotImplementedError + + def to_fileobj(self, f): + f.write(self.to_str()) + + def to_mmap(self, mm, ptr): + mm[ptr:ptr+self._size_] = self.to_str() + + +# This defines a class with a custom metaclass, we'd normally +# use "class Packable(BasePackable, metaclass=MetaPackage)", +# but that syntax is not valid in Python 2 (and likewise the +# python 2 syntax is not valid in Python 3) +def _make(): + def to_str(self): + cls = type(self) + endian = getattr(self, '_endian_', cls._endian_) + return struct.pack(endian + cls._format_, self) + return MetaPackable("Packable", (BasePackable,), {'to_str': to_str}) + + +Packable = _make() +del _make + + +def pypackable(name, pytype, format): + """ + Create a "mix-in" class with a python type and a + Packable with the given struct format + """ + size, items = _formatinfo(format) + + def __new__(cls, *args, **kwds): + if '_endian_' in kwds: + _endian_ = kwds.pop('_endian_') + else: + _endian_ = cls._endian_ + + result = pytype.__new__(cls, *args, **kwds) + result._endian_ = _endian_ + return result + + return type(Packable)(name, (pytype, Packable), { + '_format_': format, + '_size_': size, + '_items_': items, + '__new__': __new__, + }) + + +def _formatinfo(format): + """ + Calculate the size and number of items in a struct format. + """ + size = struct.calcsize(format) + return size, len(struct.unpack(format, b'\x00' * size)) + + +class MetaStructure(MetaPackable): + """ + The metaclass of Structure objects that does all the magic. + + Since we can assume that all Structures have a fixed size, + we can do a bunch of calculations up front and pack or + unpack the whole thing in one struct call. + """ + def __new__(cls, clsname, bases, dct): + fields = dct['_fields_'] + names = [] + types = [] + structmarks = [] + format = '' + items = 0 + size = 0 + + def struct_property(name, typ): + + def _get(self): + return self._objects_[name] + + def _set(self, obj): + if type(obj) is not typ: + obj = typ(obj) + self._objects_[name] = obj + + return property(_get, _set, typ.__name__) + + for name, typ in fields: + dct[name] = struct_property(name, typ) + names.append(name) + types.append(typ) + format += typ._format_ + size += typ._size_ + if (typ._items_ > 1): + structmarks.append((items, typ._items_, typ)) + items += typ._items_ + + dct['_structmarks_'] = structmarks + dct['_names_'] = names + dct['_types_'] = types + dct['_size_'] = size + dct['_items_'] = items + dct['_format_'] = format + return super(MetaStructure, cls).__new__(cls, clsname, bases, dct) + + def from_tuple(cls, tpl, **kw): + values = [] + current = 0 + for begin, length, typ in cls._structmarks_: + if begin > current: + values.extend(tpl[current:begin]) + current = begin + length + values.append(typ.from_tuple(tpl[begin:current], **kw)) + values.extend(tpl[current:]) + return cls(*values, **kw) + + +# See metaclass discussion earlier in this file +def _make(): + class_dict = {} + class_dict['_fields_'] = () + + def as_method(function): + class_dict[function.__name__] = function + + @as_method + def __init__(self, *args, **kwargs): + if len(args) == 1 and not kwargs and type(args[0]) is type(self): + kwargs = args[0]._objects_ + args = () + self._objects_ = {} + iargs = chain(izip(self._names_, args), kwargs.items()) + for key, value in iargs: + if key not in self._names_ and key != "_endian_": + raise TypeError + setattr(self, key, value) + for key, typ in izip(self._names_, self._types_): + if key not in self._objects_: + self._objects_[key] = typ() + + @as_method + def _get_packables(self): + for obj in imap(self._objects_.__getitem__, self._names_): + if hasattr(obj, '_get_packables'): + for obj in obj._get_packables(): + yield obj + + else: + yield obj + + @as_method + def to_str(self): + return struct.pack( + self._endian_ + self._format_, *self._get_packables()) + + @as_method + def __cmp__(self, other): + if type(other) is not type(self): + raise TypeError( + 'Cannot compare objects of type %r to objects of type %r' % ( + type(other), type(self))) + if sys.version_info[0] == 2: + _cmp = cmp # noqa: F821 + else: + def _cmp(a, b): + if a < b: + return -1 + elif a > b: + return 1 + elif a == b: + return 0 + else: + raise TypeError() + + for cmpval in starmap( + _cmp, izip(self._get_packables(), other._get_packables())): + if cmpval != 0: + return cmpval + return 0 + + @as_method + def __eq__(self, other): + r = self.__cmp__(other) + return r == 0 + + @as_method + def __ne__(self, other): + r = self.__cmp__(other) + return r != 0 + + @as_method + def __lt__(self, other): + r = self.__cmp__(other) + return r < 0 + + @as_method + def __le__(self, other): + r = self.__cmp__(other) + return r <= 0 + + @as_method + def __gt__(self, other): + r = self.__cmp__(other) + return r > 0 + + @as_method + def __ge__(self, other): + r = self.__cmp__(other) + return r >= 0 + + @as_method + def __repr__(self): + result = [] + result.append('<') + result.append(type(self).__name__) + for nm in self._names_: + result.append(' %s=%r' % (nm, getattr(self, nm))) + result.append('>') + return ''.join(result) + + return MetaStructure("Structure", (BasePackable,), class_dict) + + +Structure = _make() +del _make + +try: + long +except NameError: + long = int + +# export common packables with predictable names +p_char = pypackable('p_char', bytes, 'c') +p_int8 = pypackable('p_int8', int, 'b') +p_uint8 = pypackable('p_uint8', int, 'B') +p_int16 = pypackable('p_int16', int, 'h') +p_uint16 = pypackable('p_uint16', int, 'H') +p_int32 = pypackable('p_int32', int, 'i') +p_uint32 = pypackable('p_uint32', long, 'I') +p_int64 = pypackable('p_int64', long, 'q') +p_uint64 = pypackable('p_uint64', long, 'Q') +p_float = pypackable('p_float', float, 'f') +p_double = pypackable('p_double', float, 'd') + +# Deprecated names, need trick to emit deprecation warning. +p_byte = p_int8 +p_ubyte = p_uint8 +p_short = p_int16 +p_ushort = p_uint16 +p_int = p_long = p_int32 +p_uint = p_ulong = p_uint32 +p_longlong = p_int64 +p_ulonglong = p_uint64 diff --git a/lib/spack/external/macholib/util.py b/lib/spack/external/macholib/util.py new file mode 100644 index 00000000000..99b682a27f1 --- /dev/null +++ b/lib/spack/external/macholib/util.py @@ -0,0 +1,258 @@ +import os +import sys +import stat +import struct +import shutil + +from macholib import mach_o + +MAGIC = [ + struct.pack('!L', getattr(mach_o, 'MH_' + _)) + for _ in ['MAGIC', 'CIGAM', 'MAGIC_64', 'CIGAM_64'] +] +FAT_MAGIC_BYTES = struct.pack('!L', mach_o.FAT_MAGIC) +MAGIC_LEN = 4 +STRIPCMD = ['/usr/bin/strip', '-x', '-S', '-'] + +try: + unicode +except NameError: + unicode = str + + +def fsencoding(s, encoding=sys.getfilesystemencoding()): + """ + Ensure the given argument is in filesystem encoding (not unicode) + """ + if isinstance(s, unicode): + s = s.encode(encoding) + return s + + +def move(src, dst): + """ + move that ensures filesystem encoding of paths + """ + shutil.move(fsencoding(src), fsencoding(dst)) + + +def copy2(src, dst): + """ + copy2 that ensures filesystem encoding of paths + """ + shutil.copy2(fsencoding(src), fsencoding(dst)) + + +def flipwritable(fn, mode=None): + """ + Flip the writability of a file and return the old mode. Returns None + if the file is already writable. + """ + if os.access(fn, os.W_OK): + return None + old_mode = os.stat(fn).st_mode + os.chmod(fn, stat.S_IWRITE | old_mode) + return old_mode + + +class fileview(object): + """ + A proxy for file-like objects that exposes a given view of a file + """ + + def __init__(self, fileobj, start, size): + self._fileobj = fileobj + self._start = start + self._end = start + size + + def __repr__(self): + return '' % ( + self._start, self._end, self._fileobj) + + def tell(self): + return self._fileobj.tell() - self._start + + def _checkwindow(self, seekto, op): + if not (self._start <= seekto <= self._end): + raise IOError("%s to offset %d is outside window [%d, %d]" % ( + op, seekto, self._start, self._end)) + + def seek(self, offset, whence=0): + seekto = offset + if whence == 0: + seekto += self._start + elif whence == 1: + seekto += self._fileobj.tell() + elif whence == 2: + seekto += self._end + else: + raise IOError("Invalid whence argument to seek: %r" % (whence,)) + self._checkwindow(seekto, 'seek') + self._fileobj.seek(seekto) + + def write(self, bytes): + here = self._fileobj.tell() + self._checkwindow(here, 'write') + self._checkwindow(here + len(bytes), 'write') + self._fileobj.write(bytes) + + def read(self, size=sys.maxsize): + if size < 0: + raise ValueError( + "Invalid size %s while reading from %s", size, self._fileobj) + here = self._fileobj.tell() + self._checkwindow(here, 'read') + bytes = min(size, self._end - here) + return self._fileobj.read(bytes) + + +def mergecopy(src, dest): + """ + copy2, but only if the destination isn't up to date + """ + if os.path.exists(dest) and \ + os.stat(dest).st_mtime >= os.stat(src).st_mtime: + return + + copy2(src, dest) + + +def mergetree(src, dst, condition=None, copyfn=mergecopy, srcbase=None): + """ + Recursively merge a directory tree using mergecopy(). + """ + src = fsencoding(src) + dst = fsencoding(dst) + if srcbase is None: + srcbase = src + names = map(fsencoding, os.listdir(src)) + try: + os.makedirs(dst) + except OSError: + pass + errors = [] + for name in names: + srcname = os.path.join(src, name) + dstname = os.path.join(dst, name) + if condition is not None and not condition(srcname): + continue + try: + if os.path.islink(srcname): + # XXX: This is naive at best, should check srcbase(?) + realsrc = os.readlink(srcname) + os.symlink(realsrc, dstname) + elif os.path.isdir(srcname): + mergetree( + srcname, dstname, + condition=condition, copyfn=copyfn, srcbase=srcbase) + else: + copyfn(srcname, dstname) + except (IOError, os.error) as why: + errors.append((srcname, dstname, why)) + if errors: + raise IOError(errors) + + +def sdk_normalize(filename): + """ + Normalize a path to strip out the SDK portion, normally so that it + can be decided whether it is in a system path or not. + """ + if filename.startswith('/Developer/SDKs/'): + pathcomp = filename.split('/') + del pathcomp[1:4] + filename = '/'.join(pathcomp) + return filename + + +NOT_SYSTEM_FILES = [] + + +def in_system_path(filename): + """ + Return True if the file is in a system path + """ + fn = sdk_normalize(os.path.realpath(filename)) + if fn.startswith('/usr/local/'): + return False + elif fn.startswith('/System/') or fn.startswith('/usr/'): + if fn in NOT_SYSTEM_FILES: + return False + return True + else: + return False + + +def has_filename_filter(module): + """ + Return False if the module does not have a filename attribute + """ + return getattr(module, 'filename', None) is not None + + +def get_magic(): + """ + Get a list of valid Mach-O header signatures, not including the fat header + """ + return MAGIC + + +def is_platform_file(path): + """ + Return True if the file is Mach-O + """ + if not os.path.exists(path) or os.path.islink(path): + return False + # If the header is fat, we need to read into the first arch + with open(path, 'rb') as fileobj: + bytes = fileobj.read(MAGIC_LEN) + if bytes == FAT_MAGIC_BYTES: + # Read in the fat header + fileobj.seek(0) + header = mach_o.fat_header.from_fileobj(fileobj, _endian_='>') + if header.nfat_arch < 1: + return False + # Read in the first fat arch header + arch = mach_o.fat_arch.from_fileobj(fileobj, _endian_='>') + fileobj.seek(arch.offset) + # Read magic off the first header + bytes = fileobj.read(MAGIC_LEN) + for magic in MAGIC: + if bytes == magic: + return True + return False + + +def iter_platform_files(dst): + """ + Walk a directory and yield each full path that is a Mach-O file + """ + for root, dirs, files in os.walk(dst): + for fn in files: + fn = os.path.join(root, fn) + if is_platform_file(fn): + yield fn + + +def strip_files(files, argv_max=(256 * 1024)): + """ + Strip a list of files + """ + tostrip = [(fn, flipwritable(fn)) for fn in files] + while tostrip: + cmd = list(STRIPCMD) + flips = [] + pathlen = sum([len(s) + 1 for s in cmd]) + while pathlen < argv_max: + if not tostrip: + break + added, flip = tostrip.pop() + pathlen += len(added) + 1 + cmd.append(added) + flips.append((added, flip)) + else: + cmd.pop() + tostrip.append(flips.pop()) + os.spawnv(os.P_WAIT, cmd[0], cmd) + for args in flips: + flipwritable(*args) From 950338aa92545aedde357e15929be672c113afb7 Mon Sep 17 00:00:00 2001 From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Date: Thu, 26 Sep 2019 10:23:59 -0700 Subject: [PATCH 040/499] add --no-deps opt to `buildcache-create` (#12956) --- lib/spack/spack/cmd/buildcache.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/spack/spack/cmd/buildcache.py b/lib/spack/spack/cmd/buildcache.py index 5d5e6933198..5f26fb8ef94 100644 --- a/lib/spack/spack/cmd/buildcache.py +++ b/lib/spack/spack/cmd/buildcache.py @@ -61,6 +61,8 @@ def setup_parser(subparser): create.add_argument( 'packages', nargs=argparse.REMAINDER, help="specs of packages to create buildcache for") + create.add_argument('--no-deps', action='store_true', default='false', + help='Create buildcache entry wo/ dependencies') create.set_defaults(func=createtarball) install = subparsers.add_parser('install', help=installtarball.__doc__) @@ -333,6 +335,8 @@ def createtarball(args): else: tty.debug('adding matching spec %s' % match.format()) specs.add(match) + if args.no_deps is True: + continue tty.debug('recursing dependencies') for d, node in match.traverse(order='post', depth=True, From 7dae058f913a5851cbecd60322c9f98739eb221e Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Thu, 26 Sep 2019 13:04:58 -0500 Subject: [PATCH 041/499] Relocate mach-o binaries using macholib on linux. (#12946) Changes deps and rpaths for bins and libs, changes id for libs. --- lib/spack/spack/binary_distribution.py | 7 +- lib/spack/spack/relocate.py | 162 +++++++++++-------------- 2 files changed, 74 insertions(+), 95 deletions(-) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index 40e3a7c17ac..cab0ad21ea7 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -573,20 +573,19 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False, # so the pathname should be the same now that the directory layout # is confirmed workdir = os.path.join(tmpdir, os.path.basename(spec.prefix)) + install_tree(workdir, spec.prefix, symlinks=True) # cleanup os.remove(tarfile_path) os.remove(specfile_path) try: - relocate_package(workdir, spec, allow_root) + relocate_package(spec.prefix, spec, allow_root) except Exception as e: - shutil.rmtree(workdir) + shutil.rmtree(spec.prefix) tty.die(e) # Delay creating spec.prefix until verification is complete # and any relocation has been done. - else: - install_tree(workdir, spec.prefix, symlinks=True) finally: shutil.rmtree(tmpdir) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index 8873d1d725d..2c76166e92c 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -41,20 +41,20 @@ def __init__(self, file_path, old_len, new_len): (file_path, old_len, new_len)) -class MissingMachotoolsException(spack.error.SpackError): +class MissingMacholibException(spack.error.SpackError): """ Raised when the size of the file changes after binary path substitution. """ def __init__(self, error): - super(MissingMachotoolsException, self).__init__( + super(MissingMacholibException, self).__init__( "%s\n" - "Python package machotools needs to be avaiable to list\n" + "Python package macholib needs to be avaiable to list\n" "and modify a mach-o binary's rpaths, deps and id.\n" - "Use virtualenv with pip install machotools or\n" - "use spack to install the py-machotools package\n" - "spack install py-machotools\n" - "spack activate py-machotools\n" + "Use virtualenv with pip install macholib or\n" + "use spack to install the py-macholib package\n" + "spack install py-macholib\n" + "spack activate py-macholib\n" "spack load python\n" % error) @@ -275,55 +275,50 @@ def modify_macho_object(cur_path, rpaths, deps, idpath, return -def modify_object_machotools(cur_path, rpaths, deps, idpath, - new_rpaths, new_deps, new_idpath): +def modify_object_macholib(cur_path, old_dir, new_dir): """ Modify MachO binary path_name by replacing old_dir with new_dir or the relative path to spack install root. The old install dir in LC_ID_DYLIB is replaced with the new install dir - using py-machotools + using py-macholib The old install dir in LC_LOAD_DYLIB is replaced with the new install dir - using py-machotools + using py-macholib The old install dir in LC_RPATH is replaced with the new install dir using - using py-machotools + using py-macholib """ if cur_path.endswith('.o'): return try: - import machotools + from macholib.MachO import MachO + from macholib.mach_o import LC_RPATH except ImportError as e: - raise MissingMachotoolsException(e) - rewriter = machotools.rewriter_factory(cur_path) - if machotools.detect.is_dylib(cur_path): - if not new_idpath == idpath: - rewriter.install_name = new_idpath - for orig, new in zip(deps, new_deps): - if not orig == new: - rewriter.change_dependency(orig, new) - rewriter.commit() - return + raise MissingMacholibException(e) + def match_func(cpath): + return str(cpath).replace(old_dir, new_dir) + + dll = MachO(cur_path) + dll.rewriteLoadCommands(match_func) + for header in dll.headers: + for (idx, (lc, cmd, data)) in enumerate(header.commands): + if lc.cmd == LC_RPATH: + rpath = data + rpath = rpath.strip('\x00') + new_rpath = match_func(rpath) + header.rewriteDataForCommand(idx, new_rpath) -def machotools_get_paths(path_name): - """ - Examines the output of otool -l path_name for these three fields: - LC_ID_DYLIB, LC_LOAD_DYLIB, LC_RPATH and parses out the rpaths, - dependiencies and library id. - Returns these values. - """ try: - import machotools - except ImportError as e: - raise MissingMachotoolsException(e) - idpath = None - rpaths = list() - deps = list() - rewriter = machotools.rewriter_factory(path_name) - if machotools.detect.is_dylib(path_name): - idpath = rewriter.install_name - rpaths = rewriter.rpaths - deps = rewriter.dependencies - return rpaths, deps, idpath + f = open(dll.filename, 'rb+') + for header in dll.headers: + f.seek(0) + dll.write(f) + f.seek(0, 2) + f.flush() + f.close() + except Exception: + pass + + return def strings_contains_installroot(path_name, root_dir): @@ -405,48 +400,41 @@ def relocate_macho_binaries(path_names, old_dir, new_dir, allow_root): """ placeholder = set_placeholder(old_dir) for path_name in path_names: - deps = set() - idpath = None - if platform.system().lower() == 'darwin': - if path_name.endswith('.o'): - continue - else: - rpaths, deps, idpath = macho_get_paths(path_name) - else: - rpaths, deps, idpath = machotools_get_paths(path_name) - # one pass to replace placeholder - (n_rpaths, - n_deps, - n_idpath) = macho_replace_paths(placeholder, - new_dir, - rpaths, - deps, - idpath) - # another pass to replace old_dir - (new_rpaths, - new_deps, - new_idpath) = macho_replace_paths(old_dir, - new_dir, - n_rpaths, - n_deps, - n_idpath) + if path_name.endswith('.o'): + continue + if new_dir == old_dir: + continue if platform.system().lower() == 'darwin': + rpaths, deps, idpath = macho_get_paths(path_name) + # one pass to replace placeholder + (n_rpaths, + n_deps, + n_idpath) = macho_replace_paths(placeholder, + new_dir, + rpaths, + deps, + idpath) + # another pass to replace old_dir + (new_rpaths, + new_deps, + new_idpath) = macho_replace_paths(old_dir, + new_dir, + n_rpaths, + n_deps, + n_idpath) modify_macho_object(path_name, rpaths, deps, idpath, new_rpaths, new_deps, new_idpath) else: - modify_object_machotools(path_name, - rpaths, deps, idpath, - new_rpaths, new_deps, new_idpath) - - if not new_dir == old_dir: - if len(new_dir) <= len(old_dir): - replace_prefix_bin(path_name, old_dir, new_dir) - else: - tty.warn('Cannot do a binary string replacement' - ' with padding for %s' - ' because %s is longer than %s' % - (path_name, new_dir, old_dir)) + modify_object_macholib(path_name, placeholder, new_dir) + modify_object_macholib(path_name, old_dir, new_dir) + if len(new_dir) <= len(old_dir): + replace_prefix_bin(path_name, old_dir, new_dir) + else: + tty.warn('Cannot do a binary string replacement' + ' with padding for %s' + ' because %s is longer than %s' % + (path_name, new_dir, old_dir)) def relocate_elf_binaries(path_names, old_dir, new_dir, allow_root): @@ -498,21 +486,13 @@ def make_macho_binaries_relative(cur_path_names, orig_path_names, old_dir, idpath = None if platform.system().lower() == 'darwin': (rpaths, deps, idpath) = macho_get_paths(cur_path) - else: - (rpaths, deps, idpath) = machotools_get_paths(cur_path) - (new_rpaths, - new_deps, - new_idpath) = macho_make_paths_relative(orig_path, old_dir, - rpaths, deps, idpath) - if platform.system().lower() == 'darwin': + (new_rpaths, + new_deps, + new_idpath) = macho_make_paths_relative(orig_path, old_dir, + rpaths, deps, idpath) modify_macho_object(cur_path, rpaths, deps, idpath, new_rpaths, new_deps, new_idpath) - else: - modify_object_machotools(cur_path, - rpaths, deps, idpath, - new_rpaths, new_deps, new_idpath) - if (not allow_root and not file_is_relocatable(cur_path)): raise InstallRootStringException(cur_path, old_dir) From 5201d2615eff0a7ff948b5783a0d859eb53a9423 Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Thu, 26 Sep 2019 12:15:17 -0700 Subject: [PATCH 042/499] qt4: fix 'arch' string due to microarchitecture change (#12957) qt4 fails to build because it's expecting something like 'x86_64' rather than 'broadwell'. --- var/spack/repos/builtin/packages/qt/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index c67b6a76af5..fc55570eb35 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -427,7 +427,7 @@ def configure(self, spec, prefix): '-{0}gtkstyle'.format('' if '+gtk' in spec else 'no-'), '-{0}webkit'.format('' if '+webkit' in spec else 'no-'), '-{0}phonon'.format('' if '+phonon' in spec else 'no-'), - '-arch', str(spec.architecture.target), + '-arch', str(spec.target.family), ]) # Disable phonon backend until gstreamer is setup as dependency From 08a6577861883aefa41fd813904dc9f34c3b4dec Mon Sep 17 00:00:00 2001 From: Glenn P Johnson Date: Tue, 24 Sep 2019 21:01:12 -0500 Subject: [PATCH 043/499] Fix perl build when using Build.PL This fixes #12852 where perl builds that use Build.PL will fail when the shebang of the Build script produced from the configure step is too long. --- lib/spack/spack/build_systems/perl.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/lib/spack/spack/build_systems/perl.py b/lib/spack/spack/build_systems/perl.py index bdd1e7fda3a..28f1fc56083 100644 --- a/lib/spack/spack/build_systems/perl.py +++ b/lib/spack/spack/build_systems/perl.py @@ -10,6 +10,7 @@ from spack.directives import depends_on, extends from spack.package import PackageBase, run_after from spack.util.executable import Executable +from llnl.util.filesystem import filter_file class PerlPackage(PackageBase): @@ -80,6 +81,17 @@ def configure(self, spec, prefix): inspect.getmodule(self).perl(*options) + # It is possible that the shebang in the Build script that is created from + # Build.PL may be too long causing the build to fail. Patching the shebang + # does not happen until after install so set '/usr/bin/env perl' here in + # the Build script. + @run_after('configure') + def fix_shebang(self): + if self.build_method == 'Build.PL': + pattern = '#!{0}'.format(self.spec['perl'].command.path) + repl = '#!/usr/bin/env perl' + filter_file(pattern, repl, 'Build', backup=False) + def build(self, spec, prefix): """Builds a Perl package.""" self.build_executable() From fc99eddb124b4bcc887eaa3d2c22d5fe2ef42893 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Fri, 27 Sep 2019 16:59:58 -0500 Subject: [PATCH 044/499] New package: maker and dependencies (#12904) --- .../builtin/packages/maker/MpiChunk.patch | 20 ++++ .../builtin/packages/maker/install.patch | 10 ++ .../repos/builtin/packages/maker/mpi.patch | 38 ++++++++ .../repos/builtin/packages/maker/package.py | 91 +++++++++++++++++++ .../packages/perl-acme-damn/package.py | 17 ++++ .../packages/perl-alien-build/package.py | 23 +++++ .../packages/perl-alien-libxml2/package.py | 18 ++++ .../builtin/packages/perl-bio-perl/package.py | 70 ++++++++++++-- .../builtin/packages/perl-dbd-pg/package.py | 19 ++++ .../packages/perl-devel-symdump/package.py | 15 +++ .../builtin/packages/perl-error/package.py | 20 ++++ .../packages/perl-ffi-checklib/package.py | 20 ++++ .../packages/perl-file-chdir/package.py | 23 +++++ .../builtin/packages/perl-forks/package.py | 21 +++++ .../builtin/packages/perl-io-all/package.py | 30 ++++++ .../packages/perl-io-prompt/package.py | 35 +++++++ .../packages/perl-io-stringy/package.py | 26 ++++++ .../builtin/packages/perl-io-tty/package.py | 17 ++++ .../builtin/packages/perl-ipc-run/package.py | 21 +++++ .../packages/perl-libxml-perl/package.py | 17 ++++ .../perl-list-moreutils-xs/package.py | 18 ++++ .../packages/perl-mailtools/package.py | 17 ++++ .../packages/perl-path-tiny/package.py | 19 ++++ .../perl-perl-unsafe-signals/package.py | 35 +++++++ .../packages/perl-set-scalar/package.py | 15 +++ .../packages/perl-sys-sigaction/package.py | 28 ++++++ .../packages/perl-term-readkey/package.py | 1 + .../builtin/packages/perl-timedate/package.py | 17 ++++ .../packages/perl-xml-dom-xpath/package.py | 19 ++++ .../builtin/packages/perl-xml-dom/package.py | 22 +++++ .../perl-xml-filter-buffertext/package.py | 19 ++++ .../packages/perl-xml-libxml/package.py | 26 ++++++ .../perl-xml-namespacesupport/package.py | 17 ++++ .../packages/perl-xml-quote/package.py | 18 ++++ .../packages/perl-xml-regexp/package.py | 18 ++++ .../packages/perl-xml-sax-base/package.py | 19 ++++ .../packages/perl-xml-sax-writer/package.py | 22 +++++ .../builtin/packages/perl-xml-sax/package.py | 20 ++++ .../perl-xml-twig/non_interactive.patch | 27 ++++++ .../builtin/packages/perl-xml-twig/package.py | 32 +++++++ .../packages/perl-xml-writer/package.py | 27 ++++++ .../packages/perl-xml-xpathengine/package.py | 16 ++++ 42 files changed, 997 insertions(+), 6 deletions(-) create mode 100644 var/spack/repos/builtin/packages/maker/MpiChunk.patch create mode 100644 var/spack/repos/builtin/packages/maker/install.patch create mode 100644 var/spack/repos/builtin/packages/maker/mpi.patch create mode 100644 var/spack/repos/builtin/packages/maker/package.py create mode 100644 var/spack/repos/builtin/packages/perl-acme-damn/package.py create mode 100644 var/spack/repos/builtin/packages/perl-alien-build/package.py create mode 100644 var/spack/repos/builtin/packages/perl-alien-libxml2/package.py create mode 100644 var/spack/repos/builtin/packages/perl-dbd-pg/package.py create mode 100644 var/spack/repos/builtin/packages/perl-devel-symdump/package.py create mode 100644 var/spack/repos/builtin/packages/perl-error/package.py create mode 100644 var/spack/repos/builtin/packages/perl-ffi-checklib/package.py create mode 100644 var/spack/repos/builtin/packages/perl-file-chdir/package.py create mode 100644 var/spack/repos/builtin/packages/perl-forks/package.py create mode 100644 var/spack/repos/builtin/packages/perl-io-all/package.py create mode 100644 var/spack/repos/builtin/packages/perl-io-prompt/package.py create mode 100644 var/spack/repos/builtin/packages/perl-io-stringy/package.py create mode 100644 var/spack/repos/builtin/packages/perl-io-tty/package.py create mode 100644 var/spack/repos/builtin/packages/perl-ipc-run/package.py create mode 100644 var/spack/repos/builtin/packages/perl-libxml-perl/package.py create mode 100644 var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py create mode 100644 var/spack/repos/builtin/packages/perl-mailtools/package.py create mode 100644 var/spack/repos/builtin/packages/perl-path-tiny/package.py create mode 100644 var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py create mode 100644 var/spack/repos/builtin/packages/perl-set-scalar/package.py create mode 100644 var/spack/repos/builtin/packages/perl-sys-sigaction/package.py create mode 100644 var/spack/repos/builtin/packages/perl-timedate/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-dom/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-libxml/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-quote/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-regexp/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-sax-base/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-sax/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-twig/non_interactive.patch create mode 100644 var/spack/repos/builtin/packages/perl-xml-twig/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-writer/package.py create mode 100644 var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py diff --git a/var/spack/repos/builtin/packages/maker/MpiChunk.patch b/var/spack/repos/builtin/packages/maker/MpiChunk.patch new file mode 100644 index 00000000000..cbb447741f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/maker/MpiChunk.patch @@ -0,0 +1,20 @@ +--- a/lib/Process/MpiChunk.pm 2014-12-01 16:40:29.000000000 -0600 ++++ b/lib/Process/MpiChunk.pm 2019-09-23 13:23:19.779213006 -0500 +@@ -744,7 +744,7 @@ + my $safe_seq_id = $VARS->{safe_seq_id}; + my $q_seq_length = $VARS->{q_seq_length}; + +- my $TMP = GI::get_global_temp; ++ my $TMP = GI::get_global_temp::; + if($CTL_OPT{go_gffdb} && GI::is_NFS_mount($dbfile) && !GI::is_NFS_mount($TMP)){ + $dbfile = GI::localize_file($dbfile); + } +@@ -3167,7 +3167,7 @@ + my $LOG = $VARS->{LOG}; + my %CTL_OPT = %{$VARS->{CTL_OPT}}; + +- my $TMP = GI::get_global_temp; ++ my $TMP = GI::get_global_temp::; + if($CTL_OPT{go_gffdb} && GI::is_NFS_mount($dbfile) && !GI::is_NFS_mount($TMP)){ + $dbfile = GI::localize_file($dbfile); + } diff --git a/var/spack/repos/builtin/packages/maker/install.patch b/var/spack/repos/builtin/packages/maker/install.patch new file mode 100644 index 00000000000..30d8ad36409 --- /dev/null +++ b/var/spack/repos/builtin/packages/maker/install.patch @@ -0,0 +1,10 @@ +--- a/src/Build.PL 2019-09-18 21:00:16.900047731 -0500 ++++ b/src/Build.PL 2019-09-18 21:10:41.058957500 -0500 +@@ -91,7 +91,6 @@ + 'Carp' => '1.24', + #'Other::Module' => '>= 1.2, != 1.5, < 2.0', + }, +- install_base => "$FindBin::RealBin/../", + install_base_relpaths => { + arch => [qw(perl/lib)], + lib => [qw(perl/lib)], diff --git a/var/spack/repos/builtin/packages/maker/mpi.patch b/var/spack/repos/builtin/packages/maker/mpi.patch new file mode 100644 index 00000000000..92cbebf87db --- /dev/null +++ b/var/spack/repos/builtin/packages/maker/mpi.patch @@ -0,0 +1,38 @@ +diff -ruN a/src/Build.PL b/src/Build.PL +--- a/src/Build.PL 2014-12-01 16:37:10.000000000 -0600 ++++ b/src/Build.PL 2019-09-15 18:30:56.940787669 -0500 +@@ -129,9 +129,10 @@ + } + + #ask for MPI +-my $go = $build->y_n("\nMAKER supports distributed parallelization via MPI.\n". +- "Would you like to configure MAKER for MPI (This\n". +- "requires that you have an MPI client installed)?", 'N'); ++#my $go = $build->y_n("\nMAKER supports distributed parallelization via MPI.\n". ++# "Would you like to configure MAKER for MPI (This\n". ++# "requires that you have an MPI client installed)?", 'N'); ++my $go = 0; + $build->feature(mpi_support => $go); + $build->config_mpi() if($go); + +diff -ruN a/src/inc/lib/MAKER/Build.pm b/src/inc/lib/MAKER/Build.pm +--- a/src/inc/lib/MAKER/Build.pm 2014-12-01 16:37:10.000000000 -0600 ++++ b/src/inc/lib/MAKER/Build.pm 2019-09-15 18:30:25.439863837 -0500 +@@ -108,7 +108,7 @@ + $mpicc = $self->config('cc') if(! $mpicc && $self->config('cc') =~ /(^|[\/])mpicc$/); + ($mpicc) = File::Which::where('mpicc') if(!$mpicc || ! -f $mpicc); + +- $mpicc = $self->prompt("\nPlease specify the path to 'mpicc' on your system:", $mpicc); ++ #$mpicc = $self->prompt("\nPlease specify the path to 'mpicc' on your system:", $mpicc); + + while(!$mpicc || $mpicc !~ /(^|[\/])mpicc$/ || ! -f $mpicc){ + $mpicc = $self->prompt("\nCannot find 'mpicc'.\n". +@@ -139,7 +139,7 @@ + + my ($MPIDIR) = grep {-f "$_/mpi.h"} @includes; + +- $MPIDIR = $self->prompt("\nPlease specify the path to the directory containing 'mpi.h':", $MPIDIR); ++ #$MPIDIR = $self->prompt("\nPlease specify the path to the directory containing 'mpi.h':", $MPIDIR); + + while(!$MPIDIR || ! -f "$MPIDIR/mpi.h"){ + $MPIDIR = $self->prompt("\nCannot find 'mpi.h'\n.". diff --git a/var/spack/repos/builtin/packages/maker/package.py b/var/spack/repos/builtin/packages/maker/package.py new file mode 100644 index 00000000000..41363ec0a1e --- /dev/null +++ b/var/spack/repos/builtin/packages/maker/package.py @@ -0,0 +1,91 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class Maker(Package): + """MAKER is a portable and easily configurable genome annotation pipeline. + It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects + to independently annotate their genomes and to create genome databases. + MAKER identifies repeats, aligns ESTs and proteins to a genome, produces + ab-initio gene predictions and automatically synthesizes these data into + gene annotations having evidence-based quality values. MAKER is also easily + trainable: outputs of preliminary runs can be used to automatically retrain + its gene prediction algorithm, producing higher quality gene-models on + subsequent runs. MAKER's inputs are minimal and its ouputs can be directly + loaded into a GMOD database. They can also be viewed in the Apollo genome + browser; this feature of MAKER provides an easy means to annotate, view and + edit individual contigs and BACs without the overhead of a database. MAKER + should prove especially useful for emerging model organism projects with + minimal bioinformatics expertise and computer resources. + + Note: MAKER requires registration. Fill out the form at + http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi to get a + download link. Spack will search your current directory for the download + file. Alternatively, add this file to a mirror so that Spack can find it. + For instructions on how to set up a mirror, see + http://spack.readthedocs.io/en/latest/mirrors.html""" + + homepage = "http://www.yandell-lab.org/software/maker.html" + + version('2.31.10', sha256='d3979af9710d61754a3b53f6682d0e2052c6c3f36be6f2df2286d2587406f07d') + + def url_for_version(self, version): + return "file://{0}/maker-{1}.tgz".format(os.getcwd(), version) + + variant('mpi', default=True, description='Build with MPI support') + + patch('install.patch') + patch('mpi.patch') + patch('MpiChunk.patch') + + depends_on('perl', type=('build', 'run')) + depends_on('perl-module-build', type='build') + depends_on('perl-dbi', type=('build', 'run')) + depends_on('perl-dbd-pg', type=('build', 'run')) + depends_on('perl-dbd-sqlite', type=('build', 'run')) + depends_on('perl-forks', type=('build', 'run')) + depends_on('perl-file-which', type=('build', 'run')) + depends_on('perl-perl-unsafe-signals', type=('build', 'run')) + depends_on('perl-bit-vector', type=('build', 'run')) + depends_on('perl-inline-c', type=('build', 'run')) + depends_on('perl-io-all', type=('build', 'run')) + depends_on('perl-io-prompt', type=('build', 'run')) + depends_on('perl-bio-perl', type=('build', 'run')) + depends_on('blast-plus') + depends_on('snap-korf') + depends_on('repeatmasker') + depends_on('exonerate') + depends_on('augustus') + depends_on('interproscan@:4.8') + depends_on('mpi', when='+mpi') + + def install(self, spec, prefix): + if '+mpi' in spec: + with working_dir('src'): + pattern = r'my \$go = 0;' + repl = 'my $go = 1;' + filter_file(pattern, repl, 'Build.PL', backup=False) + + perl = which('perl') + rm = which('rm') + with working_dir('src'): + perl('Build.PL', '--install_base', prefix) + perl('Build', 'install') + + install_tree('lib', join_path(prefix, 'perl', 'lib')) + + # Remove scripts that do not work. The 'mpi_evaluator' and + # 'mpi_iprscan' scripts depend on a custom perl module that is not + # shipped with maker. The 'maker2chado' script depends on setting up a + # CHADO database which is out of scope here. + for package in ('maker2chado', 'maker2jbrowse', 'maker2wap', + 'mpi_evaluator', 'mpi_iprscan'): + rm('-f', join_path(prefix.bin, package)) + + # Remove old IO::Prompt perl module + rm('-r', '-f', join_path(prefix, 'perl', 'lib', 'IO')) diff --git a/var/spack/repos/builtin/packages/perl-acme-damn/package.py b/var/spack/repos/builtin/packages/perl-acme-damn/package.py new file mode 100644 index 00000000000..62fbd15301a --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-acme-damn/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlAcmeDamn(PerlPackage): + """Acme::Damn provides a single routine, damn(), which takes a blessed + reference (a Perl object), and unblesses it, to return the original + reference.""" + + homepage = "https://metacpan.org/pod/Acme::Damn" + url = "https://cpan.metacpan.org/authors/id/I/IB/IBB/Acme-Damn-0.08.tar.gz" + + version('0.08', sha256='310d2d03ff912dcd42e4d946174099f41fe3a2dd57a497d6bd65baf1759b7e0e') diff --git a/var/spack/repos/builtin/packages/perl-alien-build/package.py b/var/spack/repos/builtin/packages/perl-alien-build/package.py new file mode 100644 index 00000000000..db96518659f --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-alien-build/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlAlienBuild(PerlPackage): + """This module provides tools for building external (non-CPAN) dependencies + for CPAN. It is mainly designed to be used at install time of a CPAN + client, and work closely with Alien::Base which is used at runtime.""" + + homepage = "https://metacpan.org/pod/Alien::Build" + url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Build-1.86.tar.gz" + + version('1.86', sha256='f856a46aea72fe77daea5b1788b4ea0dc215f5704f5a35fa063171be8523e4e9') + + depends_on('perl-capture-tiny', type=('build', 'run')) + depends_on('perl-ffi-checklib', type=('build', 'run')) + depends_on('perl-file-which', type=('build', 'run')) + depends_on('perl-file-chdir', type=('build', 'run')) + depends_on('perl-path-tiny', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py new file mode 100644 index 00000000000..98c0a488d93 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlAlienLibxml2(PerlPackage): + """This module provides libxml2 for other modules to use.""" + + homepage = "https://metacpan.org/pod/Alien::Libxml2" + url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.09.tar.gz" + + version('0.10_01', sha256='2f45b308b33503292f48bf46a75fe1e653d6b209ba5caf0628d8cc103f8d61ac') + + depends_on('libxml2') + depends_on('perl-alien-build', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bio-perl/package.py index 92d0e292228..05294029015 100644 --- a/var/spack/repos/builtin/packages/perl-bio-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-bio-perl/package.py @@ -8,19 +8,65 @@ class PerlBioPerl(PerlPackage): - """Functional access to BioPerl for people who don't know objects""" + """BioPerl is the product of a community effort to produce Perl code which + is useful in biology. Examples include Sequence objects, Alignment objects + and database searching objects. These objects not only do what they are + advertised to do in the documentation, but they also interact - Alignment + objects are made from the Sequence objects, Sequence objects have access to + Annotation and SeqFeature objects and databases, Blast objects can be + converted to Alignment objects, and so on. This means that the objects + provide a coordinated and extensible framework to do computational biology. - homepage = "http://search.cpan.org/~cjfields/BioPerl-1.007002/Bio/Perl.pm" - url = "http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz" + BioPerl development focuses on Perl classes, or code that is used to create + objects representing biological entities. There are scripts provided in the + scripts/ and examples/ directories but scripts are not the main focus of + the BioPerl developers. Of course, as the objects do most of the hard work + for you, all you have to do is combine a number of objects together + sensibly to make useful scripts. - version('1.007002', 'a912c92b56d009198f1786b4cf560d5c') + The intent of the BioPerl development effort is to make reusable tools that + aid people in creating their own sites or job-specific applications. - depends_on('perl-module-build', type='build') - depends_on('perl-uri-escape', type=('build', 'run')) + The BioPerl website at http://bioperl.org also attempts to maintain links + and archives of standalone bio-related Perl tools that are not affiliated + or related to the core BioPerl effort. Check the site for useful code ideas + and contribute your own if possible.""" + + homepage = "https://metacpan.org/pod/BioPerl" + url = "https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.6.tar.gz" + + version('1.7.6', sha256='df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d') + version('1.7.2', 'a912c92b56d009198f1786b4cf560d5c', + url="http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz") + + # According to cpandeps.grinnz.com Module-Build is both a build and run + # time dependency for BioPerl + depends_on('perl-module-build', type=('build', 'run')) + depends_on('perl-uri', type=('build', 'run')) depends_on('perl-io-string', type=('build', 'run')) depends_on('perl-data-stag', type=('build', 'run')) depends_on('perl-test-most', type=('build', 'run')) + depends_on('perl-error', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-graph', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-http-message', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-io-stringy', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-ipc-run', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-list-moreutils', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-set-scalar', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-test-requiresinternet', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-dom', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-dom-xpath', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-libxml', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-sax', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-sax-base', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-sax-writer', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-twig', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-xml-writer', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-yaml', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-libwww-perl', when='@1.7.6:', type=('build', 'run')) + depends_on('perl-libxml-perl', when='@1.7.6:', type=('build', 'run')) + @when('@1.7.2') def configure(self, spec, prefix): # Overriding default configure method in order to cater to interactive # Build.pl @@ -50,3 +96,15 @@ def configure(self, spec, prefix): with open(config_answers_filename, 'r') as f: inspect.getmodule(self).perl('Build.PL', '--install_base=%s' % self.prefix, input=f) + + # Need to also override the build and install methods to make sure that the + # Build script is run through perl and not use the shebang, as it might be + # too long. This is needed because this does not pick up the + # `@run_after(configure)` step defined in `PerlPackage`. + @when('@1.7.2') + def build(self, spec, prefix): + inspect.getmodule(self).perl('Build') + + @when('@1.7.2') + def install(self, spec, prefix): + inspect.getmodule(self).perl('Build', 'install') diff --git a/var/spack/repos/builtin/packages/perl-dbd-pg/package.py b/var/spack/repos/builtin/packages/perl-dbd-pg/package.py new file mode 100644 index 00000000000..b54b7864b08 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-dbd-pg/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlDbdPg(PerlPackage): + """DBD::Pg is a Perl module that works with the DBI module to provide + access to PostgreSQL databases.""" + + homepage = "https://metacpan.org/pod/DBD::Pg" + url = "https://cpan.metacpan.org/authors/id/T/TU/TURNSTEP/DBD-Pg-3.10.0.tar.gz" + + version('3.10.0', sha256='e103268a63e2828e3d43659bdba5f743446cbbe047a766f843112eedae105f80') + + depends_on('postgresql') + depends_on('perl-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-devel-symdump/package.py b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py new file mode 100644 index 00000000000..9dfdc5ae984 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlDevelSymdump(PerlPackage): + """Devel::Symdump - dump symbol names or the symbol table""" + + homepage = "https://metacpan.org/pod/Devel::Symdump" + url = "https://cpan.metacpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.18.tar.gz" + + version('2.0604', sha256='1f9eaa557733f775ccaa852e846566274c017e6fee380aeb8d08e425cfa86d3e') diff --git a/var/spack/repos/builtin/packages/perl-error/package.py b/var/spack/repos/builtin/packages/perl-error/package.py new file mode 100644 index 00000000000..0289506bc7d --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-error/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlError(PerlPackage): + """The Error package provides two interfaces. Firstly Error provides a + procedural interface to exception handling. Secondly Error is a base class + for errors/exceptions that can either be thrown, for subsequent catch, or + can simply be recorded.""" + + homepage = "https://metacpan.org/pod/Error" + url = "https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Error-0.17028.tar.gz" + + version('0.17028', sha256='3ad85c5e58b31c8903006298424a51bba39f1840e324f5ae612eabc8b935e960') + + depends_on('perl-module-build', type='build') diff --git a/var/spack/repos/builtin/packages/perl-ffi-checklib/package.py b/var/spack/repos/builtin/packages/perl-ffi-checklib/package.py new file mode 100644 index 00000000000..461259ead0f --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-ffi-checklib/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlFfiChecklib(PerlPackage): + """This module checks whether a particular dynamic library is available for + FFI to use. It is modeled heavily on Devel::CheckLib, but will find dynamic + libraries even when development packages are not installed. It also + provides a find_lib function that will return the full path to the found + dynamic library, which can be feed directly into FFI::Platypus or another + FFI system.""" + + homepage = "https://metacpan.org/pod/FFI::CheckLib" + url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/FFI-CheckLib-0.25.tar.gz" + + version('0.25', sha256='eb36b9a7cff1764a65b1b77e01e92c26207c558a3f986d0d17d2b110fa366ba4') diff --git a/var/spack/repos/builtin/packages/perl-file-chdir/package.py b/var/spack/repos/builtin/packages/perl-file-chdir/package.py new file mode 100644 index 00000000000..b628ca12e54 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-file-chdir/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlFileChdir(PerlPackage): + """Perl's chdir() has the unfortunate problem of being very, very, very + global. If any part of your program calls chdir() or if any library you use + calls chdir(), it changes the current working directory for the *whole* + program. + + This sucks. + + File::chdir gives you an alternative, $CWD and @CWD. These two variables + combine all the power of chdir(), File::Spec and Cwd.""" + + homepage = "https://metacpan.org/pod/File::chdir" + url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1010.tar.gz" + + version('0.1011', sha256='31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79') diff --git a/var/spack/repos/builtin/packages/perl-forks/package.py b/var/spack/repos/builtin/packages/perl-forks/package.py new file mode 100644 index 00000000000..51fe7762db3 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-forks/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlForks(PerlPackage): + """The "forks" pragma allows a developer to use threads without having to + have a threaded perl, or to even run 5.8.0 or higher.""" + + homepage = "https://metacpan.org/pod/forks" + url = "https://cpan.metacpan.org/authors/id/R/RY/RYBSKEJ/forks-0.36.tar.gz" + + version('0.36', sha256='61be24e44f4c6fea230e8354678beb5b7adcfefd909a47db8f0a251b0ab65993') + + depends_on('perl-acme-damn', type=('build', 'run')) + depends_on('perl-devel-symdump', type=('build', 'run')) + depends_on('perl-list-moreutils', type=('build', 'run')) + depends_on('perl-sys-sigaction', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-io-all/package.py b/var/spack/repos/builtin/packages/perl-io-all/package.py new file mode 100644 index 00000000000..6d45ed5b8a2 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-io-all/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlIoAll(PerlPackage): + """IO::All combines all of the best Perl IO modules into a single nifty + object oriented interface to greatly simplify your everyday Perl IO idioms. + It exports a single function called io, which returns a new IO::All object. + And that object can do it all! + + The IO::All object is a proxy for IO::File, IO::Dir, IO::Socket, Tie::File, + File::Spec, File::Path, File::MimeInfo and File::ReadBackwards; as well as + all the DBM and MLDBM modules. You can use most of the methods found in + these classes and in IO::Handle (which they inherit from). IO::All adds + dozens of other helpful idiomatic methods including file stat and + manipulation functions. + + IO::All is pluggable, and modules like IO::All::LWP and IO::All::Mailto add + even more functionality. Optionally, every IO::All object can be tied to + itself. This means that you can use most perl IO builtins on it: readline, + <>, getc, print, printf, syswrite, sysread, close.""" + + homepage = "https://metacpan.org/pod/distribution/IO-All/lib/IO/All.pod" + url = "https://cpan.metacpan.org/authors/id/F/FR/FREW/IO-All-0.87.tar.gz" + + version('0.87', sha256='54e21d250c0229127e30b77a3461e10077854ec244f26fb670f1b445ed4c4d5b') diff --git a/var/spack/repos/builtin/packages/perl-io-prompt/package.py b/var/spack/repos/builtin/packages/perl-io-prompt/package.py new file mode 100644 index 00000000000..2bf41449906 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-io-prompt/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlIoPrompt(PerlPackage): + """By default, this module exports a single function prompt. It prompts the + user to enter some input, and returns an object that represents the user + input. + + You may specify various flags to the function to affect its behaviour; most + notably, it defaults to automatically chomp the input, unless the -line + flag is specified. + + Two other functions are exported at request: hand_print, which simulates + hand-typing to the console; and get_input, which is the lower-level + function that actually prompts the user for a suitable input. + + Note that this is an interim re-release. A full release with better + documentation will follow in the near future. Meanwhile, please consult the + examples directory from this module's CPAN distribution to better + understand how to make use of this module.""" + + homepage = "https://metacpan.org/pod/IO::Prompt" + url = "https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/IO-Prompt-0.997004.tar.gz" + + version('0.997004', sha256='f17bb305ee6ac8b5b203e6d826eb940c4f3f6d6f4bfe719c3b3a225f46f58615') + + depends_on('perl-module-build', type='build') + + depends_on('perl-term-readkey', type=('build', 'run')) + depends_on('perl-want', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-io-stringy/package.py b/var/spack/repos/builtin/packages/perl-io-stringy/package.py new file mode 100644 index 00000000000..826414418b6 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-io-stringy/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlIoStringy(PerlPackage): + """This toolkit primarily provides modules for performing both traditional + and object-oriented i/o) on things other than normal filehandles; in + particular, IO::Scalar, IO::ScalarArray, and IO::Lines. + + In the more-traditional IO::Handle front, we have IO::AtomicFile which may + be used to painlessly create files which are updated atomically. + + And in the "this-may-prove-useful" corner, we have IO::Wrap, whose exported + wraphandle() function will clothe anything that's not a blessed object in + an IO::Handle-like wrapper... so you can just use OO syntax and stop + worrying about whether your function's caller handed you a string, a + globref, or a FileHandle.""" + + homepage = "https://metacpan.org/pod/IO::Stringy" + url = "https://cpan.metacpan.org/authors/id/D/DS/DSKOLL/IO-stringy-2.111.tar.gz" + + version('2.111', sha256='8c67fd6608c3c4e74f7324f1404a856c331dbf48d9deda6aaa8296ea41bf199d') diff --git a/var/spack/repos/builtin/packages/perl-io-tty/package.py b/var/spack/repos/builtin/packages/perl-io-tty/package.py new file mode 100644 index 00000000000..217b4fb71bf --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-io-tty/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlIoTty(PerlPackage): + """IO::Tty is used internally by IO::Pty to create a pseudo-tty. You + wouldn't want to use it directly except to import constants, use IO::Pty. + For a list of importable constants, see IO::Tty::Constant.""" + + homepage = "https://metacpan.org/pod/IO::Tty" + url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IO-Tty-1.12.tar.gz" + + version('1.13_01', sha256='89798eba7c31d9c169ef2f38ff49490aa769b1d9a68033de365595cfaf9cc258') diff --git a/var/spack/repos/builtin/packages/perl-ipc-run/package.py b/var/spack/repos/builtin/packages/perl-ipc-run/package.py new file mode 100644 index 00000000000..228d76877f0 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-ipc-run/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlIpcRun(PerlPackage): + """IPC::Run allows you to run and interact with child processes using + files, pipes, and pseudo-ttys. Both system()-style and scripted usages are + supported and may be mixed. Likewise, functional and OO API styles are both + supported and may be mixed.""" + + homepage = "https://metacpan.org/pod/IPC::Run" + url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IPC-Run-20180523.0.tar.gz" + + version('20180523.0', sha256='3850d7edf8a4671391c6e99bb770698e1c45da55b323b31c76310913349b6c2f') + + depends_on('perl-io-tty', type=('build', 'run')) + depends_on('perl-readonly', type='build') diff --git a/var/spack/repos/builtin/packages/perl-libxml-perl/package.py b/var/spack/repos/builtin/packages/perl-libxml-perl/package.py new file mode 100644 index 00000000000..70fbfda3ab3 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-libxml-perl/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlLibxmlPerl(PerlPackage): + """libxml-perl is a collection of smaller Perl modules, scripts, and + documents for working with XML in Perl. libxml-perl software works in + combination with XML::Parser, PerlSAX, XML::DOM, XML::Grove and others.""" + + homepage = "https://metacpan.org/release/libxml-perl" + url = "https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/libxml-perl-0.08.tar.gz" + + version('0.08', sha256='4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb') diff --git a/var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py b/var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py new file mode 100644 index 00000000000..0020e883136 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlListMoreutilsXs(PerlPackage): + """List::MoreUtils::XS is a backend for List::MoreUtils. Even if it's + possible (because of user wishes) to have it practically independent from + List::MoreUtils, it technically depend on List::MoreUtils. Since it's only + a backend, the API is not public and can change without any warning.""" + + homepage = "https://metacpan.org/pod/List::MoreUtils::XS" + url = "https://cpan.metacpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-XS-0.428.tar.gz" + + version('0.428', sha256='9d9fe621429dfe7cf2eb1299c192699ddebf060953e5ebdc1b4e293c6d6dd62d') diff --git a/var/spack/repos/builtin/packages/perl-mailtools/package.py b/var/spack/repos/builtin/packages/perl-mailtools/package.py new file mode 100644 index 00000000000..9c4237c2e6c --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-mailtools/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlMailtools(PerlPackage): + """Perl module for handling mail""" + + homepage = "https://metacpan.org/release/MailTools" + url = "https://cpan.metacpan.org/authors/id/M/MA/MARKOV/MailTools-2.21.tar.gz" + + version('2.21', sha256='4ad9bd6826b6f03a2727332466b1b7d29890c8d99a32b4b3b0a8d926ee1a44cb') + + depends_on('perl-timedate', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-path-tiny/package.py b/var/spack/repos/builtin/packages/perl-path-tiny/package.py new file mode 100644 index 00000000000..e7218843876 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-path-tiny/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlPathTiny(PerlPackage): + """This module provides a small, fast utility for working with file paths. + It is friendlier to use than File::Spec and provides easy access to + functions from several other core file handling modules. It aims to be + smaller and faster than many alternatives on CPAN, while helping people do + many common things in consistent and less error-prone ways.""" + + homepage = "https://metacpan.org/pod/Path::Tiny" + url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.108.tar.gz" + + version('0.108', sha256='3c49482be2b3eb7ddd7e73a5b90cff648393f5d5de334ff126ce7a3632723ff5') diff --git a/var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py b/var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py new file mode 100644 index 00000000000..4efa679d620 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlPerlUnsafeSignals(PerlPackage): + """Quoting perl581delta: + + In Perl 5.8.0 the so-called "safe signals" were introduced. This means + that Perl no longer handles signals immediately but instead "between + opcodes", when it is safe to do so. The earlier immediate handling + easily could corrupt the internal state of Perl, resulting in + mysterious crashes. + + It's possible since perl 5.8.1 to globally disable this feature by + using the PERL_SIGNALS environment variables (as specified in + "PERL_SIGNALS" in perlrun); but there's no way to disable it locally, + for a short period of time. That's however something you might want to + do, if, for example, your Perl program calls a C routine that will + potentially run for a long time and for which you want to set a + timeout. + + This module therefore allows you to define UNSAFE_SIGNALS blocks in + which signals will be handled "unsafely". + + Note that, no matter how short you make the unsafe block, it will still + be unsafe. Use with caution.""" + + homepage = "https://metacpan.org/pod/Perl::Unsafe::Signals" + url = "https://cpan.metacpan.org/authors/id/R/RG/RGARCIA/Perl-Unsafe-Signals-0.03.tar.gz" + + version('0.03', sha256='d311ae7d73e8d0c2346dfacb82aa952322e70cd928b09d502d739e60e35f829d') diff --git a/var/spack/repos/builtin/packages/perl-set-scalar/package.py b/var/spack/repos/builtin/packages/perl-set-scalar/package.py new file mode 100644 index 00000000000..9ea860541e4 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-set-scalar/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlSetScalar(PerlPackage): + """Set::Scalar - basic set operations""" + + homepage = "https://metacpan.org/pod/Set::Scalar" + url = "https://cpan.metacpan.org/authors/id/D/DA/DAVIDO/Set-Scalar-1.29.tar.gz" + + version('1.29', sha256='a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d') diff --git a/var/spack/repos/builtin/packages/perl-sys-sigaction/package.py b/var/spack/repos/builtin/packages/perl-sys-sigaction/package.py new file mode 100644 index 00000000000..50118db5489 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-sys-sigaction/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlSysSigaction(PerlPackage): + """Prior to version 5.8.0 perl implemented 'unsafe' signal handling. The + reason it is consider unsafe, is that there is a risk that a signal will + arrive, and be handled while perl is changing internal data structures. + This can result in all kinds of subtle and not so subtle problems. For this + reason it has always been recommended that one do as little as possible in + a signal handler, and only variables that already exist be manipulated. + + Perl 5.8.0 and later versions implements 'safe' signal handling on + platforms which support the POSIX sigaction() function. This is + accomplished by having perl note that a signal has arrived, but deferring + the execution of the signal handler until such time as it is safe to do so. + Unfortunately these changes can break some existing scripts, if they + depended on a system routine being interrupted by the signal's arrival. The + perl 5.8.0 implementation was modified further in version 5.8.2""" + + homepage = "https://metacpan.org/pod/Sys::SigAction" + url = "https://cpan.metacpan.org/authors/id/L/LB/LBAXTER/Sys-SigAction-0.23.tar.gz" + + version('0.23', sha256='c4ef6c9345534031fcbbe2adc347fc7194d47afc945e7a44fac7e9563095d353') diff --git a/var/spack/repos/builtin/packages/perl-term-readkey/package.py b/var/spack/repos/builtin/packages/perl-term-readkey/package.py index d672cf6f5bd..93317e3bf78 100644 --- a/var/spack/repos/builtin/packages/perl-term-readkey/package.py +++ b/var/spack/repos/builtin/packages/perl-term-readkey/package.py @@ -18,4 +18,5 @@ class PerlTermReadkey(PerlPackage): homepage = "http://search.cpan.org/perldoc/Term::ReadKey" url = "http://www.cpan.org/authors/id/J/JS/JSTOWE/TermReadKey-2.37.tar.gz" + version('2.38', sha256='5a645878dc570ac33661581fbb090ff24ebce17d43ea53fd22e105a856a47290') version('2.37', 'e8ea15c16333ac4f8d146d702e83cc0c') diff --git a/var/spack/repos/builtin/packages/perl-timedate/package.py b/var/spack/repos/builtin/packages/perl-timedate/package.py new file mode 100644 index 00000000000..b887ce85133 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-timedate/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlTimedate(PerlPackage): + """The parser contained here will only parse absolute dates, if you want a + date parser that can parse relative dates then take a look at the Time + modules by David Muir on CPAN.""" + + homepage = "https://metacpan.org/release/TimeDate" + url = "https://cpan.metacpan.org/authors/id/G/GB/GBARR/TimeDate-2.30.tar.gz" + + version('2.30', sha256='75bd254871cb5853a6aa0403ac0be270cdd75c9d1b6639f18ecba63c15298e86') diff --git a/var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py b/var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py new file mode 100644 index 00000000000..0227d4e5097 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlDomXpath(PerlPackage): + """XML::DOM::XPath allows you to use XML::XPath methods to query a DOM. + This is often much easier than relying only on getElementsByTagName.""" + + homepage = "https://metacpan.org/pod/XML::DOM::XPath" + url = "https://cpan.metacpan.org/authors/id/M/MI/MIROD/XML-DOM-XPath-0.14.tar.gz" + + version('0.14', sha256='0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea') + + depends_on('perl-xml-dom', type=('build', 'run')) + depends_on('perl-xml-xpathengine', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-dom/package.py b/var/spack/repos/builtin/packages/perl-xml-dom/package.py new file mode 100644 index 00000000000..e0c3d97d11c --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-dom/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlDom(PerlPackage): + """This module extends the XML::Parser module by Clark Cooper. The + XML::Parser module is built on top of XML::Parser::Expat, which is a lower + level interface to James Clark's expat library.""" + + homepage = "https://metacpan.org/pod/XML::DOM" + url = "https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/XML-DOM-1.46.tar.gz" + + version('1.46', sha256='8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e') + + depends_on('perl-xml-parser', type=('build', 'run')) + depends_on('perl-xml-regexp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) + depends_on('perl-libxml-perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py b/var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py new file mode 100644 index 00000000000..59950576f03 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlFilterBuffertext(PerlPackage): + """This is a very simple filter. One common cause of grief (and programmer + error) is that XML parsers aren't required to provide character events in + one chunk. They can, but are not forced to, and most don't. This filter + does the trivial but oft-repeated task of putting all characters into a + single event.""" + + homepage = "https://metacpan.org/pod/XML::Filter::BufferText" + url = "https://cpan.metacpan.org/authors/id/R/RB/RBERJON/XML-Filter-BufferText-1.01.tar.gz" + + version('1.01', sha256='8fd2126d3beec554df852919f4739e689202cbba6a17506e9b66ea165841a75c') diff --git a/var/spack/repos/builtin/packages/perl-xml-libxml/package.py b/var/spack/repos/builtin/packages/perl-xml-libxml/package.py new file mode 100644 index 00000000000..bc6d4f4c05b --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-libxml/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlLibxml(PerlPackage): + """This module is an interface to libxml2, providing XML and HTML parsers + with DOM, SAX and XMLReader interfaces, a large subset of DOM Layer 3 + interface and a XML::XPath-like interface to XPath API of libxml2. The + module is split into several packages which are not described in this + section; unless stated otherwise, you only need to use XML::LibXML; in your + programs.""" + + homepage = "https://metacpan.org/pod/XML::LibXML" + url = "https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/XML-LibXML-2.0201.tar.gz" + + version('2.0201', sha256='e008700732502b3f1f0890696ec6e2dc70abf526cd710efd9ab7675cae199bc2') + + depends_on('libxml2') + depends_on('perl-xml-namespacesupport', type=('build', 'run')) + depends_on('perl-xml-sax', type=('build', 'run')) + depends_on('perl-xml-sax-base', type=('build', 'run')) + depends_on('perl-alien-libxml2', type='build') diff --git a/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py new file mode 100644 index 00000000000..cb7e58bcd11 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlNamespacesupport(PerlPackage): + """This module offers a simple to process namespaced XML names (unames) + from within any application that may need them. It also helps maintain a + prefix to namespace URI map, and provides a number of basic checks.""" + + homepage = "https://metacpan.org/pod/XML::NamespaceSupport" + url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-NamespaceSupport-1.12.tar.gz" + + version('1.12_9', sha256='2e84a057f0a8c845a612d212742cb94fca4fc8a433150b5721bd448f77d1e4a9') diff --git a/var/spack/repos/builtin/packages/perl-xml-quote/package.py b/var/spack/repos/builtin/packages/perl-xml-quote/package.py new file mode 100644 index 00000000000..2c6702225e2 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-quote/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlQuote(PerlPackage): + """This module provides functions to quote/dequote strings in "xml"-way. + + All functions are written in XS and are very fast; they correctly process + utf8, tied, overloaded variables and all the rest of perl "magic".""" + + homepage = "https://metacpan.org/pod/XML::Quote" + url = "https://cpan.metacpan.org/authors/id/G/GD/GDSL/XML-Quote-1.02.tar.gz" + + version('1.02', sha256='4705b86a8dcc002bffc6ff154ec5c55f0bfb6e99a3f744d1e77ae6541c6af228') diff --git a/var/spack/repos/builtin/packages/perl-xml-regexp/package.py b/var/spack/repos/builtin/packages/perl-xml-regexp/package.py new file mode 100644 index 00000000000..30ecb45a676 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-regexp/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlRegexp(PerlPackage): + """This package contains regular expressions for the following XML tokens: + BaseChar, Ideographic, Letter, Digit, Extender, CombiningChar, + NameChar, EntityRef, CharRef, Reference, Name, NmToken, and + AttValue.""" + + homepage = "https://metacpan.org/pod/XML::RegExp" + url = "https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/XML-RegExp-0.04.tar.gz" + + version('0.04', sha256='df1990096036085c8e2d45904fe180f82bfed40f1a7e05243f334ea10090fc54') diff --git a/var/spack/repos/builtin/packages/perl-xml-sax-base/package.py b/var/spack/repos/builtin/packages/perl-xml-sax-base/package.py new file mode 100644 index 00000000000..b9943e6d0d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-sax-base/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlSaxBase(PerlPackage): + """This module has a very simple task - to be a base class for PerlSAX + drivers and filters. It's default behaviour is to pass the input directly + to the output unchanged. It can be useful to use this module as a base + class so you don't have to, for example, implement the characters() + callback.""" + + homepage = "https://metacpan.org/pod/XML::SAX::Base" + url = "https://cpan.metacpan.org/authors/id/G/GR/GRANTM/XML-SAX-Base-1.09.tar.gz" + + version('1.09', sha256='66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0') diff --git a/var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py b/var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py new file mode 100644 index 00000000000..6de6611f09d --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlSaxWriter(PerlPackage): + """A new XML Writer was needed to match the SAX2 effort because quite + naturally no existing writer understood SAX2. My first intention had been + to start patching XML::Handler::YAWriter as it had previously been my + favourite writer in the SAX1 world.""" + + homepage = "https://metacpan.org/pod/XML::SAX::Writer" + url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-SAX-Writer-0.57.tar.gz" + + version('0.57', sha256='3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0') + + depends_on('perl-xml-filter-buffertext', type=('build', 'run')) + depends_on('perl-xml-namespacesupport', type=('build', 'run')) + depends_on('perl-xml-sax-base', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-sax/package.py b/var/spack/repos/builtin/packages/perl-xml-sax/package.py new file mode 100644 index 00000000000..78138fca659 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-sax/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlSax(PerlPackage): + """XML::SAX is a SAX parser access API for Perl. It includes classes and + APIs required for implementing SAX drivers, along with a factory class for + returning any SAX parser installed on the user's system.""" + + homepage = "https://metacpan.org/pod/XML::SAX" + url = "https://cpan.metacpan.org/authors/id/G/GR/GRANTM/XML-SAX-1.02.tar.gz" + + version('1.02', sha256='4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a') + + depends_on('perl-xml-namespacesupport', type=('build', 'run')) + depends_on('perl-xml-sax-base', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-twig/non_interactive.patch b/var/spack/repos/builtin/packages/perl-xml-twig/non_interactive.patch new file mode 100644 index 00000000000..0c246215e79 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-twig/non_interactive.patch @@ -0,0 +1,27 @@ +--- a/Makefile.PL 2016-06-21 05:50:27.000000000 -0500 ++++ b/Makefile.PL 2019-09-16 10:51:28.436352022 -0500 +@@ -15,23 +15,7 @@ + + my $opt= $ARGV[0] ? $ARGV[0] : ''; + +-if( $opt eq "-n") +- { @programs=(); } +-elsif( $opt eq "-y") +- { @programs= map { $_->[0] } @prompts; } +-elsif( $opt eq "-d") +- { @programs= map { $_->[0] if( $_->[1] eq 'y') } @prompts; } +-elsif( $ENV{AUTOMATED_TESTING} || $ENV{NONINTERACTIVE_TESTING}) +- { @programs=(); } +-else +- { print "run 'perl Makefile.PL -y' to install all tools,\n", +- " 'perl Makefile.PL -n' to skip installation\n"; +- foreach my $prompt (@prompts) +- { my ($program, $default, $description) = @$prompt; +- if( prompt("Do you want to install '$program' ($description)?", $default) =~ /^y/i) +- { push(@programs, $program); } +- } +- } ++@programs= map { $_->[0] } @prompts; + + MyWriteMakefile( + META_MERGE => { diff --git a/var/spack/repos/builtin/packages/perl-xml-twig/package.py b/var/spack/repos/builtin/packages/perl-xml-twig/package.py new file mode 100644 index 00000000000..e2c81fef041 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-twig/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlTwig(PerlPackage): + """This module provides a way to process XML documents. It is build on top + of XML::Parser. + + The module offers a tree interface to the document, while allowing you to + output the parts of it that have been completely processed. + + It allows minimal resource (CPU and memory) usage by building the tree only + for the parts of the documents that need actual processing, through the use + of the twig_roots and twig_print_outside_roots options. The finish and + finish_print methods also help to increase performances. + + XML::Twig tries to make simple things easy so it tries its best to takes + care of a lot of the (usually) annoying (but sometimes necessary) features + that come with XML and XML::Parser.""" + + homepage = "https://metacpan.org/pod/XML::Twig" + url = "https://cpan.metacpan.org/authors/id/M/MI/MIROD/XML-Twig-3.52.tar.gz" + + version('3.52', sha256='fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad') + + depends_on('perl-xml-parser', type=('build', 'run')) + + patch('non_interactive.patch') diff --git a/var/spack/repos/builtin/packages/perl-xml-writer/package.py b/var/spack/repos/builtin/packages/perl-xml-writer/package.py new file mode 100644 index 00000000000..29c39ca8f2d --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-writer/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlWriter(PerlPackage): + """XML::Writer is a helper module for Perl programs that write an XML + document. The module handles all escaping for attribute values and + character data and constructs different types of markup, such as tags, + comments, and processing instructions. + + By default, the module performs several well-formedness checks to catch + errors during output. This behaviour can be extremely useful during + development and debugging, but it can be turned off for production-grade + code. + + The module can operate either in regular mode in or Namespace processing + mode. In Namespace mode, the module will generate Namespace Declarations + itself, and will perform additional checks on the output.""" + + homepage = "https://metacpan.org/pod/XML::Writer" + url = "https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW/XML-Writer-0.625.tar.gz" + + version('0.625', sha256='e080522c6ce050397af482665f3965a93c5d16f5e81d93f6e2fe98084ed15fbe') diff --git a/var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py b/var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py new file mode 100644 index 00000000000..241d806d6cc --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PerlXmlXpathengine(PerlPackage): + """This module provides an XPath engine, that can be re-used by other + module/classes that implement trees.""" + + homepage = "https://metacpan.org/pod/XML::XPathEngine" + url = "https://cpan.metacpan.org/authors/id/M/MI/MIROD/XML-XPathEngine-0.14.tar.gz" + + version('0.14', sha256='d2fe7bcbbd0beba1444f4a733401e7b8aa5282fad4266d42735dd74582b2e264') From 61d41eea7f913f9beb8128e5191697aad1734c07 Mon Sep 17 00:00:00 2001 From: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com> Date: Fri, 27 Sep 2019 19:02:34 -0500 Subject: [PATCH 045/499] New package: libibumad (#12886) --- .../builtin/packages/libibumad/package.py | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 var/spack/repos/builtin/packages/libibumad/package.py diff --git a/var/spack/repos/builtin/packages/libibumad/package.py b/var/spack/repos/builtin/packages/libibumad/package.py new file mode 100644 index 00000000000..4d5a6836776 --- /dev/null +++ b/var/spack/repos/builtin/packages/libibumad/package.py @@ -0,0 +1,27 @@ + +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libibumad(CMakePackage): + """This package installs the user-space libraries and headers for libibumad. + This is a subset of the linux-rdma distribution.""" + + homepage = "https://github.com/linux-rdma/" + url = "https://github.com/linux-rdma/rdma-core/archive/v25.0.tar.gz" + + version('25.0', sha256='d735bd091d13e8a68ce650e432b5bdc934fc7f1d5fb42a6045278a5b3f7fe48b') + + depends_on('libnl') + + def build(self, spec, prefix): + with working_dir(join_path(self.build_directory, 'libibumad')): + make() + + def install(self, spec, prefix): + with working_dir(join_path(self.build_directory, 'libibumad')): + make('install') From b4c28182dcd27639eaa5233334427fd416d9e674 Mon Sep 17 00:00:00 2001 From: Kevin Huck Date: Fri, 27 Sep 2019 17:16:44 -0700 Subject: [PATCH 046/499] Tau package: turn off unsupported variants by default on OSX (#12890) --- var/spack/repos/builtin/packages/tau/package.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py index 131d5657163..0cfd580a7b8 100644 --- a/var/spack/repos/builtin/packages/tau/package.py +++ b/var/spack/repos/builtin/packages/tau/package.py @@ -8,6 +8,7 @@ import fnmatch import glob import platform +import sys from llnl.util.filesystem import join_path @@ -38,16 +39,21 @@ class Tau(Package): version('2.24', '57ce33539c187f2e5ec68f0367c76db4') version('2.23.1', '6593b47ae1e7a838e632652f0426fe72') + # Disable some default dependencies on Darwin/OSX + darwin_default = False + if sys.platform != 'darwin': + darwin_default = True + variant('scorep', default=False, description='Activates SCOREP support') variant('openmp', default=False, description='Use OpenMP threads') variant('pthreads', default=True, description='Use POSIX threads') variant('mpi', default=False, description='Specify use of TAU MPI wrapper library') variant('phase', default=False, description='Generate phase based profiles') - variant('papi', default=True, description='Activates Performance API') + variant('papi', default=darwin_default, description='Activates Performance API') variant('binutils', default=True, description='Activates support of BFD GNU Binutils') - variant('libdwarf', default=True, description='Activates support of libdwarf') - variant('libelf', default=True, description='Activates support of libelf') - variant('libunwind', default=True, description='Activates support of libunwind') + variant('libdwarf', default=darwin_default, description='Activates support of libdwarf') + variant('libelf', default=darwin_default, description='Activates support of libelf') + variant('libunwind', default=darwin_default, description='Activates support of libunwind') variant('otf2', default=True, description='Activates support of Open Trace Format (OTF)') variant('pdt', default=True, description='Use PDT for source code instrumentation') variant('comm', default=False, description=' Generate profiles with MPI communicator info') @@ -58,7 +64,7 @@ class Tau(Package): variant('shmem', default=False, description='Activates SHMEM support') variant('gasnet', default=False, description='Activates GASNET support') variant('cuda', default=False, description='Activates CUDA support') - variant('fortran', default=True, description='Activates Fortran support') + variant('fortran', default=darwin_default, description='Activates Fortran support') variant('io', default=True, description='Activates POSIX I/O support') # Support cross compiling. From c49c37af9b3664e6807169ede5dfb4ecd03643ab Mon Sep 17 00:00:00 2001 From: Ross Miller Date: Fri, 27 Sep 2019 20:19:36 -0400 Subject: [PATCH 047/499] py-adios package: restrict python dependency to <=3.6.x (#12932) The adios code (currently) won't compile against the Python 3.7 C API. This change adds a dependency on 3.6 or less. --- var/spack/repos/builtin/packages/py-adios/package.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/var/spack/repos/builtin/packages/py-adios/package.py b/var/spack/repos/builtin/packages/py-adios/package.py index a297f39fc9d..2149c0e2236 100644 --- a/var/spack/repos/builtin/packages/py-adios/package.py +++ b/var/spack/repos/builtin/packages/py-adios/package.py @@ -35,6 +35,14 @@ class PyAdios(PythonPackage): when='@{0} +mpi'.format(v), type=['build', 'link', 'run']) + # NOTE: this dependency is a work-around for a bug in Adios itself. + # Specifically, Adios uses code that was generated by Cython 0.28.2. + # This code won't compile against the Python 3.7 C API. + # See https://github.com/ornladios/ADIOS/issues/202 and + # the first entry under "Bug Fixes" at + # https://github.com/cython/cython/blob/0.29.x/CHANGES.rst + depends_on('python@:3.6') + depends_on('py-numpy', type=['build', 'run']) depends_on('mpi', when='+mpi') depends_on('py-mpi4py', type=['run'], when='+mpi') From 8db94bcc86b889959bc93f43dd136a3b53dd3594 Mon Sep 17 00:00:00 2001 From: "Daryl W. Grunau" Date: Fri, 27 Sep 2019 18:28:38 -0600 Subject: [PATCH 048/499] eospac: laws.lanl.gov -> laws-green.lanl.gov (#12970) --- .../repos/builtin/packages/eospac/package.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/eospac/package.py b/var/spack/repos/builtin/packages/eospac/package.py index a1c0c41a2ac..4399ef60398 100644 --- a/var/spack/repos/builtin/packages/eospac/package.py +++ b/var/spack/repos/builtin/packages/eospac/package.py @@ -12,21 +12,21 @@ class Eospac(Package): library. """ - homepage = "https://laws.lanl.gov/projects/data/eos.html" - list_url = "https://laws.lanl.gov/projects/data/eos/eospacReleases.php" + homepage = "http://laws-green.lanl.gov/projects/data/eos.html" + list_url = "http://laws-green.lanl.gov/projects/data/eos/eospacReleases.php" version('6.4.0', sha256='15a953beac735c68431afe86ffe33323d540d0fbbbec03ba79438dd29736051d', - url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0_612ea8c9b8ffa6d9175d9118955571d9107f1e3c.tgz") + url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0_612ea8c9b8ffa6d9175d9118955571d9107f1e3c.tgz") version('6.4.0beta.4', sha256='0ebfd8badff575ea77444aa978629dbdca3135a0b5eb373b8daba058773d4635', - url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.4_aff6429bb6868de31a980278bafa13487c2ce83f.tgz") + url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.4_aff6429bb6868de31a980278bafa13487c2ce83f.tgz") version('6.4.0beta.3', sha256='9f387ca5356519494c6f3f27adb0c165cf9f9e15e3355a67bf940a4a92eebdab', - url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.3_90ff265f62aa1780bfcd0a62dad807b6be6ed461.tgz") + url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.3_90ff265f62aa1780bfcd0a62dad807b6be6ed461.tgz") version('6.4.0beta.2', sha256='f9db46cd6c62a6f83960d802350f3e37675921af102969b293c02eb797558a53', - url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.2_69196eadbc77506561eef711f19d2f03b4ab0ffa.tgz") + url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.2_69196eadbc77506561eef711f19d2f03b4ab0ffa.tgz") version('6.4.0beta.1', sha256='14c5c804e5f628f41e8ed80bcee5a80adeb6c6f3d130715421ca99a30c7eb7e2', - url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz") + url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz") version('6.3.1', sha256='aa1112c4251c9c3c2883a7ab2c7f2abff2c339f29dbbf8421ef88b0c9df904f8', preferred=True, - url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.3.1_r20161202150449.tgz") + url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.3.1_r20161202150449.tgz") # This patch allows the use of spack's compile wrapper 'flang' patch('flang.patch', when='@:6.4.0beta.2%clang') From 3776eccc4b3ed9cc8dfe493954ef0472f56bb98e Mon Sep 17 00:00:00 2001 From: Shintaro Iwasaki Date: Sat, 28 Sep 2019 13:27:33 -0500 Subject: [PATCH 049/499] bolt: add a new version, 1.0rc2 (#12966) --- var/spack/repos/builtin/packages/bolt/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/bolt/package.py b/var/spack/repos/builtin/packages/bolt/package.py index 4ac3eac7b2a..1b0fa8106ec 100644 --- a/var/spack/repos/builtin/packages/bolt/package.py +++ b/var/spack/repos/builtin/packages/bolt/package.py @@ -22,6 +22,7 @@ class Bolt(CMakePackage): git = "https://github.com/pmodels/bolt.git" version("master", branch="master") + version("1.0rc2", "f5ca4f9fb05d6e4edbbd32635828c833") version("1.0rc1", "77733ba2ad9440c29b36d1c1411a9793") version("1.0b1", "df76beb3a7f13ae2dcaf9ab099eea87b") From 86a85b7eb22ccf69489a4bfbd947da7dfedcf233 Mon Sep 17 00:00:00 2001 From: Patrick Schratz Date: Sat, 28 Sep 2019 20:28:27 +0200 Subject: [PATCH 050/499] update neovim (#12965) --- var/spack/repos/builtin/packages/neovim/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/neovim/package.py b/var/spack/repos/builtin/packages/neovim/package.py index db398f5a2a9..4f676c62249 100644 --- a/var/spack/repos/builtin/packages/neovim/package.py +++ b/var/spack/repos/builtin/packages/neovim/package.py @@ -11,8 +11,9 @@ class Neovim(CMakePackage): """NeoVim: the future of vim""" homepage = "http://neovim.io" - url = "https://github.com/neovim/neovim/archive/v0.3.4.tar.gz" + url = "https://github.com/neovim/neovim/archive/v0.4.2.tar.gz" + version('0.4.2', sha256='9f874d3d2a74f33b931db62adebe28f8d2ec116270d1e13998b58a73348b6e56') version('0.3.4', sha256='a641108bdebfaf319844ed46b1bf35d6f7c30ef5aeadeb29ba06e19c3274bc0e') version('0.3.1', '5405bced1c929ebc245c75409cd6c7ef') version('0.3.0', 'e5fdb2025757c337c17449c296eddf5b') From 7e9365036f81391abce15f47186e58ae31aadfd6 Mon Sep 17 00:00:00 2001 From: Jaroslav Hron Date: Sat, 28 Sep 2019 20:39:45 +0200 Subject: [PATCH 051/499] correct with-xxx-lib= options (#12964) --- var/spack/repos/builtin/packages/petsc/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 1b5f0de1865..3bdee89feb1 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -316,7 +316,7 @@ def install(self, spec, prefix): if 'zlib' in spec: options.extend([ '--with-zlib-include=%s' % spec['zlib'].prefix.include, - '--with-zlib-lib=%s' % spec['zlib'].libs.ld_flags, + '--with-zlib-lib=%s' % spec['zlib'].libs.joined(), '--with-zlib=1' ]) else: From 4cebc68f064838393efe9928d867a0e3d1547542 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Sat, 28 Sep 2019 20:41:57 +0200 Subject: [PATCH 052/499] vdt: simplified recipe by removing SIMD variants (#12954) Now the support for SSE3 or AVX is tested on the selected target --- .../repos/builtin/packages/vdt/package.py | 63 +++---------------- 1 file changed, 8 insertions(+), 55 deletions(-) diff --git a/var/spack/repos/builtin/packages/vdt/package.py b/var/spack/repos/builtin/packages/vdt/package.py index b64452328f1..7341ec92d78 100644 --- a/var/spack/repos/builtin/packages/vdt/package.py +++ b/var/spack/repos/builtin/packages/vdt/package.py @@ -3,16 +3,14 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * -from spack.spec import ConflictsInSpecError - class Vdt(CMakePackage): """Vectorised math. A collection of fast and inline implementations of - mathematical functions.""" + mathematical functions. + """ homepage = "https://github.com/dpiparo/vdt" - url = "https://github.com/dpiparo/vdt/archive/v0.3.9.tar.gz" + url = "https://github.com/dpiparo/vdt/archive/v0.3.9.tar.gz" version('0.4.3', sha256='705674612ebb5c182b65a8f61f4d173eb7fe7cdeee2235b402541a492e08ace1') version('0.3.9', '80a2d73a82f7ef8257a8206ca22dd145') @@ -20,50 +18,6 @@ class Vdt(CMakePackage): version('0.3.7', 'd2621d4c489894fd1fe8e056d9a0a67c') version('0.3.6', '6eaff3bbbd5175332ccbd66cd71a741d') - simd_x86 = ('sse', 'avx', 'avx2', 'fma') - simd_all = ('sse', 'avx', 'avx2', 'fma', 'neon') - variant( - 'simd', - default='None', - values=simd_all, - description='USE simd instruction set', - multi=True - ) - - def flag_handler(self, name, flags): - arch = '' - spec = self.spec - if spec.satisfies("platform=cray"): - # FIXME; It is assumed that cray is x86_64. - # If you support arm on cray, you need to fix it. - arch = 'x86_64' - if arch != 'x86_64' and not spec.satisfies("target=x86_64:"): - for s in self.simd_x86: - if (spec.satisfies("simd={0}".format(s))): - raise ConflictsInSpecError( - spec, - [( - spec, - spec.architecture.target, - spec.variants['simd'], - 'simd=sse,avx,avx2 and fma are valid' - ' only on x86_64' - )] - ) - # FIXME: It is assumed that arm 32 bit target is arm. - if arch != 'arm' and not spec.satisfies("target=arm"): - if spec.satisfies("simd=neon"): - raise ConflictsInSpecError( - spec, - [( - spec, - spec.architecture.target, - spec.variants['simd'], - 'simd=neon is valid only on arm 32 bit' - )] - ) - return (flags, None, None) - @property def build_directory(self): d = join_path(self.stage.path, 'spack-build') @@ -73,10 +27,9 @@ def build_directory(self): def cmake_args(self): options = [] - - for s in self.simd_all: - options.append( - "-D{0}=".format(s.upper()) + - ("ON" if (s in self.spec.variants['simd'].value) else "OFF") - ) + for simd_feature in ('sse', 'avx', 'avx2', 'fma', 'neon'): + options.append("-D{0}={1}".format( + simd_feature.upper(), + "ON" if simd_feature in self.spec.target else "OFF" + )) return options From c065c25a4ccb2e29f56d7b5c534e615cec531135 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Sun, 29 Sep 2019 03:44:02 +0900 Subject: [PATCH 053/499] bowtie: fix for aarch64, and bugfix about c++11-narrowing. (#12953) --- .../packages/bowtie/fix_narrowing_err.patch | 11 +++ .../builtin/packages/bowtie/for_aarch64.patch | 68 +++++++++++++++++++ .../repos/builtin/packages/bowtie/package.py | 7 ++ 3 files changed, 86 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bowtie/fix_narrowing_err.patch create mode 100644 var/spack/repos/builtin/packages/bowtie/for_aarch64.patch diff --git a/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err.patch b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err.patch new file mode 100644 index 00000000000..ca4895dff08 --- /dev/null +++ b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err.patch @@ -0,0 +1,11 @@ +--- bowtie-1.2.3.org/alphabet.cpp 2019-09-26 12:14:35.508558749 +0900 ++++ bowtie-1.2.3/alphabet.cpp 2019-09-26 14:15:56.960009461 +0900 +@@ -274,7 +274,7 @@ + const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn"; + + char mask2iupac[16] = { +- -1, ++ static_cast(-1), + 'A', // 0001 + 'C', // 0010 + 'M', // 0011 diff --git a/var/spack/repos/builtin/packages/bowtie/for_aarch64.patch b/var/spack/repos/builtin/packages/bowtie/for_aarch64.patch new file mode 100644 index 00000000000..4dafbaaf20d --- /dev/null +++ b/var/spack/repos/builtin/packages/bowtie/for_aarch64.patch @@ -0,0 +1,68 @@ +diff -ur bowtie-1.2.3.org/Makefile bowtie-1.2.3/Makefile +--- bowtie-1.2.3.org/Makefile 2019-09-26 12:14:35.498557693 +0900 ++++ bowtie-1.2.3/Makefile 2019-09-26 12:15:17.262960932 +0900 +@@ -174,14 +174,22 @@ + ifeq (x86_64, $(shell uname -p)) + BITS=64 + endif ++ ifeq (aarch64, $(shell uname -p)) ++ BITS=64 ++ endif + endif + + ifeq (32,$(BITS)) + $(error bowtie2 compilation requires a 64-bit platform ) + endif + +-DEBUG_FLAGS = -O0 -g3 -m64 +-RELEASE_FLAGS = -O3 -m64 ++ifeq (aarch64, $(shell uname -p)) ++ DEBUG_FLAGS = -O0 -g3 ++ RELEASE_FLAGS = -O3 ++else ++ DEBUG_FLAGS = -O0 -g3 -m64 ++ RELEASE_FLAGS = -O3 -m64 ++endif + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE + +diff -ur bowtie-1.2.3.org/ebwt.h bowtie-1.2.3/ebwt.h +--- bowtie-1.2.3.org/ebwt.h 2019-09-26 12:14:35.518559804 +0900 ++++ bowtie-1.2.3/ebwt.h 2019-09-26 14:13:12.142637470 +0900 +@@ -1957,7 +1957,11 @@ + struct USE_POPCNT_INSTRUCTION { + inline static int pop64(uint64_t x) { + int64_t count; ++#ifdef __aarch64__ ++ count = __builtin_popcount(x); ++#else + asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x)); ++#endif + return count; + } + }; +diff -ur bowtie-1.2.3.org/third_party/cpuid.h bowtie-1.2.3/third_party/cpuid.h +--- bowtie-1.2.3.org/third_party/cpuid.h 2019-09-26 12:14:35.548562971 +0900 ++++ bowtie-1.2.3/third_party/cpuid.h 2019-09-26 12:17:41.677842567 +0900 +@@ -65,6 +65,7 @@ + #define bit_FSGSBASE (1 << 0) + #define bit_BMI (1 << 3) + ++#ifndef __aarch64__ + #if defined(__i386__) && defined(__PIC__) + /* %ebx may be the PIC register. */ + #if __GNUC__ >= 3 +@@ -185,3 +186,13 @@ + __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); + return 1; + } ++#endif ++#ifdef __aarch64__ ++static __inline int ++__get_cpuid (unsigned int __level, ++ unsigned int *__eax, unsigned int *__ebx, ++ unsigned int *__ecx, unsigned int *__edx) ++{ ++ return 1; ++} ++#endif diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py index 50c02c9825f..c89f8f4081a 100644 --- a/var/spack/repos/builtin/packages/bowtie/package.py +++ b/var/spack/repos/builtin/packages/bowtie/package.py @@ -45,6 +45,13 @@ class Bowtie(MakefilePackage): # https://svnweb.freebsd.org/ports?view=revision&revision=483954 patch('issue-87.patch', when='@:1.2.2 %gcc@8.0.0:') + # correspond to 'aarch64' architecture + # reference: https://github.com/BenLangmead/bowtie/pull/13 + patch('for_aarch64.patch', when='target=aarch64:') + + # measures for narrowing error + patch('fix_narrowing_err.patch') + def edit(self, spec, prefix): makefile = FileFilter('Makefile') makefile.filter('CC = .*', 'CC = ' + env['CC']) From 467261803fc32750e48b6e7357788d11488152c6 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Sat, 28 Sep 2019 20:45:01 +0200 Subject: [PATCH 054/499] raxml: simplified recipe by removing SIMD variants (#12952) Now the support for SSE3 or AVX is tested on the selected target --- .../repos/builtin/packages/raxml/package.py | 58 ++++--------------- 1 file changed, 12 insertions(+), 46 deletions(-) diff --git a/var/spack/repos/builtin/packages/raxml/package.py b/var/spack/repos/builtin/packages/raxml/package.py index 528172733dc..84a63fbd2cb 100644 --- a/var/spack/repos/builtin/packages/raxml/package.py +++ b/var/spack/repos/builtin/packages/raxml/package.py @@ -2,26 +2,22 @@ # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * -from spack.spec import ConflictsInSpecError import glob class Raxml(Package): """RAxML (Randomized Axelerated Maximum Likelihood) is a program for - sequential and parallel Maximum Likelihood based inference of large - phylogenetic trees.""" + sequential and parallel Maximum Likelihood based inference of large + phylogenetic trees. + """ homepage = "https://sco.h-its.org/exelixis/web/software/raxml" - url = "https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz" + url = "https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz" version('8.2.11', '6bd5c4e1f93003ccf13c9b59a5d080ab') variant('mpi', default=True, description='Enable MPI parallel support') variant('pthreads', default=False, description='Enable pthreads version') - variant('sse', default=False, description='Enable SSE in order to substantially speed up execution') - variant('avx', default=False, description='Enable AVX in order to substantially speed up execution') depends_on('mpi', when='+mpi') @@ -38,36 +34,6 @@ class Raxml(Package): # can't build multiple binaries in parallel without things breaking parallel = False - def flag_handler(self, name, flags): - arch = '' - spec = self.spec - if spec.satisfies("platform=cray"): - # FIXME; It is assumed that cray is x86_64. - # If you support arm on cray, you need to fix it. - arch = 'x86_64' - if arch != 'x86_64' and not spec.target.family == 'x86_64': - if spec.satisfies("+sse"): - raise ConflictsInSpecError( - spec, - [( - spec, - spec.architecture.target, - spec.variants['sse'], - '+sse is valid only on x86_64' - )] - ) - if spec.satisfies("+avx"): - raise ConflictsInSpecError( - spec, - [( - spec, - spec.architecture.target, - spec.variants['avx'], - '+avx is valid only on x86_64' - )] - ) - return (flags, None, None) - def install(self, spec, prefix): mkdirp(prefix.bin) files = glob.iglob("Makefile.*") @@ -78,11 +44,11 @@ def install(self, spec, prefix): makefile.filter('mpicc', self.spec['mpi'].mpicc) if spec.target.family == 'x86_64': - if spec.satisfies('+mpi +avx +pthreads'): + if spec.satisfies('+mpi +pthreads') and 'avx' in spec.target: make('-f', 'Makefile.AVX.HYBRID.gcc') install('raxmlHPC-HYBRID-AVX', prefix.bin) - if spec.satisfies('+mpi +sse +pthreads'): + if spec.satisfies('+mpi +pthreads') and 'sse3' in spec.target: make('-f', 'Makefile.SSE3.HYBRID.gcc') install('raxmlHPC-HYBRID-SSE3', prefix.bin) @@ -90,11 +56,11 @@ def install(self, spec, prefix): make('-f', 'Makefile.HYBRID.gcc') install('raxmlHPC-HYBRID', prefix.bin) - if spec.satisfies('+mpi +avx'): + if spec.satisfies('+mpi') and 'avx' in spec.target: make('-f', 'Makefile.AVX.MPI.gcc') install('raxmlHPC-MPI-AVX', prefix.bin) - if spec.satisfies('+mpi +sse'): + if spec.satisfies('+mpi') and 'sse3' in spec.target: make('-f', 'Makefile.SSE3.MPI.gcc') install('raxmlHPC-MPI-SSE3', prefix.bin) @@ -102,11 +68,11 @@ def install(self, spec, prefix): make('-f', 'Makefile.MPI.gcc') install('raxmlHPC-MPI', prefix.bin) - if spec.satisfies('+pthreads +avx'): + if spec.satisfies('+pthreads') and 'avx' in spec.target: make('-f', 'Makefile.AVX.PTHREADS.gcc') install('raxmlHPC-PTHREADS-AVX', prefix.bin) - if spec.satisfies('+pthreads +sse'): + if spec.satisfies('+pthreads') and 'sse3' in spec.target: make('-f', 'Makefile.SSE3.PTHREADS.gcc') install('raxmlHPC-PTHREADS-SSE3', prefix.bin) @@ -114,11 +80,11 @@ def install(self, spec, prefix): make('-f', 'Makefile.PTHREADS.gcc') install('raxmlHPC-PTHREADS', prefix.bin) - if spec.satisfies('+sse'): + if 'sse3' in spec.target: make('-f', 'Makefile.SSE3.gcc') install('raxmlHPC-SSE3', prefix.bin) - if spec.satisfies('+avx'): + if 'avx' in spec.target: make('-f', 'Makefile.AVX.gcc') install('raxmlHPC-AVX', prefix.bin) From 9117dfd11854d38b5ad3dda2101c6d3a9620ff98 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Sun, 29 Sep 2019 06:47:05 +0200 Subject: [PATCH 055/499] Add all the 'generic' architectures that are mentioned in recipes (#12958) LLVM, mesa and other packages check for these generic microarchitectures. One solution is to let Spack know they exist. --- .../llnl/util/cpu/microarchitectures.json | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 1ee782b408a..2e20cc98f80 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -825,6 +825,41 @@ "flags": "-march=armv8-a -mtune=generic" } } + }, + "arm": { + "from": null, + "vendor": "generic", + "features": [], + "compilers": { + } + }, + "ppc": { + "from": null, + "vendor": "generic", + "features": [], + "compilers": { + } + }, + "ppcle": { + "from": null, + "vendor": "generic", + "features": [], + "compilers": { + } + }, + "sparc": { + "from": null, + "vendor": "generic", + "features": [], + "compilers": { + } + }, + "sparc64": { + "from": null, + "vendor": "generic", + "features": [], + "compilers": { + } } }, "feature_aliases": { From c56f03a3baab7d851b555ffd6ef161747b423d74 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Sun, 29 Sep 2019 09:27:42 -0500 Subject: [PATCH 056/499] The perl-uri-escape package duplicates perl-uri (#12971) * The perl-uri-escape package duplicates perl-uri The Perl URI::Escape module is in the Perl URI package so the Spack perl-uri-escape package is a duplicate of the perl-uri package. This PR does the following: - replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')` in packages that dependend on perl-uri-escape - add the version from perl-uri-escape to perl-uri - remove the unneeded dependency from perl-uri - remove the perl-uri-escape package * Reinstated perl-test-needs dependency Put the perl-test-needs dependency for perl-uri back in but set it to type='test'. * For tests to succeed the type must be ('build', 'test') --- .../packages/perl-star-fusion/package.py | 2 +- .../packages/perl-uri-escape/package.py | 20 ------------------- .../builtin/packages/perl-uri/package.py | 3 ++- .../builtin/packages/transdecoder/package.py | 2 +- .../repos/builtin/packages/trinity/package.py | 2 +- .../repos/builtin/packages/xios/package.py | 2 +- 6 files changed, 6 insertions(+), 25 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/perl-uri-escape/package.py diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py index 762dee3c61c..ccab3095ad5 100644 --- a/var/spack/repos/builtin/packages/perl-star-fusion/package.py +++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py @@ -26,7 +26,7 @@ class PerlStarFusion(Package): depends_on('perl-intervaltree', type=('build', 'run')) depends_on('perl-dbi', type=('build', 'run')) depends_on('perl-dbfile', type=('build', 'run')) - depends_on('perl-uri-escape', type=('build', 'run')) + depends_on('perl-uri', type=('build', 'run')) def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/perl-uri-escape/package.py b/var/spack/repos/builtin/packages/perl-uri-escape/package.py deleted file mode 100644 index 2876bfb0a0d..00000000000 --- a/var/spack/repos/builtin/packages/perl-uri-escape/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PerlUriEscape(PerlPackage): - """This module provides functions to percent-encode and percent-decode URI - strings as defined by RFC 3986. Percent-encoding URI's is informally called - "URI escaping". This is the terminology used by this module, which predates - the formalization of the terms by the RFC by several years.""" - - homepage = "https://metacpan.org/pod/URI::Escape" - url = "https://cpan.metacpan.org/authors/id/E/ET/ETHER/URI-1.71.tar.gz" - - version('1.71', '247c3da29a794f72730e01aa5a715daf') - - depends_on('perl-extutils-makemaker', type='build') diff --git a/var/spack/repos/builtin/packages/perl-uri/package.py b/var/spack/repos/builtin/packages/perl-uri/package.py index bd96a33eec5..ddcb5ed5cfb 100644 --- a/var/spack/repos/builtin/packages/perl-uri/package.py +++ b/var/spack/repos/builtin/packages/perl-uri/package.py @@ -13,5 +13,6 @@ class PerlUri(PerlPackage): url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/URI-1.72.tar.gz" version('1.72', 'cd56d81ed429efaa97e7f3ff08851b48') + version('1.71', '247c3da29a794f72730e01aa5a715daf') - depends_on('perl-test-needs', type=('build', 'run')) + depends_on('perl-test-needs', type=('build', 'test')) diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py index f3b3c92541e..26cb4f8f715 100644 --- a/var/spack/repos/builtin/packages/transdecoder/package.py +++ b/var/spack/repos/builtin/packages/transdecoder/package.py @@ -20,7 +20,7 @@ class Transdecoder(MakefilePackage): url='https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz') depends_on('perl', type=('build', 'run')) - depends_on('perl-uri-escape', type='run') + depends_on('perl-uri', type='run') def install(self, spec, prefix): mkdirp(prefix.util) diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py index 4440c0ec543..3bfb35b61ee 100644 --- a/var/spack/repos/builtin/packages/trinity/package.py +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -53,7 +53,7 @@ class Trinity(MakefilePackage): depends_on("py-numpy", type="run") depends_on("express", type="run") depends_on("perl-dbfile", type="run") - depends_on("perl-uri-escape", type="run") + depends_on("perl-uri", type="run") depends_on("r-fastcluster", type="run") depends_on("r-ctc", type="run") depends_on("r-goseq", type="run") diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py index 74649095ff4..799bdc03d7c 100644 --- a/var/spack/repos/builtin/packages/xios/package.py +++ b/var/spack/repos/builtin/packages/xios/package.py @@ -37,7 +37,7 @@ class Xios(Package): depends_on('boost') depends_on('blitz') depends_on('perl', type='build') - depends_on('perl-uri-escape', type='build') + depends_on('perl-uri', type='build') depends_on('gmake', type='build') @when('%clang') From 97980a8f94e0c3f868dc071a24c299d05b017de5 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 28 Sep 2019 20:59:02 -0700 Subject: [PATCH 057/499] prefer Python 3 to Python 2 for running Spack The Python landscape is going to be changing in 2020, and Python 2 will be end of life. Spack should *prefer* Python 3 to Python 2 by default, but we still need to run on systems that only have Python2 available. This is trickier than it sounds, as on some systems, the `python` command is `python2`; on others it's `python3`, and RHEL8 doesn't even have the `python` command. Instead, it makes you choose `python3` or `python2`. You can thus no longer make a simple shebang to handle all the cases. This commit makes the `spack` script bilingual. It is still valid Python, but its shebang is `#!/bin/sh`, and it has a tiny bit of shell code at the beginning to pick the right python and execute itself with what it finds. This has a lot of advantages. I think this will help ensure that Spack works well in Python3 -- there are cases where we've missed things because Python2 is still the default `python` on most systems. Also, with this change, you do not lose the ability to execute the `spack` script directly with a python interpreter. This is useful for forcing your own version of python, running coverage tools, and running profiling tools. i.e., these will not break with this change: ```console $ python2 $(which spack) $ coverage run $(which spack) $ pyinstrument $(which spack) ``` These would not work if we split `spack` into a python file and a shell script (see #11783). So, this gives us the best of both worlds. We get to control our interpreter *and* remain a mostly pure python executable. --- bin/spack | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/bin/spack b/bin/spack index 7c911ce9f22..a7ebb8d1611 100755 --- a/bin/spack +++ b/bin/spack @@ -1,10 +1,26 @@ -#!/usr/bin/env python +#!/bin/sh +# -*- python -*- # # Copyright 2013-2019 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +# This file is bilingual. The following shell code finds our preferred python. +# Following line is a shell no-op, and starts a multi-line Python comment. +# See https://stackoverflow.com/a/47886254 +""":" +# prefer python3, then python, then python2 +for cmd in python3 python python2; do + command -v > /dev/null $cmd && exec $cmd $0 "$@" +done + +echo "==> Error: spack could not find a python interpreter!" >&2 +exit 1 +":""" +# Line above is a shell no-op, and ends a python multi-line comment. +# The code above runs this file with our preferred python interpreter. + from __future__ import print_function import os From a12c03250927670a45039a5f0bf651e2e84e52a2 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 28 Sep 2019 21:27:32 -0700 Subject: [PATCH 058/499] make license check slightly more lenient bin/spack now needs to have a "-*- python -*-" line after the shebang, so that emacs will interpret it as a python file instead of as a shell script. Add one line to the license check limit to accommodate this. --- lib/spack/spack/cmd/license.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/cmd/license.py b/lib/spack/spack/cmd/license.py index 7ae5f1c72b5..4c69dba0e7c 100644 --- a/lib/spack/spack/cmd/license.py +++ b/lib/spack/spack/cmd/license.py @@ -22,7 +22,7 @@ git = which('git') #: SPDX license id must appear in the first lines of a file -license_lines = 6 +license_lines = 7 #: Spack's license identifier apache2_mit_spdx = "(Apache-2.0 OR MIT)" From 139eaa13064c2f8db824abe9c29f26296408ea86 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Mon, 30 Sep 2019 22:18:09 +0900 Subject: [PATCH 059/499] otf2: add configure args to specify compiler commands. (#12711) * otf2: add configure args to specify compiler commands. * Modify the reference of the compile commands. --- var/spack/repos/builtin/packages/otf2/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py index bf5f6eb4aa9..f163c02dcc0 100644 --- a/var/spack/repos/builtin/packages/otf2/package.py +++ b/var/spack/repos/builtin/packages/otf2/package.py @@ -27,6 +27,10 @@ class Otf2(AutotoolsPackage): def configure_args(self): return [ '--enable-shared', + 'CC={0}'.format(spack_cc), + 'CXX={0}'.format(spack_cxx), + 'F77={0}'.format(spack_f77), + 'FC={0}'.format(spack_fc), 'CFLAGS={0}'.format(self.compiler.pic_flag), 'CXXFLAGS={0}'.format(self.compiler.pic_flag) ] From 7bcb306d4a5fc74fff63ea73369211e95270b911 Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Mon, 30 Sep 2019 14:02:32 -0400 Subject: [PATCH 060/499] Fix GCC environment variables for external installations (#12454) Unlike the compiler binary name search logic, the `setup_environment` in GCC's package assumes the compiler names are *exactly* `gcc`, `g++`, etc. In many external installations (Homebrew, Macports) the installation includes only *suffixed* versions such as `gcc-9`. This patch uses the GCC compiler search suffixes to actually locate the correct filenames for the installed compilers, allowing the Spack-generated module file to have useful definitions of CC, CXX, etc. It also allows for the possibility that the user's external installation of GCC is compiled without Fortran support, in which case the `FC` environment variables are not defined. --- .../repos/builtin/packages/gcc/package.py | 30 +++++++++++++++---- 1 file changed, 25 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 15acc438c34..86e2b843e43 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -8,6 +8,7 @@ from llnl.util import tty import glob +import itertools import os import sys @@ -420,8 +421,27 @@ def write_rpath_specs(self): set_install_permissions(specs_file) def setup_environment(self, spack_env, run_env): - run_env.set('CC', join_path(self.spec.prefix.bin, 'gcc')) - run_env.set('CXX', join_path(self.spec.prefix.bin, 'g++')) - run_env.set('FC', join_path(self.spec.prefix.bin, 'gfortran')) - run_env.set('F77', join_path(self.spec.prefix.bin, 'gfortran')) - run_env.set('F90', join_path(self.spec.prefix.bin, 'gfortran')) + # Search prefix directory for possibly modified compiler names + from spack.compilers.gcc import Gcc as Compiler + + # Get the contents of the installed binary directory + bin_path = self.spec.prefix.bin + bin_contents = os.listdir(bin_path) + + # Find the first non-symlink compiler binary present for each language + for lang in ['cc', 'cxx', 'fc', 'f77']: + for filename, regexp in itertools.product( + bin_contents, + Compiler.search_regexps(lang) + ): + if not regexp.match(filename): + continue + + abspath = os.path.join(bin_path, filename) + if os.path.islink(abspath): + continue + + # Set the proper environment variable + run_env.set(lang.upper(), abspath) + # Stop searching filename/regex combos for this language + break From c70f9bffe2c417c41769cf533824bb45970be326 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Mon, 30 Sep 2019 13:18:11 -0500 Subject: [PATCH 061/499] petsc, slepc: add new versions - 3.12.0 (#12979) --- var/spack/repos/builtin/packages/petsc/package.py | 6 ++++-- var/spack/repos/builtin/packages/slepc/package.py | 4 ++++ 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 3bdee89feb1..78e72b3db72 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -24,6 +24,8 @@ class Petsc(Package): version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') + version('3.12.0', 'ba9ecf69783c7ebf05bd1c91dd1d4b38bf09b7a2d5f9a774aa6bb46deff7cb14') + version('3.11.4', '319cb5a875a692a67fe5b1b90009ba8f182e21921ae645d38106544aff20c3c1') version('3.11.3', '199ad9650a9f58603b49e7fff7cd003ceb03aa231e5d37d0bf0496c6348eca81') version('3.11.2', '4d244dd7d1565d6534e776445fcf6977a6ee2a8bb2be4a36ac1e0fc1f9ad9cfa') version('3.11.1', 'cb627f99f7ce1540ebbbf338189f89a5f1ecf3ab3b5b0e357f9e46c209f1fb23') @@ -159,8 +161,8 @@ class Petsc(Package): depends_on('superlu-dist@5.2:5.2.99+int64', when='@3.8:3.9.99+superlu-dist+mpi+int64') depends_on('superlu-dist@5.4:5.4.99~int64', when='@3.10:3.10.2+superlu-dist+mpi~int64') depends_on('superlu-dist@5.4:5.4.99+int64', when='@3.10:3.10.2+superlu-dist+mpi+int64') - depends_on('superlu-dist@6.1:6.1.99~int64', when='@3.10.3:3.11.99+superlu-dist+mpi~int64') - depends_on('superlu-dist@6.1:6.1.99+int64', when='@3.10.3:3.11.99+superlu-dist+mpi+int64') + depends_on('superlu-dist@6.1:6.1.99~int64', when='@3.10.3:3.12.99+superlu-dist+mpi~int64') + depends_on('superlu-dist@6.1:6.1.99+int64', when='@3.10.3:3.12.99+superlu-dist+mpi+int64') depends_on('superlu-dist@xsdk-0.2.0~int64', when='@xsdk-0.2.0+superlu-dist+mpi~int64') depends_on('superlu-dist@xsdk-0.2.0+int64', when='@xsdk-0.2.0+superlu-dist+mpi+int64') depends_on('superlu-dist@develop~int64', when='@develop+superlu-dist+mpi~int64') diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index ac350b35e85..1dc1c7d615b 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -18,6 +18,9 @@ class Slepc(Package): maintainers = ['joseeroman', 'balay'] version('develop', branch='master') + version('3.12.0', '872831d961cf76389fafb7553231ae1a6676555850c98ea0e893c06f596b2e9e') + version('3.11.2', 'cd6a73ac0c9f689c12f2987000a7a28fa7df53fdc069fb59a2bb148699e741dd') + version('3.11.1', '4816070d4ecfeea6212c6944cee22dc7b4763df1eaf6ab7847cc5ac5132608fb') version('3.11.0', 'bf29043c311fe2c549a25e2b0835095723a3eebc1dff288a233b32913b5762a2') version('3.10.2', '0594972293f6586458a54b7c1e1121b311a9c9449060355d52bb3bf09ad6812b') version('3.10.1', 'f64787c8c2ab3d2f6db3c67d2bfe6ee84f741ce3dfde1d2f8221e131820a12a1') @@ -42,6 +45,7 @@ class Slepc(Package): # Cannot mix release and development versions of SLEPc and PETSc: depends_on('petsc@develop', when='@develop') + depends_on('petsc@3.12:3.12.99', when='@3.12:3.12.99') depends_on('petsc@3.11:3.11.99', when='@3.11:3.11.99') depends_on('petsc@3.10:3.10.99', when='@3.10:3.10.99') depends_on('petsc@3.9:3.9.99', when='@3.9:3.9.99') From 5b2b0ee9a309519dcdd75ca3715cf0517fb43bdb Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 30 Sep 2019 13:18:27 -0500 Subject: [PATCH 062/499] Revert "update neovim (#12965)" (#12978) This reverts commit 86a85b7eb22ccf69489a4bfbd947da7dfedcf233. --- var/spack/repos/builtin/packages/neovim/package.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/neovim/package.py b/var/spack/repos/builtin/packages/neovim/package.py index 4f676c62249..db398f5a2a9 100644 --- a/var/spack/repos/builtin/packages/neovim/package.py +++ b/var/spack/repos/builtin/packages/neovim/package.py @@ -11,9 +11,8 @@ class Neovim(CMakePackage): """NeoVim: the future of vim""" homepage = "http://neovim.io" - url = "https://github.com/neovim/neovim/archive/v0.4.2.tar.gz" + url = "https://github.com/neovim/neovim/archive/v0.3.4.tar.gz" - version('0.4.2', sha256='9f874d3d2a74f33b931db62adebe28f8d2ec116270d1e13998b58a73348b6e56') version('0.3.4', sha256='a641108bdebfaf319844ed46b1bf35d6f7c30ef5aeadeb29ba06e19c3274bc0e') version('0.3.1', '5405bced1c929ebc245c75409cd6c7ef') version('0.3.0', 'e5fdb2025757c337c17449c296eddf5b') From cfc17e95062a8d974bd95b881070199ffcb343f9 Mon Sep 17 00:00:00 2001 From: egreen77 <45573926+egreen77@users.noreply.github.com> Date: Mon, 30 Sep 2019 14:27:29 -0700 Subject: [PATCH 063/499] Update nano (#12980) --- .../repos/builtin/packages/nano/package.py | 54 +++++++++++++++++-- 1 file changed, 51 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/nano/package.py b/var/spack/repos/builtin/packages/nano/package.py index 684c23987f1..4cd6cf1d4b0 100644 --- a/var/spack/repos/builtin/packages/nano/package.py +++ b/var/spack/repos/builtin/packages/nano/package.py @@ -10,9 +10,57 @@ class Nano(AutotoolsPackage): """Tiny little text editor""" homepage = "http://www.nano-editor.org" - url = "https://www.nano-editor.org/dist/v2.6/nano-2.6.3.tar.gz" + url = "https://www.nano-editor.org/dist/v4/nano-4.4.tar.xz" + list_url = "https://www.nano-editor.org/dist/" + list_depth = 1 - version('2.6.3', '1213c7f17916e65afefc95054c1f90f9') - version('2.6.2', '58568a4b8a33841d774c25f285fc11c1') + # 4.x + version('4.4', sha256='2af222e0354848ffaa3af31b5cd0a77917e9cb7742cd073d762f3c32f0f582c7') + version('4.3', sha256='00d3ad1a287a85b4bf83e5f06cedd0a9f880413682bebd52b4b1e2af8cfc0d81') + version('4.2', sha256='1143defce62e391b241252ffdb6e5c1ded56cfe26d46ee81b796abe0ccc45df9') + version('4.1', sha256='86bde596a038d6fde619b49d785c0ebf0b3eaa7001a39dbe9316bd5392d221d0') + version('4.0', sha256='1e2fcfea35784624a7d86785768b772d58bb3995d1aec9176a27a113b1e9bac3') + # 3.x + version('3.2', sha256='d12773af3589994b2e4982c5792b07c6240da5b86c5aef2103ab13b401fe6349') + version('3.1', sha256='14c02ca40a5bc61c580ce2f9cb7f9fc72d5ccc9da17ad044f78f6fb3fdb7719e') + version('3.0', sha256='e0a5bca354514e64762c987c200a8758b05e7bcced3b00b3e48ea0a2d383c8a0') + # 2.9.x + version('2.9.8', sha256='c2deac31ba4d3fd27a42fafcc47ccf499296cc69a422bbecab63f2933ea85488') + version('2.9.7', sha256='b64ab017305b1777e97b5b9b07b31db8aeebfc3e8719f61e8da1cf3866d344bd') + version('2.9.6', sha256='a373507ebb4e9307a8202fbc19b5d29718025c8ec773669349211c362545d4c6') + version('2.9.5', sha256='7b8d181cb57f42fa86a380bb9ad46abab859b60383607f731b65a9077f4b4e19') + version('2.9.4', sha256='2cf9726e735f5c962af63d27c2faaead5936e45adec983659fb9e4af88ffa35a') + version('2.9.3', sha256='7783bcfd4b2d5dc0bf64d4bd07b1a19e7ba3c91da881a4249772a36b972d4012') + version('2.9.2', sha256='4eccb7451b5729ce8abae8f9a5679f32e41ae58df73ea86b850ec45b10a83d55') + version('2.9.1', sha256='6316d52d0d26af3e79a13dcb4db1c7a4aeac61b37fd9381e801a4189a2ecba7c') + version('2.9.0', sha256='d2d30c39caef53aba1ec1b4baff4186d4496f35d2411b0848242a5f2e27e129e') + # 2.8.x + version('2.8.7', sha256='fbe31746958698d73c6726ee48ad8b0612697157961a2e9aaa83b4aa53d1165a') + version('2.8.6', sha256='9a46962a3ae59db922467a095217ed23280b42d80640f932f3a59ba2a6a85776') + version('2.8.5', sha256='cb43bf11990b2839446229b0c21ed7abef67c2df861f250cc874553ca27d89c2') + version('2.8.4', sha256='c7cf264f0f3e4af43ecdbc4ec72c3b1e831c69a1a5f6512d5b0c109e6bac7b11') + version('2.8.3', sha256='62b8e55b934091edbb41e948eac3d6769cc13d18b837c38faf7226c0820b0f55') + version('2.8.2', sha256='023e8a7b38b2420d5476d7b2b4d8524d7de55c0853b4dc0b02e4a4adf7ecb9e0') + version('2.8.1', sha256='e935a8bb373345c833dff3a304c6d392775d206b94c802d9285ae80ac6b66d0b') + version('2.8.0', sha256='15c1bcf4d8888d3b56f68a0b75871cc349b81a9094f8a42d73010ffc26c85dc2') + # 2.7.x + version('2.7.5', sha256='a64d24e6bc4fc448376d038f9a755af77f8e748c9051b6f45bf85e783a7e67e4') + version('2.7.4', sha256='752170643039e2c95a433de357f0c70a8c4c4c561a90a7e7259a63e225b659b9') + version('2.7.3', sha256='d926ef5060d23bafec75dab9328bb9b9df9a08e58c56b9061d686f5698770bfc') + version('2.7.2', sha256='77016f73c686857ce8a3ec217832febb6e636122762d47ce3c6cbef6f7e390c2') + version('2.7.1', sha256='df5cbe69831d7394c0a32fb27373ab313335ea4dc586d6f4be4081eb1de857cd') + version('2.7.0', sha256='f86af39514ae74e20bef3c29cd01d1090a9aca772a70e9c9f9e70c3d14b39521') + # 2.6.x + version('2.6.3', sha256='69ecbfbaa845800f43c27d6190ca87d277f3278f81e9c55ee569181b572b7519') + version('2.6.2', sha256='22f79cc635458e0c0d110d211576f1edc03b112a62d73b914826a46547a6ac27') + version('2.6.1', sha256='45721fa6d6128068895ad71a6967ff7398d11b064b3f888e5073c97a2b6e9a81') depends_on('ncurses') + + def url_for_version(self, version): + url = "https://www.nano-editor.org/dist/v{0}/nano-{1}.tar.xz" + subdir = version.up_to(2) + major = version.up_to(1) + if int(str(major)) > 2: + subdir = major + return url.format(subdir, version) From 5b4040ea3638eee23298dabd1b821cc0451f8280 Mon Sep 17 00:00:00 2001 From: noguchi-k <55966120+noguchi-k@users.noreply.github.com> Date: Tue, 1 Oct 2019 22:54:01 +0900 Subject: [PATCH 064/499] libcerf:add CFLAGS for fujitsu compiler (#12990) * libcerf:add CFLAGS for fujitsu compiler * fix for flake8 --- var/spack/repos/builtin/packages/libcerf/package.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py index 8a203f5dddd..1451bbe52b7 100644 --- a/var/spack/repos/builtin/packages/libcerf/package.py +++ b/var/spack/repos/builtin/packages/libcerf/package.py @@ -25,5 +25,8 @@ def configure_args(self): # http://clang.debian.net/status.php?version=3.8.1&key=UNUSED_FUNCTION if spec.satisfies('%clang'): options.append('CFLAGS=-Wno-unused-function') + # fujitsu compiler has a error about unused functions too. + if spec.satisfies('%fj'): + options.append('CFLAGS=-Wno-unused-function') return options From f9396978638847da572b4121456a69ab86ac5d45 Mon Sep 17 00:00:00 2001 From: Mark Olesen Date: Tue, 1 Oct 2019 17:48:14 +0200 Subject: [PATCH 065/499] add adios2 dependency and configuration for newest OpenFOAM (#12993) --- .../repos/builtin/packages/openfoam/package.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/openfoam/package.py b/var/spack/repos/builtin/packages/openfoam/package.py index 2a1bdb6e0e2..60b49bbca83 100644 --- a/var/spack/repos/builtin/packages/openfoam/package.py +++ b/var/spack/repos/builtin/packages/openfoam/package.py @@ -286,8 +286,6 @@ class Openfoam(Package): description='With scotch/ptscotch decomposition') variant('zoltan', default=False, description='With zoltan renumbering') - # TODO?# variant('scalasca', default=False, - # TODO?# description='With scalasca profiling') variant('mgridgen', default=False, description='With mgridgen support') variant('paraview', default=False, description='Build paraview plugins and runtime post-processing') @@ -321,8 +319,7 @@ class Openfoam(Package): depends_on('parmgridgen', when='+mgridgen', type='build') depends_on('zoltan', when='+zoltan') depends_on('vtk', when='+vtk') - - # TODO?# depends_on('scalasca', when='+scalasca') + depends_on('adios2', when='@1912:') # For OpenFOAM plugins and run-time post-processing this should just be # 'paraview+plugins' but that resolves poorly. @@ -555,6 +552,7 @@ def configure(self, spec, prefix): ('LD_LIBRARY_PATH', foam_add_lib(user_mpi['libdir'])), ('PATH', foam_add_path(user_mpi['bindir'])), ], + 'adios2': {}, 'scotch': {}, 'kahip': {}, 'metis': {}, @@ -564,6 +562,15 @@ def configure(self, spec, prefix): 'vtk': [], } + # With adios2 after 1912 or develop (after 2019-10-01) + if spec.satisfies('@1912:'): + self.etc_config['adios2'] = [ + ('ADIOS2_ARCH_PATH', spec['adios2'].prefix), + ('LD_LIBRARY_PATH', + foam_add_lib(pkglib(spec['adios2'], '${ADIOS2_ARCH_PATH}'))), + ('PATH', foam_add_path('${ADIOS2_ARCH_PATH}/bin')), + ] + if '+scotch' in spec: self.etc_config['scotch'] = { 'SCOTCH_ARCH_PATH': spec['scotch'].prefix, From b9a860820a6a350ec6bddd41634affa6e88641c0 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Tue, 1 Oct 2019 10:48:40 -0500 Subject: [PATCH 066/499] hypre: add version 2.18.0 (#12992) --- var/spack/repos/builtin/packages/hypre/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 6354c59673b..83965314794 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -20,6 +20,7 @@ class Hypre(Package): maintainers = ['ulrikeyang', 'osborn9', 'balay'] version('develop', branch='master') + version('2.18.0', sha256='62591ac69f9cc9728bd6d952b65bcadd2dfe52b521081612609804a413f49b07') version('2.17.0', sha256='4674f938743aa29eb4d775211b13b089b9de84bfe5e9ea00c7d8782ed84a46d7') version('2.16.0', sha256='33f8a27041e697343b820d0426e74694670f955e21bbf3fcb07ee95b22c59e90') version('2.15.1', sha256='50d0c0c86b4baad227aa9bdfda4297acafc64c3c7256c27351f8bae1ae6f2402') From 10e4d611a5cdefec3d0845059eea29bb66bd17b2 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 1 Oct 2019 08:49:52 -0700 Subject: [PATCH 067/499] ADIOS2: 2.5.0 (#12987) Add the latest ADIOS2 release, v2.5.0 . --- var/spack/repos/builtin/packages/adios2/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index 750a08619e7..b4061aa1cff 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -16,6 +16,7 @@ class Adios2(CMakePackage): maintainers = ['ax3l', 'chuckatkins'] version('develop', branch='master') + version('2.5.0', sha256='7c8ff3bf5441dd662806df9650c56a669359cb0185ea232ecb3578de7b065329') version('2.4.0', sha256='50ecea04b1e41c88835b4b3fd4e7bf0a0a2a3129855c9cc4ba6cf6a1575106e2') version('2.3.1', sha256='3bf81ccc20a7f2715935349336a76ba4c8402355e1dc3848fcd6f4c3c5931893') version('2.2.0', sha256='77058ea2ff7224dc02ea519733de42d89112cf21ffe7474fb2fa3c5696152948') From 82a3ee0868964d9bd99ca992aaea52dc7d47a0f9 Mon Sep 17 00:00:00 2001 From: Christopher Edsall Date: Tue, 1 Oct 2019 17:47:57 +0100 Subject: [PATCH 068/499] Update chapel to current (1.19 -> 1.20) (#12991) --- var/spack/repos/builtin/packages/chapel/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/chapel/package.py b/var/spack/repos/builtin/packages/chapel/package.py index 462647565a3..689222fd8c1 100644 --- a/var/spack/repos/builtin/packages/chapel/package.py +++ b/var/spack/repos/builtin/packages/chapel/package.py @@ -11,7 +11,8 @@ class Chapel(AutotoolsPackage): portable, scalable and open-source.""" homepage = "https://chapel-lang.org/" - url = "https://github.com/chapel-lang/chapel/releases/download/1.19.0/chapel-1.19.0.tar.gz" + url = "https://github.com/chapel-lang/chapel/releases/download/1.20.0/chapel-1.20.0.tar.gz" + version('1.20.0', sha256='08bc86df13e4ad56d0447f52628b0f8e36b0476db4e19a90eeb2bd5f260baece') version('1.19.0', sha256='c2b68a20d87cc382c2f73dd1ecc6a4f42fb2f590b0b10fbc577382dd35c9e9bd') version('1.18.0', sha256='68471e1f398b074edcc28cae0be26a481078adc3edea4df663f01c6bd3b6ae0d') From 5868e0f5f2459b7587d79ad475c106665322213c Mon Sep 17 00:00:00 2001 From: Jeffrey Salmond Date: Tue, 1 Oct 2019 18:08:28 +0100 Subject: [PATCH 069/499] add new mercurial versions (#12997) --- var/spack/repos/builtin/packages/mercurial/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py index 15ed27bdc15..988e5c54679 100644 --- a/var/spack/repos/builtin/packages/mercurial/package.py +++ b/var/spack/repos/builtin/packages/mercurial/package.py @@ -11,7 +11,7 @@ class Mercurial(PythonPackage): """Mercurial is a free, distributed source control management tool.""" homepage = "https://www.mercurial-scm.org" - url = "https://www.mercurial-scm.org/release/mercurial-4.1.2.tar.gz" + url = "https://www.mercurial-scm.org/release/mercurial-5.1.1.tar.gz" import_modules = [ 'hgext', 'hgext3rd', 'mercurial', 'hgext.convert', 'hgext.fsmonitor', @@ -20,6 +20,8 @@ class Mercurial(PythonPackage): 'mercurial.httpclient', 'mercurial.pure' ] + version('5.1.1', sha256='35fc8ba5e0379c1b3affa2757e83fb0509e8ac314cbd9f1fd133cf265d16e49f') + version('4.9.1', sha256='1bdd21bb87d1e05fb5cd395d488d0e0cc2f2f90ce0fd248e31a03595da5ccb47') version('4.4.1', '37974a416d1d9525e1375c92025b16d9') version('4.1.2', '934c99808bdc8385e074b902d59b0d93') version('3.9.1', '3759dd10edb8c1a6dfb8ff0ce82658ce') From a7e64e539699a6b2387ec393f36b511e84833625 Mon Sep 17 00:00:00 2001 From: Jimmy Tang Date: Tue, 1 Oct 2019 18:24:03 +0100 Subject: [PATCH 070/499] Kaldi package: add version 7637de7 and egs (#12911) --- var/spack/repos/builtin/packages/kaldi/package.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/var/spack/repos/builtin/packages/kaldi/package.py b/var/spack/repos/builtin/packages/kaldi/package.py index 461929b2286..8455763add1 100644 --- a/var/spack/repos/builtin/packages/kaldi/package.py +++ b/var/spack/repos/builtin/packages/kaldi/package.py @@ -18,6 +18,7 @@ class Kaldi(Package): # Does not use Autotools git = "https://github.com/kaldi-asr/kaldi.git" version('master') + version('2019-07-29', commit='7637de77e0a77bf280bef9bf484e4f37c4eb9475') version('2018-07-11', commit='6f2140b032b0108bc313eefdca65151289642773') version('2015-10-07', commit='c024e8aa0a727bf76c91a318f76a1f8b0b59249e') @@ -35,6 +36,8 @@ class Kaldi(Package): # Does not use Autotools depends_on('speex', type='run') depends_on('openfst@1.4.1-patch', when='@2015-10-07') depends_on('openfst@1.6.0:', when='@2018-07-11') + depends_on('openfst@1.6.0:', when='@2019-07-29') + depends_on('cub', when='@2019-07-29:') depends_on('openfst') patch('openfst-1.4.1.patch', when='@2015-10-07') @@ -69,6 +72,9 @@ def install(self, spec, prefix): configure_args.append('--use-cuda=yes') configure_args.append('--cudatk-dir=' + spec['cuda'].prefix) + if spec.satisfies('@2019-07-29:'): + configure_args.append('--cub-root=' + spec['cub'].prefix.include) + with working_dir("src"): configure(*configure_args) make() @@ -99,3 +105,5 @@ def install(self, spec, prefix): mkdirp(join(prefix.include, root.strip("./"))) install(join(root, name), join(prefix.include, root.strip("./"))) + egs_dir = join(prefix, 'egs') + install_tree('egs', egs_dir) From 76178f31ca89e81d6f97c3fcf322bd3100322634 Mon Sep 17 00:00:00 2001 From: Jeffrey Salmond Date: Tue, 1 Oct 2019 18:29:10 +0100 Subject: [PATCH 071/499] When removing a file from a view, don't fail if it doesn't exist (#12960) Sometimes when remove_file is called on a link, that link is missing (perhaps ctrl-C happened halfway through a previous action). As removing a non-existent file is no problem, this patch changes the behavior so Spack continues rather than stopping with an error. Currently you would see ValueError: /path/to/dir is not a link tree! and now it continues with a warning. --- lib/spack/spack/filesystem_view.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py index 5385ca08038..1701af55014 100644 --- a/lib/spack/spack/filesystem_view.py +++ b/lib/spack/spack/filesystem_view.py @@ -357,6 +357,9 @@ def unmerge(self, spec, ignore=None): tree.unmerge_directories(view_dst, ignore_file) def remove_file(self, src, dest): + if not os.path.lexists(dest): + tty.warn("Tried to remove %s which does not exist" % dest) + return if not os.path.islink(dest): raise ValueError("%s is not a link tree!" % dest) # remove if dest is a hardlink/symlink to src; this will only From 245c1bb20895931263acb068a6e5a109c143fa03 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 1 Oct 2019 22:35:51 +0200 Subject: [PATCH 072/499] libaio: fixed a condition that checks whether we are running on OS X (#12976) * libaio: fixed a condition that checks whether we are running on OS X * libaio: simplified package by adding an explicit conflict for darwin * libaio: added information to the docstring * fio: added version 3.16, added conflict when using libaio, docstring * lvm2: conflict due to libaio dep, improved docstring, simpler install * mariadb: conflict due to libaio dep, improved docstring, version 10.4.7 * mariadb: the dependency on libaio is now conditional, removed conflict * mariadb: fixed a typo in previous commit Co-Authored-By: Adam J. Stewart * libaio: turned into a MakefilePackage --- .../repos/builtin/packages/fio/package.py | 16 ++++++--- .../repos/builtin/packages/libaio/package.py | 24 +++++++------ .../repos/builtin/packages/lvm2/package.py | 36 +++++++++---------- .../repos/builtin/packages/mariadb/package.py | 13 ++++--- 4 files changed, 52 insertions(+), 37 deletions(-) diff --git a/var/spack/repos/builtin/packages/fio/package.py b/var/spack/repos/builtin/packages/fio/package.py index 9f1f30273b5..29f02c8b807 100644 --- a/var/spack/repos/builtin/packages/fio/package.py +++ b/var/spack/repos/builtin/packages/fio/package.py @@ -3,15 +3,20 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * - class Fio(AutotoolsPackage): - """Flexible I/O Tester.""" + """Flexible I/O Tester. + + Fio spawns a number of threads or processes doing a particular type of I/O + action as specified by the user. fio takes a number of global parameters, + each inherited by the thread unless otherwise parameters given to them + overriding that setting is given. + """ homepage = "https://github.com/axboe/fio" - url = "https://github.com/axboe/fio/archive/fio-2.19.tar.gz" + url = "https://github.com/axboe/fio/archive/fio-2.19.tar.gz" + version('3.16', sha256='c7731a9e831581bab7104da9ea60c9f44e594438dbe95dff26726ca0285e7b93') version('2.19', '67125b60210a4daa689a4626fc66c612') variant('gui', default=False, description='Enable building of gtk gfio') @@ -24,6 +29,9 @@ class Fio(AutotoolsPackage): depends_on('py-sphinx', type='build', when='+doc') + conflicts('+libaio', when='platform=darwin', + msg='libaio does not support Darwin') + def configure_args(self): config_args = [] diff --git a/var/spack/repos/builtin/packages/libaio/package.py b/var/spack/repos/builtin/packages/libaio/package.py index 26919f67c89..638d57892d6 100644 --- a/var/spack/repos/builtin/packages/libaio/package.py +++ b/var/spack/repos/builtin/packages/libaio/package.py @@ -3,22 +3,24 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * +class Libaio(MakefilePackage): + """Linux native Asynchronous I/O interface library. -class Libaio(Package): - """This is the linux native Asynchronous I/O interface library.""" + AIO enables even a single application thread to overlap I/O operations + with other processing, by providing an interface for submitting one or + more I/O requests in one system call (io_submit()) without waiting for + completion, and a separate interface (io_getevents()) to reap completed + I/O operations associated with a given completion group. + """ homepage = "http://lse.sourceforge.net/io/aio.html" - url = "https://debian.inf.tu-dresden.de/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz" + url = "https://debian.inf.tu-dresden.de/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz" version('0.3.110', '2a35602e43778383e2f4907a4ca39ab8') - def install(self, spec, prefix): - # libaio is not supported on OS X - if spec.satisfies('arch=darwin-x86_64'): - # create a dummy directory - mkdir(prefix.lib) - return + conflicts('platform=darwin', msg="libaio is a linux specific library") - make('prefix={0}'.format(prefix), 'install') + @property + def install_targets(self): + return ['prefix={0}'.format(self.spec.prefix), 'install'] diff --git a/var/spack/repos/builtin/packages/lvm2/package.py b/var/spack/repos/builtin/packages/lvm2/package.py index 18d9ef205d4..f49c8371a21 100644 --- a/var/spack/repos/builtin/packages/lvm2/package.py +++ b/var/spack/repos/builtin/packages/lvm2/package.py @@ -3,20 +3,22 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * - class Lvm2(AutotoolsPackage): """LVM2 is the userspace toolset that provides logical volume - management facilities on linux. To use it you need 3 things: - device-mapper in your kernel, the userspace device-mapper support - library (libdevmapper) and the userspace LVM2 tools (dmsetup). These - userspace components, and associated header files, are provided by this - package. See http://sources.redhat.com/dm/ for additional information - about the device-mapper kernel and userspace components.""" + management facilities on linux. + + To use it you need 3 things: device-mapper in your kernel, the userspace + device-mapper support library (libdevmapper) and the userspace LVM2 tools + (dmsetup). These userspace components, and associated header files, are + provided by this package. + + See http://sources.redhat.com/dm/ for additional information + about the device-mapper kernel and userspace components. + """ homepage = "https://www.sourceware.org/lvm2" - url = "https://sourceware.org/pub/lvm2/releases/LVM2.2.03.05.tgz" + url = "https://sourceware.org/pub/lvm2/releases/LVM2.2.03.05.tgz" version('2.03.05', sha256='ca52815c999b20c6d25e3192f142f081b93d01f07b9d787e99664b169dba2700') version('2.03.04', sha256='f151f36fc0039997d2d9369b607b9262568b1a268afe19fd1535807355402142') @@ -35,13 +37,11 @@ def url_for_version(self, version): depends_on('libaio') depends_on('pkgconfig', type='build', when='+pkgconfig') + conflicts('platform=darwin', + msg='lvm2 depends on libaio which does not support Darwin') + def configure_args(self): - args = ['--with-confdir={0}'. - format(self.prefix.etc), - '--with-default-system-dir={0}'. - format(self.prefix.etc.lvm)] - if self.spec.satisfies('+pkgconfig'): - args.append('--enable-pkgconfig') - else: - args.append('--disable-pkgconfig') - return args + return [ + '--with-confdir={0}'.format(self.prefix.etc), + '--with-default-system-dir={0}'.format(self.prefix.etc.lvm) + ] + self.enable_or_disable('pkgconfig') diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py index fed976ef38c..c094da88651 100644 --- a/var/spack/repos/builtin/packages/mariadb/package.py +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -7,15 +7,20 @@ class Mariadb(CMakePackage): - """MariaDB turns data into structured information in a wide array of + """MariaDB Server is one of the most popular database servers + in the world. + + MariaDB turns data into structured information in a wide array of applications, ranging from banking to websites. It is an enhanced, drop-in replacement for MySQL. MariaDB is used because it is fast, scalable and robust, with a rich ecosystem of storage engines, plugins and many other - tools make it very versatile for a wide variety of use cases.""" + tools make it very versatile for a wide variety of use cases. + """ homepage = "https://mariadb.org/about/" - url = "http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-10.2.8/source/mariadb-10.2.8.tar.gz" + url = "http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-10.2.8/source/mariadb-10.2.8.tar.gz" + version('10.4.7', sha256='c8e6a6d0bb4f22c416ed675d24682a3ecfa383c5283efee70c8edf131374d817') version('10.2.8', 'f93cbd5bfde3c0d082994764ff7db580') version('10.1.23', '1a7392cc05c7c249acd4495022719ca8') version('5.5.56', '8bc7772fea3e11b0bc1a09d2278e2e32') @@ -32,7 +37,7 @@ class Mariadb(CMakePackage): depends_on('pkgconfig', type='build') depends_on('bison', type='build') depends_on('jemalloc') - depends_on('libaio') + depends_on('libaio', when='platform=linux') depends_on('libedit') depends_on('libevent', when='+nonblocking') depends_on('ncurses') From 3575f9b38228c5ddb99759c8c3b73996d644ed78 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Tue, 1 Oct 2019 14:29:01 -0700 Subject: [PATCH 073/499] GCC package: don't set CC etc. based on bin dir if it doesn't exist (#13000) 7bcb306 updated setup_environment in the GCC package to examine the bin/ directory to find alternatively-named instances of CC, but this failed to account for when GCC was being installed and failed when it attempted to list the not-yet-existing installation prefix. This commit updates the logic to skip this search if the bin/ directory doesn't exist. --- var/spack/repos/builtin/packages/gcc/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 86e2b843e43..6bdfaeccc2d 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -426,6 +426,10 @@ def setup_environment(self, spack_env, run_env): # Get the contents of the installed binary directory bin_path = self.spec.prefix.bin + + if not os.path.isdir(bin_path): + return + bin_contents = os.listdir(bin_path) # Find the first non-symlink compiler binary present for each language From 436afdd2a85b45fbbeeeb017e8a3739de4bc6128 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 1 Oct 2019 14:52:44 -0700 Subject: [PATCH 074/499] Dataspaces: Fix Fetch URL, Savanna Spec (#13001) --- var/spack/repos/builtin/packages/dataspaces/package.py | 2 +- var/spack/repos/builtin/packages/savanna/package.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/dataspaces/package.py b/var/spack/repos/builtin/packages/dataspaces/package.py index 9fa03e7e771..3e156ca8299 100644 --- a/var/spack/repos/builtin/packages/dataspaces/package.py +++ b/var/spack/repos/builtin/packages/dataspaces/package.py @@ -19,7 +19,7 @@ class Dataspaces(AutotoolsPackage): """an extreme scale data management framework.""" homepage = "http://www.dataspaces.org" - url = "http://personal.cac.rutgers.edu/TASSL/projects/data/downloads/dataspaces-1.6.2.tar.gz" + url = "https://dataspaces.rdi2.rutgers.edu/downloads/dataspaces-1.6.2.tar.gz" git = "https://github.com/melrom/dataspaces.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/savanna/package.py b/var/spack/repos/builtin/packages/savanna/package.py index 2b1075863a7..127c4966d39 100644 --- a/var/spack/repos/builtin/packages/savanna/package.py +++ b/var/spack/repos/builtin/packages/savanna/package.py @@ -21,7 +21,7 @@ class Savanna(MakefilePackage): depends_on('mpi') depends_on('stc') - depends_on('adios +fortran +zlib +sz +zfp +staging') + depends_on('adios +fortran +zlib +sz +zfp staging=dataspaces') # flexpath depends_on('mpix-launch-swift') depends_on('tau', when='+tau') From b92977492d9f329d44e356d6dbc6b1be6701f5ad Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Tue, 1 Oct 2019 15:03:28 -0700 Subject: [PATCH 075/499] binary cache: show all packages for compatible differing targets (#12943) --- lib/spack/spack/binary_distribution.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index cab0ad21ea7..510e9c234d0 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -609,7 +609,9 @@ def get_specs(force=False): tty.warn("No Spack mirrors are currently configured") return {} - path = str(spack.architecture.sys_type()) + arch = spack.architecture.sys_type() + arch_spec = 'platform=%s os=%s target=:%s' % tuple(arch.split('-')) + urls = set() for mirror_name, mirror_url in mirrors.items(): if mirror_url.startswith('file'): @@ -626,7 +628,7 @@ def get_specs(force=False): tty.msg("Finding buildcaches on %s" % mirror_url) p, links = spider(mirror_url + "/" + _build_cache_relative_path) for link in links: - if re.search("spec.yaml", link) and re.search(path, link): + if re.search("spec.yaml", link): urls.add(link) _cached_specs = [] @@ -645,7 +647,8 @@ def get_specs(force=False): # we need to mark this spec concrete on read-in. spec = Spec.from_yaml(f) spec._mark_concrete() - _cached_specs.append(spec) + if spec.satisfies(arch_spec): + _cached_specs.append(spec) return _cached_specs From c1ecd037d7ed481ee248e63dec1d43f70c1d5c5b Mon Sep 17 00:00:00 2001 From: Eduardo Arango Date: Tue, 1 Oct 2019 19:16:20 -0500 Subject: [PATCH 076/499] add singularity 3.4.1 (#12995) * add singularity 3.4.1 Signed-off-by: ArangoGutierrez * revert some changes Signed-off-by: ArangoGutierrez * add maintainers list to pkg singularity Add @alalazo and me to the Singularity maintainers list * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart --- var/spack/repos/builtin/packages/singularity/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py index 1b030cff239..ba0929c02b3 100644 --- a/var/spack/repos/builtin/packages/singularity/package.py +++ b/var/spack/repos/builtin/packages/singularity/package.py @@ -24,8 +24,10 @@ class Singularity(MakefilePackage): url = "https://github.com/sylabs/singularity/releases/download/v3.1.1/singularity-3.1.1.tar.gz" git = "https://github.com/sylabs/singularity.git" - version('develop', branch='master') + maintainers = ['ArangoGutierrez', 'alalazo'] + version('master', branch='master') + version('3.4.1', sha256='638fd7cc5ab2a20e779b8768f73baf21909148339d6c4edf6ff61349c53a70c2') version('3.4.0', sha256='eafb27f1ffbed427922ebe2b5b95d1c9c09bfeb897518867444fe230e3e35e41') version('3.3.0', sha256='070530a472e7e78492f1f142c8d4b77c64de4626c4973b0589f0d18e1fcf5b4f') version('3.2.1', sha256='d4388fb5f7e0083f0c344354c9ad3b5b823e2f3f27980e56efa7785140c9b616') From 248bc17bb0c513fad9ed0337112faba5356418c8 Mon Sep 17 00:00:00 2001 From: "Daryl W. Grunau" Date: Tue, 1 Oct 2019 18:17:10 -0600 Subject: [PATCH 077/499] go-md2man: disable module-mode (#12985) * go-md2man: disable module-mode * Update var/spack/repos/builtin/packages/go-md2man/package.py Co-Authored-By: Adam J. Stewart --- var/spack/repos/builtin/packages/go-md2man/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/go-md2man/package.py b/var/spack/repos/builtin/packages/go-md2man/package.py index 47882d94f4b..0986d416617 100644 --- a/var/spack/repos/builtin/packages/go-md2man/package.py +++ b/var/spack/repos/builtin/packages/go-md2man/package.py @@ -37,6 +37,7 @@ def install(self, spec, prefix): with working_dir('src'): env['GOPATH'] = self.stage.source_path + env['GO111MODULE'] = 'off' go = which('go') go('build', '-v', join_path( 'github.com', 'cpuguy83', 'go-md2man')) From 5c2b01ebcf8e8336f50cee64b09e158167a0f168 Mon Sep 17 00:00:00 2001 From: codeandkey Date: Tue, 1 Oct 2019 16:29:28 -0500 Subject: [PATCH 078/499] picard: add 2.20.8 --- var/spack/repos/builtin/packages/picard/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py index d42f80a3f0b..98d311b4e58 100644 --- a/var/spack/repos/builtin/packages/picard/package.py +++ b/var/spack/repos/builtin/packages/picard/package.py @@ -21,6 +21,7 @@ class Picard(Package): # They started distributing a single jar file at v2.6.0, prior to # that it was a .zip file with multiple .jar and .so files + version('2.20.8', sha256='aff92d618ee9e6bafc1ab4fbfa89fc557a0dbe596ae4b92fe3bf93ebf95c7105', expand=False) version('2.19.0', sha256='f97fc3f7a73b55cceea8b6a6488efcf1b2fbf8cad61d88645704ddd45a8c5950', expand=False) version('2.18.3', '181b1b0731fd35f0d8bd44677d8787e9', expand=False) version('2.18.0', '20045ff141e4a67512365f0b6bbd8229', expand=False) From 91488ed8f5f6870c7423971e9fc2495696c59eb4 Mon Sep 17 00:00:00 2001 From: Sinan Date: Tue, 1 Oct 2019 18:37:34 -0700 Subject: [PATCH 079/499] New package: py-python-mapnik (#12786) --- .../packages/py-python-mapnik/package.py | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-python-mapnik/package.py diff --git a/var/spack/repos/builtin/packages/py-python-mapnik/package.py b/var/spack/repos/builtin/packages/py-python-mapnik/package.py new file mode 100644 index 00000000000..6d1cf944b0d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-mapnik/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonMapnik(PythonPackage): + """ + Python bindings for mapnik + """ + + homepage = "https://github.com/mapnik/python-mapnik" + url = "https://github.com/mapnik/python-mapnik/archive/v3.0.16.tar.gz" + + version('3.0.16', sha256='643117752fa09668a1e26a360d13cd137329ae2013eb14ad92ab72fbc479fc70') + version('3.0.13', sha256='ced684745e778c0cac0edba89c09c6f9b9f1db18fc12744ed4710a88b78a3389') + + depends_on('py-setuptools', type='build') + depends_on('mapnik', type=('build', 'link', 'run')) + depends_on('boost +python+thread') + + # Package can't find boost_python without the following + def setup_environment(self, spack_env, run_env): + # Inform the package that boost python library is of form + # 'libboost_python27.so' as opposed to 'libboost_python.so' + py_ver = str(self.spec['python'].version.up_to(2).joined) + spack_env.set('BOOST_PYTHON_LIB', 'boost_python' + py_ver) From d20e3517c20633534e0d358de1e400b5f8d8a4ec Mon Sep 17 00:00:00 2001 From: Sinan Date: Tue, 1 Oct 2019 18:59:53 -0700 Subject: [PATCH 080/499] new package: py-python-ldap (#12599) * new package: py-python-ldap * fix dependency types * improvements * Update var/spack/repos/builtin/packages/py-python-ldap/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-python-ldap/package.py Co-Authored-By: Adam J. Stewart * add openldap dependency --- .../packages/py-python-ldap/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-python-ldap/package.py diff --git a/var/spack/repos/builtin/packages/py-python-ldap/package.py b/var/spack/repos/builtin/packages/py-python-ldap/package.py new file mode 100644 index 00000000000..002de856e00 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-ldap/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonLdap(PythonPackage): + """python-ldap provides an object-oriented API to access LDAP directory + servers from Python programs. + """ + + homepage = "https://www.python-ldap.org/en/python-ldap-3.2.0/" + url = "https://pypi.io/packages/source/p/python-ldap/python-ldap-3.2.0.tar.gz" + + version('3.2.0', sha256='7d1c4b15375a533564aad3d3deade789221e450052b21ebb9720fb822eccdb8e') + version('3.0.0', sha256='86746b912a2cd37a54b06c694f021b0c8556d4caeab75ef50435ada152e2fbe1') + + depends_on('openldap+client_only', type=('build', 'link', 'run')) + depends_on('py-setuptools', type='build') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-pyasn1@0.3.7:', type=('build', 'run')) + depends_on('py-pyasn1-modules@0.1.5:', type=('build', 'run')) From 1b18ec90abadf6e476a5e5fe1c82d18849c1d18d Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 26 Sep 2019 22:51:16 +0200 Subject: [PATCH 081/499] Add all compatible system types directory to module paths fixes #12915 closes #12916 Since Spack has support for specific targets it might happen that software is built for targets that are not exactly the host because it was either an explicit user request or the compiler being used is too old to support the host. Modules for different targets are written into different directories and by default Spack was adding to MODULEPATH only the directory corresponding to the current host. This PR modifies this behavior to add all the directories that are **compatible** with the current host. --- lib/spack/spack/architecture.py | 12 ++++++++++++ lib/spack/spack/main.py | 3 ++- share/spack/setup-env.csh | 5 ++++- share/spack/setup-env.sh | 4 +++- 4 files changed, 21 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index c67b63cba00..53cbc44ca53 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -493,3 +493,15 @@ def sys_type(): """ arch = Arch(platform(), 'default_os', 'default_target') return str(arch) + + +@memoized +def compatible_sys_types(): + """Returns a list of all the systypes compatible with the current host.""" + compatible_archs = [] + current_host = cpu.host() + compatible_targets = [current_host] + current_host.ancestors + for target in compatible_targets: + arch = Arch(platform(), 'default_os', target) + compatible_archs.append(str(arch)) + return compatible_archs diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py index a2220a9ba81..c3746b6b26a 100644 --- a/lib/spack/spack/main.py +++ b/lib/spack/spack/main.py @@ -585,7 +585,8 @@ def shell_set(var, value): # print sys type shell_set('_sp_sys_type', spack.architecture.sys_type()) - + shell_set('_sp_compatible_sys_types', + ':'.join(spack.architecture.compatible_sys_types())) # print roots for all module systems module_roots = spack.config.get('config:module_roots') module_to_roots = { diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh index f2b5b00006f..ac5479196d4 100755 --- a/share/spack/setup-env.csh +++ b/share/spack/setup-env.csh @@ -26,8 +26,11 @@ if ($?SPACK_ROOT) then # Set up modules and dotkit search paths in the user environment set tcl_roots = `echo $_sp_tcl_roots:q | sed 's/:/ /g'` + set compatible_sys_types = `echo $_sp_compatible_sys_types:q | sed 's/:/ /g'` foreach tcl_root ($tcl_roots:q) - _spack_pathadd MODULEPATH "$tcl_root/$_sp_sys_type" + foreach systype ($compatible_sys_types:q) + _spack_pathadd MODULEPATH "$tcl_root/$systype" + end end set dotkit_roots = `echo $_sp_dotkit_roots:q | sed 's/:/ /g'` diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index ae6d00a47b7..0fd5eb30f72 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -350,7 +350,9 @@ _sp_multi_pathadd() { setopt sh_word_split fi for pth in $2; do - _spack_pathadd "$1" "${pth}/${_sp_sys_type}" + for systype in ${_sp_compatible_sys_types}; do + _spack_pathadd "$1" "${pth}/${systype}" + done done } _sp_multi_pathadd MODULEPATH "$_sp_tcl_roots" From 22e75b77e3b10e88b0acb7878a1153cc6778deb1 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 1 Oct 2019 20:34:14 -0700 Subject: [PATCH 082/499] direnv: add info for version 2.20.0 (#13007) --- var/spack/repos/builtin/packages/direnv/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/direnv/package.py b/var/spack/repos/builtin/packages/direnv/package.py index 81c97eaaf50..816c4331858 100644 --- a/var/spack/repos/builtin/packages/direnv/package.py +++ b/var/spack/repos/builtin/packages/direnv/package.py @@ -12,6 +12,7 @@ class Direnv(Package): homepage = "https://direnv.net/" url = "https://github.com/direnv/direnv/archive/v2.11.3.tar.gz" + version('2.20.0', '75a166c2ef83a3b8dfbd0544cadb5984') version('2.11.3', '5b9728e2dabed232b4932849647fd6e5') depends_on('go', type='build') From 9dfec4a57c7331c05f0a70b657f1bbc628e34586 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Tue, 1 Oct 2019 22:54:22 -0500 Subject: [PATCH 083/499] 'spack buildcache list' should show all buildaches available. (#13002) * binary cache: show all packages for compatible differing targets * Don't restrict spack buildcache list to arch or os * Fix from merge conflict --- lib/spack/spack/binary_distribution.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index 510e9c234d0..a4624e9326f 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -609,9 +609,6 @@ def get_specs(force=False): tty.warn("No Spack mirrors are currently configured") return {} - arch = spack.architecture.sys_type() - arch_spec = 'platform=%s os=%s target=:%s' % tuple(arch.split('-')) - urls = set() for mirror_name, mirror_url in mirrors.items(): if mirror_url.startswith('file'): @@ -647,8 +644,7 @@ def get_specs(force=False): # we need to mark this spec concrete on read-in. spec = Spec.from_yaml(f) spec._mark_concrete() - if spec.satisfies(arch_spec): - _cached_specs.append(spec) + _cached_specs.append(spec) return _cached_specs From bec283080292f90f8f97dcb7ceb070a9a86ed388 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 1 Oct 2019 23:28:36 -0700 Subject: [PATCH 084/499] ZFP: CMake Package (#12999) * ZFP: CMake Package ZFP is primarily build via CMake, which will have all install logic and configuration files generated. The 0.5.0 release did not support this yet, so we toss it. * Patch ADIOS1: ZFP 0.5.1+ support * ZFP: Expose all CMake variants --- .../repos/builtin/packages/adios/package.py | 6 +- .../repos/builtin/packages/adios/zfp051.patch | 22 ++++++ .../repos/builtin/packages/adios2/package.py | 2 +- .../repos/builtin/packages/zfp/package.py | 73 ++++++++++--------- 4 files changed, 65 insertions(+), 38 deletions(-) create mode 100644 var/spack/repos/builtin/packages/adios/zfp051.patch diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index d4ea3258e22..ac9ab764682 100644 --- a/var/spack/repos/builtin/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -79,7 +79,7 @@ class Adios(AutotoolsPackage): depends_on('sz@:1.4.10', when='@:1.12.0 +sz') depends_on('sz@1.4.11.0:1.4.11.99', when='@1.13.0 +sz') depends_on('sz@1.4.12.3:1.4.12.99', when='@1.13.1: +sz') - depends_on('zfp@:0.5.0', when='+zfp') + depends_on('zfp@0.5.1:0.5.99', when='+zfp') depends_on('lz4', when='+lz4') depends_on('c-blosc@1.12.0:', when='+blosc') # optional transports & file converters @@ -101,6 +101,10 @@ class Adios(AutotoolsPackage): # https://github.com/spack/spack/issues/1683 patch('adios_1100.patch', when='@:1.10.0^hdf5@1.10:') + # ADIOS 1.13.1 is written for ZFP 0.5.0 interfaces + # https://github.com/ornladios/ADIOS/pull/204 + patch('zfp051.patch', when='@1.11.0:1.13.1') + def validate(self, spec): """Checks if incompatible variants have been activated at the same time diff --git a/var/spack/repos/builtin/packages/adios/zfp051.patch b/var/spack/repos/builtin/packages/adios/zfp051.patch new file mode 100644 index 00000000000..d602ce39ed1 --- /dev/null +++ b/var/spack/repos/builtin/packages/adios/zfp051.patch @@ -0,0 +1,22 @@ +diff --git a/src/transforms/adios_transform_zfp_common.h b/src/transforms/adios_transform_zfp_common.h +index e453d078..681198ee 100644 +--- a/src/transforms/adios_transform_zfp_common.h ++++ b/src/transforms/adios_transform_zfp_common.h +@@ -146,7 +146,7 @@ static void zfp_initialize(void* array, struct zfp_buffer* zbuff) + zbuff->error = true; + return; + } +- zfp_stream_set_accuracy(zbuff->zstream, tol, zbuff->type); ++ zfp_stream_set_accuracy(zbuff->zstream, tol); + } + else if (zbuff->mode == 1) // precision + { +@@ -172,7 +172,7 @@ static void zfp_initialize(void* array, struct zfp_buffer* zbuff) + tol = (uint) ct; + + +- zfp_stream_set_precision(zbuff->zstream, tol, zbuff->type); ++ zfp_stream_set_precision(zbuff->zstream, tol); + } + else if (zbuff->mode == 2) // rate + { diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index b4061aa1cff..2a3d3698df3 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -94,7 +94,7 @@ class Adios2(CMakePackage): depends_on('bzip2', when='+bzip2') depends_on('libpng@1.6:', when='@2.4.0: +png') # depends_on('mgard', when='@2.3.0: +mgard') - depends_on('zfp', when='+zfp') + depends_on('zfp@0.5.1:', when='+zfp') # depends_on('sz@:1.4.12', when='+sz') extends('python', when='+python') diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py index c7cf5b10386..7eb5e511d01 100644 --- a/var/spack/repos/builtin/packages/zfp/package.py +++ b/var/spack/repos/builtin/packages/zfp/package.py @@ -6,7 +6,7 @@ from spack import * -class Zfp(MakefilePackage): +class Zfp(CMakePackage): """zfp is an open source C/C++ library for high-fidelity, high-throughput lossy compression of floating-point and integer multi-dimensional arrays. @@ -15,10 +15,10 @@ class Zfp(MakefilePackage): homepage = 'http://computing.llnl.gov/projects/floating-point-compression' url = 'http://computing.llnl.gov/projects/floating-point-compression/download/zfp-0.5.2.tar.gz' + version('0.5.5', sha256='fdf7b948bab1f4e5dccfe2c2048fd98c24e417ad8fb8a51ed3463d04147393c5') version('0.5.4', sha256='768a05ed9bf10e54ac306f90b81dd17b0e7b13782f01823d7da4394fd2da8adb') - version('0.5.2', '2f0a77aa34087219a6e10b8b7d031e77') - version('0.5.1', '0ed7059a9b480635e0dd33745e213d17') - version('0.5.0', '2ab29a852e65ad85aae38925c5003654') + version('0.5.2', sha256='89e718edb966422b5898b5c37b1b0a781d4effacb511520558469e3ff7f65d7c') + version('0.5.1', sha256='867c04cf965f1c70d9725b396c6e1b5d29db55b0d69b8e87a995aaebd221b830') variant('bsws', default='64', @@ -26,41 +26,42 @@ class Zfp(MakefilePackage): multi=False, description='Bit stream word size: use smaller for finer ' 'rate granularity. Use 8 for H5Z-ZFP filter.') - + variant('strided', default=False, + description='Enable strided access for progressive zfp streams') + variant('aligned', default=False, + description='Enable aligned memory allocation') + variant('twoway', default=False, + description='Use two-way skew-associative cache') + variant('fasthash', default=False, + description='Use a faster but more collision prone hash function') + variant('profile', default=False, + description='Count cache misses') variant('shared', default=True, description='Build shared versions of the library') - def edit(self, spec, prefix): - config_file = FileFilter('Config') - config_file.filter( - r'^\s*#\s*DEFS\s*\+=\s*-DBIT_STREAM_WORD_TYPE\s*=\s*uint8', - 'DEFS += -DBIT_STREAM_WORD_TYPE=uint%s' % - spec.variants['bsws'].value) + depends_on('cmake@3.4.0:', type='build') - def build(self, spec, prefix): - with working_dir('src'): - if '~shared' in spec: - make('static') - else: - make('shared') + def cmake_args(self): + spec = self.spec - def install(self, spec, prefix): - incdir = 'include' if spec.satisfies('@0.5.1:') else 'inc' + args = [ + '-DZFP_BIT_STREAM_WORD_SIZE:STRING={0}'.format( + spec.variants['bsws'].value), + '-DZFP_WITH_BIT_STREAM_STRIDED:BOOL={0}'.format( + 'ON' if '+strided' in spec else 'OFF'), + '-DZFP_WITH_ALIGNED_ALLOC:BOOL={0}'.format( + 'ON' if '+aligned' in spec else 'OFF'), + '-DZFP_WITH_CACHE_TWOWAY:BOOL={0}'.format( + 'ON' if '+twoway' in spec else 'OFF'), + '-DBUILD_SHARED_LIBS:BOOL={0}'.format( + 'ON' if '+shared' in spec else 'OFF'), + '-DBUILD_TESTING:BOOL={0}'.format( + 'ON' if self.run_tests else 'OFF') + ] + if spec.version >= Version('0.5.2'): + args.append('-DZFP_WITH_CACHE_FAST_HASH:BOOL={0}'.format( + 'ON' if '+fasthash' in spec else 'OFF')) + args.append('-DZFP_WITH_CACHE_PROFILE:BOOL={0}'.format( + 'ON' if '+profile' in spec else 'OFF')) - # Note: ZFP package does not provide an install target - mkdirp(prefix.lib) - mkdirp(prefix.include) - # Note: ZFP package builds .so files even on OSX - if '~shared' in spec: - install('lib/libzfp.a', prefix.lib) - else: - install('lib/libzfp.so', prefix.lib) - install('%s/zfp.h' % incdir, prefix.include) - install('%s/bitstream.h' % incdir, prefix.include) - if spec.satisfies('@0.5.1:'): - mkdirp('%s/zfp' % prefix.include) - install('%s/zfp/system.h' % incdir, '%s/zfp' % prefix.include) - install('%s/zfp/types.h' % incdir, '%s/zfp' % prefix.include) - else: - install('%s/types.h' % incdir, prefix.include) - install('%s/system.h' % incdir, prefix.include) + return args From 2a739ed03e4ebe46162632f6370bd7c355586cf2 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Wed, 2 Oct 2019 11:30:28 -0500 Subject: [PATCH 085/499] Replace expensive store.reindex() call with db.add() call. (#13021) --- lib/spack/spack/cmd/buildcache.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/cmd/buildcache.py b/lib/spack/spack/cmd/buildcache.py index 5f26fb8ef94..121a6f4aa50 100644 --- a/lib/spack/spack/cmd/buildcache.py +++ b/lib/spack/spack/cmd/buildcache.py @@ -391,7 +391,7 @@ def install_tarball(spec, args): bindist.extract_tarball(spec, tarball, args.allow_root, args.unsigned, args.force) spack.hooks.post_install(spec) - spack.store.store.reindex() + spack.store.db.add(spec, spack.store.layout) else: tty.die('Download of binary cache file for spec %s failed.' % spec.format()) From 64ff27626e3b42ccbbc2b3930b943e97dafa5c16 Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Wed, 2 Oct 2019 18:39:55 +0200 Subject: [PATCH 086/499] update py-jupyter-notebook to use the real releases (#13020) * github releases are not released versions, but from-source releases * they lack the mimification of the JS/CSS components and as such require node-js and npm, this conflicts with python@3: * this commit * drops the from-source dependencies on node-js and npm and * updates the checksums to the correct sha256 hashes of the pypi releases. The pypi-tarballs are different --- .../packages/py-jupyter-notebook/package.py | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py b/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py index 45239772e8d..55c2f0f2565 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py @@ -10,24 +10,20 @@ class PyJupyterNotebook(PythonPackage): """Jupyter Interactive Notebook""" homepage = "https://github.com/jupyter/notebook" - url = "https://github.com/jupyter/notebook/archive/4.2.3.tar.gz" + url = "https://pypi.io/packages/source/n/notebook/notebook-4.2.3.tar.gz" - version('4.2.3', '5c6b0b1303adacd8972c4db21eda3e98') - version('4.2.2', '7f9717ae4fed930d187a44c0707b6379') - version('4.2.1', '4286f1eaf608257bd69cad4042c7c2fe') - version('4.2.0', '136be6b72fe9db7f0269dc7fa5652a62') - version('4.1.0', '763ab54b3fc69f6225b9659b6994e756') - version('4.0.6', 'd70d8a6d01893f4b64df9edbc0e13b52') - version('4.0.5', '2681a70e4c62aafe7ce69f1da5799ac8') - version('4.0.4', 'ab72f28f6af8107d71241a4110e92c05') - version('4.0.3', '119beea793865ee4b1673a50043ead2a') - version('4.0.2', '77f371e9a23a840d14d8a60fee7ba1b7') + version('4.2.3', sha256='39a9603d3fe88b60de2903680c965cf643acf2c16fb2c6bac1d905e1042b5851') + version('4.2.2', sha256='418ba230c9b2e7e739940cae9fb4625e10a63f038e9c95cf1a9b7a244256ba38') + version('4.2.1', sha256='a49de524dabb99f214bdf2a58f26c7892650251a23a3669c6492fb180492e197') + version('4.2.0', sha256='e10c4916c77b48394796b5b1440d61d7b210f9941194048fe20ef88948016d84') + version('4.1.0', sha256='b597437ba33538221008e21fea71cd01eda9da1515ca3963d7c74e44f4b03d90') + version('4.0.6', sha256='f62e7a6afbc00bab3615b927595d27b1874cff3218bddcbab62f97f6dae567c3') + version('4.0.4', sha256='a57852514bce1b1cf41fa0311f6cf894960cf68b083b55e6c408316b598d5648') + version('4.0.2', sha256='8478d7e2ab474855b0ff841f693983388af8662d3af1adcb861acb900274f22a') variant('terminal', default=False, description="Enable terminal functionality") depends_on('python@2.7:2.8,3.3:') - depends_on('npm', type='build') - depends_on('node-js', type=('build', 'run')) depends_on('py-jinja2', type=('build', 'run')) depends_on('py-tornado@4:', type=('build', 'run')) depends_on('py-ipython-genutils', type=('build', 'run')) From a3a0e1cd2e6e39ba94dc3a4b476b509b19da6b83 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Thu, 3 Oct 2019 01:55:08 +0900 Subject: [PATCH 087/499] fujitsu compiler: Add 'required_libs'. (#13014) --- lib/spack/spack/compilers/fj.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/lib/spack/spack/compilers/fj.py b/lib/spack/spack/compilers/fj.py index 1ddffd91af7..1868972e964 100644 --- a/lib/spack/spack/compilers/fj.py +++ b/lib/spack/spack/compilers/fj.py @@ -28,6 +28,8 @@ class Fj(spack.compiler.Compiler): version_argument = '--version' version_regex = r'\((?:FCC|FRT)\) ([\d.]+)' + required_libs = ['libfj90i', 'libfj90f', 'libfjsrcinfo'] + @classmethod def verbose_flag(cls): return "-v" From d238b9d394f5405720089dce9b72fb92bc2e32bf Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 3 Oct 2019 01:56:37 +0900 Subject: [PATCH 088/499] breseq: fix dependency and limit compiler version. (#13013) --- var/spack/repos/builtin/packages/breseq/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/breseq/package.py b/var/spack/repos/builtin/packages/breseq/package.py index b979f724cce..4d93f72112d 100644 --- a/var/spack/repos/builtin/packages/breseq/package.py +++ b/var/spack/repos/builtin/packages/breseq/package.py @@ -22,11 +22,14 @@ class Breseq(AutotoolsPackage): depends_on('automake', type='build') depends_on('libtool', type='build') depends_on('m4', type='build') - depends_on('zlib', type='build') + depends_on('zlib', type='link') depends_on('bedtools2', type='run') depends_on('r', type='run') + conflicts('%gcc@:4.8') + conflicts('%clang@:3.3') + def setup_environment(self, spack_env, run_env): spack_env.set('LDFLAGS', "-L{0}".format(self.spec['zlib'].prefix.lib)) From 7d9514d3fa87d4df7006489b681d2cf209f4b715 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 3 Oct 2019 01:57:05 +0900 Subject: [PATCH 089/499] breakdancer: missing ncurses dependency. (#13011) --- var/spack/repos/builtin/packages/breakdancer/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py index 4b24c3961b2..3ad2cdfc01a 100644 --- a/var/spack/repos/builtin/packages/breakdancer/package.py +++ b/var/spack/repos/builtin/packages/breakdancer/package.py @@ -28,6 +28,8 @@ class Breakdancer(CMakePackage): depends_on('zlib') + depends_on('ncurses', type='link') + depends_on('perl-statistics-descriptive', type='run') depends_on('perl-math-cdf', type='run') depends_on('perl-gd-graph', type='run') From 1550d5cae644f962fb12ff584a94203e6125c179 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 3 Oct 2019 01:58:25 +0900 Subject: [PATCH 090/499] ants: missing zlib dependency and fix working directory in install. (#13010) --- var/spack/repos/builtin/packages/ants/package.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/ants/package.py b/var/spack/repos/builtin/packages/ants/package.py index 28bbce2b608..870ade0037c 100644 --- a/var/spack/repos/builtin/packages/ants/package.py +++ b/var/spack/repos/builtin/packages/ants/package.py @@ -20,8 +20,13 @@ class Ants(CMakePackage): version('2.2.0', '5661b949268100ac0f7baf6d2702b4dd') + depends_on('zlib', type='link') + def install(self, spec, prefix): - with working_dir(join_path('spack-build', 'ANTS-build'), create=False): + with working_dir( + join_path(self.build_directory, 'ANTS-build'), + create=False + ): make("install") install_tree('Scripts', prefix.bin) From afca223b3da4541e79533a75d7fb1fe3e39e986e Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 2 Oct 2019 09:58:46 -0700 Subject: [PATCH 091/499] new package: openldap (#12748) * new package: openldap * fix mistake * remove template text * fix build error involving perl * flake8 * improvements * introduce multi valued variant for tls support * improve tls variant * overwrite build phase as opposed install * improve style --- .../builtin/packages/openldap/package.py | 92 +++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 var/spack/repos/builtin/packages/openldap/package.py diff --git a/var/spack/repos/builtin/packages/openldap/package.py b/var/spack/repos/builtin/packages/openldap/package.py new file mode 100644 index 00000000000..3c8a9e453e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/openldap/package.py @@ -0,0 +1,92 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Openldap(AutotoolsPackage): + """ + OpenLDAP Software is an open source implementation of the Lightweight + Directory Access Protocol. The suite includes: + + slapd - stand-alone LDAP daemon (server) + libraries implementing the LDAP protocol, and + utilities, tools, and sample clients. + """ + + homepage = "https://www.openldap.org/" + url = "ftp://ftp.openldap.org/pub/OpenLDAP/openldap-release/openldap-2.4.9.tgz" + + version('2.4.48', sha256='d9523ffcab5cd14b709fcf3cb4d04e8bc76bb8970113255f372bc74954c6074d') + + variant('client_only', default=True, description='Client only installation') + variant('icu', default=False, description='Build with unicode support') + # Below, tls=none is not an option from programming point of view + # If +client_only, configure arguments for tls won't be enabled + variant('tls', default='gnutls', description='Build with TLS support', + values=('gnutls', 'openssl'), multi=False) + + variant('perl', default=False, description='Perl backend to Slapd') + + depends_on('icu4c', when='+icu') + depends_on('gnutls', when='~client_only tls=gnutls') + depends_on('openssl', when='~client_only tls=openssl') + depends_on('unixodbc', when='~client_only') + depends_on('postgresql', when='~client_only') + depends_on('berkeley-db', when='~client_only') # for slapd + # Recommended dependencies by Linux From Scratch + # depends_on('cyrus-sasl', when='~client_only') # not avail. in spack yet + # depends_on('openslp', when='~client_only') # not avail. in spack yet + # depends_on('Pth', when='~client_only') # not avail. in spack yet + depends_on('perl', when='~client_only+perl') # for slapd + + # Ref: http://www.linuxfromscratch.org/blfs/view/svn/server/openldap.html + @when('+client_only') + def configure_args(self): + return ['CPPFLAGS=-D_GNU_SOURCE', + '--disable-static', + '--enable-dynamic', + '--disable-debug', + '--disable-slapd', + ] + + @when('~client_only') + def configure_args(self): + # Ref: https://www.openldap.org/lists/openldap-technical/201009/msg00304.html + args = ['CPPFLAGS=-D_GNU_SOURCE', # fixes a build error, see Ref above + '--disable-static', + '--disable-debug', + '--with-cyrus-sasl', + '--enable-dynamic', + '--enable-crypt', + '--enable-spasswd', + '--enable-slapd', + '--enable-modules', + '--enable-rlookups', + '--enable-backends=mod', + '--disable-ndb', + '--disable-sql', + '--disable-shell', + '--disable-bdb', + '--disable-hdb', + '--enable-overlays=mod', + ] + + if '~client_only' in self.spec: + if 'tls=gnutls' in self.spec: + args.append('--with-tls=gnutls') + if 'tls=openssl' in self.spec: + args.append('--with-tls=openssl') + + if '+perl' in self.spec: + args.append('--enable-perl') + else: + args.append('--disable-perl') + + return args + + def build(self, spec, prefix): + make('depend') + make() From 21e95e41413b81d239a5fdd8e81fb212cf792b88 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Wed, 2 Oct 2019 09:59:11 -0700 Subject: [PATCH 092/499] Singularity 3.4.1 still needs the makefile patch (#13008) * Singularity 3.4.1 still needs the makefile patch * Constrain build patch to 3.4.0:3.4.1 --- var/spack/repos/builtin/packages/singularity/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py index ba0929c02b3..ed6322304fc 100644 --- a/var/spack/repos/builtin/packages/singularity/package.py +++ b/var/spack/repos/builtin/packages/singularity/package.py @@ -41,7 +41,7 @@ class Singularity(MakefilePackage): depends_on('shadow', type='run', when='@3.3:') depends_on('cryptsetup', type=('build', 'run'), when='@3.4:') - patch('singularity_v3.4.0_remove_root_check.patch', level=0, when='@3.4.0') + patch('singularity_v3.4.0_remove_root_check.patch', level=0, when='@3.4.0:3.4.1') # Go has novel ideas about how projects should be organized. # We'll point GOPATH at the stage dir, and move the unpacked src From 210dd594a1b752fa3c1303a8ad568712b412ae97 Mon Sep 17 00:00:00 2001 From: Dan Lipsa Date: Wed, 2 Oct 2019 13:00:03 -0400 Subject: [PATCH 093/499] Add cuda to paraview build. (#12996) --- var/spack/repos/builtin/packages/paraview/package.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index d68c7519784..fc6d0e99c29 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -7,7 +7,7 @@ import os -class Paraview(CMakePackage): +class Paraview(CMakePackage, CudaPackage): """ParaView is an open-source, multi-platform data analysis and visualization application.""" @@ -234,6 +234,16 @@ def nvariant_bool(feature): '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc ]) + if '+cuda' in spec: + cmake_args.extend([ + '-DPARAVIEW_USE_CUDA:BOOL=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS:BOOL=OFF' + ]) + else: + cmake_args.extend([ + '-DPARAVIEW_USE_CUDA:BOOL=OFF', + ]) + if 'darwin' in spec.architecture: cmake_args.extend([ '-DVTK_USE_X:BOOL=OFF', From 58c01792ef678cd9c2230812dd91c8a991d3cd65 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 3 Oct 2019 02:54:31 +0900 Subject: [PATCH 094/499] cnpy: add zlib dependency. (#13016) --- var/spack/repos/builtin/packages/cnpy/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/cnpy/package.py b/var/spack/repos/builtin/packages/cnpy/package.py index 4d9d0c34f5d..c9602ac168d 100644 --- a/var/spack/repos/builtin/packages/cnpy/package.py +++ b/var/spack/repos/builtin/packages/cnpy/package.py @@ -16,6 +16,8 @@ class Cnpy(CMakePackage): version('master', branch='master') + depends_on('zlib', type='link') + def cmake_args(self): args = [] if sys.platform == 'darwin': From b85ff04681ea1864ed5a66bcbe5e242ba54ecf6e Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 3 Oct 2019 02:54:50 +0900 Subject: [PATCH 095/499] denovogear: Add missing zlib depenbdency and fix open handling error. (#13017) --- .../repos/builtin/packages/denovogear/package.py | 3 +++ .../builtin/packages/denovogear/stream-open.patch | 12 ++++++++++++ 2 files changed, 15 insertions(+) create mode 100644 var/spack/repos/builtin/packages/denovogear/stream-open.patch diff --git a/var/spack/repos/builtin/packages/denovogear/package.py b/var/spack/repos/builtin/packages/denovogear/package.py index f214d37ee3e..61651ca492b 100644 --- a/var/spack/repos/builtin/packages/denovogear/package.py +++ b/var/spack/repos/builtin/packages/denovogear/package.py @@ -22,3 +22,6 @@ class Denovogear(CMakePackage): depends_on('boost@1.47:1.60', type=('build')) depends_on('htslib@1.2:', type=('build')) depends_on('eigen', type=('build')) + depends_on('zlib', type=('link')) + + patch('stream-open.patch', when='@:1.1.1') diff --git a/var/spack/repos/builtin/packages/denovogear/stream-open.patch b/var/spack/repos/builtin/packages/denovogear/stream-open.patch new file mode 100644 index 00000000000..23d699cc7d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/denovogear/stream-open.patch @@ -0,0 +1,12 @@ +diff -ru spack-src.org/src/dng-dnm.cc spack-src/src/dng-dnm.cc +--- spack-src.org/src/dng-dnm.cc 2015-04-21 09:16:59.000000000 +0900 ++++ spack-src/src/dng-dnm.cc 2019-10-02 15:08:28.892042247 +0900 +@@ -161,7 +161,7 @@ + int writeVCFHeader(std::ofstream& fo_vcf, string op_vcf_f, string bcf_file, string ped_file, string sample) + { + fo_vcf.open(op_vcf_f.c_str()); +- if(fo_vcf == NULL) { ++ if(fo_vcf.fail()) { + cerr<<"Unable to open vcf file for writing output. Exiting !"< Date: Thu, 3 Oct 2019 02:55:05 +0900 Subject: [PATCH 096/499] cdhit: add zlib dependency. (#13015) * cdhit: add zlib dependency. * Add zlib variant. --- var/spack/repos/builtin/packages/cdhit/package.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/cdhit/package.py b/var/spack/repos/builtin/packages/cdhit/package.py index f2c1d78b6f5..0f5172bfc1e 100644 --- a/var/spack/repos/builtin/packages/cdhit/package.py +++ b/var/spack/repos/builtin/packages/cdhit/package.py @@ -17,15 +17,19 @@ class Cdhit(MakefilePackage): version('4.6.8', 'bdd73ec0cceab6653aab7b31b57c5a8b') variant('openmp', default=True, description='Compile with multi-threading support') + variant('zlib', default=True, description='Compile with zlib') depends_on('perl', type=('build', 'run')) + depends_on('zlib', when='+zlib', type='link') def build(self, spec, prefix): mkdirp(prefix.bin) + make_args = [] if '~openmp' in spec: - make('openmp=no') - else: - make() + make_args.append('openmp=no') + if '~zlib' in spec: + make_args.append('zlib=no') + make(*make_args) def setup_environment(self, spack_env, run_env): spack_env.set('PREFIX', prefix.bin) From d99b92febdd709ac741551752262b0aff896efa0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tiziano=20M=C3=BCller?= Date: Wed, 2 Oct 2019 21:31:19 +0200 Subject: [PATCH 097/499] libint + cp2k: 2-stage build with 'tune' and 'fortran' variants (#12475) * libint: switch to 2-stage build for 2.6.0+ * libint: add tune and fortran variants * cp2k: add support for libint >= 2.0 * cp2k: use pkg-config for linking libxc --- .../repos/builtin/packages/cp2k/package.py | 66 ++++++++++----- .../repos/builtin/packages/libint/package.py | 82 +++++++++++++++++++ 2 files changed, 128 insertions(+), 20 deletions(-) diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index 23edfd10b21..36b94926dab 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -61,6 +61,14 @@ class Cp2k(MakefilePackage, CudaPackage): variant('cuda_blas', default=False, description=('Use CUBLAS for general matrix operations in DBCSR')) + HFX_LMAX_RANGE = range(4, 8) + + variant('lmax', + description='Maximum supported angular momentum (HFX and others)', + default='5', + values=list(HFX_LMAX_RANGE), + multi=False) + depends_on('python', type='build') depends_on('fftw@3:', when='~openmp') @@ -80,11 +88,19 @@ class Cp2k(MakefilePackage, CudaPackage): depends_on('libxsmm@1.11:~header-only', when='smm=libxsmm') # use pkg-config (support added in libxsmm-1.10) to link to libxsmm depends_on('pkgconfig', type='build', when='smm=libxsmm') + # ... and in CP2K 7.0+ for linking to libint2 + depends_on('pkgconfig', type='build', when='@7.0:') # libint & libxc are always statically linked - depends_on('libint@1.1.4:1.2', when='@3.0:', type='build') + depends_on('libint@1.1.4:1.2', when='@3.0:6.9', type='build') + for lmax in HFX_LMAX_RANGE: + # libint2 can be linked dynamically again + depends_on('libint@2.6.0:+fortran tune=cp2k-lmax-{0}'.format(lmax), + when='@7.0: lmax={0}'.format(lmax)) + depends_on('libxc@2.2.2:', when='+libxc@:5.5999', type='build') - depends_on('libxc@4.0.3:', when='+libxc@6.0:', type='build') + depends_on('libxc@4.0.3:', when='+libxc@6.0:6.9', type='build') + depends_on('libxc@4.0.3:', when='+libxc@7.0:') depends_on('mpi@2:', when='+mpi') depends_on('scalapack', when='+mpi') @@ -169,13 +185,17 @@ def edit(self, spec, prefix): dflags = ['-DNDEBUG'] cppflags = [ - '-D__FFTW3', '-D__LIBINT', - '-D__LIBINT_MAX_AM=6', - '-D__LIBDERIV_MAX_AM1=5', + '-D__FFTW3', fftw.headers.cpp_flags, ] + if '@:6.9' in spec: + cppflags += [ + '-D__LIBINT_MAX_AM=6', + '-D__LIBDERIV_MAX_AM1=5', + ] + if '^mpi@3:' in spec: cppflags.append('-D__MPI_VERSION=3') elif '^mpi@2:' in spec: @@ -220,14 +240,18 @@ def edit(self, spec, prefix): if 'superlu-dist@4.3' in spec: ldflags.insert(0, '-Wl,--allow-multiple-definition') - # libint-1.x.y has to be linked statically to work around - # inconsistencies in its Fortran interface definition - # (short-int vs int) which otherwise causes segfaults at runtime - # due to wrong offsets into the shared library symbols. - libs.extend([ - os.path.join(spec['libint'].libs.directories[0], 'libderiv.a'), - os.path.join(spec['libint'].libs.directories[0], 'libint.a'), - ]) + if '@:6.9' in spec: + # libint-1.x.y has to be linked statically to work around + # inconsistencies in its Fortran interface definition + # (short-int vs int) which otherwise causes segfaults at runtime + # due to wrong offsets into the shared library symbols. + libs.extend([ + os.path.join(spec['libint'].libs.directories[0], 'libderiv.a'), + os.path.join(spec['libint'].libs.directories[0], 'libint.a'), + ]) + else: + fcflags += ['$(shell pkg-config --cflags libint2)'] + libs += ['$(shell pkg-config --libs libint2)'] if '+plumed' in self.spec: dflags.extend(['-D__PLUMED2']) @@ -286,14 +310,16 @@ def edit(self, spec, prefix): libs.append(wannier) if '+libxc' in spec: - libxc = spec['libxc:fortran,static'] - cppflags += [ - '-D__LIBXC', - libxc.headers.cpp_flags - ] + cppflags += ['-D__LIBXC'] - ldflags.append(libxc.libs.search_flags) - libs.append(str(libxc.libs)) + if '@:6.9' in spec: + libxc = spec['libxc:fortran,static'] + cppflags += [libxc.headers.cpp_flags] + ldflags.append(libxc.libs.search_flags) + libs.append(str(libxc.libs)) + else: + fcflags += ['$(shell pkg-config --cflags libxcf03)'] + libs += ['$(shell pkg-config --libs libxcf03)'] if '+pexsi' in self.spec: cppflags.append('-D__LIBPEXSI') diff --git a/var/spack/repos/builtin/packages/libint/package.py b/var/spack/repos/builtin/packages/libint/package.py index 08094d5c680..d58e4fec1d3 100644 --- a/var/spack/repos/builtin/packages/libint/package.py +++ b/var/spack/repos/builtin/packages/libint/package.py @@ -3,9 +3,19 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os from spack import * +TUNE_VARIANTS = ( + 'none', + 'cp2k-lmax-4', + 'cp2k-lmax-5', + 'cp2k-lmax-6', + 'cp2k-lmax-7', +) + + class Libint(AutotoolsPackage): """Libint is a high-performance library for computing Gaussian integrals in quantum mechanics. @@ -14,6 +24,7 @@ class Libint(AutotoolsPackage): homepage = "https://github.com/evaleev/libint" url = "https://github.com/evaleev/libint/archive/v2.1.0.tar.gz" + version('2.6.0', sha256='4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa') version('2.4.2', sha256='86dff38065e69a3a51d15cfdc638f766044cb87e5c6682d960c14f9847e2eac3') version('2.4.1', sha256='0513be124563fdbbc7cd3c7043e221df1bda236a037027ba9343429a27db8ce4') version('2.4.0', sha256='52eb16f065406099dcfaceb12f9a7f7e329c9cfcf6ed9bfacb0cff7431dd6019') @@ -22,6 +33,12 @@ class Libint(AutotoolsPackage): version('1.1.6', sha256='f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6') version('1.1.5', sha256='ec8cd4a4ba1e1a98230165210c293632372f0e573acd878ed62e5ec6f8b6174b') + variant('fortran', default=False, + description='Build & install Fortran bindings') + variant('tune', default='none', multi=False, + values=TUNE_VARIANTS, + description='Tune libint for use with the given package') + # Build dependencies depends_on('autoconf@2.52:', type='build') depends_on('automake', type='build') @@ -31,6 +48,11 @@ class Libint(AutotoolsPackage): depends_on('boost', when='@2:') depends_on('gmp', when='@2:') + for tvariant in TUNE_VARIANTS[1:]: + conflicts('tune={0}'.format(tvariant), when='@:2.5.99', + msg=('for versions prior to 2.6, tuning for specific' + 'codes/configurations is not supported')) + def url_for_version(self, version): base_url = "https://github.com/evaleev/libint/archive" if version == Version('1.0.0'): @@ -45,6 +67,10 @@ def autoreconf(self, spec, prefix): aclocal('-I', 'lib/autoconf') autoconf() + if '@2.6.0:' in spec: + # skip tarball creation and removal of dir with generated code + filter_file(r'^(export::.*)\s+tgz$', r'\1', 'export/Makefile') + @property def optflags(self): flags = '-O2' @@ -89,4 +115,60 @@ def configure_args(self): '--with-libint-max-am=5', '--with-libderiv-max-am1=4' ]) + + if '@2.6.0:' in self.spec: + config_args += ['--with-libint-exportdir=generated'] + + tune_value = self.spec.variants['tune'].value + if tune_value.startswith('cp2k'): + lmax = int(tune_value.split('-lmax-')[1]) + config_args += [ + '--enable-eri=1', + '--enable-eri2=1', + '--enable-eri3=1', + '--with-max-am={0}'.format(lmax), + '--with-eri-max-am={0},{1}'.format(lmax, lmax - 1), + '--with-eri2-max-am={0},{1}'.format(lmax + 2, lmax + 1), + '--with-eri3-max-am={0},{1}'.format(lmax + 2, lmax + 1), + '--with-opt-am=3', + # keep code-size at an acceptable limit, + # cf. https://github.com/evaleev/libint/wiki#program-specific-notes: + '--enable-generic-code', + '--disable-unrolling', + ] + return config_args + + @property + def build_targets(self): + if '@2.6.0:' in self.spec: + return ['export'] + + return [] + + @when('@2.6.0:') + def install(self, spec, prefix): + """ + Starting from libint 2.6.0 we're using the 2-stage build + to get support for the Fortran bindings, required by some + packages (CP2K notably). + """ + + # upstream says that using configure/make for the generated code + # is deprecated and one should use CMake, but with the currently + # recent 2.7.0.b1 it still doesn't work + with working_dir(os.path.join(self.build_directory, 'generated')): + # straight from the AutotoolsPackage class: + options = [ + '--prefix={0}'.format(prefix), + '--enable-shared', + '--with-cxx-optflags={0}'.format(self.optflags), + ] + + if '+fortran' in spec: + options += ['--enable-fortran'] + + configure = Executable('./configure') + configure(*options) + make() + make('install') From b084d095bc72d4455620b8b54fa5ff87e810cee4 Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 2 Oct 2019 13:50:57 -0700 Subject: [PATCH 098/499] New package: mapnik (#12708) --- .../repos/builtin/packages/mapnik/package.py | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mapnik/package.py diff --git a/var/spack/repos/builtin/packages/mapnik/package.py b/var/spack/repos/builtin/packages/mapnik/package.py new file mode 100644 index 00000000000..de3e1ffb90f --- /dev/null +++ b/var/spack/repos/builtin/packages/mapnik/package.py @@ -0,0 +1,54 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Mapnik(AutotoolsPackage): + """ + mapnik combines pixel-perfect image output with lightning-fast + cartographic algorithms, and exposes interfaces in C++, Python, and Node + """ + + homepage = "https://mapnik.org/" + url = "https://github.com/mapnik/mapnik/releases/download/v3.0.22/mapnik-v3.0.22.tar.bz2" + + version('3.0.22', sha256='930612ad9e604b6a29b9cea1bc1de85cf7cf2b2b8211f57ec8b6b94463128ab9') + + depends_on('python', type=('build', 'run')) + # Build fails with boost@1.70 + depends_on('boost@:1.69.0+regex+filesystem+system+icu+program_options cxxstd=11') + depends_on('icu4c') + depends_on('zlib') + depends_on('freetype') + depends_on('libxml2') + depends_on('harfbuzz') + depends_on('libpng') + depends_on('libjpeg') + depends_on('libtiff') + depends_on('proj') + depends_on('cairo') + depends_on('postgresql', type=('build', 'link', 'run')) + depends_on('gdal', type=('build', 'link', 'run')) + depends_on('sqlite+rtree', type=('build', 'link', 'run')) + depends_on('libwebp') + + conflicts('%gcc@9.0.0:') + + def setup_environment(self, spack_env, run_env): + spec = self.spec + spack_env.set('GDAL_DATA', spec['gdal'].prefix.share.gdal) + + def configure_args(self): + return [ + 'CXXFLAGS="-std=c++11"', + 'PREFIX=' + self.prefix, + 'BOOST_INCLUDES=' + self.spec['boost'].prefix.include, + 'BOOST_LIBS=' + self.spec['boost'].prefix.lib.directories[0], + 'PROJ_INCLUDES=' + self.spec['proj'].prefix.include, + 'PROJ_LIBS=' + self.spec['proj'].prefix.lib.directories[0], + 'CAIRO_INCLUDES=' + self.spec['cairo'].prefix.include, + 'CAIRO_LIBS=' + self.spec['cairo'].prefix.lib.directories[0], + ] From b11984767b79f05d261ef112a46e09bc1939204f Mon Sep 17 00:00:00 2001 From: Miroslav Stoyanov <30537612+mkstoyanov@users.noreply.github.com> Date: Wed, 2 Oct 2019 19:35:49 -0400 Subject: [PATCH 099/499] added tasmanian version 7.0 to spack (#13003) --- .../builtin/packages/tasmanian/addons70.patch | 25 +++++++++++++++++++ .../builtin/packages/tasmanian/package.py | 16 +++++++++--- .../packages/tasmanian/packageconf70.patch | 15 +++++++++++ 3 files changed, 52 insertions(+), 4 deletions(-) create mode 100644 var/spack/repos/builtin/packages/tasmanian/addons70.patch create mode 100644 var/spack/repos/builtin/packages/tasmanian/packageconf70.patch diff --git a/var/spack/repos/builtin/packages/tasmanian/addons70.patch b/var/spack/repos/builtin/packages/tasmanian/addons70.patch new file mode 100644 index 00000000000..8d983c6308b --- /dev/null +++ b/var/spack/repos/builtin/packages/tasmanian/addons70.patch @@ -0,0 +1,25 @@ +diff --git a/Addons/CMakeLists.txt b/Addons/CMakeLists.txt +index 1279ada..0b6d9be 100644 +--- a/Addons/CMakeLists.txt ++++ b/Addons/CMakeLists.txt +@@ -49,19 +49,7 @@ endif() + + # The Tasmanian MPI capabilities are templated into the Addons + if (Tasmanian_ENABLE_MPI) +- target_link_libraries(Tasmanian_addons INTERFACE ${MPI_CXX_LIBRARIES}) +- +- if (DEFINED MPI_CXX_INCLUDE_PATH) +- target_include_directories(Tasmanian_addons INTERFACE "${MPI_CXX_INCLUDE_PATH}") +- endif() +- +- if(DEFINED MPI_CXX_COMPILE_FLAGS) +- target_compile_options(Tasmanian_addons INTERFACE "${MPI_CXX_COMPILE_FLAGS}") +- endif() +- +- if(DEFINED MPI_CXX_LINK_FLAGS) +- set_target_properties(Tasmanian_addons PROPERTIES INTERFACE_LINK_OPTIONS "${MPI_CXX_LINK_FLAGS}") +- endif() ++ target_link_libraries(Tasmanian_addons INTERFACE MPI::MPI_CXX) + + add_executable(Tasmanian_mpitester testMPI.cpp testMPI.hpp testMPIDream.hpp) + set_target_properties(Tasmanian_mpitester PROPERTIES OUTPUT_NAME "mpitester") diff --git a/var/spack/repos/builtin/packages/tasmanian/package.py b/var/spack/repos/builtin/packages/tasmanian/package.py index a7c2672250e..e8dbe58113d 100644 --- a/var/spack/repos/builtin/packages/tasmanian/package.py +++ b/var/spack/repos/builtin/packages/tasmanian/package.py @@ -12,13 +12,14 @@ class Tasmanian(CMakePackage): interpolation as well as parameter calibration.""" homepage = 'http://tasmanian.ornl.gov' - url = 'https://github.com/ORNL/TASMANIAN/archive/v6.0.tar.gz' + url = 'https://github.com/ORNL/TASMANIAN/archive/v7.0.tar.gz' git = 'https://github.com/ORNL/TASMANIAN.git' maintainers = ['mkstoyanov'] version('develop', branch='master') + version('7.0', '60916a3dee3d23c1c41ca8005238f66e') # use for xsdk-0.5.0 version('6.0', '43dcb1d2bcb2f2c829ad046d0e91e83d') # use for xsdk-0.4.0 version('5.1', '5d904029a24470a6acf4a87d3339846e') @@ -54,7 +55,9 @@ class Tasmanian(CMakePackage): description='CMake build type', values=('Debug', 'Release')) - depends_on('cmake@3.5.1:', type='build') + depends_on('cmake@2.8:', type='build') + depends_on('cmake@3.5:', type='build', when='@6.0:') + depends_on('cmake@3.10:', type='build', when='@7.0:') depends_on('python@2.7:', when='+python', type=('build', 'run')) depends_on('py-numpy', when='+python', type=('build', 'run')) @@ -68,7 +71,8 @@ class Tasmanian(CMakePackage): depends_on('cuda@8.0.61:', when='+cuda', type=('build', 'run')) depends_on('cuda@8.0.61:', when='+magma', type=('build', 'run')) - depends_on('magma@2.4.0:', when='+magma', type=('build', 'run')) + depends_on('magma@2.4.0:', when='+magma @6.0:', type=('build', 'run')) + depends_on('magma@2.5.0:', when='+magma @7.0:', type=('build', 'run')) conflicts('-cuda', when='+magma') # currently MAGMA only works with CUDA @@ -77,6 +81,10 @@ class Tasmanian(CMakePackage): conflicts('+mpi', when='@:5.1') # MPI is broken prior to 6.0 conflicts('+xsdkflags', when='@:5.1') # 6.0 is the first version included in xSDK + # patching some bugs + patch('addons70.patch', when='@7.0') + patch('packageconf70.patch', when='@7.0') + def cmake_args(self): spec = self.spec @@ -85,7 +93,7 @@ def cmake_args(self): '-DUSE_XSDK_DEFAULTS:BOOL=ON', '-DXSDK_ENABLE_PYTHON:BOOL={0}'.format( 'ON' if '+python' in spec else 'OFF'), - '-DTasmanian_ENABLE_MPI:BOOL={0}'.format( + '-DTPL_ENABLE_MPI:BOOL={0}'.format( 'ON' if '+mpi' in spec else 'OFF'), '-DXSDK_ENABLE_OPENMP:BOOL={0}'.format( 'ON' if '+openmp' in spec else 'OFF'), diff --git a/var/spack/repos/builtin/packages/tasmanian/packageconf70.patch b/var/spack/repos/builtin/packages/tasmanian/packageconf70.patch new file mode 100644 index 00000000000..c53255687f0 --- /dev/null +++ b/var/spack/repos/builtin/packages/tasmanian/packageconf70.patch @@ -0,0 +1,15 @@ +diff --git a/Config/TasmanianConfig.in.cmake b/Config/TasmanianConfig.in.cmake +index 8912e4c..df54aaf 100644 +--- a/Config/TasmanianConfig.in.cmake ++++ b/Config/TasmanianConfig.in.cmake +@@ -7,6 +7,10 @@ cmake_minimum_required(VERSION 3.10) + # but this doesn't seem to work, not sure if this is a "relocatable package" (low concern) + include("@CMAKE_INSTALL_PREFIX@/lib/@CMAKE_PROJECT_NAME@/@CMAKE_PROJECT_NAME@.cmake") + ++if (@Tasmanian_ENABLE_MPI@) ++ find_package(MPI REQUIRED) ++endif() ++ + add_executable(Tasmanian::tasgrid IMPORTED) + set_property(TARGET Tasmanian::tasgrid PROPERTY IMPORTED_LOCATION "@CMAKE_INSTALL_PREFIX@/bin/tasgrid${CMAKE_EXECUTABLE_SUFFIX_CXX}") + From 76b9c561109e4a19375231fd6e8fd8a1c7947f34 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 3 Oct 2019 07:15:01 +0200 Subject: [PATCH 100/499] Remove support for generating dotkit files (#11986) Dotkit is being used only at a few sites and has been deprecated on new machines. This commit removes all the code that provide support for the generation of dotkit module files. A new validator named "deprecatedProperties" has been added to the jsonschema validators. It permits to prompt a warning message or exit with an error if a property that has been marked as deprecated is encountered. * Removed references to dotkit in the docs * Removed references to dotkit in setup-env-test.sh * Added a unit test for the 'deprecatedProperties' schema validator --- etc/spack/defaults/config.yaml | 1 - etc/spack/defaults/modules.yaml | 1 - lib/spack/docs/basic_usage.rst | 13 +--- lib/spack/docs/config_yaml.rst | 1 - lib/spack/docs/configuration.rst | 2 - lib/spack/docs/getting_started.rst | 2 +- lib/spack/docs/module_file_support.rst | 50 ++++------------ lib/spack/spack/cmd/module.py | 2 - lib/spack/spack/cmd/modules/__init__.py | 1 - lib/spack/spack/cmd/modules/dotkit.py | 19 ------ lib/spack/spack/cmd/unuse.py | 23 ------- lib/spack/spack/cmd/use.py | 24 -------- lib/spack/spack/hooks/__init__.py | 2 +- lib/spack/spack/main.py | 1 - lib/spack/spack/modules/__init__.py | 6 +- lib/spack/spack/modules/dotkit.py | 60 ------------------- lib/spack/spack/schema/__init__.py | 27 ++++++++- lib/spack/spack/schema/config.py | 7 +++ lib/spack/spack/schema/modules.py | 18 +++++- lib/spack/spack/schema/upstreams.py | 3 +- lib/spack/spack/test/cmd/module.py | 3 +- lib/spack/spack/test/data/config/modules.yaml | 1 - .../data/modules/dotkit/autoload_direct.yaml | 5 -- .../modules/dotkit/override_template.yaml | 5 -- lib/spack/spack/test/modules/dotkit.py | 51 ---------------- lib/spack/spack/test/schema.py | 25 ++++++++ share/spack/csh/spack.csh | 34 ++++------- share/spack/qa/setup-env-test.sh | 32 +--------- share/spack/setup-env.csh | 8 +-- share/spack/setup-env.sh | 37 ++++-------- share/spack/spack-completion.bash | 49 +-------------- share/spack/templates/modules/modulefile.dk | 31 ---------- .../override-module-templates/package.py | 1 - .../repos/builtin/packages/go/package.py | 2 +- 34 files changed, 121 insertions(+), 426 deletions(-) delete mode 100644 lib/spack/spack/cmd/modules/dotkit.py delete mode 100644 lib/spack/spack/cmd/unuse.py delete mode 100644 lib/spack/spack/cmd/use.py delete mode 100644 lib/spack/spack/modules/dotkit.py delete mode 100644 lib/spack/spack/test/data/modules/dotkit/autoload_direct.yaml delete mode 100644 lib/spack/spack/test/data/modules/dotkit/override_template.yaml delete mode 100644 lib/spack/spack/test/modules/dotkit.py delete mode 100644 share/spack/templates/modules/modulefile.dk diff --git a/etc/spack/defaults/config.yaml b/etc/spack/defaults/config.yaml index 1b6d83f3591..d6c9551d93b 100644 --- a/etc/spack/defaults/config.yaml +++ b/etc/spack/defaults/config.yaml @@ -32,7 +32,6 @@ config: module_roots: tcl: $spack/share/spack/modules lmod: $spack/share/spack/lmod - dotkit: $spack/share/spack/dotkit # Temporary locations Spack can try to use for builds. diff --git a/etc/spack/defaults/modules.yaml b/etc/spack/defaults/modules.yaml index b5ea65da95b..1d91b0c88c4 100644 --- a/etc/spack/defaults/modules.yaml +++ b/etc/spack/defaults/modules.yaml @@ -16,7 +16,6 @@ modules: enable: - tcl - - dotkit prefix_inspections: bin: - PATH diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index 1c61a388995..f6ceb2a9e69 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -1190,24 +1190,15 @@ Using Extensions ^^^^^^^^^^^^^^^^ There are three ways to get ``numpy`` working in Python. The first is -to use :ref:`shell-support`. You can simply ``use`` or ``load`` the +to use :ref:`shell-support`. You can simply ``load`` the module for the extension, and it will be added to the ``PYTHONPATH`` -in your current shell. - -For tcl modules: +in your current shell: .. code-block:: console $ spack load python $ spack load py-numpy -or, for dotkit: - -.. code-block:: console - - $ spack use python - $ spack use py-numpy - Now ``import numpy`` will succeed for as long as you keep your current session open. diff --git a/lib/spack/docs/config_yaml.rst b/lib/spack/docs/config_yaml.rst index 92030b8ac9d..53398f55c2d 100644 --- a/lib/spack/docs/config_yaml.rst +++ b/lib/spack/docs/config_yaml.rst @@ -74,7 +74,6 @@ the location for each type of module. e.g.: module_roots: tcl: $spack/share/spack/modules lmod: $spack/share/spack/lmod - dotkit: $spack/share/spack/dotkit See :ref:`modules` for details. diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst index c89a90f2e91..7721c07a8e1 100644 --- a/lib/spack/docs/configuration.rst +++ b/lib/spack/docs/configuration.rst @@ -463,7 +463,6 @@ account all scopes. For example, to see the fully merged module_roots: tcl: $spack/share/spack/modules lmod: $spack/share/spack/lmod - dotkit: $spack/share/spack/dotkit build_stage: - $tempdir/$user/spack-stage - ~/.spack/stage @@ -514,7 +513,6 @@ down the problem: /home/myuser/spack/etc/spack/defaults/config.yaml:32 module_roots: /home/myuser/spack/etc/spack/defaults/config.yaml:33 tcl: $spack/share/spack/modules /home/myuser/spack/etc/spack/defaults/config.yaml:34 lmod: $spack/share/spack/lmod - /home/myuser/spack/etc/spack/defaults/config.yaml:35 dotkit: $spack/share/spack/dotkit /home/myuser/spack/etc/spack/defaults/config.yaml:49 build_stage: /home/myuser/spack/etc/spack/defaults/config.yaml:50 - $tempdir/$user/spack-stage /home/myuser/spack/etc/spack/defaults/config.yaml:51 - ~/.spack/stage diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst index ec3dc51eedf..eeeffcc25f3 100644 --- a/lib/spack/docs/getting_started.rst +++ b/lib/spack/docs/getting_started.rst @@ -71,7 +71,7 @@ This automatically adds Spack to your ``PATH`` and allows the ``spack`` command to be used to execute spack :ref:`commands ` and :ref:`useful packaging commands `. -If :ref:`environment-modules or dotkit ` is +If :ref:`environment-modules ` is installed and available, the ``spack`` command can also load and unload :ref:`modules `. diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst index f6dbdf3f190..7ce2398af2c 100644 --- a/lib/spack/docs/module_file_support.rst +++ b/lib/spack/docs/module_file_support.rst @@ -13,8 +13,8 @@ The use of module systems to manage user environment in a controlled way is a common practice at HPC centers that is often embraced also by individual programmers on their development machines. To support this common practice Spack integrates with `Environment Modules -`_ , `LMod -`_ and `Dotkit `_ by +`_ and `LMod +`_ by providing post-install hooks that generate module files and commands to manipulate them. .. note:: @@ -67,7 +67,7 @@ to load the ``cmake`` module: $ module load cmake-3.7.2-gcc-6.3.0-fowuuby Neither of these is particularly pretty, easy to remember, or -easy to type. Luckily, Spack has its own interface for using modules and dotkits. +easy to type. Luckily, Spack has its own interface for using modules. ^^^^^^^^^^^^^ Shell support @@ -108,20 +108,10 @@ that the startup time may be slightly increased because of that. ^^^^^^^^^^^^^^^^^^^^^^^ Once you have shell support enabled you can use the same spec syntax -you're used to: +you're used to and you can use the same shortened names you use +everywhere else in Spack. -========================= ========================== -Modules Dotkit -========================= ========================== -``spack load `` ``spack use `` -``spack unload `` ``spack unuse `` -========================= ========================== - -And you can use the same shortened names you use everywhere else in -Spack. - -For example, if you are using dotkit, this will add the ``mpich`` -package built with ``gcc`` to your path: +For example this will add the ``mpich`` package built with ``gcc`` to your path: .. code-block:: console @@ -129,17 +119,10 @@ package built with ``gcc`` to your path: # ... wait for install ... - $ spack use mpich %gcc@4.4.7 # dotkit - Prepending: mpich@3.0.4%gcc@4.4.7 (ok) + $ spack load mpich %gcc@4.4.7 # modules $ which mpicc ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc -Or, similarly if you are using modules, you could type: - -.. code-block:: console - - $ spack load mpich %gcc@4.4.7 # modules - These commands will add appropriate directories to your ``PATH``, ``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH``. When you no longer want to use a package, you can type unload or unuse similarly: @@ -147,13 +130,12 @@ want to use a package, you can type unload or unuse similarly: .. code-block:: console $ spack unload mpich %gcc@4.4.7 # modules - $ spack unuse mpich %gcc@4.4.7 # dotkit .. note:: - These ``use``, ``unuse``, ``load``, and ``unload`` subcommands are + The ``load`` and ``unload`` subcommands are only available if you have enabled Spack's shell support *and* you - have dotkit or modules installed on your machine. + have environment-modules installed on your machine. ^^^^^^^^^^^^^^^^^^^^^^ Ambiguous module names @@ -292,8 +274,6 @@ that can be generated by Spack: +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+ | | **Hook name** | **Default root directory** | **Default template file** | **Compatible tools** | +=============================+====================+===============================+==============================================+======================+ - | **Dotkit** | ``dotkit`` | share/spack/dotkit | share/spack/templates/modules/modulefile.dk | DotKit | - +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+ | **TCL - Non-Hierarchical** | ``tcl`` | share/spack/modules | share/spack/templates/modules/modulefile.tcl | Env. Modules/LMod | +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+ | **Lua - Hierarchical** | ``lmod`` | share/spack/lmod | share/spack/templates/modules/modulefile.lua | LMod | @@ -377,7 +357,7 @@ are named ``modules.yaml``. The default configuration: .. literalinclude:: _spack_root/etc/spack/defaults/modules.yaml :language: yaml -activates the hooks to generate ``tcl`` and ``dotkit`` module files and inspects +activates the hooks to generate ``tcl`` module files and inspects the installation folder of each package for the presence of a set of subdirectories (``bin``, ``man``, ``share/man``, etc.). If any is found its full path is prepended to the environment variables listed below the folder name. @@ -399,12 +379,9 @@ to the generator being customized: modules: enable: - tcl - - dotkit - lmod tcl: # contains environment modules specific customizations - dotkit: - # contains dotkit specific customizations lmod: # contains lmod specific customizations @@ -590,15 +567,14 @@ do so by using the environment blacklist: .. code-block:: yaml modules: - dotkit: + tcl: all: filter: # Exclude changes to any of these variables environment_blacklist: ['CPATH', 'LIBRARY_PATH'] -The configuration above will generate dotkit module files that will not contain -modifications to either ``CPATH`` or ``LIBRARY_PATH`` and environment module -files that instead will contain these modifications. +The configuration above will generate module files that will not contain +modifications to either ``CPATH`` or ``LIBRARY_PATH``. .. _autoloading-dependencies: diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index b337e454ef1..86a27786dab 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -7,7 +7,6 @@ import llnl.util.tty as tty -import spack.cmd.modules.dotkit import spack.cmd.modules.lmod import spack.cmd.modules.tcl @@ -23,7 +22,6 @@ def setup_parser(subparser): sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command') - spack.cmd.modules.dotkit.add_command(sp, _subcommands) spack.cmd.modules.lmod.add_command(sp, _subcommands) spack.cmd.modules.tcl.add_command(sp, _subcommands) diff --git a/lib/spack/spack/cmd/modules/__init__.py b/lib/spack/spack/cmd/modules/__init__.py index 33367f6c88d..4f1e640f6c3 100644 --- a/lib/spack/spack/cmd/modules/__init__.py +++ b/lib/spack/spack/cmd/modules/__init__.py @@ -137,7 +137,6 @@ def loads(module_type, specs, args, out=sys.stdout): module_commands = { 'tcl': 'module load ', 'lmod': 'module load ', - 'dotkit': 'use ' } d = { diff --git a/lib/spack/spack/cmd/modules/dotkit.py b/lib/spack/spack/cmd/modules/dotkit.py deleted file mode 100644 index fae242a1990..00000000000 --- a/lib/spack/spack/cmd/modules/dotkit.py +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -import functools - -import spack.cmd.modules - - -def add_command(parser, command_dict): - dotkit_parser = parser.add_parser( - 'dotkit', help='manipulate dotkit module files' - ) - spack.cmd.modules.setup_parser(dotkit_parser) - - command_dict['dotkit'] = functools.partial( - spack.cmd.modules.modules_cmd, module_type='dotkit' - ) diff --git a/lib/spack/spack/cmd/unuse.py b/lib/spack/spack/cmd/unuse.py deleted file mode 100644 index 930fa316d04..00000000000 --- a/lib/spack/spack/cmd/unuse.py +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -import argparse -from spack.cmd.common import print_module_placeholder_help - -description = "remove package from environment using dotkit" -section = "modules" -level = "long" - - -def setup_parser(subparser): - """Parser is only constructed so that this prints a nice help - message with -h. """ - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help='spec of package to unuse with dotkit') - - -def unuse(parser, args): - print_module_placeholder_help() diff --git a/lib/spack/spack/cmd/use.py b/lib/spack/spack/cmd/use.py deleted file mode 100644 index 1a17eb7cf22..00000000000 --- a/lib/spack/spack/cmd/use.py +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -import argparse -from spack.cmd.common import print_module_placeholder_help, arguments - -description = "add package to environment using dotkit" -section = "modules" -level = "long" - - -def setup_parser(subparser): - """Parser is only constructed so that this prints a nice help - message with -h. """ - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help='spec of package to use with dotkit') - arguments.add_common_arguments(subparser, ['recurse_dependencies']) - - -def use(parser, args): - print_module_placeholder_help() diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py index d17e25b1ac7..3938f9e6d3d 100644 --- a/lib/spack/spack/hooks/__init__.py +++ b/lib/spack/spack/hooks/__init__.py @@ -19,7 +19,7 @@ * post_uninstall(spec) This can be used to implement support for things like module - systems (e.g. modules, dotkit, etc.) or to add other custom + systems (e.g. modules, lmod, etc.) or to add other custom features. """ import os.path diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py index c3746b6b26a..0984aa3b006 100644 --- a/lib/spack/spack/main.py +++ b/lib/spack/spack/main.py @@ -591,7 +591,6 @@ def shell_set(var, value): module_roots = spack.config.get('config:module_roots') module_to_roots = { 'tcl': list(), - 'dotkit': list(), 'lmod': list() } for name, path in module_roots.items(): diff --git a/lib/spack/spack/modules/__init__.py b/lib/spack/spack/modules/__init__.py index f1897ab943c..20864b5f271 100644 --- a/lib/spack/spack/modules/__init__.py +++ b/lib/spack/spack/modules/__init__.py @@ -4,24 +4,20 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) """This package contains code for creating environment modules, which can -include dotkits, TCL non-hierarchical modules, LUA hierarchical modules, and -others. +include TCL non-hierarchical modules, LUA hierarchical modules, and others. """ from __future__ import absolute_import -from .dotkit import DotkitModulefileWriter from .tcl import TclModulefileWriter from .lmod import LmodModulefileWriter __all__ = [ - 'DotkitModulefileWriter', 'TclModulefileWriter', 'LmodModulefileWriter' ] module_types = { - 'dotkit': DotkitModulefileWriter, 'tcl': TclModulefileWriter, 'lmod': LmodModulefileWriter } diff --git a/lib/spack/spack/modules/dotkit.py b/lib/spack/spack/modules/dotkit.py deleted file mode 100644 index 3d8d97770f6..00000000000 --- a/lib/spack/spack/modules/dotkit.py +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -"""This module implements the classes necessary to generate dotkit modules.""" -import os.path - -import spack.config -from .common import BaseConfiguration, BaseFileLayout -from .common import BaseContext, BaseModuleFileWriter - -#: Dotkit specific part of the configuration -configuration = spack.config.get('modules:dotkit', {}) - -#: Caches the configuration {spec_hash: configuration} -configuration_registry = {} - - -def make_configuration(spec): - """Returns the dotkit configuration for spec""" - key = spec.dag_hash() - try: - return configuration_registry[key] - except KeyError: - return configuration_registry.setdefault( - key, DotkitConfiguration(spec) - ) - - -def make_layout(spec): - """Returns the layout information for spec """ - conf = make_configuration(spec) - return DotkitFileLayout(conf) - - -def make_context(spec): - """Returns the context information for spec""" - conf = make_configuration(spec) - return DotkitContext(conf) - - -class DotkitConfiguration(BaseConfiguration): - """Configuration class for dotkit module files.""" - - -class DotkitFileLayout(BaseFileLayout): - """File layout for dotkit module files.""" - - #: file extension of dotkit module files - extension = 'dk' - - -class DotkitContext(BaseContext): - """Context class for dotkit module files.""" - - -class DotkitModulefileWriter(BaseModuleFileWriter): - """Writer class for dotkit module files.""" - default_template = os.path.join('modules', 'modulefile.dk') diff --git a/lib/spack/spack/schema/__init__.py b/lib/spack/spack/schema/__init__.py index 3e26238c933..894d1cd7436 100644 --- a/lib/spack/spack/schema/__init__.py +++ b/lib/spack/spack/schema/__init__.py @@ -11,6 +11,7 @@ import six import llnl.util.lang +import llnl.util.tty import spack.spec @@ -72,11 +73,35 @@ def _validate_spec(validator, is_spec, instance, schema): '"{0}" is an invalid spec [{1}]'.format(spec_str, str(e)) ) + def _deprecated_properties(validator, deprecated, instance, schema): + if not (validator.is_type(instance, "object") or + validator.is_type(instance, "array")): + return + + # Get a list of the deprecated properties, return if there is none + deprecated_properties = [ + x for x in instance if x in deprecated['properties'] + ] + if not deprecated_properties: + return + + # Retrieve the template message + msg = deprecated['message'] + is_error = deprecated['error'] + if not is_error: + for entry in deprecated_properties: + llnl.util.tty.warn(msg.format(property=entry)) + else: + import jsonschema + for entry in deprecated_properties: + yield jsonschema.ValidationError(msg.format(property=entry)) + return jsonschema.validators.extend( jsonschema.Draft4Validator, { "validate_spec": _validate_spec, "properties": _set_defaults, - "patternProperties": _set_pp_defaults + "patternProperties": _set_pp_defaults, + "deprecatedProperties": _deprecated_properties } ) diff --git a/lib/spack/spack/schema/config.py b/lib/spack/spack/schema/config.py index 31e7f9b283d..4c49cbca6ad 100644 --- a/lib/spack/spack/schema/config.py +++ b/lib/spack/spack/schema/config.py @@ -41,6 +41,13 @@ 'lmod': {'type': 'string'}, 'dotkit': {'type': 'string'}, }, + 'deprecatedProperties': { + 'properties': ['dotkit'], + 'message': 'specifying a "{property}" module root has no ' + 'effect [support for {property} module files' + ' has been dropped]', + 'error': False + }, }, 'source_cache': {'type': 'string'}, 'misc_cache': {'type': 'string'}, diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py index 1da9dbd5861..14f185cfcc1 100644 --- a/lib/spack/spack/schema/modules.py +++ b/lib/spack/spack/schema/modules.py @@ -135,7 +135,16 @@ 'default': [], 'items': { 'type': 'string', - 'enum': ['tcl', 'dotkit', 'lmod']}}, + 'enum': ['tcl', 'dotkit', 'lmod'] + }, + 'deprecatedProperties': { + 'properties': ['dotkit'], + 'message': 'cannot enable "{property}" in modules.yaml ' + '[support for {property} module files has been' + ' dropped]', + 'error': False + }, + }, 'lmod': { 'allOf': [ # Base configuration @@ -164,6 +173,13 @@ ] }, }, + 'deprecatedProperties': { + 'properties': ['dotkit'], + 'message': 'the section "{property}" in modules.yaml has no effect' + ' [support for {property} module files has been ' + 'dropped]', + 'error': False + }, }, } diff --git a/lib/spack/spack/schema/upstreams.py b/lib/spack/spack/schema/upstreams.py index 4bbbac17bed..5925782af2c 100644 --- a/lib/spack/spack/schema/upstreams.py +++ b/lib/spack/spack/schema/upstreams.py @@ -20,8 +20,7 @@ 'type': 'object', 'properties': { 'tcl': {'type': 'string'}, - 'lmod': {'type': 'string'}, - 'dotkit': {'type': 'string'} + 'lmod': {'type': 'string'} } } } diff --git a/lib/spack/spack/test/cmd/module.py b/lib/spack/spack/test/cmd/module.py index 6222401d660..ac8b48a9e86 100644 --- a/lib/spack/spack/test/cmd/module.py +++ b/lib/spack/spack/test/cmd/module.py @@ -21,7 +21,6 @@ def _module_files(module_type, *specs): @pytest.fixture(scope='module', autouse=True) def ensure_module_files_are_there(database): - module('dotkit', 'refresh', '-y') module('tcl', 'refresh', '-y') @@ -39,7 +38,7 @@ def failure_args(request): @pytest.fixture( - params=['dotkit', 'tcl', 'lmod'] + params=['tcl', 'lmod'] ) def module_type(request): return request.param diff --git a/lib/spack/spack/test/data/config/modules.yaml b/lib/spack/spack/test/data/config/modules.yaml index 25fe2088e7e..adc16e896b2 100644 --- a/lib/spack/spack/test/data/config/modules.yaml +++ b/lib/spack/spack/test/data/config/modules.yaml @@ -16,7 +16,6 @@ modules: enable: - tcl - - dotkit prefix_inspections: bin: - PATH diff --git a/lib/spack/spack/test/data/modules/dotkit/autoload_direct.yaml b/lib/spack/spack/test/data/modules/dotkit/autoload_direct.yaml deleted file mode 100644 index 2636d6265ba..00000000000 --- a/lib/spack/spack/test/data/modules/dotkit/autoload_direct.yaml +++ /dev/null @@ -1,5 +0,0 @@ -enable: - - dotkit -dotkit: - all: - autoload: 'direct' diff --git a/lib/spack/spack/test/data/modules/dotkit/override_template.yaml b/lib/spack/spack/test/data/modules/dotkit/override_template.yaml deleted file mode 100644 index 8da581689fd..00000000000 --- a/lib/spack/spack/test/data/modules/dotkit/override_template.yaml +++ /dev/null @@ -1,5 +0,0 @@ -enable: - - dotkit -dotkit: - all: - template: 'override_from_modules.txt' diff --git a/lib/spack/spack/test/modules/dotkit.py b/lib/spack/spack/test/modules/dotkit.py deleted file mode 100644 index 951fb383434..00000000000 --- a/lib/spack/spack/test/modules/dotkit.py +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - - -import pytest -import spack.modules.dotkit - -#: Class of the writer tested in this module -writer_cls = spack.modules.dotkit.DotkitModulefileWriter - - -@pytest.mark.usefixtures('config', 'mock_packages') -class TestDotkit(object): - - def test_dotkit(self, modulefile_content, module_configuration): - """Tests the generation of a dotkit file that loads dependencies - automatically. - """ - - module_configuration('autoload_direct') - content = modulefile_content('mpileaks arch=x86-linux') - - assert '#c spack' in content - assert '#d mpileaks @2.3' in content - assert len([x for x in content if 'dk_op' in x]) == 2 - - def test_override_template_in_package( - self, modulefile_content, module_configuration - ): - """Tests overriding a template from and attribute in the package.""" - - module_configuration('autoload_direct') - content = modulefile_content('override-module-templates') - - assert 'Override successful!' in content - - def test_override_template_in_modules_yaml( - self, modulefile_content, module_configuration - ): - """Tests overriding a template from `modules.yaml`""" - - module_configuration('override_template') - - # Check that this takes precedence over an attribute in the package - content = modulefile_content('override-module-templates') - assert 'Override even better!' in content - - content = modulefile_content('mpileaks arch=x86-linux') - assert 'Override even better!' in content diff --git a/lib/spack/spack/test/schema.py b/lib/spack/spack/test/schema.py index 88c824513a0..9149b77b370 100644 --- a/lib/spack/spack/test/schema.py +++ b/lib/spack/spack/test/schema.py @@ -114,3 +114,28 @@ def test_schema_validation(meta_schema, config_name): # If this validation throws the test won't pass jsonschema.validate(schema, meta_schema) + + +def test_deprecated_properties(module_suffixes_schema): + # Test that an error is reported when 'error: True' + module_suffixes_schema['deprecatedProperties'] = { + 'properties': ['tcl'], + 'message': '{property} not allowed', + 'error': True + } + v = spack.schema.Validator(module_suffixes_schema) + data = {'tcl': {'all': {'suffixes': {'^python': 'py'}}}} + + with pytest.raises(jsonschema.ValidationError, match='tcl not allowed'): + v.validate(data) + + # Test that just a warning is reported when 'error: False' + module_suffixes_schema['deprecatedProperties'] = { + 'properties': ['tcl'], + 'message': '{property} not allowed', + 'error': False + } + v = spack.schema.Validator(module_suffixes_schema) + data = {'tcl': {'all': {'suffixes': {'^python': 'py'}}}} + # The next validation doesn't raise anymore + v.validate(data) diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh index 01be6165724..ac893d72b10 100644 --- a/share/spack/csh/spack.csh +++ b/share/spack/csh/spack.csh @@ -5,27 +5,27 @@ ######################################################################## # This is a wrapper around the spack command that forwards calls to -# 'spack use' and 'spack unuse' to shell functions. This in turn -# allows them to be used to invoke dotkit functions. +# 'spack load' and 'spack unload' to shell functions. This in turn +# allows them to be used to invoke environment-modules functions. # -# 'spack use' is smarter than just 'use' because it converts its -# arguments into a unique spack spec that is then passed to dotkit +# 'spack load' is smarter than just 'load' because it converts its +# arguments into a unique Spack spec that is then passed to environment-modules # commands. This allows the user to use packages without knowing all # their installation details. # -# e.g., rather than requring a full spec for libelf, the user can type: +# e.g., rather than requiring a full spec for libelf, the user can type: # -# spack use libelf +# spack load libelf # -# This will first find the available libelf dotkits and use a +# This will first find the available libelf module file and use a # matching one. If there are two versions of libelf, the user would # need to be more specific, e.g.: # -# spack use libelf@0.8.13 +# spack load libelf@0.8.13 # # This is very similar to how regular spack commands work and it # avoids the need to come up with a user-friendly naming scheme for -# spack dotfiles. +# spack module files. ######################################################################## # accumulate initial flags for main spack command set _sp_flags = "" @@ -104,8 +104,6 @@ case env: breaksw endsw endif -case use: -case unuse: case load: case unload: set _sp_module_args="""" @@ -115,22 +113,10 @@ case unload: set _sp_spec = ($_sp_spec) endif - # Here the user has run use or unuse with a spec. Find a matching + # Here the user has run load or unload with a spec. Find a matching # spec using 'spack module find', then use the appropriate module # tool's commands to add/remove the result from the environment. switch ($_sp_subcommand) - case "use": - set _sp_full_spec = ( "`\spack $_sp_flags module dotkit find $_sp_spec`" ) - if ( $? == 0 ) then - use $_sp_module_args $_sp_full_spec - endif - breaksw - case "unuse": - set _sp_full_spec = ( "`\spack $_sp_flags module dotkit find $_sp_spec`" ) - if ( $? == 0 ) then - unuse $_sp_module_args $_sp_full_spec - endif - breaksw case "load": # _sp_module_args may be "-r" for recursive spec retrieval set _sp_full_spec = ( "`\spack $_sp_flags module tcl find $_sp_module_args $_sp_spec`" ) diff --git a/share/spack/qa/setup-env-test.sh b/share/spack/qa/setup-env-test.sh index 6515a99d8c1..e16e31fffbc 100755 --- a/share/spack/qa/setup-env-test.sh +++ b/share/spack/qa/setup-env-test.sh @@ -167,7 +167,7 @@ is_not_set() { # ----------------------------------------------------------------------- -# Instead of invoking the module/use/dotkit commands, we print the +# Instead of invoking the module commands, we print the # arguments that Spack invokes the command with, so we can check that # Spack passes the expected arguments in the tests below. # @@ -177,14 +177,6 @@ module() { echo module "$@" } -use() { - echo use "$@" -} - -unuse() { - echo unuse "$@" -} - # ----------------------------------------------------------------------- # Setup test environment and do some preliminary checks # ----------------------------------------------------------------------- @@ -219,11 +211,9 @@ echo "Creating a mock package installation" spack -m install --fake a a_install=$(spack location -i a) a_module=$(spack -m module tcl find a) -a_dotkit=$(spack -m module dotkit find a) b_install=$(spack location -i b) b_module=$(spack -m module tcl find b) -b_dotkit=$(spack -m module dotkit find b) # create a test environment for tesitng environment commands echo "Creating a mock environment" @@ -304,26 +294,6 @@ contains "usage: spack unload " spack -m unload -h contains "usage: spack unload " spack -m unload -h d contains "usage: spack unload " spack -m unload --help -title 'Testing `spack use`' -contains "use $b_dotkit" spack -m use b -fails spack -m use -l -contains "use -l --arg $b_dotkit" spack -m use -l --arg b -contains "use $b_dotkit $a_dotkit" spack -m use -r a -contains "use $b_dotkit $a_dotkit" spack -m use --dependencies a -fails spack -m use d -contains "usage: spack use " spack -m use -h -contains "usage: spack use " spack -m use -h d -contains "usage: spack use " spack -m use --help - -title 'Testing `spack unuse`' -contains "unuse $b_dotkit" spack -m unuse b -fails spack -m unuse -l -contains "unuse -l --arg $b_dotkit" spack -m unuse -l --arg b -fails spack -m unuse d -contains "usage: spack unuse " spack -m unuse -h -contains "usage: spack unuse " spack -m unuse -h d -contains "usage: spack unuse " spack -m unuse --help - title 'Testing `spack env`' contains "usage: spack env " spack env -h contains "usage: spack env " spack env --help diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh index ac5479196d4..b49597918c0 100755 --- a/share/spack/setup-env.csh +++ b/share/spack/setup-env.csh @@ -6,7 +6,7 @@ # # This file is part of Spack and sets up the spack environment for -# csh and tcsh. This includes dotkit support, module support, and +# csh and tcsh. This includes environment modules and lmod support, and # it also puts spack in your path. Source it like this: # # setenv SPACK_ROOT /path/to/spack @@ -24,7 +24,7 @@ if ($?SPACK_ROOT) then _spack_pathadd PATH "$SPACK_ROOT/bin" eval `spack --print-shell-vars csh` - # Set up modules and dotkit search paths in the user environment + # Set up module search paths in the user environment set tcl_roots = `echo $_sp_tcl_roots:q | sed 's/:/ /g'` set compatible_sys_types = `echo $_sp_compatible_sys_types:q | sed 's/:/ /g'` foreach tcl_root ($tcl_roots:q) @@ -33,10 +33,6 @@ if ($?SPACK_ROOT) then end end - set dotkit_roots = `echo $_sp_dotkit_roots:q | sed 's/:/ /g'` - foreach dotkit_root ($dotkit_roots) - _spack_pathadd DK_NODE "$dotkit_root/$_sp_sys_type" - end else echo "ERROR: Sourcing spack setup-env.csh requires setting SPACK_ROOT to " echo " the root of your spack installation." diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index 0fd5eb30f72..d5cad059a61 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -7,8 +7,8 @@ ######################################################################## # # This file is part of Spack and sets up the spack environment for bash, -# zsh, and dash (sh). This includes dotkit support, module support, and -# it also puts spack in your path. The script also checks that at least +# zsh, and dash (sh). This includes environment modules and lmod support, +# and it also puts spack in your path. The script also checks that at least # module support exists, and provides suggestions if it doesn't. Source # it like this: # @@ -16,27 +16,27 @@ # ######################################################################## # This is a wrapper around the spack command that forwards calls to -# 'spack use' and 'spack unuse' to shell functions. This in turn -# allows them to be used to invoke dotkit functions. +# 'spack load' and 'spack unload' to shell functions. This in turn +# allows them to be used to invoke environment modules functions. # -# 'spack use' is smarter than just 'use' because it converts its -# arguments into a unique spack spec that is then passed to dotkit +# 'spack load' is smarter than just 'load' because it converts its +# arguments into a unique Spack spec that is then passed to module # commands. This allows the user to use packages without knowing all # their installation details. # # e.g., rather than requiring a full spec for libelf, the user can type: # -# spack use libelf +# spack load libelf # -# This will first find the available libelf dotkits and use a +# This will first find the available libelf module file and use a # matching one. If there are two versions of libelf, the user would # need to be more specific, e.g.: # -# spack use libelf@0.8.13 +# spack load libelf@0.8.13 # # This is very similar to how regular spack commands work and it # avoids the need to come up with a user-friendly naming scheme for -# spack dotfiles. +# spack module files. ######################################################################## spack() { @@ -140,7 +140,7 @@ spack() { fi return ;; - "use"|"unuse"|"load"|"unload") + "load"|"unload") # Shift any other args for use off before parsing spec. _sp_subcommand_args="" _sp_module_args="" @@ -161,20 +161,6 @@ spack() { # tool's commands to add/remove the result from the environment. # If spack module command comes back with an error, do nothing. case $_sp_subcommand in - "use") - if _sp_full_spec=$(command spack $_sp_flags module dotkit find $_sp_subcommand_args "$@"); then - use $_sp_module_args $_sp_full_spec - else - $(exit 1) - fi - ;; - "unuse") - if _sp_full_spec=$(command spack $_sp_flags module dotkit find $_sp_subcommand_args "$@"); then - unuse $_sp_module_args $_sp_full_spec - else - $(exit 1) - fi - ;; "load") if _sp_full_spec=$(command spack $_sp_flags module tcl find $_sp_subcommand_args "$@"); then module load $_sp_module_args $_sp_full_spec @@ -356,7 +342,6 @@ _sp_multi_pathadd() { done } _sp_multi_pathadd MODULEPATH "$_sp_tcl_roots" -_sp_multi_pathadd DK_NODE "$_sp_dotkit_roots" # Add programmable tab completion for Bash # diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash index bd6675dd160..935092aedb9 100755 --- a/share/spack/spack-completion.bash +++ b/share/spack/spack-completion.bash @@ -760,7 +760,7 @@ function _spack_module { then compgen -W "-h --help" -- "$cur" else - compgen -W "lmod tcl dotkit" -- "$cur" + compgen -W "lmod tcl" -- "$cur" fi } @@ -812,53 +812,6 @@ function _spack_module_tcl_rm { fi } -function _spack_module_dotkit { - if $list_options - then - compgen -W "-h --help" -- "$cur" - else - compgen -W "refresh find rm loads" -- "$cur" - fi -} - - -function _spack_module_dotkit_find { - if $list_options - then - compgen -W "-h --help --full-path -r --dependencies" -- "$cur" - else - compgen -W "$(_installed_packages)" -- "$cur" - fi -} - -function _spack_module_dotkit_loads { - if $list_options - then - compgen -W "-h --help --input-only -p --prefix -x --exclude - -r --dependencies" -- "$cur" - else - compgen -W "$(_installed_packages)" -- "$cur" - fi - -} - -function _spack_module_dotkit_refresh { - if $list_options - then - compgen -W "-h --help --delete-tree -y --yes-to-all" -- "$cur" - else - compgen -W "$(_installed_packages)" -- "$cur" - fi -} - -function _spack_module_dotkit_rm { - if $list_options - then - compgen -W "-h --help -y --yes-to-all" -- "$cur" - else - compgen -W "$(_installed_packages)" -- "$cur" - fi -} function _spack_module_lmod { if $list_options diff --git a/share/spack/templates/modules/modulefile.dk b/share/spack/templates/modules/modulefile.dk deleted file mode 100644 index c3f6d2dce1e..00000000000 --- a/share/spack/templates/modules/modulefile.dk +++ /dev/null @@ -1,31 +0,0 @@ -{% block header %} -{% if category %} -#c {{ category }} -{% endif %} -{% if short_description %} -#d {{ short_description }} -{% endif %} -{% if long_description %} -{{ long_description| textwrap(72)| prepend_to_line('#h ')| join() }} -{% endif %} -{% endblock %} - -{% block autoloads %} -{% for module in autoload %} -dk_op {{ module }} -{% endfor %} -{% endblock %} - -{% block environment %} -{% for command_name, cmd in environment_modifications %} -{% if command_name == 'PrependPath' %} -dk_alter {{ cmd.name }} {{ cmd.value }} -{% endif %} -{% if command_name == 'RemovePath' %} -dk_unalter {{ cmd.name }} {{ cmd.value }} -{% endif %} -{% if command_name == 'SetEnv' %} -dk_setenv {{ cmd.name }} {{ cmd.value }} -{% endif %} -{% endfor %} -{% endblock %} diff --git a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py index 818591a15b4..f3cad009aa8 100644 --- a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py +++ b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py @@ -12,7 +12,6 @@ class OverrideModuleTemplates(Package): version('1.0', 'foobarbaz') - dotkit_template = 'override.txt' tcl_template = 'override.txt' lmod_template = 'override.txt' diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 11f2ff79451..e8a20515f91 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -134,6 +134,6 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # This *MUST* be first, this is where new code is installed spack_env.set('GOPATH', ':'.join(path_components)) - # Allow packages to find this when using module or dotkit + # Allow packages to find this when using module files run_env.prepend_path('GOPATH', ':'.join( [dependent_spec.prefix] + path_components)) From 78577c0a90d79a22634644370e2e1f0f9cf138c7 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 3 Oct 2019 10:31:03 +0200 Subject: [PATCH 101/499] Generic x86_64 code compiled with GCC uses non deprecated mtune flags (#13022) fixes #12928 --- lib/spack/llnl/util/cpu/microarchitectures.json | 17 ++++++++++++----- lib/spack/spack/test/llnl/util/cpu.py | 4 +++- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 2e20cc98f80..ad985ba9941 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -49,11 +49,18 @@ "vendor": "generic", "features": [], "compilers": { - "gcc": { - "versions": "4:", - "name": "x86-64", - "flags": "-march={name} -mtune={name}" - } + "gcc": [ + { + "versions": "4.2.0:", + "name": "x86-64", + "flags": "-march={name} -mtune=generic" + }, + { + "versions": "4.0:4.1.2", + "name": "x86-64", + "flags": "-march={name} -mtune={name}" + } + ] } }, "nocona": { diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 836514cc3c7..9af784d1032 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -190,7 +190,9 @@ def test_target_json_schema(): @pytest.mark.parametrize('target_name,compiler,version,expected_flags', [ - ('x86_64', 'gcc', '4.9.3', '-march=x86-64 -mtune=x86-64'), + ('x86_64', 'gcc', '4.9.3', '-march=x86-64 -mtune=generic'), + ('x86_64', 'gcc', '4.2.0', '-march=x86-64 -mtune=generic'), + ('x86_64', 'gcc', '4.1.1', '-march=x86-64 -mtune=x86-64'), ('nocona', 'gcc', '4.9.3', '-march=nocona -mtune=nocona'), ('nehalem', 'gcc', '4.9.3', '-march=nehalem -mtune=nehalem'), ('nehalem', 'gcc', '4.8.5', '-march=corei7 -mtune=corei7'), From b973f038fda813964f92ab9a4fe7f994ea0640f4 Mon Sep 17 00:00:00 2001 From: Chuck Atkins Date: Thu, 3 Oct 2019 10:05:02 -0400 Subject: [PATCH 102/499] Update ECP Data & Vis SDK packages (#13027) * ecp-io-sdk: Add faodel and sort variants * ecp-viz-sdk: Re-enable catalyst, sort variants, turn on by default * ecp-io-sdk and ecp-viz-sdk: Fix dependency variants --- .../builtin/packages/ecp-io-sdk/package.py | 19 +++++++------ .../builtin/packages/ecp-viz-sdk/package.py | 28 +++++++++---------- 2 files changed, 23 insertions(+), 24 deletions(-) diff --git a/var/spack/repos/builtin/packages/ecp-io-sdk/package.py b/var/spack/repos/builtin/packages/ecp-io-sdk/package.py index dd0f09eff98..774704ff0f3 100644 --- a/var/spack/repos/builtin/packages/ecp-io-sdk/package.py +++ b/var/spack/repos/builtin/packages/ecp-io-sdk/package.py @@ -16,26 +16,27 @@ class EcpIoSdk(CMakePackage): version('1.0', branch='master') - variant('hdf5', default=True, description="Enable HDF5") variant('adios2', default=True, description="Enable ADIOS2") - variant('pnetcdf', default=True, description="Enable PNetCDF") variant('darshan', default=True, description="Enable Darshan") + variant('faodel', default=False, description="Enable FAODEL") + variant('hdf5', default=True, description="Enable HDF5") variant('mercury', default=True, description="Enable Mercury") + variant('pnetcdf', default=True, description="Enable PNetCDF") variant('unifyfs', default=True, description="Enable UnifyFS") variant('veloc', default=True, description="Enable VeloC") # Currently no spack packages # variant('romio', default=False, description="Enable ROMIO") - # variant('faodel', default=False, description="Enable FAODEL") - depends_on('hdf5', when='+hdf5') - depends_on('adios2', when='+adios2') - depends_on('parallel-netcdf', when='+pnetcdf') - depends_on('veloc', when='+veloc') - depends_on('unifyfs', when='+unifyfs') + depends_on('adios2+mpi+fortran+zfp+hdf5', when='+adios2') depends_on('darshan-runtime', when='+darshan') depends_on('darshan-util', when='+darshan') - depends_on('mercury', when='+mercury') + depends_on('faodel+mpi+hdf5', when='+faodel') + depends_on('hdf5+mpi+fortran', when='+hdf5') + depends_on('mercury+mpi+ofi+sm', when='+mercury') + depends_on('parallel-netcdf+fortran+pic', when='+pnetcdf') + depends_on('unifyfs+fortran+numa', when='+unifyfs') + depends_on('veloc', when='+veloc') def cmake_args(self): return ['-DIO=ON'] diff --git a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py index 734982799b9..f86330613c4 100644 --- a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py +++ b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py @@ -16,31 +16,29 @@ class EcpVizSdk(CMakePackage): version('1.0', branch='master') - variant('paraview', default=False, description="Enable ParaView") - variant('vtkm', default=False, description="Enable VTK-m") - variant('zfp', default=False, description="Enable ZFP") - variant('sz', default=False, description="Enable SZ") - - # TODO: fix +osmesa~rendering conflict - variant('catalyst', default=False, description="Enable Catalyst") - - # Unsatisfiable dependencies: hdf5 and netcdf - # variant('visit', default=False, description="Enable VisIt") + variant('catalyst', default=True, description="Enable Catalyst") + variant('paraview', default=True, description="Enable ParaView") + variant('sz', default=True, description="Enable SZ") + variant('vtkm', default=True, description="Enable VTK-m") + variant('zfp', default=True, description="Enable ZFP") # Broken dependency: vtk-h # variant('ascent', default=False, description="Enable Ascent") + # Outstanding build issues + # variant('visit', default=False, description="Enable VisIt") + # Missing spack package # variant('cinema', default=False, description="Enable Cinema") # variant('rover', default=False, description="Enable ROVER") - depends_on('paraview', when='+paraview') - depends_on('catalyst', when='+catalyst') - depends_on('vtkm', when='+vtkm') depends_on('ascent', when='+ascent') - depends_on('visit', when='+visit') - depends_on('zfp', when='+zfp') + depends_on('catalyst', when='+catalyst') + depends_on('paraview', when='+paraview') depends_on('sz', when='+sz') + depends_on('visit', when='+visit') + depends_on('vtkm', when='+vtkm') + depends_on('zfp', when='+zfp') def cmake_args(self): return ['-DVIZ=ON'] From dac34147c017e35043f93c2be2959377b5a9a50e Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 3 Oct 2019 09:48:42 -0500 Subject: [PATCH 103/499] Add EasyBuild 4.0.0 (#13024) * Add EasyBuild 4.0.0 * Update homepage, remove no longer required deps * Replace version ranges with fixed versions --- .../repos/builtin/packages/easybuild/package.py | 16 +++++++++++----- .../packages/py-easybuild-easyblocks/package.py | 12 +++++++++--- .../py-easybuild-easyconfigs/package.py | 14 ++++++++++---- .../packages/py-easybuild-framework/package.py | 17 +++++++++++------ 4 files changed, 41 insertions(+), 18 deletions(-) diff --git a/var/spack/repos/builtin/packages/easybuild/package.py b/var/spack/repos/builtin/packages/easybuild/package.py index 043481874b2..0430639762a 100644 --- a/var/spack/repos/builtin/packages/easybuild/package.py +++ b/var/spack/repos/builtin/packages/easybuild/package.py @@ -11,11 +11,17 @@ class Easybuild(PythonPackage): for (scientific) software on HPC systems. """ - homepage = 'http://hpcugent.github.io/easybuild/' - url = 'https://pypi.io/packages/source/e/easybuild/easybuild-3.1.2.tar.gz' + homepage = 'https://easybuilders.github.io/easybuild/' + url = 'https://pypi.io/packages/source/e/easybuild/easybuild-4.0.0.tar.gz' + maintainers = ['boegel'] + version('4.0.0', sha256='21bcc1048525ad6219667cc97a7421b5388068c670cabba356712e474896de40') version('3.1.2', 'c2d901c2a71f51b24890fa69c3a46383') - depends_on('py-easybuild-framework@3.1.2', when='@3.1.2', type='run') - depends_on('py-easybuild-easyblocks@3.1.2', when='@3.1.2', type='run') - depends_on('py-easybuild-easyconfigs@3.1.2', when='@3.1.2', type='run') + depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) + depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) + + for v in ['@4.0.0', '@3.1.2']: + depends_on('py-easybuild-framework' + v, when=v, type='run') + depends_on('py-easybuild-easyblocks' + v, when=v, type='run') + depends_on('py-easybuild-easyconfigs' + v, when=v, type='run') diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py index 181a25febcd..8719f6924f3 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py @@ -11,9 +11,15 @@ class PyEasybuildEasyblocks(PythonPackage): installation framework for (scientific) software on HPC systems. """ - homepage = 'http://hpcugent.github.io/easybuild/' - url = 'https://pypi.io/packages/source/e/easybuild-easyblocks/easybuild-easyblocks-3.1.2.tar.gz' + homepage = 'https://easybuilders.github.io/easybuild' + url = 'https://pypi.io/packages/source/e/easybuild-easyblocks/easybuild-easyblocks-4.0.0.tar.gz' + maintainers = ['boegel'] + version('4.0.0', sha256='a0fdef6c33c786e323bde1b28bab942fd8e535c26842877d705e692e85b31b07') version('3.1.2', 'be08da30c07e67ed3e136e8d38905fbc') - depends_on('py-easybuild-framework@3.1:', when='@3.1:', type='run') + depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) + depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) + + for v in ['@3.1.2', '@4.0.0']: + depends_on('py-easybuild-framework' + v, when=v, type='run') diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py index 9f9d69c2cbb..cc610917ffa 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py @@ -11,10 +11,16 @@ class PyEasybuildEasyconfigs(PythonPackage): installation framework for (scientific) software on HPC systems. """ - homepage = 'http://hpcugent.github.io/easybuild/' - url = 'https://pypi.io/packages/source/e/easybuild-easyconfigs/easybuild-easyconfigs-3.1.2.tar.gz' + homepage = 'https://easybuilders.github.io/easybuild' + url = 'https://pypi.io/packages/source/e/easybuild-easyconfigs/easybuild-easyconfigs-4.0.0.tar.gz' + maintainers = ['boegel'] + version('4.0.0', sha256='90d4e8f8abb11e7ae2265745bbd1241cd69d02570e9b4530175c4b2e2aba754e') version('3.1.2', '13a4a97fe8a5b9a94f885661cf497d13') - depends_on('py-easybuild-framework@3.1:', when='@3.1:', type='run') - depends_on('py-easybuild-easyblocks@3.1.2:', when='@3.1.2', type='run') + depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) + depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) + + for v in ['@3.1.2', '@4.0.0']: + depends_on('py-easybuild-framework{0}:'.format(v), when=v + ':', type='run') + depends_on('py-easybuild-easyblocks{0}:'.format(v), when=v, type='run') diff --git a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py index feb31e680b7..47e78c51d1e 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py @@ -11,12 +11,17 @@ class PyEasybuildFramework(PythonPackage): for (scientific) software on HPC systems. """ - homepage = 'http://hpcugent.github.io/easybuild/' - url = 'https://pypi.io/packages/source/e/easybuild-framework/easybuild-framework-3.1.2.tar.gz' + homepage = 'https://easybuilders.github.io/easybuild' + url = 'https://pypi.io/packages/source/e/easybuild-framework/easybuild-framework-4.0.0.tar.gz' + maintainers = ['boegel'] + version('4.0.0', sha256='f5c40345cc8b9b5750f53263ade6c9c3a8cd3dfab488d58f76ac61a8ca7c5a77') version('3.1.2', '283bc5f6bdcb90016b32986d52fd04a8') - depends_on('python@2.6:2.8', type='run') - depends_on('py-setuptools', type=('build', 'run')) - depends_on('py-vsc-base@2.5.4:', when='@2.9:', type='run') - depends_on('py-vsc-install', type='run') # only required for tests (python -O -m test.framework.suite) + depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) + depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) + depends_on('py-setuptools', when='@:3', type=('build', 'run')) + depends_on('py-vsc-base@2.5.4:', when='@2.9:3', type='run') + + # Only required for tests (python -O -m test.framework.suite) + depends_on('py-vsc-install', when='@:3', type='test') From 24f8d1042bfb6b3abe33816903d45667b44f3926 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 3 Oct 2019 10:31:32 -0500 Subject: [PATCH 104/499] Update compilers.yaml location in Getting Started docs (#13029) --- lib/spack/docs/getting_started.rst | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst index eeeffcc25f3..b7ba386bb29 100644 --- a/lib/spack/docs/getting_started.rst +++ b/lib/spack/docs/getting_started.rst @@ -190,7 +190,7 @@ where the compiler is installed. For example: .. code-block:: console $ spack compiler find /usr/local/tools/ic-13.0.079 - ==> Added 1 new compiler to ~/.spack/compilers.yaml + ==> Added 1 new compiler to ~/.spack/linux/compilers.yaml intel@13.0.079 Or you can run ``spack compiler find`` with no arguments to force @@ -202,7 +202,7 @@ installed, but you know that new compilers have been added to your $ module load gcc-4.9.0 $ spack compiler find - ==> Added 1 new compiler to ~/.spack/compilers.yaml + ==> Added 1 new compiler to ~/.spack/linux/compilers.yaml gcc@4.9.0 This loads the environment module for gcc-4.9.0 to add it to @@ -247,7 +247,7 @@ Manual compiler configuration ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If auto-detection fails, you can manually configure a compiler by -editing your ``~/.spack/compilers.yaml`` file. You can do this by running +editing your ``~/.spack//compilers.yaml`` file. You can do this by running ``spack config edit compilers``, which will open the file in your ``$EDITOR``. Each compiler configuration in the file looks like this: @@ -263,7 +263,7 @@ Each compiler configuration in the file looks like this: cxx: /usr/local/bin/icpc-15.0.024-beta f77: /usr/local/bin/ifort-15.0.024-beta fc: /usr/local/bin/ifort-15.0.024-beta - spec: intel@15.0.0: + spec: intel@15.0.0 For compilers that do not support Fortran (like ``clang``), put ``None`` for ``f77`` and ``fc``: @@ -469,18 +469,21 @@ Fortran. install GCC with Spack (``spack install gcc``) or with Homebrew (``brew install gcc``). -#. The only thing left to do is to edit ``~/.spack/compilers.yaml`` to provide +#. The only thing left to do is to edit ``~/.spack/darwin/compilers.yaml`` to provide the path to ``gfortran``: .. code-block:: yaml compilers: - darwin-x86_64: - clang@7.3.0-apple: - cc: /usr/bin/clang - cxx: /usr/bin/clang++ - f77: /path/to/bin/gfortran - fc: /path/to/bin/gfortran + - compiler: + ... + paths: + cc: /usr/bin/clang + cxx: /usr/bin/clang++ + f77: /path/to/bin/gfortran + fc: /path/to/bin/gfortran + spec: clang@11.0.0-apple + If you used Spack to install GCC, you can get the installation prefix by ``spack location -i gcc`` (this will only work if you have a single version From 69acb024a5693d9cbabbb66c81b0957e68ef8995 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 3 Oct 2019 10:32:00 -0500 Subject: [PATCH 105/499] Add py-flye 2.6 (#13025) --- .../repos/builtin/packages/py-flye/package.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-flye/package.py b/var/spack/repos/builtin/packages/py-flye/package.py index 589d41965b1..03705a7a3ac 100644 --- a/var/spack/repos/builtin/packages/py-flye/package.py +++ b/var/spack/repos/builtin/packages/py-flye/package.py @@ -11,11 +11,22 @@ class PyFlye(PythonPackage): reads""" homepage = "https://github.com/fenderglass/Flye" - url = "https://github.com/fenderglass/Flye/archive/2.4.2.tar.gz" + url = "https://github.com/fenderglass/Flye/archive/2.6.tar.gz" + version('2.6', sha256='5bdc44b84712794fa4264eed690d8c65c0d72f495c7bbf2cd15b634254809131') version('2.4.2', sha256='5b74d4463b860c9e1614ef655ab6f6f3a5e84a7a4d33faf3b29c7696b542c51a') - depends_on('python@2.7:2.8', type=('build', 'run')) + # https://github.com/fenderglass/Flye/blob/flye/docs/INSTALL.md + depends_on('python@2.7:2.8,3.5:', when='@2.6:', type=('build', 'run')) + depends_on('python@2.7:2.8', when='@:2.5', type=('build', 'run')) + depends_on('py-setuptools', when='@2.6:', type='build') + depends_on('gmake', type='build') + depends_on('zlib') + + msg = 'C++ compiler with C++11 support required' + conflicts('%gcc@:4.7', msg=msg) + conflicts('%clang@:3.2', msg=msg) + # Requires Apple Clang 5.0+ but no way to specify that right now def setup_environment(self, spack_env, run_env): if self.spec.target.family == 'aarch64': From bef702d0f393ab7b72565dc279512bbea8a46c8d Mon Sep 17 00:00:00 2001 From: Owen Solberg Date: Thu, 3 Oct 2019 16:23:47 -0700 Subject: [PATCH 106/499] updated manta checksum (#13038) --- var/spack/repos/builtin/packages/manta/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/manta/package.py b/var/spack/repos/builtin/packages/manta/package.py index 52e7d772987..0922e3f0352 100644 --- a/var/spack/repos/builtin/packages/manta/package.py +++ b/var/spack/repos/builtin/packages/manta/package.py @@ -12,6 +12,7 @@ class Manta(CMakePackage): homepage = "https://github.com/Illumina/manta" url = "https://github.com/Illumina/manta/releases/download/v1.3.2/manta-1.3.2.release_src.tar.bz2" + version('1.6.0', sha256='c846d61b02483265c09d58bd85dacf5326a94f38179b5ae4f70694be96e1368f') version('1.5.0', sha256='9aa1a59c9cb8d2dd33724a42959c9398aff7840c5bf3c895d2483a8093b3d2dc') version('1.4.0', '582d10f3bc56aecfa5c24931af3742b4') version('1.3.2', '83f43fe1a12605c1e9803d1020b24bd1') From 882843974bc5cde5ad5342dbf6a11e59e8af888c Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 3 Oct 2019 16:57:20 -0700 Subject: [PATCH 107/499] Update cctools to v7.0.18 (#13037) - add version/checksum info for v7.0.18 - update checksum for v6.1.1 to use sha256, while I have the editor open... --- var/spack/repos/builtin/packages/cctools/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/cctools/package.py b/var/spack/repos/builtin/packages/cctools/package.py index d58c73ddff5..fb546fc628c 100644 --- a/var/spack/repos/builtin/packages/cctools/package.py +++ b/var/spack/repos/builtin/packages/cctools/package.py @@ -15,7 +15,8 @@ class Cctools(AutotoolsPackage): homepage = "https://github.com/cooperative-computing-lab/cctools" url = "https://github.com/cooperative-computing-lab/cctools/archive/release/6.1.1.tar.gz" - version('6.1.1', '9b43cdb3aceebddc1608c77184590619') + version('7.0.18', sha256='5b6f3c87ae68dd247534a5c073eb68cb1a60176a7f04d82699fbc05e649a91c2') + version('6.1.1', sha256='97f073350c970d6157f80891b3bf6d4f3eedb5f031fea386dc33e22f22b8af9d') depends_on('openssl') depends_on('perl+shared', type=('build', 'run')) From 4e7ea627c8534d5209494308b43121b6f5e9d94b Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Fri, 4 Oct 2019 05:17:16 +0200 Subject: [PATCH 108/499] fix ipykernel dependency, newer versions are python3-only (#13019) * fix ipykernel dependency, newer versions are python3-only * Update var/spack/repos/builtin/packages/py-ipykernel/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/py-ipykernel/package.py Co-Authored-By: Adam J. Stewart --- var/spack/repos/builtin/packages/py-ipykernel/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-ipykernel/package.py b/var/spack/repos/builtin/packages/py-ipykernel/package.py index 499ae703ced..ad4046018ff 100644 --- a/var/spack/repos/builtin/packages/py-ipykernel/package.py +++ b/var/spack/repos/builtin/packages/py-ipykernel/package.py @@ -24,8 +24,9 @@ class PyIpykernel(PythonPackage): version('4.1.1', '51376850c46fb006e1f8d1cd353507c5') version('4.1.0', '638a43e4f8a15872f749090c3f0827b6') - depends_on('python@2.7:2.8,3.3:') - depends_on('py-setuptools', type='build') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) + depends_on('python@3.4:', when='@5:', type=('build', 'run')) + depends_on('py-setuptools', type='build', when='@5:') depends_on('py-traitlets@4.1.0:', type=('build', 'run')) depends_on('py-tornado@4.0:', when='@:4.999', type=('build', 'run')) depends_on('py-tornado@4.2:', when='@5.0.0:', type=('build', 'run')) From c97be22ff55f7854900fe0b9334d9ca9c4ee98ad Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 4 Oct 2019 12:18:12 +0900 Subject: [PATCH 109/499] ngmlr: add zlib dependency. (#13041) --- var/spack/repos/builtin/packages/ngmlr/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/ngmlr/package.py b/var/spack/repos/builtin/packages/ngmlr/package.py index 18367964336..72033007a66 100644 --- a/var/spack/repos/builtin/packages/ngmlr/package.py +++ b/var/spack/repos/builtin/packages/ngmlr/package.py @@ -15,3 +15,5 @@ class Ngmlr(CMakePackage): url = "https://github.com/philres/ngmlr/archive/v0.2.5.tar.gz" version('0.2.5', '1b2b1aaeb6a3accc8b9f3e5c29e77037') + + depends_on('zlib', type='link') From 58a64f69e70078bc2d187309337568186e80639e Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 4 Oct 2019 12:18:27 +0900 Subject: [PATCH 110/499] muse: add zlib dependency. (#13040) --- var/spack/repos/builtin/packages/muse/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/muse/package.py b/var/spack/repos/builtin/packages/muse/package.py index 32e7f63e7c5..eb4685a2f65 100644 --- a/var/spack/repos/builtin/packages/muse/package.py +++ b/var/spack/repos/builtin/packages/muse/package.py @@ -14,6 +14,8 @@ class Muse(MakefilePackage): version('1.0-rc', 'c63fdb48c041f6f9545879f1a7e4da58') + depends_on('zlib', type='link') + def install(self, spec, prefix): mkdir(prefix.bin) install('MuSE', prefix.bin.MuSE) From bb1d0ff6fbbe76bd96f12cf2a1e0a4a0a83067b5 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 4 Oct 2019 12:18:55 +0900 Subject: [PATCH 111/499] metabat: Add zlib and ncurses dependency. (#13034) --- var/spack/repos/builtin/packages/metabat/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/metabat/package.py b/var/spack/repos/builtin/packages/metabat/package.py index 0e95cb8d0c2..12623f528e1 100644 --- a/var/spack/repos/builtin/packages/metabat/package.py +++ b/var/spack/repos/builtin/packages/metabat/package.py @@ -18,6 +18,8 @@ class Metabat(SConsPackage): depends_on('boost@1.55.0:', type=('build', 'run')) depends_on('perl', type='run') + depends_on('zlib', type='link') + depends_on('ncurses', type='link') def setup_environment(self, spack_env, run_env): spack_env.set('BOOST_ROOT', self.spec['boost'].prefix) From 2233a7b49335b00ca792771050370f5dae3e4c24 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 4 Oct 2019 12:19:22 +0900 Subject: [PATCH 112/499] liblbxutil: Add zlib dependency. (#13033) --- var/spack/repos/builtin/packages/liblbxutil/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/liblbxutil/package.py b/var/spack/repos/builtin/packages/liblbxutil/package.py index 63155cb2360..f9e4da68c9e 100644 --- a/var/spack/repos/builtin/packages/liblbxutil/package.py +++ b/var/spack/repos/builtin/packages/liblbxutil/package.py @@ -18,6 +18,7 @@ class Liblbxutil(AutotoolsPackage): depends_on('xproto', type='build') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') + depends_on('zlib', type='link') # There is a bug in the library that causes the following messages: # undefined symbol: Xfree From 4046e10b951cf6c5f420fa125d6bea23103b60f8 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 4 Oct 2019 12:19:43 +0900 Subject: [PATCH 113/499] hapcut2: add zlib dependency. (#13032) --- var/spack/repos/builtin/packages/hapcut2/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/hapcut2/package.py b/var/spack/repos/builtin/packages/hapcut2/package.py index d2a16bddd4c..69eb5073d59 100644 --- a/var/spack/repos/builtin/packages/hapcut2/package.py +++ b/var/spack/repos/builtin/packages/hapcut2/package.py @@ -17,6 +17,8 @@ class Hapcut2(MakefilePackage): version('2017-07-10', commit='2966b94c2c2f97813b757d4999b7a6471df1160e', submodules=True) + depends_on('zlib', type='link') + def install(self, spec, prefix): mkdirp(prefix.bin) with working_dir('build'): From b89fa3e01a67308ec41398e2a888526b014664cb Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 4 Oct 2019 12:19:58 +0900 Subject: [PATCH 114/499] fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030) --- .../packages/fastqvalidator/chromosome.patch | 26 +++++++++++++++++++ .../packages/fastqvalidator/package.py | 3 +++ 2 files changed, 29 insertions(+) create mode 100644 var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch diff --git a/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch b/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch new file mode 100644 index 00000000000..579444868e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch @@ -0,0 +1,26 @@ +commit 3a10afe08c209dbacc3eca7794a5a8c0a42ee566 +Author: jonathonl +Date: Thu Sep 20 11:57:06 2018 -0400 + + Removes erroneous deletes in Chromosome constructor. + +diff --git a/general/Chromosome.cpp b/general/Chromosome.cpp +index ac2ff5c..2d773e8 100644 +--- a/general/Chromosome.cpp ++++ b/general/Chromosome.cpp +@@ -27,7 +27,6 @@ Chromosome::Chromosome(GenomeSequence* gs, const char* chromosomeName) + Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) + { + std::string s(genomseSequenceFileName); +- if (this->gs) delete gs; + gs = new GenomeSequence; + assert(gs); + gs->setReferenceName(s); +@@ -39,7 +38,6 @@ Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromos + + Chromosome::Chromosome(const std::string& genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) + { +- if (this->gs) delete gs; + gs = new GenomeSequence; + assert(gs); + gs->setReferenceName(genomseSequenceFileName); diff --git a/var/spack/repos/builtin/packages/fastqvalidator/package.py b/var/spack/repos/builtin/packages/fastqvalidator/package.py index 4395892e175..9397eec2a09 100644 --- a/var/spack/repos/builtin/packages/fastqvalidator/package.py +++ b/var/spack/repos/builtin/packages/fastqvalidator/package.py @@ -20,6 +20,9 @@ class Fastqvalidator(MakefilePackage): commit='9db9c23e176a6ce6f421a3c21ccadedca892ac0c' ) + depends_on('zlib', type='link') + patch('chromosome.patch', when='@2017-01-10', working_dir='libStatGen') + @property def build_targets(self): return ['LIB_PATH_GENERAL={0}'.format( From 938bae1ab6954fca20678a3e5a7e4a23aaa448f5 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 4 Oct 2019 12:20:13 +0900 Subject: [PATCH 115/499] graphmap: add zlib dependency. (#13031) --- var/spack/repos/builtin/packages/graphmap/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/graphmap/package.py b/var/spack/repos/builtin/packages/graphmap/package.py index 2bb7105d945..28dab0f28d8 100644 --- a/var/spack/repos/builtin/packages/graphmap/package.py +++ b/var/spack/repos/builtin/packages/graphmap/package.py @@ -14,6 +14,8 @@ class Graphmap(MakefilePackage): version('0.3.0', commit='eb8c75d68b03be95464318afa69b645a59f8f6b7') + depends_on('zlib', type='link') + def edit(self, spec, prefix): mkdirp(prefix.bin) makefile = FileFilter('Makefile') From 46e319ecd484130cdda9b95c64b16ccea3e6c282 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Fri, 4 Oct 2019 12:20:55 +0900 Subject: [PATCH 116/499] boost: Use gcc toolset for bootstrap with Fujitsu compiler. (#12876) --- var/spack/repos/builtin/packages/boost/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 79d91b99ba5..4f0655dbacd 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -253,7 +253,7 @@ def determine_bootstrap_options(self, spec, with_libs, options): boost_toolset_id = self.determine_toolset(spec) # Arm compiler bootstraps with 'gcc' (but builds as 'clang') - if spec.satisfies('%arm'): + if spec.satisfies('%arm') or spec.satisfies('%fj'): options.append('--with-toolset=gcc') else: options.append('--with-toolset=%s' % boost_toolset_id) From 2cd800306d6ce408d35fae4453c66a4d8dfe1f30 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Fri, 4 Oct 2019 05:32:42 +0200 Subject: [PATCH 117/499] fftw: simplify the recipe and make use of specific targets (#12889) * fftw: grouped precisions in a single variant * fftw: simd options are now based on target features and not on variants * fftw: simplified computing the selected precisions --- .../repos/builtin/packages/fftw/package.py | 191 +++++++----------- 1 file changed, 68 insertions(+), 123 deletions(-) diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py index d719f973bd7..841f8272aba 100644 --- a/var/spack/repos/builtin/packages/fftw/package.py +++ b/var/spack/repos/builtin/packages/fftw/package.py @@ -3,12 +3,12 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * -from spack.spec import ConflictsInSpecError +import os +import os.path import llnl.util.lang -# os is used for rename, etc in patch() -import os + +from spack import * class Fftw(AutotoolsPackage): @@ -20,7 +20,7 @@ class Fftw(AutotoolsPackage): library of choice for most applications.""" homepage = "http://www.fftw.org" - url = "http://www.fftw.org/fftw-3.3.4.tar.gz" + url = "http://www.fftw.org/fftw-3.3.4.tar.gz" list_url = "http://www.fftw.org/download.html" version('3.3.8', '8aac833c943d8e90d51b697b27d4384d') @@ -35,84 +35,32 @@ class Fftw(AutotoolsPackage): patch('pgi-3.3.6-pl2.patch', when="@3.3.6-pl2%pgi", level=0) variant( - 'float', default=True, - description='Produces a single precision version of the library') - variant( - 'double', default=True, - description='Produces a double precision version of the library') - variant( - 'long_double', default=True, - description='Produces a long double precision version of the library') - variant( - 'quad', default=False, - description='Produces a quad precision version of the library ' - '(works only with GCC and libquadmath)') + 'precision', values=any_combination_of( + 'float', 'double', 'long_double', 'quad' + ).prohibit_empty_set().with_default('float,double'), + description='Build the selected floating-point precision libraries' + ) variant('openmp', default=False, description="Enable OpenMP support.") variant('mpi', default=True, description='Activate MPI support') variant( 'pfft_patches', default=False, description='Add extra transpose functions for PFFT compatibility') - variant( - 'simd', - default='generic-simd128,generic-simd256', - values=( - 'sse', 'sse2', 'avx', 'avx2', 'avx512', # Intel - 'avx-128-fma', 'kcvi', # Intel - 'altivec', 'vsx', # IBM - 'neon', # ARM - 'generic-simd128', 'generic-simd256' # Generic - ), - description='Optimizations that are enabled in this build', - multi=True - ) - variant('fma', default=False, description='Activate support for fma') - depends_on('mpi', when='+mpi') depends_on('automake', type='build', when='+pfft_patches') depends_on('autoconf', type='build', when='+pfft_patches') depends_on('libtool', type='build', when='+pfft_patches') + # https://github.com/FFTW/fftw3/commit/902d0982522cdf6f0acd60f01f59203824e8e6f3 conflicts('%gcc@8:8.9999', when="@3.3.7") + conflicts('precision=long_double', when='@2.1.5', + msg='Long double precision is not supported in FFTW 2') + conflicts('precision=quad', when='@2.1.5', + msg='Quad precision is not supported in FFTW 2') provides('fftw-api@2', when='@2.1.5') provides('fftw-api@3', when='@3:') - def flag_handler(self, name, flags): - arch = "" - spec = self.spec - target_simds = { - ('x86_64',): ('sse', 'sse2', 'avx', 'avx2', 'avx512', - 'avx-128-fma', 'kcvi'), - ('ppc', 'ppc64le', 'power7'): ('altivec', 'vsx'), - ('arm',): ('neon',) - } - - if spec.satisfies("platform=cray"): - # FIXME; It is assumed that cray is x86_64. - # If you support arm on cray, you need to fix it. - arch = "x86_64" - - for targets, simds in target_simds.items(): - if ( - (arch not in targets) - and str(spec.target.family) not in targets - ): - if any(spec.satisfies('simd={0}'.format(x)) for x in simds): - raise ConflictsInSpecError( - spec, - [( - spec, - spec.architecture.target, - spec.variants['simd'], - 'simd={0} are valid only on {1}'.format( - ','.join(target_simds[targets]), - ','.join(targets) - ) - )] - ) - return (flags, None, None) - @property def libs(self): @@ -157,6 +105,11 @@ def autoreconf(self, spec, prefix): autoreconf = which('autoreconf') autoreconf('-ifv') + @property + def selected_precisions(self): + """Precisions that have been selected in this build""" + return self.spec.variants['precision'].value + def configure(self, spec, prefix): # Base options options = [ @@ -184,68 +137,60 @@ def configure(self, spec, prefix): if '+mpi' in spec: options.append('--enable-mpi') - # SIMD support - float_options, double_options = [], [] - if spec.satisfies('@3:', strict=True): - for opts in (float_options, double_options): - opts += self.enable_or_disable('simd') - opts += self.enable_or_disable('fma') + # Specific SIMD support. Note there's SSE support too for float, but + # given that it can be activated only for float and that most machines + # are new enough to have SSE2 it has been skipped not to complicate the + # recipe further. + simd_features = ['sse2', 'avx', 'avx2', 'avx512', 'avx-128-fma', + 'kcvi', 'altivec', 'vsx', 'neon'] + simd_options = [] + for feature in simd_features: + msg = '--enable-{0}' if feature in spec.target else '--disable-{0}' + simd_options.append(msg.format(feature)) + # If no features are found, enable the generic ones + if not any(f in spec.target for f in simd_features): + simd_options += [ + '--enable-generic-simd128', + '--enable-generic-simd256' + ] + + simd_options += [ + '--enable-fma' if 'fma' in spec.target else '--disable-fma' + ] + + # Double is the default precision, for all the others we need + # to enable the corresponding option. + enable_precision = { + 'float': ['--enable-float'], + 'double': None, + 'long_double': ['--enable-long-double'], + 'quad': ['--enable-quad-precision'] + } + + # Different precisions must be configured and compiled one at a time configure = Executable('../configure') + for precision in self.selected_precisions: + opts = (enable_precision[precision] or []) + options[:] - # Build double/float/long double/quad variants - if '+double' in spec: - with working_dir('double', create=True): - configure(*(options + double_options)) - if '+float' in spec: - with working_dir('float', create=True): - configure('--enable-float', *(options + float_options)) - if spec.satisfies('@3:+long_double'): - with working_dir('long-double', create=True): - configure('--enable-long-double', *options) - if spec.satisfies('@3:+quad'): - with working_dir('quad', create=True): - configure('--enable-quad-precision', *options) + # SIMD optimizations are available only for float and double + # starting from FFTW 3 + if precision in ('float', 'double') and spec.satisfies('@3:'): + opts += simd_options + + with working_dir(precision, create=True): + configure(*opts) + + def for_each_precision_make(self, *targets): + for precision in self.selected_precisions: + with working_dir(precision): + make(*targets) def build(self, spec, prefix): - if '+double' in spec: - with working_dir('double'): - make() - if '+float' in spec: - with working_dir('float'): - make() - if spec.satisfies('@3:+long_double'): - with working_dir('long-double'): - make() - if spec.satisfies('@3:+quad'): - with working_dir('quad'): - make() + self.for_each_precision_make() def check(self): - spec = self.spec - if '+double' in spec: - with working_dir('double'): - make("check") - if '+float' in spec: - with working_dir('float'): - make("check") - if spec.satisfies('@3:+long_double'): - with working_dir('long-double'): - make("check") - if spec.satisfies('@3:+quad'): - with working_dir('quad'): - make("check") + self.for_each_precision_make('check') def install(self, spec, prefix): - if '+double' in spec: - with working_dir('double'): - make("install") - if '+float' in spec: - with working_dir('float'): - make("install") - if spec.satisfies('@3:+long_double'): - with working_dir('long-double'): - make("install") - if spec.satisfies('@3:+quad'): - with working_dir('quad'): - make("install") + self.for_each_precision_make('install') From 437236781ddaf40e8725d96866b4e402db1a03f8 Mon Sep 17 00:00:00 2001 From: Felix Thaler Date: Fri, 4 Oct 2019 16:56:12 +0000 Subject: [PATCH 118/499] LLVM 9.0.0 (#13050) --- var/spack/repos/builtin/packages/llvm/package.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 5946d6c784f..4b879e3fbd8 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -180,6 +180,22 @@ class Llvm(CMakePackage): 'libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk', } }, + { + 'version': '9.0.0', + 'md5': '0fd4283ff485dffb71a4f1cc8fd3fc72', + 'resources': { + 'compiler-rt': 'c92b8a1aed654463962d77445ebee10b', + 'openmp': 'aea2a701d5d62605bf82cfc2bb57cd0f', + 'polly': '5cd3222a5d7f96cf789dd0bdba14d0fc', + 'libcxx': '3b26e4c37aac2650b594668437a57966', + 'libcxxabi': 'bd8799cc69c7660c7a4729019fbfe286', + 'cfe': '0df6971e2f99b1e99e7bfb533e4067af', + 'clang-tools-extra': '6d1b6e8a9c24ccf98b6ed4f63dbb6356', + 'lldb': '963b43e591d9501965e932fc4218d1a0', + 'lld': 'aa70e956ddbe0c7bff029b8358ff6c44', + 'libunwind': 'ea60ad42e59193ae99bf239d69dfa086' + } + }, { 'version': '8.0.0', 'md5': '74818f431563603515a62be1ee69a142', From cb89949018d0a881d9d548b986bb8eba9e6f1dc3 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Sat, 5 Oct 2019 03:14:09 +0900 Subject: [PATCH 119/499] migrate: add zlib dependency. (#13039) * migrate: add zlib dependency. * flake8. * autotools related tools change to build. --- var/spack/repos/builtin/packages/migrate/package.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/migrate/package.py b/var/spack/repos/builtin/packages/migrate/package.py index c5e7a59ad39..90ccd1abd52 100644 --- a/var/spack/repos/builtin/packages/migrate/package.py +++ b/var/spack/repos/builtin/packages/migrate/package.py @@ -19,15 +19,19 @@ class Migrate(AutotoolsPackage): variant('mpi', default=False, description='Build MPI binaries') - depends_on('autoconf') - depends_on('automake') - depends_on('libtool') - depends_on('m4') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('zlib', type='link') depends_on('openmpi', type=('build', 'link', 'run'), when='+mpi') configure_directory = 'src' + def configure_args(self): + return ['--with-zlib=system'] + def build(self, spec, prefix): with working_dir('src'): # this software is written with parts both in C and C++. From 3cb4547348aad8c0caf5db3000c0fc1567a5e3d0 Mon Sep 17 00:00:00 2001 From: Cody Balos Date: Fri, 4 Oct 2019 11:48:56 -0700 Subject: [PATCH 120/499] superlu-dist: add openmp variant (#13052) --- var/spack/repos/builtin/packages/superlu-dist/package.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index d5009540885..75b9c32856b 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -31,6 +31,7 @@ class SuperluDist(CMakePackage): version('5.0.0', '78d1d6460ff16b3f71e4bcd7306397574d54d421249553ccc26567f00a10bfc6') variant('int64', default=False, description='Build with 64 bit integers') + variant('openmp', default=False, description='Build with OpenMP support (needs a good multithreaded BLAS implementation for good performance)') variant('shared', default=True, description='Build shared libraries') depends_on('mpi') @@ -58,6 +59,11 @@ def cmake_args(self): else: args.append('-DXSDK_INDEX_SIZE=32') + if '+openmp' in spec: + args.append('-Denable_openmp=ON') + else: + args.append('-Denable_openmp=OFF') + if '+shared' in spec: args.append('-DBUILD_SHARED_LIBS:BOOL=ON') else: From b1cdf8bd57054ac4e56b022cacdf66c1b3d55c69 Mon Sep 17 00:00:00 2001 From: Robert Maynard Date: Fri, 4 Oct 2019 15:12:58 -0400 Subject: [PATCH 121/499] Update the VTK-m package with better defaults and cuda corrections (#12850) --- .../repos/builtin/packages/vtkm/package.py | 22 ++++++++++++++----- 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/vtkm/package.py b/var/spack/repos/builtin/packages/vtkm/package.py index b899ef54725..19f0c74afe4 100644 --- a/var/spack/repos/builtin/packages/vtkm/package.py +++ b/var/spack/repos/builtin/packages/vtkm/package.py @@ -6,6 +6,7 @@ from spack import * import os +import sys class Vtkm(CMakePackage, CudaPackage): @@ -21,6 +22,7 @@ class Vtkm(CMakePackage, CudaPackage): git = "https://gitlab.kitware.com/vtk/vtk-m.git" version('master', branch='master') + version('1.4.0', "b0d76bbf5a69c18ec6f1fca4f7858047b65330bd") version('1.3.0', "d9f6e274dec2ea01273cccaba356d23ca88c5a25") version('1.2.0', "3295fed86012226c107e1f2605ca7cc583586b63") version('1.1.0', "6aab1c0885f6ffaaffcf07930873d0df") @@ -29,15 +31,15 @@ class Vtkm(CMakePackage, CudaPackage): # can overwhelm compilers with too many symbols variant('build_type', default='Release', description='CMake build type', values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel')) - variant("shared", default=True, description="build shared libs") + variant("shared", default=False, description="build shared libs") variant("cuda", default=False, description="build cuda support") variant("doubleprecision", default=True, description='enable double precision') - variant("logging", default=False, description="build logging support") + variant("logging", default=True, description="build logging support") variant("mpi", default=False, description="build mpi support") - variant("openmp", default=False, description="build openmp support") + variant("openmp", default=(sys.platform != 'darwin'), description="build openmp support") variant("rendering", default=True, description="build rendering support") - variant("tbb", default=True, description="build TBB support") + variant("tbb", default=(sys.platform == 'darwin'), description="build TBB support") variant("64bitids", default=False, description="enable 64 bits ids") @@ -46,9 +48,16 @@ class Vtkm(CMakePackage, CudaPackage): depends_on("cuda", when="+cuda") depends_on("mpi", when="+mpi") + conflicts("~shared", when="~pic") + def cmake_args(self): spec = self.spec options = [] + gpu_name_table = {'20': 'fermi', + '30': 'kepler', '32': 'kepler', '35': 'kepler', + '50': 'maxwell', '52': 'maxwell', '53': 'maxwell', + '60': 'pascal', '61': 'pascal', '62': 'pascal', + '70': 'turing', '72': 'turing', '75': 'turing'} with working_dir('spack-build', create=True): options = ["-DVTKm_ENABLE_TESTING:BOOL=OFF"] # shared vs static libs @@ -60,9 +69,10 @@ def cmake_args(self): if "+cuda" in spec: options.append("-DVTKm_ENABLE_CUDA:BOOL=ON") if 'cuda_arch' in spec.variants: - cuda_arch = spec.variants['cuda_arch'].value + cuda_value = spec.variants['cuda_arch'].value + name = gpu_name_table[cuda_value[0]] options.append( - '-DVTKm_CUDA_Architecture={0}'.format(cuda_arch[0])) + '-DVTKm_CUDA_Architecture={0}'.format(name)) else: # this fix is necessary if compiling platform has cuda, but # no devices (this's common for front end nodes on hpc clus From e366f6ba3996f815be01fc8ef92ad4ef5e134c67 Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Fri, 4 Oct 2019 22:31:43 +0200 Subject: [PATCH 122/499] llvm: update link to the document explaining codesign (#13047) Change-Id: I01242cbb43b0c62a659739a5d7e9d998dd27e794 --- var/spack/repos/builtin/packages/llvm/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 4b879e3fbd8..be385873f67 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -619,8 +619,8 @@ def check_darwin_lldb_codesign_requirement(self): except ProcessError: explanation = ('The "lldb_codesign" identity must be available' - ' to build LLVM with LLDB. See https://llvm.org/' - 'svn/llvm-project/lldb/trunk/docs/code-signing' + ' to build LLVM with LLDB. See https://github.com/' + 'jevinskie/llvm-lldb/blob/master/docs/code-signing' '.txt for details on how to create this identity.') raise RuntimeError(explanation) From a362cf5ff6dcea353560409b9430ca82150b5918 Mon Sep 17 00:00:00 2001 From: Federico Ficarelli Date: Sat, 5 Oct 2019 01:42:09 +0200 Subject: [PATCH 123/499] grpc: new package (#13054) * Add grpc@1.23.1 * Let version in url match actual one --- .../repos/builtin/packages/grpc/package.py | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 var/spack/repos/builtin/packages/grpc/package.py diff --git a/var/spack/repos/builtin/packages/grpc/package.py b/var/spack/repos/builtin/packages/grpc/package.py new file mode 100644 index 00000000000..20d09541ff2 --- /dev/null +++ b/var/spack/repos/builtin/packages/grpc/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Grpc(CMakePackage): + """A high performance, open-source universal RPC framework.""" + + homepage = "https://grpc.io" + url = "https://github.com/grpc/grpc/archive/v1.23.1.tar.gz" + + version('1.23.1', sha256='dd7da002b15641e4841f20a1f3eb1e359edb69d5ccf8ac64c362823b05f523d9') + + variant('codegen', default=True, + description='Builds code generation plugins for protobuf ' + 'compiler (protoc)') + + depends_on('protobuf') + depends_on('openssl') + depends_on('zlib') + depends_on('cares') + + def cmake_args(self): + args = [ + '-DgRPC_BUILD_CODEGEN:Bool={0}'.format( + 'ON' if '+codegen' in self.spec else 'OFF'), + '-DgRPC_BUILD_CSHARP_EXT:Bool=OFF', + '-DgRPC_INSTALL:Bool=ON', + # Tell grpc to skip vendoring and look for deps via find_package: + '-DgRPC_CARES_PROVIDER:String=package', + '-DgRPC_ZLIB_PROVIDER:String=package', + '-DgRPC_SSL_PROVIDER:String=package', + '-DgRPC_PROTOBUF_PROVIDER:String=package', + '-DgRPC_USE_PROTO_LITE:Bool=OFF', + '-DgRPC_PROTOBUF_PACKAGE_TYPE:String=CONFIG', + # Disable tests: + '-DgRPC_BUILD_TESTS:BOOL=OFF', + '-DgRPC_GFLAGS_PROVIDER:String=none', + '-DgRPC_BENCHMARK_PROVIDER:String=none', + ] + return args From 6a1021b81cb3e0de3510c5d0b410d49055d73f0e Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Sat, 5 Oct 2019 08:42:21 +0200 Subject: [PATCH 124/499] bugfix: issue with custom dotkit root in config.yaml (#13046) When removing support for dotkit in #11986 the code trying to set the paths of the various module files was not updated to skip it. This results in a failure because of a key error after the deprecation warning is displayed to user. This commit fixes the issue and adds a unit test for regression. Note that code for Spack chains has been updated accordingly but no unit test has been added for that case. --- lib/spack/spack/main.py | 9 ++++++++- lib/spack/spack/test/config.py | 17 +++++++++++++++++ 2 files changed, 25 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py index 0984aa3b006..89b4d3dc85e 100644 --- a/lib/spack/spack/main.py +++ b/lib/spack/spack/main.py @@ -588,11 +588,14 @@ def shell_set(var, value): shell_set('_sp_compatible_sys_types', ':'.join(spack.architecture.compatible_sys_types())) # print roots for all module systems - module_roots = spack.config.get('config:module_roots') module_to_roots = { 'tcl': list(), 'lmod': list() } + module_roots = spack.config.get('config:module_roots') + module_roots = dict( + (k, v) for k, v in module_roots.items() if k in module_to_roots + ) for name, path in module_roots.items(): path = spack.util.path.canonicalize_path(path) module_to_roots[name].append(path) @@ -601,6 +604,10 @@ def shell_set(var, value): 'upstreams') or {} for install_properties in other_spack_instances.values(): upstream_module_roots = install_properties.get('modules', {}) + upstream_module_roots = dict( + (k, v) for k, v in upstream_module_roots.items() + if k in module_to_roots + ) for module_type, root in upstream_module_roots.items(): module_to_roots[module_type].append(root) diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index cf0de708561..631fbabe8b8 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -16,6 +16,7 @@ import spack.paths import spack.config +import spack.main import spack.schema.compilers import spack.schema.config import spack.schema.env @@ -759,3 +760,19 @@ def test_bad_compilers_yaml(tmpdir): - compiler: fenfironfent: /bad/value """) + + +@pytest.mark.regression('13045') +def test_dotkit_in_config_does_not_raise( + mock_config, write_config_file, capsys +): + write_config_file('config', + {'config': {'module_roots': {'dotkit': '/some/path'}}}, + 'high') + spack.main.print_setup_info('sh') + captured = capsys.readouterr() + + # Check that we set the variables we expect and that + # we throw a a deprecation warning without raising + assert '_sp_sys_type' in captured[0] # stdout + assert 'Warning' in captured[1] # stderr From c45ecafd71025b9d5edce99f3c22a23e63fa5781 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 5 Oct 2019 04:39:55 -0500 Subject: [PATCH 125/499] procps: new package (#13043) --- .../repos/builtin/packages/procps/package.py | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 var/spack/repos/builtin/packages/procps/package.py diff --git a/var/spack/repos/builtin/packages/procps/package.py b/var/spack/repos/builtin/packages/procps/package.py new file mode 100644 index 00000000000..ff51b4e57a9 --- /dev/null +++ b/var/spack/repos/builtin/packages/procps/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Procps(AutotoolsPackage): + """Command line and full screen utilities for browsing procfs, a "pseudo" + file system dynamically generated by the kernel to provide information + about the status of entries in its process table.""" + + homepage = "https://gitlab.com/procps-ng/procps" + git = "https://gitlab.com/procps-ng/procps.git" + + version('master', branch='master') + version('3.3.15', tag='v3.3.15') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('pkgconfig@0.9.0:', type='build') + depends_on('dejagnu', type='test') + depends_on('libiconv') + depends_on('gettext') + depends_on('ncurses') + + conflicts('platform=darwin', msg='procps is linux-only') + + def autoreconf(self, spec, prefix): + sh = which('sh') + sh('autogen.sh') + + def configure_args(self): + return [ + '--with-libiconv-prefix={0}'.format(self.spec['libiconv'].prefix), + '--with-libintl-prefix={0}'.format(self.spec['gettext'].prefix), + '--with-ncurses', + # Required to avoid libintl linking errors + '--disable-nls', + ] From e78ca6608796f6ba67ddd348f2e6df9b9c457a9b Mon Sep 17 00:00:00 2001 From: Teodor Nikolov Date: Sun, 6 Oct 2019 03:36:59 +0200 Subject: [PATCH 126/499] New package: cxxopts (#13035) * New package: cxxopts * Use +unicode instead of unicode=True - Make the unicode option more explicit * [cxxopts] Fix white space warnings --- .../repos/builtin/packages/cxxopts/package.py | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 var/spack/repos/builtin/packages/cxxopts/package.py diff --git a/var/spack/repos/builtin/packages/cxxopts/package.py b/var/spack/repos/builtin/packages/cxxopts/package.py new file mode 100644 index 00000000000..cb3ff6e8003 --- /dev/null +++ b/var/spack/repos/builtin/packages/cxxopts/package.py @@ -0,0 +1,42 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Cxxopts(CMakePackage): + """Lightweight C++ command line option parser""" + + homepage = "https://github.com/jarro2783/cxxopts" + url = "https://github.com/jarro2783/cxxopts/archive/v2.2.0.tar.gz" + + version('2.2.0', sha256='447dbfc2361fce9742c5d1c9cfb25731c977b405f9085a738fbd608626da8a4d') + version('2.1.2', sha256='95f524c6615a2067e935e02ef74b013b17efa339df0a3c9db3e91fc0afbaf269') + version('2.1.1', sha256='e19216251427d04f0273e6487c0246ae2dbb4154bf178f43896af8fa1ef89f3f') + version('2.1.0', sha256='7672c79e5e48dd0cb1935c6efe65d2695d96fa764bf06c493d2db25a3cf633b4') + version('2.0.0', sha256='f575a12645743032c27a7bc661e8598f249a8453d7f5388bcae66ac3b089399e') + version('1.4.4', sha256='1d0eedb39ecbc64a0f82d8b6fe40d5c8e611501702969cfbd14a07ce6ddb8501') + version('1.4.3', sha256='9103d6d75a3f599728256ce89922a8cd348bfe5874de62ca1436f605f194c52e') + version('1.4.2', sha256='8fc5e16e68ddf549465f8bec6b56adaccfab9d183093616ddd4d3e80115844cb') + version('1.4.1', sha256='c5ccfe99bd3db0604d077c968b39a42d61333a64d171fe84d7037d6c0dcc996d') + version('1.4.0', sha256='60d4a482ec603ef4efa2603978596716884b33e24d39af6ddca52b4a30f7107b') + + variant('unicode', default=False, + description='Enables unicode support using the ICU library.') + + depends_on('cmake@3.1.0:', type='build') + depends_on('icu4c', when='+unicode') + + def cmake_args(self): + args = ['-DCXXOPTS_ENABLE_INSTALL=ON', + '-DCXXOPTS_BUILD_EXAMPLES=OFF', + '-DCXXOPTS_BUILD_TESTS=OFF'] + + if '+unicode' in self.spec: + args.append('-DCXXOPTS_USE_UNICODE_HELP=ON') + else: + args.append('-DCXXOPTS_USE_UNICODE_HELP=OFF') + + return args From 608f7321016d5a9937930d3163fdef9af0a194af Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 5 Oct 2019 20:37:44 -0500 Subject: [PATCH 127/499] expect: fix darwin install name (#13042) * expect: fix darwin install name * Fix expect binary as well --- var/spack/repos/builtin/packages/expect/package.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/var/spack/repos/builtin/packages/expect/package.py b/var/spack/repos/builtin/packages/expect/package.py index 01becf4b3f9..1c431e9d999 100644 --- a/var/spack/repos/builtin/packages/expect/package.py +++ b/var/spack/repos/builtin/packages/expect/package.py @@ -58,3 +58,15 @@ def symlink_library(self): link_name = join_path(self.prefix.lib, link_name) symlink(target, link_name) + + @run_after('install') + def darwin_fix(self): + # The shared library is not installed correctly on Darwin; fix this + if self.spec.satisfies('platform=darwin'): + fix_darwin_install_name( + join_path(self.prefix.lib, 'expect{0}'.format(self.version))) + + old = 'libexpect{0}.dylib'.format(self.version) + new = glob.glob(join_path(self.prefix.lib, 'expect*', 'libexpect*'))[0] + install_name_tool = Executable('install_name_tool') + install_name_tool('-change', old, new, self.prefix.bin.expect) From c6b8d79ea6960609ec62fada1ab210725a464886 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Sun, 6 Oct 2019 10:58:43 +0900 Subject: [PATCH 128/499] Package/fujitsu mpi (#12807) * fujitsu-mpi: commit new package * Add homepage. * * Modified the MPI commands to a simple form. * Unnecessary processing has been deleted. * Add conflict for all compilers except the Fujitsu compiler. * Fix typo. * Delete versions. * Delete conditions for specifying the Fujitsu compiler. --- .../builtin/packages/fujitsu-mpi/package.py | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 var/spack/repos/builtin/packages/fujitsu-mpi/package.py diff --git a/var/spack/repos/builtin/packages/fujitsu-mpi/package.py b/var/spack/repos/builtin/packages/fujitsu-mpi/package.py new file mode 100644 index 00000000000..3370cc3b217 --- /dev/null +++ b/var/spack/repos/builtin/packages/fujitsu-mpi/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class FujitsuMpi(Package): + """Fujitsu MPI implementation only for Fujitsu compiler.""" + + homepage = "https://www.fujitsu.com/us/" + + conflicts('%arm') + conflicts('%cce') + conflicts('%clang') + conflicts('%gcc') + conflicts('%intel') + conflicts('%nag') + conflicts('%pgi') + conflicts('%xl') + conflicts('%xl_r') + + provides('mpi@3.1:') + + def install(self, spec, prefix): + raise InstallError( + 'Fujitsu MPI is not installable; it is vendor supplied') + + def setup_dependent_package(self, module, dependent_spec): + self.spec.mpicc = self.prefix.bin.mpifcc + self.spec.mpicxx = self.prefix.bin.mpiFCC + self.spec.mpif77 = self.prefix.bin.mpifrt + self.spec.mpifc = self.prefix.bin.mpifrt + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('MPICC', self.prefix.bin.mpifcc) + spack_env.set('MPICXX', self.prefix.bin.mpiFCC) + spack_env.set('MPIF77', self.prefix.bin.mpifrt) + spack_env.set('MPIF90', self.prefix.bin.mpifrt) From bdb92f2d91605dd8a93ef16f0d7fcf6595f5b012 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sun, 6 Oct 2019 04:03:35 +0200 Subject: [PATCH 129/499] Consistently support pkg-config files in share subdirectory (#12838) While the build environment already takes share/pkgconfig into account, the generated module files etc. only consider lib/pkgconfig and lib64/pkgconfig. --- etc/spack/defaults/modules.yaml | 2 ++ lib/spack/docs/environments.rst | 2 +- lib/spack/spack/environment.py | 3 ++- lib/spack/spack/test/config.py | 1 + lib/spack/spack/test/data/config/modules.yaml | 2 ++ lib/spack/spack/test/environment_modifications.py | 1 + 6 files changed, 9 insertions(+), 2 deletions(-) diff --git a/etc/spack/defaults/modules.yaml b/etc/spack/defaults/modules.yaml index 1d91b0c88c4..77c976510bd 100644 --- a/etc/spack/defaults/modules.yaml +++ b/etc/spack/defaults/modules.yaml @@ -35,6 +35,8 @@ modules: - PKG_CONFIG_PATH lib64/pkgconfig: - PKG_CONFIG_PATH + share/pkgconfig: + - PKG_CONFIG_PATH '': - CMAKE_PREFIX_PATH diff --git a/lib/spack/docs/environments.rst b/lib/spack/docs/environments.rst index 664e6e2cce8..6ce67f0067a 100644 --- a/lib/spack/docs/environments.rst +++ b/lib/spack/docs/environments.rst @@ -764,7 +764,7 @@ ACLOCAL_PATH share/aclocal LD_LIBRARY_PATH lib, lib64 LIBRARY_PATH lib, lib64 CPATH include -PKG_CONFIG_PATH lib/pkgconfig, lib64/pkgconfig +PKG_CONFIG_PATH lib/pkgconfig, lib64/pkgconfig, share/pkgconfig CMAKE_PREFIX_PATH . =================== ========= diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index adb062d1cbc..84c77df6b0e 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -949,7 +949,8 @@ def _shell_vars(self): ('LD_LIBRARY_PATH', ['lib', 'lib64']), ('LIBRARY_PATH', ['lib', 'lib64']), ('CPATH', ['include']), - ('PKG_CONFIG_PATH', ['lib/pkgconfig', 'lib64/pkgconfig']), + ('PKG_CONFIG_PATH', ['lib/pkgconfig', 'lib64/pkgconfig', + 'share/pkgconfig']), ('CMAKE_PREFIX_PATH', ['']), ] diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index 631fbabe8b8..163fc392d3d 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -507,6 +507,7 @@ def test_keys_are_ordered(): 'include', 'lib/pkgconfig', 'lib64/pkgconfig', + 'share/pkgconfig', '' ) diff --git a/lib/spack/spack/test/data/config/modules.yaml b/lib/spack/spack/test/data/config/modules.yaml index adc16e896b2..f610087fb18 100644 --- a/lib/spack/spack/test/data/config/modules.yaml +++ b/lib/spack/spack/test/data/config/modules.yaml @@ -37,5 +37,7 @@ modules: - PKG_CONFIG_PATH lib64/pkgconfig: - PKG_CONFIG_PATH + share/pkgconfig: + - PKG_CONFIG_PATH '': - CMAKE_PREFIX_PATH diff --git a/lib/spack/spack/test/environment_modifications.py b/lib/spack/spack/test/environment_modifications.py index a57ac743640..1e1759ddbc9 100644 --- a/lib/spack/spack/test/environment_modifications.py +++ b/lib/spack/spack/test/environment_modifications.py @@ -28,6 +28,7 @@ def test_inspect_path(tmpdir): 'include': ['CPATH'], 'lib/pkgconfig': ['PKG_CONFIG_PATH'], 'lib64/pkgconfig': ['PKG_CONFIG_PATH'], + 'share/pkgconfig': ['PKG_CONFIG_PATH'], '': ['CMAKE_PREFIX_PATH'] } From 19e6f55647a33e1d5039b0bef0803ce9469c49b3 Mon Sep 17 00:00:00 2001 From: Pariksheet Nanda Date: Sat, 5 Oct 2019 22:07:18 -0400 Subject: [PATCH 130/499] doc: fix #12245 non-functional libdwarf dependency (#12515) Applying accepted fix from spack/spack.io#4 --- lib/spack/docs/features.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/spack/docs/features.rst b/lib/spack/docs/features.rst index c4de4ef416c..a242eab5955 100644 --- a/lib/spack/docs/features.rst +++ b/lib/spack/docs/features.rst @@ -60,14 +60,14 @@ Customize dependencies ---------------------- Spack allows *dependencies* of a particular installation to be -customized extensively. Suppose that ``mpileaks`` depends indirectly -on ``libelf`` and ``libdwarf``. Using ``^``, users can add custom +customized extensively. Suppose that ``hdf5`` depends +on ``openmpi`` and indirectly on ``hwloc``. Using ``^``, users can add custom configurations for the dependencies: .. code-block:: console - # Install mpileaks and link it with specific versions of libelf and libdwarf - $ spack install mpileaks@1.1.2 %gcc@4.7.3 +debug ^libelf@0.8.12 ^libdwarf@20130729+debug + # Install hdf5 and link it with specific versions of openmpi and hwloc + $ spack install hdf5@1.10.1 %gcc@4.7.3 +debug ^openmpi+cuda fabrics=auto ^hwloc+gl ------------------------ Non-destructive installs From 070a536e490fe428814d88bd1b03df0259db67d1 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 6 Oct 2019 04:13:39 +0200 Subject: [PATCH 131/499] qt: help pick up dependencies (#11172) * qt: help pick up dependencies * qt: add 5.12.5 --- .../repos/builtin/packages/pcre2/package.py | 7 ++++ .../repos/builtin/packages/qt/package.py | 37 ++++++++++++++++--- 2 files changed, 39 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py index a78bdb213e0..f29708b26bf 100644 --- a/var/spack/repos/builtin/packages/pcre2/package.py +++ b/var/spack/repos/builtin/packages/pcre2/package.py @@ -28,3 +28,10 @@ def configure_args(self): args.append('--enable-pcre2-32') return args + + @property + def libs(self): + libs = find_libraries('libpcre2*', + root=self.prefix.lib, + recursive=False) + return libs diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index fc55570eb35..8585f6a2723 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -21,6 +21,8 @@ class Qt(Package): phases = ['configure', 'build', 'install'] + version('5.12.5', 'a2299e21db7767caf98242767bffb18a2a88a42fee2d6a393bedd234f8c91298') + version('5.12.2', '59b8cb4e728450b21224dcaaa40eb25bafc5196b6988f2225c394c6b7f881ff5') version('5.11.3', '859417642713cee2493ee3646a7fee782c9f1db39e41d7bb1322bba0c5f0ff4d') version('5.11.2', 'c6104b840b6caee596fa9a35bc5f57f67ed5a99d6a36497b6fe66f990a53ca81') version('5.10.0', 'c5e275ab0ed7ee61d0f4b82cd471770d') @@ -70,7 +72,7 @@ class Qt(Package): # fix installation of pkgconfig files # see https://github.com/Homebrew/homebrew-core/pull/5951 - patch('restore-pc-files.patch', when='@5.9: platform=darwin') + patch('restore-pc-files.patch', when='@5.9:5.11 platform=darwin') patch('qt3accept.patch', when='@3.3.8b') patch('qt3krell.patch', when='@3.3.8b+krellpatch') @@ -302,6 +304,7 @@ def patch(self): @property def common_config_args(self): # incomplete list is here http://doc.qt.io/qt-5/configure-options.html + openssl = self.spec['openssl'] config_args = [ '-prefix', self.prefix, '-v', @@ -309,6 +312,9 @@ def common_config_args(self): '-{0}opengl'.format('' if '+opengl' in self.spec else 'no-'), '-release', '-confirm-license', + '-openssl-linked', + '{0}'.format(openssl.libs.search_flags), + '{0}'.format(openssl.headers.include_flags), '-optimized-qmake', '-no-pch', ] @@ -344,19 +350,39 @@ def common_config_args(self): config_args.append('-static') if self.spec.satisfies('@5:'): - config_args.append('-system-harfbuzz') - config_args.append('-system-pcre') + pcre = self.spec['pcre'] if self.spec.satisfies('@5.0:5.8') \ + else self.spec['pcre2'] + harfbuzz = self.spec['harfbuzz'] + config_args.extend([ + '-system-harfbuzz', + '{0}'.format(harfbuzz.libs.search_flags), + '{0}'.format(harfbuzz.headers.include_flags), + '-system-pcre', + '{0}'.format(pcre.libs.search_flags), + '{0}'.format(pcre.headers.include_flags) + ]) if self.spec.satisfies('@5.7:'): - config_args.append('-system-doubleconversion') + dc = self.spec['double-conversion'] + config_args.extend([ + '-system-doubleconversion', + '{0}'.format(dc.libs.search_flags), + '{0}'.format(dc.headers.include_flags) + ]) if '@:5.7.1' in self.spec: config_args.append('-no-openvg') else: # FIXME: those could work for other versions + png = self.spec['libpng'] + jpeg = self.spec['jpeg'] config_args.extend([ '-system-libpng', + '{0}'.format(png.libs.search_flags), + '{0}'.format(png.headers.include_flags), '-system-libjpeg', + '{0}'.format(jpeg.libs.search_flags), + '{0}'.format(jpeg.headers.include_flags), '-system-zlib' ]) @@ -387,11 +413,12 @@ def common_config_args(self): '' if '+framework' in self.spec else 'no-')) if '@5:' in self.spec and MACOS_VERSION: config_args.extend([ - '-no-xinput2', '-no-xcb-xlib', '-no-pulseaudio', '-no-alsa', ]) + if self.spec.satisfies('@:5.11'): + config_args.append('-no-xinput2') # FIXME: else: -system-xcb ? From f34162a5b88569b6c5dd0ee2865503860c5a4957 Mon Sep 17 00:00:00 2001 From: Oliver Breitwieser Date: Sun, 6 Oct 2019 16:15:29 +0200 Subject: [PATCH 132/499] Add missing py-contextlib2 (#13056) Change-Id: I8e0a90d4aa2c9f46230a6fe35ce5f4fa44672faf --- .../packages/py-contextlib2/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-contextlib2/package.py diff --git a/var/spack/repos/builtin/packages/py-contextlib2/package.py b/var/spack/repos/builtin/packages/py-contextlib2/package.py new file mode 100644 index 00000000000..edf31e99f3b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-contextlib2/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyContextlib2(PythonPackage): + """contextlib2 is a backport of the standard library's contextlib module to + earlier Python versions.""" + + homepage = "https://contextlib2.readthedocs.io/en/stable/" + url = "https://github.com/jazzband/contextlib2/archive/v0.6.0.tar.gz" + + version('0.6.0', sha256='4f18e2f28bb642aae9447aacec93b1319c8ee838711553c0a2bd906753f2ad33') + + depends_on('py-setuptools', type='build') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) From ba72114ba21781dee662300b8d53e7e44b0fd702 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Sun, 6 Oct 2019 16:16:25 +0200 Subject: [PATCH 133/499] unrar: Add package (#12908) --- .../repos/builtin/packages/unrar/package.py | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 var/spack/repos/builtin/packages/unrar/package.py diff --git a/var/spack/repos/builtin/packages/unrar/package.py b/var/spack/repos/builtin/packages/unrar/package.py new file mode 100644 index 00000000000..79bf9d31f78 --- /dev/null +++ b/var/spack/repos/builtin/packages/unrar/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Unrar(MakefilePackage): + """RAR archive extraction utility""" + + homepage = "https://www.rarlab.com" + url = "https://www.rarlab.com/rar/unrarsrc-5.8.2.tar.gz" + + version( + "5.8.2", + sha256="33386623fd3fb153b56292df4a6a69b457e69e1803b6d07b614e5fd22fb33dda", + ) + + version( + "5.8.1", + sha256="035f1f436f0dc2aea09aec146b9cc3e47ca2442f2c62b4ad9374c7c9cc20e632", + ) + + def edit(self, spec, prefix): + makefile = FileFilter("makefile") + makefile.filter( + "LIBFLAGS=-fPIC", "LIBFLAGS={0}".format(self.compiler.pic_flag) + ) + makefile.filter("DESTDIR=/usr", "DESTDIR={0}".format(self.prefix)) From 3d247d9567e700f7bc27c84a8687bf86013e7944 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Sun, 6 Oct 2019 16:20:29 +0200 Subject: [PATCH 134/499] freeimage: new package (#13049) * freeimage: new package * Address comments. * Whitespace --- .../packages/freeimage/install_fixes.patch | 15 +++++++++++ .../builtin/packages/freeimage/package.py | 25 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 var/spack/repos/builtin/packages/freeimage/install_fixes.patch create mode 100644 var/spack/repos/builtin/packages/freeimage/package.py diff --git a/var/spack/repos/builtin/packages/freeimage/install_fixes.patch b/var/spack/repos/builtin/packages/freeimage/install_fixes.patch new file mode 100644 index 00000000000..21c9fadde97 --- /dev/null +++ b/var/spack/repos/builtin/packages/freeimage/install_fixes.patch @@ -0,0 +1,15 @@ +--- a/Makefile.gnu 2015-03-10 09:04:00.000000000 +0100 ++++ b/Makefile.gnu 2019-03-15 13:20:12.480698778 +0100 +@@ -71,9 +71,9 @@ + + install: + install -d $(INCDIR) $(INSTALLDIR) +- install -m 644 -o root -g root $(HEADER) $(INCDIR) +- install -m 644 -o root -g root $(STATICLIB) $(INSTALLDIR) +- install -m 755 -o root -g root $(SHAREDLIB) $(INSTALLDIR) ++ install -m 644 $(HEADER) $(INCDIR) ++ install -m 644 $(STATICLIB) $(INSTALLDIR) ++ install -m 755 $(SHAREDLIB) $(INSTALLDIR) + ln -sf $(SHAREDLIB) $(INSTALLDIR)/$(VERLIBNAME) + ln -sf $(VERLIBNAME) $(INSTALLDIR)/$(LIBNAME) + # ldconfig diff --git a/var/spack/repos/builtin/packages/freeimage/package.py b/var/spack/repos/builtin/packages/freeimage/package.py new file mode 100644 index 00000000000..2f1293c1f4b --- /dev/null +++ b/var/spack/repos/builtin/packages/freeimage/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Freeimage(MakefilePackage): + """FreeImage is an Open Source library project for developers who would like + to support popular graphics image formats like PNG, BMP, JPEG, TIFF and + others as needed by today's multimedia applications""" + + homepage = "http://freeimage.sourceforge.net/" + + version('3.18.0', 'f8ba138a3be233a3eed9c456e42e2578') + + patch('install_fixes.patch', when='@3.18.0') + + def edit(self, spec, prefix): + env["DESTDIR"] = prefix + + def url_for_version(self, version): + url = "https://downloads.sourceforge.net/project/freeimage/Source%20Distribution/{0}/FreeImage{1}.zip" + return url.format(version, version.joined) From 79bd6bbd04bcf33f9574f95dc2fc1ecad6403dda Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 6 Oct 2019 21:28:34 +0200 Subject: [PATCH 135/499] gnuplot: add 5.2.7 and fix qt dep (#13058) --- var/spack/repos/builtin/packages/gnuplot/package.py | 2 ++ var/spack/repos/builtin/packages/qt/package.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py index c33b207cf20..63578e2f5de 100644 --- a/var/spack/repos/builtin/packages/gnuplot/package.py +++ b/var/spack/repos/builtin/packages/gnuplot/package.py @@ -26,6 +26,7 @@ class Gnuplot(AutotoolsPackage): # dependency of readline. Fix it with a small patch patch('term_include.patch') + version('5.2.7', '97fe503ff3b2e356fe2ae32203fc7fd2cf9cef1f46b60fe46dc501a228b9f4ed') version('5.2.5', '039db2cce62ddcfd31a6696fe576f4224b3bc3f919e66191dfe2cdb058475caa') version('5.2.2', '60aedd08998160593199459dea8467fe') version('5.2.0', '0bd8f9af84c0ad2fa9de16772c366416') @@ -64,6 +65,7 @@ class Gnuplot(AutotoolsPackage): depends_on('pango@1.10:', when='+cairo') depends_on('libx11', when='+X') depends_on('qt@5.7:+opengl', when='+qt') + depends_on('qt+framework', when='+qt platform=darwin') def configure_args(self): # see https://github.com/Homebrew/homebrew-core/blob/master/Formula/gnuplot.rb diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 8585f6a2723..2df6befa710 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -51,7 +51,7 @@ class Qt(Package): description="Build the Webkit extension") variant('examples', default=False, description="Build examples.") - variant('framework', default=False, + variant('framework', default=bool(MACOS_VERSION), description="Build as a macOS Framework package.") variant('tools', default=True, description="Build tools, including Qt Designer.") From 7d0e7efabb8d7ea01b2d7f163065e76a17e135b4 Mon Sep 17 00:00:00 2001 From: Paul Date: Sun, 6 Oct 2019 19:22:05 -0600 Subject: [PATCH 136/499] Added go 1.13.1 and 1.12.10 (#12977) --- var/spack/repos/builtin/packages/go/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index e8a20515f91..ec56df2d1ad 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -35,7 +35,9 @@ class Go(Package): extendable = True + version('1.13.1', sha256='81f154e69544b9fa92b1475ff5f11e64270260d46e7e36c34aafc8bc96209358') version('1.13', sha256='3fc0b8b6101d42efd7da1da3029c0a13f22079c0c37ef9730209d8ec665bf122') + version('1.12.10', sha256='f56e48fce80646d3c94dcf36d3e3f490f6d541a92070ad409b87b6bbb9da3954') version('1.12.9', sha256='ab0e56ed9c4732a653ed22e232652709afbf573e710f56a07f7fdeca578d62fc') version('1.12.8', sha256='11ad2e2e31ff63fcf8a2bdffbe9bfa2e1845653358daed593c8c2d03453c9898') version('1.12.6', sha256='c96c5ccc7455638ae1a8b7498a030fe653731c8391c5f8e79590bce72f92b4ca') From c8c795e7dbde22dc47c9ae285a4dd59004b115b1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 7 Oct 2019 04:11:17 -0500 Subject: [PATCH 137/499] watch: added new package (#13044) --- .../repos/builtin/packages/watch/package.py | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 var/spack/repos/builtin/packages/watch/package.py diff --git a/var/spack/repos/builtin/packages/watch/package.py b/var/spack/repos/builtin/packages/watch/package.py new file mode 100644 index 00000000000..760bd8b187e --- /dev/null +++ b/var/spack/repos/builtin/packages/watch/package.py @@ -0,0 +1,49 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Watch(AutotoolsPackage): + """Executes a program periodically, showing output fullscreen.""" + + # Note: there is a separate procps package, but it doesn't build on macOS. + # This package only contains the `watch` program, a subset of procps which + # does build on macOS. + # https://github.com/NixOS/nixpkgs/issues/18929#issuecomment-249388571 + homepage = "https://gitlab.com/procps-ng/procps" + git = "https://gitlab.com/procps-ng/procps.git" + + version('master', branch='master') + version('3.3.15', tag='v3.3.15') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('pkgconfig@0.9.0:', type='build') + depends_on('ncurses') + + # https://github.com/Homebrew/homebrew-core/blob/master/Formula/watch.rb + def autoreconf(self, spec, prefix): + sh = which('sh') + sh('autogen.sh') + + def configure_args(self): + return [ + '--with-ncurses', + # Required to avoid libintl linking errors + '--disable-nls', + ] + + def build(self, spec, prefix): + make('watch') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + mkdirp(prefix.man.man1) + + install('watch', prefix.bin) + install('watch.1', prefix.man.man1) From 9faee51e22967b289dc7d8aabe0dffd36a0f85ba Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Mon, 7 Oct 2019 18:53:23 +0200 Subject: [PATCH 138/499] Spack environments can concretize specs together (#11372) This PR adds a 'concretize' entry to an environment's spec.yaml file which controls how user specs are concretized. By default it is set to 'separately' which means that each spec added by the user is concretized separately (the behavior of environments before this PR). If set to 'together', the environment will concretize all of the added user specs together; this means that all specs and their dependencies will be consistent with each other (for example, a user could develop code linked against the set of libraries in the environment without conflicts). If the environment was previously concretized, this will re-concretize all specs, in which case previously-installed specs may no longer be used by the environment (in this sense, adding a new spec to an environment with 'concretize: together' can be significantly more expensive). The 'concretize: together' setting is not compatible with Spec matrices; this PR adds a check to look for multiple instances of the same package added to the environment and fails early when 'concretize: together' is set (to avoid confusing messages about conflicts later on). --- lib/spack/docs/environments.rst | 52 ++++++++++++++++++++++-- lib/spack/spack/environment.py | 70 ++++++++++++++++++++++++++++++++- lib/spack/spack/schema/env.py | 5 +++ lib/spack/spack/test/cmd/env.py | 48 ++++++++++++++++++++++ 4 files changed, 171 insertions(+), 4 deletions(-) diff --git a/lib/spack/docs/environments.rst b/lib/spack/docs/environments.rst index 6ce67f0067a..1ce765210fe 100644 --- a/lib/spack/docs/environments.rst +++ b/lib/spack/docs/environments.rst @@ -292,19 +292,37 @@ or $ spack -E myenv add python +.. _environments_concretization: + ^^^^^^^^^^^^ Concretizing ^^^^^^^^^^^^ Once some user specs have been added to an environment, they can be -concretized. The following command will concretize all user specs -that have been added and not yet concretized: +concretized. *By default specs are concretized separately*, one after +the other. This mode of operation permits to deploy a full +software stack where multiple configurations of the same package +need to be installed alongside each other. Central installations done +at HPC centers by system administrators or user support groups +are a common case that fits in this behavior. +Environments *can also be configured to concretize all +the root specs in a self-consistent way* to ensure that +each package in the environment comes with a single configuration. This +mode of operation is usually what is required by software developers that +want to deploy their development environment. + +Regardless of which mode of operation has been chosen, the following +command will ensure all the root specs are concretized according to the +constraints that are prescribed in the configuration: .. code-block:: console [myenv]$ spack concretize -This command will re-concretize all specs: +In the case of specs that are not concretized together, the command +above will concretize only the specs that were added and not yet +concretized. Forcing a re-concretization of all the specs can be done +instead with this command: .. code-block:: console @@ -467,6 +485,34 @@ Appending to this list in the yaml is identical to using the ``spack add`` command from the command line. However, there is more power available from the yaml file. +""""""""""""""""""" +Spec concretization +""""""""""""""""""" + +Specs can be concretized separately or together, as already +explained in :ref:`environments_concretization`. The behavior active +under any environment is determined by the ``concretization`` property: + +.. code-block:: yaml + + spack: + specs: + - ncview + - netcdf + - nco + - py-sphinx + concretization: together + +which can currently take either one of the two allowed values ``together`` or ``separately`` +(the default). + +.. admonition:: Re-concretization of user specs + + When concretizing specs together the entire set of specs will be + re-concretized after any addition of new user specs, to ensure that + the environment remains consistent. When instead the specs are concretized + separately only the new specs will be re-concretized after any addition. + """"""""""""" Spec Matrices """"""""""""" diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 84c77df6b0e..ab8d7e14f18 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -3,6 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import collections import os import re import sys @@ -19,6 +20,7 @@ import llnl.util.tty as tty from llnl.util.tty.color import colorize +import spack.concretize import spack.error import spack.hash_types as ht import spack.repo @@ -514,6 +516,9 @@ def __init__(self, path, init_file=None, with_view=None): path to the view. """ self.path = os.path.abspath(path) + # This attribute will be set properly from configuration + # during concretization + self.concretization = None self.clear() if init_file: @@ -591,6 +596,9 @@ def _read_manifest(self, f): for name, values in enable_view.items()) else: self.views = {} + # Retrieve the current concretization strategy + configuration = config_dict(self.yaml) + self.concretization = configuration.get('concretization') @property def user_specs(self): @@ -845,6 +853,59 @@ def concretize(self, force=False): self.concretized_order = [] self.specs_by_hash = {} + # Pick the right concretization strategy + if self.concretization == 'together': + return self._concretize_together() + if self.concretization == 'separately': + return self._concretize_separately() + + msg = 'concretization strategy not implemented [{0}]' + raise SpackEnvironmentError(msg.format(self.concretization)) + + def _concretize_together(self): + """Concretization strategy that concretizes all the specs + in the same DAG. + """ + # Exit early if the set of concretized specs is the set of user specs + user_specs_did_not_change = not bool( + set(self.user_specs) - set(self.concretized_user_specs) + ) + if user_specs_did_not_change: + return [] + + # Check that user specs don't have duplicate packages + counter = collections.defaultdict(int) + for user_spec in self.user_specs: + counter[user_spec.name] += 1 + + duplicates = [] + for name, count in counter.items(): + if count > 1: + duplicates.append(name) + + if duplicates: + msg = ('environment that are configured to concretize specs' + ' together cannot contain more than one spec for each' + ' package [{0}]'.format(', '.join(duplicates))) + raise SpackEnvironmentError(msg) + + # Proceed with concretization + self.concretized_user_specs = [] + self.concretized_order = [] + self.specs_by_hash = {} + + concrete_specs = spack.concretize.concretize_specs_together( + *self.user_specs + ) + concretized_specs = [x for x in zip(self.user_specs, concrete_specs)] + for abstract, concrete in concretized_specs: + self._add_concrete_spec(abstract, concrete) + return concretized_specs + + def _concretize_separately(self): + """Concretization strategy that concretizes separately one + user spec after the other. + """ # keep any concretized specs whose user specs are still in the manifest old_concretized_user_specs = self.concretized_user_specs old_concretized_order = self.concretized_order @@ -875,6 +936,13 @@ def install(self, user_spec, concrete_spec=None, **install_args): This will automatically concretize the single spec, but it won't affect other as-yet unconcretized specs. """ + if self.concretization == 'together': + msg = 'cannot install a single spec in an environment that is ' \ + 'configured to be concretized together. Run instead:\n\n' \ + ' $ spack add \n' \ + ' $ spack install\n' + raise SpackEnvironmentError(msg) + spec = Spec(user_spec) if self.add(spec): @@ -1292,7 +1360,7 @@ def write(self): def __enter__(self): self._previous_active = _active_environment activate(self) - return + return self def __exit__(self, exc_type, exc_val, exc_tb): deactivate() diff --git a/lib/spack/spack/schema/env.py b/lib/spack/spack/schema/env.py index 2a3afb0aef3..0af877185a7 100644 --- a/lib/spack/spack/schema/env.py +++ b/lib/spack/spack/schema/env.py @@ -119,6 +119,11 @@ } } ] + }, + 'concretization': { + 'type': 'string', + 'enum': ['together', 'separately'], + 'default': 'separately' } } ) diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py index 45b409df392..b7f3e5e325d 100644 --- a/lib/spack/spack/test/cmd/env.py +++ b/lib/spack/spack/test/cmd/env.py @@ -1694,3 +1694,51 @@ def test_env_activate_csh_prints_shell_output( assert "setenv SPACK_ENV" in out assert "set prompt=" in out assert "alias despacktivate" in out + + +def test_concretize_user_specs_together(): + e = ev.create('coconcretization') + e.concretization = 'together' + + # Concretize a first time using 'mpich' as the MPI provider + e.add('mpileaks') + e.add('mpich') + e.concretize() + + assert all('mpich' in spec for _, spec in e.concretized_specs()) + assert all('mpich2' not in spec for _, spec in e.concretized_specs()) + + # Concretize a second time using 'mpich2' as the MPI provider + e.remove('mpich') + e.add('mpich2') + e.concretize() + + assert all('mpich2' in spec for _, spec in e.concretized_specs()) + assert all('mpich' not in spec for _, spec in e.concretized_specs()) + + # Concretize again without changing anything, check everything + # stays the same + e.concretize() + + assert all('mpich2' in spec for _, spec in e.concretized_specs()) + assert all('mpich' not in spec for _, spec in e.concretized_specs()) + + +def test_cant_install_single_spec_when_concretizing_together(): + e = ev.create('coconcretization') + e.concretization = 'together' + + with pytest.raises(ev.SpackEnvironmentError, match=r'cannot install'): + e.install('zlib') + + +def test_duplicate_packages_raise_when_concretizing_together(): + e = ev.create('coconcretization') + e.concretization = 'together' + + e.add('mpileaks+opt') + e.add('mpileaks~opt') + e.add('mpich') + + with pytest.raises(ev.SpackEnvironmentError, match=r'cannot contain more'): + e.concretize() From 9600eb4f5a81cc090c08935456fb66de79da120c Mon Sep 17 00:00:00 2001 From: Oliver Breitwieser Date: Tue, 8 Oct 2019 03:55:22 +0200 Subject: [PATCH 139/499] py-apipkg: Fix mix up of checksums (#13066) Change-Id: Ibae329c5a6cf7e3741a879612da523e11e3b0ab9 --- var/spack/repos/builtin/packages/py-apipkg/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-apipkg/package.py b/var/spack/repos/builtin/packages/py-apipkg/package.py index 4617805259c..676462d5cbe 100644 --- a/var/spack/repos/builtin/packages/py-apipkg/package.py +++ b/var/spack/repos/builtin/packages/py-apipkg/package.py @@ -12,8 +12,8 @@ class PyApipkg(PythonPackage): homepage = "https://pypi.python.org/pypi/apipkg" url = "https://pypi.io/packages/source/a/apipkg/apipkg-1.4.tar.gz" - version('1.5', sha256='2e38399dbe842891fe85392601aab8f40a8f4cc5a9053c326de35a1cc0297ac6') - version('1.4', sha256='37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6') + version('1.5', sha256='37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6') + version('1.4', sha256='2e38399dbe842891fe85392601aab8f40a8f4cc5a9053c326de35a1cc0297ac6') depends_on('py-setuptools@30.3.0:', type='build') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) From 72d8febc4eb889f51378ebf5b9b4b2f9dd0f5ea1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 8 Oct 2019 01:59:33 -0500 Subject: [PATCH 140/499] Add macOS Catalina support (#13070) --- lib/spack/spack/operating_systems/mac_os.py | 34 +++++++++++++-------- 1 file changed, 22 insertions(+), 12 deletions(-) diff --git a/lib/spack/spack/operating_systems/mac_os.py b/lib/spack/spack/operating_systems/mac_os.py index 7ebd1ce8d24..2f98c0cd79c 100644 --- a/lib/spack/spack/operating_systems/mac_os.py +++ b/lib/spack/spack/operating_systems/mac_os.py @@ -32,19 +32,29 @@ class MacOs(OperatingSystem): """ def __init__(self): - """ Autodetects the mac version from a dictionary. Goes back as - far as 10.6 snowleopard. If the user has an older mac then - the version will just be a generic mac_os. + """Autodetects the mac version from a dictionary. + + If the mac version is too old or too new for Spack to recognize, + will use a generic "macos" version string until Spack is updated. """ - mac_releases = {'10.6': "snowleopard", - "10.7": "lion", - "10.8": "mountainlion", - "10.9": "mavericks", - "10.10": "yosemite", - "10.11": "elcapitan", - "10.12": "sierra", - "10.13": "highsierra", - "10.14": "mojave"} + mac_releases = { + '10.0': 'cheetah', + '10.1': 'puma', + '10.2': 'jaguar', + '10.3': 'panther', + '10.4': 'tiger', + '10.5': 'leopard', + '10.6': 'snowleopard', + '10.7': 'lion', + '10.8': 'mountainlion', + '10.9': 'mavericks', + '10.10': 'yosemite', + '10.11': 'elcapitan', + '10.12': 'sierra', + '10.13': 'highsierra', + '10.14': 'mojave', + '10.15': 'catalina', + } mac_ver = str(macos_version().up_to(2)) name = mac_releases.get(mac_ver, "macos") From 66b9009a0713f9ce1d63f518ab1528af7587eaa5 Mon Sep 17 00:00:00 2001 From: Phil Carns Date: Tue, 8 Oct 2019 02:19:27 -0500 Subject: [PATCH 141/499] pmdk: added v 1.7 (#13067) --- var/spack/repos/builtin/packages/pmdk/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/pmdk/package.py b/var/spack/repos/builtin/packages/pmdk/package.py index feafda5da90..2f8aca78e04 100644 --- a/var/spack/repos/builtin/packages/pmdk/package.py +++ b/var/spack/repos/builtin/packages/pmdk/package.py @@ -18,6 +18,7 @@ class Pmdk(Package): git = "https://github.com/pmem/pmdk.git" version('develop', branch='master') + version('1.7', sha256='865ce1b422bc83109cb4a63dcff8fd1077eea3617e668faf6a043208d8be03ca') version('1.6', sha256='3b99e6c30709326a94d2e73a9247a8dfb58d0a394c5b7714e5c3d8a3ad2e2e9f') version('1.5', sha256='6b069d7207febeb62440e89245e8b18fcdf40b6170d2ec2ef33c252ed16db2d4') From 1213aec7ed29cc89b1e9e0a90f5e62af7b2572fa Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 3 Oct 2019 16:13:55 +0200 Subject: [PATCH 142/499] travis: bump python version for flake8 and build tests --- .travis.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index c94f3e748c4..33c0346eaf7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,7 +18,7 @@ jobs: fast_finish: true include: - stage: 'style checks' - python: '2.7' + python: '3.7' os: linux language: python env: TEST_SUITE=flake8 @@ -58,17 +58,17 @@ jobs: language: python env: [ TEST_SUITE=build, 'SPEC=mpich' ] # astyle (MakefilePackage) - - python: '2.7' + - python: '3.7' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=astyle' ] # tut (WafPackage) - - python: '2.7' + - python: '3.7' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=tut' ] # py-setuptools (PythonPackage) - - python: '2.7' + - python: '3.7' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=py-setuptools' ] @@ -78,17 +78,17 @@ jobs: # language: python # env: [ TEST_SUITE=build, 'SPEC=perl-dbi' ] # openjpeg (CMakePackage + external cmake) - - python: '2.7' + - python: '3.7' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=openjpeg' ] # r-rcpp (RPackage + external R) - - python: '2.7' + - python: '3.7' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=r-rcpp' ] # mpich (AutotoolsPackage) - - python: '3.6' + - python: '3.7' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=mpich' ] From 4377cc7066c133728b2ffa2f3a3acba7e94d19c6 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 8 Oct 2019 18:07:38 -0700 Subject: [PATCH 143/499] Add headsup note re cryptsetup patch for v2.2.2 (#13076) --- var/spack/repos/builtin/packages/cryptsetup/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/cryptsetup/package.py b/var/spack/repos/builtin/packages/cryptsetup/package.py index 9bee30ef9f8..1ff2c98c66f 100644 --- a/var/spack/repos/builtin/packages/cryptsetup/package.py +++ b/var/spack/repos/builtin/packages/cryptsetup/package.py @@ -14,6 +14,8 @@ class Cryptsetup(AutotoolsPackage): list_url = "https://www.kernel.org/pub/linux/utils/cryptsetup/" list_depth = 1 + # If you're adding newer versions, check whether the patch below + # still needs to be applied. version('2.2.1', sha256='94e79a31ed38bdb0acd9af7ccca1605a2ac62ca850ed640202876b1ee11c1c61') depends_on('libuuid', type=('build', 'link')) @@ -31,6 +33,8 @@ class Cryptsetup(AutotoolsPackage): # Upstream includes support for discovering the location of the libintl # library but is missing the bit in the Makefile.ac that includes it in # the LDFLAGS. See https://gitlab.com/cryptsetup/cryptsetup/issues/479 + # This *should* be unnecessary starting with release 2.2.2, see + # https://gitlab.com/cryptsetup/cryptsetup/issues/479#note_227617031 patch('autotools-libintl.patch') def url_for_version(self, version): From 6a99b7e2629b487dc774157f83b7c357ab08ef34 Mon Sep 17 00:00:00 2001 From: wspear Date: Tue, 8 Oct 2019 18:08:32 -0700 Subject: [PATCH 144/499] Added py-pamela package. Dependency of py-jupyterhub. (#13075) --- .../repos/builtin/packages/py-pamela/package.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pamela/package.py diff --git a/var/spack/repos/builtin/packages/py-pamela/package.py b/var/spack/repos/builtin/packages/py-pamela/package.py new file mode 100644 index 00000000000..28ad7d47ef9 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pamela/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPamela(PythonPackage): + """Python wrapper for PAM""" + + homepage = "https://pypi.org/project/pamela/" + url = "https://pypi.io/packages/source/p/pamela/pamela-1.0.0.tar.gz" + + version('1.0.0', sha256='65c9389bef7d1bb0b168813b6be21964df32016923aac7515bdf05366acbab6c') + + depends_on('py-setuptools', type='build') From e3f69f8ce6cf4264e78c1915945d9598f8df4d0b Mon Sep 17 00:00:00 2001 From: Mark Olesen Date: Wed, 9 Oct 2019 03:42:44 +0200 Subject: [PATCH 145/499] Build older openfoam (#13071) * adjust building of OpenFOAM 1806 and earlier - spack now unpacks into spack-src, but earlier OpenFOAM versions still expect particular directory names (eg, OpenFOAM-v1806). Resolve by creating a symlink during patching. * replace openfoam 1806 patch with URL version --- .../packages/openfoam/1806-have-kahip.patch | 17 ---------------- .../builtin/packages/openfoam/package.py | 20 +++++++++++++++++-- 2 files changed, 18 insertions(+), 19 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/openfoam/1806-have-kahip.patch diff --git a/var/spack/repos/builtin/packages/openfoam/1806-have-kahip.patch b/var/spack/repos/builtin/packages/openfoam/1806-have-kahip.patch deleted file mode 100644 index 3e10a441456..00000000000 --- a/var/spack/repos/builtin/packages/openfoam/1806-have-kahip.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- OpenFOAM-v1806/wmake/scripts/have_kahip-ORIG 2018-06-28 16:39:32.000000000 +0200 -+++ OpenFOAM-v1806/wmake/scripts/have_kahip 2018-08-11 13:37:18.250219013 +0200 -@@ -83,10 +83,10 @@ - # FOAM_EXT_LIBBIN is allowed to be unset - library=$(findFirstFile \ - $FOAM_EXT_LIBBIN/$library \ -- $METIS_ARCH_PATH/lib/$static \ -- $METIS_ARCH_PATH/lib/$library \ -- $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \ -- $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \ -+ $KAHIP_ARCH_PATH/lib/$static \ -+ $KAHIP_ARCH_PATH/lib/$library \ -+ $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \ -+ $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \ - ) - elif isSystem "$KAHIP_ARCH_PATH" - then diff --git a/var/spack/repos/builtin/packages/openfoam/package.py b/var/spack/repos/builtin/packages/openfoam/package.py index 60b49bbca83..a2c82cf0540 100644 --- a/var/spack/repos/builtin/packages/openfoam/package.py +++ b/var/spack/repos/builtin/packages/openfoam/package.py @@ -337,7 +337,11 @@ class Openfoam(Package): # Version-specific patches patch('1612-spack-patches.patch', when='@1612') - patch('1806-have-kahip.patch', when='@1806') + # kahip patch (wmake) + patch('https://develop.openfoam.com/Development/OpenFOAM-plus/commit/4068c03c616a4964472e06d5fb5b9bc2dd0bf1b7.patch', + when='@1806', + sha256='21f1ab68c82dfa41ed1a4439427c94c43ddda02c84175c30da623d905d3e5d61' + ) # Some user config settings # default: 'compile-option': 'RpathOpt', @@ -364,7 +368,7 @@ class Openfoam(Package): # def url_for_version(self, version): - # Prior to 'v1706' and additional '+' in the naming + # Prior to 1706 had additional '+' in the naming fmt = self.list_url if version <= Version('1612'): fmt += 'v{0}+/OpenFOAM-v{0}+.tgz' @@ -481,6 +485,18 @@ def patch(self): Where needed, apply filter as an alternative to normal patching.""" add_extra_files(self, self.common, self.assets) + # Prior to 1812, required OpenFOAM-v{VER} directory when sourcing + projdir = "OpenFOAM-v{0}".format(self.version) + if not os.path.exists(join_path(self.stage.path, projdir)): + tty.info('Added directory link {0}'.format(projdir)) + os.symlink( + os.path.relpath( + self.stage.source_path, + self.stage.path + ), + join_path(self.stage.path, projdir) + ) + # Avoid WM_PROJECT_INST_DIR for ThirdParty # This modification is non-critical edits = { From 8de453af5454cb37cd63b0e64dff4a6f73d6d875 Mon Sep 17 00:00:00 2001 From: wspear Date: Tue, 8 Oct 2019 18:43:44 -0700 Subject: [PATCH 146/499] Fixed hash of version .0.5 and added latest version (.0.7.1) (#13077) --- .../repos/builtin/packages/py-prometheus-client/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-prometheus-client/package.py b/var/spack/repos/builtin/packages/py-prometheus-client/package.py index c8926a56e5b..a89649b9673 100644 --- a/var/spack/repos/builtin/packages/py-prometheus-client/package.py +++ b/var/spack/repos/builtin/packages/py-prometheus-client/package.py @@ -10,8 +10,9 @@ class PyPrometheusClient(PythonPackage): """Prometheus instrumentation library for Python applications.""" homepage = "https://pypi.org/project/prometheus_client/" - url = "https://pypi.io/packages/source/p/prometheus_client/prometheus_client-0.5.0.tar.gz" + url = "https://pypi.io/packages/source/p/prometheus_client/prometheus_client-0.7.1.tar.gz" - version('0.5.0', sha256='2d7f7af343dec0a96ee849b1bba18aad9f767bf16d5eb5f0c11cae837bf22731') + version('0.7.1', sha256='71cd24a2b3eb335cb800c7159f423df1bd4dcd5171b234be15e3f31ec9f622da') + version('0.5.0', sha256='e8c11ff5ca53de6c3d91e1510500611cafd1d247a937ec6c588a0a7cc3bef93c') depends_on('py-setuptools', type='build') From 2794e52ddd58aced74300ce5cd1a2ca30825dd90 Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Tue, 8 Oct 2019 20:46:15 -0500 Subject: [PATCH 147/499] QMCPACK Oct2019 fix buglets (#13069) * Support different CMake build types correctly. * LIBXML2 variables no longer used. * Fix E501 as part of https://github.com/spack/spack/pull/13069 --- .../repos/builtin/packages/qmcpack/package.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py index 771c01d8c22..67041e455a1 100644 --- a/var/spack/repos/builtin/packages/qmcpack/package.py +++ b/var/spack/repos/builtin/packages/qmcpack/package.py @@ -33,7 +33,9 @@ class Qmcpack(CMakePackage, CudaPackage): version('3.1.0', tag='v3.1.0') # These defaults match those in the QMCPACK manual - variant('debug', default=False, description='Build debug version') + variant('build_type', default='Release', + description='The build type to build', + values=('Debug', 'Release', 'RelWithDebInfo')) variant('mpi', default=True, description='Build with MPI support') variant('phdf5', default=True, description='Build with parallel collective I/O') variant('complex', default=False, @@ -184,10 +186,14 @@ def cmake_args(self): # Currently FFTW_HOME and LIBXML2_HOME are used by CMake. # Any CMake warnings about other variables are benign. - xml2_prefix = spec['libxml2'].prefix - args.append('-DLIBXML2_HOME={0}'.format(xml2_prefix)) - args.append('-DLibxml2_INCLUDE_DIRS={0}'.format(xml2_prefix.include)) - args.append('-DLibxml2_LIBRARY_DIRS={0}'.format(xml2_prefix.lib)) + # Starting with QMCPACK 3.8.0, CMake uses the builtin find(libxml2) + # function + if spec.satisfies('@:3.7.0'): + xml2_prefix = spec['libxml2'].prefix + args.append('-DLIBXML2_HOME={0}'.format(xml2_prefix)) + args.append( + '-DLibxml2_INCLUDE_DIRS={0}'.format(xml2_prefix.include)) + args.append('-DLibxml2_LIBRARY_DIRS={0}'.format(xml2_prefix.lib)) if '^fftw@3:' in spec: fftw_prefix = spec['fftw'].prefix From 2e4bcf223c7d1bf1184b85d94d8267a91d078354 Mon Sep 17 00:00:00 2001 From: wspear Date: Tue, 8 Oct 2019 18:48:11 -0700 Subject: [PATCH 148/499] Added py-certipy package. Dependency of py-jupyterhub. (#13068) * Added py-certipy package. Dependency of py-jupyterhub. * Changed url to pypi --- .../builtin/packages/py-certipy/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-certipy/package.py diff --git a/var/spack/repos/builtin/packages/py-certipy/package.py b/var/spack/repos/builtin/packages/py-certipy/package.py new file mode 100644 index 00000000000..7bbf223d901 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-certipy/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCertipy(PythonPackage): + """A simple python tool for creating certificate authorities + and certificates on the fly.""" + + homepage = "https://pypi.org/project/certipy/" + url = "https://pypi.io/packages/source/c/certipy/certipy-0.1.3.tar.gz" + + version('0.1.3', sha256='695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859') + + depends_on('py-setuptools', type='build') + depends_on('py-pyopenssl', type=('build', 'run')) From fdc91a17051918ffdda6619fee2d0240e5783474 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Wed, 9 Oct 2019 10:48:37 +0900 Subject: [PATCH 149/499] tabix: add zlib dependency. (#13064) --- var/spack/repos/builtin/packages/tabix/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/tabix/package.py b/var/spack/repos/builtin/packages/tabix/package.py index 96cf6131c53..47208e6e7ae 100644 --- a/var/spack/repos/builtin/packages/tabix/package.py +++ b/var/spack/repos/builtin/packages/tabix/package.py @@ -16,6 +16,7 @@ class Tabix(MakefilePackage): depends_on('perl', type=('build', 'run')) depends_on('python', type=('build', 'run')) + depends_on('zlib', type='link') def install(self, spec, prefix): mkdirp(prefix.bin) From f1e1693a6a8e018bf2b7eae43d21fd7c311106e2 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Wed, 9 Oct 2019 10:50:51 +0900 Subject: [PATCH 150/499] seqprep: add zlib dependency. (#13062) --- var/spack/repos/builtin/packages/seqprep/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/seqprep/package.py b/var/spack/repos/builtin/packages/seqprep/package.py index 8fc632e07ff..738091d5e74 100644 --- a/var/spack/repos/builtin/packages/seqprep/package.py +++ b/var/spack/repos/builtin/packages/seqprep/package.py @@ -15,6 +15,8 @@ class Seqprep(MakefilePackage): version('1.3.2', 'b6a4f5491dfdb0ce38bf791454151468') + depends_on('zlib', type='link') + def install(self, spec, prefix): mkdirp(prefix.bin) install('SeqPrep', prefix.bin) From 529d0f3e37684ebba5b62ea2d861cb6a846c4e03 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Wed, 9 Oct 2019 10:51:04 +0900 Subject: [PATCH 151/499] psmc: add zlib dependency. (#13061) --- var/spack/repos/builtin/packages/psmc/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/psmc/package.py b/var/spack/repos/builtin/packages/psmc/package.py index 8c32c867bb3..8db04ce5bc9 100644 --- a/var/spack/repos/builtin/packages/psmc/package.py +++ b/var/spack/repos/builtin/packages/psmc/package.py @@ -15,6 +15,8 @@ class Psmc(MakefilePackage): version('2016-1-21', commit='e5f7df5d00bb75ec603ae0beff62c0d7e37640b9') + depends_on('zlib', type='link') + def setup_environment(self, spack_env, run_env): run_env.prepend_path('PATH', prefix.bin.utils) From b0bf528ab3aa155c5115371b972105c8cf8c462a Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Wed, 9 Oct 2019 10:51:39 +0900 Subject: [PATCH 152/499] perl-perlio-gzip: add zlib dependency. (#13060) --- .../repos/builtin/packages/perl-perlio-gzip/package.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py index 31f07921c91..d7f68d420b2 100644 --- a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py +++ b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py @@ -14,3 +14,9 @@ class PerlPerlioGzip(PerlPackage): version('0.20', '0393eae5d0b23df6cf40ed44af7d711c') version('0.19', 'dbcfc1450f6b593b65048b8ced061c98') + + depends_on('zlib', type='link') + + def configure_args(self): + p = self.spec['zlib'].prefix.include + return ['INC=-I{0}'.format(p)] From acbb2af5282cad203448b0875ad5ce91abde7d9a Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 9 Oct 2019 14:13:37 +0200 Subject: [PATCH 153/499] "No Spack mirror configured": demoted the warning to a debug message (#13082) fixes #12010 --- lib/spack/spack/binary_distribution.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index a4624e9326f..6a1935b922b 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -606,7 +606,7 @@ def get_specs(force=False): mirrors = spack.config.get('mirrors') if len(mirrors) == 0: - tty.warn("No Spack mirrors are currently configured") + tty.debug("No Spack mirrors are currently configured") return {} urls = set() From 469bef880a402ce8d7b4b3b804c18f32884c6fb4 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 9 Oct 2019 21:45:31 +0200 Subject: [PATCH 154/499] mysql: Add missing dependencies (#12717) This also changes the default for cxxstd from 98 to 14 because (at least) newer versions of mysql do not compile with 98 (tested with gcc@9). --- var/spack/repos/builtin/packages/mysql/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/mysql/package.py b/var/spack/repos/builtin/packages/mysql/package.py index db1ab0ff3ce..9c5656ad974 100644 --- a/var/spack/repos/builtin/packages/mysql/package.py +++ b/var/spack/repos/builtin/packages/mysql/package.py @@ -44,7 +44,7 @@ class Mysql(CMakePackage): variant('client_only', default=False, description='Build and install client only.') variant('cxxstd', - default='98', + default='14', values=('98', '11', '14', '17'), multi=False, description='Use the specified C++ standard when building.') @@ -69,6 +69,8 @@ class Mysql(CMakePackage): depends_on('cmake@2.8.12:', type='build', when='@8.0.0:') depends_on('gmake@3.75:', type='build') + depends_on('pkgconfig', type='build', when='@5.7.0:') + depends_on('doxygen', type='build', when='@8.0.0:') # Each version of MySQL requires a specific version of boost # See BOOST_PACKAGE_NAME in cmake/boost.cmake @@ -100,8 +102,9 @@ class Mysql(CMakePackage): depends_on('ncurses') depends_on('openssl') + depends_on('libtirpc', when='@5.7.0:') depends_on('perl', type=['build', 'test'], when='@:7.99.99') - depends_on('bison@2.1:', type='build', when='@develop') + depends_on('bison@2.1:', type='build') depends_on('m4', type='build', when='@develop platform=solaris') patch('fix-no-server-5.5.patch', level=1, when='@5.5.0:5.5.999') From 5b879459c7b20ca5d5f18136bb025a4001fdeb7b Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Wed, 9 Oct 2019 20:36:47 -0500 Subject: [PATCH 155/499] Buildcache: pass string.encode('utf-8') for old_dir and new_dir to replace_prefix_bin. (#13114) This should fix a Python3 error from concatenating strings and bytes. --- lib/spack/spack/relocate.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index 2c76166e92c..3794189d79d 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -429,7 +429,8 @@ def relocate_macho_binaries(path_names, old_dir, new_dir, allow_root): modify_object_macholib(path_name, placeholder, new_dir) modify_object_macholib(path_name, old_dir, new_dir) if len(new_dir) <= len(old_dir): - replace_prefix_bin(path_name, old_dir, new_dir) + replace_prefix_bin(path_name, old_dir.encode('utf-8'), + new_dir.encode('utf-8')) else: tty.warn('Cannot do a binary string replacement' ' with padding for %s' From 2e2b1a5e02033b85db7f427cc947399e7259c7ca Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Thu, 10 Oct 2019 05:22:52 +0200 Subject: [PATCH 156/499] qt: Add 5.13.1 and missing zlib flags (#13109) --- var/spack/repos/builtin/packages/qt/package.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 2df6befa710..bf76caa0084 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -21,6 +21,7 @@ class Qt(Package): phases = ['configure', 'build', 'install'] + version('5.13.1', 'adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e') version('5.12.5', 'a2299e21db7767caf98242767bffb18a2a88a42fee2d6a393bedd234f8c91298') version('5.12.2', '59b8cb4e728450b21224dcaaa40eb25bafc5196b6988f2225c394c6b7f881ff5') version('5.11.3', '859417642713cee2493ee3646a7fee782c9f1db39e41d7bb1322bba0c5f0ff4d') @@ -376,6 +377,7 @@ def common_config_args(self): # FIXME: those could work for other versions png = self.spec['libpng'] jpeg = self.spec['jpeg'] + zlib = self.spec['zlib'] config_args.extend([ '-system-libpng', '{0}'.format(png.libs.search_flags), @@ -383,7 +385,9 @@ def common_config_args(self): '-system-libjpeg', '{0}'.format(jpeg.libs.search_flags), '{0}'.format(jpeg.headers.include_flags), - '-system-zlib' + '-system-zlib', + '{0}'.format(zlib.libs.search_flags), + '{0}'.format(zlib.headers.include_flags) ]) if '@:5.7.0' in self.spec: From 4ef64b64d118ed03c7c57fad9ef18eb5632ab140 Mon Sep 17 00:00:00 2001 From: Francesco Di Natale Date: Wed, 9 Oct 2019 20:23:19 -0700 Subject: [PATCH 157/499] Add new versions of py-maestrowf (#13081) * Addition of 1.1.3 and 1.1.4 * Addition of conditional enum-34 installation. * Update var/spack/repos/builtin/packages/py-maestrowf/package.py Addition of versioning for pyyaml. Co-Authored-By: Adam J. Stewart * Addition of enum34 back to older versions 1.1.3 and below. --- var/spack/repos/builtin/packages/py-maestrowf/package.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-maestrowf/package.py b/var/spack/repos/builtin/packages/py-maestrowf/package.py index f5b419439c1..0dcfd381d29 100644 --- a/var/spack/repos/builtin/packages/py-maestrowf/package.py +++ b/var/spack/repos/builtin/packages/py-maestrowf/package.py @@ -13,14 +13,19 @@ class PyMaestrowf(PythonPackage): homepage = "https://github.com/LLNL/maestrowf/" url = "https://github.com/LLNL/maestrowf/archive/v1.1.2.tar.gz" + maintainers = ['FrankD412'] + + version('1.1.4', 'e2da101fb1cad9a164d375eccb1f07ce') + version('1.1.3', '0299e4ae3ec8b8c0296df0efaa8b517f') version('1.1.2', 'a9e05d82910cd2dd077321fb9b0c8dcd') version('1.1.1', 'd38bbf634de4f29fd01d1864ba2f70e0') version('1.1.0', '3c20bf36fbb85d14c3bfdb865944a409') version('1.0.1', '6838fc8bdc7ca0c1adbb6a0333f005b4') depends_on('py-setuptools', type='build') - depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-pyyaml@4.2b1:', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) - depends_on('py-enum34', type=('build', 'run')) + depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3') + depends_on('py-enum34', type=('build', 'run'), when='@:1.1.3') depends_on('py-tabulate', type=('build', 'run'), when='@1.1.0:') depends_on('py-filelock', type=('build', 'run'), when='@1.1.0:') From e7e67fdfeca6b07a51d8594a2a0aa4ff6bfbba91 Mon Sep 17 00:00:00 2001 From: wspear Date: Wed, 9 Oct 2019 20:23:33 -0700 Subject: [PATCH 158/499] Added latest versions to py-traitlets (#13079) * Added latest versions to py-traitlets * Added missing dependencies --- var/spack/repos/builtin/packages/py-traitlets/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-traitlets/package.py b/var/spack/repos/builtin/packages/py-traitlets/package.py index 8463b8402b4..5c125acd311 100644 --- a/var/spack/repos/builtin/packages/py-traitlets/package.py +++ b/var/spack/repos/builtin/packages/py-traitlets/package.py @@ -12,6 +12,8 @@ class PyTraitlets(PythonPackage): homepage = "https://pypi.python.org/pypi/traitlets" url = "https://github.com/ipython/traitlets/archive/4.3.1.tar.gz" + version('4.3.3', sha256='b686c1aadf6ee5a9ee4c22df23bc5cd5bb7b5cfa18afe092e0a139cc2f05fe2e') + version('4.3.2', sha256='370f938ad730d52272ef74f96f831cb21138f6168e46fe582fe256c35cc656ce') version('4.3.1', '146a4885ea64079f62a33b2049841543') version('4.3.0', '17af8d1306a401c42dbc92a080722422') version('4.2.2', 'ffc03056dc5c8d1fc5dbd6eac76e1e46') @@ -21,7 +23,8 @@ class PyTraitlets(PythonPackage): version('4.0.0', 'b5b95ea5941fd9619b4704dfd8201568') version('4.0', '14544e25ccf8e920ed1cbf833852481f') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) depends_on('py-decorator', type=('build', 'run')) depends_on('py-ipython-genutils', type=('build', 'run')) - depends_on('py-enum34', when='^python@:3.3', type=('build', 'run')) From c8289fcd90e31ec4e1ebd08fa80ebdc9ffde1271 Mon Sep 17 00:00:00 2001 From: wspear Date: Wed, 9 Oct 2019 20:23:55 -0700 Subject: [PATCH 159/499] Added latest versions of SQLAlchemy 1.3.X, 1.2.X and 1.1.X (#13078) * Added latest versions of SQLAlchemy 1.3.X, 1.2.X and 1.1.X * Added missing dependencies --- .../repos/builtin/packages/py-sqlalchemy/package.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py index 3d3b198c582..8eea38eeee4 100644 --- a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py +++ b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py @@ -10,6 +10,15 @@ class PySqlalchemy(PythonPackage): """The Python SQL Toolkit and Object Relational Mapper""" homepage = 'http://www.sqlalchemy.org/' - url = "https://pypi.io/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz" + url = "https://pypi.io/packages/source/S/SQLAlchemy/SQLAlchemy-1.3.9.tar.gz" + version('1.3.9', sha256='272a835758908412e75e87f75dd0179a51422715c125ce42109632910526b1fd') + version('1.2.19', sha256='5bb2c4fc2bcc3447ad45716c66581eab982c007dcf925482498d8733f86f17c7') + version('1.1.18', sha256='8b0ec71af9291191ba83a91c03d157b19ab3e7119e27da97932a4773a3f664a9') version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-pytest@2.5.2:3.9.0,3.9.3:', type='test') + depends_on('py-mock', type='test') + depends_on('py-pytest-xdist', type='test') From d93cacfa5cc3bc01104185a1aea9382a2afd228d Mon Sep 17 00:00:00 2001 From: Rob Latham Date: Wed, 9 Oct 2019 21:24:17 -0600 Subject: [PATCH 160/499] libfabric: new upstream release 1.8.1 (#13053) --- var/spack/repos/builtin/packages/libfabric/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py index d26b80f622e..6cb06f3c01f 100644 --- a/var/spack/repos/builtin/packages/libfabric/package.py +++ b/var/spack/repos/builtin/packages/libfabric/package.py @@ -15,6 +15,8 @@ class Libfabric(AutotoolsPackage): git = "https://github.com/ofiwg/libfabric.git" version('develop', branch='master') + version('1.8.1', sha256='3c560b997f9eafd89f961dd8e8a29a81aad3e39aee888e3f3822da419047dc88', + url='https://github.com/ofiwg/libfabric/releases/download/v1.8.1/libfabric-1.8.1.tar.bz2') version('1.8.0', sha256='c4763383a96af4af52cd81b3b094227f5cf8e91662f861670965994539b7ee37', url='https://github.com/ofiwg/libfabric/releases/download/v1.8.0/libfabric-1.8.0.tar.bz2') version('1.7.1', sha256='312e62c57f79b7274f89c41823932c00b15f1cc8de9c1f8dce17cd7fdae66fa1') From e69efded329ebbcf5ccf74ef137dc1a80bd4b4a6 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Thu, 10 Oct 2019 11:34:50 +0200 Subject: [PATCH 161/499] py-line-profiler: add 2.1.2, re-run cython if needed (#13102) * py-line-profiler: add 2.1.2, re-run cython if needed See rkern/line_profiler#166. * Update var/spack/repos/builtin/packages/py-line-profiler/package.py Co-Authored-By: Adam J. Stewart --- .../builtin/packages/py-line-profiler/package.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-line-profiler/package.py b/var/spack/repos/builtin/packages/py-line-profiler/package.py index 4276a89c4da..2399602e775 100644 --- a/var/spack/repos/builtin/packages/py-line-profiler/package.py +++ b/var/spack/repos/builtin/packages/py-line-profiler/package.py @@ -3,6 +3,8 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os + from spack import * @@ -12,9 +14,20 @@ class PyLineProfiler(PythonPackage): homepage = "https://github.com/rkern/line_profiler" url = "https://pypi.io/packages/source/l/line_profiler/line_profiler-2.0.tar.gz" + version('2.1.2', sha256='efa66e9e3045aa7cb1dd4bf0106e07dec9f80bc781a993fbaf8162a36c20af5c') version('2.0', 'fc93c6bcfac3b7cb1912cb28836d7ee6') - depends_on('python@2.5:') + depends_on('python@2.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-cython', type='build') depends_on('py-ipython@0.13:', type=('build', 'run')) + + # See https://github.com/rkern/line_profiler/issues/166 + @run_before('build') + @when('^python@3.7:') + def fix_cython(self): + cython = self.spec['py-cython'].command + for root, _, files in os.walk('.'): + for fn in files: + if fn.endswith('.pyx'): + cython(os.path.join(root, fn)) From a042a7e91e07c06d9774ccedd775b80d9299b90b Mon Sep 17 00:00:00 2001 From: wspear Date: Thu, 10 Oct 2019 07:06:01 -0700 Subject: [PATCH 162/499] Added new versions to py-tornado (#13080) * Added new versions to py-tornado * Removed all but the latest new version --- var/spack/repos/builtin/packages/py-tornado/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-tornado/package.py b/var/spack/repos/builtin/packages/py-tornado/package.py index 5373185e0ed..666d2a0a02c 100644 --- a/var/spack/repos/builtin/packages/py-tornado/package.py +++ b/var/spack/repos/builtin/packages/py-tornado/package.py @@ -10,13 +10,15 @@ class PyTornado(PythonPackage): """Tornado is a Python web framework and asynchronous networking library.""" homepage = "https://github.com/tornadoweb/tornado" - url = "https://github.com/tornadoweb/tornado/archive/v4.4.0.tar.gz" + url = "https://github.com/tornadoweb/tornado/archive/v6.0.3.tar.gz" + version('6.0.3', sha256='a97ac3b8c95867e534b48cb6fbbf156f5ca5b20c423bb06894c17b240d7a18fc') version('4.4.0', 'c28675e944f364ee96dda3a8d2527a87ed28cfa3') depends_on('py-setuptools', type='build') # requirements from setup.py + depends_on('python@3.5:', when='@6:', type=('build', 'run')) depends_on('py-backports-ssl-match-hostname', when='^python@:2.7.8', type=('build', 'run')) depends_on('py-singledispatch', when='^python@:3.3', type=('build', 'run')) depends_on('py-certifi', when='^python@:3.3', type=('build', 'run')) From dd64bdc3130ac23f06ff6f4397428912b5c1a793 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Thu, 10 Oct 2019 09:11:15 -0500 Subject: [PATCH 163/499] hypre: add compatibility patch for petsc/mfem build failures (#13116) --- .../builtin/packages/hypre/hypre21800-compat.patch | 12 ++++++++++++ var/spack/repos/builtin/packages/hypre/package.py | 1 + 2 files changed, 13 insertions(+) create mode 100644 var/spack/repos/builtin/packages/hypre/hypre21800-compat.patch diff --git a/var/spack/repos/builtin/packages/hypre/hypre21800-compat.patch b/var/spack/repos/builtin/packages/hypre/hypre21800-compat.patch new file mode 100644 index 00000000000..7f0c84e8cf6 --- /dev/null +++ b/var/spack/repos/builtin/packages/hypre/hypre21800-compat.patch @@ -0,0 +1,12 @@ +diff --git a/src/parcsr_mv/_hypre_parcsr_mv.h b/src/parcsr_mv/_hypre_parcsr_mv.h +index db08548d1..119d0b3d9 100644 +--- a/src/parcsr_mv/_hypre_parcsr_mv.h ++++ b/src/parcsr_mv/_hypre_parcsr_mv.h +@@ -800,6 +800,7 @@ HYPRE_Int hypre_ParCSRMatrixCopy ( hypre_ParCSRMatrix *A , hypre_ParCSRMatrix *B + HYPRE_Int hypre_FillResponseParToCSRMatrix ( void *p_recv_contact_buf , HYPRE_Int contact_size , HYPRE_Int contact_proc , void *ro , MPI_Comm comm , void **p_send_response_buf , HYPRE_Int *response_message_size ); + hypre_ParCSRMatrix *hypre_ParCSRMatrixUnion ( hypre_ParCSRMatrix *A , hypre_ParCSRMatrix *B ); + hypre_ParCSRMatrix* hypre_ParCSRMatrixClone ( hypre_ParCSRMatrix *A, HYPRE_Int copy_data ); ++#define hypre_ParCSRMatrixCompleteClone(A) hypre_ParCSRMatrixClone(A,0) + hypre_ParCSRMatrix* hypre_ParCSRMatrixClone_v2 ( hypre_ParCSRMatrix *A, HYPRE_Int copy_data, HYPRE_Int memory_location ); + #ifdef HYPRE_USING_CUDA + //hypre_int hypre_ParCSRMatrixIsManaged(hypre_ParCSRMatrix *a); diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 83965314794..fc5bf923c7d 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -59,6 +59,7 @@ class Hypre(Package): patch('darwin-shared-libs-for-hypre-2.14.0.patch', when='+shared@2.14.0 platform=darwin') patch('superlu-dist-link-2.15.0.patch', when='+superlu-dist @2.15:2.16.0') patch('superlu-dist-link-2.14.0.patch', when='+superlu-dist @:2.14.0') + patch('hypre21800-compat.patch', when='@2.18.0') depends_on("mpi", when='+mpi') depends_on("blas") From f904e47c4ec0cfe55539ab99fd627355cdb2cd3f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:06:44 -0500 Subject: [PATCH 164/499] Add sqlite 3.30.0 (#13098) --- var/spack/repos/builtin/packages/sqlite/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py index 51897713c89..2be29341d85 100644 --- a/var/spack/repos/builtin/packages/sqlite/package.py +++ b/var/spack/repos/builtin/packages/sqlite/package.py @@ -14,6 +14,7 @@ class Sqlite(AutotoolsPackage): """ homepage = "https://www.sqlite.org" + version('3.30.0', sha256='e0a8cf4c7a87455e55e10413d16f358ca121ccec687fe1301eac95e2d340fc58') version('3.29.0', sha256='8e7c1e2950b5b04c5944a981cb31fffbf9d2ddda939d536838ebc854481afd5b') version('3.28.0', sha256='d61b5286f062adfce5125eaf544d495300656908e61fca143517afcc0a89b7c3') version('3.27.2', sha256='50c39e85ea28b5ecfdb3f9e860afe9ba606381e21836b2849efca6a0bfe6ef6e') From 01b87259e2880c76fab85bd7f5defdc98e9e592b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:07:05 -0500 Subject: [PATCH 165/499] ncurses: https -> http (#13097) --- var/spack/repos/builtin/packages/ncurses/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index 4915fcb092a..7d599893e1f 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -17,7 +17,8 @@ class Ncurses(AutotoolsPackage): SYSV-curses enhancements over BSD curses.""" homepage = "http://invisible-island.net/ncurses/ncurses.html" - url = "https://ftpmirror.gnu.org/ncurses/ncurses-6.1.tar.gz" + # URL must remain http:// so Spack can bootstrap curl + url = "http://ftpmirror.gnu.org/ncurses/ncurses-6.1.tar.gz" version('6.1', '98c889aaf8d23910d2b92d65be2e737a') version('6.0', 'ee13d052e1ead260d7c28071f46eefb1') From 4a5bdd1afd91760a543407b6654081ae7258c211 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:07:24 -0500 Subject: [PATCH 166/499] gdbm: https -> http (#13096) --- var/spack/repos/builtin/packages/gdbm/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/gdbm/package.py b/var/spack/repos/builtin/packages/gdbm/package.py index bbfcf75891a..9d19b2bced8 100644 --- a/var/spack/repos/builtin/packages/gdbm/package.py +++ b/var/spack/repos/builtin/packages/gdbm/package.py @@ -14,7 +14,8 @@ class Gdbm(AutotoolsPackage): manipulate a hashed database.""" homepage = "http://www.gnu.org.ua/software/gdbm/gdbm.html" - url = "https://ftpmirror.gnu.org/gdbm/gdbm-1.13.tar.gz" + # URL must remain http:// so Spack can bootstrap curl + url = "http://ftpmirror.gnu.org/gdbm/gdbm-1.13.tar.gz" version('1.18.1', '86e613527e5dba544e73208f42b78b7c022d4fa5a6d5498bf18c8d6f745b91dc') version('1.14.1', 'c2ddcb3897efa0f57484af2bd4f4f848') From 0cf69804378f636f9784a5b4593d234157282737 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:07:48 -0500 Subject: [PATCH 167/499] Add readline 8.0 (#13095) --- var/spack/repos/builtin/packages/readline/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py index 2fba5f5cbcd..906b26c3ef1 100644 --- a/var/spack/repos/builtin/packages/readline/package.py +++ b/var/spack/repos/builtin/packages/readline/package.py @@ -15,8 +15,10 @@ class Readline(AutotoolsPackage): csh-like history expansion on previous commands.""" homepage = "http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html" - url = "https://ftpmirror.gnu.org/readline/readline-7.0.tar.gz" + # URL must remain http:// so Spack can bootstrap curl + url = "http://ftpmirror.gnu.org/readline/readline-8.0.tar.gz" + version('8.0', sha256='e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461') version('7.0', '205b03a87fc83dab653b628c59b9fc91') version('6.3', '33c8fb279e981274f485fd91da77e94a') From f35c845330f765be4098957a9ee4ddc93159a294 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:08:19 -0500 Subject: [PATCH 168/499] Add pkgconf 1.6.3 (#13094) --- var/spack/repos/builtin/packages/pkgconf/package.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/pkgconf/package.py b/var/spack/repos/builtin/packages/pkgconf/package.py index 84e137d1086..ce4221d4d4e 100644 --- a/var/spack/repos/builtin/packages/pkgconf/package.py +++ b/var/spack/repos/builtin/packages/pkgconf/package.py @@ -13,11 +13,13 @@ class Pkgconf(AutotoolsPackage): maintaining compatibility.""" homepage = "http://pkgconf.org/" - url = "http://distfiles.dereferenced.org/pkgconf/pkgconf-1.5.4.tar.xz" + # URL must remain http:// so Spack can bootstrap curl + url = "http://distfiles.dereferenced.org/pkgconf/pkgconf-1.6.3.tar.xz" - version('1.6.1', '22b9ee38438901f9d60f180e5182821180854fa738fd071f593ea26a81da208c') - version('1.6.0', '6135a3abb576672ba54a899860442ba185063f0f90dae5892f64f7bae8e1ece5') - version('1.5.4', '9c5864a4e08428ef52f05a41c948529555458dec6d283b50f8b7d32463c54664') + version('1.6.3', sha256='61f0b31b0d5ea0e862b454a80c170f57bad47879c0c42bd8de89200ff62ea210') + version('1.6.1', sha256='22b9ee38438901f9d60f180e5182821180854fa738fd071f593ea26a81da208c') + version('1.6.0', sha256='6135a3abb576672ba54a899860442ba185063f0f90dae5892f64f7bae8e1ece5') + version('1.5.4', sha256='9c5864a4e08428ef52f05a41c948529555458dec6d283b50f8b7d32463c54664') version('1.4.2', '678d242b4eef1754bba6a58642af10bb') version('1.4.0', 'c509c0dad5a70aa4bc3210557b7eafce') version('1.3.10', '9b63707bf6f8da6efb3868101d7525fe') From ace11d857f5c7ff6ddbdfbfc5cbdd0a898f16468 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:08:40 -0500 Subject: [PATCH 169/499] Add latest Perl releases (#13093) --- var/spack/repos/builtin/packages/perl/package.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py index 2d1ed46f872..715ed9732db 100644 --- a/var/spack/repos/builtin/packages/perl/package.py +++ b/var/spack/repos/builtin/packages/perl/package.py @@ -31,14 +31,15 @@ class Perl(Package): # Perl doesn't use Autotools, it should subclass Package # explanation of version numbering scheme # Development releases (odd numbers) - version('5.25.11', '37a398682c36cd85992b34b5c1c25dc1') + version('5.31.4', sha256='418a7e6fe6485cc713a86d1227ef112f0bb3f80322e3b715ffe42851d97804a5') # Maintenance releases (even numbers, recommended) - version('5.28.0', sha256='7e929f64d4cb0e9d1159d4a59fc89394e27fa1f7004d0836ca0d514685406ea8') - version('5.26.2', 'dc0fea097f3992a8cd53f8ac0810d523', preferred=True) - version('5.24.1', '765ef511b5b87a164e2531403ee16b3c') + version('5.30.0', sha256='851213c754d98ccff042caa40ba7a796b2cee88c5325f121be5cbb61bbf975f2', preferred=True) # End of life releases + version('5.28.0', sha256='7e929f64d4cb0e9d1159d4a59fc89394e27fa1f7004d0836ca0d514685406ea8') + version('5.26.2', 'dc0fea097f3992a8cd53f8ac0810d523') + version('5.24.1', '765ef511b5b87a164e2531403ee16b3c') version('5.22.4', '31a71821682e02378fcdadeed85688b8') version('5.22.3', 'aa4f236dc2fc6f88b871436b8d0fda95') version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b') From db8178d99a355eeb7bd9d664e1d6c4560c50d571 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:09:02 -0500 Subject: [PATCH 170/499] Add latest openssl releases (#13092) --- var/spack/repos/builtin/packages/openssl/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index e3d6fefee46..d3ebcc5d183 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -19,12 +19,13 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package homepage = "http://www.openssl.org" # URL must remain http:// so Spack can bootstrap curl - url = "http://www.openssl.org/source/openssl-1.0.2m.tar.gz" - list_url = "https://www.openssl.org/source/old/" + url = "http://www.openssl.org/source/openssl-1.1.1d.tar.gz" + list_url = "http://www.openssl.org/source/old/" list_depth = 1 # The latest stable version is the 1.1.1 series. This is also our Long Term # Support (LTS) version, supported until 11th September 2023. + version('1.1.1d', sha256='1e3a91bc1f9dfce01af26026f856e064eab4c8ee0a8f457b5ae30b40b8b711f2') version('1.1.1c', sha256='f6fb3079ad15076154eda9413fed42877d668e7069d9b87396d0804fdb3f4c90') version('1.1.1b', sha256='5c557b023230413dfb0756f3137a13e6d726838ccd1430888ad15bfb2b43ea4b') version('1.1.1a', sha256='fc20130f8b7cbd2fb918b2f14e2f429e109c31ddd0fb38fc5d71d9ffed3f9f41') @@ -32,6 +33,7 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package # The 1.1.0 series is currently only receiving security fixes and will go # out of support on 11th September 2019. + version('1.1.0l', sha256='74a2f756c64fd7386a29184dc0344f4831192d61dc2481a93a4c5dd727f41148') version('1.1.0k', sha256='efa4965f4f773574d6cbda1cf874dbbe455ab1c0d4f906115f867d30444470b1') version('1.1.0j', sha256='31bec6c203ce1a8e93d5994f4ed304c63ccf07676118b6634edded12ad1b3246') version('1.1.0i', sha256='ebbfc844a8c8cc0ea5dc10b86c9ce97f401837f3fa08c17b2cdadc118253cf99') @@ -43,6 +45,7 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package # Our previous LTS version (1.0.2 series) will continue to be supported # until 31st December 2019 (security fixes only during the last year of # support). + version('1.0.2t', sha256='14cb464efe7ac6b54799b34456bd69558a749a4931ecfd9cf9f71d7881cac7bc') version('1.0.2s', sha256='cabd5c9492825ce5bd23f3c3aeed6a97f8142f606d893df216411f07d1abab96') version('1.0.2r', sha256='ae51d08bba8a83958e894946f15303ff894d75c2b8bbd44a852b64e3fe11d0d6') version('1.0.2p', sha256='50a98e07b1a89eb8f6a99477f262df71c6fa7bef77df4dc83025a2845c827d00') From c570c09cbf0558e6db11f23090c4fad8fec642d1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:09:28 -0500 Subject: [PATCH 171/499] Add libsigsegv 2.12 (#13089) --- var/spack/repos/builtin/packages/libsigsegv/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py index aceb24006b3..63f8de66c85 100644 --- a/var/spack/repos/builtin/packages/libsigsegv/package.py +++ b/var/spack/repos/builtin/packages/libsigsegv/package.py @@ -10,12 +10,13 @@ class Libsigsegv(AutotoolsPackage): """GNU libsigsegv is a library for handling page faults in user mode.""" homepage = "https://www.gnu.org/software/libsigsegv/" - url = "https://ftpmirror.gnu.org/libsigsegv/libsigsegv-2.11.tar.gz" - - patch('patch.new_config_guess', when='@2.10') + url = "https://ftpmirror.gnu.org/libsigsegv/libsigsegv-2.12.tar.gz" + version('2.12', sha256='3ae1af359eebaa4ffc5896a1aee3568c052c99879316a1ab57f8fe1789c390b6') version('2.11', 'a812d9481f6097f705599b218eea349f') version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f') + patch('patch.new_config_guess', when='@2.10') + def configure_args(self): return ['--enable-shared'] From 15d7e2efd50d0441d186903faf984d5b116601a2 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:09:46 -0500 Subject: [PATCH 172/499] Add libiconv 1.16 (#13088) --- var/spack/repos/builtin/packages/libiconv/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py index 9942abefed0..9aeb1ec7b03 100644 --- a/var/spack/repos/builtin/packages/libiconv/package.py +++ b/var/spack/repos/builtin/packages/libiconv/package.py @@ -11,8 +11,9 @@ class Libiconv(AutotoolsPackage): and the iconv program for character set conversion.""" homepage = "https://www.gnu.org/software/libiconv/" - url = "https://ftpmirror.gnu.org/libiconv/libiconv-1.15.tar.gz" + url = "https://ftpmirror.gnu.org/libiconv/libiconv-1.16.tar.gz" + version('1.16', sha256='e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04') version('1.15', 'ace8b5f2db42f7b3b3057585e80d9808') version('1.14', 'e34509b1623cec449dfeb73d7ce9c6c6') From 4d2b300da0043b64baafeb949075b4190797d303 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:10:03 -0500 Subject: [PATCH 173/499] Add isl 0.21 (#13087) --- var/spack/repos/builtin/packages/isl/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/isl/package.py b/var/spack/repos/builtin/packages/isl/package.py index c4f803b8b77..eddb99a0f9c 100644 --- a/var/spack/repos/builtin/packages/isl/package.py +++ b/var/spack/repos/builtin/packages/isl/package.py @@ -11,8 +11,10 @@ class Isl(AutotoolsPackage): sets and relations of integer points bounded by affine constraints.""" homepage = "http://isl.gforge.inria.fr" - url = "http://isl.gforge.inria.fr/isl-0.19.tar.bz2" + url = "http://isl.gforge.inria.fr/isl-0.21.tar.bz2" + version('0.21', sha256='d18ca11f8ad1a39ab6d03d3dcb3365ab416720fcb65b42d69f34f51bf0a0e859') + version('0.20', sha256='b587e083eb65a8b394e833dea1744f21af3f0e413a448c17536b5549ae42a4c2') version('0.19', sha256='d59726f34f7852a081fbd3defd1ab2136f174110fc2e0c8d10bb122173fa9ed8') version('0.18', sha256='6b8b0fd7f81d0a957beb3679c81bbb34ccc7568d5682844d8924424a0dadcb1b') version('0.15', sha256='8ceebbf4d9a81afa2b4449113cee4b7cb14a687d7a549a963deb5e2a41458b6b') From f940e8616cb0347f85faf7fe2c4f90baa6af9490 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:10:19 -0500 Subject: [PATCH 174/499] Add gettext 0.20.1 (#13086) --- var/spack/repos/builtin/packages/gettext/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py index bd608c99bb3..2d42fe25295 100644 --- a/var/spack/repos/builtin/packages/gettext/package.py +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -10,8 +10,9 @@ class Gettext(AutotoolsPackage): """GNU internationalization (i18n) and localization (l10n) library.""" homepage = "https://www.gnu.org/software/gettext/" - url = "https://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz" + url = "https://ftpmirror.gnu.org/gettext/gettext-0.20.1.tar.xz" + version('0.20.1', sha256='53f02fbbec9e798b0faaf7c73272f83608e835c6288dd58be6c9bb54624a3800') version('0.19.8.1', 'df3f5690eaa30fd228537b00cb7b7590') version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') From e925dbcefe727529e9d8f4c90cf135fffc5c07fc Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:10:48 -0500 Subject: [PATCH 175/499] Add expat 2.2.9 (#13085) --- var/spack/repos/builtin/packages/expat/package.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index 9fd6995b967..83387ccee13 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -11,7 +11,12 @@ class Expat(AutotoolsPackage): """Expat is an XML parser library written in C.""" homepage = "https://libexpat.github.io/" - url = "https://github.com/libexpat/libexpat/releases/download/R_2_2_2/expat-2.2.2.tar.bz2" + url = "https://github.com/libexpat/libexpat/releases/download/R_2_2_9/expat-2.2.9.tar.bz2" + + version('2.2.9', sha256='f1063084dc4302a427dabcca499c8312b3a32a29b7d2506653ecc8f950a9a237') + version('2.2.5', '789e297f547980fc9ecc036f9a070d49') + version('2.2.2', '1ede9a41223c78528b8c5d23e69a2667') + version('2.2.0', '2f47841c829facb346eb6e3fab5212e2') # Version 2.2.2 introduced a requirement for a high quality # entropy source. "Older" linux systems (aka CentOS 7) do not @@ -23,11 +28,8 @@ class Expat(AutotoolsPackage): # `~libbsd`. variant('libbsd', default=sys.platform != 'darwin', description="Use libbsd (for high quality randomness)") - depends_on('libbsd', when="@2.2.1:+libbsd") - version('2.2.5', '789e297f547980fc9ecc036f9a070d49') - version('2.2.2', '1ede9a41223c78528b8c5d23e69a2667') - version('2.2.0', '2f47841c829facb346eb6e3fab5212e2') + depends_on('libbsd', when="@2.2.1:+libbsd") def url_for_version(self, version): url = 'https://github.com/libexpat/libexpat/releases/download/R_{0}/expat-{1}.tar.bz2' From 02564ef4ab0ecced2a820990143fd831a4fe2881 Mon Sep 17 00:00:00 2001 From: Jannek Squar Date: Thu, 10 Oct 2019 19:13:00 +0200 Subject: [PATCH 176/499] sublime-text: New version, adapt install process (#13074) * Added new version, reworked installation process * Removed explicit addition to PATH --- .../repos/builtin/packages/sublime-text/package.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py index 0386d100310..e3f89592b73 100644 --- a/var/spack/repos/builtin/packages/sublime-text/package.py +++ b/var/spack/repos/builtin/packages/sublime-text/package.py @@ -11,9 +11,10 @@ class SublimeText(Package): prose.""" homepage = "http://www.sublimetext.com/" - url = "https://download.sublimetext.com/sublime_text_3_build_3176_x64.tar.bz2" + url = "https://download.sublimetext.com/sublime_text_3_build_3211_x64.tar.bz2" - version('3.2.1.3207', 'acb64f1de024a0f004888096afa101051e48d96c7a3e7fe96e11312d524938c4') + version('3.2.2.3211', sha256='0b3c8ca5e6df376c3c24a4b9ac2e3b391333f73b229bc6e87d0b4a5f636d74ee') + version('3.2.1.3207', sha256='acb64f1de024a0f004888096afa101051e48d96c7a3e7fe96e11312d524938c4') version('3.1.1.3176', '7d4c8c5167224888d901e8cbafb6ec7f') version('3.0.3126', 'acc34252b0ea7dff1f581c5db1564dcb') version('2.0.2', '699cd26d7fe0bada29eb1b2cd7b50e4b') @@ -39,8 +40,9 @@ def url_for_version(self, version): return "https://download.sublimetext.com/sublime_text_{0}_build_{1}_x64.tar.bz2".format(version[0], version[-1]) def install(self, spec, prefix): - # Sublime text comes as a pre-compiled binary. install_tree('.', prefix) - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix) + src = join_path(prefix, 'sublime_text') + dst = join_path(prefix, 'bin') + mkdirp(dst) + force_symlink(src, join_path(dst, 'sublime_text')) + force_symlink(src, join_path(dst, 'subl')) From 06dffaefed3d83d83031ef4e3708d0e80f5097d2 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:48:16 -0500 Subject: [PATCH 177/499] Add tar 1.32 (#13099) --- var/spack/repos/builtin/packages/tar/package.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py index f69f4daae27..6c00cdd6893 100644 --- a/var/spack/repos/builtin/packages/tar/package.py +++ b/var/spack/repos/builtin/packages/tar/package.py @@ -11,15 +11,23 @@ class Tar(AutotoolsPackage): other kinds of manipulation.""" homepage = "https://www.gnu.org/software/tar/" - url = "https://ftpmirror.gnu.org/tar/tar-1.29.tar.gz" + url = "https://ftpmirror.gnu.org/tar/tar-1.32.tar.gz" - version('1.31', 'b471be6cb68fd13c4878297d856aebd50551646f4e3074906b1a74549c40d5a2') + version('1.32', sha256='b59549594d91d84ee00c99cf2541a3330fed3a42c440503326dab767f2fbb96c') + version('1.31', sha256='b471be6cb68fd13c4878297d856aebd50551646f4e3074906b1a74549c40d5a2') version('1.30', 'e0c5ed59e4dd33d765d6c90caadd3c73') - version('1.29', 'cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0') + version('1.29', sha256='cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0') version('1.28', '6ea3dbea1f2b0409b234048e021a9fd7') + depends_on('libiconv') + patch('tar-pgi.patch', when='@1.29') patch('config-pgi.patch', when='@:1.29') patch('se-selinux.patch', when='@:1.29') patch('argp-pgi.patch', when='@:1.29') patch('gnutar-configure-xattrs.patch', when='@1.28') + + def configure_args(self): + return [ + '--with-libiconv-prefix={0}'.format(self.spec['libiconv'].prefix), + ] From c131a725af7e27fd8b80683e6af1ddfc986ca2c4 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:48:32 -0500 Subject: [PATCH 178/499] Add mpfr 4.0.2 (#13091) --- var/spack/repos/builtin/packages/mpfr/package.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py index 82665eb49f4..e0fd6885d3a 100644 --- a/var/spack/repos/builtin/packages/mpfr/package.py +++ b/var/spack/repos/builtin/packages/mpfr/package.py @@ -10,9 +10,10 @@ class Mpfr(AutotoolsPackage): """The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.""" - homepage = "http://www.mpfr.org" - url = "https://ftpmirror.gnu.org/mpfr/mpfr-4.0.1.tar.bz2" + homepage = "https://www.mpfr.org/" + url = "https://ftpmirror.gnu.org/mpfr/mpfr-4.0.2.tar.bz2" + version('4.0.2', sha256='c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc') version('4.0.1', '8c21d8ac7460493b2b9f3ef3cc610454') version('4.0.0', 'ef619f3bb68039e35c4a219e06be72d0') version('3.1.6', '320c28198def956aeacdb240b46b8969') @@ -23,11 +24,13 @@ class Mpfr(AutotoolsPackage): # mpir is a drop-in replacement for gmp depends_on('gmp@4.1:') # 4.2.3 or higher is recommended - depends_on('gmp@5.0:', when='@4.0.0:') # http://www.mpfr.org/mpfr-4.0.0/ + depends_on('gmp@5.0:', when='@4.0.0:') # https://www.mpfr.org/mpfr-4.0.0/ # Check the Bugs section of old release pages for patches. - # http://www.mpfr.org/mpfr-X.Y.Z/#bugs + # https://www.mpfr.org/mpfr-X.Y.Z/#bugs patches = { + '4.0.2': 'f2d2a530acb5e70e1a9d5b80881dbb4a504d56535c4bc103d83e0bb630172029', + '4.0.1': '5230aab653fa8675fc05b5bdd3890e071e8df49a92a9d58c4284024affd27739', '3.1.6': '66a5d58364113a21405fc53f4a48f4e8', '3.1.5': '1dc5fe65feb5607b89fe0f410d53b627', '3.1.4': 'd124381573404fe83654c7d5a79aeabf', @@ -36,7 +39,7 @@ class Mpfr(AutotoolsPackage): } for ver, checksum in patches.items(): - patch('http://www.mpfr.org/mpfr-{0}/allpatches'.format(ver), + patch('https://www.mpfr.org/mpfr-{0}/allpatches'.format(ver), when='@' + ver, sha256=checksum) def configure_args(self): From 7af8c206ace3e6fd99bef11501e1def601bbdd78 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 10 Oct 2019 12:48:49 -0500 Subject: [PATCH 179/499] Add patches and missing dependency to bash (#13084) --- .../repos/builtin/packages/bash/package.py | 23 ++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py index 4b15080e12e..24842d1ad22 100644 --- a/var/spack/repos/builtin/packages/bash/package.py +++ b/var/spack/repos/builtin/packages/bash/package.py @@ -19,6 +19,26 @@ class Bash(AutotoolsPackage): depends_on('ncurses') depends_on('readline@5.0:') + depends_on('libiconv') + + patches = [ + ('5.0', '001', 'f2fe9e1f0faddf14ab9bfa88d450a75e5d028fedafad23b88716bd657c737289'), + ('5.0', '002', '87e87d3542e598799adb3e7e01c8165bc743e136a400ed0de015845f7ff68707'), + ('5.0', '003', '4eebcdc37b13793a232c5f2f498a5fcbf7da0ecb3da2059391c096db620ec85b'), + ('5.0', '004', '14447ad832add8ecfafdce5384badd933697b559c4688d6b9e3d36ff36c62f08'), + ('5.0', '005', '5bf54dd9bd2c211d2bfb34a49e2c741f2ed5e338767e9ce9f4d41254bf9f8276'), + ('5.0', '006', 'd68529a6ff201b6ff5915318ab12fc16b8a0ebb77fda3308303fcc1e13398420'), + ('5.0', '007', '17b41e7ee3673d8887dd25992417a398677533ab8827938aa41fad70df19af9b'), + ('5.0', '008', 'eec64588622a82a5029b2776e218a75a3640bef4953f09d6ee1f4199670ad7e3'), + ('5.0', '009', 'ed3ca21767303fc3de93934aa524c2e920787c506b601cc40a4897d4b094d903'), + ('5.0', '010', 'd6fbc325f0b5dc54ddbe8ee43020bced8bd589ddffea59d128db14b2e52a8a11'), + ('5.0', '011', '2c4de332b91eaf797abbbd6c79709690b5cbd48b12e8dfe748096dbd7bf474ea'), + ] + + for ver, num, checksum in patches: + ver = Version(ver) + patch('https://ftpmirror.gnu.org/bash/bash-{0}-patches/bash{1}-{2}'.format(ver, ver.joined, num), + level=0, when='@{0}'.format(ver), sha256=checksum) def configure_args(self): spec = self.spec @@ -27,7 +47,8 @@ def configure_args(self): 'LIBS=-lncursesw', '--with-curses', '--enable-readline', - '--with-installed-readline={0}'.format(spec['readline'].prefix), + '--with-installed-readline', + '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix), ] def check(self): From 77444dff106524b0b33f664e5fe1f4512ec511d7 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 9 Oct 2019 23:32:27 +0200 Subject: [PATCH 180/499] ArchSpec: fix constraint satisfaction for targets fixes #13111 Due to a missing case we were treating a single target that was not equal to the one we were comparing to as a range open on the right. --- lib/spack/spack/spec.py | 4 ++++ lib/spack/spack/test/spec_semantics.py | 5 +++++ 2 files changed, 9 insertions(+) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 99246ebb02c..0cde672de25 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -395,6 +395,10 @@ def _satisfies_target(self, other_target, strict): if not sep and self_target == t_min: return True + if not sep and self_target != t_min: + return False + + # Check against a range min_ok = self_target.microarchitecture >= t_min if t_min else True max_ok = self_target.microarchitecture <= t_max if t_max else True diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py index 0c52bd1c108..a183742e655 100644 --- a/lib/spack/spack/test/spec_semantics.py +++ b/lib/spack/spack/test/spec_semantics.py @@ -972,7 +972,12 @@ def test_forwarding_of_architecture_attributes(self): ('libelf target=haswell', 'target=:haswell', True), ('libelf target=haswell', 'target=icelake,:nocona', False), ('libelf target=haswell', 'target=haswell,:nocona', True), + # Check that a single target is not treated as the start + # or the end of an open range + ('libelf target=haswell', 'target=x86_64', False), + ('libelf target=x86_64', 'target=haswell', False), ]) + @pytest.mark.regression('13111') def test_target_constraints(self, spec, constraint, expected_result): s = Spec(spec) assert s.satisfies(constraint) is expected_result From b07460ab5f01bae693cfc73d3128c29ee9fb2c47 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 2 Oct 2019 08:35:32 +0200 Subject: [PATCH 181/499] Added NEON to the list of features required for the aarch64 family Both floating-point and NEON are required in all standard ARMv8 implementations. Theoretically though specialized markets can support no NEON or floating-point at all. Source: https://developer.arm.com/docs/den0024/latest/aarch64-floating-point-and-neon On the other hand the base procedure call standard for Aarch64 "assumes the availability of the vector registers for passing floating-point and SIMD arguments". Further "the Arm 64-bit architecture defines two mandatory register banks: a general-purpose register bank which can be used for scalar integer processing and pointer arithmetic; and a SIMD and Floating-Point register bank". Source: https://developer.arm.com/docs/ihi0055/latest/procedure-call-standard-for-the-arm-64-bit-architecture This makes customization of Aarch64 with no NEON instruction set available so unlikely that we can consider them a feature of the generic family. --- lib/spack/llnl/util/cpu/microarchitectures.json | 6 ++++++ lib/spack/spack/test/llnl/util/cpu.py | 1 + 2 files changed, 7 insertions(+) diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index ad985ba9941..5a288c58098 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -904,6 +904,12 @@ "any_of": [ "sse4_2" ] + }, + "neon": { + "reason": "NEON is required in all standard ARMv8 implementations", + "families": [ + "aarch64" + ] } } } diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 9af784d1032..9c65825a52c 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -156,6 +156,7 @@ def test_architecture_family(target_name, expected_family): ('skylake', 'sse3'), ('power8', 'altivec'), ('broadwell', 'sse4.1'), + ('aarch64', 'neon') ]) def test_features_query(target_name, feature): target = llnl.util.cpu.targets[target_name] From 87cdfa2c255e86b9f89790349f2d8479c0eb86b8 Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren Date: Tue, 17 Sep 2019 19:27:33 -0700 Subject: [PATCH 182/499] Add support for nested "overrides" scopes. --- lib/spack/spack/config.py | 26 ++++++++++++++++-- lib/spack/spack/test/config.py | 48 ++++++++++++++++++++++++++++++++++ 2 files changed, 72 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index c73b5047f53..4a684986ebb 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -32,6 +32,7 @@ import copy import os +import re import sys import multiprocessing from contextlib import contextmanager @@ -354,6 +355,15 @@ def highest_precedence_scope(self): """Non-internal scope with highest precedence.""" return next(reversed(self.file_scopes), None) + def matching_scopes(self, reg_expr): + """ + List of all scopes whose names match the provided regular expression. + + For example, matching_scopes(r'^command') will return all scopes + whose names begin with `command`. + """ + return [s for s in self.scopes.values() if re.search(reg_expr, s.name)] + def _validate_scope(self, scope): """Ensure that scope is valid in this configuration. @@ -539,13 +549,25 @@ def override(path_or_scope, value=None): an internal config scope for it and push/pop that scope. """ + base_name = 'overrides-' if isinstance(path_or_scope, ConfigScope): overrides = path_or_scope config.push_scope(path_or_scope) else: - overrides = InternalConfigScope('overrides') + # Ensure the new override gets a unique scope name + current_overrides = [s.name for s in + config.matching_scopes(r'^{0}'.format(base_name))] + num_overrides = len(current_overrides) + while True: + scope_name = '{0}{1}'.format(base_name, num_overrides) + if scope_name in current_overrides: + num_overrides += 1 + else: + break + + overrides = InternalConfigScope(scope_name) config.push_scope(overrides) - config.set(path_or_scope, value, scope='overrides') + config.set(path_or_scope, value, scope=scope_name) yield config diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index 163fc392d3d..99e1d7499c0 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -627,6 +627,54 @@ def test_add_command_line_scopes(tmpdir, mutable_config): spack.config._add_command_line_scopes(mutable_config, [str(tmpdir)]) +@pytest.mark.nomockstage +def test_nested_override(): + """Ensure proper scope naming of nested overrides.""" + # WARNING: Base name must match that used in `config.py`s `override()`. + base_name = 'overrides-' + + def _check_scopes(num_expected, debug_values): + scope_names = [s.name for s in spack.config.config.scopes.values()] + + for i in range(num_expected): + name = '{0}{1}'.format(base_name, i) + assert name in scope_names + + data = spack.config.config.get_config('config', name) + assert data['debug'] == debug_values[i] + + # Check results from single and nested override + with spack.config.override('config:debug', True): + with spack.config.override('config:debug', False): + _check_scopes(2, [True, False]) + + _check_scopes(1, [True]) + + +@pytest.mark.nomockstage +def test_alternate_override(monkeypatch): + """Ensure proper scope naming of override when conflict present.""" + # WARNING: Base name must match that used in `config.py`s `override()`. + base_name = 'overrides-' + + def _matching_scopes(regexpr): + return [spack.config.InternalConfigScope('{0}1'.format(base_name))] + + # Check that the alternate naming works + monkeypatch.setattr(spack.config.config, 'matching_scopes', + _matching_scopes) + + with spack.config.override('config:debug', False): + name = '{0}2'.format(base_name) + + scope_names = [s.name for s in spack.config.config.scopes.values() if + s.name.startswith(base_name)] + assert name in scope_names + + data = spack.config.config.get_config('config', name) + assert data['debug'] is False + + def test_immutable_scope(tmpdir): config_yaml = str(tmpdir.join('config.yaml')) with open(config_yaml, 'w') as f: From 93a44c822c23ee3c12543148e058c784a63495f2 Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren Date: Tue, 17 Sep 2019 19:28:24 -0700 Subject: [PATCH 183/499] tests: cleanup config:build_stage handling (fixes #12651, #12798) --- lib/spack/spack/config.py | 5 +- lib/spack/spack/stage.py | 29 ++-- lib/spack/spack/test/config.py | 11 +- lib/spack/spack/test/conftest.py | 31 ++-- lib/spack/spack/test/stage.py | 253 ++++++++++++------------------- 5 files changed, 129 insertions(+), 200 deletions(-) diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index 4a684986ebb..1af8ad757b4 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -110,6 +110,9 @@ #: this is shorter and more readable than listing all choices scopes_metavar = '{defaults,system,site,user}[/PLATFORM]' +#: Base name for the (internal) overrides scope. +overrides_base_name = 'overrides-' + def first_existing(dictionary, keys): """Get the value of the first key in keys that is in the dictionary.""" @@ -549,11 +552,11 @@ def override(path_or_scope, value=None): an internal config scope for it and push/pop that scope. """ - base_name = 'overrides-' if isinstance(path_or_scope, ConfigScope): overrides = path_or_scope config.push_scope(path_or_scope) else: + base_name = overrides_base_name # Ensure the new override gets a unique scope name current_overrides = [s.name for s in config.matching_scopes(r'^{0}'.format(base_name))] diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index 4e950482cfe..537a97b10e9 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -91,18 +91,29 @@ def _first_accessible_path(paths): def _resolve_paths(candidates): - """Resolve paths, removing extra $user from $tempdir if needed.""" + """ + Resolve candidate paths and make user-related adjustments. + + Adjustments involve removing extra $user from $tempdir if $tempdir includes + $user and appending $user if it is not present in the path. + """ temp_path = sup.canonicalize_path('$tempdir') - tmp_has_usr = getpass.getuser() in temp_path.split(os.path.sep) + user = getpass.getuser() + tmp_has_usr = user in temp_path.split(os.path.sep) paths = [] for path in candidates: - # First remove the extra `$user` node from a `$tempdir/$user` entry - # for hosts that automatically append `$user` to `$tempdir`. + # Remove the extra `$user` node from a `$tempdir/$user` entry for + # hosts that automatically append `$user` to `$tempdir`. if path.startswith(os.path.join('$tempdir', '$user')) and tmp_has_usr: path = os.path.join('$tempdir', path[15:]) - paths.append(sup.canonicalize_path(path)) + # Ensure the path is unique per user. + can_path = sup.canonicalize_path(path) + if user not in can_path: + can_path = os.path.join(can_path, user) + + paths.append(can_path) return paths @@ -125,14 +136,6 @@ def get_stage_root(): raise StageError("No accessible stage paths in:", ' '.join(resolved_candidates)) - # Ensure that path is unique per user in an attempt to avoid - # conflicts in shared temporary spaces. Emulate permissions from - # `tempfile.mkdtemp`. - user = getpass.getuser() - if user not in path: - path = os.path.join(path, user) - mkdirp(path, mode=stat.S_IRWXU) - _stage_root = path return _stage_root diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index 99e1d7499c0..2de4e552811 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -627,14 +627,13 @@ def test_add_command_line_scopes(tmpdir, mutable_config): spack.config._add_command_line_scopes(mutable_config, [str(tmpdir)]) -@pytest.mark.nomockstage def test_nested_override(): """Ensure proper scope naming of nested overrides.""" - # WARNING: Base name must match that used in `config.py`s `override()`. - base_name = 'overrides-' + base_name = spack.config.overrides_base_name def _check_scopes(num_expected, debug_values): - scope_names = [s.name for s in spack.config.config.scopes.values()] + scope_names = [s.name for s in spack.config.config.scopes.values() if + s.name.startswith(base_name)] for i in range(num_expected): name = '{0}{1}'.format(base_name, i) @@ -651,11 +650,9 @@ def _check_scopes(num_expected, debug_values): _check_scopes(1, [True]) -@pytest.mark.nomockstage def test_alternate_override(monkeypatch): """Ensure proper scope naming of override when conflict present.""" - # WARNING: Base name must match that used in `config.py`s `override()`. - base_name = 'overrides-' + base_name = spack.config.overrides_base_name def _matching_scopes(regexpr): return [spack.config.InternalConfigScope('{0}1'.format(base_name))] diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py index c193e66eee7..7795303edae 100644 --- a/lib/spack/spack/test/conftest.py +++ b/lib/spack/spack/test/conftest.py @@ -17,7 +17,7 @@ import pytest import ruamel.yaml as yaml -from llnl.util.filesystem import remove_linked_tree +from llnl.util.filesystem import mkdirp, remove_linked_tree import spack.architecture import spack.compilers @@ -122,34 +122,27 @@ def reset_compiler_cache(): spack.compilers._compiler_cache = {} -@pytest.fixture -def clear_stage_root(monkeypatch): - """Ensure spack.stage._stage_root is not set at test start.""" - monkeypatch.setattr(spack.stage, '_stage_root', None) - yield - - @pytest.fixture(scope='function', autouse=True) -def mock_stage(clear_stage_root, tmpdir_factory, request): +def mock_stage(tmpdir_factory, monkeypatch, request): """Establish the temporary build_stage for the mock archive.""" - # Workaround to skip mock_stage for 'nomockstage' test cases + # The approach with this autouse fixture is to set the stage root + # instead of using spack.config.override() to avoid configuration + # conflicts with dozens of tests that rely on other configuration + # fixtures, such as config. if 'nomockstage' not in request.keywords: + # Set the build stage to the requested path new_stage = tmpdir_factory.mktemp('mock-stage') new_stage_path = str(new_stage) - # Set test_stage_path as the default directory to use for test stages. - current = spack.config.get('config:build_stage') - spack.config.set('config', - {'build_stage': new_stage_path}, scope='user') + # Ensure the source directory exists within the new stage path + source_path = os.path.join(new_stage_path, + spack.stage._source_path_subdir) + mkdirp(source_path) - # Ensure the source directory exists - source_path = new_stage.join(spack.stage._source_path_subdir) - source_path.ensure(dir=True) + monkeypatch.setattr(spack.stage, '_stage_root', new_stage_path) yield new_stage_path - spack.config.set('config', {'build_stage': current}, scope='user') - # Clean up the test stage directory if os.path.isdir(new_stage_path): shutil.rmtree(new_stage_path) diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py index 5e21c48cc40..cb3204bc5ff 100644 --- a/lib/spack/spack/test/stage.py +++ b/lib/spack/spack/test/stage.py @@ -13,7 +13,7 @@ import pytest -from llnl.util.filesystem import mkdirp, working_dir +from llnl.util.filesystem import mkdirp, touch, working_dir import spack.paths import spack.stage @@ -40,9 +40,6 @@ _include_hidden = 2 _include_extra = 3 -# Some standard unix directory that does NOT include the username -_non_user_root = os.path.join(os.path.sep, 'opt') - # Mock fetch directories are expected to appear as follows: # @@ -70,6 +67,13 @@ # +@pytest.fixture +def clear_stage_root(monkeypatch): + """Ensure spack.stage._stage_root is not set at test start.""" + monkeypatch.setattr(spack.stage, '_stage_root', None) + yield + + def check_expand_archive(stage, stage_name, expected_file_list): """ Ensure the expanded archive directory contains the expected structure and @@ -176,83 +180,22 @@ def get_stage_path(stage, stage_name): return stage.path +# TODO: Revisit use of the following fixture (and potentially leveraging +# the `mock_stage` path in `mock_stage_archive`) per discussions in +# #12857. See also #13065. @pytest.fixture -def bad_stage_path(): - """Temporarily ensure there is no accessible path for staging.""" - current = spack.config.get('config:build_stage') - spack.config.set('config', {'build_stage': '/no/such/path'}, scope='user') - yield - spack.config.set('config', {'build_stage': current}, scope='user') +def tmp_build_stage_dir(tmpdir, clear_stage_root): + """Use a temporary test directory for the stage root.""" + test_path = str(tmpdir.join('stage')) + with spack.config.override('config:build_stage', test_path): + yield tmpdir, spack.stage.get_stage_root() + + shutil.rmtree(test_path) @pytest.fixture -def non_user_path_for_stage(monkeypatch): - """Temporarily use a Linux-standard non-user path for staging. """ - def _can_access(path, perms): - return True - - current = spack.config.get('config:build_stage') - spack.config.set('config', {'build_stage': [_non_user_root]}, scope='user') - monkeypatch.setattr(os, 'access', _can_access) - yield - spack.config.set('config', {'build_stage': current}, scope='user') - - -@pytest.fixture -def instance_path_for_stage(): - """ - Temporarily use the "traditional" spack instance stage path for staging. - - Note that it can be important for other tests that the previous settings be - restored when the test case is over. - """ - current = spack.config.get('config:build_stage') - base = canonicalize_path(os.path.join('$spack', 'test-stage')) - mkdirp(base) - path = tempfile.mkdtemp(dir=base) - spack.config.set('config', {'build_stage': path}, scope='user') - yield - spack.config.set('config', {'build_stage': current}, scope='user') - shutil.rmtree(base) - - -@pytest.fixture -def tmp_path_for_stage(tmpdir): - """ - Use a temporary test directory for staging. - - Note that it can be important for other tests that the previous settings be - restored when the test case is over. - """ - current = spack.config.get('config:build_stage') - spack.config.set('config', {'build_stage': [str(tmpdir)]}, scope='user') - yield tmpdir - spack.config.set('config', {'build_stage': current}, scope='user') - - -@pytest.fixture -def tmp_build_stage_dir(tmpdir): - """Establish the temporary build_stage for the mock archive.""" - test_stage_path = tmpdir.join('stage') - - # Set test_stage_path as the default directory to use for test stages. - current = spack.config.get('config:build_stage') - spack.config.set('config', - {'build_stage': [str(test_stage_path)]}, scope='user') - - yield (tmpdir, test_stage_path) - - spack.config.set('config', {'build_stage': current}, scope='user') - - -@pytest.fixture -def mock_stage_archive(clear_stage_root, tmp_build_stage_dir, request): - """ - Create the directories and files for the staged mock archive. - - Note that it can be important for other tests that the previous settings be - restored when the test case is over. - """ +def mock_stage_archive(tmp_build_stage_dir): + """Create the directories and files for the staged mock archive.""" # Mock up a stage area that looks like this: # # tmpdir/ test_files_dir @@ -265,7 +208,7 @@ def mock_stage_archive(clear_stage_root, tmp_build_stage_dir, request): # def create_stage_archive(expected_file_list=[_include_readme]): tmpdir, test_stage_path = tmp_build_stage_dir - test_stage_path.ensure(dir=True) + mkdirp(test_stage_path) # Create the archive directory and associated file archive_dir = tmpdir.join(_archive_base) @@ -733,82 +676,87 @@ def test_resolve_paths(self): assert spack.stage._resolve_paths([]) == [] + # resolved path without user appends user paths = [os.path.join(os.path.sep, 'a', 'b', 'c')] - assert spack.stage._resolve_paths(paths) == paths - - tmp = '$tempdir' - paths = [os.path.join(tmp, 'stage'), os.path.join(tmp, '$user')] - can_paths = [canonicalize_path(paths[0]), canonicalize_path(tmp)] user = getpass.getuser() - if user not in can_paths[1].split(os.path.sep): - can_paths[1] = os.path.join(can_paths[1], user) + can_paths = [os.path.join(paths[0], user)] assert spack.stage._resolve_paths(paths) == can_paths - def test_get_stage_root_bad_path(self, clear_stage_root, bad_stage_path): + # resolved path with node including user does not append user + paths = [os.path.join(os.path.sep, 'spack-{0}'.format(user), 'stage')] + assert spack.stage._resolve_paths(paths) == paths + + # resolve paths where user + tmp = '$tempdir' + can_tmpdir = canonicalize_path(tmp) + temp_has_user = user in can_tmpdir.split(os.sep) + paths = [os.path.join(tmp, 'stage'), os.path.join(tmp, '$user')] + can_paths = [canonicalize_path(p) for p in paths] + + if temp_has_user: + can_paths[1] = can_tmpdir + else: + can_paths[0] = os.path.join(can_paths[0], user) + + assert spack.stage._resolve_paths(paths) == can_paths + + def test_get_stage_root_bad_path(self, clear_stage_root): """Ensure an invalid stage path root raises a StageError.""" - with pytest.raises(spack.stage.StageError, - match="No accessible stage paths in"): - assert spack.stage.get_stage_root() is None + with spack.config.override('config:build_stage', '/no/such/path'): + with pytest.raises(spack.stage.StageError, + match="No accessible stage paths in"): + spack.stage.get_stage_root() # Make sure the cached stage path values are unchanged. assert spack.stage._stage_root is None - def test_get_stage_root_non_user_path(self, clear_stage_root, - non_user_path_for_stage): - """Ensure a non-user stage root includes the username.""" - # The challenge here is whether the user has access to the standard - # non-user path. If not, the path should still appear in the error. + @pytest.mark.parametrize( + 'path,purged', [('stage-1234567890abcdef1234567890abcdef', True), + ('stage-abcdef12345678900987654321fedcba', True), + ('stage-a1b2c3', False)]) + def test_stage_purge(self, tmpdir, clear_stage_root, path, purged): + """Test purging of stage directories.""" + stage_dir = tmpdir.join('stage') + stage_path = str(stage_dir) + + test_dir = stage_dir.join(path) + test_dir.ensure(dir=True) + test_path = str(test_dir) + + with spack.config.override('config:build_stage', stage_path): + stage_root = spack.stage.get_stage_root() + assert stage_path == stage_root + + spack.stage.purge() + + if purged: + assert not os.path.exists(test_path) + else: + assert os.path.exists(test_path) + shutil.rmtree(test_path) + + def test_get_stage_root_in_spack(self, clear_stage_root): + """Ensure an instance path is an accessible build stage path.""" + + base = canonicalize_path(os.path.join('$spack', '.spack-test-stage')) + mkdirp(base) + test_path = tempfile.mkdtemp(dir=base) + try: - path = spack.stage.get_stage_root() - assert getpass.getuser() in path.split(os.path.sep) + with spack.config.override('config:build_stage', test_path): + path = spack.stage.get_stage_root() - # Make sure the cached stage path values are changed appropriately. - assert spack.stage._stage_root == path - except OSError as e: - expected = os.path.join(_non_user_root, getpass.getuser()) - assert expected in str(e) + assert 'spack' in path.split(os.path.sep) - # Make sure the cached stage path values are unchanged. - assert spack.stage._stage_root is None + # Make sure cached stage path value was changed appropriately + assert spack.stage._stage_root == test_path - def test_get_stage_root_tmp(self, clear_stage_root, tmp_path_for_stage): - """Ensure a temp path stage root is a suitable temp path.""" - assert spack.stage._stage_root is None + # Make sure the directory exists + assert os.path.isdir(spack.stage._stage_root) - tmpdir = tmp_path_for_stage - path = spack.stage.get_stage_root() - assert path == str(tmpdir) - assert 'test_get_stage_root_tmp' in path - - # Make sure the cached stage path values are changed appropriately. - assert spack.stage._stage_root == path - - # Add then purge a few directories - dir1 = tmpdir.join('stage-1234567890abcdef1234567890abcdef') - dir1.ensure(dir=True) - dir2 = tmpdir.join('stage-abcdef12345678900987654321fedcba') - dir2.ensure(dir=True) - dir3 = tmpdir.join('stage-a1b2c3') - dir3.ensure(dir=True) - - spack.stage.purge() - assert not os.path.exists(str(dir1)) - assert not os.path.exists(str(dir2)) - assert os.path.exists(str(dir3)) - - # Cleanup - shutil.rmtree(str(dir3)) - - def test_get_stage_root_in_spack(self, clear_stage_root, - instance_path_for_stage): - """Ensure an instance path stage root is a suitable path.""" - assert spack.stage._stage_root is None - - path = spack.stage.get_stage_root() - assert 'spack' in path.split(os.path.sep) - - # Make sure the cached stage path values are changed appropriately. - assert spack.stage._stage_root == path + finally: + # Clean up regardless of outcome + shutil.rmtree(base) def test_stage_constructor_no_fetcher(self): """Ensure Stage constructor with no URL or fetch strategy fails.""" @@ -879,34 +827,19 @@ def test_diystage_preserve_file(self, tmpdir): _file.read() == _readme_contents -@pytest.fixture -def tmp_build_stage_nondir(tmpdir): - """Establish the temporary build_stage pointing to non-directory.""" - test_stage_path = tmpdir.join('stage', 'afile') - test_stage_path.ensure(dir=False) - - # Set test_stage_path as the default directory to use for test stages. - current = spack.config.get('config:build_stage') - stage_dir = os.path.dirname(str(test_stage_path)) - spack.config.set('config', {'build_stage': [stage_dir]}, scope='user') - - yield test_stage_path - - spack.config.set('config', {'build_stage': current}, scope='user') - - def test_stage_create_replace_path(tmp_build_stage_dir): """Ensure stage creation replaces a non-directory path.""" _, test_stage_path = tmp_build_stage_dir - test_stage_path.ensure(dir=True) + mkdirp(test_stage_path) - nondir = test_stage_path.join('afile') - nondir.ensure(dir=False) + nondir = os.path.join(test_stage_path, 'afile') + touch(nondir) path = str(nondir) stage = Stage(path, name='') - stage.create() # Should ensure the path is converted to a dir + stage.create() + # Ensure the stage path is "converted" to a directory assert os.path.isdir(stage.path) From 884964d551d763ae22376e522ad01e23b5121bca Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Thu, 10 Oct 2019 21:52:29 -0500 Subject: [PATCH 184/499] Fix f18 install method (#13123) * Install method is broken and not needed. Built-in install method works fine. Just delete. * Change version to master. --- var/spack/repos/builtin/packages/f18/package.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/f18/package.py b/var/spack/repos/builtin/packages/f18/package.py index 7a2269ae83a..3b0a4d8b4f9 100644 --- a/var/spack/repos/builtin/packages/f18/package.py +++ b/var/spack/repos/builtin/packages/f18/package.py @@ -14,10 +14,6 @@ class F18(CMakePackage): git = "https://github.com/flang-compiler/f18" - version('develop', branch='master') + version('master', branch='master') - depends_on('llvm@6.0.0+clang', when='@develop') - - def install(self, spec, prefix): - mkdirp(prefix.bin) - install("spack-build/tools/f18/bin/f18", prefix.bin) + depends_on('llvm@6.0.0+clang', when='@master') From fd97f5c491ca3943e7b990382c3aa9befca14551 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Fri, 11 Oct 2019 07:55:15 +0200 Subject: [PATCH 185/499] Fixed constraints in recipes for packages that depends on fftw (#13125) --- var/spack/repos/builtin/packages/abinit/package.py | 5 +++-- var/spack/repos/builtin/packages/accfft/package.py | 2 +- var/spack/repos/builtin/packages/libemos/package.py | 2 +- var/spack/repos/builtin/packages/relion/package.py | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py index 196efaa19c6..70df84c709d 100644 --- a/var/spack/repos/builtin/packages/abinit/package.py +++ b/var/spack/repos/builtin/packages/abinit/package.py @@ -71,8 +71,9 @@ class Abinit(AutotoolsPackage): # depends_on('elpa~openmp', when='+elpa+mpi~openmp') # depends_on('elpa+openmp', when='+elpa+mpi+openmp') - depends_on('fftw+float', when='~openmp') - depends_on('fftw+float+openmp', when='+openmp') + depends_on('fftw precision=float') + depends_on('fftw~openmp', when='~openmp') + depends_on('fftw+openmp', when='+openmp') depends_on('netcdf-fortran', when='+hdf5') depends_on('hdf5+mpi', when='+mpi+hdf5') # required for NetCDF-4 support diff --git a/var/spack/repos/builtin/packages/accfft/package.py b/var/spack/repos/builtin/packages/accfft/package.py index bdc3f52f66f..8c200b76f9c 100644 --- a/var/spack/repos/builtin/packages/accfft/package.py +++ b/var/spack/repos/builtin/packages/accfft/package.py @@ -20,7 +20,7 @@ class Accfft(CMakePackage, CudaPackage): variant('shared', default=True, description='Enables the build of shared libraries') # See: http://accfft.org/articles/install/#installing-dependencies - depends_on('fftw+float+double~mpi+openmp') + depends_on('fftw precision=float,double ~mpi+openmp') depends_on('parallel-netcdf', when='+pnetcdf') diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py index 3d1cd2eaf57..30bd081a634 100644 --- a/var/spack/repos/builtin/packages/libemos/package.py +++ b/var/spack/repos/builtin/packages/libemos/package.py @@ -28,7 +28,7 @@ class Libemos(CMakePackage): depends_on('eccodes', when='grib=eccodes') depends_on('grib-api', when='grib=grib-api') - depends_on('fftw+float+double') + depends_on('fftw precision=float,double') depends_on('cmake@2.8.11:', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py index c767baaaabd..a9ab80b8495 100644 --- a/var/spack/repos/builtin/packages/relion/package.py +++ b/var/spack/repos/builtin/packages/relion/package.py @@ -37,7 +37,7 @@ class Relion(CMakePackage, CudaPackage): # relion will not build with newer versions of cmake # per https://github.com/3dem/relion/issues/380 depends_on('cmake@3:3.9.4', type='build') - depends_on('fftw+float+double') + depends_on('fftw precision=float,double') depends_on('fltk', when='+gui') depends_on('libtiff') From d248b0e9d5c322576620eb5270f7d95b7c1e9df0 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Fri, 11 Oct 2019 03:21:45 -0500 Subject: [PATCH 186/499] Fix python3 errors from string and byte concatenation (#13141) --- lib/spack/spack/binary_distribution.py | 9 ++-- lib/spack/spack/relocate.py | 70 +++++++++++++++----------- 2 files changed, 47 insertions(+), 32 deletions(-) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index 6a1935b922b..ca8fbd31d16 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -461,10 +461,11 @@ def relocate_package(workdir, spec, allow_root): Relocate the given package """ buildinfo = read_buildinfo_file(workdir) - new_path = spack.store.layout.root - new_prefix = spack.paths.prefix - old_path = buildinfo['buildpath'] - old_prefix = buildinfo.get('spackprefix', '/not/in/buildinfo/dictionary') + new_path = str(spack.store.layout.root) + new_prefix = str(spack.paths.prefix) + old_path = str(buildinfo['buildpath']) + old_prefix = str(buildinfo.get('spackprefix', + '/not/in/buildinfo/dictionary')) rel = buildinfo.get('relative_rpaths', False) if rel: return diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index 3794189d79d..8e4350a7b1b 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -10,7 +10,6 @@ import spack.repo import spack.cmd import llnl.util.lang -import llnl.util.filesystem as fs from spack.util.executable import Executable, ProcessError import llnl.util.tty as tty @@ -290,23 +289,15 @@ def modify_object_macholib(cur_path, old_dir, new_dir): return try: from macholib.MachO import MachO - from macholib.mach_o import LC_RPATH except ImportError as e: raise MissingMacholibException(e) def match_func(cpath): - return str(cpath).replace(old_dir, new_dir) + rpath = cpath.replace(old_dir, new_dir) + return rpath dll = MachO(cur_path) dll.rewriteLoadCommands(match_func) - for header in dll.headers: - for (idx, (lc, cmd, data)) in enumerate(header.commands): - if lc.cmd == LC_RPATH: - rpath = data - rpath = rpath.strip('\x00') - new_rpath = match_func(rpath) - header.rewriteDataForCommand(idx, new_rpath) - try: f = open(dll.filename, 'rb+') for header in dll.headers: @@ -364,6 +355,26 @@ def needs_text_relocation(m_type, m_subtype): return (m_type == "text") +def replace_prefix_text(path_name, old_dir, new_dir): + """ + Replace old install prefix with new install prefix + in text files using utf-8 encoded strings. + """ + + def replace(match): + return match.group().replace(old_dir.encode('utf-8'), + new_dir.encode('utf-8')) + with open(path_name, 'rb+') as f: + data = f.read() + f.seek(0) + pat = re.compile(old_dir.encode('utf-8')) + if not pat.search(data): + return + ndata = pat.sub(replace, data) + f.write(ndata) + f.truncate() + + def replace_prefix_bin(path_name, old_dir, new_dir): """ Attempt to replace old install prefix with new install prefix @@ -372,23 +383,27 @@ def replace_prefix_bin(path_name, old_dir, new_dir): """ def replace(match): - occurances = match.group().count(old_dir) - padding = (len(old_dir) - len(new_dir)) * occurances + occurances = match.group().count(old_dir.encode('utf-8')) + olen = len(old_dir.encode('utf-8')) + nlen = len(new_dir.encode('utf-8')) + padding = (olen - nlen) * occurances if padding < 0: return data - return match.group().replace(old_dir, new_dir) + b'\0' * padding + return match.group().replace(old_dir.encode('utf-8'), + new_dir.encode('utf-8')) + b'\0' * padding with open(path_name, 'rb+') as f: data = f.read() f.seek(0) original_data_len = len(data) - pat = re.compile(re.escape(old_dir) + b'([^\0]*?)\0') + pat = re.compile(old_dir.encode('utf-8') + b'([^\0]*?)\0') + if not pat.search(data): + return ndata = pat.sub(replace, data) - new_data_len = len(ndata) - if not new_data_len == original_data_len: + if not len(ndata) == original_data_len: raise BinaryStringReplacementException( - path_name, original_data_len, new_data_len) - f.write(data) + path_name, original_data_len, len(ndata)) + f.write(ndata) f.truncate() @@ -429,8 +444,8 @@ def relocate_macho_binaries(path_names, old_dir, new_dir, allow_root): modify_object_macholib(path_name, placeholder, new_dir) modify_object_macholib(path_name, old_dir, new_dir) if len(new_dir) <= len(old_dir): - replace_prefix_bin(path_name, old_dir.encode('utf-8'), - new_dir.encode('utf-8')) + replace_prefix_bin(path_name, old_dir, + new_dir) else: tty.warn('Cannot do a binary string replacement' ' with padding for %s' @@ -563,16 +578,15 @@ def relocate_links(path_names, old_dir, new_dir): def relocate_text(path_names, oldpath, newpath, oldprefix, newprefix): """ - Replace old path with new path in text file path_name + Replace old path with new path in text files + including the path the the spack sbang script. """ - fs.filter_file('%s' % oldpath, '%s' % newpath, *path_names, - backup=False, string=True) sbangre = '#!/bin/bash %s/bin/sbang' % oldprefix sbangnew = '#!/bin/bash %s/bin/sbang' % newprefix - fs.filter_file(sbangre, sbangnew, *path_names, - backup=False, string=True) - fs.filter_file(oldprefix, newprefix, *path_names, - backup=False, string=True) + for path_name in path_names: + replace_prefix_text(path_name, oldpath, newpath) + replace_prefix_text(path_name, sbangre, sbangnew) + replace_prefix_text(path_name, oldprefix, newprefix) def substitute_rpath(orig_rpath, topdir, new_root_path): From 8dd95c17053ee0f19bc0afe18822ed341ae77852 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Fri, 11 Oct 2019 14:49:27 +0200 Subject: [PATCH 187/499] Fixed options to compile generic code on ppc64 and ppc64le --- lib/spack/llnl/util/cpu/microarchitectures.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 5a288c58098..88e2bb665f1 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -729,6 +729,7 @@ "features": [], "compilers": { "gcc": { + "name": "powerpc64", "versions": "4:", "flags": "-mcpu={name} -mtune={name}" } @@ -783,6 +784,7 @@ "features": [], "compilers": { "gcc": { + "name": "powerpc64le", "versions": "4:", "flags": "-mcpu={name} -mtune={name}" } From f8a4a3802c294977f44bf9a7881363c3a3def32d Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Fri, 11 Oct 2019 10:52:53 +0200 Subject: [PATCH 188/499] Autotools build system to patch config.guess based on a range check --- lib/spack/spack/build_systems/autotools.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py index b8fb6dc0b94..eb237bcc4e6 100644 --- a/lib/spack/spack/build_systems/autotools.py +++ b/lib/spack/spack/build_systems/autotools.py @@ -87,8 +87,9 @@ def _do_patch_config_guess(self): config.guess fails for PPC64LE for version prior to a 2013-06-10 build date (automake 1.13.4) and for ARM (aarch64).""" - if not self.patch_config_guess or (not self.spec.satisfies( - 'target=ppc64le') and not self.spec.satisfies('target=aarch64') + if not self.patch_config_guess or ( + not self.spec.satisfies('target=ppc64le:') and + not self.spec.satisfies('target=aarch64:') ): return my_config_guess = None From 87fa7c15fc1f529debf7b010a5e3cd8ee4fb3f04 Mon Sep 17 00:00:00 2001 From: Matthew LeGendre Date: Fri, 11 Oct 2019 12:23:29 -0700 Subject: [PATCH 189/499] Add adiak package, version 0.1.1 --- .../repos/builtin/packages/adiak/package.py | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 var/spack/repos/builtin/packages/adiak/package.py diff --git a/var/spack/repos/builtin/packages/adiak/package.py b/var/spack/repos/builtin/packages/adiak/package.py new file mode 100644 index 00000000000..774ef198c07 --- /dev/null +++ b/var/spack/repos/builtin/packages/adiak/package.py @@ -0,0 +1,38 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Adiak(CMakePackage): + """Adiak collects metadata about HPC application runs and provides it + to tools.""" + + homepage = "https://github.com/LLNL/Adiak" + url = "https://github.com/LLNL/Adiak/releases/download/v0.1/adiak-v0.1.1.tar.gz" + + variant('mpi', default=True, description='Build with MPI support') + variant('shared', default=True, description='Build dynamic libraries') + + version('0.1.1', sha256='438e4652e15e206cd0019423d829fd4f2329323ff0c8861d9586bae051d9624b') + + depends_on('mpi', when='+mpi') + + def cmake_args(self): + args = [] + if self.spec.satisfies('+mpi'): + args.append('-DMPICXX=%s' % self.spec['mpi'].mpicxx) + args.append('-DMPICC=%s' % self.spec['mpi'].mpicc) + args.append('-DENABLE_MPI=ON') + else: + args.append('-DENABLE_MPI=OFF') + + if (self.spec.satisfies('+shared')): + args.append('-DBUILD_SHARED_LIBS=ON') + else: + args.append('-DBUILD_SHARED_LIBS=OFF') + + args.append('-DENABLE_TESTS=OFF') + return args From 62927654dd26db7a6a45c8bb307bf1cf6ba3470d Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Thu, 10 Oct 2019 22:44:41 -0700 Subject: [PATCH 190/499] checksums: use sha256 checksums everywhere We'd like to use a consistent checksum scheme everywhere so that we can: a) incorporate archive checksums into our specs and have a consistent hashing algorithm across all specs. b) index mirrors with a consistent type of checksum, and not one that is dependent on how spack packages are written. - [x] convert existing md5, sha224, sha512, sha1 checksums to sha256 --- .../repos/builtin/packages/abinit/package.py | 10 +- .../repos/builtin/packages/abyss/package.py | 4 +- .../repos/builtin/packages/ack/package.py | 8 +- .../builtin/packages/activeharmony/package.py | 2 +- .../builtin/packages/adept-utils/package.py | 4 +- .../repos/builtin/packages/adios/package.py | 14 +- 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.../packages/xcursor-themes/package.py | 2 +- .../builtin/packages/xcursorgen/package.py | 2 +- .../builtin/packages/xdbedizzy/package.py | 2 +- .../builtin/packages/xditview/package.py | 2 +- .../repos/builtin/packages/xdm/package.py | 2 +- .../builtin/packages/xdpyinfo/package.py | 2 +- .../builtin/packages/xdriinfo/package.py | 2 +- .../repos/builtin/packages/xedit/package.py | 2 +- .../builtin/packages/xerces-c/package.py | 6 +- .../repos/builtin/packages/xev/package.py | 2 +- .../builtin/packages/xextproto/package.py | 2 +- .../repos/builtin/packages/xeyes/package.py | 2 +- .../packages/xf86bigfontproto/package.py | 2 +- .../repos/builtin/packages/xf86dga/package.py | 2 +- .../builtin/packages/xf86dgaproto/package.py | 2 +- .../builtin/packages/xf86driproto/package.py | 2 +- .../builtin/packages/xf86miscproto/package.py | 2 +- .../builtin/packages/xf86rushproto/package.py | 2 +- .../packages/xf86vidmodeproto/package.py | 2 +- .../repos/builtin/packages/xfd/package.py | 4 +- .../builtin/packages/xfindproxy/package.py | 2 +- .../builtin/packages/xfontsel/package.py | 2 +- .../repos/builtin/packages/xfs/package.py | 2 +- .../repos/builtin/packages/xfsinfo/package.py | 2 +- .../repos/builtin/packages/xfwp/package.py | 2 +- .../repos/builtin/packages/xgamma/package.py | 2 +- .../repos/builtin/packages/xgc/package.py | 2 +- .../repos/builtin/packages/xhost/package.py | 2 +- .../builtin/packages/xineramaproto/package.py | 2 +- .../repos/builtin/packages/xinit/package.py | 2 +- .../repos/builtin/packages/xinput/package.py | 2 +- .../repos/builtin/packages/xkbcomp/package.py | 2 +- .../repos/builtin/packages/xkbdata/package.py | 2 +- .../repos/builtin/packages/xkbevd/package.py | 2 +- .../builtin/packages/xkbprint/package.py | 2 +- .../builtin/packages/xkbutils/package.py | 2 +- .../packages/xkeyboard-config/package.py | 2 +- .../repos/builtin/packages/xkill/package.py | 2 +- .../repos/builtin/packages/xload/package.py | 2 +- .../repos/builtin/packages/xlogo/package.py | 2 +- .../builtin/packages/xlsatoms/package.py | 2 +- .../builtin/packages/xlsclients/package.py | 2 +- .../builtin/packages/xlsfonts/package.py | 2 +- .../repos/builtin/packages/xmag/package.py | 2 +- .../repos/builtin/packages/xman/package.py | 2 +- .../builtin/packages/xmessage/package.py | 2 +- .../repos/builtin/packages/xmh/package.py | 2 +- .../repos/builtin/packages/xmlf90/package.py | 2 +- .../repos/builtin/packages/xmlto/package.py | 2 +- .../repos/builtin/packages/xmodmap/package.py | 2 +- .../repos/builtin/packages/xmore/package.py | 2 +- .../builtin/packages/xorg-cf-files/package.py | 2 +- .../builtin/packages/xorg-docs/package.py | 2 +- .../builtin/packages/xorg-gtest/package.py | 2 +- .../builtin/packages/xorg-server/package.py | 2 +- .../packages/xorg-sgml-doctools/package.py | 2 +- .../builtin/packages/xphelloworld/package.py | 2 +- .../builtin/packages/xplsprinters/package.py | 2 +- .../repos/builtin/packages/xpr/package.py | 2 +- .../packages/xprehashprinterlist/package.py | 2 +- .../repos/builtin/packages/xprop/package.py | 2 +- .../repos/builtin/packages/xproto/package.py | 4 +- .../xproxymanagementprotocol/package.py | 2 +- .../repos/builtin/packages/xqilla/package.py | 2 +- .../repos/builtin/packages/xrandr/package.py | 2 +- .../repos/builtin/packages/xrdb/package.py | 2 +- .../builtin/packages/xrefresh/package.py | 2 +- .../repos/builtin/packages/xrootd/package.py | 24 +- .../repos/builtin/packages/xrx/package.py | 2 +- .../repos/builtin/packages/xsbench/package.py | 4 +- .../repos/builtin/packages/xscope/package.py | 2 +- .../repos/builtin/packages/xsd/package.py | 2 +- .../builtin/packages/xsdktrilinos/package.py | 4 +- .../repos/builtin/packages/xset/package.py | 2 +- .../builtin/packages/xsetmode/package.py | 2 +- .../builtin/packages/xsetpointer/package.py | 2 +- .../builtin/packages/xsetroot/package.py | 2 +- .../repos/builtin/packages/xsimd/package.py | 4 +- .../repos/builtin/packages/xsm/package.py | 2 +- .../repos/builtin/packages/xssp/package.py | 20 +- .../builtin/packages/xstdcmap/package.py | 2 +- .../packages/xtensor-python/package.py | 2 +- .../repos/builtin/packages/xtensor/package.py | 4 +- .../repos/builtin/packages/xterm/package.py | 2 +- .../repos/builtin/packages/xtl/package.py | 6 +- .../repos/builtin/packages/xtrans/package.py | 2 +- .../repos/builtin/packages/xtrap/package.py | 2 +- .../repos/builtin/packages/xts/package.py | 2 +- .../builtin/packages/xvidtune/package.py | 2 +- .../repos/builtin/packages/xvinfo/package.py | 2 +- .../repos/builtin/packages/xwd/package.py | 2 +- .../builtin/packages/xwininfo/package.py | 2 +- .../repos/builtin/packages/xwud/package.py | 2 +- .../repos/builtin/packages/xxhash/package.py | 16 +- .../repos/builtin/packages/xz/package.py | 8 +- .../repos/builtin/packages/yajl/package.py | 2 +- .../repos/builtin/packages/yambo/package.py | 6 +- .../builtin/packages/yaml-cpp/package.py | 4 +- .../repos/builtin/packages/yasm/package.py | 2 +- .../repos/builtin/packages/z3/package.py | 6 +- .../repos/builtin/packages/zeromq/package.py | 16 +- .../repos/builtin/packages/zip/package.py | 2 +- .../repos/builtin/packages/zlib/package.py | 6 +- .../repos/builtin/packages/zoltan/package.py | 8 +- .../repos/builtin/packages/zstd/package.py | 4 +- 2344 files changed, 5728 insertions(+), 5754 deletions(-) mode change 100755 => 100644 var/spack/repos/builtin/packages/minisign/package.py mode change 100755 => 100644 var/spack/repos/builtin/packages/poppler/package.py mode change 100755 => 100644 var/spack/repos/builtin/packages/signify/package.py mode change 100755 => 100644 var/spack/repos/builtin/packages/texstudio/package.py diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py index 70df84c709d..98953214a77 100644 --- a/var/spack/repos/builtin/packages/abinit/package.py +++ b/var/spack/repos/builtin/packages/abinit/package.py @@ -30,12 +30,12 @@ class Abinit(AutotoolsPackage): homepage = 'http://www.abinit.org' url = 'https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz' - version('8.10.3', '969303cf21526cef2a6a08118a3d30ae') - version('8.8.2', '72d7046c7ff31b9f17afe050ecdfb3a5') - version('8.6.3', '6c34d2cec0cf0008dd25b8ec1b6d3ee8') - version('8.2.2', '5f25250e06fdc0815c224ffd29858860') + version('8.10.3', sha256='ed626424b4472b93256622fbb9c7645fa3ffb693d4b444b07d488771ea7eaa75') + version('8.8.2', sha256='15216703bd56a799a249a112b336d07d733627d3756487a4b1cb48ebb625c3e7') + version('8.6.3', sha256='82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65') + version('8.2.2', sha256='e43544a178d758b0deff3011c51ef7c957d7f2df2ce8543366d68016af9f3ea1') # Versions before 8.0.8b are not supported. - version('8.0.8b', 'abc9e303bfa7f9f43f95598f87d84d5d') + version('8.0.8b', sha256='37ad5f0f215d2a36e596383cb6e54de3313842a0390ce8d6b48a423d3ee25af2') variant('mpi', default=True, description='Builds with MPI support. Requires MPI2+') diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py index cd9ed984763..361d3e96c7c 100644 --- a/var/spack/repos/builtin/packages/abyss/package.py +++ b/var/spack/repos/builtin/packages/abyss/package.py @@ -15,8 +15,8 @@ class Abyss(AutotoolsPackage): url = "https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz" version('2.1.4', sha256='2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc') - version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798') - version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c') + version('2.0.2', sha256='d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df') + version('1.5.2', sha256='8a52387f963afb7b63db4c9b81c053ed83956ea0a3981edcad554a895adf84b1') variant('maxk', values=int, default=0, description='''set the maximum k-mer length. diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py index 03875384087..efbe029b32f 100644 --- a/var/spack/repos/builtin/packages/ack/package.py +++ b/var/spack/repos/builtin/packages/ack/package.py @@ -16,10 +16,10 @@ class Ack(Package): homepage = "http://beyondgrep.com/" url = "http://beyondgrep.com/ack-2.14-single-file" - version('2.22', 'eea9d4daef7c262751f15ca9b3b70317', expand=False) - version('2.18', 'e8ebfd7a7ec8476bffd4686bf7b14fd7', expand=False) - version('2.16', '7085b5a5c76fda43ff049410870c8535', expand=False) - version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False) + version('2.22', sha256='fd0617585b88517a3d41d3d206c1dc38058c57b90dfd88c278049a41aeb5be38', expand=False) + version('2.18', sha256='6e41057c8f50f661d800099471f769209480efa53b8a886969d7ec6db60a2208', expand=False) + version('2.16', sha256='7f39f08ebb78ed160a41293d7f42ff1bdcdaf57aee859bc4c4888bdf4abee7f2', expand=False) + version('2.14', sha256='1d203cfbc52ce8f49e3992be1cd3e4d7d5dfb7daa3739e8628aa9858ccc5b9df', expand=False) depends_on('perl') diff --git a/var/spack/repos/builtin/packages/activeharmony/package.py b/var/spack/repos/builtin/packages/activeharmony/package.py index b1764fb30d4..f53ed791b66 100644 --- a/var/spack/repos/builtin/packages/activeharmony/package.py +++ b/var/spack/repos/builtin/packages/activeharmony/package.py @@ -12,7 +12,7 @@ class Activeharmony(Package): homepage = "http://www.dyninst.org/harmony" url = "http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.5.tar.gz" - version('4.5', 'caee5b864716d376e2c25d739251b2a9') + version('4.5', sha256='31d9990c8dd36724d336707d260aa4d976e11eaa899c4c7cc11f80a56cdac684') def install(self, spec, prefix): make("CFLAGS=-O3") diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py index 114d7bf225d..b5f03b3c9fb 100644 --- a/var/spack/repos/builtin/packages/adept-utils/package.py +++ b/var/spack/repos/builtin/packages/adept-utils/package.py @@ -12,8 +12,8 @@ class AdeptUtils(CMakePackage): homepage = "https://github.com/llnl/adept-utils" url = "https://github.com/llnl/adept-utils/archive/v1.0.tar.gz" - version('1.0.1', '731a310717adcb004d9d195130efee7d') - version('1.0', '5c6cd9badce56c945ac8551e34804397') + version('1.0.1', sha256='259f777aeb368ede3583d3617bb779f0fde778319bf2122fdd216bdf223c015e') + version('1.0', sha256='fed29366c9bcf5f3799220ae3b351d2cb338e2aa42133d61584ea650aa8d6ff7') depends_on('boost') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index ac9ab764682..4b8e417a11b 100644 --- a/var/spack/repos/builtin/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -20,13 +20,13 @@ class Adios(AutotoolsPackage): maintainers = ['ax3l'] version('develop', branch='master') - version('1.13.1', '958aed11240d7f5a065ab5ee271ecb44') - version('1.13.0', '68af36b821debbdf4748b20320a990ce') - version('1.12.0', '84a1c71b6698009224f6f748c5257fc9') - version('1.11.1', '5639bfc235e50bf17ba9dafb14ea4185') - version('1.11.0', '5eead5b2ccf962f5e6d5f254d29d5238') - version('1.10.0', 'eff450a4c0130479417cfd63186957f3') - version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678') + version('1.13.1', sha256='b1c6949918f5e69f701cabfe5987c0b286793f1057d4690f04747852544e157b') + version('1.13.0', sha256='7b5ee8ff7a5f7215f157c484b20adb277ec0250f87510513edcc25d2c4739f50') + version('1.12.0', sha256='22bc22c157322abec2d1a0817a259efd9057f88c2113e67d918a9a5ebcb3d88d') + version('1.11.1', sha256='9f5c10b9471a721ba57d1cf6e5a55a7ad139a6c12da87b4dc128539e9eef370e') + version('1.11.0', sha256='e89d14ccbe7181777225e0ba6c272c0941539b8ccd440e72ed5a9457441dae83') + version('1.10.0', sha256='6713069259ee7bfd4d03f47640bf841874e9114bab24e7b0c58e310c42a0ec48') + version('1.9.0', sha256='23b2bb70540d51ab0855af0b205ca484fd1bd963c39580c29e3133f9e6fffd46') variant('shared', default=True, description='Builds a shared version of the library') diff --git a/var/spack/repos/builtin/packages/adlbx/package.py b/var/spack/repos/builtin/packages/adlbx/package.py index 3df61b2a1c5..6abab59d801 100644 --- a/var/spack/repos/builtin/packages/adlbx/package.py +++ b/var/spack/repos/builtin/packages/adlbx/package.py @@ -15,9 +15,9 @@ class Adlbx(AutotoolsPackage): git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') - version('0.9.2', 'a7d9e208eb3b49b8bb857562f6bb61bb') - version('0.9.1', '07151ddef5fb83d8f4b40700013d9daf') - version('0.8.0', '34ade59ce3be5bc296955231d47a27dd') + version('0.9.2', sha256='524902d648001b689a98492402d754a607b8c1d0734699154063c1a4f3410d4a') + version('0.9.1', sha256='8913493fe0c097ff13c721ab057514e5bdb55f6318d4e3512692ab739c3190b3') + version('0.8.0', md5='34ade59ce3be5bc296955231d47a27dd') depends_on('exmcutils@master', when='@master') depends_on('exmcutils@:0.5.3', when='@:0.8.0') diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py index 857f2e9ca54..cb83d4d68d1 100644 --- a/var/spack/repos/builtin/packages/adol-c/package.py +++ b/var/spack/repos/builtin/packages/adol-c/package.py @@ -16,10 +16,10 @@ class AdolC(AutotoolsPackage): git = "https://gitlab.com/adol-c/adol-c.git" version('develop', branch='master') - version('2.6.3', 'f78f67f70d5874830a1ad1c0f54e54f7') - version('2.6.2', '0f9547584c99c0673e4f81cf64e8d865') - version('2.6.1', '1032b28427d6e399af4610e78c0f087b') - version('2.5.2', '96f81b80e93cca57398066ea4afe28f0') + version('2.6.3', sha256='6ed74580695a0d2c960581e5430ebfcd380eb5da9337daf488bf2e89039e9c21') + version('2.6.2', sha256='f6326e7ba994d02074816132d4461915221069267c31862b31fab7020965c658') + version('2.6.1', sha256='037089e0f64224e5e6255b61af4fe7faac080533fd778b76fe946e52491918b5') + version('2.5.2', sha256='2fa514d9799989d6379738c2bcf75070d9834e4d227eb32a5b278840893b2af9') variant('advanced_branching', default=False, description='Enable advanced branching to reduce retaping') diff --git a/var/spack/repos/builtin/packages/aegean/package.py b/var/spack/repos/builtin/packages/aegean/package.py index c7bf40d171f..9c5778b8512 100644 --- a/var/spack/repos/builtin/packages/aegean/package.py +++ b/var/spack/repos/builtin/packages/aegean/package.py @@ -15,7 +15,7 @@ class Aegean(MakefilePackage): homepage = "http://brendelgroup.github.io/AEGeAn/" url = "https://github.com/BrendelGroup/AEGeAn/archive/v0.15.2.tar.gz" - version('0.15.2', 'd7d73f5f132ff52340975b636564e949') + version('0.15.2', sha256='734c9dd23ab3415c3966083bfde5fb72c81e6ace84e08ee3fe0d4c338331d975') depends_on('genometools') diff --git a/var/spack/repos/builtin/packages/albert/package.py b/var/spack/repos/builtin/packages/albert/package.py index 0bce5632005..1d94483f4f5 100644 --- a/var/spack/repos/builtin/packages/albert/package.py +++ b/var/spack/repos/builtin/packages/albert/package.py @@ -13,7 +13,7 @@ class Albert(MakefilePackage): homepage = "https://people.cs.clemson.edu/~dpj/albertstuff/albert.html" url = "https://github.com/kentavv/Albert/archive/v4.0a_opt4.tar.gz" - version('4.0a_opt4', '79e3d9623602f2ca5db7d84c81d4eb8c') + version('4.0a_opt4', sha256='80b9ee774789c9cd123072523cfb693c443c3624708a58a5af177a51f36b2c79') depends_on('readline') diff --git a/var/spack/repos/builtin/packages/alglib/package.py b/var/spack/repos/builtin/packages/alglib/package.py index 7394a8b6964..30a1c0b2c40 100644 --- a/var/spack/repos/builtin/packages/alglib/package.py +++ b/var/spack/repos/builtin/packages/alglib/package.py @@ -16,7 +16,7 @@ class Alglib(MakefilePackage): homepage = "http://www.alglib.net" url = "http://www.alglib.net/translator/re/alglib-3.11.0.cpp.gpl.tgz" - version('3.11.0', 'f87bb05349924d486e8809590dee9f80') + version('3.11.0', sha256='34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0') def url_for_version(self, version): return 'http://www.alglib.net/translator/re/alglib-{0}.cpp.gpl.tgz'.format(version.dotted) diff --git a/var/spack/repos/builtin/packages/allpaths-lg/package.py b/var/spack/repos/builtin/packages/allpaths-lg/package.py index adf63d42dc8..c8d580d08e6 100644 --- a/var/spack/repos/builtin/packages/allpaths-lg/package.py +++ b/var/spack/repos/builtin/packages/allpaths-lg/package.py @@ -13,7 +13,7 @@ class AllpathsLg(AutotoolsPackage): homepage = "http://www.broadinstitute.org/software/allpaths-lg/blog/" url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz" - version('52488', 'bde9008e236d87708a48eb83af6d6d5b') + version('52488', sha256='035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542') # compiles with gcc 4.7.0 to 4.9.4) conflicts('%gcc@:4.6.4,5.1.0:') diff --git a/var/spack/repos/builtin/packages/alsa-lib/package.py b/var/spack/repos/builtin/packages/alsa-lib/package.py index a1775b3a306..b79bcd3d7ca 100644 --- a/var/spack/repos/builtin/packages/alsa-lib/package.py +++ b/var/spack/repos/builtin/packages/alsa-lib/package.py @@ -14,4 +14,4 @@ class AlsaLib(AutotoolsPackage): homepage = "https://www.alsa-project.org" url = "ftp://ftp.alsa-project.org/pub/lib/alsa-lib-1.1.4.1.tar.bz2" - version('1.1.4.1', '29fa3e69122d3cf3e8f0e01a0cb1d183') + version('1.1.4.1', sha256='91bb870c14d1c7c269213285eeed874fa3d28112077db061a3af8010d0885b76') diff --git a/var/spack/repos/builtin/packages/amg2013/package.py b/var/spack/repos/builtin/packages/amg2013/package.py index 24b378738a1..5954bb615f3 100644 --- a/var/spack/repos/builtin/packages/amg2013/package.py +++ b/var/spack/repos/builtin/packages/amg2013/package.py @@ -17,7 +17,7 @@ class Amg2013(MakefilePackage): homepage = "https://computing.llnl.gov/projects/co-design/amg2013" url = "https://computing.llnl.gov/projects/co-design/download/amg2013.tgz" - version('master', '9d918d2a69528b83e6e0aba6ba601fef', + version('master', sha256='b03771d84a04e3dbbbe32ba5648cd7b789e5853b938dd501e17d23d43f13c50f', url='https://computing.llnl.gov/projects/co-design/download/amg2013.tgz') variant('openmp', default=True, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/aml/package.py b/var/spack/repos/builtin/packages/aml/package.py index 8b3ebdb3aab..41cd9085e5e 100644 --- a/var/spack/repos/builtin/packages/aml/package.py +++ b/var/spack/repos/builtin/packages/aml/package.py @@ -11,7 +11,7 @@ class Aml(AutotoolsPackage): homepage = "https://xgitlab.cels.anl.gov/argo/aml" url = "https://www.mcs.anl.gov/research/projects/argo/downloads/aml-0.1.0.tar.gz" - version('0.1.0', 'f704397fe568bcb334ee0cbc4f9e066e') + version('0.1.0', sha256='cc89a8768693f1f11539378b21cdca9f0ce3fc5cb564f9b3e4154a051dcea69b') depends_on('numactl') diff --git a/var/spack/repos/builtin/packages/ampliconnoise/package.py b/var/spack/repos/builtin/packages/ampliconnoise/package.py index 481e81db57e..381871bd69c 100644 --- a/var/spack/repos/builtin/packages/ampliconnoise/package.py +++ b/var/spack/repos/builtin/packages/ampliconnoise/package.py @@ -13,7 +13,7 @@ class Ampliconnoise(MakefilePackage): homepage = "https://code.google.com/archive/p/ampliconnoise/" url = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/ampliconnoise/AmpliconNoiseV1.29.tar.gz" - version('1.29', 'd6723e6f9cc71d7eb6f1a65ba4643aac') + version('1.29', sha256='0bf946806d77ecaf0994ad8ebf9a5e98ad33c809f6def5c9340a16c367918167') depends_on('mpi@2:') depends_on('gsl') diff --git a/var/spack/repos/builtin/packages/andi/package.py b/var/spack/repos/builtin/packages/andi/package.py index 96e47b67d5d..c01c48f7f9f 100644 --- a/var/spack/repos/builtin/packages/andi/package.py +++ b/var/spack/repos/builtin/packages/andi/package.py @@ -13,7 +13,7 @@ class Andi(AutotoolsPackage): homepage = "https://github.com/EvolBioInf/andi" url = "https://github.com/EvolBioInf/andi/archive/v0.10.tar.gz" - version('0.10', '3aaba7961798bb4aaa546baa44e469d8') + version('0.10', sha256='1ff371de0b6db4080e402ded2687947dc2d6913e28626edec21dcf5149489ee8') depends_on('m4', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/angsd/package.py b/var/spack/repos/builtin/packages/angsd/package.py index d5b7358def2..7959f2b20cb 100644 --- a/var/spack/repos/builtin/packages/angsd/package.py +++ b/var/spack/repos/builtin/packages/angsd/package.py @@ -16,8 +16,8 @@ class Angsd(MakefilePackage): homepage = "https://github.com/ANGSD/angsd" url = "https://github.com/ANGSD/angsd/archive/0.919.tar.gz" - version('0.921', '3702db035396db602c7f74728b1a5a1f') - version('0.919', '79d342f49c24ac00d35934f2617048d4') + version('0.921', sha256='8892d279ce1804f9e17fe2fc65a47e5498e78fc1c1cb84d2ca2527fd5c198772') + version('0.919', sha256='c2ea718ca5a5427109f4c3415e963dcb4da9afa1b856034e25c59c003d21822a') depends_on('htslib') conflicts('^htslib@1.6:', when='@0.919') diff --git a/var/spack/repos/builtin/packages/ant/package.py b/var/spack/repos/builtin/packages/ant/package.py index d70533c9f06..68c5047d1d8 100644 --- a/var/spack/repos/builtin/packages/ant/package.py +++ b/var/spack/repos/builtin/packages/ant/package.py @@ -15,11 +15,11 @@ class Ant(Package): homepage = "http://ant.apache.org/" url = "https://archive.apache.org/dist/ant/source/apache-ant-1.9.7-src.tar.gz" - version('1.10.0', '2260301bb7734e34d8b96f1a5fd7979c') - version('1.9.9', '22c9d40dabafbec348aaada226581239') - version('1.9.8', '16253d516d5c33c4af9ef8fafcf1004b') - version('1.9.7', 'a2fd9458c76700b7be51ef12f07d4bb1') - version('1.9.6', '29b7507c9053e301d2b85091f2aec6f0') + version('1.10.0', sha256='1f78036c38753880e16fb755516c8070187a78fe4b2e99b59eda5b81b58eccaf') + version('1.9.9', sha256='d6a0c93777ab27db36212d77c5733ac80d17fe24e83f947df23a8e0ad4ac48cc') + version('1.9.8', sha256='5f4daf56e66fc7a71de772920ca27c15eac80cf1fcf41f3b4f2d535724942681') + version('1.9.7', sha256='648b3f3787bb0cb6226978b6d4898eb7e21ae391385357a5f824972dd910a1c8') + version('1.9.6', sha256='550d2aaf828785e30870c227056942c2a552da961db6010cedb2fbcfa8e3268d') depends_on('java') diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py index 984a0c6944f..0cb10751a90 100644 --- a/var/spack/repos/builtin/packages/antlr/package.py +++ b/var/spack/repos/builtin/packages/antlr/package.py @@ -16,7 +16,7 @@ class Antlr(AutotoolsPackage): homepage = "http://www.antlr2.org/" url = "http://www.antlr2.org/download/antlr-2.7.7.tar.gz" - version('2.7.7', '01cc9a2a454dd33dcd8c856ec89af090') + version('2.7.7', sha256='853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9') # Fixes build with recent versions of GCC patch('gcc.patch') diff --git a/var/spack/repos/builtin/packages/ants/package.py b/var/spack/repos/builtin/packages/ants/package.py index 870ade0037c..903be43a485 100644 --- a/var/spack/repos/builtin/packages/ants/package.py +++ b/var/spack/repos/builtin/packages/ants/package.py @@ -18,7 +18,7 @@ class Ants(CMakePackage): homepage = "http://stnava.github.io/ANTs/" url = "https://github.com/ANTsX/ANTs/archive/v2.2.0.tar.gz" - version('2.2.0', '5661b949268100ac0f7baf6d2702b4dd') + version('2.2.0', sha256='62f8f9ae141cb45025f4bb59277c053acf658d4a3ba868c9e0f609af72e66b4a') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py index f15c3b7f309..09c69e1dcb5 100644 --- a/var/spack/repos/builtin/packages/apex/package.py +++ b/var/spack/repos/builtin/packages/apex/package.py @@ -12,7 +12,7 @@ class Apex(CMakePackage): homepage = "http://github.com/khuck/xpress-apex" url = "http://github.com/khuck/xpress-apex/archive/v0.1.tar.gz" - version('0.1', 'e224a0b9033e23a9697ce2a3c307a0a3') + version('0.1', sha256='bb0be37f8f8133fe492998515bcf66a4df452c28a995d317228fbed9b18e6a92') depends_on("binutils+libiberty") depends_on("boost@1.54:") diff --git a/var/spack/repos/builtin/packages/applewmproto/package.py b/var/spack/repos/builtin/packages/applewmproto/package.py index e02e44b4bca..171ced2bf5c 100644 --- a/var/spack/repos/builtin/packages/applewmproto/package.py +++ b/var/spack/repos/builtin/packages/applewmproto/package.py @@ -16,7 +16,7 @@ class Applewmproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/applewmproto" url = "https://www.x.org/archive/individual/proto/applewmproto-1.4.2.tar.gz" - version('1.4.2', 'ecc8a4424a893ce120f5652dba62e9e6') + version('1.4.2', sha256='ff8ac07d263a23357af2d6ff0cca3c1d56b043ddf7797a5a92ec624f4704df2e') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/appres/package.py b/var/spack/repos/builtin/packages/appres/package.py index 45a347684e5..cb53cdf7d84 100644 --- a/var/spack/repos/builtin/packages/appres/package.py +++ b/var/spack/repos/builtin/packages/appres/package.py @@ -15,7 +15,7 @@ class Appres(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/appres" url = "https://www.x.org/archive/individual/app/appres-1.0.4.tar.gz" - version('1.0.4', 'f82aabe6bbb8960781b63c6945bb361b') + version('1.0.4', sha256='22cb6f639c891ffdbb5371bc50a88278185789eae6907d05e9e0bd1086a80803') depends_on('libx11') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py index 465ac894025..bebce244fa3 100644 --- a/var/spack/repos/builtin/packages/apr-util/package.py +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -12,8 +12,8 @@ class AprUtil(AutotoolsPackage): homepage = 'https://apr.apache.org/' url = 'http://archive.apache.org/dist/apr/apr-util-1.6.0.tar.gz' - version('1.6.0', '3b03dbff60728a4f4c33f5d929e8b35a') - version('1.5.4', '866825c04da827c6e5f53daff5569f42') + version('1.6.0', sha256='483ef4d59e6ac9a36c7d3fd87ad7b9db7ad8ae29c06b9dd8ff22dda1cc416389') + version('1.5.4', sha256='976a12a59bc286d634a21d7be0841cc74289ea9077aa1af46be19d1a6e844c19') variant('crypto', default=True, description='Enable crypto support') variant('gdbm', default=False, description='Enable GDBM support') diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py index c337d76ba60..9efefa1002f 100644 --- a/var/spack/repos/builtin/packages/apr/package.py +++ b/var/spack/repos/builtin/packages/apr/package.py @@ -12,5 +12,5 @@ class Apr(AutotoolsPackage): homepage = 'https://apr.apache.org/' url = 'http://archive.apache.org/dist/apr/apr-1.6.2.tar.gz' - version('1.6.2', '8672e78514e3fcef2643127c524bf0f9') - version('1.5.2', '98492e965963f852ab29f9e61b2ad700') + version('1.6.2', sha256='4fc24506c968c5faf57614f5d0aebe0e9d0b90afa47a883e1a1ca94f15f4a42e') + version('1.5.2', sha256='1af06e1720a58851d90694a984af18355b65bb0d047be03ec7d659c746d6dbdb') diff --git a/var/spack/repos/builtin/packages/aragorn/package.py b/var/spack/repos/builtin/packages/aragorn/package.py index 285efe9ec7c..1befdaf866b 100644 --- a/var/spack/repos/builtin/packages/aragorn/package.py +++ b/var/spack/repos/builtin/packages/aragorn/package.py @@ -13,8 +13,8 @@ class Aragorn(Package): homepage = "http://mbio-serv2.mbioekol.lu.se/ARAGORN" url = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz" - version('1.2.38', '1df0ed600069e6f520e5cd989de1eaf0') - version('1.2.36', 'ab06032589e45aa002f8616333568e9ab11034b3a675f922421e5f1c3e95e7b5') + version('1.2.38', sha256='4b84e3397755fb22cc931c0e7b9d50eaba2a680df854d7a35db46a13cecb2126') + version('1.2.36', sha256='ab06032589e45aa002f8616333568e9ab11034b3a675f922421e5f1c3e95e7b5') phases = ['build', 'install'] diff --git a/var/spack/repos/builtin/packages/argobots/package.py b/var/spack/repos/builtin/packages/argobots/package.py index 7ceca52c706..80950bf3f14 100644 --- a/var/spack/repos/builtin/packages/argobots/package.py +++ b/var/spack/repos/builtin/packages/argobots/package.py @@ -20,9 +20,9 @@ class Argobots(AutotoolsPackage): git = "https://github.com/pmodels/argobots.git" version("develop", branch="master") - version("1.0rc1", "729c018f3353976cb79c07ecaa13319d") - version("1.0b1", "5eeab7b2c639d08bbea22db3026cdf39") - version("1.0a1", "9d29d57d14d718f93b505178f6ba3e08") + version("1.0rc1", sha256="2dc4487556dce602655a6535f501136f0edc3575708029c80b1af6dccd069ce7") + version("1.0b1", sha256="480b85b0e8db288400088a57c2dc5639f556843b06b0492841920c38348a2a3e") + version("1.0a1", sha256="bef93e06026ddeba8809474923176803e64d08e1425672cd7c5b424c797d5d9d") variant("valgrind", default=False, description="Enable Valgrind") diff --git a/var/spack/repos/builtin/packages/argp-standalone/package.py b/var/spack/repos/builtin/packages/argp-standalone/package.py index 7fa5d76bbf0..fe75693bd38 100644 --- a/var/spack/repos/builtin/packages/argp-standalone/package.py +++ b/var/spack/repos/builtin/packages/argp-standalone/package.py @@ -14,7 +14,7 @@ class ArgpStandalone(AutotoolsPackage): homepage = "https://www.lysator.liu.se/~nisse/misc" url = "https://www.lysator.liu.se/~nisse/misc/argp-standalone-1.3.tar.gz" - version('1.3', '720704bac078d067111b32444e24ba69') + version('1.3', sha256='dec79694da1319acd2238ce95df57f3680fea2482096e483323fddf3d818d8be') # Homebrew (https://github.com/Homebrew/homebrew-core) patches # argp-standalone to work on Darwin; the patchfile below was taken diff --git a/var/spack/repos/builtin/packages/argtable/package.py b/var/spack/repos/builtin/packages/argtable/package.py index fe4b0066def..d78f5fcef1c 100644 --- a/var/spack/repos/builtin/packages/argtable/package.py +++ b/var/spack/repos/builtin/packages/argtable/package.py @@ -14,4 +14,4 @@ class Argtable(AutotoolsPackage): homepage = "http://argtable.sourceforge.net/" url = "https://sourceforge.net/projects/argtable/files/argtable/argtable-2.13/argtable2-13.tar.gz/download" - version('2-13', '156773989d0d6406cea36526d3926668') + version('2-13', sha256='8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf') diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index ba789c8f177..7709bcd3201 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -14,13 +14,13 @@ class Armadillo(CMakePackage): homepage = "http://arma.sourceforge.net/" url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" - version('8.100.1', 'd9762d6f097e0451d0cfadfbda295e7c') - version('7.950.1', 'c06eb38b12cae49cab0ce05f96147147') + version('8.100.1', sha256='54773f7d828bd3885c598f90122b530ded65d9b195c9034e082baea737cd138d') + version('7.950.1', sha256='a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b') # NOTE: v7.900.1 download url seems broken is no v7.950.1? - version('7.900.1', '5ef71763bd429a3d481499878351f3be') - version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d') - version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2') - version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e') + version('7.900.1', md5='5ef71763bd429a3d481499878351f3be') + version('7.500.0', md5='7d316fdf3c3c7ea92b64704180ae315d') + version('7.200.2', md5='b21585372d67a8876117fd515d8cf0a2') + version('7.200.1', md5='ed86d6df0058979e107502e1fe3e469e') variant('hdf5', default=False, description='Include HDF5 support') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 5bb2a64cffe..f7628cc5aec 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -42,10 +42,10 @@ class ArpackNg(Package): version('3.7.0', sha256='972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6') version('3.6.3', sha256='64f3551e5a2f8497399d82af3076b6a33bf1bc95fc46bbcabe66442db366f453') version('3.6.2', sha256='673c8202de996fd3127350725eb1818e534db4e79de56d5dcee8c00768db599a') - version('3.6.0', 'f2607c1d5f80e922d55751fbed86a8ec') - version('3.5.0', '9762c9ae6d739a9e040f8201b1578874') - version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4') - version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5') + version('3.6.0', sha256='3c88e74cc10bba81dc2c72c4f5fff38a800beebaa0b4c64d321c28c9203b37ea') + version('3.5.0', sha256='50f7a3e3aec2e08e732a487919262238f8504c3ef927246ec3495617dde81239') + version('3.4.0', sha256='69e9fa08bacb2475e636da05a6c222b17c67f1ebeab3793762062248dd9d842f') + version('3.3.0', sha256='ad59811e7d79d50b8ba19fd908f92a3683d883597b2c7759fdcc38f6311fe5b3') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/arrow/package.py b/var/spack/repos/builtin/packages/arrow/package.py index 6ef75ea3431..c3ce7da229a 100644 --- a/var/spack/repos/builtin/packages/arrow/package.py +++ b/var/spack/repos/builtin/packages/arrow/package.py @@ -15,10 +15,10 @@ class Arrow(CMakePackage): homepage = "http://arrow.apache.org" url = "https://github.com/apache/arrow/archive/apache-arrow-0.9.0.tar.gz" - version('0.12.1', 'aae68622edc3dcadaa16b2d25ae3f00290d5233100321993427b03bcf5b1dd3b') - version('0.11.0', '0ac629a7775d86108e403eb66d9f1a3d3bdd6b3a497a86228aa4e8143364b7cc') - version('0.9.0', 'ebbd36c362b9e1d398ca612f6d2531ec') - version('0.8.0', '56436f6f61ccc68686b7e0ea30bf4d09') + version('0.12.1', sha256='aae68622edc3dcadaa16b2d25ae3f00290d5233100321993427b03bcf5b1dd3b') + version('0.11.0', sha256='0ac629a7775d86108e403eb66d9f1a3d3bdd6b3a497a86228aa4e8143364b7cc') + version('0.9.0', sha256='65f89a3910b6df02ac71e4d4283db9b02c5b3f1e627346c7b6a5982ae994af91') + version('0.8.0', sha256='c61a60c298c30546fc0b418a35be66ef330fb81b06c49928acca7f1a34671d54') depends_on('boost@1.60:') depends_on('cmake@3.2.0:', type='build') diff --git a/var/spack/repos/builtin/packages/asciidoc/package.py b/var/spack/repos/builtin/packages/asciidoc/package.py index 276c121e496..e8f71a0b3f9 100644 --- a/var/spack/repos/builtin/packages/asciidoc/package.py +++ b/var/spack/repos/builtin/packages/asciidoc/package.py @@ -13,7 +13,7 @@ class Asciidoc(AutotoolsPackage): homepage = "http://asciidoc.org" url = "http://downloads.sourceforge.net/project/asciidoc/asciidoc/8.6.9/asciidoc-8.6.9.tar.gz" - version('8.6.9', 'c59018f105be8d022714b826b0be130a') + version('8.6.9', sha256='78db9d0567c8ab6570a6eff7ffdf84eadd91f2dfc0a92a2d0105d323cab4e1f0') depends_on('libxml2') depends_on('libxslt') diff --git a/var/spack/repos/builtin/packages/asciidoctor/package.py b/var/spack/repos/builtin/packages/asciidoctor/package.py index 5ea167d636c..951d833f1a9 100644 --- a/var/spack/repos/builtin/packages/asciidoctor/package.py +++ b/var/spack/repos/builtin/packages/asciidoctor/package.py @@ -12,7 +12,7 @@ class Asciidoctor(Package): homepage = "https://asciidoctor.org/" url = "https://rubygems.org/downloads/asciidoctor-1.5.8.gem" - version('1.5.8', '5f55200cab8d1cfcf561e66d3f477159', expand=False) + version('1.5.8', sha256='9deaa93eacadda48671e18395b992eafba35d08f25ddbe28d25bb275831a8d62', expand=False) extends('ruby') diff --git a/var/spack/repos/builtin/packages/aspcud/package.py b/var/spack/repos/builtin/packages/aspcud/package.py index 0a269bc51db..b209e4c6cc1 100644 --- a/var/spack/repos/builtin/packages/aspcud/package.py +++ b/var/spack/repos/builtin/packages/aspcud/package.py @@ -18,7 +18,7 @@ class Aspcud(CMakePackage): homepage = "https://potassco.org/aspcud" url = "https://github.com/potassco/aspcud/archive/v1.9.4.tar.gz" - version('1.9.4', '35e5c663a25912e4bdc94f168e827ed2') + version('1.9.4', sha256='3645f08b079e1cc80e24cd2d7ae5172a52476d84e3ec5e6a6c0034492a6ea885') depends_on('boost', type=('build')) depends_on('cmake', type=('build')) diff --git a/var/spack/repos/builtin/packages/aspell/package.py b/var/spack/repos/builtin/packages/aspell/package.py index 60ea89e6650..84a3f0ec719 100644 --- a/var/spack/repos/builtin/packages/aspell/package.py +++ b/var/spack/repos/builtin/packages/aspell/package.py @@ -16,7 +16,7 @@ class Aspell(AutotoolsPackage): extendable = True # support activating dictionaries - version('0.60.6.1', 'e66a9c9af6a60dc46134fdacf6ce97d7') + version('0.60.6.1', sha256='f52583a83a63633701c5f71db3dc40aab87b7f76b29723aeb27941eff42df6e1') patch('darwin.patch', when='platform=darwin') patch('issue-519.patch', when='@:0.60.6.1') diff --git a/var/spack/repos/builtin/packages/aspell6-de/package.py b/var/spack/repos/builtin/packages/aspell6-de/package.py index 081c6f236e1..d73a80c5c7f 100644 --- a/var/spack/repos/builtin/packages/aspell6-de/package.py +++ b/var/spack/repos/builtin/packages/aspell6-de/package.py @@ -12,4 +12,4 @@ class Aspell6De(AspellDictPackage): homepage = "http://aspell.net/" url = "https://ftpmirror.gnu.org/aspell/dict/de/aspell6-de-20030222-1.tar.bz2" - version('6-de-20030222-1', '5950c5c8a36fc93d4d7616591bace6a6') + version('6-de-20030222-1', sha256='ba6c94e11bc2e0e6e43ce0f7822c5bba5ca5ac77129ef90c190b33632416e906') diff --git a/var/spack/repos/builtin/packages/aspell6-en/package.py b/var/spack/repos/builtin/packages/aspell6-en/package.py index 1611e8c9f9e..5464c811418 100644 --- a/var/spack/repos/builtin/packages/aspell6-en/package.py +++ b/var/spack/repos/builtin/packages/aspell6-en/package.py @@ -12,4 +12,4 @@ class Aspell6En(AspellDictPackage): homepage = "http://aspell.net/" url = "https://ftpmirror.gnu.org/aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2" - version('2017.01.22-0', 'a6e002076574de9dc4915967032a1dab') + version('2017.01.22-0', sha256='93c73fae3eab5ea3ca6db3cea8770715a820f1b7d6ea2b932dd66a17f8fd55e1') diff --git a/var/spack/repos/builtin/packages/aspell6-es/package.py b/var/spack/repos/builtin/packages/aspell6-es/package.py index 0aa1148fd9c..cf6892c80cb 100644 --- a/var/spack/repos/builtin/packages/aspell6-es/package.py +++ b/var/spack/repos/builtin/packages/aspell6-es/package.py @@ -12,4 +12,4 @@ class Aspell6Es(AspellDictPackage): homepage = "http://aspell.net/" url = "https://ftpmirror.gnu.org/aspell/dict/es/aspell6-es-1.11-2.tar.bz2" - version('1.11-2', '8406336a89c64e47e96f4153d0af70c4') + version('1.11-2', sha256='ad367fa1e7069c72eb7ae37e4d39c30a44d32a6aa73cedccbd0d06a69018afcc') diff --git a/var/spack/repos/builtin/packages/aspera-cli/package.py b/var/spack/repos/builtin/packages/aspera-cli/package.py index f20b9f49e0b..f0a2debfa6e 100644 --- a/var/spack/repos/builtin/packages/aspera-cli/package.py +++ b/var/spack/repos/builtin/packages/aspera-cli/package.py @@ -13,7 +13,7 @@ class AsperaCli(Package): homepage = "https://asperasoft.com" url = "https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh" - version('3.7.7', 'e92140d809e7e65112a5d1cd49c442cf', + version('3.7.7', sha256='83efd03b699bdb1cac6c62befb3812342d6122217f4944f732ae7a135d578966', url='https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh', expand=False) diff --git a/var/spack/repos/builtin/packages/assimp/package.py b/var/spack/repos/builtin/packages/assimp/package.py index 60ea4a05936..610086a0bbb 100644 --- a/var/spack/repos/builtin/packages/assimp/package.py +++ b/var/spack/repos/builtin/packages/assimp/package.py @@ -13,7 +13,7 @@ class Assimp(CMakePackage): homepage = "https://www.assimp.org" url = "https://github.com/assimp/assimp/archive/v4.0.1.tar.gz" - version('4.0.1', '23a6301c728a413aafbfa1cca19ba91f') + version('4.0.1', sha256='60080d8ab4daaab309f65b3cffd99f19eb1af8d05623fff469b9b652818e286e') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/astral/package.py b/var/spack/repos/builtin/packages/astral/package.py index b04620db3be..f3a110a1bd3 100644 --- a/var/spack/repos/builtin/packages/astral/package.py +++ b/var/spack/repos/builtin/packages/astral/package.py @@ -16,7 +16,7 @@ class Astral(Package): version('5.6.1', sha256='b49a67c9fe19c0c92a89dc2f1a3928840e698a53054a595c61546ca98448a076', url='https://github.com/smirarab/ASTRAL/archive/untagged-697f19dbce69929ece09.tar.gz') - version('4.10.7', '38c81020570254e3f5c75d6c3c27fc6d') + version('4.10.7', sha256='314b49e0129ec06a7c78a1b60d590259ede6a5e75253407031e108d8048fcc79') depends_on('java', type=('build', 'run')) depends_on('zip', type='build') diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py index e1e668b2376..2d086a5eb59 100644 --- a/var/spack/repos/builtin/packages/astyle/package.py +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -17,11 +17,11 @@ class Astyle(MakefilePackage): # Gentoo alternative # url = "http://distfiles.gentoo.org/distfiles/astyle_3.0.1_linux.tar.gz" - version('3.1', '7712622f62661b1d8cb1062d7fedc390') - version('3.0.1', 'c301f09679efa2e1eb6e6b5fd33788b4') - version('2.06', 'ff588e7fcede824591cf5b9085df109d') - version('2.05.1', '4142d178047d7040da3e0e2f1b030a1a') - version('2.04', '30b1193a758b0909d06e7ee8dd9627f6') + version('3.1', sha256='cbcc4cf996294534bb56f025d6f199ebfde81aa4c271ccbd5ee1c1a3192745d7') + version('3.0.1', sha256='6c3ab029e0e4a75e2e603d449014374aa8269218fdd03a4aaa46ab743b1912fd') + version('2.06', sha256='3b7212210dc139e8f648e004b758c0be1b3ceb1694b22a879202d2b833db7c7e') + version('2.05.1', sha256='fbdfc6f1966a972d19a215927266c76d4183eee235ed1e2bd7ec551c2a270eac') + version('2.04', sha256='70b37f4853c418d1e2632612967eebf1bdb93dfbe558c51d7d013c9b4e116b60') parallel = False diff --git a/var/spack/repos/builtin/packages/at-spi2-atk/package.py b/var/spack/repos/builtin/packages/at-spi2-atk/package.py index b023dd75f4e..1e1fee8fe47 100644 --- a/var/spack/repos/builtin/packages/at-spi2-atk/package.py +++ b/var/spack/repos/builtin/packages/at-spi2-atk/package.py @@ -15,8 +15,8 @@ class AtSpi2Atk(MesonPackage): list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk" list_depth = 1 - version('2.26.2', '355c7916a69513490cb83ad34016b169') - version('2.26.1', 'eeec6cead3350dca48a235271c105b3e') + version('2.26.2', sha256='61891f0abae1689f6617a963105a3f1dcdab5970c4a36ded9c79a7a544b16a6e') + version('2.26.1', sha256='b4f0c27b61dbffba7a5b5ba2ff88c8cee10ff8dac774fa5b79ce906853623b75') depends_on('pkgconfig', type='build') depends_on('at-spi2-core@2.28.0:') diff --git a/var/spack/repos/builtin/packages/at-spi2-core/package.py b/var/spack/repos/builtin/packages/at-spi2-core/package.py index b63151f3db3..97d582b18db 100644 --- a/var/spack/repos/builtin/packages/at-spi2-core/package.py +++ b/var/spack/repos/builtin/packages/at-spi2-core/package.py @@ -16,7 +16,7 @@ class AtSpi2Core(MesonPackage): list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-core" list_depth = 1 - version('2.28.0', '9c42f79636ed1c0e908b7483d789b32e') + version('2.28.0', sha256='42a2487ab11ce43c288e73b2668ef8b1ab40a0e2b4f94e80fca04ad27b6f1c87') depends_on('glib@2.56.1:') depends_on('dbus@1.12.8:') diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py index b66d372a4d8..f3931e0cedd 100644 --- a/var/spack/repos/builtin/packages/atk/package.py +++ b/var/spack/repos/builtin/packages/atk/package.py @@ -18,9 +18,9 @@ class Atk(Package): list_depth = 1 version('2.30.0', sha256='dd4d90d4217f2a0c1fee708a555596c2c19d26fef0952e1ead1938ab632c027b') - version('2.28.1', 'dfb5e7474220afa3f4ca7e45af9f3a11') - version('2.20.0', '5187b0972f4d3905f285540b31395e20') - version('2.14.0', 'ecb7ca8469a5650581b1227d78051b8b') + version('2.28.1', sha256='cd3a1ea6ecc268a2497f0cd018e970860de24a6d42086919d6bf6c8e8d53f4fc') + version('2.20.0', sha256='493a50f6c4a025f588d380a551ec277e070b28a82e63ef8e3c06b3ee7c1238f0') + version('2.14.0', sha256='2875cc0b32bfb173c066c22a337f79793e0c99d2cc5e81c4dac0d5a523b8fbad') depends_on('meson@0.40.1:', type='build', when='@2.28:') depends_on('meson@0.46.0:', type='build', when='@2.29:') diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index 528f26ac82a..da539def1c4 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -20,18 +20,18 @@ class Atlas(Package): # Developer (unstable) version('3.11.41', sha256='477d567a8d683e891d786e9e8bb6ad6659daa9ba18e8dd0e2f70b7a54095f8de') - version('3.11.39', '5f3252fa980f5f060f93edd4669321e2') - version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825') + version('3.11.39', sha256='584bd44572746142bf19348139530c18f4538ce41d94330ff86ede38c36eddc9') + version('3.11.34', sha256='b6d42af3afd4fe54ef3a04a070fc7e75f6d8ac9f7d4886b636fe27ebfcbdf91f') # Stable - version('3.10.3', 'd6ce4f16c2ad301837cfb3dade2f7cef', preferred=True) - version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da') + version('3.10.3', sha256='2688eb733a6c5f78a18ef32144039adcd62fabce66f2eb51dd59dde806a6d2b7', preferred=True) + version('3.10.2', sha256='3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f') # not all packages (e.g. Trilinos@12.6.3) stopped using deprecated in 3.6.0 # Lapack routines. Stick with 3.5.0 until this is fixed. resource(name='lapack', url='http://www.netlib.org/lapack/lapack-3.5.0.tgz', - md5='b1d3e3e425b2e44a06760ff173104bdf', + sha256='9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', destination='spack-resource-lapack', when='@3:') diff --git a/var/spack/repos/builtin/packages/atom-dft/package.py b/var/spack/repos/builtin/packages/atom-dft/package.py index 0cb5b85a19f..89e63234eef 100644 --- a/var/spack/repos/builtin/packages/atom-dft/package.py +++ b/var/spack/repos/builtin/packages/atom-dft/package.py @@ -13,7 +13,7 @@ class AtomDft(MakefilePackage): homepage = "https://departments.icmab.es/leem/siesta/Pseudopotentials/" url = "https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/atom-4.2.6.tgz" - version('4.2.6', 'c0c80cf349f951601942ed6c7cb0256b') + version('4.2.6', sha256='489f0d883af35525647a8b8f691e7845c92fe6b5a25b13e1ed368edfd0391ed2') depends_on('libgridxc') depends_on('xmlf90') diff --git a/var/spack/repos/builtin/packages/atompaw/package.py b/var/spack/repos/builtin/packages/atompaw/package.py index 01572527fda..b5f5898b0fc 100644 --- a/var/spack/repos/builtin/packages/atompaw/package.py +++ b/var/spack/repos/builtin/packages/atompaw/package.py @@ -18,8 +18,8 @@ class Atompaw(Package): homepage = "http://users.wfu.edu/natalie/papers/pwpaw/man.html" url = "http://users.wfu.edu/natalie/papers/pwpaw/atompaw-4.0.0.13.tar.gz" - version('4.0.0.13', 'af4a042380356f6780183c4b325aad1d') - version('3.1.0.3', 'c996a277e11707887177f47bbb229aa6') + version('4.0.0.13', sha256='cbd73f11f3e9cc3ff2e5f3ec87498aeaf439555903d0b95a72f3b0a021902020') + version('3.1.0.3', sha256='15fe9a0369bdcc366370a0ecaa67e803ae54534b479ad63c4c7494a04fa3ea78') depends_on("lapack") depends_on("blas") diff --git a/var/spack/repos/builtin/packages/atop/package.py b/var/spack/repos/builtin/packages/atop/package.py index 505e8f00937..f7c253b2981 100644 --- a/var/spack/repos/builtin/packages/atop/package.py +++ b/var/spack/repos/builtin/packages/atop/package.py @@ -11,7 +11,7 @@ class Atop(Package): homepage = "http://www.atoptool.nl/index.php" url = "http://www.atoptool.nl/download/atop-2.2-3.tar.gz" - version('2.2-3', '034dc1544f2ec4e4d2c739d320dc326d') + version('2.2-3', sha256='c785b8a2355be28b3de6b58a8ea4c4fcab8fadeaa57a99afeb03c66fac8e055d') depends_on('zlib') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index 6424fcdc18d..18b30d29d40 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -18,9 +18,9 @@ class Augustus(MakefilePackage): version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2') version('3.3.1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab', url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz') - version('3.3', '93691d9aafc7d3d0e1adf31ec308507f', + version('3.3', sha256='b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee', url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz') - version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830', + version('3.2.3', sha256='a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514', url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index 35b89691241..29a4a7cbbe2 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -12,10 +12,10 @@ class Autoconf(AutotoolsPackage): homepage = 'https://www.gnu.org/software/autoconf/' url = 'https://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz' - version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b') - version('2.62', '6c1f3b3734999035d77da5024aab4fbd') - version('2.59', 'd4d45eaa1769d45e59dcb131a4af17a0') - version('2.13', '9de56d4a161a723228220b0f425dc711') + version('2.69', sha256='954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969') + version('2.62', sha256='83aa747e6443def0ebd1882509c53f5a2133f502ddefa21b3de141c433914bdd') + version('2.59', sha256='9cd05c73c5fcb1f5ccae53dd6cac36bb8cb9c7b3e97ffae5a7c05c72594c88d8') + version('2.13', sha256='f0611136bee505811e9ca11ca7ac188ef5323a8e2ef19cffd3edb3cf08fd791e') # Note: m4 is not a pure build-time dependency of autoconf. m4 is # needed when autoconf runs, not only when autoconf is built. diff --git a/var/spack/repos/builtin/packages/autodock-vina/package.py b/var/spack/repos/builtin/packages/autodock-vina/package.py index 65f4d2fe0ed..2ce0555529c 100644 --- a/var/spack/repos/builtin/packages/autodock-vina/package.py +++ b/var/spack/repos/builtin/packages/autodock-vina/package.py @@ -13,7 +13,7 @@ class AutodockVina(MakefilePackage): homepage = "http://vina.scripps.edu/" url = "http://vina.scripps.edu/download/autodock_vina_1_1_2.tgz" - version('1_1_2', 'b467b71ee77dd155b65b1c5364e4220f') + version('1_1_2', sha256='b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776') depends_on('boost@1.65.0') diff --git a/var/spack/repos/builtin/packages/autogen/package.py b/var/spack/repos/builtin/packages/autogen/package.py index a5ea2129247..de3e2e0dfda 100644 --- a/var/spack/repos/builtin/packages/autogen/package.py +++ b/var/spack/repos/builtin/packages/autogen/package.py @@ -17,7 +17,7 @@ class Autogen(AutotoolsPackage): list_url = "https://ftp.gnu.org/gnu/autogen" list_depth = 1 - version('5.18.12', '551d15ccbf5b5fc5658da375d5003389') + version('5.18.12', sha256='805c20182f3cb0ebf1571d3b01972851c56fb34348dfdc38799fd0ec3b2badbe') variant('xml', default=True, description='Enable XML support') diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py index bd5dbf21a47..2ac1ab33cf3 100644 --- a/var/spack/repos/builtin/packages/automaded/package.py +++ b/var/spack/repos/builtin/packages/automaded/package.py @@ -21,7 +21,7 @@ class Automaded(CMakePackage): homepage = "https://github.com/llnl/AutomaDeD" url = "https://github.com/llnl/AutomaDeD/archive/v1.0.tar.gz" - version('1.0', '16a3d4def2c4c77d0bc4b21de8b3ab03') + version('1.0', sha256='600740cdd594cc6968c7bcb285d0829eb0ddbd5597c32c06c6ae5d9929a2625d') depends_on('mpi') depends_on('boost') diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py index c3f159cc2c9..4c460d8ddef 100644 --- a/var/spack/repos/builtin/packages/automake/package.py +++ b/var/spack/repos/builtin/packages/automake/package.py @@ -12,12 +12,12 @@ class Automake(AutotoolsPackage): homepage = 'http://www.gnu.org/software/automake/' url = 'https://ftpmirror.gnu.org/automake/automake-1.15.tar.gz' - version('1.16.1', '608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8') - version('1.15.1', '988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260') - version('1.15', '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924') - version('1.14.1', '814c2333f350ce00034a1fe718e0e4239998ceea7b0aff67e9fd273ed6dfc23b') - version('1.13.4', '4c93abc0bff54b296f41f92dd3aa1e73e554265a6f719df465574983ef6f878c') - version('1.11.6', '53dbf1945401c43f4ce19c1971baecdbf8bc32e0f37fa3f49fe7b6992d0d2030') + version('1.16.1', sha256='608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8') + version('1.15.1', sha256='988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260') + version('1.15', sha256='7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924') + version('1.14.1', sha256='814c2333f350ce00034a1fe718e0e4239998ceea7b0aff67e9fd273ed6dfc23b') + version('1.13.4', sha256='4c93abc0bff54b296f41f92dd3aa1e73e554265a6f719df465574983ef6f878c') + version('1.11.6', sha256='53dbf1945401c43f4ce19c1971baecdbf8bc32e0f37fa3f49fe7b6992d0d2030') depends_on('autoconf', type='build') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/axel/package.py b/var/spack/repos/builtin/packages/axel/package.py index d6424f3a851..056803110a1 100644 --- a/var/spack/repos/builtin/packages/axel/package.py +++ b/var/spack/repos/builtin/packages/axel/package.py @@ -12,7 +12,7 @@ class Axel(AutotoolsPackage): homepage = "https://github.com/axel-download-accelerator/axel" url = "https://github.com/axel-download-accelerator/axel/archive/v2.16.1.tar.gz" - version('2.16.1', '3aaa7052458c66c1547bf1133609d0f2') + version('2.16.1', sha256='64529add74df3db828f704b42d4ec3fcdacb8142c84f051f9213637c337e706c') depends_on('m4', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py index 2f15ea73f0e..47e134daf86 100644 --- a/var/spack/repos/builtin/packages/bamtools/package.py +++ b/var/spack/repos/builtin/packages/bamtools/package.py @@ -13,12 +13,12 @@ class Bamtools(CMakePackage): homepage = "https://github.com/pezmaster31/bamtools" url = "https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz" - version('2.5.1', '98e90632058f85bd5eed6088b3ff912e') - version('2.5.0', 'dd4185bdba6e3adf2c24b7f93a57233d') - version('2.4.1', '41cadf513f2744256851accac2bc7baa') - version('2.4.0', '6139d00c1b1fe88fe15d094d8a74d8b9') - version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc') - version('2.2.3', '6eccd3e45e4ba12a68daa3298998e76d') + version('2.5.1', sha256='4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc') + version('2.5.0', sha256='85e02e04998a67cbda7ab68cdab36cee133db024e814b34e06bb617b627caf9c') + version('2.4.1', sha256='933a0c1a83c88c1dac8078c0c0e82f6794c75cb927265399404bc2cc2611204b') + version('2.4.0', sha256='f1fe82b8871719e0fb9ed7be73885f5d0815dd5c7277ee33bd8f67ace961e13e') + version('2.3.0', sha256='288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af') + version('2.2.3', sha256='92ddef44801a1f8f01ce1a397f83e0f8b5e1ae8ad92c620f2dafaaf8d54cf178') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/bamutil/package.py b/var/spack/repos/builtin/packages/bamutil/package.py index 69c2bcfb072..49bb4a96dd7 100644 --- a/var/spack/repos/builtin/packages/bamutil/package.py +++ b/var/spack/repos/builtin/packages/bamutil/package.py @@ -15,7 +15,7 @@ class Bamutil(MakefilePackage): homepage = "http://genome.sph.umich.edu/wiki/BamUtil" url = "http://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz" - version('1.0.13', '08b7d0bb1d60be104a11f0e54ddf4a79') + version('1.0.13', sha256='16c1d01c37d1f98b98c144f3dd0fda6068c1902f06bd0989f36ce425eb0c592b') depends_on('zlib', type=('build', 'link')) diff --git a/var/spack/repos/builtin/packages/barrnap/package.py b/var/spack/repos/builtin/packages/barrnap/package.py index 54a7d96ce32..e5bb5ac8641 100644 --- a/var/spack/repos/builtin/packages/barrnap/package.py +++ b/var/spack/repos/builtin/packages/barrnap/package.py @@ -12,9 +12,9 @@ class Barrnap(Package): homepage = "https://github.com/tseemann/barrnap" url = "https://github.com/tseemann/barrnap/archive/0.8.tar.gz" - version('0.8', 'd02ccb800d60fa824bae946dd4fa2358') - version('0.7', 'ef2173e250f06cca7569c03404c9d4ab6a908ef7643e28901fbe9a732d20c09b') - version('0.6', '272642a41634623bda34dccdce487ab791925fa769e3e575d53014956a1f9dce') + version('0.8', sha256='82004930767e92b61539c0de27ff837b8b7af01236e565f1473c63668cf0370f') + version('0.7', sha256='ef2173e250f06cca7569c03404c9d4ab6a908ef7643e28901fbe9a732d20c09b') + version('0.6', sha256='272642a41634623bda34dccdce487ab791925fa769e3e575d53014956a1f9dce') depends_on('hmmer@3.1b:', type='run') diff --git a/var/spack/repos/builtin/packages/bash-completion/package.py b/var/spack/repos/builtin/packages/bash-completion/package.py index e586c7b0010..1b16fa2a1d8 100644 --- a/var/spack/repos/builtin/packages/bash-completion/package.py +++ b/var/spack/repos/builtin/packages/bash-completion/package.py @@ -14,8 +14,8 @@ class BashCompletion(AutotoolsPackage): git = "https://github.com/scop/bash-completion.git" version('develop', branch='master') - version('2.7', 'f72c9e2e877d188c3159956a3496a450e7279b76') - version('2.3', '67e50f5f3c804350b43f2b664c33dde811d24292') + version('2.7', sha256='dba2b88c363178622b61258f35d82df64dc8d279359f599e3b93eac0375a416c') + version('2.3', sha256='d92fcef5f6e3bbc68a84f0a7b063a1cd07b4000cc6e275cd1ff83863ab3b322a') # Build dependencies depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py index 24842d1ad22..906e98ee5d3 100644 --- a/var/spack/repos/builtin/packages/bash/package.py +++ b/var/spack/repos/builtin/packages/bash/package.py @@ -12,10 +12,10 @@ class Bash(AutotoolsPackage): homepage = "https://www.gnu.org/software/bash/" url = "https://ftpmirror.gnu.org/bash/bash-4.4.tar.gz" - version('5.0', sha256='b4a80f2ac66170b2913efbfb9f2594f1f76c7b1afd11f799e22035d63077fb4d') - version('4.4.12', '7c112970cbdcadfc331e10eeb5f6aa41') - version('4.4', '148888a7c95ac23705559b6f477dfe25') - version('4.3', '81348932d5da294953e15d4814c74dd1') + version('5.0', sha256='b4a80f2ac66170b2913efbfb9f2594f1f76c7b1afd11f799e22035d63077fb4d') + version('4.4.12', sha256='57d8432be54541531a496fd4904fdc08c12542f43605a9202594fa5d5f9f2331') + version('4.4', sha256='d86b3392c1202e8ff5a423b302e6284db7f8f435ea9f39b5b1b20fd3ac36dfcb') + version('4.3', sha256='afc687a28e0e24dc21b988fa159ff9dbcf6b7caa92ade8645cc6d5605cd024d4') depends_on('ncurses') depends_on('readline@5.0:') diff --git a/var/spack/repos/builtin/packages/bats/package.py b/var/spack/repos/builtin/packages/bats/package.py index 74baeb9bbe7..279116bb30c 100644 --- a/var/spack/repos/builtin/packages/bats/package.py +++ b/var/spack/repos/builtin/packages/bats/package.py @@ -12,7 +12,7 @@ class Bats(Package): homepage = "https://github.com/sstephenson/bats" url = "https://github.com/sstephenson/bats/archive/v0.4.0.tar.gz" - version('0.4.0', 'aeeddc0b36b8321930bf96fce6ec41ee') + version('0.4.0', sha256='480d8d64f1681eee78d1002527f3f06e1ac01e173b761bc73d0cf33f4dc1d8d7') def install(self, spec, prefix): bash = which("bash") diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py index 51e4e510507..b976301f3aa 100644 --- a/var/spack/repos/builtin/packages/bazel/package.py +++ b/var/spack/repos/builtin/packages/bazel/package.py @@ -17,24 +17,24 @@ class Bazel(Package): homepage = "https://www.bazel.io" url = "https://github.com/bazelbuild/bazel/releases/download/0.11.1/bazel-0.11.1-dist.zip" - version('0.17.2', '9805c0593e781295126af6b8be8cc7a9') - version('0.16.1', 'c333d903c5275286e79316eb19dd742d') - version('0.15.0', 'fb6b928b62f068697bd66ad6d13aad53') - version('0.14.1', '841900316b3ec9b996babe1c5b0b92e1') - version('0.13.0', '64a5124025c1618b550faec64a9b6fa3') - version('0.12.0', 'b5d67564ceecfe2005a885fe2ffe0da3') - version('0.11.1', '80daac6b100b7f8e2b17d133150eba44') - version('0.11.0', 'e6caf93a805b45c33367028e575b91dd') - version('0.10.1', 'a7e5b9576993b752e31bd2d3259a14c5') - version('0.10.0', 'c2f15b34255099d25e94fce7283e5cd2') - version('0.9.0', '7fda74c163108f7c180bbc513bc8123b') - version('0.4.5', '2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b') - version('0.4.4', '5e7c52b89071efc41277e2f0057d258f') - version('0.3.1', '5c959467484a7fc7dd2e5e4a1e8e866b') - version('0.3.0', '33a2cb457d28e1bee9282134769b9283') - version('0.2.3', '393a491d690e43caaba88005efe6da91') - version('0.2.2b', '75081804f073cbd194da1a07b16cba5f') - version('0.2.2', '644bc4ea7f429d835e74f255dc1054e6') + version('0.17.2', sha256='b6e87acfa0a405bb8b3417c58477b66d5bc27dc0d31ba6fa12bc255b9278d33b') + version('0.16.1', sha256='09c66b94356c82c52f212af52a81ac28eb06de1313755a2f23eeef84d167b36c') + version('0.15.0', sha256='c3b716e6625e6b8c323350c95cd3ae0f56aeb00458dddd10544d5bead8a7b602') + version('0.14.1', sha256='d49cdcd82618ae7a7a190e6f0a80d9bf85c1a66b732f994f37732dc14ffb0025') + version('0.13.0', sha256='82e9035084660b9c683187618a29aa896f8b05b5f16ae4be42a80b5e5b6a7690') + version('0.12.0', sha256='3b3e7dc76d145046fdc78db7cac9a82bc8939d3b291e53a7ce85315feb827754') + version('0.11.1', sha256='e8d762bcc01566fa50952c8028e95cfbe7545a39b8ceb3a0d0d6df33b25b333f') + version('0.11.0', sha256='abfeccc94728cb46be8dbb3507a23ccffbacef9fbda96a977ef4ea8d6ab0d384') + version('0.10.1', sha256='708248f6d92f2f4d6342006c520f22dffa2f8adb0a9dc06a058e3effe7fee667') + version('0.10.0', sha256='47e0798caaac4df499bce5fe554a914abd884a855a27085a4473de1d737d9548') + version('0.9.0', sha256='efb28fed4ffcfaee653e0657f6500fc4cbac61e32104f4208da385676e76312a') + version('0.4.5', sha256='2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b') + version('0.4.4', sha256='d52a21dda271ae645711ce99c70cf44c5d3a809138e656bbff00998827548ebb') + version('0.3.1', md5='5c959467484a7fc7dd2e5e4a1e8e866b') + version('0.3.0', md5='33a2cb457d28e1bee9282134769b9283') + version('0.2.3', md5='393a491d690e43caaba88005efe6da91') + version('0.2.2b', md5='75081804f073cbd194da1a07b16cba5f') + version('0.2.2', md5='644bc4ea7f429d835e74f255dc1054e6') depends_on('java@8:', type=('build', 'link', 'run')) depends_on('zip') diff --git a/var/spack/repos/builtin/packages/bbmap/package.py b/var/spack/repos/builtin/packages/bbmap/package.py index e232e9f3954..47197d1c17f 100644 --- a/var/spack/repos/builtin/packages/bbmap/package.py +++ b/var/spack/repos/builtin/packages/bbmap/package.py @@ -13,7 +13,7 @@ class Bbmap(Package): url = "https://downloads.sourceforge.net/project/bbmap/BBMap_38.63.tar.gz" version('38.63', sha256='089064104526c8d696164aefa067f935b888bc71ef95527c72a98c17ee90a01f') - version('37.36', '1e1086e1fae490a7d03c5a065b1c262f') + version('37.36', sha256='befe76d7d6f3d0f0cd79b8a01004a2283bdc0b5ab21b0743e9dbde7c7d79e8a9') depends_on('java') diff --git a/var/spack/repos/builtin/packages/bc/package.py b/var/spack/repos/builtin/packages/bc/package.py index f12bccf16af..99dc0b1d99d 100644 --- a/var/spack/repos/builtin/packages/bc/package.py +++ b/var/spack/repos/builtin/packages/bc/package.py @@ -14,7 +14,7 @@ class Bc(AutotoolsPackage): homepage = "https://www.gnu.org/software/bc" url = "https://ftpmirror.gnu.org/bc/bc-1.07.tar.gz" - version('1.07', 'e91638a947beadabf4d7770bdbb3d512') + version('1.07', sha256='55cf1fc33a728d7c3d386cc7b0cb556eb5bacf8e0cb5a3fcca7f109fc61205ad') depends_on('ed', type='build') depends_on('texinfo', type='build') diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py index 34182f930d9..cfdea1a3c93 100644 --- a/var/spack/repos/builtin/packages/bcftools/package.py +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -16,12 +16,12 @@ class Bcftools(AutotoolsPackage): url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2" version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8') - version('1.8', 'ba6c2fb7eb6dcb208f00ab8b22df475c') - version('1.7', 'c972db68d17af9da3a18963f4e5aeca8') - version('1.6', 'c4dba1e8cb55db0f94b4c47724b4f9fa') - version('1.4', '50ccf0a073bd70e99cdb3c8be830416e') - version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb') - version('1.2', '8044bed8fce62f7072fc6835420f0906') + version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced') + version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1') + version('1.6', sha256='293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982') + version('1.4', sha256='8fb1b0a47ed4e1f9d7c70129d7993aa650da1688fd931b10646d1c4707ae234d') + version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924') + version('1.2', sha256='53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6') depends_on('libzip', when='@1.8:') diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py index 8250b231125..d884fbd965a 100644 --- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py +++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py @@ -19,13 +19,13 @@ class Bcl2fastq2(Package): homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html" - version('2.20.0.422', '4dc99f1af208498b7279b66556329488') - version('2.19.1.403', 'baba7a02767fd868e87cb36781d2be26') - version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c') + version('2.20.0.422', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3') + version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806') + version('2.18.0.12', md5='fbe06492117f65609c41be0c27e3215c') # 2.17.1.14 is no longer distributed. If you have a copy of the # source tarball, you can drop it into a local mirror w/ the name # mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there. - version('2.17.1.14', '7426226c6db095862e636b95c38608d3') + version('2.17.1.14', md5='7426226c6db095862e636b95c38608d3') conflicts('platform=darwin', msg='malloc.h/etc requirements break build on macs') diff --git a/var/spack/repos/builtin/packages/bdftopcf/package.py b/var/spack/repos/builtin/packages/bdftopcf/package.py index f521b96403d..38576dbed3b 100644 --- a/var/spack/repos/builtin/packages/bdftopcf/package.py +++ b/var/spack/repos/builtin/packages/bdftopcf/package.py @@ -17,7 +17,7 @@ class Bdftopcf(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/bdftopcf" url = "https://www.x.org/archive/individual/app/bdftopcf-1.0.5.tar.gz" - version('1.0.5', '456416d33e0d41a96b5a3725d99e1be3') + version('1.0.5', sha256='78a5ec945de1d33e6812167b1383554fda36e38576849e74a9039dc7364ff2c3') depends_on('libxfont') diff --git a/var/spack/repos/builtin/packages/bdw-gc/package.py b/var/spack/repos/builtin/packages/bdw-gc/package.py index 526dd28beef..5d5f882bab9 100644 --- a/var/spack/repos/builtin/packages/bdw-gc/package.py +++ b/var/spack/repos/builtin/packages/bdw-gc/package.py @@ -14,8 +14,8 @@ class BdwGc(AutotoolsPackage): url = "https://www.hboehm.info/gc/gc_source/gc-8.0.0.tar.gz" version('8.0.0', sha256='8f23f9a20883d00af2bff122249807e645bdf386de0de8cbd6cce3e0c6968f04') - version('7.6.0', 'bf46ccbdaccfa3186c2ab87191c8855a') - version('7.4.4', '96d18b0448a841c88d56e4ab3d180297') + version('7.6.0', sha256='a14a28b1129be90e55cd6f71127ffc5594e1091d5d54131528c24cd0c03b7d90') + version('7.4.4', sha256='e5ca9b628b765076b6ab26f882af3a1a29cde786341e08b9f366604f74e4db84') variant('libatomic-ops', default=True, description='Use external libatomic-ops') diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py index df2270c9553..85210b0af89 100644 --- a/var/spack/repos/builtin/packages/bear/package.py +++ b/var/spack/repos/builtin/packages/bear/package.py @@ -12,8 +12,8 @@ class Bear(CMakePackage): homepage = "https://github.com/rizsotto/Bear" url = "https://github.com/rizsotto/Bear/archive/2.0.4.tar.gz" - version('2.2.0', '87250cc3a9a697e7d1e8972253a35259') - version('2.0.4', 'fd8afb5e8e18f8737ba06f90bd77d011') + version('2.2.0', sha256='6bd61a6d64a24a61eab17e7f2950e688820c72635e1cf7ea8ea7bf9482f3b612') + version('2.0.4', sha256='33ea117b09068aa2cd59c0f0f7535ad82c5ee473133779f1cc20f6f99793a63e') depends_on('python') depends_on('cmake@2.8:', type='build') diff --git a/var/spack/repos/builtin/packages/beast1/package.py b/var/spack/repos/builtin/packages/beast1/package.py index de148c0a6c1..4d895e814cc 100644 --- a/var/spack/repos/builtin/packages/beast1/package.py +++ b/var/spack/repos/builtin/packages/beast1/package.py @@ -13,8 +13,8 @@ class Beast1(Package): homepage = "http://beast.community/" version('1.10.4', sha256='be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8') - version('1.10.0', 'bcf2f2c074319360ec8a2ebad57d2e57') - version('1.8.4', 'cb8752340c1f77a22d39ca4fe09687b0') + version('1.10.0', md5='bcf2f2c074319360ec8a2ebad57d2e57') + version('1.8.4', sha256='c14e93976008463108aefa34ecc23287ab70703caccf4962e36e295207120d78') variant('beagle', default=True, description='Build with libbeagle support') diff --git a/var/spack/repos/builtin/packages/beast2/package.py b/var/spack/repos/builtin/packages/beast2/package.py index 57bfd2fcd75..299fbba8493 100644 --- a/var/spack/repos/builtin/packages/beast2/package.py +++ b/var/spack/repos/builtin/packages/beast2/package.py @@ -18,7 +18,7 @@ class Beast2(Package): url = "https://github.com/CompEvol/beast2/releases/download/v2.4.6/BEAST.v2.4.6.Linux.tgz" version('2.5.2', sha256='2feb2281b4f7cf8f7de1a62de50f52a8678ed0767fc72f2322e77dde9b8cd45f') - version('2.4.6', 'b446f4ab121df9b991f7bb7ec94c8217') + version('2.4.6', sha256='84029c5680cc22f95bef644824130090f5f12d3d7f48d45cb4efc8e1d6b75e93') depends_on('java') diff --git a/var/spack/repos/builtin/packages/bedops/package.py b/var/spack/repos/builtin/packages/bedops/package.py index e01193f8319..02f85d9b823 100644 --- a/var/spack/repos/builtin/packages/bedops/package.py +++ b/var/spack/repos/builtin/packages/bedops/package.py @@ -15,9 +15,9 @@ class Bedops(MakefilePackage): homepage = "https://bedops.readthedocs.io" url = "https://github.com/bedops/bedops/archive/v2.4.30.tar.gz" - version('2.4.35', 'b425b3e05fd4cd1024ef4dd8bf04b4e5') - version('2.4.34', 'fc467d96134a0efe8b134e638af87a1a') - version('2.4.30', '4e5d9f7b7e5432b28aef8d17a22cffab') + version('2.4.35', sha256='da0265cf55ef5094834318f1ea4763d7a3ce52a6900e74f532dd7d3088c191fa') + version('2.4.34', sha256='533a62a403130c048d3378e6a975b73ea88d156d4869556a6b6f58d90c52ed95') + version('2.4.30', sha256='218e0e367aa79747b2f90341d640776eea17befc0fdc35b0cec3c6184098d462') @property def build_targets(self): diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py index 25f374dba1b..80c1359719e 100644 --- a/var/spack/repos/builtin/packages/bedtools2/package.py +++ b/var/spack/repos/builtin/packages/bedtools2/package.py @@ -15,11 +15,11 @@ class Bedtools2(Package): homepage = "https://github.com/arq5x/bedtools2" url = "https://github.com/arq5x/bedtools2/archive/v2.26.0.tar.gz" - version('2.27.1', '8e0afcab95a824e42a6e99c5436a8438') - version('2.27.0', '052f22eb214ef2e7e7981b3c01167302') - version('2.26.0', '52227e7efa6627f0f95d7d734973233d') - version('2.25.0', '534fb4a7bf0d0c3f05be52a0160d8e3d') - version('2.23.0', '4fa3671b3a3891eefd969ad3509222e3') + version('2.27.1', sha256='edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112') + version('2.27.0', sha256='e91390b567e577d337c15ca301e264b0355441f5ab90fa4f971622e3043e0ca0') + version('2.26.0', sha256='15db784f60a11b104ccbc9f440282e5780e0522b8d55d359a8318a6b61897977') + version('2.25.0', sha256='159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb') + version('2.23.0', sha256='9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/beforelight/package.py b/var/spack/repos/builtin/packages/beforelight/package.py index 103e2bc0c3e..512b77373c4 100644 --- a/var/spack/repos/builtin/packages/beforelight/package.py +++ b/var/spack/repos/builtin/packages/beforelight/package.py @@ -15,7 +15,7 @@ class Beforelight(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/beforelight" url = "https://www.x.org/archive/individual/app/beforelight-1.0.5.tar.gz" - version('1.0.5', 'f0433eb6df647f36bbb5b38fb2beb22a') + version('1.0.5', sha256='93bb3c457d6d5e8def3180fdee07bc84d1b7f0e5378a95812e2193cd51455cdc') depends_on('libx11') depends_on('libxscrnsaver') diff --git a/var/spack/repos/builtin/packages/benchmark/package.py b/var/spack/repos/builtin/packages/benchmark/package.py index d35325a545e..07bd2790f0c 100644 --- a/var/spack/repos/builtin/packages/benchmark/package.py +++ b/var/spack/repos/builtin/packages/benchmark/package.py @@ -19,11 +19,11 @@ class Benchmark(CMakePackage): version('develop', branch='master') version('1.5.0', sha256='3c6a165b6ecc948967a1ead710d4a181d7b0fbcaa183ef7ea84604994966221a') version('1.4.1', sha256='f8e525db3c42efc9c7f3bc5176a8fa893a9a9920bbd08cef30fb56a51854d60d') - version('1.4.0', 'ccfaf2cd93ae20191b94f730b945423e') - version('1.3.0', '19ce86516ab82d6ad3b17173cf307aac') - version('1.2.0', '48d0b090cd7a84af2c4a28c8dc963c74') - version('1.1.0', '66b2a23076cf70739525be0092fc3ae3') - version('1.0.0', '1474ff826f8cd68067258db75a0835b8') + version('1.4.0', sha256='616f252f37d61b15037e3c2ef956905baf9c9eecfeab400cb3ad25bae714e214') + version('1.3.0', sha256='f19559475a592cbd5ac48b61f6b9cedf87f0b6775d1443de54cfe8f53940b28d') + version('1.2.0', sha256='3dcc90c158838e2ac4a7ad06af9e28eb5877cf28252a81e55eb3c836757d3070') + version('1.1.0', sha256='e7334dd254434c6668e33a54c8f839194c7c61840d52f4b6258eee28e9f3b20e') + version('1.0.0', sha256='d2206c263fc1a7803d4b10e164e0c225f6bcf0d5e5f20b87929f137dee247b54') variant('build_type', default='RelWithDebInfo', description='The build type to build', diff --git a/var/spack/repos/builtin/packages/berkeley-db/package.py b/var/spack/repos/builtin/packages/berkeley-db/package.py index 7cce0622d57..244f7ddaa12 100644 --- a/var/spack/repos/builtin/packages/berkeley-db/package.py +++ b/var/spack/repos/builtin/packages/berkeley-db/package.py @@ -12,10 +12,10 @@ class BerkeleyDb(AutotoolsPackage): homepage = "http://www.oracle.com/technetwork/database/database-technologies/berkeleydb/overview/index.html" url = "http://download.oracle.com/berkeley-db/db-5.3.28.tar.gz" - version('5.3.28', 'b99454564d5b4479750567031d66fe24') - version('6.0.35', 'c65a4d3e930a116abaaf69edfc697f25') - version('6.1.29', '7f4d47302dfec698fe088e5285c9098e') - version('6.2.32', '33491b4756cb44b91c3318b727e71023') + version('5.3.28', sha256='e0a992d740709892e81f9d93f06daf305cf73fb81b545afe72478043172c3628') + version('6.0.35', sha256='24421affa8ae436fe427ae4f5f2d1634da83d3d55a5ad6354a98eeedb825de55') + version('6.1.29', sha256='b3c18180e4160d97dd197ba1d37c19f6ea2ec91d31bbfaf8972d99ba097af17d') + version('6.2.32', sha256='a9c5e2b004a5777aa03510cfe5cd766a4a3b777713406b02809c17c8e0e7a8fb') configure_directory = 'dist' build_directory = 'spack-build' diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py index 33cab8a2c79..41d31097bdf 100644 --- a/var/spack/repos/builtin/packages/bertini/package.py +++ b/var/spack/repos/builtin/packages/bertini/package.py @@ -14,7 +14,7 @@ class Bertini(AutotoolsPackage): homepage = "https://bertini.nd.edu/" url = "https://bertini.nd.edu/BertiniSource_v1.5.tar.gz" - version('1.5', 'e3f6cc6e7f9a0cf1d73185e8671af707') + version('1.5', sha256='a9a68a96e180fe6a93ba1bc1d61f522784c9a053b049b2cbd98008b5b6deec3c') variant('mpi', default=True, description='Compile in parallel') diff --git a/var/spack/repos/builtin/packages/bigreqsproto/package.py b/var/spack/repos/builtin/packages/bigreqsproto/package.py index 98089b13559..ef6eecfd81a 100644 --- a/var/spack/repos/builtin/packages/bigreqsproto/package.py +++ b/var/spack/repos/builtin/packages/bigreqsproto/package.py @@ -15,7 +15,7 @@ class Bigreqsproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/bigreqsproto" url = "https://www.x.org/archive/individual/proto/bigreqsproto-1.1.2.tar.gz" - version('1.1.2', '9b83369ac7a5eb2bf54c8f34db043a0e') + version('1.1.2', sha256='de68a1a9dd1a1219ad73531bff9f662bc62fcd777387549c43cd282399f4a6ea') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index ad4c8a76a5a..9f42882f03b 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -14,16 +14,16 @@ class Binutils(AutotoolsPackage): url = "https://ftpmirror.gnu.org/binutils/binutils-2.28.tar.bz2" version('2.32', sha256='de38b15c902eb2725eac6af21183a5f34ea4634cb0bcef19612b50e5ed31072d') - version('2.31.1', 'ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0') - version('2.29.1', '9af59a2ca3488823e453bb356fe0f113') - version('2.28', '9e8340c96626b469a603c15c9d843727') - version('2.27', '2869c9bf3e60ee97c74ac2a6bf4e9d68') - version('2.26', '64146a0faa3b411ba774f47d41de239f') + version('2.31.1', sha256='ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0') + version('2.29.1', sha256='1509dff41369fb70aed23682351b663b56db894034773e6dbf7d5d6071fc55cc') + version('2.28', sha256='6297433ee120b11b4b0a1c8f3512d7d73501753142ab9e2daa13c5a3edd32a72') + version('2.27', sha256='369737ce51587f92466041a97ab7d2358c6d9e1b6490b3940eb09fb0a9a6ac88') + version('2.26', sha256='c2ace41809542f5237afc7e3b8f32bb92bc7bc53c6232a84463c423b0714ecd9') version('2.25.1', sha256='b5b14added7d78a8d1ca70b5cb75fef57ce2197264f4f5835326b0df22ac9f22') - version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66') - version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b') - version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') - version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') + version('2.25', sha256='22defc65cfa3ef2a3395faaea75d6331c6e62ea5dfacfed3e2ec17b08c882923') + version('2.24', sha256='e5e8c5be9664e7f7f96e0d09919110ab5ad597794f5b1809871177a0f0f14137') + version('2.23.2', sha256='fe914e56fed7a9ec2eb45274b1f2e14b0d8b4f41906a5194eac6883cfe5c1097') + version('2.20.1', sha256='71d37c96451333c5c0b84b170169fdcb138bbb27397dc06281905d9717c8ed64') variant('plugins', default=False, description="enable plugins, needed for gold linker") diff --git a/var/spack/repos/builtin/packages/bioawk/package.py b/var/spack/repos/builtin/packages/bioawk/package.py index f8a90fe1230..c01be2d8d5a 100644 --- a/var/spack/repos/builtin/packages/bioawk/package.py +++ b/var/spack/repos/builtin/packages/bioawk/package.py @@ -15,7 +15,7 @@ class Bioawk(MakefilePackage): homepage = "https://github.com/lh3/bioawk" url = "https://github.com/lh3/bioawk/archive/v1.0.zip" - version('1.0', 'e423942689f944369de270900978be28') + version('1.0', sha256='316a6561dda41e8327b85106db3704e94e23d7a89870392d19ef8559f7859e2d') depends_on('zlib') depends_on('bison', type=('build')) diff --git a/var/spack/repos/builtin/packages/bismark/package.py b/var/spack/repos/builtin/packages/bismark/package.py index 4421e29a3d5..057ccd1dad5 100644 --- a/var/spack/repos/builtin/packages/bismark/package.py +++ b/var/spack/repos/builtin/packages/bismark/package.py @@ -13,8 +13,8 @@ class Bismark(Package): homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark" url = "https://github.com/FelixKrueger/Bismark/archive/0.19.0.tar.gz" - version('0.19.0', 'f403654aded77bf0d1dac1203867ded1') - version('0.18.2', '42334b7e3ed53ba246f30f1f846b4af8') + version('0.19.0', sha256='91707737f96a0574956a282b635abad7560e7d90bee188a67a7807b2470deae2') + version('0.18.2', sha256='83391c5b5af33047178e7774ac25f5a69ce9315c13ae02f016baf7c50b73e702') depends_on('bowtie2', type='run') depends_on('perl', type='run') diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index 29161702daa..f1eb5503879 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -16,9 +16,9 @@ class Bison(AutotoolsPackage): homepage = "http://www.gnu.org/software/bison/" url = "https://ftpmirror.gnu.org/bison/bison-3.0.4.tar.gz" - version('3.0.5', '41ad57813157b61bfa47e33067a9d6f0') - version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8') - version('2.7', 'ded660799e76fb1667d594de1f7a0da9') + version('3.0.5', sha256='cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566') + version('3.0.4', sha256='b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e') + version('2.7', sha256='19bbe7374fd602f7a6654c131c21a15aebdc06cc89493e8ff250cb7f9ed0a831') depends_on('diffutils', type='build') depends_on('m4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/bitmap/package.py b/var/spack/repos/builtin/packages/bitmap/package.py index 71a57089555..af6b2582f91 100644 --- a/var/spack/repos/builtin/packages/bitmap/package.py +++ b/var/spack/repos/builtin/packages/bitmap/package.py @@ -12,7 +12,7 @@ class Bitmap(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/bitmap" url = "https://www.x.org/archive/individual/app/bitmap-1.0.8.tar.gz" - version('1.0.8', '0ca600041bb0836ae7c9f5db5ce09091') + version('1.0.8', sha256='1a2fbd10a2ca5cd93f7b77bbb0555b86d8b35e0fc18d036b1607c761755006fc') depends_on('libx11') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/blasr-libcpp/package.py b/var/spack/repos/builtin/packages/blasr-libcpp/package.py index d1bba64eccc..40693d9e89d 100644 --- a/var/spack/repos/builtin/packages/blasr-libcpp/package.py +++ b/var/spack/repos/builtin/packages/blasr-libcpp/package.py @@ -15,7 +15,7 @@ class BlasrLibcpp(Package): homepage = "https://github.com/PacificBiosciences/blasr_libcpp" url = "https://github.com/PacificBiosciences/blasr_libcpp/archive/5.3.1.tar.gz" - version('5.3.1', 'ca770042cbca508d5ff12dff0d645045') + version('5.3.1', sha256='45a673255bfe7e29ed1f5bdb6410aa45cb6b907400d038c3da9daf1058b09156') depends_on('pbbam') depends_on('hdf5+cxx@1.8.12:1.8.99') diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py index 9979d959853..a25f1486da3 100644 --- a/var/spack/repos/builtin/packages/blasr/package.py +++ b/var/spack/repos/builtin/packages/blasr/package.py @@ -13,7 +13,7 @@ class Blasr(Package): homepage = "https://github.com/PacificBiosciences/blasr/wiki" url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz" - version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a') + version('5.3.1', sha256='ff7da5a03096294572e6c64340354da5c5ee1c86c277e7b899f2c170c1ac4049') depends_on('ncurses') depends_on('hdf5+cxx@1.8.12:1.8.99') diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py index 7722e1b2a4e..71ba17eb4af 100644 --- a/var/spack/repos/builtin/packages/blast-plus/package.py +++ b/var/spack/repos/builtin/packages/blast-plus/package.py @@ -26,8 +26,8 @@ class BlastPlus(AutotoolsPackage): version('2.9.0', sha256='a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257') version('2.8.1', sha256='e03dd1a30e37cb8a859d3788a452c5d70ee1f9102d1ee0f93b2fbd145925118f') version('2.7.1', sha256='10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca') - version('2.6.0', 'c8ce8055b10c4d774d995f88c7cc6225') - version('2.2.30', 'f8e9a5eb368173142fe6867208b73715') + version('2.6.0', sha256='0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996') + version('2.2.30', sha256='26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40') # homebrew sez: Fixed upstream in future version > 2.6 # But this bug sez that it will be fixed in 2.6 diff --git a/var/spack/repos/builtin/packages/blat/package.py b/var/spack/repos/builtin/packages/blat/package.py index 349b8e18952..7b2f5de6492 100644 --- a/var/spack/repos/builtin/packages/blat/package.py +++ b/var/spack/repos/builtin/packages/blat/package.py @@ -13,7 +13,7 @@ class Blat(Package): homepage = "https://genome.ucsc.edu/FAQ/FAQblat.html" url = "https://users.soe.ucsc.edu/~kent/src/blatSrc35.zip" - version('35', '16e546b8843b85e0b0f2fa603cd78724') + version('35', sha256='06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620') depends_on('libpng') diff --git a/var/spack/repos/builtin/packages/blaze/package.py b/var/spack/repos/builtin/packages/blaze/package.py index e2eef8c4df1..531449a3203 100644 --- a/var/spack/repos/builtin/packages/blaze/package.py +++ b/var/spack/repos/builtin/packages/blaze/package.py @@ -26,19 +26,19 @@ class Blaze(CMakePackage): version('3.5', sha256='f50d4a57796b8012d3e6d416667d9abe6f4d95994eb9deb86cd4491381dec624') version('3.4', sha256='fd474ab479e81d31edf27d4a529706b418f874caa7b046c67489128c20dda66f') version('3.3', sha256='138cbb7b95775c10bf56a5ab3596a32205751299b19699984b6ed55b1bf989d0') - version('3.2', '47bd4a4f1b6292f5a6f71ed9d5287480') - version('3.1', '2938e015f0d274e8d62ee5c4c0c1e9f3') - version('3.0', '0c4cefb0be7b5a27ed8a377941be1ab1') - version('2.6', 'f7b515eeffd5cce92eb02dc6f8905f4d') - version('2.5', '53a862763c275046ff0a8f07dfd3985b') - version('2.4', '7cf2e963a73d3c95ced0f7eaa0ae3677') - version('2.3', '2f8ca52d23447ac75a03bb43b12ef774') - version('2.2', '686a514108d7f3c6c7325ed57c171a59') - version('2.1', 'e5e419a2b35f0a36cd9d7527a250c56a') - version('2.0', 'aeb6a865e9e3810ee55456f961458a8e') - version('1.5', '5b77b605ee5ad35631bb3039737142c9') - version('1.4', '3f06d710161954ccae0975d87f1069ca') - version('1.3', 'ebd7f91fc5fca4108bfd16a86f9abd82') - version('1.2', 'b1511324456c3f70fce198a2b63e71ef') - version('1.1', '5e52ebe68217f2e50d66dfdb9803d51e') - version('1.0', 'a46508a2965ace9d89ded30a386d9548') + version('3.2', sha256='fb7e83d3a8c1ba04d3a51234708092b75a1abf3b7c4d0db5e6cf3cbed771b869') + version('3.1', sha256='a122d6758d9ada7ab516417f7b5ad186a4a9b390bba682f009df6585f5550716') + version('3.0', sha256='d66abaf4633d60b6e6472f6ecd7db7b4fb5f74a4afcfdf00c92e1ea61f2e0870') + version('2.6', sha256='a6b927db14b43fad483670dfa2acd7ecc94fd53085cdf18f262d2dc613857fb6') + version('2.5', sha256='5faeca8a26e04f70a5b3f94e88ef1fbe96a89e3722cd89e5f9d4bc8267b33d41') + version('2.4', sha256='34af70c8bb4da5fd0017b7c47e5efbfef9aadbabc5aae416582901a4059d1fa3') + version('2.3', sha256='785089db7f15684c24018b931f9f564954a79389166ac1f3e256a56c667d49f2') + version('2.2', sha256='448e70a440d71afa6325bae254ca7367b10e61431084adbf2ac679dbd5da78d2') + version('2.1', sha256='b982c03236c6a7ae396850eba0ef8fb1642ddf6448531063bf7239d9ff3290fd') + version('2.0', sha256='7bdf555e97455a2f42f40396b32caa9cf3e52bdd1877e0289115825113f4dcb2') + version('1.5', sha256='5c69b605b712616dcd29fa25abecb20b977ef318207ef96176ab67b2ad891e1e') + version('1.4', sha256='2e48d2e5a3a06abb23716829501bb0b825c58ad156faab6df0cfeef1bcdfbc82') + version('1.3', sha256='361bfbf2d2bf8557d123da3af8abc70e4c3b13d9c94a8227aeb751e06acdb8cf') + version('1.2', sha256='16f56d4f61dca229fa7e17a0d1e348a1f3246c65cded2df5db33babebf8f9b9d') + version('1.1', sha256='6add20eb9c176ea9f8091c49b101f46d1a1a6bd9c31553a6eff5e53603f0527f') + version('1.0', sha256='ee13cfd467c1a4b0fe7cc58b61b846eae862167a90dd2e60559626a30418b5a3') diff --git a/var/spack/repos/builtin/packages/bliss/package.py b/var/spack/repos/builtin/packages/bliss/package.py index 3c03dcbb898..3134aa9293f 100644 --- a/var/spack/repos/builtin/packages/bliss/package.py +++ b/var/spack/repos/builtin/packages/bliss/package.py @@ -14,7 +14,7 @@ class Bliss(Package): homepage = "http://www.tcs.hut.fi/Software/bliss/" url = "http://www.tcs.hut.fi/Software/bliss/bliss-0.73.zip" - version('0.73', '72f2e310786923b5c398ba0fc40b42ce') + version('0.73', sha256='f57bf32804140cad58b1240b804e0dbd68f7e6bf67eba8e0c0fa3a62fd7f0f84') # Note: Bliss can also be built without gmp, but we don't support this yet diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py index 22cdba5e928..005de899c4c 100644 --- a/var/spack/repos/builtin/packages/blitz/package.py +++ b/var/spack/repos/builtin/packages/blitz/package.py @@ -11,8 +11,8 @@ class Blitz(AutotoolsPackage): homepage = "http://github.com/blitzpp/blitz" url = "https://github.com/blitzpp/blitz/archive/1.0.1.tar.gz" - version('1.0.1', 'fe43e2cf6c9258bc8b369264dd008971') - version('1.0.0', '971c43e22318bbfe8da016e6ef596234') + version('1.0.1', sha256='b62fc3f07b64b264307b01fec5e4f2793e09a68dcb5378984aedbc2e4b3adcef') + version('1.0.0', sha256='79c06ea9a0585ba0e290c8140300e3ad19491c45c1d90feb52819abc3b58a0c1') build_targets = ['lib'] diff --git a/var/spack/repos/builtin/packages/bmake/package.py b/var/spack/repos/builtin/packages/bmake/package.py index d7d57932eab..bce12a14406 100644 --- a/var/spack/repos/builtin/packages/bmake/package.py +++ b/var/spack/repos/builtin/packages/bmake/package.py @@ -12,8 +12,8 @@ class Bmake(Package): homepage = "http://www.crufty.net/help/sjg/bmake.htm" url = "http://www.crufty.net/ftp/pub/sjg/bmake-20180512.tar.gz" - version('20180512', '48ba5933833a7f224d76ce482eedfec0') - version('20171207', '5d7f2f85f16c4a6ba34ceea68957447f') + version('20180512', sha256='ac3cd262065fcc20c1dec7c95f06306c8138b3e17025b949343a06a8980a5508') + version('20171207', sha256='1703667e53a0498c0903b20612ebcbb41b886a94b238624cfeadd91a4111d39a') phases = ['configure', 'build', 'install'] diff --git a/var/spack/repos/builtin/packages/bml/package.py b/var/spack/repos/builtin/packages/bml/package.py index 343a46e8854..95bf6e1b25c 100644 --- a/var/spack/repos/builtin/packages/bml/package.py +++ b/var/spack/repos/builtin/packages/bml/package.py @@ -17,10 +17,10 @@ class Bml(CMakePackage): version('develop', branch='master') version('1.3.1', sha256='17145eda96aa5e550dcbff1ee7ce62b45723af8210b1ab70c5975ec792fa3d13') - version('1.3.0', '2bf8546b27a89666dab3e8f4873cd117') - version('1.2.3', '8133137fb56a27fade44d1588449c2ac') - version('1.2.2', 'c86959cb0188e9d0a9a2cbad03b2782d') - version('1.1.0', '271adecee08aee678be9eeceee06b6fb') + version('1.3.0', sha256='d9465079fe77210eb2af2dcf8ed96802edf5bb76bfbfdbcc97e206c8cd460b07') + version('1.2.3', sha256='9a2ee6c47d2445bfdb34495497ea338a047e9e4767802af47614d9ff94b0c523') + version('1.2.2', sha256='89ab78f9fe8395fe019cc0495a1d7b69875b5708069faeb831ddb9a6a9280a8a') + version('1.1.0', sha256='29162f1f7355ad28b44d3358206ccd3c7ac7794ee13788483abcbd2f8063e7fc') variant('shared', default=True, description='Build shared libs') variant('mpi', default=True, description='Build with MPI Support') diff --git a/var/spack/repos/builtin/packages/bolt/package.py b/var/spack/repos/builtin/packages/bolt/package.py index 1b0fa8106ec..981dfae6112 100644 --- a/var/spack/repos/builtin/packages/bolt/package.py +++ b/var/spack/repos/builtin/packages/bolt/package.py @@ -22,9 +22,9 @@ class Bolt(CMakePackage): git = "https://github.com/pmodels/bolt.git" version("master", branch="master") - version("1.0rc2", "f5ca4f9fb05d6e4edbbd32635828c833") - version("1.0rc1", "77733ba2ad9440c29b36d1c1411a9793") - version("1.0b1", "df76beb3a7f13ae2dcaf9ab099eea87b") + version("1.0rc2", sha256="662ab0bb9583e8d733e8af62a97b41828e8bfe4bd65902f1195b986901775a45") + version("1.0rc1", sha256="c08cde0695b9d1252ab152425be96eb29c70d764e3083e276c013804883a15a4") + version("1.0b1", sha256="fedba46ad2f8835dd1cec1a9a52bcc9d8923071dc40045d0360517d09cd1a57d") depends_on('argobots') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/bookleaf-cpp/package.py b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py index f85f32d62fe..0dcbc7646e9 100644 --- a/var/spack/repos/builtin/packages/bookleaf-cpp/package.py +++ b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py @@ -16,8 +16,8 @@ class BookleafCpp(CMakePackage): version('develop', branch='develop') version('2.0.2', sha256='787ade5045415d71d9bad55fe9f93598f3a0548d13e2ff80e752cc99f62fe6d3') - version('2.0.1', '34a5a9e7b2b5ffc98562656a4406ba5b') - version('2.0', '69819ebcbae5eaa63d1a4de2c77cac85') + version('2.0.1', sha256='1286f916f59d1f3bf325041854e8c203894e293c5e26d5b19b9362ee02082983') + version('2.0', sha256='3c14344c31385bec9e089f9babf815566c4fcf98a47822f663afa2cefb0e90e1') variant('typhon', default=True, description='Use Typhon') variant('parmetis', default=False, description='Use ParMETIS') diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 4f0655dbacd..40fda7c362d 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -24,50 +24,50 @@ class Boost(Package): list_depth = 1 version('develop', branch='develop', submodules=True) - version('1.70.0', '5b2e5ccc454503cfbba6c1221f5d495f0de279ea') - version('1.69.0', 'ea6eee4b5999f9c02105386850f63a53f0250eaa') - version('1.68.0', '18863a7cae4d58ae85eb63d400f774f60a383411') - version('1.67.0', '694ae3f4f899d1a80eb7a3b31b33be73c423c1ae') - version('1.66.0', 'b6b284acde2ad7ed49b44e856955d7b1ea4e9459') - version('1.65.1', '41d7542ce40e171f3f7982aff008ff0d') - version('1.65.0', '5512d3809801b0a1b9dd58447b70915d') + version('1.70.0', sha256='430ae8354789de4fd19ee52f3b1f739e1fba576f0aded0897c3c2bc00fb38778') + version('1.69.0', sha256='8f32d4617390d1c2d16f26a27ab60d97807b35440d45891fa340fc2648b04406') + version('1.68.0', sha256='7f6130bc3cf65f56a618888ce9d5ea704fa10b462be126ad053e80e553d6d8b7') + version('1.67.0', sha256='2684c972994ee57fc5632e03bf044746f6eb45d4920c343937a465fd67a5adba') + version('1.66.0', sha256='5721818253e6a0989583192f96782c4a98eb6204965316df9f5ad75819225ca9') + version('1.65.1', sha256='9807a5d16566c57fd74fb522764e0b134a8bbe6b6e8967b83afefd30dcd3be81') + version('1.65.0', sha256='ea26712742e2fb079c2a566a31f3266973b76e38222b9f88b387e3c8b2f9902c') # NOTE: 1.64.0 seems fine for *most* applications, but if you need # +python and +mpi, there seem to be errors with out-of-date # API calls from mpi/python. # See: https://github.com/spack/spack/issues/3963 - version('1.64.0', '93eecce2abed9d2442c9676914709349') - version('1.63.0', '1c837ecd990bb022d07e7aab32b09847') - version('1.62.0', '5fb94629535c19e48703bdb2b2e9490f') - version('1.61.0', '6095876341956f65f9d35939ccea1a9f') - version('1.60.0', '65a840e1a0b13a558ff19eeb2c4f0cbe') - version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87') - version('1.58.0', 'b8839650e61e9c1c0a89f371dd475546') - version('1.57.0', '1be49befbdd9a5ce9def2983ba3e7b76') - version('1.56.0', 'a744cf167b05d72335f27c88115f211d') - version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354') - version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279') - version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2') - version('1.52.0', '3a855e0f919107e0ca4de4d84ad3f750') - version('1.51.0', '4b6bd483b692fd138aef84ed2c8eb679') - version('1.50.0', '52dd00be775e689f55a987baebccc462') - version('1.49.0', '0d202cb811f934282dea64856a175698') - version('1.48.0', 'd1e9a7a7f532bb031a3c175d86688d95') - version('1.47.0', 'a2dc343f7bc7f83f8941e47ed4a18200') - version('1.46.1', '7375679575f4c8db605d426fc721d506') - version('1.46.0', '37b12f1702319b73876b0097982087e0') - version('1.45.0', 'd405c606354789d0426bc07bea617e58') - version('1.44.0', 'f02578f5218f217a9f20e9c30e119c6a') - version('1.43.0', 'dd49767bfb726b0c774f7db0cef91ed1') - version('1.42.0', '7bf3b4eb841b62ffb0ade2b82218ebe6') - version('1.41.0', '8bb65e133907db727a2a825c5400d0a6') - version('1.40.0', 'ec3875caeac8c52c7c129802a8483bd7') - version('1.39.0', 'a17281fd88c48e0d866e1a12deecbcc0') - version('1.38.0', '5eca2116d39d61382b8f8235915cb267') - version('1.37.0', '8d9f990bfb7e83769fa5f1d6f065bc92') - version('1.36.0', '328bfec66c312150e4c2a78dcecb504b') - version('1.35.0', 'dce952a7214e72d6597516bcac84048b') - version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5') - version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0') + version('1.64.0', sha256='7bcc5caace97baa948931d712ea5f37038dbb1c5d89b43ad4def4ed7cb683332') + version('1.63.0', sha256='beae2529f759f6b3bf3f4969a19c2e9d6f0c503edcb2de4a61d1428519fcb3b0') + version('1.62.0', sha256='36c96b0f6155c98404091d8ceb48319a28279ca0333fba1ad8611eb90afb2ca0') + version('1.61.0', sha256='a547bd06c2fd9a71ba1d169d9cf0339da7ebf4753849a8f7d6fdb8feee99b640') + version('1.60.0', sha256='686affff989ac2488f79a97b9479efb9f2abae035b5ed4d8226de6857933fd3b') + version('1.59.0', sha256='727a932322d94287b62abb1bd2d41723eec4356a7728909e38adb65ca25241ca') + version('1.58.0', sha256='fdfc204fc33ec79c99b9a74944c3e54bd78be4f7f15e260c0e2700a36dc7d3e5') + version('1.57.0', sha256='910c8c022a33ccec7f088bd65d4f14b466588dda94ba2124e78b8c57db264967') + version('1.56.0', sha256='134732acaf3a6e7eba85988118d943f0fa6b7f0850f65131fff89823ad30ff1d') + version('1.55.0', sha256='fff00023dd79486d444c8e29922f4072e1d451fc5a4d2b6075852ead7f2b7b52') + version('1.54.0', sha256='047e927de336af106a24bceba30069980c191529fd76b8dff8eb9a328b48ae1d') + version('1.53.0', sha256='f88a041b01882b0c9c5c05b39603ec8383fb881f772f6f9e6e6fd0e0cddb9196') + version('1.52.0', sha256='222b6afd7723f396f5682c20130314a10196d3999feab5ba920d2a6bf53bac92') + version('1.51.0', sha256='fb2d2335a29ee7fe040a197292bfce982af84a645c81688a915c84c925b69696') + version('1.50.0', sha256='c9ace2b8c81fa6703d1d17c7e478de3bc51101c5adbdeb3f6cb72cf3045a8529') + version('1.49.0', sha256='dd748a7f5507a7e7af74f452e1c52a64e651ed1f7263fce438a06641d2180d3c') + version('1.48.0', sha256='1bf254b2d69393ccd57a3cdd30a2f80318a005de8883a0792ed2f5e2598e5ada') + version('1.47.0', sha256='815a5d9faac4dbd523fbcf3fe1065e443c0bbf43427c44aa423422c6ec4c2e31') + version('1.46.1', sha256='e1dfbf42b16e5015c46b98e9899c423ca4d04469cbeee05e43ea19236416d883') + version('1.46.0', sha256='2f90f60792fdc25e674b8a857a0bcbb8d01199651719c90d5c4f8c61c08eba59') + version('1.45.0', sha256='55ed3ec51d5687e8224c988e22bef215dacce04e037d9f689569a80c4377a6d5') + version('1.44.0', sha256='45c328029d97d1f1dc7ff8c9527cd0c5cc356636084a800bca2ee4bfab1978db') + version('1.43.0', sha256='344f100b1aa410e812cabf0e4130728a80be042bf346135516b9187853806120') + version('1.42.0', sha256='4b1eb95bd250ce15ac66435d6167f225b072b0d3a7eb72477a31847a9ca9e609') + version('1.41.0', sha256='1ef94e6749eaf13318284b4f629be063544c7015b45e38113b975ac1945cc726') + version('1.40.0', sha256='36cf4a239b587067a4923fdf6e290525a14c3af29829524fa73f3dec6841530c') + version('1.39.0', sha256='44785eae8c6cce61a29a8a51f9b737e57b34d66baa7c0bcd4af188832b8018fd') + version('1.38.0', sha256='3ee3a45af4d2fabf343b9e05cfbe033c35d63719b45a6554d5849e4a34216066') + version('1.37.0', sha256='d52ef49f70b1b9addc4e0d1a3a2a1966227f0d173c3301bac3e6d399eeac5472') + version('1.36.0', sha256='9a4a0cfbbd227c20a13519a2c41f2e707dc0d89e518a3c7bfcd381f7b7fbcdef') + version('1.35.0', sha256='f8bf7368a22ccf2e2cf77048ab2129744be4c03f8488c76ad31c0aa229b280da') + version('1.34.1', sha256='0f866c75b025a4f1340117a106595cc0675f48ba1e5a9b5c221ec7f19e96ec4c') + version('1.34.0', sha256='455cb8fa41b759272768257c2e7bdc5c47ec113245dfa533f275e787a855efd2') default_install_libs = set(['atomic', 'chrono', diff --git a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py index 84972bfa807..a193fba98b9 100644 --- a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py +++ b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py @@ -15,7 +15,7 @@ class Boostmplcartesianproduct(Package): homepage = "http://www.organicvectory.com/index.php?option=com_content&view=article&id=75:boostmplcartesianproduct&catid=42:boost&Itemid=78" url = "https://github.com/quinoacomputing/BoostMPLCartesianProduct/tarball/20161205" - version('20161205', 'b0c8534ee807484ffd161723cbc8fc04') + version('20161205', sha256='1fa8e367e4dc545b34016bf57d802858ce38baf40aff20f7c93b329895a18572') def install(self, spec, prefix): install_tree('boost/mpl', join_path(prefix.include, 'boost', 'mpl')) diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py index c89f8f4081a..0454e68e505 100644 --- a/var/spack/repos/builtin/packages/bowtie/package.py +++ b/var/spack/repos/builtin/packages/bowtie/package.py @@ -28,7 +28,7 @@ class Bowtie(MakefilePackage): version('1.2.0', sha256='dc4e7951b8eca56ce7714c47fd4e84f72badd5312ee9546c912af1963570f894') # Keeping the old 1.2 version around for reproducibility, it's not # clearly identical to 1.2.0. - version('1.2', md5='6d97f0ea1a65af11d17cc270cfac4af9', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip') + version('1.2', sha256='b1052de4253007890f6436e6361d40148bc2a5a9dd01827bb9f34097747e65f8', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip') # 1.2.2 and 1.2.2_p1 fail to build with %gcc@8.3.0 # with and without issue-87 patch diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py index b19a15cd9f2..ec54582d038 100644 --- a/var/spack/repos/builtin/packages/bowtie2/package.py +++ b/var/spack/repos/builtin/packages/bowtie2/package.py @@ -16,10 +16,10 @@ class Bowtie2(Package): version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f') version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b') - version('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9') - version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478') - version('2.3.0', '3ab33f30f00f3c30fec1355b4e569ea2') - version('2.2.5', '51fa97a862d248d7ee660efc1147c75f') + version('2.3.4.1', sha256='a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc') + version('2.3.1', sha256='33bd54f5041a31878e7e450cdcf0afba08345fa1133ce8ac6fd00bf7e521a443') + version('2.3.0', sha256='f9f841e780e78b1ae24b17981e2469e6d5add90ec22ef563af23ae2dd5ca003c') + version('2.2.5', sha256='e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0') depends_on('tbb', when='@2.3.0:') depends_on('readline', when='@2.3.1:') diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py index c3e8e86e82e..032faad56d2 100644 --- a/var/spack/repos/builtin/packages/boxlib/package.py +++ b/var/spack/repos/builtin/packages/boxlib/package.py @@ -13,7 +13,7 @@ class Boxlib(CMakePackage): homepage = "https://ccse.lbl.gov/BoxLib/" url = "https://github.com/BoxLib-Codes/BoxLib/archive/16.12.2.tar.gz" - version('16.12.2', 'a28d92a5ff3fbbdbbd0a776a59f18526') + version('16.12.2', sha256='e87faeccfcb14b3436d36c45fcd9f46ea20f65298d35c6db2a80d6332b036dd2') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py index cf026854390..da9473e2aec 100644 --- a/var/spack/repos/builtin/packages/bpp-core/package.py +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -12,7 +12,7 @@ class BppCore(CMakePackage): homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" url = "http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz" - version('2.2.0', '5789ed2ae8687d13664140cd77203477') + version('2.2.0', sha256='aacd4afddd1584ab6bfa1ff6931259408f1d39958a0bdc5f78bf1f9ee4e98b79') depends_on('cmake@2.6:', type='build') diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py index 62b35209618..f48889a8821 100644 --- a/var/spack/repos/builtin/packages/bpp-phyl/package.py +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -12,7 +12,7 @@ class BppPhyl(CMakePackage): homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" url = "http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz" - version('2.2.0', '5c40667ec0bf37e0ecaba321be932770') + version('2.2.0', sha256='f346d87bbc7858924f3c99d7d74eb4a1f7a1b926746c68d8c28e07396c64237b') depends_on('cmake@2.6:', type='build') depends_on('bpp-core') diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py index f938539b94d..74ca003851e 100644 --- a/var/spack/repos/builtin/packages/bpp-seq/package.py +++ b/var/spack/repos/builtin/packages/bpp-seq/package.py @@ -12,7 +12,7 @@ class BppSeq(CMakePackage): homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" url = "http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz" - version('2.2.0', '44adef0ff4d5ca4e69ccf258c9270633') + version('2.2.0', sha256='0927d7fb0301c1b99a7353d5876deadb4a3040776cc74e8fe1c366fe920e7b6b') depends_on('cmake@2.6:', type='build') depends_on('bpp-core') diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py index 3cfe8f3e4ee..542a5cf73e5 100644 --- a/var/spack/repos/builtin/packages/bpp-suite/package.py +++ b/var/spack/repos/builtin/packages/bpp-suite/package.py @@ -13,7 +13,7 @@ class BppSuite(CMakePackage): homepage = "http://biopp.univ-montp2.fr/wiki/index.php/BppSuite" url = "http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz" - version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4') + version('2.2.0', sha256='761fa5eec794af221d971ae70fd8c43171ad71a6bb5f20549263a1797b43f138') depends_on('cmake@2.6:', type='build') depends_on('texinfo', type='build') diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py index 2a1d6f0f43b..b971f099691 100644 --- a/var/spack/repos/builtin/packages/bracken/package.py +++ b/var/spack/repos/builtin/packages/bracken/package.py @@ -14,7 +14,7 @@ class Bracken(Package): homepage = "https://ccb.jhu.edu/software/bracken" url = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz" - version('1.0.0', 'bd91805655269c5f3becb8f8028bab6d') + version('1.0.0', sha256='8ee736535ad994588339d94d0db4c0b1ba554a619f5f96332ee09f2aabdfe176') depends_on('perl') depends_on('python@2.7:') diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py index 86d8cd2e8c2..973268a4b66 100644 --- a/var/spack/repos/builtin/packages/braker/package.py +++ b/var/spack/repos/builtin/packages/braker/package.py @@ -17,8 +17,8 @@ class Braker(Package): list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old" version('2.1.4', sha256='d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52') - version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56') - version('1.11', '297efe4cabdd239b710ac2c45d81f6a5', + version('2.1.0', md5='5f974abcceb9f96a11668fa20a6f6a56') + version('1.11', sha256='cb2d9abe1720ed58753d362eee4af3791007efc617754804882d31f9fe2eab00', url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/branson/package.py b/var/spack/repos/builtin/packages/branson/package.py index 8c3e028ee1a..38d76499d83 100644 --- a/var/spack/repos/builtin/packages/branson/package.py +++ b/var/spack/repos/builtin/packages/branson/package.py @@ -21,11 +21,11 @@ class Branson(CMakePackage): # Version 1.01 is actually deprecated and older than any of the 0.8 series. # However, its entry is left here to reflect older versions of this # spackage. - version('1.01', 'cf7095a887a8dd7d417267615bd0452a') - version('0.82', '7d83d41d0c7ab9c1c906a902165af31182da4604dd0b69aec28d709fe4d7a6ec', + version('1.01', md5='cf7095a887a8dd7d417267615bd0452a') + version('0.82', sha256='7d83d41d0c7ab9c1c906a902165af31182da4604dd0b69aec28d709fe4d7a6ec', preferred=True) - version('0.81', '493f720904791f06b49ff48c17a681532c6a4d9fa59636522cf3f9700e77efe4') - version('0.8', '85ffee110f89be00c37798700508b66b0d15de1d98c54328b6d02a9eb2cf1cb8') + version('0.81', sha256='493f720904791f06b49ff48c17a681532c6a4d9fa59636522cf3f9700e77efe4') + version('0.8', sha256='85ffee110f89be00c37798700508b66b0d15de1d98c54328b6d02a9eb2cf1cb8') depends_on('mpi@2:') depends_on('boost', when='@:0.81') diff --git a/var/spack/repos/builtin/packages/breseq/package.py b/var/spack/repos/builtin/packages/breseq/package.py index 4d93f72112d..82893663d93 100644 --- a/var/spack/repos/builtin/packages/breseq/package.py +++ b/var/spack/repos/builtin/packages/breseq/package.py @@ -16,7 +16,7 @@ class Breseq(AutotoolsPackage): version('0.33.2', sha256='c698d2d25cc7ed251ff916343a8c04f79b5540281288cb7c955f458255ac21de') version('0.33.1', sha256='e24a50e254ad026c519747313b9e42bbeb32bd766a6a06ed369bd5b9dc50e84d') - version('0.31.1', 'a4e602d5481f8692833ba3d5a3cd0394') + version('0.31.1', sha256='ffc8a7f40a5ad918234e465e9d4cdf74be02fd29091b13720c2cab1dc238cf5c') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/brigand/package.py b/var/spack/repos/builtin/packages/brigand/package.py index b70b05c1a0c..54c3b52a478 100644 --- a/var/spack/repos/builtin/packages/brigand/package.py +++ b/var/spack/repos/builtin/packages/brigand/package.py @@ -15,10 +15,10 @@ class Brigand(Package): git = "https://github.com/edouarda/brigand.git" version('master', branch='master') - version('1.3.0', '0bea9713b3b712229aed289e218d577b') - version('1.2.0', '32c0f73e7e666d33ff123334f5c9c92f') - version('1.1.0', '073b7c8e2cbda3a81bbeb1ea5b9ca0eb') - version('1.0.0', 'eeab3d437090f0bb7bc4eb69a5cd9c49') + version('1.3.0', sha256='2468107c5b9ab0b56d84797dfc6636d0aae0507ae9cd6cb1acc1de85e5787acd') + version('1.2.0', sha256='4287fa7278cc000a63e90f1a1b903952b7f606b1a3cf95c23a422d2fe96ca50d') + version('1.1.0', sha256='afdcc6909ebff6994269d3039c31698c2b511a70280072f73382b26855221f64') + version('1.0.0', sha256='8daf7686ff39792f851ef1977323808b80aab31c5f38ef0ba4e6a8faae491f8d') def install(self, spec, prefix): install_tree('include', prefix.include) diff --git a/var/spack/repos/builtin/packages/bsseeker2/package.py b/var/spack/repos/builtin/packages/bsseeker2/package.py index 3c6e0031ebe..73fd8ca24bb 100644 --- a/var/spack/repos/builtin/packages/bsseeker2/package.py +++ b/var/spack/repos/builtin/packages/bsseeker2/package.py @@ -15,7 +15,7 @@ class Bsseeker2(Package): version('2.1.8', sha256='34ebedce36a0fca9e22405d4c2c20bc978439d4a34d1d543657fbc53ff847934') version('2.1.5', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a', url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.7.tar.gz') - version('2.1.2', '5f7f0ef4071711e56b59c5c16b7f34a7', + version('2.1.2', sha256='08055dd314f85a9b74c259c2cb894ea2affdab2c7a120af3589c649e1900c5c6', url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz') depends_on('python@2.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/bucky/package.py b/var/spack/repos/builtin/packages/bucky/package.py index 9a5e95964f1..c88fd91b618 100644 --- a/var/spack/repos/builtin/packages/bucky/package.py +++ b/var/spack/repos/builtin/packages/bucky/package.py @@ -15,7 +15,7 @@ class Bucky(MakefilePackage): homepage = "http://www.stat.wisc.edu/~ane/bucky/index.html" url = "http://dstats.net/download/http://www.stat.wisc.edu/~ane/bucky/v1.4/bucky-1.4.4.tgz" - version('1.4.4', 'f0c910dd1d411d112637826519943a6d') + version('1.4.4', sha256='1621fee0d42314d9aa45d0082b358d4531e7d1d1a0089c807c1b21fbdc4e4592') # Compilation requires gcc conflicts('%cce') diff --git a/var/spack/repos/builtin/packages/bumpversion/package.py b/var/spack/repos/builtin/packages/bumpversion/package.py index 0ed4ef9792d..1f8d3d519d6 100644 --- a/var/spack/repos/builtin/packages/bumpversion/package.py +++ b/var/spack/repos/builtin/packages/bumpversion/package.py @@ -12,7 +12,7 @@ class Bumpversion(PythonPackage): homepage = "https://pypi.python.org/pypi/bumpversion" url = "https://pypi.io/packages/source/b/bumpversion/bumpversion-0.5.0.tar.gz" - version('0.5.3', 'c66a3492eafcf5ad4b024be9fca29820') - version('0.5.0', '222ba619283d6408ce1bfbb0b5b542f3') + version('0.5.3', sha256='6744c873dd7aafc24453d8b6a1a0d6d109faf63cd0cd19cb78fd46e74932c77e') + version('0.5.0', sha256='030832b9b46848e1c1ac6678dba8242a021e35e908b65565800c9650291117dc') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/busco/package.py b/var/spack/repos/builtin/packages/busco/package.py index bbd2741357c..fe3a8fbf0ae 100644 --- a/var/spack/repos/builtin/packages/busco/package.py +++ b/var/spack/repos/builtin/packages/busco/package.py @@ -16,11 +16,11 @@ class Busco(PythonPackage): # TODO: check the installation procedure for version 3.0.2 # and uncomment the following line - # version('3.0.2', '31d80042bb7e96422843fa43d0acbd21') + # version('3.0.2', md5='31d80042bb7e96422843fa43d0acbd21') # There is no tag for version 3.0.1 version('3.0.1', commit='078252e00399550d7b0e8941cd4d986c8e868a83') - version('2.0.1', '4dbcc8a0c18fa8f8312c103eb2fbb4e2') + version('2.0.1', sha256='bd72a79b880370e9b61b8c722e171818c7c85d46cc1e2f80595df2738a7e220c') depends_on('python', type=('build', 'run')) depends_on('blast-plus') diff --git a/var/spack/repos/builtin/packages/butter/package.py b/var/spack/repos/builtin/packages/butter/package.py index 51f9f5b3efb..c7d2c02ef02 100644 --- a/var/spack/repos/builtin/packages/butter/package.py +++ b/var/spack/repos/builtin/packages/butter/package.py @@ -15,7 +15,7 @@ class Butter(Package): homepage = "https://github.com/MikeAxtell/butter" url = "https://github.com/MikeAxtell/butter/archive/v0.3.3.tar.gz" - version('0.3.3', '806ff3cb7afc1d8b75126404056c629d') + version('0.3.3', sha256='862cbe06d51fdefca18e5fe4cfa8e4df6ce92686ccbc389affe05b199ea9243b') depends_on('perl', type=('build', 'run')) depends_on('samtools') diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py index 34c8a460c29..dc4c65a62bd 100644 --- a/var/spack/repos/builtin/packages/bwa/package.py +++ b/var/spack/repos/builtin/packages/bwa/package.py @@ -12,11 +12,11 @@ class Bwa(Package): homepage = "http://github.com/lh3/bwa" url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2" - version('0.7.17', '82cba7ef695538e6a38b9d4156837381') - version('0.7.16a', 'c5115c9a5ea0406848500e4b23a7708c') - version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554') - version('0.7.13', 'f094f609438511766c434178a3635ab4') - version('0.7.12', 'e24a587baaad411d5da89516ad7a261a', + version('0.7.17', sha256='de1b4d4e745c0b7fc3e107b5155a51ac063011d33a5d82696331ecf4bed8d0fd') + version('0.7.16a', md5='c5115c9a5ea0406848500e4b23a7708c') + version('0.7.15', sha256='2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515') + version('0.7.13', sha256='559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc') + version('0.7.12', sha256='285f55b7fa1f9e873eda9a9b06752378a799ecdecbc886bbd9ba238045bf62e0', url='https://github.com/lh3/bwa/archive/0.7.12.tar.gz') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/bwtool/package.py b/var/spack/repos/builtin/packages/bwtool/package.py index 791d5aecc6f..9fe48971a99 100644 --- a/var/spack/repos/builtin/packages/bwtool/package.py +++ b/var/spack/repos/builtin/packages/bwtool/package.py @@ -12,6 +12,6 @@ class Bwtool(AutotoolsPackage): homepage = "https://github.com/CRG-Barcelona/bwtool" url = "https://github.com/CRG-Barcelona/bwtool/archive/1.0.tar.gz" - version('1.0', 'cdd7a34ae457b587edfe7dc8a0bdbedd') + version('1.0', sha256='2e177573602c129e1d37e07288bdc04bef14d2c25c39636aea8c9a359400594a') depends_on('libbeato') diff --git a/var/spack/repos/builtin/packages/byobu/package.py b/var/spack/repos/builtin/packages/byobu/package.py index 2eb321e1176..672a0e61ad2 100644 --- a/var/spack/repos/builtin/packages/byobu/package.py +++ b/var/spack/repos/builtin/packages/byobu/package.py @@ -13,8 +13,8 @@ class Byobu(AutotoolsPackage): homepage = "http://www.byobu.co" url = "https://launchpad.net/byobu/trunk/5.123/+download/byobu_5.123.orig.tar.gz" - version('5.127', '4bafc7cb69ff5b0ab6998816d58cd1ef7175e5de75abc1dd7ffd6d5288a4f63b') - version('5.125', 'f90f15771325e8be9360f301b52182d2') - version('5.123', '961e0072c01c78c9ce4c20d1aa1b0dc4') + version('5.127', sha256='4bafc7cb69ff5b0ab6998816d58cd1ef7175e5de75abc1dd7ffd6d5288a4f63b') + version('5.125', sha256='5022c82705a5d57f1d4e8dcb1819fd04628af2d4b4618b7d44fa27ebfcdda9db') + version('5.123', sha256='2e5a5425368d2f74c0b8649ce88fc653420c248f6c7945b4b718f382adc5a67d') depends_on('tmux', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py index a20bb4c376f..83b5fabf0f5 100644 --- a/var/spack/repos/builtin/packages/bzip2/package.py +++ b/var/spack/repos/builtin/packages/bzip2/package.py @@ -16,9 +16,9 @@ class Bzip2(Package): homepage = "https://sourceware.org/bzip2/" url = "https://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz" - version('1.0.8', 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269') - version('1.0.7', 'e768a87c5b1a79511499beb41500bcc4caf203726fff46a6f5f9ad27fe08ab2b') - version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b') + version('1.0.8', sha256='ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269') + version('1.0.7', sha256='e768a87c5b1a79511499beb41500bcc4caf203726fff46a6f5f9ad27fe08ab2b') + version('1.0.6', sha256='a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd') variant('shared', default=True, description='Enables the build of shared libraries.') diff --git a/var/spack/repos/builtin/packages/c-lime/package.py b/var/spack/repos/builtin/packages/c-lime/package.py index d8cf5ffe2b4..c8550e7ded3 100644 --- a/var/spack/repos/builtin/packages/c-lime/package.py +++ b/var/spack/repos/builtin/packages/c-lime/package.py @@ -15,4 +15,4 @@ class CLime(AutotoolsPackage): homepage = "https://usqcd-software.github.io/c-lime/" url = "https://github.com/usqcd-software/c-lime/archive/qio2-3-9.tar.gz" - version('2-3-9', '28257e7ae75dc68c7c920e3e16db0ec9') + version('2-3-9', sha256='7b9aeadd4dfec50e24da3e7e729f56abf95c9192612c41515fe27b2158773aac') diff --git a/var/spack/repos/builtin/packages/caffe/package.py b/var/spack/repos/builtin/packages/caffe/package.py index 1ed5f22801f..1484d2bdedb 100644 --- a/var/spack/repos/builtin/packages/caffe/package.py +++ b/var/spack/repos/builtin/packages/caffe/package.py @@ -14,11 +14,11 @@ class Caffe(CMakePackage): homepage = "http://caffe.berkeleyvision.org" url = "https://github.com/BVLC/caffe/archive/1.0.tar.gz" - version('1.0', '5fbb0e32e7cd8de3de46e6fe6e4cd2b5') - version('rc5', '692bd3580b7576485cde6b1e03eb5a6d') - version('rc4', 'd86eeb38b1400097d32ffcabdec75b55') - version('rc3', '84e39223115753b48312a8bf48c31f59') - version('rc2', 'c331932e34b5e2f5022fcc34c419080f') + version('1.0', sha256='71d3c9eb8a183150f965a465824d01fe82826c22505f7aa314f700ace03fa77f') + version('rc5', sha256='06592aa8f5254335df3e244dafacc15765e2c60479b4bf2e7c887e8e023802fb') + version('rc4', sha256='018792411d75ee34b6107216550cca2a1d668d45cb366033ba3c647e6a3018df') + version('rc3', sha256='0884207bfba0fbc8b263b87d30f9304f7094eec3a48f975177d142f8c72b6e3b') + version('rc2', sha256='55c9c20870b30ce398e19e4f1a62ade1eff08fce51e28fa5604035b711978eec') variant('cuda', default=False, description='Builds with support for GPUs via CUDA and cuDNN') diff --git a/var/spack/repos/builtin/packages/cairo/package.py b/var/spack/repos/builtin/packages/cairo/package.py index e57100d8aab..c752122e50e 100644 --- a/var/spack/repos/builtin/packages/cairo/package.py +++ b/var/spack/repos/builtin/packages/cairo/package.py @@ -14,9 +14,9 @@ class Cairo(AutotoolsPackage): url = "https://www.cairographics.org/releases/cairo-1.16.0.tar.xz" version('1.16.0', sha256='5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331') - version('1.14.12', '490025a0ba0622a853010f49fb6343f29fb70b9b') - version('1.14.8', 'c6f7b99986f93c9df78653c3e6a3b5043f65145e') - version('1.14.0', '53cf589b983412ea7f78feee2e1ba9cea6e3ebae') + version('1.14.12', sha256='8c90f00c500b2299c0a323dd9beead2a00353752b2092ead558139bd67f7bf16') + version('1.14.8', sha256='d1f2d98ae9a4111564f6de4e013d639cf77155baf2556582295a0f00a9bc5e20') + version('1.14.0', sha256='2cf5f81432e77ea4359af9dcd0f4faf37d015934501391c311bfd2d19a0134b7') variant('X', default=False, description="Build with X11 support") variant('pdf', default=False, description="Enable cairo's PDF surface backend feature") diff --git a/var/spack/repos/builtin/packages/cairomm/package.py b/var/spack/repos/builtin/packages/cairomm/package.py index 724754b9607..2443d1536c1 100644 --- a/var/spack/repos/builtin/packages/cairomm/package.py +++ b/var/spack/repos/builtin/packages/cairomm/package.py @@ -12,8 +12,8 @@ class Cairomm(AutotoolsPackage): homepage = "https://www.cairographics.org/cairomm/" url = "https://cairographics.org/releases/cairomm-1.6.4.tar.gz" - version('1.6.4', '63561c62536173a98f03005dfe55c90e') - version('1.6.2', 'eac5d159e4cba98e32ea174483dee24e') + version('1.6.4', sha256='3cb2c898d0ceb94ad2deb722b50a3a6ee46abdda741ecd6e5a40517c85ecea4c') + version('1.6.2', sha256='068edc1743d92ff1d102141ba7597ba02a47379f9cb97799b0c3310848b56eff') depends_on('cairo') depends_on('libsigcpp') diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py index 3bd7ab39bd1..fe3b9d18a03 100644 --- a/var/spack/repos/builtin/packages/callpath/package.py +++ b/var/spack/repos/builtin/packages/callpath/package.py @@ -13,9 +13,9 @@ class Callpath(CMakePackage): homepage = "https://github.com/llnl/callpath" url = "https://github.com/llnl/callpath/archive/v1.0.1.tar.gz" - version('1.0.4', '39d2e06bfa316dec1085b874092e4b08') - version('1.0.2', 'b1994d5ee7c7db9d27586fc2dcf8f373') - version('1.0.1', '0047983d2a52c5c335f8ba7f5bab2325') + version('1.0.4', sha256='4949974d60f18bb34e44e5a4e60032c39624dde5c3f16d557b3a6845eead4e2e') + version('1.0.2', sha256='cbe42bba8b9dda259dcbe7e16ebd7ecd005eabf7e9ccf169535b03110df75c84') + version('1.0.1', sha256='9bd9723126f80d0b518c28e5298ad0fa8d8dbc6a3f03fee5ae5449cf4c9a550f') depends_on('elf', type='link') depends_on('libdwarf') diff --git a/var/spack/repos/builtin/packages/candle-benchmarks/package.py b/var/spack/repos/builtin/packages/candle-benchmarks/package.py index af396d70abb..af517463b09 100644 --- a/var/spack/repos/builtin/packages/candle-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/candle-benchmarks/package.py @@ -15,7 +15,7 @@ class CandleBenchmarks(Package): tags = ['proxy-app', 'ecp-proxy-app'] version('0.1', sha256='767f74f43ee3a5d4e0f26750f2a96b8433e25a9cd4f2d29938ac8acf263ab58d') - version('0.0', '6eced30dc15374bc9f90a86d0396e470') + version('0.0', md5='6eced30dc15374bc9f90a86d0396e470') variant('mpi', default=True, description='Build with MPI support') diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py index d4da5142dfd..fd66cef27c5 100644 --- a/var/spack/repos/builtin/packages/cantera/package.py +++ b/var/spack/repos/builtin/packages/cantera/package.py @@ -15,8 +15,8 @@ class Cantera(SConsPackage): url = "https://github.com/Cantera/cantera/archive/v2.3.0.tar.gz" version('2.4.0', sha256='0dc771693b657d8f4ba835dd229939e5b9cfd8348d2f5ba82775451a524365a5') - version('2.3.0', 'aebbd8d891cb1623604245398502b72e') - version('2.2.1', '9d1919bdef39ddec54485fc8a741a3aa') + version('2.3.0', sha256='06624f0f06bdd2acc9c0dba13443d945323ba40f68a9d422d95247c02e539b57') + version('2.2.1', sha256='c7bca241848f541466f56e479402521c618410168e8983e2b54ae48888480e1e') variant('python', default=False, description='Build the Cantera Python module') diff --git a/var/spack/repos/builtin/packages/canu/package.py b/var/spack/repos/builtin/packages/canu/package.py index a364983d9e7..01d7ad8ff1c 100644 --- a/var/spack/repos/builtin/packages/canu/package.py +++ b/var/spack/repos/builtin/packages/canu/package.py @@ -16,7 +16,7 @@ class Canu(MakefilePackage): version('1.8', sha256='30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4') version('1.7.1', sha256='c314659c929ee05fd413274f391463a93f19b8337eabb7ee5de1ecfc061caafa') version('1.7', sha256='c5be54b0ad20729093413e7e722a19637d32e966dc8ecd2b579ba3e4958d378a') - version('1.5', '65df275baa28ecf11b15dfd7343361e3') + version('1.5', sha256='06e2c6d7b9f6d325b3b468e9c1a5de65e4689aed41154f2cee5ccd2cef0d5cf6') depends_on('gnuplot', type='run') depends_on('jdk', type='run') diff --git a/var/spack/repos/builtin/packages/cap3/package.py b/var/spack/repos/builtin/packages/cap3/package.py index fe334710100..99da025c689 100644 --- a/var/spack/repos/builtin/packages/cap3/package.py +++ b/var/spack/repos/builtin/packages/cap3/package.py @@ -12,7 +12,7 @@ class Cap3(Package): homepage = "http://seq.cs.iastate.edu/" url = "http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar" - version('2015-02-11', '5393d937978ecc5f18fcb741140e1f02', + version('2015-02-11', sha256='3aff30423e052887925b32f31bdd76764406661f2be3750afbf46341c3d38a06', url='http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/cares/package.py b/var/spack/repos/builtin/packages/cares/package.py index 0a3371b2e14..f3b35ee6103 100644 --- a/var/spack/repos/builtin/packages/cares/package.py +++ b/var/spack/repos/builtin/packages/cares/package.py @@ -14,7 +14,7 @@ class Cares(CMakePackage): git = "https://github.com/c-ares/c-ares.git" version('develop', branch='master') - version('1.13.0', 'cdb21052a7eb85261da22f83c0654cfd') + version('1.13.0', sha256='7c48c57706a38691041920e705d2a04426ad9c68d40edd600685323f214b2d57') def url_for_version(self, version): url = "https://github.com/c-ares/c-ares/archive/cares-{0}.tar.gz" diff --git a/var/spack/repos/builtin/packages/casacore/package.py b/var/spack/repos/builtin/packages/casacore/package.py index f9e18ff3a72..816a5fbca2a 100644 --- a/var/spack/repos/builtin/packages/casacore/package.py +++ b/var/spack/repos/builtin/packages/casacore/package.py @@ -12,7 +12,7 @@ class Casacore(CMakePackage): homepage = "https://github.com/casacore/casacore" url = "https://github.com/casacore/casacore/archive/v2.4.1.tar.gz" - version('2.4.1', '88fdbdadbc1320290c36f1605d3bd9e7') + version('2.4.1', sha256='58eccc875053b2c6fe44fe53b6463030ef169597ec29926936f18d27b5087d63') variant('openmp', default=False, description='Build OpenMP support') variant('shared', default=True, description='Build shared libraries') diff --git a/var/spack/repos/builtin/packages/cask/package.py b/var/spack/repos/builtin/packages/cask/package.py index 3f62b1309eb..28afef887f3 100644 --- a/var/spack/repos/builtin/packages/cask/package.py +++ b/var/spack/repos/builtin/packages/cask/package.py @@ -18,9 +18,9 @@ class Cask(Package): homepage = "http://cask.readthedocs.io/en/latest/" url = "https://github.com/cask/cask/archive/v0.7.4.tar.gz" - version('0.8.1', '25196468a7ce634cfff14733678be6ba') + version('0.8.1', sha256='8739ba608f23c79b3426faa8b068d5d1bc096c7305ce30b1163babd354be821c') # version 0.8.0 is broken - version('0.7.4', 'c973a7db43bc980dd83759a5864a1260') + version('0.7.4', sha256='b183ea1c50fc215c9040f402b758ecc335901fbc2c3afd4a7302386c888d437d') depends_on('emacs', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/casper/package.py b/var/spack/repos/builtin/packages/casper/package.py index ab43c7994ca..088a0b49b1d 100644 --- a/var/spack/repos/builtin/packages/casper/package.py +++ b/var/spack/repos/builtin/packages/casper/package.py @@ -15,7 +15,7 @@ class Casper(MakefilePackage): homepage = "http://best.snu.ac.kr/casper/index.php?name=main" url = "http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz" - version('0.8.2', '9e83d32ff46b876f33eb1d7b545ec9c2') + version('0.8.2', sha256='3005e165cebf8ce4e12815b7660a833e0733441b5c7e5ecbfdccef7414b0c914') depends_on('jellyfish@2.2.3:') depends_on('boost') diff --git a/var/spack/repos/builtin/packages/catalyst/package.py b/var/spack/repos/builtin/packages/catalyst/package.py index 1289ace5241..a37574a8888 100644 --- a/var/spack/repos/builtin/packages/catalyst/package.py +++ b/var/spack/repos/builtin/packages/catalyst/package.py @@ -22,16 +22,16 @@ class Catalyst(CMakePackage): maintainers = ['chuckatkins', 'danlipsa'] version('5.6.0', sha256='5b49cb96ab78eee0427e25200530ac892f9a3da7725109ce1790f8010cb5b377') - version('5.5.2', '7eb93c31a1e5deb7098c3b4275e53a4a') - version('5.5.1', 'a7d92a45837b67c3371006cc45163277') - version('5.5.0', 'a8f2f41edadffdcc89b37fdc9aa7f005') - version('5.4.1', '4030c70477ec5a85aa72d6fc86a30753') - version('5.4.0', 'b92847605bac9036414b644f33cb7163') - version('5.3.0', '68fbbbe733aa607ec13d1db1ab5eba71') - version('5.2.0', '4570d1a2a183026adb65b73c7125b8b0') - version('5.1.2', '44fb32fc8988fcdfbc216c9e40c3e925') - version('5.0.1', 'fdf206113369746e2276b95b257d2c9b') - version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378') + version('5.5.2', sha256='64561f34c4402b88f3cb20a956842394dde5838efd7ebb301157a837114a0e2d') + version('5.5.1', sha256='a6e67a95a7a5711a2b5f95f38ccbff4912262b3e1b1af7d6b9afe8185aa85c0d') + version('5.5.0', sha256='1b619e326ff574de808732ca9a7447e4cd14e94ae6568f55b6581896cd569dff') + version('5.4.1', sha256='390d0f5dc66bf432e202a39b1f34193af4bf8aad2355338fa5e2778ea07a80e4') + version('5.4.0', sha256='f488d84a53b1286d2ee1967e386626c8ad05a6fe4e6cbdaa8d5e042f519f94a9') + version('5.3.0', sha256='046631bbf00775edc927314a3db207509666c9c6aadc7079e5159440fd2f88a0') + version('5.2.0', sha256='894e42ef8475bb49e4e7e64f4ee2c37c714facd18bfbb1d6de7f69676b062c96') + version('5.1.2', sha256='ff02b7307a256b7c6e8ad900dee5796297494df7f9a0804fe801eb2f66e6a187') + version('5.0.1', sha256='caddec83ec284162a2cbc46877b0e5a9d2cca59fb4ab0ea35b0948d2492950bb') + version('4.4.0', sha256='c2dc334a89df24ce5233b81b74740fc9f10bc181cd604109fd13f6ad2381fc73') variant('python', default=False, description='Enable Python support') variant('python3', default=False, description='Enable Python3 support') diff --git a/var/spack/repos/builtin/packages/catch/package.py b/var/spack/repos/builtin/packages/catch/package.py index e4dbde3a1ce..a9d8cb412b5 100644 --- a/var/spack/repos/builtin/packages/catch/package.py +++ b/var/spack/repos/builtin/packages/catch/package.py @@ -36,34 +36,34 @@ class Catch(CMakePackage): # releases 2.3.0+ changed to "catch2/catch.hpp" header version('2.2.3', sha256='45e5e12cc5a98e098b0960d70c0d99b7168b711e85fb947dcd4d68ec3f8b8826') version('2.2.2', sha256='e93aacf012579093fe6b4e686ff0488975cabee1e6b4e4f27a0acd898e8f09fd') - version('2.2.1', '54e56803c84890636bd7fe6c3856b104') - version('2.1.0', '70b44068976d46d48f3cd8796f675691d3bc726b') - version('2.0.1', '5c191a031edebd0525640ed2f38cbf64bacb1803') - version('1.12.1', '7d89cffd9d61f4fdcbdb373b70cc92d1') - version('1.12.0', '8fb0a64144a2c1572dd930254c7bbdf504ecbe2d') - version('1.11.0', '3c03a022d8ba8dbbc931e1ce9fb28faec4890b8d') - version('1.10.0', 'c2033ca00b616e7e703623c68220cf5a8e12bba4') - version('1.9.7', '7ea41b48a23bd83f377f05a9dfde2be230cfc1b4') - version('1.9.6', 'e6ae3a50c6e4da64410979dcd4b2bb3f7ba1c364') - version('1.9.5', '7ba2bb12b5398b8b9ab7a7907f4cd345a55e179a') - version('1.9.4', 'b48fce35161160def587bd0d8f0e95969b20b786') - version('1.9.3', 'c0db82118496a2dd0637aad352f31d9356bffc28') - version('1.9.2', '627fd94d466c0f71ba84010adf82771ed3ce85c7') - version('1.9.1', '331e4a5cd32fe4c36b4bea15e5198346f18b5c3f') - version('1.9.0', '5bb46e99eea39224189a8a0442ec7790c635a7b0') - version('1.8.2', '34b8a2da76befeeaeafc393569538222605dda51') - version('1.8.1', 'd5f4ae9603fe27c313bc5b5b23c233bdce5c57f7') - version('1.8.0', '7fa6bfc50e6dbb6fd1352f41496650d56a86ac1a') - version('1.7.2', '45b0ab04b6da75ce56de25a81f0b0de4c7a62179') - version('1.7.1', '3a55985aacd5a5ff8a87c1490bbf65f0122647dc') - version('1.7.0', '6f9869cc066721d525bb03e8a9423b806c362140') - version('1.6.1', 'e88de5b611c07d5d402142d3dc20b63350fdf76c') - version('1.6.0', '21273cbed050b8d4785231d04812d5addf5b71b7') - version('1.5.9', '341bee0b642f0dc9bb6fb41243a068239468b703') - version('1.5.0', '2d14342c72f12b3f4b975cf6aa8594c8ad43d773') - version('1.4.0', '3b3b76a842508386be40d73849627bbe12fb5b7f') - version('1.3.5', '2cfd78bce21368355c7d3880df88716084df2186') - version('1.3.0', '24cd4e6518273fea20becd47a2e1edbee7ec209a') + version('2.2.1', sha256='3938bc896f8de570bc56d25606fc128437ee53590a95cf3e005710176a1a1ce4') + version('2.1.0', sha256='a8f9805174916c23bf59ed45f72c21ce092e2848c139f4c6d396aeeb5ce2dfb3') + version('2.0.1', sha256='5f31b93712e65d363f257ad0f0c02cfbed7a3988979d5f320ad7771e513d4cc8') + version('1.12.1', sha256='9a0b4722a9864fa0728241ecca2e4c1b3de8e60a5d6fe3f92dec7b8bbfbc850d') + version('1.12.0', sha256='adab7275bddcd8b5ba28478db513371137188beef5ef40489edb1c34fe2bf421') + version('1.11.0', sha256='b6f30b548aa15e42d299f3fdb15f69df4777c1b20ca24d8d7dee552d76870eff') + version('1.10.0', sha256='6e5e686c9e83ff92d622dd04281e9893957a812cfc97d2d1028a988e4bc6a31e') + version('1.9.7', sha256='175245fba4e76dca8528289c0ae23690c2270bd0fde51b8b145a5576cf70e785') + version('1.9.6', sha256='5dc4b9b38d8755173987bb47af29491656e413b64eb06e1a03cfb9c26bae0a0e') + version('1.9.5', sha256='6531b3817066ea8ab96e7a7fbda7e68a43134e6e62fdc5d8c394a451d54b1b9b') + version('1.9.4', sha256='d40a17198b0c45c1f8164e3af71a2ce759e71d08772c9066b36ccd7781fb5e64') + version('1.9.3', sha256='2e3a48781d7e57cb7afdfc3c189c8a05d99ebb7f62cc8813b63c9b75cd6045dc') + version('1.9.2', sha256='b42070df2ff568bb407d327c431cfbc19a40bd06a19228956772dc32e8c9eb45') + version('1.9.1', sha256='d3fd58730471969b46ed234f5995927cf4324b33474c3746bf17ad3cbc40132d') + version('1.9.0', sha256='acf3d9c864e06866f9993c71017d672fa7b951347402155b365e58e117ec9c2c') + version('1.8.2', sha256='85e7acf9df4763e7df3e832df393eaf52b52a1d0bfc4ab751566e3bdbe616642') + version('1.8.1', sha256='12fd706b63251f8fae1c32013815de33decec4e63a4a8f99af0af1fe0690c53d') + version('1.8.0', sha256='713d6a6d98f7402bcc2d10a00121a37aec284e6b34b34121d2a09fc1c838e5bc') + version('1.7.2', sha256='4aeca774db0ebbea0f86548e1c742fbc4c67c8cf0da550fbfe3e55efa1cc2178') + version('1.7.1', sha256='46b289866f9b44c850cc1e48d0ead479494fd8ef0cdb9eda88b1dfd5b990556a') + version('1.7.0', sha256='55ff8904d1215aadaa003ae50e1ad82747c655004b43bf30c656cb20e1c89050') + version('1.6.1', sha256='83ad2744529b3b507eee188dba23baf6b5c038fccbbe4b3256172c04420292e4') + version('1.6.0', sha256='9a7aed27cc58eee0e694135503dcc7fc99c7ec254416cff44fe10166a5f1f68c') + version('1.5.9', sha256='0ba04d0eefcf5a1d4c9e9e79f051f1f93de704ea4429a247f69ec76c2c6647cd') + version('1.5.0', sha256='bbf0ce7f72a1a8892956bc4caba9ead930b8662d908baa0b2e2ec6b164307d22') + version('1.4.0', sha256='57512b298ca3e2ff44e87c17c926d5f9edf29e13549480e912fddfab5ba63b74') + version('1.3.5', sha256='f15730d81b4173fb860ce3561768de7d41bbefb67dc031d7d1f5ae2c07f0a472') + version('1.3.0', sha256='245f6ee73e2fea66311afa1da59e5087ddab8b37ce64994ad88506e8af28c6ac') @when('+single_header') def cmake(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/cbench/package.py b/var/spack/repos/builtin/packages/cbench/package.py index 9c3ead53127..8c00aeeaddf 100644 --- a/var/spack/repos/builtin/packages/cbench/package.py +++ b/var/spack/repos/builtin/packages/cbench/package.py @@ -17,7 +17,7 @@ class Cbench(MakefilePackage): list_url = "https://sourceforge.net/projects/cbench/files/cbench/" list_depth = 1 - version('1.3.0', '2fb112876fdc96165d14e019b4a26f2e') + version('1.3.0', sha256='b40fdafd14869b86819e5906a107b0735290a1e58bae229d8166514a72f58732') depends_on('mpi') depends_on('blas') diff --git a/var/spack/repos/builtin/packages/cblas/package.py b/var/spack/repos/builtin/packages/cblas/package.py index e0416050740..7ade542e2fb 100644 --- a/var/spack/repos/builtin/packages/cblas/package.py +++ b/var/spack/repos/builtin/packages/cblas/package.py @@ -14,7 +14,7 @@ class Cblas(Package): homepage = "http://www.netlib.org/blas/_cblas/" # tarball has no version, but on the date below, this MD5 was correct. - version('2015-06-06', '1e8830f622d2112239a4a8a83b84209a', + version('2015-06-06', sha256='0f6354fd67fabd909baf57ced2ef84e962db58fae126e4f41b21dd4fec60a2a3', url='http://www.netlib.org/blas/blast-forum/cblas.tgz') depends_on('blas') diff --git a/var/spack/repos/builtin/packages/ccache/package.py b/var/spack/repos/builtin/packages/ccache/package.py index fca6a277b71..ef6a0d79b61 100644 --- a/var/spack/repos/builtin/packages/ccache/package.py +++ b/var/spack/repos/builtin/packages/ccache/package.py @@ -14,12 +14,12 @@ class Ccache(AutotoolsPackage): homepage = "https://ccache.samba.org/" url = "https://www.samba.org/ftp/ccache/ccache-3.3.4.tar.gz" - version('3.3.4', '61326f1edac7cd211a7018458dfe2d86') - version('3.3.3', 'ea1f95303749b9ac136c617d1b333eef') - version('3.3.2', 'b966d56603e1fad2bac22930e5f01830') - version('3.3.1', '7102ef024cff09d353b3f4c48379b40b') - version('3.3', 'b7ac8fdd556f93831618483325fbb1ef') - version('3.2.9', '8f3f6e15e75a0e6020166927d41bd0b3') + version('3.3.4', sha256='1348b54e7c35dd2f8d17923389e03c546e599cfbde6459d2f31cf6f1521ec538') + version('3.3.3', sha256='87a399a2267cfac3f36411fbc12ff8959f408cffd050ad15fe423df88e977e8f') + version('3.3.2', sha256='bf4a150dea611a206a933e122bd545dd6c5111d319505e0e30fef75f88651847') + version('3.3.1', sha256='4101f9937cd6e8f50d0a5882f7e9a7312ba42c01ff41e4f359c94ae2c9b87879') + version('3.3', sha256='b220fce435fe3d86b8b90097e986a17f6c1f971e0841283dd816adb238c5fd6a') + version('3.2.9', sha256='1e13961b83a3d215c4013469c149414a79312a22d3c7bf9f946abac9ee33e63f') depends_on('gperf') depends_on('libxslt') diff --git a/var/spack/repos/builtin/packages/cdd/package.py b/var/spack/repos/builtin/packages/cdd/package.py index 28eb125e578..b2d11c0bcec 100644 --- a/var/spack/repos/builtin/packages/cdd/package.py +++ b/var/spack/repos/builtin/packages/cdd/package.py @@ -16,7 +16,7 @@ class Cdd(Package): homepage = "https://www.inf.ethz.ch/personal/fukudak/cdd_home/cdd.html" url = "http://www.cs.mcgill.ca/~fukuda/download/cdd/cdd-061a.tar.gz" - version('0.61a', '22c24a7a9349dd7ec0e24531925a02d9') + version('0.61a', sha256='637a1909bbd8aa4d32667da08f9e9ac687bf7d3ef1b8af5bd227e91a3cd4019b') depends_on("libtool", type="build") diff --git a/var/spack/repos/builtin/packages/cddlib/package.py b/var/spack/repos/builtin/packages/cddlib/package.py index acf4e36373b..60d352c0ba1 100644 --- a/var/spack/repos/builtin/packages/cddlib/package.py +++ b/var/spack/repos/builtin/packages/cddlib/package.py @@ -16,7 +16,7 @@ class Cddlib(AutotoolsPackage): homepage = "https://www.inf.ethz.ch/personal/fukudak/cdd_home/" url = "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-094h.tar.gz" - version('0.94h', '1467d270860bbcb26d3ebae424690e7c') + version('0.94h', sha256='fe6d04d494683cd451be5f6fe785e147f24e8ce3ef7387f048e739ceb4565ab5') # Note: It should be possible to build cddlib also without gmp diff --git a/var/spack/repos/builtin/packages/cdhit/package.py b/var/spack/repos/builtin/packages/cdhit/package.py index 0f5172bfc1e..a2ba8c72bb7 100644 --- a/var/spack/repos/builtin/packages/cdhit/package.py +++ b/var/spack/repos/builtin/packages/cdhit/package.py @@ -14,7 +14,7 @@ class Cdhit(MakefilePackage): url = "https://github.com/weizhongli/cdhit/archive/V4.6.8.tar.gz" version('4.8.1', sha256='f8bc3cdd7aebb432fcd35eed0093e7a6413f1e36bbd2a837ebc06e57cdb20b70') - version('4.6.8', 'bdd73ec0cceab6653aab7b31b57c5a8b') + version('4.6.8', sha256='37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949') variant('openmp', default=True, description='Compile with multi-threading support') variant('zlib', default=True, description='Compile with zlib') diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py index bdc5aef2957..77111281865 100644 --- a/var/spack/repos/builtin/packages/cdo/package.py +++ b/var/spack/repos/builtin/packages/cdo/package.py @@ -19,15 +19,15 @@ class Cdo(AutotoolsPackage): version('1.9.7.1', sha256='3771952e065bcf935d43e492707370ed2a0ecb59a06bea24f9ab69d77943962c', url='https://code.mpimet.mpg.de/attachments/download/20124/cdo-1.9.7.1.tar.gz') - version('1.9.6', '322f56c5e13f525c585ee5318d4435db', url='https://code.mpimet.mpg.de/attachments/download/19299/cdo-1.9.6.tar.gz') - version('1.9.5', '0c60f2c94dc5c76421ecf363153a5043', url='https://code.mpimet.mpg.de/attachments/download/18264/cdo-1.9.5.tar.gz') - version('1.9.4', '377c9e5aa7d8cbcb4a6c558abb2eb053', url='https://code.mpimet.mpg.de/attachments/download/17374/cdo-1.9.4.tar.gz') - version('1.9.3', '13ae222164413dbd53532b03b072def5', url='https://code.mpimet.mpg.de/attachments/download/16435/cdo-1.9.3.tar.gz') - version('1.9.2', '38e68d34f0b5b44a52c3241be6831423', url='https://code.mpimet.mpg.de/attachments/download/16035/cdo-1.9.2.tar.gz') - version('1.9.1', 'e60a89f268ba24cee5c461f2c217829e', url='https://code.mpimet.mpg.de/attachments/download/15653/cdo-1.9.1.tar.gz') - version('1.9.0', '2d88561b3b4a880df0422a62e5027e40', url='https://code.mpimet.mpg.de/attachments/download/15187/cdo-1.9.0.tar.gz') - version('1.8.2', '6a2e2f99b7c67ee9a512c40a8d4a7121', url='https://code.mpimet.mpg.de/attachments/download/14686/cdo-1.8.2.tar.gz') - version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31', url='https://code.mpimet.mpg.de/attachments/download/12760/cdo-1.7.2.tar.gz') + version('1.9.6', sha256='b31474c94548d21393758caa33f35cf7f423d5dfc84562ad80a2bdcb725b5585', url='https://code.mpimet.mpg.de/attachments/download/19299/cdo-1.9.6.tar.gz') + version('1.9.5', sha256='48ed65cc5b436753c8e7f9eadd8aa97376698ce230ceafed2a4350a5b1a27148', url='https://code.mpimet.mpg.de/attachments/download/18264/cdo-1.9.5.tar.gz') + version('1.9.4', sha256='3d1c0fd3f7d38c5d3d88139ca1546c9d24e1b1ff752a794a4194dfe624695def', url='https://code.mpimet.mpg.de/attachments/download/17374/cdo-1.9.4.tar.gz') + version('1.9.3', sha256='e83a3de7b402600c0d9a5df18073d36d133ff9719d3c561a0efa90f9c1599f3f', url='https://code.mpimet.mpg.de/attachments/download/16435/cdo-1.9.3.tar.gz') + version('1.9.2', sha256='d1c5092167034a48e4b8ada24cf78a1d4b84e364ffbb08b9ca70d13f428f300c', url='https://code.mpimet.mpg.de/attachments/download/16035/cdo-1.9.2.tar.gz') + version('1.9.1', sha256='33cba3cfcc27e5896769143c5f8e2f300ca14c7a40d1f19ffd1ed24b49ea3d55', url='https://code.mpimet.mpg.de/attachments/download/15653/cdo-1.9.1.tar.gz') + version('1.9.0', sha256='df367f8c3abf4ab085bcfc61e0205b28a5ecc69b7b83ba398b4d3c874dd69008', url='https://code.mpimet.mpg.de/attachments/download/15187/cdo-1.9.0.tar.gz') + version('1.8.2', sha256='6ca6c1263af2237737728ac937a275f8aa27680507636a6b6320f347c69a369a', url='https://code.mpimet.mpg.de/attachments/download/14686/cdo-1.8.2.tar.gz') + version('1.7.2', sha256='4c43eba7a95f77457bfe0d30fb82382b3b5f2b0cf90aca6f0f0a008f6cc7e697', url='https://code.mpimet.mpg.de/attachments/download/12760/cdo-1.7.2.tar.gz') variant('netcdf', default=True, description='Enable NetCDF support') variant('grib2', default='eccodes', values=('eccodes', 'grib-api', 'none'), diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py index b066da4446a..4d598c03db4 100644 --- a/var/spack/repos/builtin/packages/ceed/package.py +++ b/var/spack/repos/builtin/packages/ceed/package.py @@ -18,10 +18,10 @@ class Ceed(Package): homepage = "https://ceed.exascaleproject.org" url = 'file://' + os.path.dirname(__file__) + '/README.md' - sha1 = 'b2eefd95c09ba573f663a761b84811a2d7e39788' + sha256 = '418c4b6b6a098648e25befdc28cdf9c351ecea9deaa660c0d9a674f8c6917122' - version('2.0.0', sha1, expand=False) - version('1.0.0', sha1, expand=False) + version('2.0.0', sha256, expand=False) + version('1.0.0', sha256, expand=False) variant('cuda', default=False, description='Build MAGMA; enable CUDA support in libCEED and OCCA') diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index f05f5cbc33e..0d0735f713a 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -18,14 +18,14 @@ class Cereal(CMakePackage): homepage = "http://uscilab.github.io/cereal/" url = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz" - version('1.2.2', '4c56c7b9499dba79404250ef9a040481') - version('1.2.1', '64476ed74c19068ee543b53ad3992261') - version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b') - version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9') - version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27') - version('1.1.0', '9f2d5f72e935c54f4c6d23e954ce699f') - version('1.0.0', 'd1bacca70a95cec0ddbff68b0871296b') - version('0.9.1', '8872d4444ff274ce6cd1ed364d0fc0ad') + version('1.2.2', sha256='1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4') + version('1.2.1', sha256='7d321c22ea1280b47ddb06f3e9702fcdbb2910ff2f3df0a2554804210714434e') + version('1.2.0', sha256='1ccf3ed205a7a2f0d6a060415b123f1ae0d984cd4435db01af8de11a2eda49c1') + version('1.1.2', sha256='45607d0de1d29e84d03bf8eecf221eb2912005b63f02314fbade9fbabfd37b8d') + version('1.1.1', sha256='ec5e2b2c8f145d86eb7c079300360bb06f708527187834f3f127e9a12b07e9cf') + version('1.1.0', sha256='69113debdac9de561f499af4cf7755b2e8c3afa92649b8178b34a7c6bbe4f12f') + version('1.0.0', sha256='51c31c84d4c9e410e56d8bfc3424076b3234f11aa349ac8cda3db9f18118c125') + version('0.9.1', sha256='2a99722df9c3d0f75267f732808a4d7e564cb5a35318a3d1c00086e2ef139385') patch("Boost.patch") patch("Boost2.patch", when="@1.2.2:") diff --git a/var/spack/repos/builtin/packages/ceres-solver/package.py b/var/spack/repos/builtin/packages/ceres-solver/package.py index 85d6b4f20f8..fa081154f7e 100644 --- a/var/spack/repos/builtin/packages/ceres-solver/package.py +++ b/var/spack/repos/builtin/packages/ceres-solver/package.py @@ -17,7 +17,7 @@ class CeresSolver(CMakePackage): homepage = "http://ceres-solver.org" url = "http://ceres-solver.org/ceres-solver-1.12.0.tar.gz" - version('1.12.0', '278a7b366881cc45e258da71464114d9') + version('1.12.0', sha256='745bfed55111e086954126b748eb9efe20e30be5b825c6dec3c525cf20afc895') depends_on('eigen@3:') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/cfitsio/package.py b/var/spack/repos/builtin/packages/cfitsio/package.py index 46be24c2293..b41261c18b3 100644 --- a/var/spack/repos/builtin/packages/cfitsio/package.py +++ b/var/spack/repos/builtin/packages/cfitsio/package.py @@ -14,10 +14,10 @@ class Cfitsio(AutotoolsPackage): homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' url = 'http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3450.tar.gz' - version('3.450', 'f470849bb43561d9a9b1925eeb7f7f0d') - version('3.420', '26e5c0dfb85b8d00f536e706305caa13') - version('3.410', '8a4a66fcdd816aae41768baa0b025552') - version('3.370', 'abebd2d02ba5b0503c633581e3bfa116') + version('3.450', sha256='bf6012dbe668ecb22c399c4b7b2814557ee282c74a7d5dc704eb17c30d9fb92e') + version('3.420', sha256='6c10aa636118fa12d9a5e2e66f22c6436fb358da2af6dbf7e133c142e2ac16b8') + version('3.410', sha256='a556ac7ea1965545dcb4d41cfef8e4915eeb8c0faa1b52f7ff70870f8bb5734c') + version('3.370', sha256='092897c6dae4dfe42d91d35a738e45e8236aa3d8f9b3ffc7f0e6545b8319c63a') variant('bzip2', default=True, description='Enable bzip2 support') variant('shared', default=True, description='Build shared libraries') diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py index 7b0bcee6b9d..2252655c85a 100644 --- a/var/spack/repos/builtin/packages/cgal/package.py +++ b/var/spack/repos/builtin/packages/cgal/package.py @@ -16,13 +16,13 @@ class Cgal(CMakePackage): homepage = 'http://www.cgal.org/' url = 'https://github.com/CGAL/cgal/releases/download/releases/CGAL-4.11/CGAL-4.11.tar.xz' - version('4.13', '3e3dd7a64febda58be54c3cbeba329ab6a73b72d4d7647ba4931ecd1fad0e3bc') - version('4.12', 'b12fd24dedfa889a04abfaea565a88bd') - version('4.11', '0e9566046e402f8dc514caef11155864') - version('4.9.1', '820ef17ffa7ed87af6cc9918a961d966') - version('4.9', 'ee31343dbc4bf7b5b7501ec1650e9233') - version('4.7', '623d91fb2ab0a35049dc6098a0f235cc') - version('4.6.3', '6953897544d41ffcc63ffe58b32a688f') + version('4.13', sha256='3e3dd7a64febda58be54c3cbeba329ab6a73b72d4d7647ba4931ecd1fad0e3bc') + version('4.12', sha256='442ef4fffb2ad6e4141e5a7902993ae6a4e73f7cb641fae1010bb586f6ca5e3f') + version('4.11', sha256='27a7762e5430f5392a1fe12a3a4abdfe667605c40224de1c6599f49d66cfbdd2') + version('4.9.1', sha256='56557da971b5310c2678ffc5def4109266666ff3adc7babbe446797ee2b90cca') + version('4.9', sha256='63ac5df71f912f34f2f0f2e54a303578df51f4ec2627db593a65407d791f9039') + version('4.7', sha256='50bd0a1cad7a8957b09012f831eebaf7d670e2a3467e8f365ec0c71fa5436369') + version('4.6.3', sha256='e338027b8767c0a7a6e4fd8679182d1b83b5b1a0da0a1fe4546e7c0ca094fc21') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/cgm/package.py b/var/spack/repos/builtin/packages/cgm/package.py index baa8e25bbc1..d572e1b73fd 100644 --- a/var/spack/repos/builtin/packages/cgm/package.py +++ b/var/spack/repos/builtin/packages/cgm/package.py @@ -13,10 +13,10 @@ class Cgm(AutotoolsPackage): homepage = "http://sigma.mcs.anl.gov/cgm-library" url = "http://ftp.mcs.anl.gov/pub/fathom/cgm-16.0.tar.gz" - version('16.0', 'a68aa5954d82502ff75d5eb91a29a01c') - version('13.1.1', '4e8dbc4ba8f65767b29f985f7a23b01f') - version('13.1.0', 'a6c7b22660f164ce893fb974f9cb2028') - version('13.1', '95f724bda04919fc76818a5b7bc0b4ed') + version('16.0', sha256='b98afe70c64efa19decc5ff01602e8c7afc6b22ce646cad30dc92ecfdce6e23d') + version('13.1.1', sha256='ffde54f0c86055b06cad911bbd4297b88c3fb124c873b03ebee626f807b8ab87') + version('13.1.0', sha256='c81bead4b919bd0cea9dbc61b219e316718d940bd3dc70825c58efbf0a0acdc3') + version('13.1', sha256='985aa6c5db4257999af6f2bdfcb24f2bce74191cdcd98e937700db7fd9f6b549') variant("mpi", default=True, description='enable mpi support') variant("oce", default=False, description='enable oce geometry kernel') diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py index 3f91686f86f..4183d923b7c 100644 --- a/var/spack/repos/builtin/packages/charliecloud/package.py +++ b/var/spack/repos/builtin/packages/charliecloud/package.py @@ -25,7 +25,7 @@ class Charliecloud(MakefilePackage): version('0.9.2', sha256='8d0e4804d412beef720a66f886a0a78bce42f3269e880ebf11f602581f8047d4') version('0.9.1', sha256='8e69150a271285da71ece7a09b48251ef6593f72207c5126741d9976aa737d95') version('0.9.0', sha256='7e74cb16e31fd9d502198f7509bab14d1049ec68ba90b15e277e76f805db9458') - version('0.2.4', 'b112de661c2c360174b42c99022c1967') + version('0.2.4', sha256='b9a8ff54b9d296e30b2cf5d64a7e732ad09e14b989645aaa5eee8a1dc7ee34e5') depends_on('python@3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py index baeed83b7b5..c667ff28ef9 100644 --- a/var/spack/repos/builtin/packages/charmpp/package.py +++ b/var/spack/repos/builtin/packages/charmpp/package.py @@ -22,15 +22,15 @@ class Charmpp(Package): git = "https://github.com/UIUC-PPL/charm.git" version("develop", branch="charm") - version("6.9.0", "85ed660e46eeb7a6fc6b32deab08226f647c244241948f6b592ebcd2b6050cbd") - version("6.8.2", "a887a34b638a5b2f7fcf7ff3c262496d") - version("6.8.1", "3e95ffa760909154ef16b643c9bb8193") - version("6.8.0", "54df066a5aefb0bbc1a263c2383c2bba") - version("6.7.1", "a8e20cf85e9c8721158f5bbd0ade48d9") - version("6.7.0", "35a39a7975f1954a7db2d76736158231") - version("6.6.1", "9554230f741e2599deaaac4d9d93d7ab") - version("6.6.0", "31e95901b3f7324d52107e6ad000fcc8") - version("6.5.1", "034d99458474a3ab96d8bede8a691a5d") + version("6.9.0", sha256="85ed660e46eeb7a6fc6b32deab08226f647c244241948f6b592ebcd2b6050cbd") + version("6.8.2", sha256="08e6001b0e9cd00ebde179f76098767149bf7e454f29028fb9a8bfb55778698e") + version("6.8.1", sha256="bf39666bb9f8bad1cd17dafa3cdf35c7ef64dfaeda835cf66ae530b7baab7583") + version("6.8.0", sha256="deca68622932ea0c677aa764d6d24cd169a2fd99c06e7d7b6947c0f18ec2f8f3") + version("6.7.1", sha256="744a093874fbac03b6ae8be3ce434eff46b2ee778561e860802ed578e0810fdf") + version("6.7.0", sha256="6b0d8215a180c90cf6ee33ff39f66726934df34aaeeed59650dd3a0cc54d0c87") + version("6.6.1", sha256="2aa16fd3015dce0a0932ab5253578a72ddbcb889bc0d23584c42b28446915467") + version("6.6.0", sha256="c916010f2d4cc2c6bd30ea19764839d0298fb56d1696d8ff08d9fa9a61dfb1c9") + version("6.5.1", sha256="68aa43e2a6e476e116a7e80e385c25c6ac6497807348025505ba8bfa256ed34a") # Support OpenMPI; see # diff --git a/var/spack/repos/builtin/packages/check/package.py b/var/spack/repos/builtin/packages/check/package.py index a787a92e5f4..ed7e933bc8a 100644 --- a/var/spack/repos/builtin/packages/check/package.py +++ b/var/spack/repos/builtin/packages/check/package.py @@ -17,4 +17,4 @@ class Check(AutotoolsPackage): homepage = "https://libcheck.github.io/check/index.html" url = "https://downloads.sourceforge.net/project/check/check/0.10.0/check-0.10.0.tar.gz" - version('0.10.0', '53c5e5c77d090e103a17f3ed7fd7d8b8') + version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052') diff --git a/var/spack/repos/builtin/packages/cistem/package.py b/var/spack/repos/builtin/packages/cistem/package.py index 68d552b51db..4fdde6c1b4b 100644 --- a/var/spack/repos/builtin/packages/cistem/package.py +++ b/var/spack/repos/builtin/packages/cistem/package.py @@ -15,7 +15,7 @@ class Cistem(AutotoolsPackage): homepage = "https://cistem.org/" url = "https://cistem.org/system/tdf/upload3/cistem-1.0.0-beta-source-code.tar.gz?file=1&type=cistem_details&id=37&force=0" - version('1.0.0-beta', '479f395b30ad630df3cbba9c56eb29c2') + version('1.0.0-beta', sha256='c62068f53d0a269ffa1bfff34641597d3795989a930686437fba9eed7a991af6') depends_on('wxwidgets@3.0.2') depends_on('fftw') diff --git a/var/spack/repos/builtin/packages/clapack/package.py b/var/spack/repos/builtin/packages/clapack/package.py index aa09b464f2c..758d0df5ef9 100644 --- a/var/spack/repos/builtin/packages/clapack/package.py +++ b/var/spack/repos/builtin/packages/clapack/package.py @@ -18,7 +18,7 @@ class Clapack(MakefilePackage): homepage = "http://www.netlib.org/clapack/" url = "http://www.netlib.org/clapack/clapack.tgz" - version('3.2.1', '040da31f3a7d4fbc9ac376c748d18d1f') + version('3.2.1', sha256='6dc4c382164beec8aaed8fd2acc36ad24232c406eda6db462bd4c41d5e455fac') variant('external-blas', default=True, description='Build with external BLAS (ATLAS here).') diff --git a/var/spack/repos/builtin/packages/cleaveland4/package.py b/var/spack/repos/builtin/packages/cleaveland4/package.py index bfcce42bc0b..ba4eb32c328 100644 --- a/var/spack/repos/builtin/packages/cleaveland4/package.py +++ b/var/spack/repos/builtin/packages/cleaveland4/package.py @@ -13,7 +13,7 @@ class Cleaveland4(Package): homepage = "https://github.com/MikeAxtell/CleaveLand4" url = "https://github.com/MikeAxtell/CleaveLand4/archive/v4.4.tar.gz" - version('4.4', 'cf62a1de715a612fc8bd5a62364e69db') + version('4.4', sha256='bf7fe6ad730ea2bfb2e0c0f863734f189073a69b1754532012f1261b368b24e7') depends_on('perl', type=('build', 'run')) depends_on('perl-math-cdf', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/clfft/package.py b/var/spack/repos/builtin/packages/clfft/package.py index 0bb0e1a5e53..2dd4e790fec 100644 --- a/var/spack/repos/builtin/packages/clfft/package.py +++ b/var/spack/repos/builtin/packages/clfft/package.py @@ -12,7 +12,7 @@ class Clfft(CMakePackage): homepage = "https://github.com/clMathLibraries/clFFT" url = "https://github.com/clMathLibraries/clFFT/archive/v2.12.2.tar.gz" - version('2.12.2', '9104d85f9f2f3c58dd8efc0e4b06496f') + version('2.12.2', sha256='e7348c146ad48c6a3e6997b7702202ad3ee3b5df99edf7ef00bbacc21e897b12') variant('client', default=True, description='build client and callback client') diff --git a/var/spack/repos/builtin/packages/clingo/package.py b/var/spack/repos/builtin/packages/clingo/package.py index 8804d8226c4..3a221868664 100644 --- a/var/spack/repos/builtin/packages/clingo/package.py +++ b/var/spack/repos/builtin/packages/clingo/package.py @@ -19,7 +19,7 @@ class Clingo(CMakePackage): homepage = "https://potassco.org/clingo/" url = "https://github.com/potassco/clingo/archive/v5.2.2.tar.gz" - version('5.2.2', 'd46a1567f772eebad85c6300d55d2cc3') + version('5.2.2', sha256='da1ef8142e75c5a6f23c9403b90d4f40b9f862969ba71e2aaee9a257d058bfcf') depends_on('doxygen', type=('build')) depends_on('python') diff --git a/var/spack/repos/builtin/packages/cloc/package.py b/var/spack/repos/builtin/packages/cloc/package.py index fd12f0b7cb2..7a6ca7fe426 100644 --- a/var/spack/repos/builtin/packages/cloc/package.py +++ b/var/spack/repos/builtin/packages/cloc/package.py @@ -14,7 +14,7 @@ class Cloc(Package): url = "https://github.com/AlDanial/cloc/releases/download/1.74/cloc-1.74.tar.gz" version('1.80', sha256='082f53530eee3f9ee84ec449eca59a77ff114250cd7daf9519679537b5b21d67') - version('1.74', '1372da13a83862c186aa0b6b0c9b86f5') + version('1.74', sha256='55ac423d5766c74236700a47838ed66bea47ba42e1d594fdd894074ba3eb0567') depends_on('perl') diff --git a/var/spack/repos/builtin/packages/cloog/package.py b/var/spack/repos/builtin/packages/cloog/package.py index 203567b10d2..70bd67c370e 100644 --- a/var/spack/repos/builtin/packages/cloog/package.py +++ b/var/spack/repos/builtin/packages/cloog/package.py @@ -16,9 +16,9 @@ class Cloog(Package): url = "http://www.bastoul.net/cloog/pages/download/count.php3?url=./cloog-0.18.1.tar.gz" list_url = "http://www.bastoul.net/cloog/pages/download" - version('0.18.1', 'e34fca0540d840e5d0f6427e98c92252') - version('0.18.0', 'be78a47bd82523250eb3e91646db5b3d') - version('0.17.0', '0aa3302c81f65ca62c114e5264f8a802') + version('0.18.1', sha256='02500a4edd14875f94fe84cbeda4290425cb0c1c2474c6f75d75a303d64b4196') + version('0.18.0', sha256='1c4aa8dde7886be9cbe0f9069c334843b21028f61d344a2d685f88cb1dcf2228') + version('0.17.0', sha256='f265f5069830c03d2919a7673c0963495437d6d79a8cbd3474cde2d4e3291e04') depends_on("gmp") depends_on("isl") diff --git a/var/spack/repos/builtin/packages/cloverleaf/package.py b/var/spack/repos/builtin/packages/cloverleaf/package.py index 144059127aa..6d81f1c9c59 100644 --- a/var/spack/repos/builtin/packages/cloverleaf/package.py +++ b/var/spack/repos/builtin/packages/cloverleaf/package.py @@ -20,7 +20,7 @@ class Cloverleaf(MakefilePackage): tags = ['proxy-app'] - version('1.1', '65652b30a64eb237ec844a6fdd4cd518') + version('1.1', sha256='de87f7ee6b917e6b3d243ccbbe620370c62df890e3ef7bdbab46569b57be132f') variant('build', default='ref', description='Type of Parallelism Build', values=('cuda', 'mpi_only', 'openacc_cray', diff --git a/var/spack/repos/builtin/packages/cloverleaf3d/package.py b/var/spack/repos/builtin/packages/cloverleaf3d/package.py index e96c50a290a..59aba4a0015 100644 --- a/var/spack/repos/builtin/packages/cloverleaf3d/package.py +++ b/var/spack/repos/builtin/packages/cloverleaf3d/package.py @@ -21,7 +21,7 @@ class Cloverleaf3d(MakefilePackage): tags = ['proxy-app'] - version('1.0', '2e86cadd7612487f9da4ddeb1a6de939') + version('1.0', sha256='78d591728c61bdfd6175b3930df7652e09ed04fbcd01b3fc86fb2aa0f237a8ef') variant('openacc', default=False, description='Enable OpenACC Support') diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustalo/package.py index 5201a1cecce..59b7606e6ce 100644 --- a/var/spack/repos/builtin/packages/clustalo/package.py +++ b/var/spack/repos/builtin/packages/clustalo/package.py @@ -12,6 +12,6 @@ class Clustalo(AutotoolsPackage): homepage = "http://www.clustal.org/omega/" url = "http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz" - version('1.2.4', '6c0459f4c463a30e942ce7e0efc91422') + version('1.2.4', sha256='8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee') depends_on('argtable') diff --git a/var/spack/repos/builtin/packages/clustalw/package.py b/var/spack/repos/builtin/packages/clustalw/package.py index 957e960e642..d279adc4a03 100644 --- a/var/spack/repos/builtin/packages/clustalw/package.py +++ b/var/spack/repos/builtin/packages/clustalw/package.py @@ -12,4 +12,4 @@ class Clustalw(AutotoolsPackage): homepage = "http://www.clustal.org/clustal2/" url = "http://www.clustal.org/download/2.1/clustalw-2.1.tar.gz" - version('2.1', '144df8440a0ae083d5167616c8ceeb41') + version('2.1', sha256='e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index ee844af77cb..c94d6aff0ba 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -23,44 +23,44 @@ class Cmake(Package): version('3.14.2', sha256='a3cbf562b99270c0ff192f692139e98c605f292bfdbc04d70da0309a5358e71e') version('3.14.1', sha256='7321be640406338fc12590609c42b0fae7ea12980855c1be363d25dcd76bb25f') version('3.14.0', sha256='aa76ba67b3c2af1946701f847073f4652af5cbd9f141f221c97af99127e75502') - version('3.13.4', 'fdd928fee35f472920071d1c7f1a6a2b72c9b25e04f7a37b409349aef3f20e9b') - version('3.13.3', '665f905036b1f731a2a16f83fb298b1fb9d0f98c382625d023097151ad016b25') - version('3.13.2', 'c925e7d2c5ba511a69f43543ed7b4182a7d446c274c7480d0e42cd933076ae25') - version('3.13.1', 'befe1ce6d672f2881350e94d4e3cc809697dd2c09e5b708b76c1dae74e1b2210') - version('3.13.0', '4058b2f1a53c026564e8936698d56c3b352d90df067b195cb749a97a3d273c90') - version('3.12.4', '5255584bfd043eb717562cff8942d472f1c0e4679c4941d84baadaa9b28e3194') - version('3.12.3', 'acbf13af31a741794106b76e5d22448b004a66485fc99f6d7df4d22e99da164a') - version('3.12.2', '6e7c550cfa1c2e216b35903dc70d80af') - version('3.12.1', '10109246a51102bfda45ff3935275fbf') - version('3.12.0', 'ab4aa7df9301c94cdd6f8ee4fe66458b') - version('3.11.4', '72e168b3bad2f9c34dcebbad7af56ff0') - version('3.11.3', '3f923154ed47128f13b08eacd207d9ee') - version('3.11.2', 'd2d554c05fc07cfae7846d2aa205f12a') - version('3.11.1', '12a3177477e4e2c7bc514193d421dafe') - version('3.11.0', 'f3ebc79b5dec85b49abe75958ffa1a03') - version('3.10.3', '1c38c67295ca696aeafd8c059d748b38') - version('3.10.2', '732808e17fc14dc8cee50d51518c34eb') - version('3.10.1', '9a726e5ec69618b172aa4b06d18c3998') - version('3.10.0', 'f3f8e70ca3055f3cd288f89ff233057e') - version('3.9.6', '084b1c8b2efc1c1ba432dea37243c0ae') - version('3.9.4', '33769e001bdcd788f565bf378692e5ae') - version('3.9.0', '180e23b4c9b55915d271b315297f6951') - version('3.8.2', 'b5dff61f6a7f1305271ab3f6ae261419') - version('3.8.1', 'e8ef820ddf7a650845252bca846696e7') - version('3.8.0', 'f28cba717ba38ad82a488daed8f45b5b') - version('3.7.2', '79bd7e65cd81ea3aa2619484ad6ff25a') - version('3.7.1', 'd031d5a06e9f1c5367cdfc56fbd2a1c8') - version('3.6.1', 'd6dd661380adacdb12f41b926ec99545') - version('3.6.0', 'aa40fbecf49d99c083415c2411d12db9') - version('3.5.2', '701386a1b5ec95f8d1075ecf96383e02') - version('3.5.1', 'ca051f4a66375c89d1a524e726da0296') - version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e') - version('3.4.3', '4cb3ff35b2472aae70f542116d616e63') - version('3.4.0', 'cd3034e0a44256a0917e254167217fc8') - version('3.3.1', '52638576f4e1e621fed6c3410d3a1b12') - version('3.1.0', '188eb7dc9b1b82b363bc51c0d3f1d461') - version('3.0.2', 'db4c687a31444a929d2fdc36c4dfb95f') - version('2.8.10.2', '097278785da7182ec0aea8769d06860c') + version('3.13.4', sha256='fdd928fee35f472920071d1c7f1a6a2b72c9b25e04f7a37b409349aef3f20e9b') + version('3.13.3', sha256='665f905036b1f731a2a16f83fb298b1fb9d0f98c382625d023097151ad016b25') + version('3.13.2', sha256='c925e7d2c5ba511a69f43543ed7b4182a7d446c274c7480d0e42cd933076ae25') + version('3.13.1', sha256='befe1ce6d672f2881350e94d4e3cc809697dd2c09e5b708b76c1dae74e1b2210') + version('3.13.0', sha256='4058b2f1a53c026564e8936698d56c3b352d90df067b195cb749a97a3d273c90') + version('3.12.4', sha256='5255584bfd043eb717562cff8942d472f1c0e4679c4941d84baadaa9b28e3194') + version('3.12.3', sha256='acbf13af31a741794106b76e5d22448b004a66485fc99f6d7df4d22e99da164a') + version('3.12.2', sha256='0f97485799e51a7070cc11494f3e02349b0fc3a24cc12b082e737bf67a0581a4') + version('3.12.1', sha256='c53d5c2ce81d7a957ee83e3e635c8cda5dfe20c9d501a4828ee28e1615e57ab2') + version('3.12.0', sha256='d0781a90f6cdb9049d104ac16a150f9350b693498b9dea8a0331e799db6b9d69') + version('3.11.4', sha256='8f864e9f78917de3e1483e256270daabc4a321741592c5b36af028e72bff87f5') + version('3.11.3', sha256='287135b6beb7ffc1ccd02707271080bbf14c21d80c067ae2c0040e5f3508c39a') + version('3.11.2', sha256='5ebc22bbcf2b4c7a20c4190d42c084cf38680a85b1a7980a2f1d5b4a52bf5248') + version('3.11.1', sha256='57bebc6ca4d1d42c6385249d148d9216087e0fda57a47dc5c858790a70217d0c') + version('3.11.0', sha256='c313bee371d4d255be2b4e96fd59b11d58bc550a7c78c021444ae565709a656b') + version('3.10.3', sha256='0c3a1dcf0be03e40cf4f341dda79c96ffb6c35ae35f2f911845b72dab3559cf8') + version('3.10.2', sha256='80d0faad4ab56de07aa21a7fc692c88c4ce6156d42b0579c6962004a70a3218b') + version('3.10.1', sha256='7be36ee24b0f5928251b644d29f5ff268330a916944ef4a75e23ba01e7573284') + version('3.10.0', sha256='b3345c17609ea0f039960ef470aa099de9942135990930a57c14575aae884987') + version('3.9.6', sha256='7410851a783a41b521214ad987bb534a7e4a65e059651a2514e6ebfc8f46b218') + version('3.9.4', sha256='b5d86f12ae0072db520fdbdad67405f799eb728b610ed66043c20a92b4906ca1') + version('3.9.0', sha256='167701525183dbb722b9ffe69fb525aa2b81798cf12f5ce1c020c93394dfae0f') + version('3.8.2', sha256='da3072794eb4c09f2d782fcee043847b99bb4cf8d4573978d9b2024214d6e92d') + version('3.8.1', sha256='ce5d9161396e06501b00e52933783150a87c33080d4bdcef461b5b7fd24ac228') + version('3.8.0', sha256='cab99162e648257343a20f61bcd0b287f5e88e36fcb2f1d77959da60b7f35969') + version('3.7.2', sha256='dc1246c4e6d168ea4d6e042cfba577c1acd65feea27e56f5ff37df920c30cae0') + version('3.7.1', sha256='449a5bce64dbd4d5b9517ebd1a1248ed197add6ad27934478976fd5f1f9330e1') + version('3.6.1', sha256='28ee98ec40427d41a45673847db7a905b59ce9243bb866eaf59dce0f58aaef11') + version('3.6.0', sha256='fd05ed40cc40ef9ef99fac7b0ece2e0b871858a82feade48546f5d2940147670') + version('3.5.2', sha256='92d8410d3d981bb881dfff2aed466da55a58d34c7390d50449aa59b32bb5e62a') + version('3.5.1', sha256='93d651a754bcf6f0124669646391dd5774c0fc4d407c384e3ae76ef9a60477e8') + version('3.5.0', sha256='92c83ad8a4fd6224cf6319a60b399854f55b38ebe9d297c942408b792b1a9efa') + version('3.4.3', sha256='b73f8c1029611df7ed81796bf5ca8ba0ef41c6761132340c73ffe42704f980fa') + version('3.4.0', sha256='a5b82bf6ace6c481cdb911fd5d372a302740cbefd387e05297cb37f7468d1cea') + version('3.3.1', sha256='cd65022c6a0707f1c7112f99e9c981677fdd5518f7ddfa0f778d4cee7113e3d6') + version('3.1.0', sha256='8bdc3fa3f2da81bc10c772a6b64cc9052acc2901d42e1e1b2588b40df224aad9') + version('3.0.2', sha256='6b4ea61eadbbd9bec0ccb383c29d1f4496eacc121ef7acf37c7a24777805693e') + version('2.8.10.2', sha256='ce524fb39da06ee6d47534bbcec6e0b50422e18b62abc4781a4ba72ea2910eb1') # Revert the change that introduced a regression when parsing mpi link # flags, see: https://gitlab.kitware.com/cmake/cmake/issues/19516 diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py index cbc125b6b43..89cf3b3b235 100644 --- a/var/spack/repos/builtin/packages/cmocka/package.py +++ b/var/spack/repos/builtin/packages/cmocka/package.py @@ -11,9 +11,9 @@ class Cmocka(CMakePackage): homepage = "https://cmocka.org/" url = "https://cmocka.org/files/1.1/cmocka-1.1.1.tar.xz" - version('1.1.1', '6fbff4e42589566eda558db98b97623e') - version('1.1.0', '59c9aa5735d9387fb591925ec53523ec') - version('1.0.1', 'ed861e501a21a92b2af63e466df2015e') + version('1.1.1', sha256='f02ef48a7039aa77191d525c5b1aee3f13286b77a13615d11bc1148753fc0389') + version('1.1.0', sha256='e960d3bf1be618634a4b924f18bb4d6f20a825c109a8ad6d1af03913ba421330') + version('1.0.1', md5='ed861e501a21a92b2af63e466df2015e') depends_on('cmake@2.6.0:', type='build') diff --git a/var/spack/repos/builtin/packages/cmor/package.py b/var/spack/repos/builtin/packages/cmor/package.py index 864e57ffd37..31460e1645a 100644 --- a/var/spack/repos/builtin/packages/cmor/package.py +++ b/var/spack/repos/builtin/packages/cmor/package.py @@ -16,9 +16,9 @@ class Cmor(AutotoolsPackage): url = "https://github.com/PCMDI/cmor/archive/3.4.0.tar.gz" version('3.4.0', sha256='e700a6d50f435e6ffdedf23bf6832b7d37fe21dc78815e1372f218d1d52bd2cb') - version('3.3.0', 'cfdeeddab1aedb823e26ec38723bd67e') - version('3.2.0', 'b48105105d4261012c19cd65e89ff7a6') - version('3.1.2', '72f7227159c901e4bcf80d2c73a8ce77') + version('3.3.0', sha256='b763707272c470fc6f7077d9c541591a60f9075b52f5f0298eaf2cb2f2fff4d2') + version('3.2.0', sha256='8d49899549dd4c08197739300d507e6fc2b4a5cfe2bfd3e6b44e8e3eaf79b132') + version('3.1.2', sha256='ee58b6d405f081e4e0633af931b7992f1a570953b71ece17c01ab9e15889211a') variant('fortran', default=True, description='Enable Fortran API') variant('python', default=False, description='Enable PYTHON support') diff --git a/var/spack/repos/builtin/packages/cntk/package.py b/var/spack/repos/builtin/packages/cntk/package.py index b87897ae55e..3f7ede7eaf5 100644 --- a/var/spack/repos/builtin/packages/cntk/package.py +++ b/var/spack/repos/builtin/packages/cntk/package.py @@ -16,7 +16,7 @@ class Cntk(Package): git = "https://github.com/Microsoft/CNTK.git" version('master', branch='master') - version('2.0', '8038780f1169ceea578e5ef4d69e4c6f') + version('2.0', sha256='3adee17f166e2a682dfb551ca017ae5c3836ca9772c0af14215a7e76254f201c') variant('opencv', default=False, description="Enable OpenCV support.") variant('kaldi', default=False, description="Enable Kaldi support.") diff --git a/var/spack/repos/builtin/packages/cnvnator/package.py b/var/spack/repos/builtin/packages/cnvnator/package.py index 42216cf3248..7ac9e01d786 100644 --- a/var/spack/repos/builtin/packages/cnvnator/package.py +++ b/var/spack/repos/builtin/packages/cnvnator/package.py @@ -13,7 +13,7 @@ class Cnvnator(MakefilePackage): homepage = "https://github.com/abyzovlab/CNVnator" url = "https://github.com/abyzovlab/CNVnator/archive/v0.3.3.tar.gz" - version('0.3.3', 'f9fc0c2e79abe85decab00d3748d8904') + version('0.3.3', sha256='58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1') depends_on('samtools') depends_on('htslib') diff --git a/var/spack/repos/builtin/packages/codar-cheetah/package.py b/var/spack/repos/builtin/packages/codar-cheetah/package.py index d3c76ccc506..a7a8dca46ac 100644 --- a/var/spack/repos/builtin/packages/codar-cheetah/package.py +++ b/var/spack/repos/builtin/packages/codar-cheetah/package.py @@ -16,7 +16,7 @@ class CodarCheetah(Package): git = "https://github.com/CODARcode/cheetah.git" version('develop', branch='master') - version('0.1', '6918021f74fa7a2f1de26c0bb31a63ef') + version('0.1', sha256='281564f8ae57a70ce28457616fde26247ea4efb29e55c7bf89a782a259a1a028') depends_on('python@3:', type=('build', 'run')) depends_on('savanna') diff --git a/var/spack/repos/builtin/packages/colm/package.py b/var/spack/repos/builtin/packages/colm/package.py index 67d073bcdf3..6e2eed2de88 100644 --- a/var/spack/repos/builtin/packages/colm/package.py +++ b/var/spack/repos/builtin/packages/colm/package.py @@ -16,4 +16,4 @@ class Colm(AutotoolsPackage): homepage = "http://www.colm.net/open-source/colm" url = "http://www.colm.net/files/colm/colm-0.12.0.tar.gz" - version('0.12.0', '079a1ed44f71d48a349d954096c8e411') + version('0.12.0', sha256='7b545d74bd139f5c622975d243c575310af1e4985059a1427b6fdbb1fb8d6e4d') diff --git a/var/spack/repos/builtin/packages/colordiff/package.py b/var/spack/repos/builtin/packages/colordiff/package.py index ddc05024770..eb59fcf472a 100644 --- a/var/spack/repos/builtin/packages/colordiff/package.py +++ b/var/spack/repos/builtin/packages/colordiff/package.py @@ -12,7 +12,7 @@ class Colordiff(Package): homepage = "https://www.colordiff.org" url = "https://www.colordiff.org/colordiff-1.0.18.tar.gz" - version('1.0.18', '07658f09a44f30a3b5c1cea9c132baed') + version('1.0.18', sha256='29cfecd8854d6e19c96182ee13706b84622d7b256077df19fbd6a5452c30d6e0') depends_on('perl') diff --git a/var/spack/repos/builtin/packages/comd/package.py b/var/spack/repos/builtin/packages/comd/package.py index 8db93de6ab5..1f42ca1cbf0 100644 --- a/var/spack/repos/builtin/packages/comd/package.py +++ b/var/spack/repos/builtin/packages/comd/package.py @@ -23,7 +23,7 @@ class Comd(MakefilePackage): git = "https://github.com/ECP-copa/CoMD.git" version('develop', branch='master') - version('1.1', '5051310a8d2c93cccba63de40bcfaa78') + version('1.1', sha256='4e85f86f043681a1ef72940fc24a4c71356a36afa45446f7cfe776abad6aa252') variant('mpi', default=True, description='Build with MPI support') variant('openmp', default=False, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/commons-lang/package.py b/var/spack/repos/builtin/packages/commons-lang/package.py index f5596af846d..daf88df9756 100644 --- a/var/spack/repos/builtin/packages/commons-lang/package.py +++ b/var/spack/repos/builtin/packages/commons-lang/package.py @@ -21,8 +21,8 @@ class CommonsLang(Package): homepage = "http://commons.apache.org/proper/commons-lang/" url = "https://archive.apache.org/dist/commons/lang/binaries/commons-lang-2.6-bin.tar.gz" - version('2.6', '444075803459bffebfb5e28877861d23') - version('2.4', '5ff5d890e46021a2dbd77caba80f90f2') + version('2.6', sha256='ff6a244bb71a9a1c859e81cb744d0ce698c20e04f13a7ef7dbffb99c8122752c') + version('2.4', sha256='00e6b3174e31196d726c14302c8e7e9ba9b8409d57a8a9821c7648beeda31c5e') extends('jdk') depends_on('java@2:', type='run') diff --git a/var/spack/repos/builtin/packages/commons-lang3/package.py b/var/spack/repos/builtin/packages/commons-lang3/package.py index 935506b4983..4309e406201 100644 --- a/var/spack/repos/builtin/packages/commons-lang3/package.py +++ b/var/spack/repos/builtin/packages/commons-lang3/package.py @@ -21,7 +21,7 @@ class CommonsLang3(Package): homepage = "http://commons.apache.org/proper/commons-lang/" url = "https://archive.apache.org/dist/commons/lang/binaries/commons-lang3-3.7-bin.tar.gz" - version('3.7', 'c7577443639dc6efadc80f1cbc7fced5') + version('3.7', sha256='94dc8289ce90b77b507d9257784d9a43b402786de40c164f6e3990e221a2a4d2') extends('jdk') depends_on('java@7:', type='run') diff --git a/var/spack/repos/builtin/packages/commons-logging/package.py b/var/spack/repos/builtin/packages/commons-logging/package.py index 81904aaddad..b5b7a8189b0 100644 --- a/var/spack/repos/builtin/packages/commons-logging/package.py +++ b/var/spack/repos/builtin/packages/commons-logging/package.py @@ -21,9 +21,9 @@ class CommonsLogging(Package): homepage = "http://commons.apache.org/proper/commons-logging/" url = "http://archive.apache.org/dist/commons/logging/binaries/commons-logging-1.2-bin.tar.gz" - version('1.2', 'ac043ce7ab3374eb4ed58354a6b2c3de') - version('1.1.3', 'b132f9a1e875677ae6b449406cff2a78') - version('1.1.1', 'e5de09672af9b386c30a311654d8541a') + version('1.2', sha256='3f758805c7290d9c6d22d1451587c9f7232744aef4c984e88aa683cdea0587bd') + version('1.1.3', sha256='9e7093c93529792563b5c19ab5cccb73ef4ca7d82b886bdec6d0af182ba9908a') + version('1.1.1', sha256='88c721d66f570a87f710a2449f0e3bffea86489d9dd2fa70b805104c4f8d69e6') extends('jdk') depends_on('java', type='run') diff --git a/var/spack/repos/builtin/packages/compiz/package.py b/var/spack/repos/builtin/packages/compiz/package.py index 1fa81b6d1cd..36bd995dae8 100644 --- a/var/spack/repos/builtin/packages/compiz/package.py +++ b/var/spack/repos/builtin/packages/compiz/package.py @@ -17,7 +17,7 @@ class Compiz(AutotoolsPackage): homepage = "http://www.compiz.org/" url = "https://www.x.org/archive/individual/app/compiz-0.7.8.tar.gz" - version('0.7.8', 'e99977d9170a7bd5d571004eed038428') + version('0.7.8', sha256='b46f52b776cc78e85357a07688d04b36ec19c65eadeaf6f6cfcca7b8515e6503') depends_on('libxcb') depends_on('libxcomposite') diff --git a/var/spack/repos/builtin/packages/compositeproto/package.py b/var/spack/repos/builtin/packages/compositeproto/package.py index b5e214f1e26..96286eaa96d 100644 --- a/var/spack/repos/builtin/packages/compositeproto/package.py +++ b/var/spack/repos/builtin/packages/compositeproto/package.py @@ -15,7 +15,7 @@ class Compositeproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/compositeproto" url = "https://www.x.org/archive/individual/proto/compositeproto-0.4.2.tar.gz" - version('0.4.2', '2dea7c339432b3363faf2d29c208e7b5') + version('0.4.2', sha256='22195b7e50036440b1c6b3b2d63eb03dfa6e71c8a1263ed1f07b0f31ae7dad50') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py index 3b4fb3e8272..af1cc70c85a 100644 --- a/var/spack/repos/builtin/packages/conduit/package.py +++ b/var/spack/repos/builtin/packages/conduit/package.py @@ -39,11 +39,11 @@ class Conduit(Package): version('master', branch='master', submodules=True, preferred=True) version('0.4.0', sha256='c228e6f0ce5a9c0ffb98e0b3d886f2758ace1a4b40d00f3f118542c0747c1f52') - version('0.3.1', 'b98d1476199a46bde197220cd9cde042') - version('0.3.0', '6396f1d1ca16594d7c66d4535d4f898e') + version('0.3.1', sha256='7b358ca03bb179876291d4a55d6a1c944b7407a80a588795b9e47940b1990521') + version('0.3.0', sha256='52e9cf5720560e5f7492876c39ef2ea20ae73187338361d2744bdf67567da155') # note: checksums on github automatic release source tars changed ~9/17 - version('0.2.1', 'ed7358af3463ba03f07eddd6a6e626ff') - version('0.2.0', 'a7b398d493fd71b881a217993a9a29d4') + version('0.2.1', sha256='796576b9c69717c52f0035542c260eb7567aa351ee892d3fbe3521c38f1520c4') + version('0.2.0', sha256='31eff8dbc654a4b235cfcbc326a319e1752728684296721535c7ca1c9b463061') maintainers = ['cyrush'] diff --git a/var/spack/repos/builtin/packages/connect-proxy/package.py b/var/spack/repos/builtin/packages/connect-proxy/package.py index b340ccc8409..fdd303fba71 100644 --- a/var/spack/repos/builtin/packages/connect-proxy/package.py +++ b/var/spack/repos/builtin/packages/connect-proxy/package.py @@ -13,7 +13,7 @@ class ConnectProxy(MakefilePackage): homepage = "https://bitbucket.org/gotoh/connect" url = "https://bitbucket.org/gotoh/connect/get/1.105.tar.bz2" - version('1.105', '07366026b1f81044ecd8da9b5b5b51321327ecdf6ba23576271a311bbd69d403') + version('1.105', sha256='07366026b1f81044ecd8da9b5b5b51321327ecdf6ba23576271a311bbd69d403') def install(self, spec, prefix): mkdir(prefix.bin) diff --git a/var/spack/repos/builtin/packages/constype/package.py b/var/spack/repos/builtin/packages/constype/package.py index 1058ce52ee5..2587cb236f8 100644 --- a/var/spack/repos/builtin/packages/constype/package.py +++ b/var/spack/repos/builtin/packages/constype/package.py @@ -16,7 +16,7 @@ class Constype(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/constype" url = "https://www.x.org/archive/individual/app/constype-1.0.4.tar.gz" - version('1.0.4', '2333b9ac9fd32e58b05afa651c4590a3') + version('1.0.4', sha256='ec09aff369cf1d527fd5b8075fb4dd0ecf89d905190cf1a0a0145d5e523f913d') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/coreutils/package.py b/var/spack/repos/builtin/packages/coreutils/package.py index eab3c634bc9..ff5239900c1 100644 --- a/var/spack/repos/builtin/packages/coreutils/package.py +++ b/var/spack/repos/builtin/packages/coreutils/package.py @@ -15,8 +15,8 @@ class Coreutils(AutotoolsPackage): homepage = "http://www.gnu.org/software/coreutils/" url = "https://ftpmirror.gnu.org/coreutils/coreutils-8.26.tar.xz" - version('8.29', '960cfe75a42c9907c71439f8eb436303') - version('8.26', 'd5aa2072f662d4118b9f4c63b94601a6') - version('8.23', 'abed135279f87ad6762ce57ff6d89c41') + version('8.29', sha256='92d0fa1c311cacefa89853bdb53c62f4110cdfda3820346b59cbd098f40f955e') + version('8.26', sha256='155e94d748f8e2bc327c66e0cbebdb8d6ab265d2f37c3c928f7bf6c3beba9a8e') + version('8.23', sha256='ec43ca5bcfc62242accb46b7f121f6b684ee21ecd7d075059bf650ff9e37b82d') build_directory = 'spack-build' diff --git a/var/spack/repos/builtin/packages/corset/package.py b/var/spack/repos/builtin/packages/corset/package.py index 55729a82736..afc74f6ca45 100644 --- a/var/spack/repos/builtin/packages/corset/package.py +++ b/var/spack/repos/builtin/packages/corset/package.py @@ -13,7 +13,7 @@ class Corset(Package): homepage = "https://github.com/Oshlack/Corset/wiki" url = "https://github.com/Oshlack/Corset/releases/download/version-1.06/corset-1.06-linux64.tar.gz" - version('1.06', '0a6d0bb1f2d1bdbcb8b47656a7f12f23') + version('1.06', sha256='4aff83844461cea1edfce3d89776236c300650fc02b497cc9f11eba42d161b60') def url_for_version(self, version): url = 'https://github.com/Oshlack/Corset/releases/download/version-{0}/corset-{0}-linux64.tar.gz' diff --git a/var/spack/repos/builtin/packages/cosmomc/package.py b/var/spack/repos/builtin/packages/cosmomc/package.py index e9326bb9bd2..a4a4a4a4b98 100644 --- a/var/spack/repos/builtin/packages/cosmomc/package.py +++ b/var/spack/repos/builtin/packages/cosmomc/package.py @@ -19,8 +19,8 @@ class Cosmomc(Package): homepage = "http://cosmologist.info/cosmomc/" url = "https://github.com/cmbant/CosmoMC/archive/Nov2016.tar.gz" - version('2016.11', '98620cb746352f68fb0c1196e9a070ac') - version('2016.06', '92dc651d1407cca6ea9228992165f5cb') + version('2016.11', sha256='b83edbf043ff83a4dde9bc14c56a09737dbc41ffe247a8e9c9a26892ed8745ba') + version('2016.06', sha256='23fa23eef40846c17d3740be63a7fefde13880cbb81545a44d14034277d9ffc0') def url_for_version(self, version): names = {'2016.11': "Nov2016", diff --git a/var/spack/repos/builtin/packages/cppcheck/package.py b/var/spack/repos/builtin/packages/cppcheck/package.py index b23c38d10eb..d7405825c9c 100644 --- a/var/spack/repos/builtin/packages/cppcheck/package.py +++ b/var/spack/repos/builtin/packages/cppcheck/package.py @@ -12,10 +12,10 @@ class Cppcheck(MakefilePackage): url = "https://downloads.sourceforge.net/project/cppcheck/cppcheck/1.78/cppcheck-1.78.tar.bz2" version('1.87', sha256='e3b0a46747822471df275417d4b74b56ecac88367433e7428f39288a32c581ca') - version('1.81', '0c60a1d00652044ef511bdd017689938') - version('1.78', 'f02d0ee0a4e71023703c6c5efff6cf9d') - version('1.72', '2bd36f91ae0191ef5273bb7f6dc0d72e') - version('1.68', 'c015195f5d61a542f350269030150708') + version('1.81', sha256='bb694f37ae0b5fed48c6cdc2fb5e528daf32cefc64e16b1a520c5411323cf27e') + version('1.78', sha256='e42696f7d6321b98cb479ad9728d051effe543b26aca8102428f60b9850786b1') + version('1.72', sha256='9460b184ff2d8dd15344f3e2f42f634c86e4dd3303e1e9b3f13dc67536aab420') + version('1.68', sha256='add6e5e12b05ca02b356cd0ec7420ae0dcafddeaef183b4dfbdef59c617349b1') variant('htmlreport', default=False, description="Install cppcheck-htmlreport") diff --git a/var/spack/repos/builtin/packages/cppunit/package.py b/var/spack/repos/builtin/packages/cppunit/package.py index 1307c165530..b85f06218a4 100644 --- a/var/spack/repos/builtin/packages/cppunit/package.py +++ b/var/spack/repos/builtin/packages/cppunit/package.py @@ -13,7 +13,7 @@ class Cppunit(AutotoolsPackage): url = "http://dev-www.libreoffice.org/src/cppunit-1.13.2.tar.gz" version('1.14.0', sha256='3d569869d27b48860210c758c4f313082103a5e58219a7669b52bfd29d674780') - version('1.13.2', '0eaf8bb1dcf4d16b12bec30d0732370390d35e6f') + version('1.13.2', sha256='3f47d246e3346f2ba4d7c9e882db3ad9ebd3fcbd2e8b732f946e0e3eeb9f429f') variant('cxxstd', default='default', diff --git a/var/spack/repos/builtin/packages/cppzmq/package.py b/var/spack/repos/builtin/packages/cppzmq/package.py index 79aac8a3d05..0adaebf9c3c 100644 --- a/var/spack/repos/builtin/packages/cppzmq/package.py +++ b/var/spack/repos/builtin/packages/cppzmq/package.py @@ -15,7 +15,7 @@ class Cppzmq(CMakePackage): version('develop', branch='master') version('4.3.0', sha256='27d1f56406ba94ee779e639203218820975cf68174f92fbeae0f645df0fcada4') - version('4.2.2', 'bd809b47296e77fe9f192bd9dafd5cc3') + version('4.2.2', sha256='3ef50070ac5877c06c6bb25091028465020e181bbfd08f110294ed6bc419737d') depends_on('cmake@3.0.0:', type='build') depends_on('zeromq@4.2.5', when='@4.3.0') diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py index bf8cef10b8e..e3ea8d16b96 100644 --- a/var/spack/repos/builtin/packages/cram/package.py +++ b/var/spack/repos/builtin/packages/cram/package.py @@ -11,7 +11,7 @@ class Cram(CMakePackage): homepage = "https://github.com/llnl/cram" url = "http://github.com/llnl/cram/archive/v1.0.1.tar.gz" - version('1.0.1', 'c73711e945cf5dc603e44395f6647f5e') + version('1.0.1', sha256='985888018f6481c3e9ab4f1d1788e25725d8b92a1cf52b1366ee93793614709a') extends('python@2.7:') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 16e1ad90d4e..f4b53701366 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -16,14 +16,14 @@ class Cryptopp(MakefilePackage): homepage = "http://www.cryptopp.com" url = "http://www.cryptopp.com/cryptopp700.zip" - version('7.0.0', '8f34884b572901b6ede89bd18f1c7ef6') + version('7.0.0', sha256='a4bc939910edd3d29fb819a6fc0dfdc293f686fa62326f61c56d72d0a366ceb0') version('6.1.0', sha256='21289d2511101a9350c87c8eb1f4982d4a266e8037b19dab79a32cc13ea108c7') version('6.0.0', sha256='64ac2db96b3f1b7a23675e2be95d16c96055edffa2d5e2de6245fdb6baa92dda') version('5.6.5', sha256='a75ef486fe3128008bbb201efee3dcdcffbe791120952910883b26337ec32c34') version('5.6.4', sha256='be430377b05c15971d5ccb6e44b4d95470f561024ed6d701fe3da3a188c84ad7') - version('5.6.3', '3c5b70e2ec98b7a24988734446242d07') - version('5.6.2', '7ed022585698df48e65ce9218f6c6a67') - version('5.6.1', '96cbeba0907562b077e26bcffb483828') + version('5.6.3', sha256='9390670a14170dd0f48a6b6b06f74269ef4b056d4718a1a329f6f6069dc957c9') + version('5.6.2', sha256='5cbfd2fcb4a6b3aab35902e2e0f3b59d9171fee12b3fc2b363e1801dfec53574') + version('5.6.1', sha256='98e74d8cb17a38033354519ac8ba9c5d98a6dc00bf5d1ec3c533c2e8ec86f268') depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/cscope/package.py b/var/spack/repos/builtin/packages/cscope/package.py index 106cfed7427..061bd805867 100644 --- a/var/spack/repos/builtin/packages/cscope/package.py +++ b/var/spack/repos/builtin/packages/cscope/package.py @@ -12,7 +12,7 @@ class Cscope(AutotoolsPackage): homepage = "http://cscope.sourceforge.net/" url = "http://downloads.sourceforge.net/project/cscope/cscope/15.8b/cscope-15.8b.tar.gz" - version('15.8b', '8f9409a238ee313a96f9f87fe0f3b176') + version('15.8b', sha256='4889d091f05aa0845384b1e4965aa31d2b20911fb2c001b2cdcffbcb7212d3af') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/csdp/package.py b/var/spack/repos/builtin/packages/csdp/package.py index cc7a0777c91..81574dc0c00 100644 --- a/var/spack/repos/builtin/packages/csdp/package.py +++ b/var/spack/repos/builtin/packages/csdp/package.py @@ -14,7 +14,7 @@ class Csdp(MakefilePackage): homepage = "https://projects.coin-or.org/Csdp" url = "http://www.coin-or.org/download/source/Csdp/Csdp-6.1.1.tgz" - version('6.1.1', '8388e8988e337bb5c1291068828de801') + version('6.1.1', sha256='0558a46ac534e846bf866b76a9a44e8a854d84558efa50988ffc092f99a138b9') depends_on('atlas') diff --git a/var/spack/repos/builtin/packages/ctffind/package.py b/var/spack/repos/builtin/packages/ctffind/package.py index 1e895ff91ca..03ec76b6c04 100644 --- a/var/spack/repos/builtin/packages/ctffind/package.py +++ b/var/spack/repos/builtin/packages/ctffind/package.py @@ -12,7 +12,7 @@ class Ctffind(AutotoolsPackage): homepage = "http://grigoriefflab.janelia.org/ctffind4" url = "http://grigoriefflab.janelia.org/sites/default/files/ctffind-4.1.8.tar.gz" - version('4.1.8', '8ae9d9abe363141a3792981b5a2fae94') + version('4.1.8', sha256='bec43c0b8d32878c740d6284ef6d9d22718c80dc62270be18d1d44e8b84b2729') depends_on('wxwidgets') depends_on('fftw@3:') diff --git a/var/spack/repos/builtin/packages/cub/package.py b/var/spack/repos/builtin/packages/cub/package.py index 0429e864137..81e71ff6c27 100644 --- a/var/spack/repos/builtin/packages/cub/package.py +++ b/var/spack/repos/builtin/packages/cub/package.py @@ -13,9 +13,9 @@ class Cub(Package): homepage = "https://nvlabs.github.com/cub" url = "https://github.com/NVlabs/cub/archive/1.6.4.zip" - version('1.7.1', '028ac43922a4538596338ad5aef0f0c4') - version('1.6.4', '924fc12c0efb17264c3ad2d611ed1c51') - version('1.4.1', '74a36eb84e5b5f0bf54aa3df39f660b2') + version('1.7.1', sha256='50b8777b83093fdfdab429a61fccdbfbbb991b3bbc08385118e5ad58e8f62e1d') + version('1.6.4', md5='924fc12c0efb17264c3ad2d611ed1c51') + version('1.4.1', md5='74a36eb84e5b5f0bf54aa3df39f660b2') def install(self, spec, prefix): mkdirp(prefix.include) diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py index c341d24ac2a..89297a86bf1 100644 --- a/var/spack/repos/builtin/packages/cube/package.py +++ b/var/spack/repos/builtin/packages/cube/package.py @@ -17,14 +17,14 @@ class Cube(AutotoolsPackage): homepage = "http://www.scalasca.org/software/cube-4.x/download.html" url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubegui-4.4.2.tar.gz" - version('4.4.4', '9b7b96d5a64b558a9017cc3599bba93a42095534e018e3de9b1f80ab6d04cc34') - version('4.4.3', 'bf4b0f2ff68507ff82ba24eb4895aed961710dae16d783c222a12f152440cf36') - version('4.4.2', '29b6479616a524f8325f5031a883963bf965fb92569de33271a020f08650ec7b') - version('4.4', '0620bae3ac357d0486ce7f5f97e448eeb2494c9a31865b679380ee08c6750e70') - version('4.3.5', 'e5dce986e3c6381ea3a5fcb66c553adc') - version('4.3.4', '50f73060f55311cb12c5b3cb354d59fa') - version('4.3.3', '07e109248ed8ffc7bdcce614264a2909') - version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20') + version('4.4.4', sha256='9b7b96d5a64b558a9017cc3599bba93a42095534e018e3de9b1f80ab6d04cc34') + version('4.4.3', sha256='bf4b0f2ff68507ff82ba24eb4895aed961710dae16d783c222a12f152440cf36') + version('4.4.2', sha256='29b6479616a524f8325f5031a883963bf965fb92569de33271a020f08650ec7b') + version('4.4', sha256='0620bae3ac357d0486ce7f5f97e448eeb2494c9a31865b679380ee08c6750e70') + version('4.3.5', sha256='1dc26f473e8bb4cdbdd411224c3c2026a394f3e936f1918000dc65a222753912') + version('4.3.4', sha256='34c55fc5d0c84942c0845a7324d84cde09f3bc1b3fae6a0f9556f7ea0e201065') + version('4.3.3', sha256='ce8e1bff5a208fe5700a0194170be85bbd8f554e1aa1514b4afc5129326c7f83') + version('4.2.3', sha256='b30c6998bcc54f795bcd6de3cfbef9c3cec094f782820174b533f628b0e60765') variant('gui', default=True, description='Build Cube GUI') diff --git a/var/spack/repos/builtin/packages/cubelib/package.py b/var/spack/repos/builtin/packages/cubelib/package.py index ea4f76929c6..0d229a54c4c 100644 --- a/var/spack/repos/builtin/packages/cubelib/package.py +++ b/var/spack/repos/builtin/packages/cubelib/package.py @@ -12,10 +12,10 @@ class Cubelib(AutotoolsPackage): homepage = "http://www.scalasca.org/software/cube-4.x/download.html" url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubelib-4.4.tar.gz" - version('4.4.4', 'adb8216ee3b7701383884417374e7ff946edb30e56640307c65465187dca7512') - version('4.4.3', 'bcd4fa81a5ba37194e590a5d7c3e6c44b448f5e156a175837b77c21206847a8d') - version('4.4.2', '843335c7d238493f1b4cb8e07555ccfe99a3fa521bf162e9d8eaa6733aa1f949') - version('4.4', 'c903f3c44d3228ebefd00c831966988e') + version('4.4.4', sha256='adb8216ee3b7701383884417374e7ff946edb30e56640307c65465187dca7512') + version('4.4.3', sha256='bcd4fa81a5ba37194e590a5d7c3e6c44b448f5e156a175837b77c21206847a8d') + version('4.4.2', sha256='843335c7d238493f1b4cb8e07555ccfe99a3fa521bf162e9d8eaa6733aa1f949') + version('4.4', sha256='77548e1732fa5e82b13cc8465c8a21349bf42b45a382217d2e70d18576741d5c') depends_on('pkgconfig', type='build') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/cubew/package.py b/var/spack/repos/builtin/packages/cubew/package.py index e4aeb907647..dd032952267 100644 --- a/var/spack/repos/builtin/packages/cubew/package.py +++ b/var/spack/repos/builtin/packages/cubew/package.py @@ -12,10 +12,10 @@ class Cubew(AutotoolsPackage): homepage = "http://www.scalasca.org/software/cube-4.x/download.html" url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubew-4.4.tar.gz" - version('4.4.3', '93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501') - version('4.4.2', '31a71e9a05e6523de2b86b4026821bbb75fb411eb5b18ae38b27c1f44158014a') - version('4.4.1', 'c09e3f5a3533ebedee2cc7dfaacd7bac4680c14c3fa540669466583a23f04b67') - version('4.4', 'e9beb140719c2ad3d971e1efb99e0916') + version('4.4.3', sha256='93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501') + version('4.4.2', sha256='31a71e9a05e6523de2b86b4026821bbb75fb411eb5b18ae38b27c1f44158014a') + version('4.4.1', sha256='c09e3f5a3533ebedee2cc7dfaacd7bac4680c14c3fa540669466583a23f04b67') + version('4.4', sha256='b1d6fecb546bc645ced430ea3fc166e85835f3b997d4e5f0dece71919fc95a99') depends_on('pkgconfig', type='build') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py index a1c80f5a834..f388bf4c73d 100644 --- a/var/spack/repos/builtin/packages/cuda/package.py +++ b/var/spack/repos/builtin/packages/cuda/package.py @@ -26,19 +26,19 @@ class Cuda(Package): url="https://developer.download.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda_10.1.243_418.87.00_linux.run") version('10.0.130', sha256='92351f0e4346694d0fcb4ea1539856c9eb82060c25654463bfd8574ec35ee39a', expand=False, url="https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux") - version('9.2.88', 'dd6e33e10d32a29914b7700c7b3d1ca0', expand=False, + version('9.2.88', sha256='8d02cc2a82f35b456d447df463148ac4cc823891be8820948109ad6186f2667c', expand=False, url="https://developer.nvidia.com/compute/cuda/9.2/Prod/local_installers/cuda_9.2.88_396.26_linux") - version('9.1.85', '67a5c3933109507df6b68f80650b4b4a', expand=False, + version('9.1.85', sha256='8496c72b16fee61889f9281449b5d633d0b358b46579175c275d85c9205fe953', expand=False, url="https://developer.nvidia.com/compute/cuda/9.1/Prod/local_installers/cuda_9.1.85_387.26_linux") - version('9.0.176', '7a00187b2ce5c5e350e68882f42dd507', expand=False, + version('9.0.176', sha256='96863423feaa50b5c1c5e1b9ec537ef7ba77576a3986652351ae43e66bcd080c', expand=False, url="https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda_9.0.176_384.81_linux-run") - version('8.0.61', '33e1bd980e91af4e55f3ef835c103f9b', expand=False, + version('8.0.61', sha256='9ceca9c2397f841024e03410bfd6eabfd72b384256fbed1c1e4834b5b0ce9dc4', expand=False, url="https://developer.nvidia.com/compute/cuda/8.0/Prod2/local_installers/cuda_8.0.61_375.26_linux-run") - version('8.0.44', '6dca912f9b7e2b7569b0074a41713640', expand=False, + version('8.0.44', sha256='64dc4ab867261a0d690735c46d7cc9fc60d989da0d69dc04d1714e409cacbdf0', expand=False, url="https://developer.nvidia.com/compute/cuda/8.0/prod/local_installers/cuda_8.0.44_linux-run") - version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False, + version('7.5.18', sha256='08411d536741075131a1858a68615b8b73c51988e616e83b835e4632eea75eec', expand=False, url="http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/cuda_7.5.18_linux.run") - version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False, + version('6.5.14', sha256='f3e527f34f317314fe8fcd8c85f10560729069298c0f73105ba89225db69da48', expand=False, url="http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run") # macOS Mojave drops NVIDIA graphics card support -- official NVIDIA diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py index 8bb374aea48..b56aacab4fe 100644 --- a/var/spack/repos/builtin/packages/cudnn/package.py +++ b/var/spack/repos/builtin/packages/cudnn/package.py @@ -13,29 +13,29 @@ class Cudnn(Package): homepage = "https://developer.nvidia.com/cudnn" - version('7.5.1-10.1-x86_64', '24017f4a56159d48fd5a31c8a930167b', + version('7.5.1-10.1-x86_64', sha256='2c833f43c9147d9a25a20947a4c5a5f5c33b2443240fd767f63b330c482e68e0', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.1-linux-x64-v7.5.1.10.tgz') - version('7.5.1-10.1-ppc64le', 'ec0993be21e0998fc12116e4c46bce02', + version('7.5.1-10.1-ppc64le', sha256='a9e23bc83c970daec20874ccd1d8d80b648adf15440ecd0164818b330b1e2663', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.1-linux-ppc64le-v7.5.1.10.tgz') - version('7.5.1-10.0-x86_64', '703ed4be4d242ff4bc0ca48aaf2029bc', + version('7.5.1-10.0-x86_64', sha256='c0a4ec438920aa581dd567117b9c316745b4a451ac739b1e04939a3d8b229985', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.0-linux-x64-v7.5.1.10.tgz') - version('7.5.1-10.0-ppc64le', '8348cbab01970b75836d945d8a75915e', + version('7.5.1-10.0-ppc64le', sha256='d9205718da5fbab85433476f9ff61fcf4b889d216d6eea26753bbc24d115dd70', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.0-linux-ppc64le-v7.5.1.10.tgz') - version('7.5.0-10.1-x86_64', '4edc7fcfeada9f2363e97f9875154e8f', + version('7.5.0-10.1-x86_64', sha256='c31697d6b71afe62838ad2e57da3c3c9419c4e9f5635d14b683ebe63f904fbc8', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.1-linux-x64-v7.5.0.56.tgz') - version('7.5.0-10.1-ppc64le', 'b927bc91d93182cb2606e51c9eeee908', + version('7.5.0-10.1-ppc64le', sha256='15415eb714ab86ab6c7531f2cac6474b5dafd989479b062776c670b190e43638', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.1-linux-ppc64le-v7.5.0.56.tgz') - version('7.5.0-10.0-x86_64', 'b05ca261ffee1e08b496bf8a57790ee8', + version('7.5.0-10.0-x86_64', sha256='701097882cb745d4683bb7ff6c33b8a35c7c81be31bac78f05bad130e7e0b781', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.0-linux-x64-v7.5.0.56.tgz') - version('7.5.0-10.0-ppc64le', 'e9d2fcdb5340df2408fa08026a2a3e1c', + version('7.5.0-10.0-ppc64le', sha256='f0c1cbd9de553c8e2a3893915bd5fff57b30e368ef4c964d783b6a877869e93a', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.0-linux-ppc64le-v7.5.0.56.tgz') - version('7.3.0', '72666d3532850752612706601258a0b2', + version('7.3.0', sha256='403f9043ff2c7b2c5967454872275d07bca11fd41dfc7b21995eadcad6dbe49b', url='http://developer.download.nvidia.com/compute/redist/cudnn/v7.3.0/cudnn-9.0-linux-x64-v7.3.0.29.tgz') - version('7.2.1', '17e010153a4a95bf9c2df2a3c3ceea63', + version('7.2.1', sha256='cf007437b9ac6250ec63b89c25f248d2597fdd01369c80146567f78e75ce4e37', url='http://developer.download.nvidia.com/compute/redist/cudnn/v7.2.1/cudnn-9.0-linux-x64-v7.2.1.38.tgz') - version('6.0', 'a08ca487f88774e39eb6b0ef6507451d', + version('6.0', sha256='9b09110af48c9a4d7b6344eb4b3e344daa84987ed6177d5c44319732f3bb7f9c', url='http://developer.download.nvidia.com/compute/redist/cudnn/v6.0/cudnn-8.0-linux-x64-v6.0.tgz') - version('5.1', '406f4ac7f7ee8aa9e41304c143461a69', + version('5.1', sha256='c10719b36f2dd6e9ddc63e3189affaa1a94d7d027e63b71c3f64d449ab0645ce', url='http://developer.download.nvidia.com/compute/redist/cudnn/v5.1/cudnn-8.0-linux-x64-v5.1.tgz') depends_on('cuda@8:', when='@5.1:@7') diff --git a/var/spack/repos/builtin/packages/cufflinks/package.py b/var/spack/repos/builtin/packages/cufflinks/package.py index 43fd5336113..10576680c9d 100644 --- a/var/spack/repos/builtin/packages/cufflinks/package.py +++ b/var/spack/repos/builtin/packages/cufflinks/package.py @@ -13,7 +13,7 @@ class Cufflinks(Package): homepage = "http://cole-trapnell-lab.github.io/cufflinks" url = "http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz" - version('2.2.1', '7e693d182dcfda8aeef8523219ea9ea7') + version('2.2.1', sha256='39f812452cae26462e5d2671d38104d9e8ef30aaf9ab6dea8ca57f50f46448e4') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/cups/package.py b/var/spack/repos/builtin/packages/cups/package.py index c756ca5c549..bfccd89ff48 100644 --- a/var/spack/repos/builtin/packages/cups/package.py +++ b/var/spack/repos/builtin/packages/cups/package.py @@ -16,7 +16,7 @@ class Cups(AutotoolsPackage): homepage = "https://www.cups.org/" url = "https://github.com/apple/cups/releases/download/v2.2.3/cups-2.2.3-source.tar.gz" - version('2.2.3', '006a8156680a516e43c59034e31df8bf') + version('2.2.3', sha256='66701fe15838f2c892052c913bde1ba106bbee2e0a953c955a62ecacce76885f') depends_on('gnutls') diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index 07afec53ada..4ab1b53a27d 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -16,22 +16,22 @@ class Curl(AutotoolsPackage): url = "http://curl.haxx.se/download/curl-7.60.0.tar.bz2" version('7.63.0', sha256='9bab7ed4ecff77020a312d84cc5fb7eb02d58419d218f267477a724a17fd8dd8') - version('7.60.0', 'bd2aabf78ded6a9aec8a54532fd6b5d7') - version('7.59.0', 'a2192804f7c2636a09320416afcf888e') - version('7.56.0', 'e0caf257103e0c77cee5be7e9ac66ca4') - version('7.54.0', '89bb7ba87384dfbf4f1a3f953da42458') - version('7.53.1', 'fb1f03a142236840c1a77c035fa4c542') - version('7.52.1', 'dd014df06ff1d12e173de86873f9f77a') - version('7.50.3', 'bd177fd6deecce00cfa7b5916d831c5e') - version('7.50.2', '6e161179f7af4b9f8b6ea21420132719') - version('7.50.1', '015f6a0217ca6f2c5442ca406476920b') - version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab') - version('7.47.1', '9ea3123449439bbd960cd25cf98796fb') - version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148') - version('7.45.0', '62c1a352b28558f25ba6209214beadc8') - version('7.44.0', '6b952ca00e5473b16a11f05f06aa8dae') - version('7.43.0', '11bddbb452a8b766b932f859aaeeed39') - version('7.42.1', '296945012ce647b94083ed427c1877a8') + version('7.60.0', sha256='897dfb2204bd99be328279f88f55b7c61592216b0542fcbe995c60aa92871e9b') + version('7.59.0', sha256='b5920ffd6a8c95585fb95070e0ced38322790cb335c39d0dab852d12e157b5a0') + version('7.56.0', sha256='de60a4725a3d461c70aa571d7d69c788f1816d9d1a8a2ef05f864ce8f01279df') + version('7.54.0', sha256='f50ebaf43c507fa7cc32be4b8108fa8bbd0f5022e90794388f3c7694a302ff06') + version('7.53.1', sha256='1c7207c06d75e9136a944a2e0528337ce76f15b9ec9ae4bb30d703b59bf530e8') + version('7.52.1', sha256='d16185a767cb2c1ba3d5b9096ec54e5ec198b213f45864a38b3bda4bbf87389b') + version('7.50.3', sha256='7b7347d976661d02c84a1f4d6daf40dee377efdc45b9e2c77dedb8acf140d8ec') + version('7.50.2', sha256='0c72105df4e9575d68bcf43aea1751056c1d29b1040df6194a49c5ac08f8e233') + version('7.50.1', sha256='3c12c5f54ccaa1d40abc65d672107dcc75d3e1fcb38c267484334280096e5156') + version('7.49.1', sha256='eb63cec4bef692eab9db459033f409533e6d10e20942f4b060b32819e81885f1') + version('7.47.1', sha256='ddc643ab9382e24bbe4747d43df189a0a6ce38fcb33df041b9cb0b3cd47ae98f') + version('7.46.0', sha256='b7d726cdd8ed4b6db0fa1b474a3c59ebbbe4dcd4c61ac5e7ade0e0270d3195ad') + version('7.45.0', sha256='65154e66b9f8a442b57c436904639507b4ac37ec13d6f8a48248f1b4012b98ea') + version('7.44.0', sha256='1e2541bae6582bb697c0fbae49e1d3e6fad5d05d5aa80dbd6f072e0a44341814') + version('7.43.0', sha256='baa654a1122530483ccc1c58cc112fec3724a82c11c6a389f1e6a37dc8858df9') + version('7.42.1', sha256='e2905973391ec2dfd7743a8034ad10eeb58dab8b3a297e7892a41a7999cac887') variant('nghttp2', default=False, description='build nghttp2 library (requires C++11)') variant('libssh2', default=False, description='enable libssh2 support') diff --git a/var/spack/repos/builtin/packages/cvs/package.py b/var/spack/repos/builtin/packages/cvs/package.py index c4587036ea3..0ddf296eb3d 100644 --- a/var/spack/repos/builtin/packages/cvs/package.py +++ b/var/spack/repos/builtin/packages/cvs/package.py @@ -12,6 +12,6 @@ class Cvs(AutotoolsPackage): homepage = "http://www.nongnu.org/cvs/" url = "https://ftpmirror.gnu.org/non-gnu/cvs/source/feature/1.12.13/cvs-1.12.13.tar.bz2" - version('1.12.13', '93a8dacc6ff0e723a130835713235863f1f5ada9') + version('1.12.13', sha256='78853613b9a6873a30e1cc2417f738c330e75f887afdaf7b3d0800cb19ca515e') parallel = False diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index 8070b891ba5..b92de9106ad 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -11,9 +11,9 @@ class Czmq(AutotoolsPackage): homepage = "http://czmq.zeromq.org" url = "https://github.com/zeromq/czmq/archive/v4.0.2.tar.gz" - version('4.1.1', 'a2ab03cddd14399c6ba75b030a256211') - version('4.0.2', 'a65317a3fb8238cf70e3e992e381f9cc') - version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1') + version('4.1.1', sha256='b7623433547aa4b6e79722796c27ebc7c0470fea4204e920fd05e717c648f889') + version('4.0.2', sha256='794f80af7392ec8d361ad69646fc20aaa284d23fef92951334009771a732c810') + version('3.0.2', sha256='e56f8498daf70310b31c42669b2f9b753c5e747eafaff6d4fdac26d72a474b27') depends_on('libtool', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py index 40fd011b23a..fc3a31ebc2b 100644 --- a/var/spack/repos/builtin/packages/dakota/package.py +++ b/var/spack/repos/builtin/packages/dakota/package.py @@ -28,8 +28,8 @@ class Dakota(CMakePackage): homepage = 'https://dakota.sandia.gov/' url = 'https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.3-public.src.tar.gz' - version('6.9', 'a3993709c7b2ef94b44da4544dc06275', url='https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.9-release-public-src.zip') - version('6.3', '05a58d209fae604af234c894c3f73f6d') + version('6.9', sha256='ede7149843707f4b07e76aae27e6a6826734131938da8a6c1b7ed11865c7ee84', url='https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.9-release-public-src.zip') + version('6.3', sha256='0fbc310105860d77bb5c96de0e8813d75441fca1a5e6dfaf732aa095c4488d52') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/daligner/package.py b/var/spack/repos/builtin/packages/daligner/package.py index 6fcadcd5f33..2abfb2c74ed 100644 --- a/var/spack/repos/builtin/packages/daligner/package.py +++ b/var/spack/repos/builtin/packages/daligner/package.py @@ -12,7 +12,7 @@ class Daligner(MakefilePackage): homepage = "https://github.com/thegenemyers/DALIGNER" url = "https://github.com/thegenemyers/DALIGNER/archive/V1.0.tar.gz" - version('1.0', 'f1b4c396ae062caa4c0e6423ba0725ef') + version('1.0', sha256='2fb03616f0d60df767fbba7c8f0021ec940c8d822ab2011cf58bd56a8b9fb414') def edit(self, spec, prefix): makefile = FileFilter('Makefile') diff --git a/var/spack/repos/builtin/packages/damageproto/package.py b/var/spack/repos/builtin/packages/damageproto/package.py index f9504a73480..db748f547d9 100644 --- a/var/spack/repos/builtin/packages/damageproto/package.py +++ b/var/spack/repos/builtin/packages/damageproto/package.py @@ -15,7 +15,7 @@ class Damageproto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/damageproto" url = "https://www.x.org/releases/individual/proto/damageproto-1.2.1.tar.gz" - version('1.2.1', 'bf8c47b7f48625230cff155180f8ddce') + version('1.2.1', sha256='f65ccbf1de9750a527ea6e85694085b179f2d06495cbdb742b3edb2149fef303') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py index dd7e358d610..0b3c770ded9 100644 --- a/var/spack/repos/builtin/packages/darshan-runtime/package.py +++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py @@ -19,10 +19,10 @@ class DarshanRuntime(Package): git = "https://xgitlab.cels.anl.gov/darshan/darshan.git" version('develop', branch='master') - version('3.1.7', '2777e0769ec2b31dd1065f1de835dcfc') - version('3.1.6', 'ce5b8f1e69d602edd4753b57258b57c1') - version('3.1.0', '439d717323e6265b2612ed127886ae52') - version('3.0.0', '732577fe94238936268d74d7d74ebd08') + version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6') + version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856') + version('3.1.0', sha256='b847047c76759054577823fbe21075cfabb478cdafad341d480274fb1cef861c') + version('3.0.0', sha256='95232710f5631bbf665964c0650df729c48104494e887442596128d189da43e0') depends_on('mpi') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py index 7ecc042057b..33041161dd1 100644 --- a/var/spack/repos/builtin/packages/darshan-util/package.py +++ b/var/spack/repos/builtin/packages/darshan-util/package.py @@ -17,10 +17,10 @@ class DarshanUtil(Package): git = "https://xgitlab.cels.anl.gov/darshan/darshan.git" version('develop', branch='master') - version('3.1.7', '2777e0769ec2b31dd1065f1de835dcfc') - version('3.1.6', 'ce5b8f1e69d602edd4753b57258b57c1') - version('3.1.0', '439d717323e6265b2612ed127886ae52') - version('3.0.0', '732577fe94238936268d74d7d74ebd08') + version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6') + version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856') + version('3.1.0', sha256='b847047c76759054577823fbe21075cfabb478cdafad341d480274fb1cef861c') + version('3.0.0', sha256='95232710f5631bbf665964c0650df729c48104494e887442596128d189da43e0') variant('bzip2', default=False, description="Enable bzip2 compression") depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/dash/package.py b/var/spack/repos/builtin/packages/dash/package.py index ca1fdc0842d..8ce374c6ca2 100644 --- a/var/spack/repos/builtin/packages/dash/package.py +++ b/var/spack/repos/builtin/packages/dash/package.py @@ -13,7 +13,7 @@ class Dash(AutotoolsPackage): url = "https://git.kernel.org/pub/scm/utils/dash/dash.git/snapshot/dash-0.5.9.1.tar.gz" list_url = homepage - version('0.5.9.1', '0d800da0b8ddbefa1468978d314b7d09') + version('0.5.9.1', sha256='3f747013a20a3a9d2932be1a6dd1b002ca5649849b649be0af8a8da80bd8a918') depends_on('libedit', type='link') diff --git a/var/spack/repos/builtin/packages/datamash/package.py b/var/spack/repos/builtin/packages/datamash/package.py index e0f2ab94f19..dd79b61af85 100644 --- a/var/spack/repos/builtin/packages/datamash/package.py +++ b/var/spack/repos/builtin/packages/datamash/package.py @@ -14,10 +14,10 @@ class Datamash(AutotoolsPackage): homepage = "https://www.gnu.org/software/datamash/" url = "https://ftpmirror.gnu.org/datamash/datamash-1.0.5.tar.gz" - version('1.3', '47d382090e367ddb4967d640aba77b66') - version('1.1.0', '79a6affca08107a095e97e4237fc8775') - version('1.0.7', '9f317bab07454032ba9c068e7f17b04b') - version('1.0.6', 'ff26fdef0f343cb695cf1853e14a1a5b') - version('1.0.5', '9a29549dc7feca49fdc5fab696614e11') + version('1.3', sha256='eebb52171a4353aaad01921384098cf54eb96ebfaf99660e017f6d9fc96657a6') + version('1.1.0', sha256='a9e5acc86af4dd64c7ac7f6554718b40271aa67f7ff6e9819bdd919a25904bb0') + version('1.0.7', sha256='1a0b300611a5dff89e08e20773252b00f5e2c2d65b2ad789872fc7df94fa8978') + version('1.0.6', sha256='0154c25c45b5506b6d618ca8e18d0ef093dac47946ac0df464fb21e77b504118') + version('1.0.5', sha256='cb7c0b7bf654eea5bb80f10c1710c8dffab8106549fd6b4341cba140e15a9938') build_directory = 'spack-build' diff --git a/var/spack/repos/builtin/packages/dataspaces/package.py b/var/spack/repos/builtin/packages/dataspaces/package.py index 3e156ca8299..5bfa513ddeb 100644 --- a/var/spack/repos/builtin/packages/dataspaces/package.py +++ b/var/spack/repos/builtin/packages/dataspaces/package.py @@ -23,7 +23,7 @@ class Dataspaces(AutotoolsPackage): git = "https://github.com/melrom/dataspaces.git" version('develop', branch='master') - version('1.6.2', '73caa4920b6f2c0c6d6cb87640ff04be') + version('1.6.2', sha256='3c43d551c1e8198a4ab269c83928e1dc6f8054e6d41ceaee45155d91a48cf9bf') variant('dimes', default=False, diff --git a/var/spack/repos/builtin/packages/davix/package.py b/var/spack/repos/builtin/packages/davix/package.py index ace203e21be..381251a62dd 100644 --- a/var/spack/repos/builtin/packages/davix/package.py +++ b/var/spack/repos/builtin/packages/davix/package.py @@ -14,7 +14,7 @@ class Davix(CMakePackage): list_url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/" list_depth = 1 - version('0.6.8', 'e1820f4cc3fc44858ae97197a3922cce2a1130ff553b080ba19e06eb8383ddf7', + version('0.6.8', sha256='e1820f4cc3fc44858ae97197a3922cce2a1130ff553b080ba19e06eb8383ddf7', url='http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.8/davix-0.6.8.tar.gz') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py index adc59372cd7..3a578e07088 100644 --- a/var/spack/repos/builtin/packages/dbus/package.py +++ b/var/spack/repos/builtin/packages/dbus/package.py @@ -19,13 +19,13 @@ class Dbus(Package): homepage = "http://dbus.freedesktop.org/" url = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz" - version('1.12.8', '2764bf150e5aa8005b7bc0d6c388756a') - version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b') - version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36') - version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43') - version('1.8.6', '6a08ba555d340e9dfe2d623b83c0eea8') - version('1.8.4', '4717cb8ab5b80978fcadf2b4f2f72e1b') - version('1.8.2', 'd6f709bbec0a022a1847c7caec9d6068') + version('1.12.8', sha256='e2dc99e7338303393b6663a98320aba6a63421bcdaaf571c8022f815e5896eb3') + version('1.11.2', sha256='5abc4c57686fa82669ad0039830788f9b03fdc4fff487f0ccf6c9d56ba2645c9') + version('1.9.0', sha256='38ebc695b5cbbd239e0f149aa5d5395f0051a0fec1b74f21ff2921b22a31c171') + version('1.8.8', sha256='dfab263649a979d0fff64a30cac374891a8e9940350e41f3bbd7679af32bd1fd') + version('1.8.6', sha256='eded83ca007b719f32761e60fd8b9ffd0f5796a4caf455b01b5a5ef740ebd23f') + version('1.8.4', sha256='3ef63dc8d0111042071ee7f7bafa0650c6ce2d7be957ef0b7ec269495a651ff8') + version('1.8.2', sha256='5689f7411165adc953f37974e276a3028db94447c76e8dd92efe910c6d3bae08') depends_on('pkgconfig', type='build') depends_on('expat') diff --git a/var/spack/repos/builtin/packages/deconseq-standalone/package.py b/var/spack/repos/builtin/packages/deconseq-standalone/package.py index 89e02bfa146..ac451ff95ab 100644 --- a/var/spack/repos/builtin/packages/deconseq-standalone/package.py +++ b/var/spack/repos/builtin/packages/deconseq-standalone/package.py @@ -13,7 +13,7 @@ class DeconseqStandalone(Package): homepage = "http://deconseq.sourceforge.net" url = "https://sourceforge.net/projects/deconseq/files/standalone/deconseq-standalone-0.4.3.tar.gz" - version('0.4.3', 'cb3fddb90e584d89fd9c2b6b8f2e20a2') + version('0.4.3', sha256='fb4050418c26a5203220f6396263da554326657590cffd65053eb8adc465ac65') depends_on('perl@5:') diff --git a/var/spack/repos/builtin/packages/dejagnu/package.py b/var/spack/repos/builtin/packages/dejagnu/package.py index cd7ea720236..b7a86064699 100644 --- a/var/spack/repos/builtin/packages/dejagnu/package.py +++ b/var/spack/repos/builtin/packages/dejagnu/package.py @@ -13,8 +13,8 @@ class Dejagnu(AutotoolsPackage): homepage = "https://www.gnu.org/software/dejagnu/" url = "https://ftpmirror.gnu.org/dejagnu/dejagnu-1.6.tar.gz" - version('1.6', '1fdc2eb0d592c4f89d82d24dfdf02f0b') - version('1.4.4', '053f18fd5d00873de365413cab17a666') + version('1.6', sha256='00b64a618e2b6b581b16eb9131ee80f721baa2669fa0cdee93c500d1a652d763') + version('1.4.4', sha256='d0fbedef20fb0843318d60551023631176b27ceb1e11de7468a971770d0e048d') depends_on('expect') depends_on('tcl@8.5:') diff --git a/var/spack/repos/builtin/packages/denovogear/package.py b/var/spack/repos/builtin/packages/denovogear/package.py index 61651ca492b..55c1213e382 100644 --- a/var/spack/repos/builtin/packages/denovogear/package.py +++ b/var/spack/repos/builtin/packages/denovogear/package.py @@ -15,8 +15,8 @@ class Denovogear(CMakePackage): homepage = "https://github.com/denovogear/denovogear" url = "https://github.com/denovogear/denovogear/archive/v1.1.1.tar.gz" - version('1.1.1', 'da30e46851c3a774653e57f98fe62e5f') - version('1.1.0', '7d441d56462efb7ff5d3a6f6bddfd8b9') + version('1.1.1', sha256='799fe99193e9cf12320893cf020a3251022f60a49de8677a1c5a18c578fe4be2') + version('1.1.0', sha256='f818f80cd67183294c8aae312cad8311e6a9abede1f687567bb079d29f79c005') depends_on('cmake@3.1:', type=('build')) depends_on('boost@1.47:1.60', type=('build')) diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py index 832d305e8cf..b0fe51553ea 100644 --- a/var/spack/repos/builtin/packages/dia/package.py +++ b/var/spack/repos/builtin/packages/dia/package.py @@ -11,7 +11,7 @@ class Dia(Package): homepage = 'https://wiki.gnome.org/Apps/Dia' url = 'https://ftp.gnome.org/pub/gnome/sources/dia/0.97/dia-0.97.3.tar.xz' - version('0.97.3', '0e744a0f6a6c4cb6a089e4d955392c3c') + version('0.97.3', sha256='22914e48ef48f894bb5143c5efc3d01ab96e0a0cde80de11058d3b4301377d34') depends_on('intltool', type='build') depends_on('gettext', type='build') diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py index 961ea6be829..7c9df369721 100644 --- a/var/spack/repos/builtin/packages/dialign-tx/package.py +++ b/var/spack/repos/builtin/packages/dialign-tx/package.py @@ -13,7 +13,7 @@ class DialignTx(MakefilePackage): homepage = "http://dialign-tx.gobics.de/" url = "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz" - version('1.0.2', '8ccfb1d91136157324d1e513f184ca29') + version('1.0.2', sha256='fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f') build_directory = 'source' diff --git a/var/spack/repos/builtin/packages/diamond/package.py b/var/spack/repos/builtin/packages/diamond/package.py index 677c71dbcd5..2d52d22e23c 100644 --- a/var/spack/repos/builtin/packages/diamond/package.py +++ b/var/spack/repos/builtin/packages/diamond/package.py @@ -16,11 +16,11 @@ class Diamond(CMakePackage): version('0.9.25', sha256='65298f60cf9421dcc7669ce61642611cd9eeffc32f66fd39ebfa25dd64416808') version('0.9.23', sha256='0da5cdd5e5b77550ec0eaba2c6c431801cdd10d31606ca12f952b57d3d31db92') version('0.9.22', sha256='35e518cfa0ac2fbc57e422d380bdb5123c6335742dd7965b76c34c95f241b729') - version('0.9.21', '6f3c53520f3dad37dfa3183d61f21dd5') - version('0.9.20', 'd73f4955909d16456d83b30d9c294b2b') - version('0.9.19', '8565d2d3bfe407ee778eeabe7c6a7fde') - version('0.9.14', 'b9e1d0bc57f07afa05dbfbb53c31aae2') - version('0.8.38', 'd4719c8a7947ba9f743446ac95cfe644') - version('0.8.26', '0d86305ab25cc9b3bb3564188d30fff2') + version('0.9.21', sha256='3f10e089c24d24f3066f3a58fa01bf356c4044e0a0bcab081b9bf1a8d946c9b1') + version('0.9.20', sha256='5cf629baf135f54dc93728e3618ae08c64c1ecb81b3f2d2d48fcfd1c010ed8f0') + version('0.9.19', sha256='fab783f51af9010666f2b569f438fb38843d0201fe0c0e167db5b70d12459e30') + version('0.9.14', sha256='de870a7806ac0aa47b97c9b784dd7201e2c8e11a122003bde440d926211b911e') + version('0.8.38', sha256='582a7932f3aa73b0eac2275dd773818665f0b067b32a79ff5a13b0e3ca375f60') + version('0.8.26', sha256='00d2be32dad76511a767ab8e917962c0ecc572bc808080be60dec028df45439f') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/diffsplice/package.py b/var/spack/repos/builtin/packages/diffsplice/package.py index 637671843a3..cca9e0cc9c4 100644 --- a/var/spack/repos/builtin/packages/diffsplice/package.py +++ b/var/spack/repos/builtin/packages/diffsplice/package.py @@ -14,8 +14,8 @@ class Diffsplice(MakefilePackage): homepage = "http://www.netlab.uky.edu/p/bioinfo/DiffSplice" url = "http://protocols.netlab.uky.edu/~yin/download/diffsplice/diffsplice_0.1.1.tgz" - version('0.1.2beta', 'a1df6e0b50968f2c229d5d7f97327336') - version('0.1.1', 'be90e6c072402d5aae0b4e2cbb8c10ac') + version('0.1.2beta', sha256='cc06dcb9f8d98b2184f0dd5863b79bdd6a8cd33b9418e6549b7ea63e90ee1aa6') + version('0.1.1', sha256='9740426692b0e5f92b943b127014c1d9815bed2938b5dd9e9d0c5b64abbb5da6') def edit(self, spec, prefix): if spec.target.family == 'aarch64': diff --git a/var/spack/repos/builtin/packages/direnv/package.py b/var/spack/repos/builtin/packages/direnv/package.py index 816c4331858..d00c811dbbf 100644 --- a/var/spack/repos/builtin/packages/direnv/package.py +++ b/var/spack/repos/builtin/packages/direnv/package.py @@ -12,8 +12,8 @@ class Direnv(Package): homepage = "https://direnv.net/" url = "https://github.com/direnv/direnv/archive/v2.11.3.tar.gz" - version('2.20.0', '75a166c2ef83a3b8dfbd0544cadb5984') - version('2.11.3', '5b9728e2dabed232b4932849647fd6e5') + version('2.20.0', sha256='cc72525b0a5b3c2ab9a52a3696e95562913cd431f923bcc967591e75b7541bff') + version('2.11.3', sha256='2d34103a7f9645059270763a0cfe82085f6d9fe61b2a85aca558689df0e7b006') depends_on('go', type='build') diff --git a/var/spack/repos/builtin/packages/discovar/package.py b/var/spack/repos/builtin/packages/discovar/package.py index 5a36964965a..16484efe1b2 100644 --- a/var/spack/repos/builtin/packages/discovar/package.py +++ b/var/spack/repos/builtin/packages/discovar/package.py @@ -12,6 +12,6 @@ class Discovar(AutotoolsPackage): homepage = "https://software.broadinstitute.org/software/discovar/blog/" url = "ftp://ftp.broadinstitute.org/pub/crd/Discovar/latest_source_code/discovar-52488.tar.gz" - version('52488', 'e72a0b9363e25c99d8e8729c0be98364') + version('52488', sha256='c46e8f5727b3c8116d715c02e20a83e6261c762e8964d00709abfb322a501d4e') conflicts('%gcc@6:') diff --git a/var/spack/repos/builtin/packages/discovardenovo/package.py b/var/spack/repos/builtin/packages/discovardenovo/package.py index b39277a937e..d62b523bcbb 100644 --- a/var/spack/repos/builtin/packages/discovardenovo/package.py +++ b/var/spack/repos/builtin/packages/discovardenovo/package.py @@ -15,7 +15,7 @@ class Discovardenovo(AutotoolsPackage): homepage = "https://software.broadinstitute.org/software/discovar/blog/" url = "ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz" - version('52488', '2b08c77b1b998d85be8048e5efb10358') + version('52488', sha256='445445a3b75e17e276a6119434f13784a5a661a9c7277f5e10f3b6b3b8ac5771') # lots of compiler errors with GCC7, works with 4.8.5 # and devs claim it works with 4.7 so I'm assuming 4.7-4.8'll work diff --git a/var/spack/repos/builtin/packages/dmd/package.py b/var/spack/repos/builtin/packages/dmd/package.py index 1885568128d..57555244763 100644 --- a/var/spack/repos/builtin/packages/dmd/package.py +++ b/var/spack/repos/builtin/packages/dmd/package.py @@ -21,15 +21,15 @@ class Dmd(MakefilePackage): # https://wiki.dlang.org/Building_under_Posix resource(name='druntime', url='https://github.com/dlang/druntime/archive/v2.081.1.tar.gz', - md5='49c8ba48fcb1e53d553a52d8ed7f9164', + sha256='8313af32dce71f767fb0072cae699cbfe7196cf01b0ce1c5dd416a71d94f5fee', placement='druntime') resource(name='phobos', url='https://github.com/dlang/phobos/archive/v2.081.1.tar.gz', - md5='ccf4787275b490eb2ddfc6713f9e9882', + sha256='d945c6fd1be14dff5fcbf45c1e11302e12bebac56d55e4e97e48e150f2899e04', placement='phobos') resource(name='tools', url='https://github.com/dlang/tools/archive/v2.081.1.tar.gz', - md5='a3bc7ed3d60b39712ef011bf19b3d427', + sha256='71fa249dbfd278eec2b95ce577af32e623e44caf0d993905ddc189e3beec21d0', placement='tools') def setup_environment(self, spack_env, run_env): diff --git a/var/spack/repos/builtin/packages/dmxproto/package.py b/var/spack/repos/builtin/packages/dmxproto/package.py index e70d2a07263..0106b5eb8f2 100644 --- a/var/spack/repos/builtin/packages/dmxproto/package.py +++ b/var/spack/repos/builtin/packages/dmxproto/package.py @@ -16,7 +16,7 @@ class Dmxproto(AutotoolsPackage): homepage = "http://dmx.sourceforge.net/" url = "https://www.x.org/archive/individual/proto/dmxproto-2.3.1.tar.gz" - version('2.3.1', '7c52af95aac192e8de31bd9a588ce121') + version('2.3.1', sha256='3262bbf5902211a3ce88f5c6ab4528145ff84f69c52fd386ae0312bc45fb8a40') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py index a8e9a819e3c..d654f790eaf 100644 --- a/var/spack/repos/builtin/packages/docbook-xml/package.py +++ b/var/spack/repos/builtin/packages/docbook-xml/package.py @@ -15,7 +15,7 @@ class DocbookXml(Package): list_url = "https://www.oasis-open.org/docbook/xml/" list_depth = 1 - version('4.5', '03083e288e87a7e829e437358da7ef9e') + version('4.5', sha256='4e4e037a2b83c98c6c94818390d4bdd3f6e10f6ec62dd79188594e26190dc7b4') def install(self, spec, prefix): install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/dos2unix/package.py b/var/spack/repos/builtin/packages/dos2unix/package.py index 34e1a53c126..d9c5daed750 100644 --- a/var/spack/repos/builtin/packages/dos2unix/package.py +++ b/var/spack/repos/builtin/packages/dos2unix/package.py @@ -12,7 +12,7 @@ class Dos2unix(MakefilePackage): homepage = "https://waterlan.home.xs4all.nl/dos2unix.html" url = "https://waterlan.home.xs4all.nl/dos2unix/dos2unix-7.3.4.tar.gz" - version('7.3.4', '04428e77e2ead8a92c1492ba8977f1d1') + version('7.3.4', sha256='8ccda7bbc5a2f903dafd95900abb5bf5e77a769b572ef25150fde4056c5f30c5') def install(self, spec, prefix): make('prefix={0}'.format(prefix), 'install') diff --git a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py index 34d2e2275cb..5d9a3ef014a 100644 --- a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py +++ b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py @@ -17,9 +17,7 @@ class DotnetCoreSdk(Package): version('2.1.300', url='https://download.microsoft.com/download/8/8/5/88544F33-836A' '-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz', - sha224='80a6bfb1db5862804e90f819c1adeebe3d624eae0d6147e5d6694333' - 'f0458afd7d34ce73623964752971495a310ff7fcc266030ce5aef82d5de' - '7293d94d13770') + sha256='fabca4c8825182ff18e5a2f82dfe75aecd10260ee9e7c85a8c4b3d108e5d8e1b') variant('telemetry', default=False, description='allow collection of telemetry data') diff --git a/var/spack/repos/builtin/packages/double-conversion/package.py b/var/spack/repos/builtin/packages/double-conversion/package.py index 33eac0e7c49..8b0ba30815a 100644 --- a/var/spack/repos/builtin/packages/double-conversion/package.py +++ b/var/spack/repos/builtin/packages/double-conversion/package.py @@ -21,11 +21,11 @@ class DoubleConversion(CMakePackage): homepage = "https://github.com/google/double-conversion" url = "https://github.com/google/double-conversion/archive/v2.0.1.zip" - version('2.0.1', '5be77f780841af528e92986d46620b1e') - version('2.0.0', '045f7927246c368b57dcdb844ec61211') - version('1.1.5', 'ddf782373e2630c07b2691c31cee0b24') - version('1.1.4', '5df72704406d93cd54c73d73f02e2744') - version('1.1.3', 'b312152c8c66c80449d5e0325b94502e') + version('2.0.1', sha256='476aefbdc2051bbcca0d5919ebc293c90a7ad2c0cb6c4ad877d6e665f469146b') + version('2.0.0', sha256='437df89059bfa6c1c0f8703693c2584a57f75289ed7020d801c9befb23f46a26') + version('1.1.5', sha256='496fd3354fa0ff17562907632f5560c1d444ea98b6069f1436fa573949b94fb0') + version('1.1.4', sha256='24b5edce8c88f0f632c83e60e0bde11252656dc3b714ba195619c1798ff28834') + version('1.1.3', sha256='f0d1b8621592a3cf010c04c3e1c0f08455fc0fc7ee22e1583e2a63dc6d3e3871') def cmake_args(self): return ['-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true'] diff --git a/var/spack/repos/builtin/packages/dri2proto/package.py b/var/spack/repos/builtin/packages/dri2proto/package.py index dda3646259a..8fc3c35c5ab 100644 --- a/var/spack/repos/builtin/packages/dri2proto/package.py +++ b/var/spack/repos/builtin/packages/dri2proto/package.py @@ -16,7 +16,7 @@ class Dri2proto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/dri2proto/" url = "https://www.x.org/releases/individual/proto/dri2proto-2.8.tar.gz" - version('2.8', '19ea18f63d8ae8053c9fa84b60365b77') + version('2.8', sha256='7e65b031eaa6ebe23c75583d4abd993ded7add8009b4200a4db7aa10728b0f61') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/dri3proto/package.py b/var/spack/repos/builtin/packages/dri3proto/package.py index 7e322a47876..2e210afa659 100644 --- a/var/spack/repos/builtin/packages/dri3proto/package.py +++ b/var/spack/repos/builtin/packages/dri3proto/package.py @@ -16,7 +16,7 @@ class Dri3proto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/dri3proto/" url = "https://www.x.org/releases/individual/proto/dri3proto-1.0.tar.gz" - version('1.0', '25e84a49a076862277ee12aebd49ff5f') + version('1.0', sha256='e1a0dad3009ecde52c0bf44187df5f95cc9a7cc0e76dfc2f2bbf3e909fe03fa9') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/dsdp/package.py b/var/spack/repos/builtin/packages/dsdp/package.py index 5bb6d4a3c17..c12c1d1c920 100644 --- a/var/spack/repos/builtin/packages/dsdp/package.py +++ b/var/spack/repos/builtin/packages/dsdp/package.py @@ -18,7 +18,7 @@ class Dsdp(MakefilePackage): homepage = "http://www.mcs.anl.gov/hs/software/DSDP/" url = "http://www.mcs.anl.gov/hs/software/DSDP/DSDP5.8.tar.gz" - version('5.8', '37c15a3c6c3f13e31262f65ac4364b5e') + version('5.8', sha256='26aa624525a636de272c0b329e2dfd01a0d5b7827f1c1c76f393d71e37dead70') depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/dsrc/package.py b/var/spack/repos/builtin/packages/dsrc/package.py index 6954e53389b..d8d6f2c609f 100644 --- a/var/spack/repos/builtin/packages/dsrc/package.py +++ b/var/spack/repos/builtin/packages/dsrc/package.py @@ -15,7 +15,7 @@ class Dsrc(MakefilePackage): homepage = "http://sun.aei.polsl.pl/dsrc" url = "https://github.com/refresh-bio/DSRC/archive/v2.0.2.tar.gz" - version('2.0.2', '0a75deb6db948f9179df0756c259b870') + version('2.0.2', sha256='6d7abe0d72a501054a2115ccafff2e85e6383de627ec3e94ff4f03b7bb96a806') parallel = False diff --git a/var/spack/repos/builtin/packages/dtcmp/package.py b/var/spack/repos/builtin/packages/dtcmp/package.py index 95a233a4d13..43679fa6c2c 100644 --- a/var/spack/repos/builtin/packages/dtcmp/package.py +++ b/var/spack/repos/builtin/packages/dtcmp/package.py @@ -13,8 +13,8 @@ class Dtcmp(AutotoolsPackage): homepage = "https://github.com/hpc/dtcmp" url = "https://github.com/hpc/dtcmp/releases/download/v1.0.3/dtcmp-1.0.3.tar.gz" - version('1.1.0', 'af5c73f7d3a9afd90a22d0df85471d2f') - version('1.0.3', 'cdd8ccf71e8ff67de2558594a7fcd317') + version('1.1.0', sha256='fd2c4485eee560a029f62c8f227df4acdb1edc9340907f4ae2dbee59f05f057d') + version('1.0.3', sha256='1327368e2808043ad5f245cd16f0da19543de50eae02a4e22b8a1c2e0eff8f35') depends_on('mpi') depends_on('lwgrp') diff --git a/var/spack/repos/builtin/packages/ea-utils/package.py b/var/spack/repos/builtin/packages/ea-utils/package.py index c666b063c88..6eae29bc78c 100644 --- a/var/spack/repos/builtin/packages/ea-utils/package.py +++ b/var/spack/repos/builtin/packages/ea-utils/package.py @@ -14,7 +14,7 @@ class EaUtils(MakefilePackage): homepage = "http://expressionanalysis.github.io/ea-utils/" url = "https://github.com/ExpressionAnalysis/ea-utils/archive/1.04.807.tar.gz" - version('1.04.807', '5972b9f712920603b7527f46c0063a09') + version('1.04.807', sha256='aa09d25e6aa7ae71d2ce4198a98e58d563f151f8ff248e4602fa437f12b8d05f') depends_on('subversion') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/easybuild/package.py b/var/spack/repos/builtin/packages/easybuild/package.py index 0430639762a..8ada721adc3 100644 --- a/var/spack/repos/builtin/packages/easybuild/package.py +++ b/var/spack/repos/builtin/packages/easybuild/package.py @@ -16,7 +16,7 @@ class Easybuild(PythonPackage): maintainers = ['boegel'] version('4.0.0', sha256='21bcc1048525ad6219667cc97a7421b5388068c670cabba356712e474896de40') - version('3.1.2', 'c2d901c2a71f51b24890fa69c3a46383') + version('3.1.2', sha256='a966a08e41d3557d7fd3dc5322180c006d27281d9ecc1b1fce1b4518c32664d4') depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py index 2b07635077d..5bbc02f96b2 100644 --- a/var/spack/repos/builtin/packages/eccodes/package.py +++ b/var/spack/repos/builtin/packages/eccodes/package.py @@ -18,8 +18,8 @@ class Eccodes(CMakePackage): maintainers = ['skosukhin'] version('2.13.0', sha256='c5ce1183b5257929fc1f1c8496239e52650707cfab24f4e0e1f1a471135b8272') - version('2.5.0', '5a7e92c58418d855082fa573efd352aa') - version('2.2.0', 'b27e6f0a3eea5b92dac37372e4c45a62') + version('2.5.0', sha256='18ab44bc444168fd324d07f7dea94f89e056f5c5cd973e818c8783f952702e4e') + version('2.2.0', sha256='1a4112196497b8421480e2a0a1164071221e467853486577c4f07627a702f4c3') variant('netcdf', default=False, description='Enable GRIB to NetCDF conversion tool') diff --git a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py index ed5ebb13d60..ef517b92d22 100644 --- a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py +++ b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py @@ -19,7 +19,7 @@ class EclipseGcjParser(Package): maintainers = ['citibeth'] - version('4.8', 'd7cd6a27c8801e66cbaa964a039ecfdb', expand=False) + version('4.8', sha256='98fd128f1d374d9e42fd9d4836bdd249c6d511ebc6c0df17fbc1b9df96c3d781', expand=False) phases = ('build', 'install') diff --git a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py index efb4d9aaa88..68586070c87 100644 --- a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py +++ b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py @@ -23,8 +23,8 @@ class EcpProxyApps(Package): version('2.1', sha256='604da008fc4ef3bdbc25505088d610333249e3e9745eac7dbfd05b91e33e218d') version('2.0', sha256='5f3cb3a772224e738c1dab42fb34d40f6b313af51ab1c575fb334e573e41e09a') - version('1.1', '15825c318acd3726fd8e72803b1c1090') - version('1.0', '8b3f00f05e6cde88d8d913da4293ee62') + version('1.1', sha256='8537e03588c0f46bebf5b7f07146c79812f2ebfb77d29e184baa4dd5f4603ee3') + version('1.0', sha256='13d9795494dabdb4c724d2c0f322c2149b2507d2fd386ced12b54292b7ecf595') variant('candle', default=False, description='Also build CANDLE Benchmarks') diff --git a/var/spack/repos/builtin/packages/ed/package.py b/var/spack/repos/builtin/packages/ed/package.py index 7d3e01488b3..9c84e64262c 100644 --- a/var/spack/repos/builtin/packages/ed/package.py +++ b/var/spack/repos/builtin/packages/ed/package.py @@ -14,6 +14,6 @@ class Ed(AutotoolsPackage): homepage = "https://www.gnu.org/software/ed" url = "https://ftpmirror.gnu.org/ed/ed-1.4.tar.gz" - version('1.4', 'da0ddc0e0b0bec2da4b13b0d0d1bce2b') + version('1.4', sha256='db36da85ee1a9d8bafb4b041bd4c8c11becba0c43ec446353b67045de1634fda') parallel = False diff --git a/var/spack/repos/builtin/packages/editres/package.py b/var/spack/repos/builtin/packages/editres/package.py index beaf5d440aa..d32e221bd37 100644 --- a/var/spack/repos/builtin/packages/editres/package.py +++ b/var/spack/repos/builtin/packages/editres/package.py @@ -12,7 +12,7 @@ class Editres(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/editres" url = "https://www.x.org/archive/individual/app/editres-1.0.6.tar.gz" - version('1.0.6', '310c504347ca499874593ac96e935353') + version('1.0.6', sha256='85f4664ca582effb01ee972d006124569b757b9a08ae6608c3f45fc36b3b7b1a') depends_on('libxaw') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 9c658bbc8b6..0c1a86d6769 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -15,14 +15,14 @@ class Eigen(CMakePackage): url = 'https://bitbucket.org/eigen/eigen/get/3.3.4.tar.bz2' version('3.3.7', sha256='9f13cf90dedbe3e52a19f43000d71fdf72e986beb9a5436dddcd61ff9d77a3ce') - version('3.3.5', 'e83549a79d1b721da0f8899ab34edf95') - version('3.3.4', 'a7aab9f758249b86c93221ad417fbe18') - version('3.3.3', 'b2ddade41040d9cf73b39b4b51e8775b') - version('3.3.1', 'edb6799ef413b0868aace20d2403864c') - version('3.2.10', 'a85bb68c82988648c3d53ba9768d7dcbcfe105f8') - version('3.2.9', '59ab81212f8eb2534b1545a9b42c38bf618a0d71') - version('3.2.8', '64f4aef8012a424c7e079eaf0be71793ab9bc6e0') - version('3.2.7', 'cc1bacbad97558b97da6b77c9644f184') + version('3.3.5', sha256='7352bff3ea299e4c7d7fbe31c504f8eb9149d7e685dec5a12fbaa26379f603e2') + version('3.3.4', sha256='dd254beb0bafc695d0f62ae1a222ff85b52dbaa3a16f76e781dce22d0d20a4a6') + version('3.3.3', sha256='a4143fc45e4454b4b98fcea3516b3a79b8cdb3bc7fadf996d088c6a0d805fea1') + version('3.3.1', sha256='a0b4cebaabd8f371d1b364f9723585fbcc7c9640ca60273b99835e6cf115f056') + version('3.2.10', sha256='760e6656426fde71cc48586c971390816f456d30f0b5d7d4ad5274d8d2cb0a6d') + version('3.2.9', sha256='4d1e036ec1ed4f4805d5c6752b76072d67538889f4003fadf2f6e00a825845ff') + version('3.2.8', sha256='722a63d672b70f39c271c5e2a4a43ba14d12015674331790414fcb167c357e55') + version('3.2.7', sha256='e58e1a11b23cf2754e32b3c5990f318a8461a3613c7acbf6035870daa45c2f3e') variant('metis', default=False, description='Enables metis permutations in sparse algebra') diff --git a/var/spack/repos/builtin/packages/elasticsearch/package.py b/var/spack/repos/builtin/packages/elasticsearch/package.py index 65552010084..6b7be6715e3 100644 --- a/var/spack/repos/builtin/packages/elasticsearch/package.py +++ b/var/spack/repos/builtin/packages/elasticsearch/package.py @@ -15,8 +15,8 @@ class Elasticsearch(Package): homepage = "https://www.elastic.co/" url = "https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-6.2.4.tar.gz" - version('6.4.0', '5c23c99a52600b250a6871bf6a744e8b') - version('6.2.4', '692d01956fe7aee2d08ac0fbf7b7a19e') + version('6.4.0', sha256='e9786efb5cecd12adee2807c7640ba9a1ab3b484d2e87497bb8d0b6df0e24f01') + version('6.2.4', sha256='91e6f1ea1e1dd39011e7a703d2751ca46ee374665b08b0bfe17e0c0c27000e8e') depends_on('jdk', type='run') diff --git a/var/spack/repos/builtin/packages/elemental/package.py b/var/spack/repos/builtin/packages/elemental/package.py index ffa1920e747..42e7992d664 100644 --- a/var/spack/repos/builtin/packages/elemental/package.py +++ b/var/spack/repos/builtin/packages/elemental/package.py @@ -17,8 +17,8 @@ class Elemental(CMakePackage): git = "https://github.com/elemental/Elemental.git" version('develop', branch='master') - version('0.87.7', '6c1e7442021c59a36049e37ea69b8075') - version('0.87.6', '9fd29783d45b0a0e27c0df85f548abe9') + version('0.87.7', sha256='7becfdbc223e9c72e65ae876d842c48d2037d13f83e9f41cea285e21b840d7d9') + version('0.87.6', sha256='b597987c99ddd3462e0619524c5b7f711177ae8ae541b1b961e11d96e15afc64') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py index 1151034b5d8..f8d6048bf68 100644 --- a/var/spack/repos/builtin/packages/elfutils/package.py +++ b/var/spack/repos/builtin/packages/elfutils/package.py @@ -21,13 +21,13 @@ class Elfutils(AutotoolsPackage): list_url = "https://sourceware.org/elfutils/ftp" list_depth = 1 - version('0.176', '077e4f49320cad82bf17a997068b1db9') - version('0.175', '9a02b0382b78cc2d515fb950275d4c02') - version('0.174', '48bec24c0c8b2c16820326956dff9378') - version('0.173', '35decb1ebfb90d565e4c411bee4185cc') - version('0.170', '03599aee98c9b726c7a732a2dd0245d5') - version('0.168', '52adfa40758d0d39e5d5c57689bf38d6') - version('0.163', '77ce87f259987d2e54e4d87b86cbee41') + version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023') + version('0.175', sha256='f7ef925541ee32c6d15ae5cb27da5f119e01a5ccdbe9fe57bf836730d7b7a65b') + version('0.174', sha256='cdf27e70076e10a29539d89e367101d516bc4aa11b0d7777fe52139e3fcad08a') + version('0.173', sha256='b76d8c133f68dad46250f5c223482c8299d454a69430d9aa5c19123345a000ff') + version('0.170', sha256='1f844775576b79bdc9f9c717a50058d08620323c1e935458223a12f249c9e066') + version('0.168', sha256='b88d07893ba1373c7dd69a7855974706d05377766568a7d9002706d5de72c276') + version('0.163', sha256='7c774f1eef329309f3b05e730bdac50013155d437518a2ec0e24871d312f2e23') # Libraries for reading compressed DWARF sections. variant('bzip2', default=False, diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py index 75c4e7bf9fa..4a210fe3280 100644 --- a/var/spack/repos/builtin/packages/elk/package.py +++ b/var/spack/repos/builtin/packages/elk/package.py @@ -13,7 +13,7 @@ class Elk(MakefilePackage): homepage = 'http://elk.sourceforge.net/' url = 'https://sourceforge.net/projects/elk/files/elk-3.3.17.tgz' - version('3.3.17', 'f57f6230d14f3b3b558e5c71f62f0592') + version('3.3.17', sha256='c9b87ae4ef367ed43afc2d43eb961745668e40670995e8e24c13db41b7e85d73') # Elk provides these libraries, but allows you to specify your own variant('blas', default=True, diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py index cc3f75a4c0c..19fdf7a3830 100644 --- a/var/spack/repos/builtin/packages/elpa/package.py +++ b/var/spack/repos/builtin/packages/elpa/package.py @@ -16,14 +16,14 @@ class Elpa(AutotoolsPackage): version('2018.11.001', sha256='cc27fe8ba46ce6e6faa8aea02c8c9983052f8e73a00cfea38abf7613cb1e1b16') - version('2018.05.001.rc1', 'ccd77bd8036988ee624f43c04992bcdd') - version('2017.11.001', '4a437be40cc966efb07aaab84c20cd6e') - version('2017.05.003', '7c8e5e58cafab212badaf4216695700f') - version('2017.05.002', 'd0abc1ac1f493f93bf5e30ec8ab155dc') - version('2016.11.001.pre', '5656fd066cf0dcd071dbcaf20a639b37') - version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376') - version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c') - version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6') + version('2018.05.001.rc1', sha256='598c01da20600a4514ea4d503b93e977ac0367e797cab7a7c1b0e0e3e86490db') + version('2017.11.001', sha256='59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820') + version('2017.05.003', sha256='bccd49ce35a323bd734b17642aed8f2588fea4cc78ee8133d88554753bc3bf1b') + version('2017.05.002', sha256='568b71024c094d667b5cbb23045ad197ed5434071152ac608dae490ace5eb0aa') + version('2016.11.001.pre', sha256='69b67f0f6faaa2b3b5fd848127b632be32771636d2ad04583c5269d550956f92') + version('2016.05.004', sha256='08c59dc9da458bab856f489d779152e5506e04f0d4b8d6dcf114ca5fbbe46c58') + version('2016.05.003', sha256='c8da50c987351514e61491e14390cdea4bdbf5b09045261991876ed5b433fca4') + version('2015.11.001', sha256='c0761a92a31c08a4009c9688c85fc3fc8fde9b6ce05e514c3e1587cf045e9eba') variant('openmp', default=False, description='Activates OpenMP support') variant('optflags', default=True, description='Build with optimization flags') diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py index cf6e14771ed..c556c446ce4 100644 --- a/var/spack/repos/builtin/packages/emacs/package.py +++ b/var/spack/repos/builtin/packages/emacs/package.py @@ -14,12 +14,12 @@ class Emacs(AutotoolsPackage): homepage = "https://www.gnu.org/software/emacs" url = "https://ftpmirror.gnu.org/emacs/emacs-24.5.tar.gz" - version('26.2', 'fab39c90a1d825695bbaa164934c3f9b') - version('26.1', '544d2ab5eb142e9ca69adb023d17bf4b') - version('25.3', '74ddd373dc52ac05ca7a8c63b1ddbf58') - version('25.2', '0a36d1cdbba6024d4dbbac027f87995f') - version('25.1', '95c12e6a9afdf0dcbdd7d2efa26ca42c') - version('24.5', 'd74b597503a68105e61b5b9f6d065b44') + version('26.2', sha256='4f99e52a38a737556932cc57479e85c305a37a8038aaceb5156625caf102b4eb') + version('26.1', sha256='760382d5e8cdc5d0d079e8f754bce1136fbe1473be24bb885669b0e38fc56aa3') + version('25.3', sha256='f72c6a1b48b6fbaca2b991eed801964a208a2f8686c70940013db26cd37983c9') + version('25.2', sha256='505bbd6ea6c197947001d0f80bfccb6b30e1add584d6376f54d4fd6e4de72d2d') + version('25.1', sha256='763344b90db4d40e9fe90c5d14748a9dbd201ce544e2cf0835ab48a0aa4a1c67') + version('24.5', sha256='2737a6622fb2d9982e9c47fb6f2fb297bda42674e09db40fc9bcc0db4297c3b6') variant('X', default=False, description="Enable an X toolkit") variant( diff --git a/var/spack/repos/builtin/packages/emboss/package.py b/var/spack/repos/builtin/packages/emboss/package.py index ebbc6eae9c6..2ec381cd415 100644 --- a/var/spack/repos/builtin/packages/emboss/package.py +++ b/var/spack/repos/builtin/packages/emboss/package.py @@ -14,7 +14,7 @@ class Emboss(AutotoolsPackage): homepage = "http://emboss.sourceforge.net/" url = "ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz" - version('6.6.0', 'cc3fca80cb0618deb10fa0d29fe90e4b') + version('6.6.0', sha256='7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e') depends_on('libxpm') depends_on('libgd') diff --git a/var/spack/repos/builtin/packages/es/package.py b/var/spack/repos/builtin/packages/es/package.py index 2a7daf60c7e..99b846e96f4 100644 --- a/var/spack/repos/builtin/packages/es/package.py +++ b/var/spack/repos/builtin/packages/es/package.py @@ -17,6 +17,6 @@ class Es(AutotoolsPackage): homepage = "http://wryun.github.io/es-shell/" url = "https://github.com/wryun/es-shell/releases/download/v0.9.1/es-0.9.1.tar.gz" - version('0.9.1', 'bf4db55b47bcc99892468b2e0aec0c9e') + version('0.9.1', sha256='b0b41fce99b122a173a06b899a4d92e5bd3cc48b227b2736159f596a58fff4ba') depends_on('readline') diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py index e1c9748000c..007c13b8536 100644 --- a/var/spack/repos/builtin/packages/esmf/package.py +++ b/var/spack/repos/builtin/packages/esmf/package.py @@ -17,8 +17,8 @@ class Esmf(MakefilePackage): homepage = "https://www.earthsystemcog.org/projects/esmf/" url = "http://www.earthsystemmodeling.org/esmf_releases/public/ESMF_7_1_0r/esmf_7_1_0r_src.tar.gz" - version('7.1.0r', '9e455bc36a0aaa9b87e0bdedc78a47f5') - version('7.0.1', 'd3316ea79b032b8fb0cd40e5868a0261') + version('7.1.0r', sha256='ae9a5edb8d40ae97a35cbd4bd00b77061f995c77c43d36334dbb95c18b00a889') + version('7.0.1', md5='d3316ea79b032b8fb0cd40e5868a0261') variant('mpi', default=True, description='Build with MPI support') variant('lapack', default=True, description='Build with LAPACK support') diff --git a/var/spack/repos/builtin/packages/ethminer/package.py b/var/spack/repos/builtin/packages/ethminer/package.py index 9ac93aff796..996532f8788 100644 --- a/var/spack/repos/builtin/packages/ethminer/package.py +++ b/var/spack/repos/builtin/packages/ethminer/package.py @@ -12,7 +12,7 @@ class Ethminer(CMakePackage): homepage = "https://github.com/ethereum-mining/ethminer" url = "https://github.com/ethereum-mining/ethminer/archive/v0.12.0.tar.gz" - version('0.12.0', '1c7e3df8476a146702a4050ad984ae5a') + version('0.12.0', sha256='71122c8aa1be2c29e46d7f07961fa760b1eb390e4d9a2a21cf900f6482a8755a') variant('opencl', default=True, description='Enable OpenCL mining.') variant('cuda', default=False, description='Enable CUDA mining.') diff --git a/var/spack/repos/builtin/packages/etsf-io/package.py b/var/spack/repos/builtin/packages/etsf-io/package.py index 8a97d21d7eb..62096ace0f3 100644 --- a/var/spack/repos/builtin/packages/etsf-io/package.py +++ b/var/spack/repos/builtin/packages/etsf-io/package.py @@ -20,7 +20,7 @@ class EtsfIo(Package): homepage = "http://www.etsf.eu/resources/software/libraries_and_tools" url = "https://launchpad.net/etsf-io/1.0/1.0.4/+download/etsf_io-1.0.4.tar.gz" - version('1.0.4', '32d0f7143278bd925b334c69fa425da1') + version('1.0.4', sha256='3140c2cde17f578a0e6b63acb27a5f6e9352257a1371a17b9c15c3d0ef078fa4') depends_on("netcdf-fortran") depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support diff --git a/var/spack/repos/builtin/packages/everytrace/package.py b/var/spack/repos/builtin/packages/everytrace/package.py index 95734ccfdc7..1de226bdac6 100644 --- a/var/spack/repos/builtin/packages/everytrace/package.py +++ b/var/spack/repos/builtin/packages/everytrace/package.py @@ -16,7 +16,7 @@ class Everytrace(CMakePackage): maintainers = ['citibeth'] version('develop', branch='develop') - version('0.2.2', 'dd60b8bf68cbf3dc2be305a040f2fe3e') + version('0.2.2', sha256='0487276bb24e648388862d8e1d8cfe56b529f7e3d840df3fcb5b3a3dad4016e1') variant('mpi', default=True, description='Enables MPI parallelism') variant('fortran', default=True, diff --git a/var/spack/repos/builtin/packages/evieext/package.py b/var/spack/repos/builtin/packages/evieext/package.py index 4937b0d61a7..4b292ebe2b2 100644 --- a/var/spack/repos/builtin/packages/evieext/package.py +++ b/var/spack/repos/builtin/packages/evieext/package.py @@ -15,7 +15,7 @@ class Evieext(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/evieproto" url = "https://www.x.org/archive/individual/proto/evieext-1.1.1.tar.gz" - version('1.1.1', '018a7d24d0c7926d594246320bcb6a86') + version('1.1.1', sha256='e58080443c279dfb5a23c37076922df535e42bf209d21a1f3e88442cc01b4a0e') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/exabayes/package.py b/var/spack/repos/builtin/packages/exabayes/package.py index 1ff8796cd15..379f8298108 100644 --- a/var/spack/repos/builtin/packages/exabayes/package.py +++ b/var/spack/repos/builtin/packages/exabayes/package.py @@ -13,7 +13,7 @@ class Exabayes(AutotoolsPackage): homepage = "https://sco.h-its.org/exelixis/web/software/exabayes/" url = "https://sco.h-its.org/exelixis/resource/download/software/exabayes-1.5.tar.gz" - version('1.5', '6a734777b8f8eff0a520306500c8c419') + version('1.5', sha256='e401f1b4645e67e8879d296807131d0ab79bba81a1cd5afea14d7c3838b095a2') variant('mpi', default=True, description='Enable MPI parallel support') diff --git a/var/spack/repos/builtin/packages/examinimd/package.py b/var/spack/repos/builtin/packages/examinimd/package.py index 7433323ebde..4d92266f2be 100644 --- a/var/spack/repos/builtin/packages/examinimd/package.py +++ b/var/spack/repos/builtin/packages/examinimd/package.py @@ -25,7 +25,7 @@ class Examinimd(MakefilePackage): git = "https://github.com/ECP-copa/ExaMiniMD.git" version('develop', branch='master') - version('1.0', '5db7679a4b9296c0cc3b2ff3a7e8f38f') + version('1.0', sha256='d5f884ecc3a5f9723cc57a4c188da926b392605650606c1c8c34f2d1953f2534') variant('mpi', default=True, description='Build with MPI support') variant('openmp', default=False, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/exasp2/package.py b/var/spack/repos/builtin/packages/exasp2/package.py index 0a7fa5dc120..bc9c452046e 100644 --- a/var/spack/repos/builtin/packages/exasp2/package.py +++ b/var/spack/repos/builtin/packages/exasp2/package.py @@ -28,7 +28,7 @@ class Exasp2(MakefilePackage): git = "https://github.com/ECP-copa/ExaSP2.git" version('develop', branch='master') - version('1.0', 'dba545995acc73f2bd1101bcb377bff5') + version('1.0', sha256='59986ea70391a1b382d2ed22d5cf013f46c0c15e44ed95dcd875a917adfc6211') variant('mpi', default=True, description='Build With MPI Support') diff --git a/var/spack/repos/builtin/packages/exmcutils/package.py b/var/spack/repos/builtin/packages/exmcutils/package.py index 0d1b9f94b52..8d53b7a71a8 100644 --- a/var/spack/repos/builtin/packages/exmcutils/package.py +++ b/var/spack/repos/builtin/packages/exmcutils/package.py @@ -15,8 +15,8 @@ class Exmcutils(AutotoolsPackage): git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') - version('0.5.7', '69bb32f364e93e8a60865c05efbf4f52') - version('0.5.6', 'b12a8dc163e3369492ec7c1403fe86e4') + version('0.5.7', sha256='6b84f43e8928d835dbd68c735ece6a9b7c648a1a4488ec2b1d2f3c4ceec508e8') + version('0.5.6', sha256='296ba85cc828bd816c7c4de9453f589da37f32854a58ffda3586b6f371a23abf') @property def configure_directory(self): diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py index 90bc52b19d0..c7eadef01fc 100644 --- a/var/spack/repos/builtin/packages/exonerate/package.py +++ b/var/spack/repos/builtin/packages/exonerate/package.py @@ -12,7 +12,7 @@ class Exonerate(AutotoolsPackage): homepage = "http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" url = "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.4.0.tar.gz" - version('2.4.0', '126fbade003b80b663a1d530c56f1904') + version('2.4.0', sha256='f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042') depends_on('pkgconfig', type="build") depends_on('glib') diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index 83387ccee13..8e992491d61 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -14,9 +14,9 @@ class Expat(AutotoolsPackage): url = "https://github.com/libexpat/libexpat/releases/download/R_2_2_9/expat-2.2.9.tar.bz2" version('2.2.9', sha256='f1063084dc4302a427dabcca499c8312b3a32a29b7d2506653ecc8f950a9a237') - version('2.2.5', '789e297f547980fc9ecc036f9a070d49') - version('2.2.2', '1ede9a41223c78528b8c5d23e69a2667') - version('2.2.0', '2f47841c829facb346eb6e3fab5212e2') + version('2.2.5', sha256='d9dc32efba7e74f788fcc4f212a43216fc37cf5f23f4c2339664d473353aedf6') + version('2.2.2', sha256='4376911fcf81a23ebd821bbabc26fd933f3ac74833f74924342c29aad2c86046') + version('2.2.0', sha256='d9e50ff2d19b3538bd2127902a89987474e1a4db8e43a66a4d1a712ab9a504ff') # Version 2.2.2 introduced a requirement for a high quality # entropy source. "Older" linux systems (aka CentOS 7) do not diff --git a/var/spack/repos/builtin/packages/expect/package.py b/var/spack/repos/builtin/packages/expect/package.py index 1c431e9d999..ad6e24bdb9e 100644 --- a/var/spack/repos/builtin/packages/expect/package.py +++ b/var/spack/repos/builtin/packages/expect/package.py @@ -15,7 +15,7 @@ class Expect(AutotoolsPackage): homepage = "http://expect.sourceforge.net/" url = "https://sourceforge.net/projects/expect/files/Expect/5.45/expect5.45.tar.gz/download" - version('5.45', '44e1a4f4c877e9ddc5a542dfa7ecc92b') + version('5.45', sha256='b28dca90428a3b30e650525cdc16255d76bb6ccd65d448be53e620d95d5cc040') depends_on('tcl') diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py index d8428fb125c..54c3622b06e 100644 --- a/var/spack/repos/builtin/packages/extrae/package.py +++ b/var/spack/repos/builtin/packages/extrae/package.py @@ -36,7 +36,7 @@ class Extrae(AutotoolsPackage): homepage = "https://tools.bsc.es/extrae" url = "https://ftp.tools.bsc.es/extrae/extrae-3.4.1-src.tar.bz2" version('3.7.1', sha256='95810b057f95e91bfc89813eb8bd320dfe40614fc8e98c63d95c5101c56dd213') - version('3.4.1', '69001f5cfac46e445d61eeb567bc8844') + version('3.4.1', sha256='77bfec16d6b5eee061fbaa879949dcef4cad28395d6a546b1ae1b9246f142725') depends_on("autoconf", type='build') depends_on("automake", type='build') diff --git a/var/spack/repos/builtin/packages/exuberant-ctags/package.py b/var/spack/repos/builtin/packages/exuberant-ctags/package.py index a19fe56e9af..dc76106827f 100644 --- a/var/spack/repos/builtin/packages/exuberant-ctags/package.py +++ b/var/spack/repos/builtin/packages/exuberant-ctags/package.py @@ -11,4 +11,4 @@ class ExuberantCtags(AutotoolsPackage): homepage = "ctags.sourceforge.net" url = "http://downloads.sourceforge.net/project/ctags/ctags/5.8/ctags-5.8.tar.gz" - version('5.8', 'c00f82ecdcc357434731913e5b48630d') + version('5.8', sha256='0e44b45dcabe969e0bbbb11e30c246f81abe5d32012db37395eb57d66e9e99c7') diff --git a/var/spack/repos/builtin/packages/f90cache/package.py b/var/spack/repos/builtin/packages/f90cache/package.py index b60ae1de77e..1de70bafa7a 100644 --- a/var/spack/repos/builtin/packages/f90cache/package.py +++ b/var/spack/repos/builtin/packages/f90cache/package.py @@ -17,5 +17,5 @@ class F90cache(AutotoolsPackage): url = "https://perso.univ-rennes1.fr/edouard.canot/f90cache/f90cache-0.99c.tar.gz" version('0.99c', sha256='13f8297ecba73671d43376b71ef0e453bd9d6677a901d1c95f01f16cc33776e1') - version('0.99', 'e4767ae876203ed4f3e118e22204cdec', + version('0.99', sha256='be3fe77b676bc784dd45b3f65b4a5db34d858ed29156b29d8da38b24585bda7d', url='http://distfiles.exherbo.org/distfiles/f90cache-0.99.tar.bz2') diff --git a/var/spack/repos/builtin/packages/fabtests/package.py b/var/spack/repos/builtin/packages/fabtests/package.py index 6ad9acad9a0..f11e27a79d4 100644 --- a/var/spack/repos/builtin/packages/fabtests/package.py +++ b/var/spack/repos/builtin/packages/fabtests/package.py @@ -14,8 +14,8 @@ class Fabtests(AutotoolsPackage): homepage = "http://libfabric.org" url = "https://github.com/ofiwg/fabtests/releases/download/v1.5.3/fabtests-1.5.3.tar.gz" - version('1.6.0', '0441aa0aeda391b1bf1eb71250a4afbc') - version('1.5.3', 'f60cb95843ebf62e4eaa128e08ccdc7d') + version('1.6.0', sha256='dc3eeccccb005205017f5af60681ede15782ce202a0103450a6d56a7ff515a67') + version('1.5.3', sha256='3835b3bf86cd00d23df0ddba8bf317e4a195e8d5c3c2baa918b373d548f77f29') depends_on('libfabric@1.6.0', when='@1.6.0') depends_on('libfabric@1.5.3', when='@1.5.3') diff --git a/var/spack/repos/builtin/packages/fast-global-file-status/package.py b/var/spack/repos/builtin/packages/fast-global-file-status/package.py index a3f43916192..c805638fe1c 100644 --- a/var/spack/repos/builtin/packages/fast-global-file-status/package.py +++ b/var/spack/repos/builtin/packages/fast-global-file-status/package.py @@ -13,7 +13,7 @@ class FastGlobalFileStatus(AutotoolsPackage): homepage = "https://github.com/LLNL/FastGlobalFileStatus" url = 'https://github.com/LLNL/FastGlobalFileStatus/files/2271592/fastglobalfilestatus-1.1.tar.gz' - version('1.1', 'c3d764c47a60310823947c489cd0f2df') + version('1.1', sha256='e6fba4a0b7f055899fa0e05d93a435c7f1f2ec1158b9a6647dc8d2bcf9c2e164') depends_on('mrnet') depends_on('mount-point-attributes') diff --git a/var/spack/repos/builtin/packages/fastjar/package.py b/var/spack/repos/builtin/packages/fastjar/package.py index cd18b3f420e..1211b4b97b7 100644 --- a/var/spack/repos/builtin/packages/fastjar/package.py +++ b/var/spack/repos/builtin/packages/fastjar/package.py @@ -12,6 +12,6 @@ class Fastjar(AutotoolsPackage): homepage = "http://savannah.nongnu.org/projects/fastjar/" url = "http://download.savannah.gnu.org/releases/fastjar/fastjar-0.98.tar.gz" - version('0.98', 'd2d264d343d4d0e1575832cc1023c3bf') + version('0.98', sha256='f156abc5de8658f22ee8f08d7a72c88f9409ebd8c7933e9466b0842afeb2f145') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/fastmath/package.py b/var/spack/repos/builtin/packages/fastmath/package.py index 56802905fca..bc04da72378 100644 --- a/var/spack/repos/builtin/packages/fastmath/package.py +++ b/var/spack/repos/builtin/packages/fastmath/package.py @@ -16,7 +16,7 @@ class Fastmath(Package): homepage = "www.fastmath-scidac.org/" url = "https://github.com/citibeth/dummy/tarball/v1.0" - version('1.0', 'e2b724dfcc31d735897971db91be89ff') + version('1.0', sha256='402a2198e40b7e9022a99ab88ba6f0ee1c04b103fc15589b22c892859f14b60a') # BundlePackage depends_on('amrex') # default is 3 dimensions diff --git a/var/spack/repos/builtin/packages/fastme/package.py b/var/spack/repos/builtin/packages/fastme/package.py index 95b06c6f996..2b678b9ac00 100644 --- a/var/spack/repos/builtin/packages/fastme/package.py +++ b/var/spack/repos/builtin/packages/fastme/package.py @@ -13,7 +13,7 @@ class Fastme(AutotoolsPackage): homepage = "http://www.atgc-montpellier.fr/fastme/" url = "https://gite.lirmm.fr/atgc/FastME/repository/v2.1.5.1/archive.tar.gz" - version('2.1.5.1', '1059dcbd320bf4d6dd9328c582dd3d24283295026530fcfb26dbdbe068e3cd1d') + version('2.1.5.1', sha256='1059dcbd320bf4d6dd9328c582dd3d24283295026530fcfb26dbdbe068e3cd1d') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/fastphase/package.py b/var/spack/repos/builtin/packages/fastphase/package.py index 2327622fb67..381ca0a9738 100644 --- a/var/spack/repos/builtin/packages/fastphase/package.py +++ b/var/spack/repos/builtin/packages/fastphase/package.py @@ -13,7 +13,7 @@ class Fastphase(Package): homepage = "http://stephenslab.uchicago.edu/software.html" url = "http://scheet.org/code/Linuxfp.tar.gz" - version('2016-03-30', 'b48731eed9b8d0a5a321f970c5c20d8c') + version('2016-03-30', sha256='f0762eaae38b276bccb567d1519fa19bf35fd4078e57cbf13c7d7054150c4f36') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py index 6d730e8b775..ef651a4c9da 100644 --- a/var/spack/repos/builtin/packages/fastq-screen/package.py +++ b/var/spack/repos/builtin/packages/fastq-screen/package.py @@ -14,7 +14,7 @@ class FastqScreen(Package): homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" url = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.11.2.tar.gz" - version('0.11.2', 'ef79f16ee553aaa0ab2fc14ea11e5473') + version('0.11.2', sha256='a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207') depends_on('perl', type='run') depends_on('perl-gd-graph', type='run') diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py index a998d9d5e15..289cda53bb9 100644 --- a/var/spack/repos/builtin/packages/fastqc/package.py +++ b/var/spack/repos/builtin/packages/fastqc/package.py @@ -12,9 +12,9 @@ class Fastqc(Package): homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip" - version('0.11.7', '8fead05fa62c5e723f0d2157a9b5fcd4') - version('0.11.5', '3524f101c0ab0bae77c7595983170a76') - version('0.11.4', '104ff2e0e9aebf5bee1f6b068a059b0d') + version('0.11.7', sha256='59cf50876bbe5f363442eb989e43ae3eaab8d932c49e8cff2c1a1898dd721112') + version('0.11.5', sha256='dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66') + version('0.11.4', sha256='adb233f9fae7b02fe99e716664502adfec1b9a3fbb84eed4497122d6d33d1fe7') depends_on('java', type='run') depends_on('perl') # for fastqc "script", any perl will do diff --git a/var/spack/repos/builtin/packages/fasttree/package.py b/var/spack/repos/builtin/packages/fasttree/package.py index d110186f1aa..b6b2f9e2a3a 100644 --- a/var/spack/repos/builtin/packages/fasttree/package.py +++ b/var/spack/repos/builtin/packages/fasttree/package.py @@ -15,7 +15,7 @@ class Fasttree(Package): homepage = "http://www.microbesonline.org/fasttree" url = "http://www.microbesonline.org/fasttree/FastTree-2.1.10.c" - version('2.1.10', '1c2c6425a638ec0c61ef064cda687987', expand=False, url='http://www.microbesonline.org/fasttree/FastTree-2.1.10.c') + version('2.1.10', sha256='54cb89fc1728a974a59eae7a7ee6309cdd3cddda9a4c55b700a71219fc6e926d', expand=False, url='http://www.microbesonline.org/fasttree/FastTree-2.1.10.c') phases = ['build', 'install'] diff --git a/var/spack/repos/builtin/packages/fastx-toolkit/package.py b/var/spack/repos/builtin/packages/fastx-toolkit/package.py index 8aeed172cfe..a291cb4385b 100644 --- a/var/spack/repos/builtin/packages/fastx-toolkit/package.py +++ b/var/spack/repos/builtin/packages/fastx-toolkit/package.py @@ -13,7 +13,7 @@ class FastxToolkit(AutotoolsPackage): homepage = "http://hannonlab.cshl.edu/fastx_toolkit/" url = "https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2" - version('0.0.14', 'bf1993c898626bb147de3d6695c20b40') + version('0.0.14', sha256='9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806') depends_on('libgtextutils') diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py index db6cd24bf81..97020e857f5 100644 --- a/var/spack/repos/builtin/packages/fenics/package.py +++ b/var/spack/repos/builtin/packages/fenics/package.py @@ -84,43 +84,43 @@ class Fenics(CMakePackage): releases = [ { 'version': '2016.1.0', - 'md5': '92e8d00f6487a575987201f0b0d19173', + 'sha256': '6228b4d641829a4cd32141bfcd217a1596a27d5969aa00ee64ebba2b1c0fb148', 'resources': { - 'ffc': '35457ae164e481ba5c9189ebae060a47', - 'fiat': 'ac0c49942831ee434301228842bcc280', - 'instant': '0e3dbb464c4d90d691f31f0fdd63d4f6', - 'ufl': '37433336e5c9b58d1d5ab4acca9104a7', + 'ffc': '52430ce4c7d57ce1b81eb5fb304992247c944bc6a6054c8b6f42bac81702578d', + 'fiat': '851723126a71bc1ae2dc4ad6e9330bd9b54d52db390dcbbc1f3c759fb49c6aeb', + 'instant': '7bf03c8a7b61fd1e432b8f3a0405410ae68892ebb1a62a9f8118e8846bbeb0c6', + 'ufl': '8dccfe10d1251ba48a4d43a4c6c89abe076390223b500f4baf06f696294b8dd0', } }, { 'version': '1.6.0', - 'md5': '35cb4baf7ab4152a40fb7310b34d5800', + 'sha256': '67eaac5fece6e71da0559b4ca8423156f9e99a952f0620adae449ebebb6695d1', 'resources': { - 'ffc': '358faa3e9da62a1b1a717070217b793e', - 'fiat': 'f4509d05c911fd93cea8d288a78a6c6f', - 'instant': '5f2522eb032a5bebbad6597b6fe0732a', - 'ufl': 'c40c5f04eaa847377ab2323122284016', + 'ffc': '382e7713fe759694e5f07506b144eeead681e169e5a34c164ef3da30eddcc1c6', + 'fiat': '858ea3e936ad3b3558b474ffccae8a7b9dddbaafeac77e307115b23753cb1cac', + 'instant': '2347e0229531969095911fdb1de30bd77bdd7f81521ba84d81b1b4a564fc906c', + 'ufl': 'c75c4781e5104504f158cb42cd87aceffa9052e8e9db6e9764e6a5b6115d7f73', } }, { 'version': '1.5.0', - 'md5': '9b589a3534299a5e6d22c13c5eb30bb8', + 'sha256': '9b589a3534299a5e6d22c13c5eb30bb8', 'resources': { - 'ffc': '343f6d30e7e77d329a400fd8e73e0b63', - 'fiat': 'da3fa4dd8177bb251e7f68ec9c7cf6c5', - 'instant': 'b744023ded27ee9df4a8d8c6698c0d58', - 'ufl': '130d7829cf5a4bd5b52bf6d0955116fd', + 'ffc': '755be60597d66f13c1e113739e7b9b620ee4271e0f7cc1053553a568bc08e7f4', + 'fiat': '2b053fa9f70399f8903b987f98a4fa2b06df9559c07c1d5f0b2b5e43c51de670', + 'instant': '36e042de26d97f5e3d43f2f52544d91ba0f14e1c73c7d07ed7804030b43d935d', + 'ufl': '2879a5b0937502676fa55765bcb8237ff78e8b70995a118ffe1de042b20e491b', } }, ] for release in releases: - version(release['version'], release['md5'], url=base_url.format( + version(release['version'], release['sha256'], url=base_url.format( pkg='dolfin', version=release['version'])) - for rname, md5 in release['resources'].items(): + for rname, sha256 in release['resources'].items(): resource(name=rname, url=base_url.format(pkg=rname, **release), - md5=md5, + sha256=sha256, destination='depends', when='@{version}'.format(**release), placement=rname) diff --git a/var/spack/repos/builtin/packages/fermi/package.py b/var/spack/repos/builtin/packages/fermi/package.py index db9dc380c64..461b6d71d23 100644 --- a/var/spack/repos/builtin/packages/fermi/package.py +++ b/var/spack/repos/builtin/packages/fermi/package.py @@ -12,7 +12,7 @@ class Fermi(MakefilePackage): homepage = "https://github.com/lh3/fermi" url = "https://github.com/downloads/lh3/fermi/fermi-1.1.tar.bz2" - version('1.1', 'd5f006315652b6f18070b31474ca5ebb') + version('1.1', sha256='f1351b52a4ff40e5d708899e90ecf747e7af8d4eac795f6968e5b58c2ba11a67') depends_on('zlib') depends_on('perl', type='run') diff --git a/var/spack/repos/builtin/packages/fermisciencetools/package.py b/var/spack/repos/builtin/packages/fermisciencetools/package.py index 6836f0ec7c9..ce2ae604b1d 100644 --- a/var/spack/repos/builtin/packages/fermisciencetools/package.py +++ b/var/spack/repos/builtin/packages/fermisciencetools/package.py @@ -19,7 +19,7 @@ class Fermisciencetools(Package): # available, but there might be some logical errors in the configure codes, # which leads to failing in building it from source. Hopefully someone else # can figure it out and we can use the source distribution instead. - version('11r5p3', 'cf050ddddfe9251b6ebe8d3fd7de3c3f') + version('11r5p3', sha256='2f4fc32a0b2e5c0f1ddb220a0560f67e66052b7907c72dba181908dc9269ffe8') def install(self, spec, prefix): install_tree('x86_64-unknown-linux-gnu-libc2.17', prefix) diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py index 060c347e3ff..0113dfba3a9 100644 --- a/var/spack/repos/builtin/packages/ferret/package.py +++ b/var/spack/repos/builtin/packages/ferret/package.py @@ -15,8 +15,8 @@ class Ferret(Package): homepage = "http://ferret.pmel.noaa.gov/Ferret/home" url = "ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.v696.tar.gz" - version('7.2', '21c339b1bafa6939fc869428d906451f130f7e77e828c532ab9488d51cf43095') - version('6.96', '51722027c864369f41bab5751dfff8cc') + version('7.2', sha256='21c339b1bafa6939fc869428d906451f130f7e77e828c532ab9488d51cf43095') + version('6.96', sha256='7eb87156aa586cfe838ab83f08b2102598f9ab62062d540a5da8c9123816331a') depends_on("hdf5+hl") depends_on("netcdf") diff --git a/var/spack/repos/builtin/packages/ffmpeg/package.py b/var/spack/repos/builtin/packages/ffmpeg/package.py index 57ccbef9420..3a1983213eb 100644 --- a/var/spack/repos/builtin/packages/ffmpeg/package.py +++ b/var/spack/repos/builtin/packages/ffmpeg/package.py @@ -13,9 +13,9 @@ class Ffmpeg(AutotoolsPackage): homepage = "https://ffmpeg.org" url = "http://ffmpeg.org/releases/ffmpeg-4.1.1.tar.bz2" - version('4.1.1', '4a64e3cb3915a3bf71b8b60795904800') - version('4.1', 'b684fb43244a5c4caae652af9022ed5d85ce15210835bce054a33fb26033a1a5') - version('3.2.4', 'd3ebaacfa36c6e8145373785824265b4') + version('4.1.1', sha256='0cb40e3b8acaccd0ecb38aa863f66f0c6e02406246556c2992f67bf650fab058') + version('4.1', sha256='b684fb43244a5c4caae652af9022ed5d85ce15210835bce054a33fb26033a1a5') + version('3.2.4', sha256='c0fa3593a2e9e96ace3c1757900094437ad96d1d6ca19f057c378b5f394496a4') variant('shared', default=True, description='build shared libraries') diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py index 841f8272aba..82bd0c7aa72 100644 --- a/var/spack/repos/builtin/packages/fftw/package.py +++ b/var/spack/repos/builtin/packages/fftw/package.py @@ -23,12 +23,12 @@ class Fftw(AutotoolsPackage): url = "http://www.fftw.org/fftw-3.3.4.tar.gz" list_url = "http://www.fftw.org/download.html" - version('3.3.8', '8aac833c943d8e90d51b697b27d4384d') - version('3.3.7', '0d5915d7d39b3253c1cc05030d79ac47') - version('3.3.6-pl2', '927e481edbb32575397eb3d62535a856') - version('3.3.5', '6cc08a3b9c7ee06fdd5b9eb02e06f569') - version('3.3.4', '2edab8c06b24feeb3b82bbb3ebf3e7b3') - version('2.1.5', '8d16a84f3ca02a785ef9eb36249ba433') + version('3.3.8', sha256='6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303') + version('3.3.7', sha256='3b609b7feba5230e8f6dd8d245ddbefac324c5a6ae4186947670d9ac2cd25573') + version('3.3.6-pl2', sha256='a5de35c5c824a78a058ca54278c706cdf3d4abba1c56b63531c2cb05f5d57da2') + version('3.3.5', sha256='8ecfe1b04732ec3f5b7d279fdb8efcad536d555f9d1e8fabd027037d45ea8bcf') + version('3.3.4', sha256='8f0cde90929bc05587c3368d2f15cd0530a60b8a9912a8e2979a72dbe5af0982') + version('2.1.5', sha256='f8057fae1c7df8b99116783ef3e94a6a44518d49c72e2e630c24b689c6022630') patch('pfft-3.3.5.patch', when="@3.3.5:+pfft_patches", level=0) patch('pfft-3.3.4.patch', when="@3.3.4+pfft_patches", level=0) diff --git a/var/spack/repos/builtin/packages/fgsl/package.py b/var/spack/repos/builtin/packages/fgsl/package.py index d98e0fbbb62..60d3580f25d 100644 --- a/var/spack/repos/builtin/packages/fgsl/package.py +++ b/var/spack/repos/builtin/packages/fgsl/package.py @@ -16,9 +16,9 @@ class Fgsl(AutotoolsPackage): homepage = "https://github.com/reinh-bader/fgsl" url = "https://github.com/reinh-bader/fgsl/archive/v1.2.0.tar.gz" - version('1.3.0', '6d73d558c889d7ea23e510a436f28618624035e8ffa07692894f10968aa83a4b') - version('1.2.0', 'e5a4ac08eb744c963e95a46a51d76c56593836077c5ad8c47e240cae57027002') - version('1.1.0', 'a5adce3c3b279d2dacc05b74c598ff89be7ef3ae3ec59b3ec1355750c1bb4832') + version('1.3.0', sha256='6d73d558c889d7ea23e510a436f28618624035e8ffa07692894f10968aa83a4b') + version('1.2.0', sha256='e5a4ac08eb744c963e95a46a51d76c56593836077c5ad8c47e240cae57027002') + version('1.1.0', sha256='a5adce3c3b279d2dacc05b74c598ff89be7ef3ae3ec59b3ec1355750c1bb4832') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/findutils/package.py b/var/spack/repos/builtin/packages/findutils/package.py index 470821254a7..eb8009623a6 100644 --- a/var/spack/repos/builtin/packages/findutils/package.py +++ b/var/spack/repos/builtin/packages/findutils/package.py @@ -13,25 +13,25 @@ class Findutils(AutotoolsPackage): homepage = "https://www.gnu.org/software/findutils/" url = "https://ftpmirror.gnu.org/findutils/findutils-4.6.0.tar.gz" - version('4.6.0', '9936aa8009438ce185bea2694a997fc1') - version('4.4.2', '351cc4adb07d54877fa15f75fb77d39f') - version('4.4.1', '5883f569dc021eee765f330bb7a3782d') - version('4.4.0', '49e769ac4382fae6f104f99d54d0a112') - version('4.2.33', 'b7e35aa175778c84942b1fee4144988b') - version('4.2.32', 'aaa6beeb41a6f04963dff58f24a55b96') - version('4.2.31', 'a0e31a0f18a49709bf5a449867c8049a') - version('4.2.30', 'c35ff6502e0b3514c99089cb5d333c25') - version('4.2.29', '24e76434ca74ba3c2c6ad621eb64e1ff') - version('4.2.28', 'f5fb3349354ee3d94fceb81dab5c71fd') - version('4.2.27', 'f1e0ddf09f28f8102ff3b90f3b5bc920') - version('4.2.26', '9ac4e62937b1fdc4eb643d1d4bf117d3') - version('4.2.25', 'e92fef6714ffa9972f28a1a423066921') - version('4.2.23', 'ecaff8b060e8d69c10eb2391a8032e26') - version('4.2.20', '7c8e12165b221dd67a19c00d780437a4') - version('4.2.18', '8aac2498435f3f1882678fb9ebda5c34') - version('4.2.15', 'a881b15aa7170aea045bf35cc92d48e7') - version('4.1.20', 'e90ce7222daadeb8616b8db461e17cbc') - version('4.1', '3ea8fe58ef5386da75f6c707713aa059') + version('4.6.0', sha256='ded4c9f73731cd48fec3b6bdaccce896473b6d8e337e9612e16cf1431bb1169d') + version('4.4.2', sha256='434f32d171cbc0a5e72cfc5372c6fc4cb0e681f8dce566a0de5b6fccd702b62a') + version('4.4.1', sha256='77a5b85d7fe0dd9c1093e010b61f765707364ec2c89c4f432c1c616215bcc138') + version('4.4.0', sha256='fb108c2959f17baf3559da9b3854495b9bb69fb13309fdd05576c66feb661ea9') + version('4.2.33', sha256='813cd9405aceec5cfecbe96400d01e90ddad7b512d3034487176ce5258ab0f78') + version('4.2.32', sha256='87bd8804f3c2fa2fe866907377afd8d26a13948a4bb1761e5e95d0494a005217') + version('4.2.31', sha256='e0d34b8faca0b3cca0703f6c6b498afbe72f0ba16c35980c10ec9ef7724d6204') + version('4.2.30', sha256='344b9cbb4034907f80398c6a6d3724507ff4b519036f13bb811d12f702043af4') + version('4.2.29', sha256='1a9ed8db0711f8419156e786b6aecd42dd05df29e53e380d8924e696f7071ae0') + version('4.2.28', sha256='aa27de514b44eb763d276ad8f19fef31a07bd63ac7ca6870d2be5cd58de862c8') + version('4.2.27', sha256='546bc7932e716beaa960116766ea4d890f292c6fbde221ec10cdd8ec37329654') + version('4.2.26', sha256='74fa9030b97e074cbeb4f6c8ec964c5e8292cf5a62b195086113417f75ab836a') + version('4.2.25', sha256='a2bc59e80ee599368584f4ac4a6e647011700e1b5230e65eb3170c603047bb51') + version('4.2.23', sha256='d3ca95bf003685c3c34eb59e41c5c4b366fb582a53c4cfa9da0424d98ff23be3') + version('4.2.20', sha256='4e4d72a4387fcc942565c45460e632001db6bde0a46338a6a1b59b956fd3e031') + version('4.2.18', sha256='05c33f3e46fa11275f89ae968af70c83b01a2c578ec4fa5abf5c33c7e4afe44d') + version('4.2.15', sha256='5ede832e70c1691a59e6d5e5ebc2b843120d631b93cd60b905b2edeb078d3719') + version('4.1.20', sha256='8c5dd50a5ca54367fa186f6294b81ec7a365e36d670d9feac62227cb513e63ab') + version('4.1', sha256='487ecc0a6c8c90634a11158f360977e5ce0a9a6701502da6cb96a5a7ec143fac') depends_on('autoconf', type='build', when='@4.6.0') depends_on('automake', type='build', when='@4.6.0') diff --git a/var/spack/repos/builtin/packages/fio/package.py b/var/spack/repos/builtin/packages/fio/package.py index 29f02c8b807..7e52b98c30e 100644 --- a/var/spack/repos/builtin/packages/fio/package.py +++ b/var/spack/repos/builtin/packages/fio/package.py @@ -17,7 +17,7 @@ class Fio(AutotoolsPackage): url = "https://github.com/axboe/fio/archive/fio-2.19.tar.gz" version('3.16', sha256='c7731a9e831581bab7104da9ea60c9f44e594438dbe95dff26726ca0285e7b93') - version('2.19', '67125b60210a4daa689a4626fc66c612') + version('2.19', sha256='61fb03a18703269b781aaf195cb0d7931493bbb5bfcc8eb746d5d66d04ed77f7') variant('gui', default=False, description='Enable building of gtk gfio') variant('doc', default=False, description='Generate documentation') diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py index 5a06b876449..4f8d8d3aae7 100644 --- a/var/spack/repos/builtin/packages/fish/package.py +++ b/var/spack/repos/builtin/packages/fish/package.py @@ -18,6 +18,6 @@ class Fish(AutotoolsPackage): depends_on('ncurses') version('3.0.0', sha256='ea9dd3614bb0346829ce7319437c6a93e3e1dfde3b7f6a469b543b0d2c68f2cf') - version('2.7.1', 'e42bb19c7586356905a58578190be792df960fa81de35effb1ca5a5a981f0c5a') - version('2.7.0', '3a76b7cae92f9f88863c35c832d2427fb66082f98e92a02203dc900b8fa87bcb') - version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a') + version('2.7.1', sha256='e42bb19c7586356905a58578190be792df960fa81de35effb1ca5a5a981f0c5a') + version('2.7.0', sha256='3a76b7cae92f9f88863c35c832d2427fb66082f98e92a02203dc900b8fa87bcb') + version('2.2.0', sha256='a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a') diff --git a/var/spack/repos/builtin/packages/fixesproto/package.py b/var/spack/repos/builtin/packages/fixesproto/package.py index cb5ffb0146e..15f8b2c8e0c 100644 --- a/var/spack/repos/builtin/packages/fixesproto/package.py +++ b/var/spack/repos/builtin/packages/fixesproto/package.py @@ -16,7 +16,7 @@ class Fixesproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/fixesproto" url = "https://www.x.org/archive/individual/proto/fixesproto-5.0.tar.gz" - version('5.0', '1b3115574cadd4cbea1f197faa7c1de4') + version('5.0', sha256='67865a0e3cdc7dec1fd676f0927f7011ad4036c18eb320a2b41dbd56282f33b8') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/flac/package.py b/var/spack/repos/builtin/packages/flac/package.py index 3ffa8d0f1e4..7fd7761cd27 100644 --- a/var/spack/repos/builtin/packages/flac/package.py +++ b/var/spack/repos/builtin/packages/flac/package.py @@ -12,9 +12,9 @@ class Flac(AutotoolsPackage): homepage = "https://xiph.org/flac/index.html" url = "http://downloads.xiph.org/releases/flac/flac-1.3.2.tar.xz" - version('1.3.2', '454f1bfa3f93cc708098d7890d0499bd') - version('1.3.1', 'b9922c9a0378c88d3e901b234f852698') - version('1.3.0', '13b5c214cee8373464d3d65dee362cdd') + version('1.3.2', sha256='91cfc3ed61dc40f47f050a109b08610667d73477af6ef36dcad31c31a4a8d53f') + version('1.3.1', sha256='4773c0099dba767d963fd92143263be338c48702172e8754b9bc5103efe1c56c') + version('1.3.0', sha256='fa2d64aac1f77e31dfbb270aeb08f5b32e27036a52ad15e69a77e309528010dc') depends_on('libvorbis') depends_on('id3lib') diff --git a/var/spack/repos/builtin/packages/flang/package.py b/var/spack/repos/builtin/packages/flang/package.py index 364448e4bde..a09e25b5bea 100644 --- a/var/spack/repos/builtin/packages/flang/package.py +++ b/var/spack/repos/builtin/packages/flang/package.py @@ -17,8 +17,8 @@ class Flang(CMakePackage): git = "https://github.com/flang-compiler/flang.git" version('develop', branch='master') - version('20180921', '4440ed5fdc390e4b7a085fb77b44ac54') - version('20180612', '62284e26214eaaff261a922c67f6878c') + version('20180921', sha256='f33bd1f054e474f1e8a204bb6f78d42f8f6ecf7a894fdddc3999f7c272350784') + version('20180612', sha256='6af858bea013548e091371a97726ac784edbd4ff876222575eaae48a3c2920ed') depends_on('llvm@flang-develop', when='@develop') depends_on('llvm@flang-20180921', when='@20180921 target=x86_64:') diff --git a/var/spack/repos/builtin/packages/flann/package.py b/var/spack/repos/builtin/packages/flann/package.py index ac8e8def960..8746f764d60 100644 --- a/var/spack/repos/builtin/packages/flann/package.py +++ b/var/spack/repos/builtin/packages/flann/package.py @@ -21,11 +21,11 @@ class Flann(CMakePackage): homepage = "http://www.cs.ubc.ca/research/flann/" url = "https://github.com/mariusmuja/flann/archive/1.9.1.tar.gz" - version('1.9.1', '73adef1c7bf8e8b978987e7860926ea6') - version('1.8.5', '02a81640b1e9c11796a0413976dc11f5') - version('1.8.4', '774b74580e3cbc5b0d45c6ec345a64ae') - version('1.8.1', '1f51500e172f5e11fbda05f033858eb6') - version('1.8.0', '473150f592c2997e32d5ce31fd3c19a2') + version('1.9.1', sha256='b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3') + version('1.8.5', sha256='59a9925dac0705b281496ae52b5dfd79d6b69316d37015e3d3b38c859bac4f2f') + version('1.8.4', sha256='ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13') + version('1.8.1', sha256='82ff80709ca25365bca3367e87ffb4e0395fab068487314d02271bc3034591c1') + version('1.8.0', sha256='8a3eef79512870dec20b3a3e481e5e5e6da00d524b810a22ee186f13732f0fa1') def url_for_version(self, version): if version > Version('1.8.1'): diff --git a/var/spack/repos/builtin/packages/flash/package.py b/var/spack/repos/builtin/packages/flash/package.py index a12883bb208..4021f763604 100644 --- a/var/spack/repos/builtin/packages/flash/package.py +++ b/var/spack/repos/builtin/packages/flash/package.py @@ -14,7 +14,7 @@ class Flash(MakefilePackage): homepage = "https://ccb.jhu.edu/software/FLASH/" url = "https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz" - version('1.2.11', 'e4d355023a766afaaab2d62f912b605c') + version('1.2.11', sha256='685ca6f7fedda07434d8ee03c536f4763385671c4509c5bb48beb3055fd236ac') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/flatbuffers/package.py b/var/spack/repos/builtin/packages/flatbuffers/package.py index d91e61dd928..e2386155d8c 100644 --- a/var/spack/repos/builtin/packages/flatbuffers/package.py +++ b/var/spack/repos/builtin/packages/flatbuffers/package.py @@ -13,6 +13,6 @@ class Flatbuffers(CMakePackage): homepage = "http://google.github.io/flatbuffers/" url = "https://github.com/google/flatbuffers/archive/v1.9.0.tar.gz" - version('1.10.0', '3714e3db8c51e43028e10ad7adffb9a36fc4aa5b1a363c2d0c4303dd1be59a7c') - version('1.9.0', '8be7513bf960034f6873326d09521a4b') - version('1.8.0', '276cab8303c4189cbe3b8a70e0515d65') + version('1.10.0', sha256='3714e3db8c51e43028e10ad7adffb9a36fc4aa5b1a363c2d0c4303dd1be59a7c') + version('1.9.0', sha256='5ca5491e4260cacae30f1a5786d109230db3f3a6e5a0eb45d0d0608293d247e3') + version('1.8.0', sha256='c45029c0a0f1a88d416af143e34de96b3091642722aa2d8c090916c6d1498c2e') diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index 6c7891eaf24..64e9bb69dc5 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -13,13 +13,13 @@ class Flex(AutotoolsPackage): homepage = "https://github.com/westes/flex" url = "https://github.com/westes/flex/releases/download/v2.6.1/flex-2.6.1.tar.gz" - version('2.6.4', '2882e3179748cc9f9c23ec593d6adc8d') - version('2.6.3', 'a5f65570cd9107ec8a8ec88f17b31bb1') + version('2.6.4', sha256='e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995') + version('2.6.3', sha256='68b2742233e747c462f781462a2a1e299dc6207401dac8f0bbb316f48565c2aa') # Avoid flex '2.6.2' (major bug) # See issue #2554; https://github.com/westes/flex/issues/113 - version('2.6.1', '05bcd8fb629e0ae130311e8a6106fa82') - version('2.6.0', '760be2ee9433e822b6eb65318311c19d') - version('2.5.39', '5865e76ac69c05699f476515592750d7') + version('2.6.1', sha256='3c43f9e658e45e8aae3cf69fa11803d60550865f023852830d557c5f0623c13b') + version('2.6.0', sha256='cde6e46064a941a3810f7bbc612a2c39cb3aa29ce7eb775089c2515d0adfa7e9') + version('2.5.39', sha256='258d3c9c38cae05932fb470db58b6a288a361c448399e6bda2694ef72a76e7cd') variant('lex', default=True, description="Provide symlinks for lex and libl") diff --git a/var/spack/repos/builtin/packages/flint/package.py b/var/spack/repos/builtin/packages/flint/package.py index 027206d9517..c83e4f0cd2c 100644 --- a/var/spack/repos/builtin/packages/flint/package.py +++ b/var/spack/repos/builtin/packages/flint/package.py @@ -14,8 +14,8 @@ class Flint(Package): git = "https://github.com/wbhart/flint2.git" version('develop', branch='trunk') - version('2.5.2', 'cda885309362150196aed66a5e0f0383') - version('2.4.5', '6504b9deabeafb9313e57153a1730b33') + version('2.5.2', sha256='cbf1fe0034533c53c5c41761017065f85207a1b770483e98b2392315f6575e87') + version('2.4.5', sha256='e489354df00f0d84976ccdd0477028693977c87ccd14f3924a89f848bb0e01e3') # Overlap in functionality between gmp and mpir # All other dependencies must also be built with diff --git a/var/spack/repos/builtin/packages/flit/package.py b/var/spack/repos/builtin/packages/flit/package.py index bd3078314de..caf97fc474c 100644 --- a/var/spack/repos/builtin/packages/flit/package.py +++ b/var/spack/repos/builtin/packages/flit/package.py @@ -16,10 +16,10 @@ class Flit(MakefilePackage): url = "https://github.com/PRUNERS/FLiT" url = "https://github.com/PRUNERS/FLiT/archive/v2.0-alpha.1.tar.gz" - version('2.0-alpha.1', '62cf7784bcdc15b962c813b11e478159') + version('2.0-alpha.1', sha256='8de2bd400acf0f513d69f3dbf588e8984dfb18b8ccaaf684391811a0582f694b') # FIXME: fix install and build to handle the old version, which is not # installable - # version('1.0.0', '27763c89b044c5e3cfe62dd319a36a2b') + # version('1.0.0', md5='27763c89b044c5e3cfe62dd319a36a2b') conflicts("@:1.999", msg="Only can build version 2.0 and up") # Add dependencies diff --git a/var/spack/repos/builtin/packages/fltk/package.py b/var/spack/repos/builtin/packages/fltk/package.py index dd101a47096..9b4aaa6de93 100644 --- a/var/spack/repos/builtin/packages/fltk/package.py +++ b/var/spack/repos/builtin/packages/fltk/package.py @@ -21,7 +21,7 @@ class Fltk(Package): homepage = 'http://www.fltk.org/' url = 'http://fltk.org/pub/fltk/1.3.3/fltk-1.3.3-source.tar.gz' - version('1.3.3', '9ccdb0d19dc104b87179bd9fd10822e3') + version('1.3.3', sha256='f8398d98d7221d40e77bc7b19e761adaf2f1ef8bb0c30eceb7beb4f2273d0d97') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py index ba1d65e1fcc..11cb14d23c1 100644 --- a/var/spack/repos/builtin/packages/flux-core/package.py +++ b/var/spack/repos/builtin/packages/flux-core/package.py @@ -16,9 +16,9 @@ class FluxCore(AutotoolsPackage): version('master', branch='master') version('0.11.0', sha256='a4d8ff92e79b4ca19d556395bb8c5f8dc02fd9d5a8cc38c4a2c66867a96de5ea') - version('0.10.0', 'a84a1ed53a69c805c253bc940540cbf667a059b2008fd2a6a9bb890a985ead08e88dcbba68c01567f887357306fbfded41b93cc33edfa7809955ba5ba5870284') - version('0.9.0', '70eaec1005aa49e8d8cf397570789cebedfb5d917efe963390d456ee4c473eefb15b0c81ea83f60a1fd057fe7be356bbafdebcae64b499844d194c48f6aefa05') - version('0.8.0', 'b0fec05acedc530bcdf75b2477ac22f39d2adddc7af8ff76496208a5e1e8185b1b4a18677871d95c3cfbf34b05f391953651200917fe029931f4e2beb79d70df') + version('0.10.0', sha256='a70cdd228077af60c9443a5c69d3da932e447dd11697f5fef9028c48dabb3041') + version('0.9.0', sha256='7b5b4aa72704b3c4432136b9e515e0d663568e6dbfc3ecd2f91c83b65841104e') + version('0.8.0', sha256='eb4b0fe0da191acd3823ef42d415c40aae6a0c3aef62ebb27905658d045e11cc') # Avoid the infinite symlink issue # This workaround is documented in PR #3543 diff --git a/var/spack/repos/builtin/packages/flux-sched/package.py b/var/spack/repos/builtin/packages/flux-sched/package.py index 6c68c231578..5a77ed46ffb 100644 --- a/var/spack/repos/builtin/packages/flux-sched/package.py +++ b/var/spack/repos/builtin/packages/flux-sched/package.py @@ -16,9 +16,9 @@ class FluxSched(AutotoolsPackage): version('master', branch='master') version('0.7.0', sha256='69267a3aaacaedd9896fd90cfe17aef266cba4fb28c77f8123d95a31ce739a7b') - version('0.6.0', '8aad185949038c7fb6b277e6a8282947917084ebbec5c5bf0ee3a81a0dcdbe41ba18b1df837c669ae7b48ca5f1e492a5172bffa6b9feb4dda1c6a7a85abed4e8') - version('0.5.0', 'a9835c9c478aa41123a4e12672500052228aaf1ea770f74cb0901dbf4a049bd7d329e99d8d3484e39cfed1f911705030b2775dcfede39bc8bea59c6afe2549b1') - version('0.4.0', '82732641ac4594ffe9b94ca442a99e92bf5f91bc14745af92203a887a40610dd44edda3ae07f9b6c8d63799b2968d87c8da28f1488edef1310d0d12be9bd6319') + version('0.6.0', sha256='3301d4c10810414228e5969b84b75fe1285abb97453070eb5a77f386d8184f8d') + version('0.5.0', sha256='d6347f5c85c12c76364dccb39d63c007094ca9cbbbae4e8f4e98d8b1c0b07e89') + version('0.4.0', sha256='00768a0b062aec42aa9b31d9d7006efd3a3e9cb9c24878d50487643c8af15e8a') # Avoid the infinite symlink issue # This workaround is documented in PR #3543 diff --git a/var/spack/repos/builtin/packages/fluxbox/package.py b/var/spack/repos/builtin/packages/fluxbox/package.py index 63d07318d05..d4499612ba5 100644 --- a/var/spack/repos/builtin/packages/fluxbox/package.py +++ b/var/spack/repos/builtin/packages/fluxbox/package.py @@ -17,7 +17,7 @@ class Fluxbox(AutotoolsPackage): homepage = "http://fluxbox.org/" url = "http://sourceforge.net/projects/fluxbox/files/fluxbox/1.3.7/fluxbox-1.3.7.tar.gz" - version('1.3.7', 'd99d7710f9daf793e0246dae5304b595') + version('1.3.7', sha256='c99e2baa06fff1e96342b20415059d12ff1fa2917ade0173c75b2fa570295b9f') depends_on('pkgconfig', type='build') depends_on('freetype') diff --git a/var/spack/repos/builtin/packages/folly/package.py b/var/spack/repos/builtin/packages/folly/package.py index 14f12f8113f..e49b04b42ae 100644 --- a/var/spack/repos/builtin/packages/folly/package.py +++ b/var/spack/repos/builtin/packages/folly/package.py @@ -20,12 +20,12 @@ class Folly(AutotoolsPackage): homepage = "https://github.com/facebook/folly" url = "https://github.com/facebook/folly/archive/v2017.06.05.00.tar.gz" - version('2017.06.05.00', 'a25e8d646702c3e0c1400f591e485a33') - version('2016.11.14.00', '88550acdb4d4b331c0ca9922039c8727') - version('2016.11.07.00', '2f605b20ad539bccdbfd361daa92081e') - version('2016.10.31.00', 'ab3049302792f8470cef64f3a29eedec') - version('2016.10.24.00', '0445efb7c16b5c32dfbb173157e54866') - version('2016.10.17.00', 'b7e01934a45c5036fab8fdc70e9eaf4d') + version('2017.06.05.00', sha256='d22ceda4dfe33583828be1193fa3929d70c51998f0797236e293c44ef828c6d0') + version('2016.11.14.00', sha256='cde5b3e1a38d181f7c4e52d590de1c1aca58da7b27b3020d08e9aa45b4c3ed74') + version('2016.11.07.00', sha256='4400d7f0fead90d88ce4caee9f0e9aeb8008c9954ea9034e19ae7226175206ba') + version('2016.10.31.00', sha256='7bef9ee956248f68f1c4e96be67561842ee6cc030a58e132b93b9be57b6b29ea') + version('2016.10.24.00', sha256='d54b609d3750a6a1cfbda7c62e1457af60cf5efc48d7a8e6552d67909e064757') + version('2016.10.17.00', sha256='0f83685016d020111ba54ddc48c0cf33e1e0b9b35cee5ae82d5f2cbc5f6b0e82') depends_on('m4', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/font-util/package.py b/var/spack/repos/builtin/packages/font-util/package.py index 1a0a23263e5..081e3be2539 100644 --- a/var/spack/repos/builtin/packages/font-util/package.py +++ b/var/spack/repos/builtin/packages/font-util/package.py @@ -12,7 +12,7 @@ class FontUtil(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/font/util" url = "https://www.x.org/archive/individual/font/font-util-1.3.1.tar.gz" version('1.3.2', sha256='f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76') - version('1.3.1', 'd153a9af216e4498fa171faea2c82514') + version('1.3.1', sha256='34ebb0c9c14e0a392cdd5ea055c92489ad88d55ae148b2f1cfded0f3f63f2b5b') depends_on('autoconf', type='build') depends_on('automake', type='build') @@ -28,48 +28,42 @@ class FontUtil(AutotoolsPackage): fonts = [] # name, version, md5 fonts_resource = [ - ['encodings', '1.0.4', '1a631784ce204d667abcc329b851670c'], - ['font-alias', '1.0.3', '535138efe0a95f5fe521be6a6b9c4888'], - ['font-adobe-100dpi', '1.0.3', 'ba61e7953f4f5cec5a8e69c262bbc7f9'], - ['font-adobe-75dpi', '1.0.3', '7a414bb661949cec938938fd678cf649'], - ['font-adobe-utopia-100dpi', '1.0.4', - '128416eccd59b850f77a9b803681da3c'], - ['font-adobe-utopia-75dpi', '1.0.4', - '74c73a5b73c6c3224b299f1fc033e508'], - ['font-adobe-utopia-type1', '1.0.4', - 'b0676c3495acabad519ee98a94163904'], - ['font-arabic-misc', '1.0.3', '918457df65ef93f09969c6ab01071789'], - ['font-bh-100dpi', '1.0.3', '09e63a5608000531179e1ab068a35878'], - ['font-bh-75dpi', '1.0.3', '88fec4ebc4a265684bff3abdd066f14f'], - ['font-bh-ttf', '1.0.3', '4ce741ec4edaa11cd38988d355a7578b'], - ['font-bh-type1', '1.0.3', '62d4e8f782a6a0658784072a5df5ac98'], - ['font-bh-lucidatypewriter-100dpi', '1.0.3', - '5f716f54e497fb4ec1bb3a5d650ac6f7'], - ['font-bh-lucidatypewriter-75dpi', '1.0.3', - 'cab8a44ae329aab7141c7adeef0daf5a'], - ['font-bitstream-100dpi', '1.0.3', 'c27bf37e9b8039f93bd90b8131ed37ad'], - ['font-bitstream-75dpi', '1.0.3', '4ff6c5d6aebe69371e27b09ad8313d25'], - ['font-bitstream-speedo', '1.0.2', 'f0a777b351cf5adefefcf4823e0c1c01'], - ['font-bitstream-type1', '1.0.3', 'ff91738c4d3646d7999e00aa9923f2a0'], - ['font-cronyx-cyrillic', '1.0.3', '3119ba1bc7f775c162c96e17a912fe30'], - ['font-cursor-misc', '1.0.3', 'a0bf70c7e498f1cd8e3fdf6154f2bb00'], - ['font-daewoo-misc', '1.0.3', '71a7e2796f045c9d217a19c4e6c25bc1'], - ['font-dec-misc', '1.0.3', '5a9242f6b60ecf2b8c5b158322ca2a40'], - ['font-ibm-type1', '1.0.3', '2806116e4adcb89d3d5ff5faf65e57c1'], - ['font-isas-misc', '1.0.3', 'ecc3b6fbe8f5721ddf5c7fc66f73e76f'], - ['font-jis-misc', '1.0.3', 'c48ee5749ae25075d2c7a6111c195e7b'], - ['font-micro-misc', '1.0.3', '4de3f0ce500aef85f198c52ace5e66ac'], - ['font-misc-cyrillic', '1.0.3', 'e7b13da5325f62dd3f630beade6d2656'], - ['font-misc-ethiopic', '1.0.3', '02ddea9338d9d36804ad38f3daadb55a'], - ['font-misc-meltho', '1.0.3', '8380696483478449c39b04612f20eea8'], - ['font-misc-misc', '1.1.2', '23a79b92275375315129b440206c85b9'], - ['font-mutt-misc', '1.0.3', '6c2de53ba514f720e02af48eef28ff32'], - ['font-schumacher-misc', '1.1.2', '1f3386a0a690ba8117fc05b501f9f91b'], - ['font-screen-cyrillic', '1.0.4', '4cadaf2ba4c4d0f4cb9b4e7b8f0a3019'], - ['font-sun-misc', '1.0.3', '87ce97ce0582e76bc4064a4d4d10db09'], - ['font-winitzki-cyrillic', '1.0.3', - '777c667b080b33793528d5abf3247a48'], - ['font-xfree86-type1', '1.0.4', '89c33c5176cd580de6636ad50ce7777b'], + ['encodings', '1.0.4', '55861d9cf456bd717a3d30a3193402c02174ed3c0dcee828798165fe307ee324'], + ['font-alias', '1.0.3', '63087cb61d17bfc9cd6f4f9359f63a3b1dd83300a31a42fd93dca084724c6afb'], + ['font-adobe-100dpi', '1.0.3', '97d9c1e706938838e4134d74f0836ae9d9ca6705ecb405c9a0ac8fdcbd9c2159'], + ['font-adobe-75dpi', '1.0.3', '61eb1fcfec89f7435cb92cd68712fbe4ba412ca562b1f5feec1f6daa1b8544f6'], + ['font-adobe-utopia-100dpi', '1.0.4', 'e8c3417d89183b1fc383fb3e0f3948c0d01fabcb9edace8b7ec85eab8cdc18c4'], + ['font-adobe-utopia-75dpi', '1.0.4', '254be39c09da1c4e77d2a75a2969330ee2db395120a428671c50aef3ab745fc0'], + ['font-adobe-utopia-type1', '1.0.4', 'd9e86a8805b0fb78222409169d839a8531a1f5c7284ee117ff2a0af2e5016c3f'], + ['font-arabic-misc', '1.0.3', '3022b6b124f4cc6aade961f8d1306f67ff42e3b7922fb2244847f287344aefea'], + ['font-bh-100dpi', '1.0.3', '817703372f080d6508cf109011b17f3572ff31047559fe82d93b487ca4e4e2d9'], + ['font-bh-75dpi', '1.0.3', '720b6a513894bfc09a163951ec3dd8311201e08ee40e8891547b6c129ffb5fce'], + ['font-bh-ttf', '1.0.3', 'c583b4b968ffae6ea30d5b74041afeac83126682c490a9624b770d60d0e63d59'], + ['font-bh-type1', '1.0.3', 'd5602f1d749ccd31d3bc1bb6f0c5d77400de0e5e3ac5abebd2a867aa2a4081a4'], + ['font-bh-lucidatypewriter-100dpi', '1.0.3', '5e05a642182ec6a77bd7cacb913d3c86b364429329a5f223b69792d418f90ae9'], + ['font-bh-lucidatypewriter-75dpi', '1.0.3', '38301bbdb6374494f30c0b44acc7052ed8fc2289e917e648ca566fc591f0a9e0'], + ['font-bitstream-100dpi', '1.0.3', '0a8c77c1540dc376fb2bb5a02bd33ee5f3563fbac9fc07c7947cac462c4bb48a'], + ['font-bitstream-75dpi', '1.0.3', 'c43ae370932eb8a4789a5b1f9801da15228b0d4c803251785c38d82aef024a4b'], + ['font-bitstream-speedo', '1.0.2', 'aeea5f130480a3f05149bde13d240e668d8fb4b32c02b18914fcccd1182abe72'], + ['font-bitstream-type1', '1.0.3', '3399b7586c18be509cdaeceeebf754b861faa1d8799dda1aae01aeb2a7a30f01'], + ['font-cronyx-cyrillic', '1.0.3', 'd64b9bfa5fa8dedf084f1695997cc32149485d2a195c810f62a1991ab5cd5519'], + ['font-cursor-misc', '1.0.3', 'a0b146139363dd0a704c7265ff9cd9150d4ae7c0d248091a9a42093e1618c427'], + ['font-daewoo-misc', '1.0.3', '21166546b0490aa3ec73215fa4ea28d91c6027b56178800ba51426bd3d840cc3'], + ['font-dec-misc', '1.0.3', 'c4923342f6068c83fd4f5dbcf60d671c28461300db7e2aee930c8634b1e4b74a'], + ['font-ibm-type1', '1.0.3', '4509703e9e581061309cf4823bffd4a93f10f48fe192a1d8be1f183fd6ab9711'], + ['font-isas-misc', '1.0.3', '493965263070a5ee2a301dfdb2e87c1ca3c00c7882bfb3dd99368565ba558ff5'], + ['font-jis-misc', '1.0.3', '57c2db8824865117287d57d47f2c8cf4b2842d036c7475534b5054be69690c73'], + ['font-micro-misc', '1.0.3', '97ee77a9d8ca3e7caf0c78c386eb0b96e8a825ca3642ec035cfb83f5f2cf1475'], + ['font-misc-cyrillic', '1.0.3', '79dfde93d356e41c298c2c1b9c638ec1a144f438d5146d0df6219afb1c2b8818'], + ['font-misc-ethiopic', '1.0.3', 'd3b93f7f73a526919bf73a38e10ef4643cd541403a682a8068d54bbcdd9c7e27'], + ['font-misc-meltho', '1.0.3', 'eaddfc6d9b32bf38c9dc87c354be3b646a385bc8d9de6e536269f6e1ca50644e'], + ['font-misc-misc', '1.1.2', '46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + ['font-mutt-misc', '1.0.3', 'fcecbfc475dfe5826d137f8edc623ba27d58d32f069165c248a013b3c566bb59'], + ['font-schumacher-misc', '1.1.2', 'dc3b8d5890480943e735e0375f0e0d8333094fcb6d6845ba321b2e39db78d148'], + ['font-screen-cyrillic', '1.0.4', '9e82783758e8c67a9aadaf1a7222d13418a87455e4ce0a9974fb1df0278bdf74'], + ['font-sun-misc', '1.0.3', '549c6ba59979da25e85c218a26e5c527c3c24ebab2c76509c1ebc34d94fae227'], + ['font-winitzki-cyrillic', '1.0.3', '503e70ee66af34f6ec4426c0f4ae708e9d30dafdcd58f671a87c7bf56b1952a3'], + ['font-xfree86-type1', '1.0.4', '02b3839ae79ba6a7750525bb3b0c281305664b95bf63b4a0baa230a277b4f928'], ] for f_r in fonts_resource: f = f_r[0] diff --git a/var/spack/repos/builtin/packages/fontcacheproto/package.py b/var/spack/repos/builtin/packages/fontcacheproto/package.py index 8baa82fcdb8..3c7328a14c4 100644 --- a/var/spack/repos/builtin/packages/fontcacheproto/package.py +++ b/var/spack/repos/builtin/packages/fontcacheproto/package.py @@ -12,4 +12,4 @@ class Fontcacheproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/fontcacheproto" url = "https://www.x.org/archive/individual/proto/fontcacheproto-0.1.3.tar.gz" - version('0.1.3', '5a91ab914ffbfbc856e6fcde52e6f3e3') + version('0.1.3', sha256='759b4863b55a25bfc8f977d8ed969da0b99b3c823f33c674d6da5825f9df9a79') diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py index c0563ef3c0a..1b6f1e77382 100644 --- a/var/spack/repos/builtin/packages/fontconfig/package.py +++ b/var/spack/repos/builtin/packages/fontconfig/package.py @@ -11,9 +11,9 @@ class Fontconfig(AutotoolsPackage): homepage = "http://www.freedesktop.org/wiki/Software/fontconfig/" url = "http://www.freedesktop.org/software/fontconfig/release/fontconfig-2.12.3.tar.gz" - version('2.12.3', 'aca0c734c1a38eb3ba12b2447dd90ab0') - version('2.12.1', 'ce55e525c37147eee14cc2de6cc09f6c') - version('2.11.1', 'e75e303b4f7756c2b16203a57ac87eba') + version('2.12.3', sha256='ffc3cbf6dd9fcd516ee42f48306a715e66698b238933d6fa7cef02ea8b3b818e') + version('2.12.1', sha256='a9f42d03949f948a3a4f762287dbc16e53a927c91a07ee64207ebd90a9e5e292') + version('2.11.1', sha256='b6b066c7dce3f436fdc0dfbae9d36122b38094f4f53bd8dffd45e195b0540d8d') depends_on('freetype') depends_on('gperf', type='build', when='@2.12.2:') diff --git a/var/spack/repos/builtin/packages/fontsproto/package.py b/var/spack/repos/builtin/packages/fontsproto/package.py index 4329e4b8748..7165eab5585 100644 --- a/var/spack/repos/builtin/packages/fontsproto/package.py +++ b/var/spack/repos/builtin/packages/fontsproto/package.py @@ -12,7 +12,7 @@ class Fontsproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/fontsproto" url = "https://www.x.org/archive/individual/proto/fontsproto-2.1.3.tar.gz" - version('2.1.3', '0415f0360e33f3202af67c6c46782251') + version('2.1.3', sha256='72c44e63044b2b66f6fa112921621ecc20c71193982de4f198d9a29cda385c5e') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/fonttosfnt/package.py b/var/spack/repos/builtin/packages/fonttosfnt/package.py index f595947a221..b47f89b873f 100644 --- a/var/spack/repos/builtin/packages/fonttosfnt/package.py +++ b/var/spack/repos/builtin/packages/fonttosfnt/package.py @@ -12,7 +12,7 @@ class Fonttosfnt(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/fonttosfnt" url = "https://www.x.org/archive/individual/app/fonttosfnt-1.0.4.tar.gz" - version('1.0.4', 'ba77fd047a9cca400f17db8c46b06ce8') + version('1.0.4', sha256='3873636be5b3b8e4160070e8f9a7a9221b5bd5efbf740d7abaa9092e10732673') depends_on('freetype') depends_on('libfontenc') diff --git a/var/spack/repos/builtin/packages/fpc/package.py b/var/spack/repos/builtin/packages/fpc/package.py index b49e2e127ef..ccaaee5b8d1 100644 --- a/var/spack/repos/builtin/packages/fpc/package.py +++ b/var/spack/repos/builtin/packages/fpc/package.py @@ -12,7 +12,7 @@ class Fpc(Package): homepage = "https://www.freepascal.org/" url = "https://downloads.sourceforge.net/project/freepascal/Linux/3.0.2/fpc-3.0.2.x86_64-linux.tar" - version('3.0.2', 'e5721c1843cff301c5b46abfee17c890') + version('3.0.2', sha256='b5b27fdbc31b1d05b6a898f3c192d8a5083050562b29c19eb9eb018ba4482bd8') def install(self, spec, prefix): install = Executable('./install.sh') diff --git a/var/spack/repos/builtin/packages/fr-hit/package.py b/var/spack/repos/builtin/packages/fr-hit/package.py index 2b77a63b6c9..f1ea5774c03 100644 --- a/var/spack/repos/builtin/packages/fr-hit/package.py +++ b/var/spack/repos/builtin/packages/fr-hit/package.py @@ -13,7 +13,7 @@ class FrHit(Package): homepage = "http://weizhong-lab.ucsd.edu/frhit" url = "http://weizhong-lab.ucsd.edu/frhit/fr-hit-v0.7.1-2013-02-20.tar.gz" - version('0.7.1-2013-02-20', '3e8ea41ba09ab0c13e9973fe6f493f96') + version('0.7.1-2013-02-20', sha256='44dcfeb73106529fcefb02c017ec7b95b04b6523a2a57683b2bc905c142e62eb') depends_on('perl') depends_on('python@2.7:') diff --git a/var/spack/repos/builtin/packages/freeglut/package.py b/var/spack/repos/builtin/packages/freeglut/package.py index dfab6764361..bea45b795f5 100644 --- a/var/spack/repos/builtin/packages/freeglut/package.py +++ b/var/spack/repos/builtin/packages/freeglut/package.py @@ -13,7 +13,7 @@ class Freeglut(CMakePackage): homepage = "http://freeglut.sourceforge.net/" url = "http://prdownloads.sourceforge.net/freeglut/freeglut-3.0.0.tar.gz" - version('3.0.0', '90c3ca4dd9d51cf32276bc5344ec9754') + version('3.0.0', sha256='2a43be8515b01ea82bcfa17d29ae0d40bd128342f0930cd1f375f1ff999f76a2') depends_on('gl') depends_on('glu') diff --git a/var/spack/repos/builtin/packages/freeimage/package.py b/var/spack/repos/builtin/packages/freeimage/package.py index 2f1293c1f4b..a7be20f9ecc 100644 --- a/var/spack/repos/builtin/packages/freeimage/package.py +++ b/var/spack/repos/builtin/packages/freeimage/package.py @@ -13,7 +13,7 @@ class Freeimage(MakefilePackage): homepage = "http://freeimage.sourceforge.net/" - version('3.18.0', 'f8ba138a3be233a3eed9c456e42e2578') + version('3.18.0', sha256='f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd') patch('install_fixes.patch', when='@3.18.0') diff --git a/var/spack/repos/builtin/packages/freetype/package.py b/var/spack/repos/builtin/packages/freetype/package.py index e55dc8dbcd3..507228b2cce 100644 --- a/var/spack/repos/builtin/packages/freetype/package.py +++ b/var/spack/repos/builtin/packages/freetype/package.py @@ -16,9 +16,9 @@ class Freetype(AutotoolsPackage): url = "https://download.savannah.gnu.org/releases/freetype/freetype-2.9.1.tar.gz" version('2.9.1', sha256='ec391504e55498adceb30baceebd147a6e963f636eb617424bcfc47a169898ce') - version('2.7.1', '78701bee8d249578d83bb9a2f3aa3616') - version('2.7', '337139e5c7c5bd645fe130608e0fa8b5') - version('2.5.3', 'cafe9f210e45360279c730d27bf071e9') + version('2.7.1', sha256='162ef25aa64480b1189cdb261228e6c5c44f212aac4b4621e28cf2157efb59f5') + version('2.7', sha256='7b657d5f872b0ab56461f3bd310bd1c5ec64619bd15f0d8e08282d494d9cfea4') + version('2.5.3', sha256='41217f800d3f40d78ef4eb99d6a35fd85235b64f81bc56e4812d7672fca7b806') depends_on('libpng') depends_on('bzip2') diff --git a/var/spack/repos/builtin/packages/freexl/package.py b/var/spack/repos/builtin/packages/freexl/package.py index ed654f5c399..aef3a885d34 100644 --- a/var/spack/repos/builtin/packages/freexl/package.py +++ b/var/spack/repos/builtin/packages/freexl/package.py @@ -13,4 +13,4 @@ class Freexl(AutotoolsPackage): homepage = "http://www.gaia-gis.it" url = "http://www.gaia-gis.it/gaia-sins/freexl-1.0.5.tar.gz" - version('1.0.5', '3ed2a0486f03318820b25f0ccae5e14d') + version('1.0.5', sha256='3dc9b150d218b0e280a3d6a41d93c1e45f4d7155829d75f1e5bf3e0b0de6750d') diff --git a/var/spack/repos/builtin/packages/fslsfonts/package.py b/var/spack/repos/builtin/packages/fslsfonts/package.py index 6b24306dbf6..c01b606f8a2 100644 --- a/var/spack/repos/builtin/packages/fslsfonts/package.py +++ b/var/spack/repos/builtin/packages/fslsfonts/package.py @@ -12,7 +12,7 @@ class Fslsfonts(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/fslsfonts" url = "https://www.x.org/archive/individual/app/fslsfonts-1.0.5.tar.gz" - version('1.0.5', 'ef781bd6a7b529d3ed7a256055715730') + version('1.0.5', sha256='27e58d2313835ce0f08cf47c59a43798b122f605a55f54b170db27b57a492007') depends_on('libfs') diff --git a/var/spack/repos/builtin/packages/fstobdf/package.py b/var/spack/repos/builtin/packages/fstobdf/package.py index fe39cd5b7cf..b5704593b87 100644 --- a/var/spack/repos/builtin/packages/fstobdf/package.py +++ b/var/spack/repos/builtin/packages/fstobdf/package.py @@ -15,7 +15,7 @@ class Fstobdf(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/fstobdf" url = "https://www.x.org/archive/individual/app/fstobdf-1.0.6.tar.gz" - version('1.0.6', '6d3f24673fcb9ce266f49dc140bbf250') + version('1.0.6', sha256='bb903ae76cbcb0a08a71f06762b64db7d5c2064f6e88e8dc3a604e76d0bcb93d') depends_on('libx11') depends_on('libfs') diff --git a/var/spack/repos/builtin/packages/ftgl/package.py b/var/spack/repos/builtin/packages/ftgl/package.py index b1dbd03a99e..5e6641005bb 100644 --- a/var/spack/repos/builtin/packages/ftgl/package.py +++ b/var/spack/repos/builtin/packages/ftgl/package.py @@ -17,7 +17,7 @@ class Ftgl(AutotoolsPackage): list_depth = 1 version('2.1.3-rc5', sha256='5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b') - version('2.1.2', 'f81c0a7128192ba11e036186f9a968f2') + version('2.1.2', sha256='2759cbd5fac0b631e8b012923cd0d2add320f6e541b399a7cda37163ad034075') variant('doc', default=False, description='Build docs') conflicts('+doc', when='@2.1.3-rc5') diff --git a/var/spack/repos/builtin/packages/funhpc/package.py b/var/spack/repos/builtin/packages/funhpc/package.py index cc65cb8607b..4fce8b68d54 100644 --- a/var/spack/repos/builtin/packages/funhpc/package.py +++ b/var/spack/repos/builtin/packages/funhpc/package.py @@ -15,13 +15,13 @@ class Funhpc(CMakePackage): git = "https://github.com/eschnett/FunHPC.cxx.git" version('develop', branch='master') - version('1.3.0', '71a1e57c4d882cdf001f29122edf7fc6') - version('1.2.0', 'ba2bbeea3091e999b6b85eaeb1b67a83') - version('1.1.1', '7b9ef638b02fffe35b75517e8eeff580') - version('1.1.0', '897bd968c42cd4f14f86fcf67da70444') - version('1.0.0', 'f34e71ccd5548b42672e692c913ba5ee') - version('0.1.1', 'f0248710f2de88ed2a595ad40d99997c') - version('0.1.0', '00f7dabc08ed1ab77858785ce0809f50') + version('1.3.0', sha256='140e60f55a307f21117bd43fa16db35d60c0df5ef37e17a4da1cb3f5da5e29c1') + version('1.2.0', md5='ba2bbeea3091e999b6b85eaeb1b67a83') + version('1.1.1', md5='7b9ef638b02fffe35b75517e8eeff580') + version('1.1.0', md5='897bd968c42cd4f14f86fcf67da70444') + version('1.0.0', md5='f34e71ccd5548b42672e692c913ba5ee') + version('0.1.1', md5='f0248710f2de88ed2a595ad40d99997c') + version('0.1.0', md5='00f7dabc08ed1ab77858785ce0809f50') variant('pic', default=True, description="Produce position-independent code") diff --git a/var/spack/repos/builtin/packages/fyba/package.py b/var/spack/repos/builtin/packages/fyba/package.py index d713d2a4b28..4c63ac84c52 100644 --- a/var/spack/repos/builtin/packages/fyba/package.py +++ b/var/spack/repos/builtin/packages/fyba/package.py @@ -14,7 +14,7 @@ class Fyba(AutotoolsPackage): homepage = "https://github.com/kartverket/fyba" url = "https://github.com/kartverket/fyba/archive/4.1.1.tar.gz" - version('4.1.1', 'ab687582efdef26593796271529a10cb') + version('4.1.1', sha256='99f658d52e8fd8997118bb6207b9c121500700996d9481a736683474e2534179') # configure: error: cannot find install-sh or install.sh force_autoreconf = True diff --git a/var/spack/repos/builtin/packages/g4ensdfstate/package.py b/var/spack/repos/builtin/packages/g4ensdfstate/package.py index 6297c60c13d..ad065f92339 100644 --- a/var/spack/repos/builtin/packages/g4ensdfstate/package.py +++ b/var/spack/repos/builtin/packages/g4ensdfstate/package.py @@ -12,8 +12,8 @@ class G4ensdfstate(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4ENSDFSTATE.2.1.tar.gz" - version('2.1', '933e7f99b1c70f24694d12d517dfca36d82f4e95b084c15d86756ace2a2790d9') - version('2.2', 'dd7e27ef62070734a4a709601f5b3bada6641b111eb7069344e4f99a01d6e0a6') + version('2.1', sha256='933e7f99b1c70f24694d12d517dfca36d82f4e95b084c15d86756ace2a2790d9') + version('2.2', sha256='dd7e27ef62070734a4a709601f5b3bada6641b111eb7069344e4f99a01d6e0a6') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4ndl/package.py b/var/spack/repos/builtin/packages/g4ndl/package.py index 76a9d7ad851..05c3d292d70 100644 --- a/var/spack/repos/builtin/packages/g4ndl/package.py +++ b/var/spack/repos/builtin/packages/g4ndl/package.py @@ -12,7 +12,7 @@ class G4ndl(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4NDL.4.5.tar.gz" - version('4.5', 'cba928a520a788f2bc8229c7ef57f83d0934bb0c6a18c31ef05ef4865edcdf8e') + version('4.5', sha256='cba928a520a788f2bc8229c7ef57f83d0934bb0c6a18c31ef05ef4865edcdf8e') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4neutronxs/package.py b/var/spack/repos/builtin/packages/g4neutronxs/package.py index bc639823160..650823c4884 100644 --- a/var/spack/repos/builtin/packages/g4neutronxs/package.py +++ b/var/spack/repos/builtin/packages/g4neutronxs/package.py @@ -13,7 +13,7 @@ class G4neutronxs(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4NEUTRONXS.1.4.tar.gz" - version('1.4', '57b38868d7eb060ddd65b26283402d4f161db76ed2169437c266105cca73a8fd') + version('1.4', sha256='57b38868d7eb060ddd65b26283402d4f161db76ed2169437c266105cca73a8fd') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4photonevaporation/package.py b/var/spack/repos/builtin/packages/g4photonevaporation/package.py index 3c98f36fcf0..29f18d05d78 100644 --- a/var/spack/repos/builtin/packages/g4photonevaporation/package.py +++ b/var/spack/repos/builtin/packages/g4photonevaporation/package.py @@ -12,8 +12,8 @@ class G4photonevaporation(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PhotonEvaporation.4.3.2.tar.gz" - version('4.3.2', 'd4641a6fe1c645ab2a7ecee09c34e5ea584fb10d63d2838248bfc487d34207c7') - version('5.2', '83607f8d36827b2a7fca19c9c336caffbebf61a359d0ef7cee44a8bcf3fc2d1f') + version('4.3.2', sha256='d4641a6fe1c645ab2a7ecee09c34e5ea584fb10d63d2838248bfc487d34207c7') + version('5.2', sha256='83607f8d36827b2a7fca19c9c336caffbebf61a359d0ef7cee44a8bcf3fc2d1f') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4pii/package.py b/var/spack/repos/builtin/packages/g4pii/package.py index cb1a52d3b6a..a58c638b624 100644 --- a/var/spack/repos/builtin/packages/g4pii/package.py +++ b/var/spack/repos/builtin/packages/g4pii/package.py @@ -12,7 +12,7 @@ class G4pii(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PII.1.3.tar.gz" - version('1.3', '6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926') + version('1.3', sha256='6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4radioactivedecay/package.py b/var/spack/repos/builtin/packages/g4radioactivedecay/package.py index aa04798bc82..d69dda62183 100644 --- a/var/spack/repos/builtin/packages/g4radioactivedecay/package.py +++ b/var/spack/repos/builtin/packages/g4radioactivedecay/package.py @@ -12,8 +12,8 @@ class G4radioactivedecay(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4RadioactiveDecay.5.1.1.tar.gz" - version('5.1.1', 'f7a9a0cc998f0d946359f2cb18d30dff1eabb7f3c578891111fc3641833870ae') - version('5.2', '99c038d89d70281316be15c3c98a66c5d0ca01ef575127b6a094063003e2af5d') + version('5.1.1', sha256='f7a9a0cc998f0d946359f2cb18d30dff1eabb7f3c578891111fc3641833870ae') + version('5.2', sha256='99c038d89d70281316be15c3c98a66c5d0ca01ef575127b6a094063003e2af5d') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4realsurface/package.py b/var/spack/repos/builtin/packages/g4realsurface/package.py index 8f5746f96df..dd68dcdd250 100644 --- a/var/spack/repos/builtin/packages/g4realsurface/package.py +++ b/var/spack/repos/builtin/packages/g4realsurface/package.py @@ -12,9 +12,9 @@ class G4realsurface(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/RealSurface.1.0.tar.gz" - version('1.0', '3e2d2506600d2780ed903f1f2681962e208039329347c58ba1916740679020b1') - version('2.1', '2a287adbda1c0292571edeae2082a65b7f7bd6cf2bf088432d1d6f889426dcf3') - version('2.1.1', '90481ff97a7c3fa792b7a2a21c9ed80a40e6be386e581a39950c844b2dd06f50') + version('1.0', sha256='3e2d2506600d2780ed903f1f2681962e208039329347c58ba1916740679020b1') + version('2.1', sha256='2a287adbda1c0292571edeae2082a65b7f7bd6cf2bf088432d1d6f889426dcf3') + version('2.1.1', sha256='90481ff97a7c3fa792b7a2a21c9ed80a40e6be386e581a39950c844b2dd06f50') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4saiddata/package.py b/var/spack/repos/builtin/packages/g4saiddata/package.py index 928e7093fe4..dc40f6024f4 100644 --- a/var/spack/repos/builtin/packages/g4saiddata/package.py +++ b/var/spack/repos/builtin/packages/g4saiddata/package.py @@ -12,7 +12,7 @@ class G4saiddata(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4SAIDDATA.1.1.tar.gz" - version('1.1', 'a38cd9a83db62311922850fe609ecd250d36adf264a88e88c82ba82b7da0ed7f') + version('1.1', sha256='a38cd9a83db62311922850fe609ecd250d36adf264a88e88c82ba82b7da0ed7f') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/g4tendl/package.py b/var/spack/repos/builtin/packages/g4tendl/package.py index ee58b772825..cc2b0f06664 100644 --- a/var/spack/repos/builtin/packages/g4tendl/package.py +++ b/var/spack/repos/builtin/packages/g4tendl/package.py @@ -12,8 +12,8 @@ class G4tendl(Package): homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4TENDL.1.3.tar.gz" - version('1.3', '52ad77515033a5d6f995c699809b464725a0e62099b5e55bf07c8bdd02cd3bce') - version('1.3.2', '3b2987c6e3bee74197e3bd39e25e1cc756bb866c26d21a70f647959fc7afb849') + version('1.3', sha256='52ad77515033a5d6f995c699809b464725a0e62099b5e55bf07c8bdd02cd3bce') + version('1.3.2', sha256='3b2987c6e3bee74197e3bd39e25e1cc756bb866c26d21a70f647959fc7afb849') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) diff --git a/var/spack/repos/builtin/packages/gapbs/package.py b/var/spack/repos/builtin/packages/gapbs/package.py index 5a805925e5c..c587c3f5b83 100644 --- a/var/spack/repos/builtin/packages/gapbs/package.py +++ b/var/spack/repos/builtin/packages/gapbs/package.py @@ -20,7 +20,7 @@ class Gapbs(MakefilePackage): homepage = "http://gap.cs.berkeley.edu/benchmark.html" url = "https://github.com/sbeamer/gapbs/archive/v1.0.tar.gz" - version('1.0', 'ac2efa793f44e58553449f42b9779f3ff2d47634') + version('1.0', sha256='a7516998c4994592053c7aa0c76282760a8e009865a6b7a1c7c40968be1ca55d') variant('serial', default=False, description='Version with no parallelism') diff --git a/var/spack/repos/builtin/packages/gapcloser/package.py b/var/spack/repos/builtin/packages/gapcloser/package.py index ee5df4b04c5..99e7ec65842 100644 --- a/var/spack/repos/builtin/packages/gapcloser/package.py +++ b/var/spack/repos/builtin/packages/gapcloser/package.py @@ -13,7 +13,7 @@ class Gapcloser(Package): homepage = "https://sourceforge.net/projects/soapdenovo2/files/GapCloser/" url = "https://downloads.sourceforge.net/project/soapdenovo2/GapCloser/bin/r6/GapCloser-bin-v1.12-r6.tgz" - version('1.12-r6', '42b4e4256bdc9f9f31a391a359256209') + version('1.12-r6', sha256='8ca1a7e521dabc551ab4436d2b6e32536df670fae1c0e0fcb9242ae3a53db579') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/gasnet/package.py b/var/spack/repos/builtin/packages/gasnet/package.py index 890028bda9e..e98593f6325 100644 --- a/var/spack/repos/builtin/packages/gasnet/package.py +++ b/var/spack/repos/builtin/packages/gasnet/package.py @@ -18,10 +18,10 @@ class Gasnet(AutotoolsPackage): version('2019.3.0', sha256='97fe19bb5ab32d14a96d2dd19d0f03048f68bb20ca83abe0c00cdab40e86eba5') version('1.32.0', sha256='42e4774b3bbc7c142f77c41b6ce86b594f579073f46c31f47f424c7e31ee1511') - version('1.30.0', '2ddb1d8397d62acfd389095ca8da72f6') - version('1.28.2', '6ca0463dc2430570e40646c4d1e97b36') - version('1.28.0', 'b44446d951d3d8954aa1570e3556ba61') - version('1.24.0', 'c8afdf48381e8b5a7340bdb32ca0f41a') + version('1.30.0', sha256='b5d8c98c53174a98a41efb4ec9dedb62c0a9e8fa111bb6460cd4493beb80d497') + version('1.28.2', sha256='7903fd8ebdd03bcda20a66e3fcedef2f8b384324591aa91b8370f3360f6384eb') + version('1.28.0', sha256='a7999fbaa1f220c2eb9657279c7e7cccd1b21865d5383c9a5685cfe05a0702bc') + version('1.24.0', sha256='76b4d897d5e2261ef83d0885c192e8ac039e32cb2464f11eb64eb3f9f2df38c0') variant('ibv', default=False, description="Support InfiniBand") variant('mpi', default=True, description="Support MPI") diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py index f9d6ff04149..8f620daba57 100644 --- a/var/spack/repos/builtin/packages/gatk/package.py +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -40,13 +40,13 @@ class Gatk(Package): ) version( "3.8-1", - "a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c", + sha256="a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c", extension="tar.bz2", url="https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef", ) version( "3.8-0", - "0581308d2a25f10d11d3dfd0d6e4d28e", + sha256="d1017b851f0cc6442b75ac88dd438e58203fa3ef1d1c38eb280071ae3803b9f1", extension="tar.gz", url="https://software.broadinstitute.org/gatk/download/auth?package=GATK", ) diff --git a/var/spack/repos/builtin/packages/gawk/package.py b/var/spack/repos/builtin/packages/gawk/package.py index 0dd1c5009b2..a3e7268fc8e 100644 --- a/var/spack/repos/builtin/packages/gawk/package.py +++ b/var/spack/repos/builtin/packages/gawk/package.py @@ -23,7 +23,7 @@ class Gawk(AutotoolsPackage): homepage = "https://www.gnu.org/software/gawk/" url = "https://ftpmirror.gnu.org/gawk/gawk-4.1.4.tar.xz" - version('4.1.4', '4e7dbc81163e60fd4f0b52496e7542c9') + version('4.1.4', sha256='53e184e2d0f90def9207860531802456322be091c7b48f23fdc79cda65adc266') depends_on('gettext') depends_on('libsigsegv') diff --git a/var/spack/repos/builtin/packages/gblocks/package.py b/var/spack/repos/builtin/packages/gblocks/package.py index 50429fa5b09..08b732d906a 100644 --- a/var/spack/repos/builtin/packages/gblocks/package.py +++ b/var/spack/repos/builtin/packages/gblocks/package.py @@ -14,7 +14,7 @@ class Gblocks(Package): homepage = "http://molevol.cmima.csic.es/castresana/Gblocks.html" url = "http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z" - version('0.91b', 'c2c752ae4cbfda0b8bf09e6662585252') + version('0.91b', sha256='563658f03cc5e76234a8aa705bdc149398defec813d3a0c172b5f94c06c880dc') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 6bdfaeccc2d..5551ba0cac1 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -25,39 +25,39 @@ class Gcc(AutotoolsPackage): version('develop', svn=svn + 'trunk') - version('9.2.0', 'a12dff52af876aee0fd89a8d09cdc455f35ec46845e154023202392adc164848faf8ee881b59b681b696e27c69fd143a214014db4214db62f9891a1c8365c040') - version('9.1.0', 'b6134df027e734cee5395afd739fcfa4ea319a6017d662e54e89df927dea19d3fff7a6e35d676685383034e3db01c9d0b653f63574c274eeb15a2cb0bc7a1f28') + version('9.2.0', sha256='ea6ef08f121239da5695f76c9b33637a118dcf63e24164422231917fa61fb206') + version('9.1.0', sha256='79a66834e96a6050d8fe78db2c3b32fb285b230b855d0a66288235bc04b327a0') - version('8.3.0', '1811337ae3add9680cec64968a2509d085b6dc5b6783fc1e8c295e3e47416196fd1a3ad8dfe7e10be2276b4f62c357659ce2902f239f60a8648548231b4b5802') - version('8.2.0', '64898a165f67e136d802a92e7633bf1b06c85266027e52127ea025bf5fc2291b5e858288aac0bdba246e6cdf7c6ec88bc8e0e7f3f6f1985f4297710cafde56ed') - version('8.1.0', '65f7c65818dc540b3437605026d329fc') + version('8.3.0', sha256='64baadfe6cc0f4947a84cb12d7f0dfaf45bb58b7e92461639596c21e02d97d2c') + version('8.2.0', sha256='196c3c04ba2613f893283977e6011b2345d1cd1af9abeac58e916b1aab3e0080') + version('8.1.0', sha256='1d1866f992626e61349a1ccd0b8d5253816222cdc13390dcfaa74b093aa2b153') - version('7.4.0', 'eddde28d04f334aec1604456e536416549e9b1aa137fc69204e65eb0c009fe51') - version('7.3.0', 'be2da21680f27624f3a87055c4ba5af2') - version('7.2.0', 'ff370482573133a7fcdd96cd2f552292') - version('7.1.0', '6bf56a2bca9dac9dbbf8e8d1036964a8') + version('7.4.0', sha256='eddde28d04f334aec1604456e536416549e9b1aa137fc69204e65eb0c009fe51') + version('7.3.0', sha256='832ca6ae04636adbb430e865a1451adf6979ab44ca1c8374f61fba65645ce15c') + version('7.2.0', sha256='1cf7adf8ff4b5aa49041c8734bbcf1ad18cc4c94d0029aae0f4e48841088479a') + version('7.1.0', sha256='8a8136c235f64c6fef69cac0d73a46a1a09bb250776a050aec8f9fc880bebc17') - version('6.5.0', '7ef1796ce497e89479183702635b14bb7a46b53249209a5e0f999bebf4740945') - version('6.4.0', '11ba51a0cfb8471927f387c8895fe232') - version('6.3.0', '677a7623c7ef6ab99881bc4e048debb6') - version('6.2.0', '9768625159663b300ae4de2f4745fcc4') - version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1') + version('6.5.0', sha256='7ef1796ce497e89479183702635b14bb7a46b53249209a5e0f999bebf4740945') + version('6.4.0', sha256='850bf21eafdfe5cd5f6827148184c08c4a0852a37ccf36ce69855334d2c914d4') + version('6.3.0', sha256='f06ae7f3f790fbf0f018f6d40e844451e6bc3b7bc96e128e63b09825c1f8b29f') + version('6.2.0', sha256='9944589fc722d3e66308c0ce5257788ebd7872982a718aa2516123940671b7c5') + version('6.1.0', sha256='09c4c85cabebb971b1de732a0219609f93fc0af5f86f6e437fd8d7f832f1a351') - version('5.5.0', '0f70424213b4a1113c04ba66ddda0c1f') - version('5.4.0', '4c626ac2a83ef30dfb9260e6f59c2b30') - version('5.3.0', 'c9616fd448f980259c31de613e575719') - version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467') - version('5.1.0', 'd5525b1127d07d215960e6051c5da35e') + version('5.5.0', sha256='530cea139d82fe542b358961130c69cfde8b3d14556370b65823d2f91f0ced87') + version('5.4.0', sha256='608df76dec2d34de6558249d8af4cbee21eceddbcb580d666f7a5a583ca3303a') + version('5.3.0', sha256='b84f5592e9218b73dbae612b5253035a7b34a9a1f7688d2e1bfaaf7267d5c4db') + version('5.2.0', sha256='5f835b04b5f7dd4f4d2dc96190ec1621b8d89f2dc6f638f9f8bc1b1014ba8cad') + version('5.1.0', sha256='b7dafdf89cbb0e20333dbf5b5349319ae06e3d1a30bf3515b5488f7e89dca5ad') - version('4.9.4', '87c24a4090c1577ba817ec6882602491') - version('4.9.3', '6f831b4d251872736e8e9cc09746f327') - version('4.9.2', '4df8ee253b7f3863ad0b86359cd39c43') - version('4.9.1', 'fddf71348546af523353bd43d34919c1') - version('4.8.5', '80d2c2982a3392bb0b89673ff136e223') - version('4.8.4', '5a84a30839b2aca22a2d723de2a626ec') - version('4.7.4', '4c696da46297de6ae77a82797d2abe28') - version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4') - version('4.5.4', '27e459c2566b8209ab064570e1b378f7') + version('4.9.4', sha256='6c11d292cd01b294f9f84c9a59c230d80e9e4a47e5c6355f046bb36d4f358092') + version('4.9.3', sha256='2332b2a5a321b57508b9031354a8503af6fdfb868b8c1748d33028d100a8b67e') + version('4.9.2', sha256='2020c98295856aa13fda0f2f3a4794490757fc24bcca918d52cc8b4917b972dd') + version('4.9.1', sha256='d334781a124ada6f38e63b545e2a3b8c2183049515a1abab6d513f109f1d717e') + version('4.8.5', sha256='22fb1e7e0f68a63cee631d85b20461d1ea6bda162f03096350e38c8d427ecf23') + version('4.8.4', sha256='4a80aa23798b8e9b5793494b8c976b39b8d9aa2e53cd5ed5534aff662a7f8695') + version('4.7.4', sha256='92e61c6dc3a0a449e62d72a38185fda550168a86702dea07125ebd3ec3996282') + version('4.6.4', sha256='35af16afa0b67af9b8eb15cafb76d2bc5f568540552522f5dc2c88dd45d977e8') + version('4.5.4', sha256='eef3f0456db8c3d992cbb51d5d32558190bc14f3bc19383dd93acc27acc6befc') # We specifically do not add 'all' variant here because: # (i) Ada, Go, Jit, and Objective-C++ are not default languages. diff --git a/var/spack/repos/builtin/packages/gccmakedep/package.py b/var/spack/repos/builtin/packages/gccmakedep/package.py index 7d8cc1e49e3..de623d4b387 100644 --- a/var/spack/repos/builtin/packages/gccmakedep/package.py +++ b/var/spack/repos/builtin/packages/gccmakedep/package.py @@ -12,6 +12,6 @@ class Gccmakedep(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/util/gccmakedep/" url = "https://www.x.org/archive/individual/util/gccmakedep-1.0.3.tar.gz" - version('1.0.3', '127ddb6131eb4a56fdf6644a63ade788') + version('1.0.3', sha256='f9e2e7a590e27f84b6708ab7a81e546399b949bf652fb9b95193e0e543e6a548') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/gconf/package.py b/var/spack/repos/builtin/packages/gconf/package.py index 771251fca08..a3ed72b9cb7 100644 --- a/var/spack/repos/builtin/packages/gconf/package.py +++ b/var/spack/repos/builtin/packages/gconf/package.py @@ -12,7 +12,7 @@ class Gconf(AutotoolsPackage): homepage = "https://projects.gnome.org/gconf/" url = "http://ftp.gnome.org/pub/gnome/sources/GConf/3.2/GConf-3.2.6.tar.xz" - version('3.2.6', '2b16996d0e4b112856ee5c59130e822c') + version('3.2.6', sha256='1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c') depends_on('glib@2.14.0:') depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index 60bc3ce0961..1d26562f066 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -17,17 +17,17 @@ class Gdb(AutotoolsPackage): version('8.3', sha256='b2266ec592440d0eec18ee1790f8558b3b8a2845b76cc83a872e39b501ce8a28') version('8.2.1', sha256='0107985f1edb8dddef6cdd68a4f4e419f5fec0f488cc204f0b7d482c0c6c9282') - version('8.2', '0783c6d86775c5aff06cccc8a3d7cad8') - version('8.1', '0c85ecbb43569ec43b1c9230622e84ab') - version('8.0.1', 'bb45869f8126a84ea2ba13a8c0e7c90e') - version('8.0', '9bb49d134916e73b2c01d01bf20363df') - version('7.12.1', '06c8f40521ed65fe36ebc2be29b56942') - version('7.11', 'f585059252836a981ea5db9a5f8ce97f') - version('7.10.1', 'b93a2721393e5fa226375b42d567d90b') - version('7.10', 'fa6827ad0fd2be1daa418abb11a54d86') - version('7.9.1', 'f3b97de919a9dba84490b2e076ec4cb0') - version('7.9', '8f8ced422fe462a00e0135a643544f17') - version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc') + version('8.2', sha256='847e4b65e5a7b872e86019dd59659029e2b06cae962e0ef345f169dcb4b851b8') + version('8.1', sha256='e54a2322da050e4b00785370a282b9b8f0b25861ec7cfbbce0115e253eea910e') + version('8.0.1', sha256='52017d33cab5b6a92455a1a904046d075357abf24153470178c0aadca2d479c5') + version('8.0', sha256='8968a19e14e176ee026f0ca777657c43456514ad41bb2bc7273e8c4219555ac9') + version('7.12.1', sha256='142057eacecfb929d52b561eb47a1103c7d504cec3f659dd8a5ae7bc378f7e77') + version('7.11', sha256='9382f5534aa0754169e1e09b5f1a3b77d1fa8c59c1e57617e06af37cb29c669a') + version('7.10.1', sha256='ff14f8050e6484508c73cbfa63731e57901478490ca1672dc0b5e2b03f6af622') + version('7.10', sha256='50690e6d6b7917a6544190ec9401eaafb555e3cef8981709ea9870296c383ce5') + version('7.9.1', sha256='4994ad986726ac4128a6f1bd8020cd672e9a92aa76b80736563ef992992764ef') + version('7.9', sha256='d282508cb7df0cb8b2cf659032ce1bede7b5725796e3ac90f3cd9d65844a65f2') + version('7.8.2', sha256='fd9a9784ca24528aac8a4e6b8d7ae7e8cf0784e128cd67a185c986deaf6b9929') variant('python', default=True, description='Compile with Python support') variant('xz', default=True, description='Compile with lzma support') diff --git a/var/spack/repos/builtin/packages/gdbm/package.py b/var/spack/repos/builtin/packages/gdbm/package.py index 9d19b2bced8..478772d87c7 100644 --- a/var/spack/repos/builtin/packages/gdbm/package.py +++ b/var/spack/repos/builtin/packages/gdbm/package.py @@ -17,14 +17,14 @@ class Gdbm(AutotoolsPackage): # URL must remain http:// so Spack can bootstrap curl url = "http://ftpmirror.gnu.org/gdbm/gdbm-1.13.tar.gz" - version('1.18.1', '86e613527e5dba544e73208f42b78b7c022d4fa5a6d5498bf18c8d6f745b91dc') - version('1.14.1', 'c2ddcb3897efa0f57484af2bd4f4f848') - version('1.13', '8929dcda2a8de3fd2367bdbf66769376') - version('1.12', '9ce96ff4c99e74295ea19040931c8fb9') - version('1.11', '72c832680cf0999caedbe5b265c8c1bd') - version('1.10', '88770493c2559dc80b561293e39d3570') - version('1.9.1', '59f6e4c4193cb875964ffbe8aa384b58') - version('1.9', '1f0e8e6691edd61bdd6b697b8c02528d') + version('1.18.1', sha256='86e613527e5dba544e73208f42b78b7c022d4fa5a6d5498bf18c8d6f745b91dc') + version('1.14.1', sha256='cdceff00ffe014495bed3aed71c7910aa88bf29379f795abc0f46d4ee5f8bc5f') + version('1.13', sha256='9d252cbd7d793f7b12bcceaddda98d257c14f4d1890d851c386c37207000a253') + version('1.12', sha256='d97b2166ee867fd6ca5c022efee80702d6f30dd66af0e03ed092285c3af9bcea') + version('1.11', sha256='8d912f44f05d0b15a4a5d96a76f852e905d051bb88022fcdfd98b43be093e3c3') + version('1.10', sha256='23f8134c5b94bbfb06d756a6b78f074fba6e6028cf2fe01341d40b26db773441') + version('1.9.1', sha256='6025852637772b0699f2294b5f14fd4a084bca3c8161d29d64d1f30d6d1a9aed') + version('1.9', sha256='f85324d7de3777db167581fd5d3493d2daa3e85e195a8ae9afc05b34551b6e57') depends_on("readline") diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py index 78d455242e4..5981d6381ec 100644 --- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py +++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py @@ -19,7 +19,7 @@ class GdkPixbuf(Package): list_depth = 1 version('2.38.0', sha256='dd50973c7757bcde15de6bcd3a6d462a445efd552604ae6435a0532fbbadae47') - version('2.31.2', '6be6bbc4f356d4b79ab4226860ab8523') + version('2.31.2', sha256='9e467ed09894c802499fb2399cd9a89ed21c81700ce8f27f970a833efb1e47aa') depends_on('meson@0.46.0:', type='build', when='@2.37.92:') depends_on('meson@0.45.0:', type='build', when='@2.37.0:') diff --git a/var/spack/repos/builtin/packages/gdl/package.py b/var/spack/repos/builtin/packages/gdl/package.py index a7b1ce5e65f..eef7ada1c01 100644 --- a/var/spack/repos/builtin/packages/gdl/package.py +++ b/var/spack/repos/builtin/packages/gdl/package.py @@ -17,7 +17,7 @@ class Gdl(CMakePackage): url = "https://github.com/gnudatalanguage/gdl/archive/v0.9.9.tar.gz" version('0.9.9', sha256='ad5de3fec095a5c58b46338dcc7367d2565c093794ab1bbcf180bba1a712cf14') - version('0.9.8', '447b0362e1df5ea8af814a969e89d3ec') + version('0.9.8', sha256='0e22df7314feaf18a76ae39ee57eea2ac8c3633bc095acbc25e1e07277d7c98b') variant('graphicsmagick', default=False, diff --git a/var/spack/repos/builtin/packages/geant4-data/package.py b/var/spack/repos/builtin/packages/geant4-data/package.py index d93b1114340..cd11e18e599 100644 --- a/var/spack/repos/builtin/packages/geant4-data/package.py +++ b/var/spack/repos/builtin/packages/geant4-data/package.py @@ -14,8 +14,8 @@ class Geant4Data(Package): homepage = "http://geant4.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.3.html" - version('10.03.p03', '2248ad436613897d9fad93bdb99d9446', expand=False) - version('10.04', 'c49194b96e65ed4527d34d22a9860972', expand=False) + version('10.03.p03', sha256='3e0d4d4e6854c8667d930fd5beaec09b7e6ec41f4847935e5d6a2720d0094b30', expand=False) + version('10.04', sha256='f67fb899b99348a1a7e471a05f249f972e7e303c78238fc5f693b99968642255', expand=False) # geant4@10.03.p03 depends_on("g4abla@3.0", when='@10.03.p03 ') diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py index f2934817df8..d0a4c111e76 100644 --- a/var/spack/repos/builtin/packages/geant4/package.py +++ b/var/spack/repos/builtin/packages/geant4/package.py @@ -17,8 +17,8 @@ class Geant4(CMakePackage): homepage = "http://geant4.cern.ch/" url = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz" - version('10.04', 'b84beeb756821d0c61f7c6c93a2b83de') - version('10.03.p03', 'ccae9fd18e3908be78784dc207f2d73b') + version('10.04', sha256='f6d883132f110eb036c69da2b21df51f13c585dc7b99d4211ddd32f4ccee1670') + version('10.03.p03', sha256='a164f49c038859ab675eec474d08c9d02be8c4be9c0c2d3aa8e69adf89e1e138') variant('qt', default=False, description='Enable Qt support') variant('vecgeom', default=False, description='Enable vecgeom support') diff --git a/var/spack/repos/builtin/packages/gearshifft/package.py b/var/spack/repos/builtin/packages/gearshifft/package.py index 961b79c3424..d889b053843 100644 --- a/var/spack/repos/builtin/packages/gearshifft/package.py +++ b/var/spack/repos/builtin/packages/gearshifft/package.py @@ -14,7 +14,7 @@ class Gearshifft(CMakePackage): maintainers = ['ax3l'] - version('0.2.1-lw', 'c3208b767b24255b488a83e5d9e517ea') + version('0.2.1-lw', sha256='04ba7401615ab29a37089c0dce8580270c0c4aa1ba328c9d438d6e4f163899c5') variant('cufft', default=True, description='Compile gearshifft_cufft') diff --git a/var/spack/repos/builtin/packages/genomefinisher/package.py b/var/spack/repos/builtin/packages/genomefinisher/package.py index a9b38a67b63..ed8f28650f7 100644 --- a/var/spack/repos/builtin/packages/genomefinisher/package.py +++ b/var/spack/repos/builtin/packages/genomefinisher/package.py @@ -16,7 +16,7 @@ class Genomefinisher(Package): homepage = "http://gfinisher.sourceforge.net" url = "https://sourceforge.net/projects/gfinisher/files/GenomeFinisher_1.4.zip" - version('1.4', 'bd9bbca656fe15ecbe615c4732714bc7') + version('1.4', sha256='8efbebaab4b577c72193f14c2c362b96fb949981fd66d2cca1364839af8bf1e3') depends_on('java@8:', type='run') diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py index 92afca50fd1..e76b0df92c4 100644 --- a/var/spack/repos/builtin/packages/genometools/package.py +++ b/var/spack/repos/builtin/packages/genometools/package.py @@ -13,7 +13,7 @@ class Genometools(MakefilePackage): homepage = "http://genometools.org/" url = "http://genometools.org/pub/genometools-1.5.9.tar.gz" - version('1.5.9', 'e400d69092f9f13db09b33f9dea39d2e') + version('1.5.9', sha256='36923198a4214422886fd1425ef986bd7e558c73b94194982431cfd3dc7eb387') depends_on('perl', type=('build', 'run')) depends_on('cairo') diff --git a/var/spack/repos/builtin/packages/geopm/package.py b/var/spack/repos/builtin/packages/geopm/package.py index 767a73a4ce5..154d9e4ceb8 100644 --- a/var/spack/repos/builtin/packages/geopm/package.py +++ b/var/spack/repos/builtin/packages/geopm/package.py @@ -31,9 +31,9 @@ class Geopm(AutotoolsPackage): version('0.6.1', sha256='0ca42853f90885bf213df190c3462b8675c143cc843aee0d8b8a0e30802b55a9') version('0.6.0', sha256='95ccf256c2b7cb35838978152479569d154347c3065af1639ed17be1399182d3') version('0.5.1', sha256='db247af55f7000b6e4628af099956349b68a637500b9d4fe8d8fb13687124d53') - version('0.5.0', '61b454bc74d4606fe84818aef16c1be4') - version('0.4.0', 'd4cc8fffe521296dab379857d7e2064d') - version('0.3.0', '568fd37234396fff134f8d57b60f2b83') + version('0.5.0', sha256='cdc123ea68b6d918dcc578a39a7a38275a5d711104364eb889abed15029f4060') + version('0.4.0', sha256='7d165f5a5fe0f19ca586bd81a4631202effb542e9d762cc9cc86ad6ef7afcad9') + version('0.3.0', sha256='73b45d36e7d2431d308038fc8c50a521a1d214c5ce105a17fba440f28509d907') # Variants reflecting most ./configure --help options variant('debug', default=False, description='Enable debug.') diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py index d369bccfc4b..7d241198d2d 100644 --- a/var/spack/repos/builtin/packages/geos/package.py +++ b/var/spack/repos/builtin/packages/geos/package.py @@ -19,22 +19,22 @@ class Geos(AutotoolsPackage): maintainers = ['adamjstewart'] version('3.7.2', sha256='2166e65be6d612317115bfec07827c11b403c3f303e0a7420a2106bc999d7707') - version('3.6.2', 'a32142343c93d3bf151f73db3baa651f') - version('3.6.1', 'c97e338b3bc81f9848656e9d693ca6cc') - version('3.6.0', '55de5fdf075c608d2d7b9348179ee649') - version('3.5.1', '2e3e1ccbd42fee9ec427106b65e43dc0') - version('3.5.0', '136842690be7f504fba46b3c539438dd') - version('3.4.3', '77f2c2cca1e9f49bc1bece9037ac7a7a') - version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae') - version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e') - version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488') - version('3.3.9', '4794c20f07721d5011c93efc6ccb8e4e') - version('3.3.8', '75be476d0831a2d14958fed76ca266de') - version('3.3.7', '95ab996d22672b067d92c7dee2170460') - version('3.3.6', '6fadfb941541875f4976f75fb0bbc800') - version('3.3.5', '2ba61afb7fe2c5ddf642d82d7b16e75b') - version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1') - version('3.3.3', '8454e653d7ecca475153cc88fd1daa26') + version('3.6.2', sha256='045a13df84d605a866602f6020fc6cbf8bf4c42fb50de237a08926e1d7d7652a') + version('3.6.1', sha256='4a2e4e3a7a09a7cfda3211d0f4a235d9fd3176ddf64bd8db14b4ead266189fc5') + version('3.6.0', sha256='1fe7644f3240c8422b0143830ff142e44e8b01333c12f67681ccaab92142f2ea') + version('3.5.1', sha256='e6bb0a7ba0e142b1e952fae9d946b2b532fa05a5c384e458f7cb8990e1fcac32') + version('3.5.0', sha256='49982b23bcfa64a53333dab136b82e25354edeb806e5a2e2f5b8aa98b1d0ae02') + version('3.4.3', sha256='cfbf68079117c1c2b76411636444ff41d73c31093c4cab9dcc9a8c1bbe7e3897') + version('3.4.2', sha256='15e8bfdf7e29087a957b56ac543ea9a80321481cef4d4f63a7b268953ad26c53') + version('3.4.1', sha256='d07ac375f3edd12425d6ce5a96db9739d5ff358cbdf60c6804f7a9e565af8ff2') + version('3.4.0', sha256='3b2106d9baeede39d70e22672598d40cb63ee901f54436c774b250726d7bbdd5') + version('3.3.9', sha256='3e2156165d593f3e85df9ac223170b2c11de3cb4697e4c7a761c3ffbf04fe0ee') + version('3.3.8', sha256='ebecd4d1a71bcc28e5e883296cd8c52a80d5596335e74728f320989734fa503b') + version('3.3.7', sha256='fd01c21b54a3c48cac3e7885f26d4ca10ea9944238776b8ce03489e5e45c592b') + version('3.3.6', sha256='7ee6c1da9a1b87a3e29209e7cddbf19d36f9689d8e44fec2c9bcf6a1b1be3898') + version('3.3.5', sha256='3b513fbe2d155364d61e76d9c250d6d8e75b5166783a233596c744373cb5874f') + version('3.3.4', sha256='cd5400aa5f3fe32246dfed5d238c5017e1808162c865c016480b3e6c07271904') + version('3.3.3', sha256='dfcf4bd70ab212a5b7bad21d01b84748f101a545092b56dafdc3882ef3bddec9') # Ruby bindings are fully supported variant('ruby', default=False, description='Enable Ruby support') diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py index 2d42fe25295..070ad067811 100644 --- a/var/spack/repos/builtin/packages/gettext/package.py +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -13,8 +13,8 @@ class Gettext(AutotoolsPackage): url = "https://ftpmirror.gnu.org/gettext/gettext-0.20.1.tar.xz" version('0.20.1', sha256='53f02fbbec9e798b0faaf7c73272f83608e835c6288dd58be6c9bb54624a3800') - version('0.19.8.1', 'df3f5690eaa30fd228537b00cb7b7590') - version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + version('0.19.8.1', sha256='105556dbc5c3fbbc2aa0edb46d22d055748b6f5c7cd7a8d99f8e7eb84e938be4') + version('0.19.7', sha256='378fa86a091cec3acdece3c961bb8d8c0689906287809a8daa79dc0c6398d934') # Recommended variants variant('curses', default=True, description='Use libncurses') diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py index add74ff9ee8..8baa8667a0e 100644 --- a/var/spack/repos/builtin/packages/gflags/package.py +++ b/var/spack/repos/builtin/packages/gflags/package.py @@ -16,7 +16,7 @@ class Gflags(CMakePackage): homepage = "https://gflags.github.io/gflags" url = "https://github.com/gflags/gflags/archive/v2.1.2.tar.gz" - version('2.1.2', 'ac432de923f9de1e9780b5254884599f') + version('2.1.2', sha256='d8331bd0f7367c8afd5fcb5f5e85e96868a00fd24b7276fa5fcee1e5575c2662') depends_on('cmake@2.8.12:', type='build') diff --git a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py index 0bebcbd26c7..be37b5347fa 100644 --- a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py +++ b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py @@ -13,7 +13,7 @@ class GhostscriptFonts(Package): homepage = "http://ghostscript.com/" url = "https://www.imagemagick.org/download/delegates/ghostscript-fonts-std-8.11.tar.gz" - version('8.11', '6865682b095f8c4500c54b285ff05ef6') + version('8.11', sha256='0eb6f356119f2e49b2563210852e17f57f9dcc5755f350a69a46a0d641a0c401') def install(self, spec, prefix): fdir = join_path(prefix.share, 'font') diff --git a/var/spack/repos/builtin/packages/ghostscript/package.py b/var/spack/repos/builtin/packages/ghostscript/package.py index df90b8ed91e..3ccf0de51f3 100644 --- a/var/spack/repos/builtin/packages/ghostscript/package.py +++ b/var/spack/repos/builtin/packages/ghostscript/package.py @@ -14,8 +14,8 @@ class Ghostscript(AutotoolsPackage): url = "https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs926/ghostscript-9.26.tar.gz" version('9.26', sha256='831fc019bd477f7cc2d481dc5395ebfa4a593a95eb2fe1eb231a97e450d7540d') - version('9.21', '5f213281761d2750fcf27476c404d17f') - version('9.18', '33a47567d7a591c00a253caddd12a88a') + version('9.21', sha256='02bceadbc4dddeb6f2eec9c8b1623d945d355ca11b8b4df035332b217d58ce85') + version('9.18', sha256='5fc93079749a250be5404c465943850e3ed5ffbc0d5c07e10c7c5ee8afbbdb1b') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py index 945377d15ba..3f31891c70f 100644 --- a/var/spack/repos/builtin/packages/giflib/package.py +++ b/var/spack/repos/builtin/packages/giflib/package.py @@ -13,7 +13,7 @@ class Giflib(AutotoolsPackage): homepage = "http://giflib.sourceforge.net/" url = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2" - version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b') + version('5.1.4', sha256='df27ec3ff24671f80b29e6ab1c4971059c14ac3db95406884fc26574631ba8d5') patch('bsd-head.patch') diff --git a/var/spack/repos/builtin/packages/git-imerge/package.py b/var/spack/repos/builtin/packages/git-imerge/package.py index 68954afad89..67ef3ea6144 100644 --- a/var/spack/repos/builtin/packages/git-imerge/package.py +++ b/var/spack/repos/builtin/packages/git-imerge/package.py @@ -27,8 +27,8 @@ class GitImerge(MakefilePackage): homepage = "https://github.com/mhagger/git-imerge" url = "https://github.com/mhagger/git-imerge/archive/v1.1.0.tar.gz" - version('1.1.0', '94a44dcbe5e764d75770a24517572a76') - version('1.0.0', 'e5e69a22610828cc33bf2cbd31685438') + version('1.1.0', sha256='62692f43591cc7d861689c60b68c55d7b10c7a201c1026096a7efc771df2ca28') + version('1.0.0', sha256='2ef3a49a6d54c4248ef2541efc3c860824fc8295a7226760f24f0bb2c5dd41f2') depends_on('python@2.6:') depends_on('py-argparse', when='^python@2.6') diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py index 823c34c7a4b..6a9f5b7b2ee 100644 --- a/var/spack/repos/builtin/packages/gl2ps/package.py +++ b/var/spack/repos/builtin/packages/gl2ps/package.py @@ -13,7 +13,7 @@ class Gl2ps(CMakePackage): homepage = "http://www.geuz.org/gl2ps/" url = "http://geuz.org/gl2ps/src/gl2ps-1.3.9.tgz" - version('1.3.9', '377b2bcad62d528e7096e76358f41140') + version('1.3.9', sha256='8a680bff120df8bcd78afac276cdc38041fed617f2721bade01213362bcc3640') variant('png', default=True, description='Enable PNG support') variant('zlib', default=True, description='Enable compression using ZLIB') diff --git a/var/spack/repos/builtin/packages/glew/package.py b/var/spack/repos/builtin/packages/glew/package.py index e8c0a1db1d5..d2fe265380e 100644 --- a/var/spack/repos/builtin/packages/glew/package.py +++ b/var/spack/repos/builtin/packages/glew/package.py @@ -12,7 +12,7 @@ class Glew(Package): homepage = "http://glew.sourceforge.net/" url = "https://sourceforge.net/projects/glew/files/glew/2.0.0/glew-2.0.0.tgz/download" - version('2.0.0', '2a2cd7c98f13854d2fcddae0d2b20411') + version('2.0.0', sha256='c572c30a4e64689c342ba1624130ac98936d7af90c3103f9ce12b8a0c5736764') depends_on("cmake", type='build') depends_on("gl") diff --git a/var/spack/repos/builtin/packages/glfmultiples/package.py b/var/spack/repos/builtin/packages/glfmultiples/package.py index 1b4ec6259af..74162517e60 100644 --- a/var/spack/repos/builtin/packages/glfmultiples/package.py +++ b/var/spack/repos/builtin/packages/glfmultiples/package.py @@ -15,7 +15,7 @@ class Glfmultiples(MakefilePackage): homepage = "https://genome.sph.umich.edu/wiki/GlfMultiples" url = "http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz" - version('2010-06-16', '64bf6bb7c76543f4c8fabce015a3cb11') + version('2010-06-16', sha256='f7abef6f6b043e9052fb408bb2aae6d0d97d907aedc1b3e02dd0db08eb81b979') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index 0414c0619f7..f6265771d7c 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -21,16 +21,16 @@ class Glib(AutotoolsPackage): homepage = "https://developer.gnome.org/glib/" url = "https://ftp.gnome.org/pub/gnome/sources/glib/2.53/glib-2.53.1.tar.xz" - version('2.56.3', 'a9a4c5b4c81b6c75bc140bdf5e32120ef3ce841b7413214ecf5f987acec74cb2') - version('2.56.2', 'd64abd16813501c956c4e123ae79f47f1b58de573df9fdd3b0795f1e2c1aa789') - version('2.56.1', '40ef3f44f2c651c7a31aedee44259809b6f03d3d20be44545cd7d177221c0b8d') - version('2.56.0', 'f2b59392f2fb514bbe7791dda0c36da5') - version('2.55.1', '9cbb6b3c7e75ba75575588497c7707b6') - version('2.53.1', '3362ef4da713f834ea26904caf3a75f5') - version('2.49.7', '397ead3fcf325cb921d54e2c9e7dfd7a') - version('2.49.4', 'e2c87c03017b0cd02c4c73274b92b148') - version('2.48.1', '67bd3b75c9f6d5587b457dc01cdcd5bb') - version('2.42.1', '89c4119e50e767d3532158605ee9121a') + version('2.56.3', sha256='a9a4c5b4c81b6c75bc140bdf5e32120ef3ce841b7413214ecf5f987acec74cb2') + version('2.56.2', sha256='d64abd16813501c956c4e123ae79f47f1b58de573df9fdd3b0795f1e2c1aa789') + version('2.56.1', sha256='40ef3f44f2c651c7a31aedee44259809b6f03d3d20be44545cd7d177221c0b8d') + version('2.56.0', sha256='ecef6e17e97b8d9150d0e8a4b3edee1ac37331213b8a2a87a083deea408a0fc7') + version('2.55.1', sha256='0cbb3d31c9d181bbcc97cba3d9dbe3250f75e2da25e5f7c8bf5a993fe54baf6a') + version('2.53.1', sha256='c8740f1d1a138086eede889b596a511fddda180646ab2f1d98aed4fdb6be7f72') + version('2.49.7', sha256='0fd13406ca31d6f654c3be620e0adaaa4f9fb788e164e265e33edf4b21e64ef6') + version('2.49.4', sha256='9e914f9d7ebb88f99f234a7633368a7c1133ea21b5cac9db2a33bc25f7a0e0d1') + version('2.48.1', sha256='74411bff489cb2a3527bac743a51018841a56a4d896cc1e0d0d54f8166a14612') + version('2.42.1', sha256='8f3f0865280e45b8ce840e176ef83bcfd511148918cc8d39df2ee89b67dcf89a') variant('libmount', default=False, description='Build with libmount support') variant( diff --git a/var/spack/repos/builtin/packages/glibmm/package.py b/var/spack/repos/builtin/packages/glibmm/package.py index b6ba636faa6..5e43576f6ff 100644 --- a/var/spack/repos/builtin/packages/glibmm/package.py +++ b/var/spack/repos/builtin/packages/glibmm/package.py @@ -12,9 +12,9 @@ class Glibmm(AutotoolsPackage): homepage = "https://developer.gnome.org/glib/" url = "https://ftp.gnome.org/pub/GNOME/sources/glibmm/2.19/glibmm-2.19.3.tar.gz" - version('2.19.3', 'b50180bb93f501172a2ac4c54e83e88a') - version('2.16.0', '24390d2da1734205f1e572f24d4942f0') - version('2.4.8', 'fa8b2889cd845752446c6ce15a94bb32') + version('2.19.3', sha256='23958368535c19188b1241c4615dcf1f35e80e0922a04236bb9247dcd8fe0a2b') + version('2.16.0', sha256='99795b9c6e58e490df740a113408092bf47a928427cbf178d77c35adcb6a57a3') + version('2.4.8', sha256='78b97bfa1d001cc7b398f76bf09005ba55b45ae20780b297947a1a71c4f07e1f') depends_on('libsigcpp') depends_on('glib') diff --git a/var/spack/repos/builtin/packages/glimmer/package.py b/var/spack/repos/builtin/packages/glimmer/package.py index 3b046271565..f6543f12369 100644 --- a/var/spack/repos/builtin/packages/glimmer/package.py +++ b/var/spack/repos/builtin/packages/glimmer/package.py @@ -12,7 +12,7 @@ class Glimmer(MakefilePackage): homepage = "https://ccb.jhu.edu/software/glimmer" - version('3.02b', '344d012ae12596de905866fe9eb7f16c') + version('3.02b', sha256='ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6') build_directory = 'src' diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py index 5d2baa92985..4e9f8194e80 100644 --- a/var/spack/repos/builtin/packages/glm/package.py +++ b/var/spack/repos/builtin/packages/glm/package.py @@ -14,6 +14,6 @@ class Glm(CMakePackage): homepage = "https://github.com/g-truc/glm" url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz" - version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8') + version('0.9.7.1', sha256='285a0dc8f762b4e523c8710fbd97accaace0c61f45bc8be2bdb0deed07b0e6f3') depends_on('cmake@2.6:', type='build') diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py index ae3a247e608..3d8231491ff 100644 --- a/var/spack/repos/builtin/packages/global/package.py +++ b/var/spack/repos/builtin/packages/global/package.py @@ -13,7 +13,7 @@ class Global(Package): homepage = "http://www.gnu.org/software/global" url = "http://tamacom.com/global/global-6.5.tar.gz" - version('6.5', 'dfec818b4f53d91721e247cf7b218078') + version('6.5', sha256='4afd12db1aa600277b39113cc2d61dc59bd6c6b4ee8033da8bb6dd0c39a4c6a9') depends_on('exuberant-ctags', type=('build', 'run')) depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/globalarrays/package.py b/var/spack/repos/builtin/packages/globalarrays/package.py index d088140edbe..a42d95f0c9a 100644 --- a/var/spack/repos/builtin/packages/globalarrays/package.py +++ b/var/spack/repos/builtin/packages/globalarrays/package.py @@ -16,13 +16,13 @@ class Globalarrays(AutotoolsPackage): homepage = "http://hpc.pnl.gov/globalarrays/" url = "https://github.com/GlobalArrays/ga/releases/download/v5.7/ga-5.7.tar.gz" - version('5.7', 'bb9a441a6b4fbb8b52b58c2d3f4cd07f') - version('5.6.5', '90da628dc72048deeda3f0cd095cb5b3') - version('5.6.4', '051901b316c9766b8ba54306bff7f6b3') - version('5.6.3', 'df3cf6cc8288d9f202b7fd0ea82f5491') - version('5.6.2', '901e4612203bac45059be524fc1abfb7') - version('5.6.1', '674c0ea9bf413840b1ff1e669de73fca') - version('5.6', '49d7e997daed094eeb9565423879ba36') + version('5.7', sha256='3ed1ab47adfda7bceb7beca12fc05a2e1631732f0e55bbaf9036dad4e3da4774') + version('5.6.5', sha256='17a7111dfe67d44cf0888c7b79abd48bf4968874f26b3f16cce9fd04e2c72bb9') + version('5.6.4', sha256='3daf742053502755c0b581041a56f8f7086af05980c7146d194b0fd6526ee14f') + version('5.6.3', sha256='e8818825d4f72c8433f416a9ae2bba203a521e9bc73d80f96c2250deaef4bc40') + version('5.6.2', sha256='3eb1c92d41235f3386e0215f04aaab1aae30a2bce191f9fb6436b2cd8b9544ba') + version('5.6.1', sha256='b324deed49f930f55203e1d18294ce07dd02680b9ac0728ebc54f94a12557ebc') + version('5.6', sha256='a228dfbae9a6cfaae34694d7e56f589ac758e959b58f4bc49e6ef44058096767') variant('int64', default=False, description='Compile with 64 bit indices support') variant('blas', default=False, description='Enable BLAS') diff --git a/var/spack/repos/builtin/packages/glog/package.py b/var/spack/repos/builtin/packages/glog/package.py index 98c5224d539..362e6c9a022 100644 --- a/var/spack/repos/builtin/packages/glog/package.py +++ b/var/spack/repos/builtin/packages/glog/package.py @@ -12,9 +12,9 @@ class Glog(Package): homepage = "https://github.com/google/glog" url = "https://github.com/google/glog/archive/v0.3.5.tar.gz" - version('0.3.5', '5df6d78b81e51b90ac0ecd7ed932b0d4') - version('0.3.4', 'df92e05c9d02504fb96674bc776a41cb') - version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0') + version('0.3.5', sha256='7580e408a2c0b5a89ca214739978ce6ff480b5e7d8d7698a2aa92fadc484d1e0') + version('0.3.4', sha256='ce99d58dce74458f7656a68935d7a0c048fa7b4626566a71b7f4e545920ceb10') + version('0.3.3', sha256='544e178644bd9b454768c2c91716c3b8365cc5d47adfbdbaecd8cf3fa17adfcb') depends_on('gflags') depends_on('cmake', when="@0.3.5:") diff --git a/var/spack/repos/builtin/packages/glpk/package.py b/var/spack/repos/builtin/packages/glpk/package.py index 17b707d57a8..05ed3fdc7eb 100644 --- a/var/spack/repos/builtin/packages/glpk/package.py +++ b/var/spack/repos/builtin/packages/glpk/package.py @@ -16,9 +16,9 @@ class Glpk(AutotoolsPackage): homepage = "https://www.gnu.org/software/glpk" url = "https://ftpmirror.gnu.org/glpk/glpk-4.65.tar.gz" - version('4.65', '470a984a8b1c0e027bdb6d5859063fe8') - version('4.61', '3ce3e224a8b6e75a1a0b378445830f21') - version('4.57', '237531a54f73155842f8defe51aedb0f') + version('4.65', sha256='4281e29b628864dfe48d393a7bedd781e5b475387c20d8b0158f329994721a10') + version('4.61', sha256='9866de41777782d4ce21da11b88573b66bb7858574f89c28be6967ac22dfaba9') + version('4.57', sha256='7323b2a7cc1f13e45fc845f0fdca74f4daea2af716f5ad2d4d55b41e8394275c') variant( 'gmp', default=False, description='Activates support for GMP library' diff --git a/var/spack/repos/builtin/packages/glproto/package.py b/var/spack/repos/builtin/packages/glproto/package.py index 6dda3c89548..9ef44273030 100644 --- a/var/spack/repos/builtin/packages/glproto/package.py +++ b/var/spack/repos/builtin/packages/glproto/package.py @@ -15,7 +15,7 @@ class Glproto(AutotoolsPackage): homepage = "https://www.x.org/wiki/" url = "https://www.x.org/archive/individual/proto/glproto-1.4.17.tar.gz" - version('1.4.17', 'd69554c1b51a83f2c6976a640819911b') + version('1.4.17', sha256='9d8130fec2b98bd032db7730fa092dd9dec39f3de34f4bb03ceb43b9903dbc96') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/glvis/package.py b/var/spack/repos/builtin/packages/glvis/package.py index b8d78a56ac4..e893c127300 100644 --- a/var/spack/repos/builtin/packages/glvis/package.py +++ b/var/spack/repos/builtin/packages/glvis/package.py @@ -36,22 +36,22 @@ class Glvis(MakefilePackage): version('develop', branch='master') version('3.4', - '289fbd2e09d4456e5fee6162bdc3e0b4c8c8d54625f3547ad2a69fef319279e7', + sha256='289fbd2e09d4456e5fee6162bdc3e0b4c8c8d54625f3547ad2a69fef319279e7', url='https://bit.ly/glvis-3-4', extension='.tar.gz') version('3.3', - 'e24d7c5cb53f208b691c872fe82ea898242cfdc0fd68dd0579c739e070dcd800', + sha256='e24d7c5cb53f208b691c872fe82ea898242cfdc0fd68dd0579c739e070dcd800', url='http://goo.gl/C0Oadw', extension='.tar.gz') version('3.2', - 'c82cb110396e63b6436a770c55eb6d578441eaeaf3f9cc20436c242392e44e80', + sha256='c82cb110396e63b6436a770c55eb6d578441eaeaf3f9cc20436c242392e44e80', url='http://goo.gl/hzupg1', extension='.tar.gz') version('3.1', - '793e984ddfbf825dcd13dfe1ca00eccd686cd40ad30c8789ba80ee175a1b488c', + sha256='793e984ddfbf825dcd13dfe1ca00eccd686cd40ad30c8789ba80ee175a1b488c', url='http://goo.gl/gQZuu9', extension='tar.gz') diff --git a/var/spack/repos/builtin/packages/gmake/package.py b/var/spack/repos/builtin/packages/gmake/package.py index f8efd690bae..baa4aa50808 100644 --- a/var/spack/repos/builtin/packages/gmake/package.py +++ b/var/spack/repos/builtin/packages/gmake/package.py @@ -13,8 +13,8 @@ class Gmake(AutotoolsPackage): homepage = "https://www.gnu.org/software/make/" url = "https://ftpmirror.gnu.org/make/make-4.2.1.tar.gz" - version('4.2.1', '7d0dcb6c474b258aab4d54098f2cf5a7') - version('4.0', 'b5e558f981326d9ca1bfdb841640721a') + version('4.2.1', sha256='e40b8f018c1da64edd1cc9a6fce5fa63b2e707e404e20cad91fbae337c98a5b7') + version('4.0', sha256='fc42139fb0d4b4291929788ebaf77e2a4de7eaca95e31f3634ef7d4932051f69') variant('guile', default=False, description='Support GNU Guile for embedded scripting') variant('nls', default=True, description='Enable Native Language Support') diff --git a/var/spack/repos/builtin/packages/gmap-gsnap/package.py b/var/spack/repos/builtin/packages/gmap-gsnap/package.py index 5411347c574..ba938f09810 100644 --- a/var/spack/repos/builtin/packages/gmap-gsnap/package.py +++ b/var/spack/repos/builtin/packages/gmap-gsnap/package.py @@ -17,10 +17,10 @@ class GmapGsnap(AutotoolsPackage): version('2019-05-12', sha256='3dc1b6ee4f6c049c07bcf4a5aba30eb2d732997241cdcad818dab571719f8008') version('2019-02-15', sha256='7e82b9867a1e561b4816fb2f2fb916294077c384c6a88bb94cce39bfe71ab3ac') version('2018-07-04', sha256='a9f8c1f0810df65b2a089dc10be79611026f4c95e4681dba98fea3d55d598d24') - version('2018-03-25', 'f08e65c1e4d9574a3eb7f15f8ca6af16') - version('2018-02-12', '13152aedeef9ac66be915fc6bf6464f2') - version('2017-06-16', 'fcc91b8bdd4bf12ae3124de0c00db0c0') - version('2014-12-28', '1ab07819c9e5b5b8970716165ccaa7da') + version('2018-03-25', sha256='a65bae6115fc50916ad7425d0b5873b611c002690bf35026bfcfc41ee0c0265a') + version('2018-02-12', sha256='5dedddab7f08f9924a995332ebc7bdbe2621fcd67021690707c876d865091fcc') + version('2017-06-16', sha256='2a277a6d45cade849be3bfb7b0f69f61ab79744af821a88eb1d599b32f358f8d') + version('2014-12-28', sha256='108433f3e3ea89b8117c8bb36d396913225caf1261d46ce6d89709ff1b44025d') depends_on('zlib') depends_on('bzip2') diff --git a/var/spack/repos/builtin/packages/gmime/package.py b/var/spack/repos/builtin/packages/gmime/package.py index 2333de5681e..7b8a66298fe 100644 --- a/var/spack/repos/builtin/packages/gmime/package.py +++ b/var/spack/repos/builtin/packages/gmime/package.py @@ -14,7 +14,7 @@ class Gmime(AutotoolsPackage): homepage = "http://spruce.sourceforge.net/gmime/" url = "https://download.gnome.org/sources/gmime/2.6/gmime-2.6.23.tar.xz" - version('2.6.23', '247072236d84bd0fbbff299d69bdf333') + version('2.6.23', sha256='7149686a71ca42a1390869b6074815106b061aaeaaa8f2ef8c12c191d9a79f6a') depends_on('glib@2.18.0:') depends_on('libgpg-error') diff --git a/var/spack/repos/builtin/packages/gmodel/package.py b/var/spack/repos/builtin/packages/gmodel/package.py index 3f02ca3497c..fecf45a967c 100644 --- a/var/spack/repos/builtin/packages/gmodel/package.py +++ b/var/spack/repos/builtin/packages/gmodel/package.py @@ -17,4 +17,4 @@ class Gmodel(CMakePackage): homepage = "https://github.com/ibaned/gmodel" url = "https://github.com/ibaned/gmodel/archive/v2.1.0.tar.gz" - version('2.1.0', '80df0c6dc413a9ffa0f0e7b65118b05b643ba3e1bfcac28fb91d2d3ad017fda0') + version('2.1.0', sha256='80df0c6dc413a9ffa0f0e7b65118b05b643ba3e1bfcac28fb91d2d3ad017fda0') diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index 7daf4b2f882..b9c034008b5 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -13,14 +13,14 @@ class Gmp(AutotoolsPackage): homepage = "https://gmplib.org" url = "https://ftpmirror.gnu.org/gmp/gmp-6.1.2.tar.bz2" - version('6.1.2', '8ddbb26dc3bd4e2302984debba1406a5') - version('6.1.1', '4c175f86e11eb32d8bf9872ca3a8e11d') - version('6.1.0', '86ee6e54ebfc4a90b643a65e402c4048') - version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470') - version('6.0.0', '6ef5869ae735db9995619135bd856b84') - version('5.1.3', 'a082867cbca5e898371a97bb27b31fea') + version('6.1.2', sha256='5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2') + version('6.1.1', sha256='a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6') + version('6.1.0', sha256='498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8') + version('6.0.0a', sha256='7f8e9a804b9c6d07164cf754207be838ece1219425d64e28cfa3e70d5c759aaf') + version('6.0.0', md5='6ef5869ae735db9995619135bd856b84') + version('5.1.3', sha256='752079520b4690531171d0f4532e40f08600215feefede70b24fabdc6f1ab160') # Old version needed for a binary package in ghc-bootstrap - version('4.3.2', 'dd60683d7057917e34630b4a787932e8') + version('4.3.2', sha256='936162c0312886c21581002b79932829aa048cfaf9937c6265aeaa14f1cd1775') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index f96e724b4f3..05afa72aa11 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -20,12 +20,12 @@ class Gmsh(CMakePackage): url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz' version('4.2.2', sha256='e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc') - version('4.0.0', 'fb0c8afa37425c6f4315ab3b3124e9e102fcf270a35198423a4002796f04155f') - version('3.0.6', '9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b') - version('3.0.1', '830b5400d9f1aeca79c3745c5c9fdaa2900cdb2fa319b664a5d26f7e615c749f') - version('2.16.0', 'e829eaf32ea02350a385202cc749341f2a3217c464719384b18f653edd028eea') - version('2.15.0', '992a4b580454105f719f5bc05441d3d392ab0b4b80d4ea07b61ca3bdc974070a') - version('2.12.0', '7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09') + version('4.0.0', sha256='fb0c8afa37425c6f4315ab3b3124e9e102fcf270a35198423a4002796f04155f') + version('3.0.6', sha256='9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b') + version('3.0.1', sha256='830b5400d9f1aeca79c3745c5c9fdaa2900cdb2fa319b664a5d26f7e615c749f') + version('2.16.0', sha256='e829eaf32ea02350a385202cc749341f2a3217c464719384b18f653edd028eea') + version('2.15.0', sha256='992a4b580454105f719f5bc05441d3d392ab0b4b80d4ea07b61ca3bdc974070a') + version('2.12.0', sha256='7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09') version('develop', branch='master', git='https://gitlab.onelab.info/gmsh/gmsh.git') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/gnat/package.py b/var/spack/repos/builtin/packages/gnat/package.py index 4c37d662091..5fe1b8488fc 100644 --- a/var/spack/repos/builtin/packages/gnat/package.py +++ b/var/spack/repos/builtin/packages/gnat/package.py @@ -23,7 +23,7 @@ class Gnat(MakefilePackage): # dependencies are already in Spack. # This is the GPL release for Linux x86-64 - version('2016', '9741107cca1a6a4ddb0d5e8de824a90c', extension='tar.gz', + version('2016', sha256='d083c01e054d0aeda7c67967306cfa5a8df12268664f9098a2d9b331aa24dfe7', extension='tar.gz', url="http://mirrors.cdn.adacore.com/art/5739cefdc7a447658e0b016b") phases = ['install'] diff --git a/var/spack/repos/builtin/packages/gnupg/package.py b/var/spack/repos/builtin/packages/gnupg/package.py index 90e3481c206..b05f468dee3 100644 --- a/var/spack/repos/builtin/packages/gnupg/package.py +++ b/var/spack/repos/builtin/packages/gnupg/package.py @@ -14,8 +14,8 @@ class Gnupg(AutotoolsPackage): url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.2.3.tar.bz2" version('2.2.15', sha256='cb8ce298d7b36558ffc48aec961b14c830ff1783eef7a623411188b5e0f5d454') - version('2.2.3', '6911c0127e4231ce52d60f26029dba68') - version('2.1.21', '685ebf4c3a7134ba0209c96b18b2f064') + version('2.2.3', sha256='cbd37105d139f7aa74f92b6f65d136658682094b0e308666b820ae4b984084b4') + version('2.1.21', sha256='7aead8a8ba75b69866f583b6c747d91414d523bfdfbe9a8e0fe026b16ba427dd') depends_on('libgcrypt') depends_on('libassuan@2.4:', when='@:2.2.3') diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py index 63578e2f5de..ff2fdd53765 100644 --- a/var/spack/repos/builtin/packages/gnuplot/package.py +++ b/var/spack/repos/builtin/packages/gnuplot/package.py @@ -26,14 +26,14 @@ class Gnuplot(AutotoolsPackage): # dependency of readline. Fix it with a small patch patch('term_include.patch') - version('5.2.7', '97fe503ff3b2e356fe2ae32203fc7fd2cf9cef1f46b60fe46dc501a228b9f4ed') - version('5.2.5', '039db2cce62ddcfd31a6696fe576f4224b3bc3f919e66191dfe2cdb058475caa') - version('5.2.2', '60aedd08998160593199459dea8467fe') - version('5.2.0', '0bd8f9af84c0ad2fa9de16772c366416') - version('5.0.7', '8eaafddb0b12795f82ed6dd2a6ebbe80') - version('5.0.6', '8ec46520a86a61163a701b00404faf1a') - version('5.0.5', 'c5e96fca73afbee4f57cbc1bfce6b3b8') - version('5.0.1', '79b4f9e203728f76b60b28bcd402d3c7') + version('5.2.7', sha256='97fe503ff3b2e356fe2ae32203fc7fd2cf9cef1f46b60fe46dc501a228b9f4ed') + version('5.2.5', sha256='039db2cce62ddcfd31a6696fe576f4224b3bc3f919e66191dfe2cdb058475caa') + version('5.2.2', sha256='a416d22f02bdf3873ef82c5eb7f8e94146795811ef808e12b035ada88ef7b1a1') + version('5.2.0', sha256='7dfe6425a1a6b9349b1fb42dae46b2e52833b13e807a78a613024d6a99541e43') + version('5.0.7', sha256='0ad760ff013b4a9cf29853fa9b50c50030a33cd8fb86220a23abb466655136fc') + version('5.0.6', sha256='5bbe4713e555c2e103b7d4ffd45fca69551fff09cf5c3f9cb17428aaacc9b460') + version('5.0.5', sha256='25f3e0bf192e01115c580f278c3725d7a569eb848786e12b455a3fda70312053') + version('5.0.1', sha256='7cbc557e71df581ea520123fb439dea5f073adcc9010a2885dc80d4ed28b3c47') variant('wx', default=False, description='Activates wxWidgets terminal') diff --git a/var/spack/repos/builtin/packages/gnutls/package.py b/var/spack/repos/builtin/packages/gnutls/package.py index 86830ff3b40..85110651771 100644 --- a/var/spack/repos/builtin/packages/gnutls/package.py +++ b/var/spack/repos/builtin/packages/gnutls/package.py @@ -21,10 +21,10 @@ class Gnutls(AutotoolsPackage): version('3.6.8', sha256='aa81944e5635de981171772857e72be231a7e0f559ae0292d2737de475383e83') version('3.6.7.1', sha256='881b26409ecd8ea4c514fd3fbdb6fae5fab422ca7b71116260e263940a4bbbad') version('3.5.19', sha256='1936eb64f03aaefd6eb16cef0567457777618573826b94d03376bb6a4afadc44') - version('3.5.13', '4fd41ad86572933c2379b4cc321a0959') - version('3.5.10', '336c03a71ba90184ffd0388075dde504') - version('3.5.9', '0ab25eb6a1509345dd085bc21a387951') - version('3.3.9', 'ff61b77e39d09f1140ab5a9cf52c58b6') + version('3.5.13', sha256='79f5480ad198dad5bc78e075f4a40c4a315a1b2072666919d2d05a08aec13096') + version('3.5.10', sha256='af443e86ba538d4d3e37c4732c00101a492fe4b56a55f4112ff0ab39dbe6579d') + version('3.5.9', sha256='82b10f0c4ef18f4e64ad8cef5dbaf14be732f5095a41cf366b4ecb4050382951') + version('3.3.9', sha256='39166de5293a9d30ef1cd0a4d97f01fdeed7d7dbf8db95392e309256edcb13c1') variant('zlib', default=True, description='Enable zlib compression support') variant('guile', default=False, description='Enable Guile bindings') diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py index 4744e12362b..e5bfcef3807 100644 --- a/var/spack/repos/builtin/packages/go-bootstrap/package.py +++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py @@ -24,11 +24,11 @@ class GoBootstrap(Package): # See: https://golang.org/doc/install/source#go14 and # https://github.com/golang/go/issues/17545 and # https://github.com/golang/go/issues/16352 - version('1.4-bootstrap-20171003', 'dbf727a4b0e365bf88d97cbfde590016', + version('1.4-bootstrap-20171003', sha256='f4ff5b5eb3a3cae1c993723f3eab519c5bae18866b5e5f96fe1102f0cb5c3e52', url='https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz') - version('1.4-bootstrap-20170531', 'd2cc61cb9f829b3510ee39c0c5568014', + version('1.4-bootstrap-20170531', sha256='49f806f66762077861b7de7081f586995940772d29d4c45068c134441a743fa2', url='https://storage.googleapis.com/golang/go1.4-bootstrap-20170531.tar.gz') - version('1.4-bootstrap-20161024', '76e42c8152e8560ded880a6d1d1f53cb', + version('1.4-bootstrap-20161024', sha256='398c70d9d10541ba9352974cc585c43220b6d8dbcd804ba2c9bd2fbf35fab286', url='https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz') provides('golang@:1.4-bootstrap-20171003') diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index ec56df2d1ad..1090718ea33 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -45,24 +45,24 @@ class Go(Package): version('1.11.13', sha256='5032095fd3f641cafcce164f551e5ae873785ce7b07ca7c143aecd18f7ba4076') version('1.11.11', sha256='1fff7c33ef2522e6dfaf6ab96ec4c2a8b76d018aae6fc88ce2bd40f2202d0f8c') version('1.11.10', sha256='df27e96a9d1d362c46ecd975f1faa56b8c300f5c529074e9ea79bdd885493c1b') - version('1.11.5', 'bc1ef02bb1668835db1390a2e478dcbccb5dd16911691af9d75184bbe5aa943e') - version('1.11.4', '4cfd42720a6b1e79a8024895fa6607b69972e8e32446df76d6ce79801bbadb15') - version('1.11.2', '042fba357210816160341f1002440550e952eb12678f7c9e7e9d389437942550') - version('1.11.1', '558f8c169ae215e25b81421596e8de7572bd3ba824b79add22fba6e284db1117') - version('1.11', 'afc1e12f5fe49a471e3aae7d906c73e9d5b1fdd36d52d72652dde8f6250152fb') - version('1.10.3', '567b1cc66c9704d1c019c50bef946272e911ec6baf244310f87f4e678be155f2') - version('1.10.2', '6264609c6b9cd8ed8e02ca84605d727ce1898d74efa79841660b2e3e985a98bd') - version('1.10.1', '589449ff6c3ccbff1d391d4e7ab5bb5d5643a5a41a04c99315e55c16bbf73ddc') - version('1.9.5', 'f1c2bb7f32bbd8fa7a19cc1608e0d06582df32ff5f0340967d83fb0017c49fbc') - version('1.9.2', '44105c865a1a810464df79233a05a568') - version('1.9.1', '27bce1ffb05f4f6bd90d90081e5d4169') - version('1.9', 'da2d44ea384076efec43ee1f8b7d45d2') - version('1.8.3', '64e9380e07bba907e26a00cf5fcbe77e') - version('1.8.1', '409dd21e7347dd1ea9efe64a700073cc') - version('1.8', '7743960c968760437b6e39093cfe6f67') - version('1.7.5', '506de2d870409e9003e1440bcfeb3a65') - version('1.7.4', '49c1076428a5d3b5ad7ac65233fcca2f') - version('1.6.4', 'b023240be707b34059d2c114d3465c92') + version('1.11.5', sha256='bc1ef02bb1668835db1390a2e478dcbccb5dd16911691af9d75184bbe5aa943e') + version('1.11.4', sha256='4cfd42720a6b1e79a8024895fa6607b69972e8e32446df76d6ce79801bbadb15') + version('1.11.2', sha256='042fba357210816160341f1002440550e952eb12678f7c9e7e9d389437942550') + version('1.11.1', sha256='558f8c169ae215e25b81421596e8de7572bd3ba824b79add22fba6e284db1117') + version('1.11', sha256='afc1e12f5fe49a471e3aae7d906c73e9d5b1fdd36d52d72652dde8f6250152fb') + version('1.10.3', sha256='567b1cc66c9704d1c019c50bef946272e911ec6baf244310f87f4e678be155f2') + version('1.10.2', sha256='6264609c6b9cd8ed8e02ca84605d727ce1898d74efa79841660b2e3e985a98bd') + version('1.10.1', sha256='589449ff6c3ccbff1d391d4e7ab5bb5d5643a5a41a04c99315e55c16bbf73ddc') + version('1.9.5', sha256='f1c2bb7f32bbd8fa7a19cc1608e0d06582df32ff5f0340967d83fb0017c49fbc') + version('1.9.2', sha256='665f184bf8ac89986cfd5a4460736976f60b57df6b320ad71ad4cef53bb143dc') + version('1.9.1', sha256='a84afc9dc7d64fe0fa84d4d735e2ece23831a22117b50dafc75c1484f1cb550e') + version('1.9', sha256='a4ab229028ed167ba1986825751463605264e44868362ca8e7accc8be057e993') + version('1.8.3', sha256='5f5dea2447e7dcfdc50fa6b94c512e58bfba5673c039259fd843f68829d99fa6') + version('1.8.1', sha256='33daf4c03f86120fdfdc66bddf6bfff4661c7ca11c5da473e537f4d69b470e57') + version('1.8', sha256='406865f587b44be7092f206d73fc1de252600b79b3cacc587b74b5ef5c623596') + version('1.7.5', sha256='4e834513a2079f8cbbd357502cccaac9507fd00a1efe672375798858ff291815') + version('1.7.4', sha256='4c189111e9ba651a2bb3ee868aa881fab36b2f2da3409e80885ca758a6b614cc') + version('1.6.4', sha256='8796cc48217b59595832aa9de6db45f58706dae68c9c7fbbd78c9fdbe3cd9032') provides('golang') diff --git a/var/spack/repos/builtin/packages/gobject-introspection/package.py b/var/spack/repos/builtin/packages/gobject-introspection/package.py index 35d210d7202..20996c981f7 100644 --- a/var/spack/repos/builtin/packages/gobject-introspection/package.py +++ b/var/spack/repos/builtin/packages/gobject-introspection/package.py @@ -15,9 +15,9 @@ class GobjectIntrospection(Package): homepage = "https://wiki.gnome.org/Projects/GObjectIntrospection" url = "http://ftp.gnome.org/pub/gnome/sources/gobject-introspection/1.49/gobject-introspection-1.49.2.tar.xz" - version('1.56.1', '5b2875ccff99ff7baab63a34b67f8c920def240e178ff50add809e267d9ea24b') - version('1.49.2', 'c47a76b05b2d8438089f519922180747') - version('1.48.0', '01301fa9019667d48e927353e08bc218') + version('1.56.1', sha256='5b2875ccff99ff7baab63a34b67f8c920def240e178ff50add809e267d9ea24b') + version('1.49.2', sha256='73d59470ba1a546b293f54d023fd09cca03a951005745d86d586b9e3a8dde9ac') + version('1.48.0', sha256='fa275aaccdbfc91ec0bc9a6fd0562051acdba731e7d584b64a277fec60e75877') depends_on("glib@2.49.2:", when="@1.49.2:") # version 1.48.0 build fails with glib 2.49.4 diff --git a/var/spack/repos/builtin/packages/gource/package.py b/var/spack/repos/builtin/packages/gource/package.py index 3bbcb8b64ef..a47bfc68219 100644 --- a/var/spack/repos/builtin/packages/gource/package.py +++ b/var/spack/repos/builtin/packages/gource/package.py @@ -12,7 +12,7 @@ class Gource(AutotoolsPackage): homepage = "http://gource.io" url = "https://github.com/acaudwell/Gource/releases/download/gource-0.44/gource-0.44.tar.gz" - version('0.44', '79cda1bfaad16027d59cce55455bfab88b57c69d') + version('0.44', sha256='2604ca4442305ffdc5bb1a7bac07e223d59c846f93567be067e8dfe2f42f097c') depends_on('automake', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/gperf/package.py b/var/spack/repos/builtin/packages/gperf/package.py index 6b761475805..1262f8a5c0e 100644 --- a/var/spack/repos/builtin/packages/gperf/package.py +++ b/var/spack/repos/builtin/packages/gperf/package.py @@ -17,6 +17,6 @@ class Gperf(AutotoolsPackage): homepage = "https://www.gnu.org/software/gperf/" url = "https://ftpmirror.gnu.org/gperf/gperf-3.0.4.tar.gz" - version('3.0.4', 'c1f1db32fb6598d6a93e6e88796a8632') + version('3.0.4', sha256='767112a204407e62dbc3106647cf839ed544f3cf5d0f0523aaa2508623aad63e') # NOTE: `make check` is known to fail tests diff --git a/var/spack/repos/builtin/packages/gperftools/package.py b/var/spack/repos/builtin/packages/gperftools/package.py index cbdb8e8dcfe..e2452c871d4 100644 --- a/var/spack/repos/builtin/packages/gperftools/package.py +++ b/var/spack/repos/builtin/packages/gperftools/package.py @@ -15,8 +15,8 @@ class Gperftools(AutotoolsPackage): homepage = "https://github.com/gperftools/gperftools" url = "https://github.com/gperftools/gperftools/releases/download/gperftools-2.7/gperftools-2.7.tar.gz" - version('2.7', '1ee8c8699a0eff6b6a203e59b43330536b22bbcbe6448f54c7091e5efb0763c9') - version('2.4', '982a37226eb42f40714e26b8076815d5ea677a422fb52ff8bfca3704d9c30a2d') - version('2.3', '093452ad45d639093c144b4ec732a3417e8ee1f3744f2b0f8d45c996223385ce') + version('2.7', sha256='1ee8c8699a0eff6b6a203e59b43330536b22bbcbe6448f54c7091e5efb0763c9') + version('2.4', sha256='982a37226eb42f40714e26b8076815d5ea677a422fb52ff8bfca3704d9c30a2d') + version('2.3', sha256='093452ad45d639093c144b4ec732a3417e8ee1f3744f2b0f8d45c996223385ce') depends_on("unwind") diff --git a/var/spack/repos/builtin/packages/gplates/package.py b/var/spack/repos/builtin/packages/gplates/package.py index fbd0a49eff5..7e4022b3a8a 100644 --- a/var/spack/repos/builtin/packages/gplates/package.py +++ b/var/spack/repos/builtin/packages/gplates/package.py @@ -17,8 +17,8 @@ class Gplates(CMakePackage): homepage = 'https://www.gplates.org' url = 'https://sourceforge.net/projects/gplates/files/gplates/2.0/gplates-2.0.0-unixsrc.tar.bz2/download' - version('2.1.0', '5a52242520d7e243c541e164c8417b23f4e17fcd79ed81f865b2c13628bb0e07') - version('2.0.0', '9e95874b35a01f4c9bff5845a1621ad5') + version('2.1.0', sha256='5a52242520d7e243c541e164c8417b23f4e17fcd79ed81f865b2c13628bb0e07') + version('2.0.0', sha256='1c27d3932a851153baee7cec48e57c2bbc87e4eea02f8a986882515ba4b44c0b') depends_on('cmake@2.8.8:', type='build') depends_on('ninja', type='build') diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py index 6c62c5b1bef..c6db417c676 100644 --- a/var/spack/repos/builtin/packages/grackle/package.py +++ b/var/spack/repos/builtin/packages/grackle/package.py @@ -18,10 +18,10 @@ class Grackle(Package): homepage = 'http://grackle.readthedocs.io/en/grackle-3.1/' url = 'https://bitbucket.org/grackle/grackle/get/grackle-3.1.tar.bz2' - version('3.1', 'cee7799dc505010e2e875950561bbbe1') - version('3.0', 'dc85e664da7e70b65b3ef7164477a959') - version('2.2', 'ec49ed1db5a42db21f478285150c2ba3') - version('2.0.1', 'a9624ad13a60c592c1a0a4ea8e1ae86d') + version('3.1', sha256='504fb080c7f8578c92dcde76cf9e8b851331a38ac76fc4a784df4ecbe1ff2ae8') + version('3.0', sha256='9219033332188d615e49135a3b030963f076b3afee098592b0c3e9f8bafdf504') + version('2.2', sha256='b1d201313c924df38d1e677015f7c31dce42083ef6a0e0936bb9410ccd8a3655') + version('2.0.1', sha256='8f784aaf53d98ddb52b448dc51eb9ec452261a2dbb360170a798693b85165f7d') variant('float', default=False, description='Build with float') diff --git a/var/spack/repos/builtin/packages/gradle/package.py b/var/spack/repos/builtin/packages/gradle/package.py index 4054f19a9a9..7566cbf7be8 100644 --- a/var/spack/repos/builtin/packages/gradle/package.py +++ b/var/spack/repos/builtin/packages/gradle/package.py @@ -17,46 +17,46 @@ class Gradle(Package): homepage = "https://gradle.org" url = "https://services.gradle.org/distributions/gradle-3.4-all.zip" - version('4.8.1', 'bf87b4c64bb6a43861f1964fb8a7f3bc') - version('3.4', '5ae23dbd730dea22eb79cd97a072f06a') - version('3.3', '355f61e9c5d092d49577765ab3712dc0') - version('3.2.1', 'd44dba900ff364103e1f45c0f4b27bbe') - version('3.2', '296cb0e8a94bf72dd80ff7f0ebbf33ed') - version('3.1', '21b34a8c6bae67c729b37b4bd59cf9d0') - version('3.0', '0a7533599b86909c85b117e897501165') - version('2.14.1', 'f74b094923ae76f15f138d42373bb4bc') - version('2.14', 'e069dca1ec042665d61c85caeb4b32ed') - version('2.13', '8e7b31a8b8500752c3d80bd683d120c1') - version('2.12', '42cce06d8fe3a7125ac9b2a6dcc13927') - version('2.11', 'd99911cb2d0e86293e1793efc61cd642') - version('2.10', 'c5d8e57186b60c6d6485682f9907b257') - version('2.9', '1ee1a98b9a73c24633c14abf7f2a5189') - version('2.8', '9f0e8b0c195d7ea6335a724bc90622a9') - version('2.7', '77a77e364c1e2005c62909e6f51a434a') - version('2.6', '6947e873602b3668b2f3cd8e2dd228f1') - version('2.5', '17295dee02217cbe4f07b0d8bb72c467') - version('2.4', 'e1528eeca5c66579ebaee4c7c13bec2a') - version('2.3', '26c527220d869dbd6bb8cd903dd044e1') - version('2.2.1', '1107fbaf94ab7eae26d76d71b5f8db13') - version('2.2', '143830aea6bbed4ee77baa3dd191745f') - version('2.1', '603c07bc1fa737809ef0d9bc5b11960a') - version('2.0', '1d0853b99e6097ea3dea5f3604dc0846') - version('1.12', 'f957126d8e84d7ee7c859d02c2ae1fc1') - version('1.11', '36d2e8f0d5059c815496775af5f688b4') - version('1.10', 'c7ea1213cee7cf2272c5189dbc6f983b') - version('1.9', 'cc0a214649b283cc9594b5b82cb84ce5') - version('1.8', '1733ee0850618a73b54c9ba407de56b6') - version('1.5', '80e60e3b71f1745bbf06f41795ac2908') - version('1.4', 'cc934cab80bed0caccaa096b83cd4d67') - version('1.3', 'f6bce3798f4ee184926592e9a6893e0e') - version('1.2', 'c4741339370bd5e825b2abb9f2cb5b40') - version('1.1', 'afb37b4b35a30ebd5d758c333c147ce9') - version('1.0', '7697cb1e78c7e7362aa422d1790238bd') - version('0.9.2', '8574a445267ce3ad21558e300d854d24') - version('0.9.1', '8fa0acfbcdf01a8425c1f797f5079e21') - version('0.9', '9da1eb9fb32d9c303de5fd5568694634') - version('0.8', '73a0ed51b6ec00a7d3a9d242d51aae60') - version('0.7', 'a8417dbbd62f7013002cb55a44f12cc3') + version('4.8.1', sha256='ce1645ff129d11aad62dab70d63426fdce6cfd646fa309dc5dc5255dd03c7c11') + version('3.4', sha256='37c2fdce55411e4c89b896c292cae1f8f437862c8433c8a74cfc3805d7670c0a') + version('3.3', sha256='71a787faed83c4ef21e8464cc8452b941b5fcd575043aa29d39d15d879be89f7') + version('3.2.1', sha256='0209696f1723f607c475109cf3ed8b51c8a91bb0cda05af0d4bd980bdefe75cd') + version('3.2', sha256='e25ff599ff268182b597c371ed94eb3c225496af5d4e7eb9dcbb08d30f93a9ec') + version('3.1', sha256='43be380834a13e28e9504c21f67fe1a8895ab54f314a6596601896dca7213482') + version('3.0', sha256='9c8b7564ea6a911b5b9fcadd60f3a6cea4238413c8b1e1dd14400a50954aab99') + version('2.14.1', sha256='88a910cdf2e03ebbb5fe90f7ecf534fc9ac22e12112dc9a2fee810c598a76091') + version('2.14', sha256='65bbc0ef9c48be86fb06522fc927d59dcc7c04266f2bb8156be76971f7c3fc4a') + version('2.13', sha256='fb126ed684150f9dc39a811cbcf4daada4292fd387ed998c151ff2cf2536d94d') + version('2.12', sha256='d8b1948a575dc9ec13e03db94502ce91815d73da023f611296c04b852164cb5f') + version('2.11', sha256='a1242e4db8f979998796b1844e608c2acf8f8f54df518bbb3d5954e52253ba71') + version('2.10', sha256='496d60c331f8666f99b66d08ff67a880697a7e85a9d9b76ff08814cf97f61a4c') + version('2.9', sha256='4647967f8de78d6d6d8093cdac50f368f8c2b8038f41a5afe1c3bce4c69219a9') + version('2.8', sha256='65f3880dcb5f728b9d198b14d7f0a678d35ecd33668efc219815a9b4713848be') + version('2.7', sha256='2ba0aaa11a3e96ec0af31d532d808e1f09cc6dcad0954e637902a1ab544b9e60') + version('2.6', sha256='5489234fc9c9733fc4115055618763ccb4d916d667980e6ab4fa57fc81197d16') + version('2.5', sha256='b71ab21fa5e91dcc6a4bd723b13403e8610a6e1b4b9d4b314ff477820de00bf9') + version('2.4', sha256='371cb9fbebbe9880d147f59bab36d61eee122854ef8c9ee1ecf12b82368bcf10') + version('2.3', sha256='515962aeec8c3e67b97f0c13c4575beeed1b5da16181d8b9054416339edc8c2d') + version('2.2.1', sha256='1d7c28b3731906fd1b2955946c1d052303881585fc14baedd675e4cf2bc1ecab') + version('2.2', sha256='65fc05f787c7344cc8834dc13a445c91ea3712a987f5958b8489422484d7371b') + version('2.1', sha256='b351ab27da6e06a74ba290213638b6597f2175f5071e6f96a0a205806720cb81') + version('2.0', sha256='11c32ed95c0ed44e091154391d69008ac5ec25ad897bc881547e6942a03aeb13') + version('1.12', sha256='cf111fcb34804940404e79eaf307876acb8434005bc4cc782d260730a0a2a4f2') + version('1.11', sha256='07e58cd960722c419eb0f6a807228e7179bb43bc266f390cde4632abdacdd659') + version('1.10', sha256='cd1a0f532258369c414a56b3e73b7bd7f087cf515b7c71dcb9091598c4a8d815') + version('1.9', sha256='eeb919fe734bc4a63aaf75c05c19bc55c8bccc925b0eca4269c67f7e8cf48efb') + version('1.8', sha256='4f03076116841743808c2f2c1ae2041d03adebe09ab80356b87516c7ed055e40') + version('1.5', sha256='fecf73744c5695e2a3078104072ae2a9fdec17e36dc058dc20adf8c7be8af13b') + version('1.4', sha256='436771c854cc665c790a6c452a2878dfbdaaf9d14e505a58127b407bb05b013f') + version('1.3', sha256='c8572e9579e2300c5e2e8ae8f1a2433d9fd7ad9a4b1e721a5ee588c72fbf7799') + version('1.2', sha256='ea66177dd532da09cb28d050e880961df5bd7ba014eda709c76f2c022f069282') + version('1.1', sha256='00519a961f7f902123368c5bfe4c01be607628410620c8c8a466fbb0de8c6715') + version('1.0', sha256='510258aa9907a8b406a118eed1f57cfe7994c4fe0a37a6f08403fe3620526504') + version('0.9.2', sha256='a9b33c1cb7c056a7bd26b588301ce80f0b6e3872d18b0f1cb80ab74af0e62404') + version('0.9.1', sha256='6b9e2033e856ed99b968d71c2dc5174dc5637c10d5e4cc9502a51e86f45709eb') + version('0.9', sha256='a06117e826ea8713f61e47b2fe2d7621867c56f4c44e4e8012552584e08b9c1b') + version('0.8', sha256='42e0db29f2e0be4eeadfe77b6491d9e2b21b95abb92fc494dfcf8615f2126910') + version('0.7', sha256='ca902f52f0789ab94762f7081b06461f8d3a03540ab73bf2d642f2d03e8558ef') depends_on('java') diff --git a/var/spack/repos/builtin/packages/grandr/package.py b/var/spack/repos/builtin/packages/grandr/package.py index 4dda7753d81..7e3becc72ff 100644 --- a/var/spack/repos/builtin/packages/grandr/package.py +++ b/var/spack/repos/builtin/packages/grandr/package.py @@ -12,7 +12,7 @@ class Grandr(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/app/grandr" url = "https://www.x.org/archive/individual/app/grandr-0.1.tar.gz" - version('0.1', '707109a105f2ab1bb216e6e6a5a10ba4') + version('0.1', sha256='67a049c8dccdb48897efbd86c2b1d3b0ff5ce3c7859c46b0297d64c881b36d24') depends_on('gtkplus@2.0.0:') depends_on('gconf') diff --git a/var/spack/repos/builtin/packages/graph500/package.py b/var/spack/repos/builtin/packages/graph500/package.py index 99c78abcfcd..2367a7a6235 100644 --- a/var/spack/repos/builtin/packages/graph500/package.py +++ b/var/spack/repos/builtin/packages/graph500/package.py @@ -12,7 +12,7 @@ class Graph500(MakefilePackage): homepage = "https://graph500.org" url = "https://github.com/graph500/graph500/archive/graph500-3.0.0.tar.gz" - version('3.0.0', 'a2ebb4783b21e2d86387a217776395e3') + version('3.0.0', sha256='887dcff56999987fba4953c1c5696d50e52265fe61b6ffa8bb14cc69ff27e8a0') depends_on('mpi@2.0:') diff --git a/var/spack/repos/builtin/packages/graphicsmagick/package.py b/var/spack/repos/builtin/packages/graphicsmagick/package.py index efd5b7d6a92..24015ea0457 100644 --- a/var/spack/repos/builtin/packages/graphicsmagick/package.py +++ b/var/spack/repos/builtin/packages/graphicsmagick/package.py @@ -18,7 +18,7 @@ class Graphicsmagick(AutotoolsPackage): homepage = "http://www.graphicsmagick.org/" url = "https://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.29/GraphicsMagick-1.3.29.tar.xz/download" - version('1.3.29', 'ddde0dd239592db50c5378472355c03c') + version('1.3.29', sha256='e18df46a6934c8c12bfe274d09f28b822f291877f9c81bd9a506f879a7610cd4') depends_on('bzip2') depends_on('ghostscript') diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py index 5588b27bc0a..c5f4d8bae74 100644 --- a/var/spack/repos/builtin/packages/graphlib/package.py +++ b/var/spack/repos/builtin/packages/graphlib/package.py @@ -11,7 +11,7 @@ class Graphlib(CMakePackage): homepage = "https://github.com/LLNL/graphlib" url = "https://github.com/LLNL/graphlib/archive/v2.0.0.tar.gz" - version('2.0.0', '43c6df84f1d38ba5a5dce0ae19371a70') - version('3.0.0', '625d199f97ab1b84cbc8daabcaee5e2a') + version('2.0.0', sha256='4f4aa1193167c41c8491dec3cf22b1e52a8f0842faab88b7945972f02d2adbcd') + version('3.0.0', sha256='c3d889f7bc25b9662426605e52f14cd16f9c05b034738a343890707f5f5681f1') depends_on('cmake@2.6:', type='build') diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py index 1c42d450691..f480d95fe3e 100644 --- a/var/spack/repos/builtin/packages/grass/package.py +++ b/var/spack/repos/builtin/packages/grass/package.py @@ -14,12 +14,12 @@ class Grass(AutotoolsPackage): homepage = "http://grass.osgeo.org" - version('7.6.1', '9ca74f9010d013f735737a90c65d8a7f') - version('7.4.4', '98ae22f8a97a83a4d99a537236639e9c') - version('7.4.3', '4f4462af7a95fe84ee21f3dd585dcb05') - version('7.4.2', 'bb3fc005e707f762c8fee36095e1df7f') - version('7.4.1', 'bf7add62cbeb05a3ed5ad832344ba524') - version('7.4.0', '15b9eb019d6c132c1a65455b3283cf69') + version('7.6.1', sha256='9e25c99cafd16ed8f5e2dca75b5a10dc2af0568dbedf3fc39f1c5a0a9c840b0b') + version('7.4.4', sha256='96a39e273103f7375a670eba94fa3e5dad2819c5c5664c9aee8f145882a94e8c') + version('7.4.3', sha256='004e65693ee97fd4d5dc7ad244e3286a115dccd88964d04be61c07db6574b399') + version('7.4.2', sha256='18eb19bc0aa4cd7be3f30f79ac83f9d0a29c63657f4c1b05bf4c5d5d57a8f46d') + version('7.4.1', sha256='560b8669caaafa9e8dbd4bbf2b4b4bbab7dca1cc46ee828eaf26c744fe0635fc') + version('7.4.0', sha256='cb6fa188e030a3a447fc5451fbe0ecbeb4069ee2fd1bf52ed8e40e9b89e293cc') variant('cxx', default=True, description='Add c++ functionality') variant('tiff', default=True, description='Add TIFF functionality') diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py index 90f04729153..b54e9093673 100644 --- a/var/spack/repos/builtin/packages/grib-api/package.py +++ b/var/spack/repos/builtin/packages/grib-api/package.py @@ -17,10 +17,10 @@ class GribApi(CMakePackage): maintainers = ['skosukhin'] - version('1.24.0', 'dcc549069cdeeaa1959732c36ab3136f') - version('1.21.0', 'eb64c5eb72e6e90841237cba9d644016') - version('1.17.0', 'bca7114d2c3100501a08190a146818d2') - version('1.16.0', '8c7fdee03344e4379d400ae20976a460') + version('1.24.0', sha256='6b0d443cb0802c5de652e5816c5b88734cb3ead454eb932c5ec12ef8d4f77bcd') + version('1.21.0', sha256='50c2b58303ab578c55735e6c21c72ffc24f82a5bf52565550f54d49cb60e8a90') + version('1.17.0', sha256='55cbb4fdcb4ee1be6a27cece9ae7e26070beb8ab6cb7e77773db3fb0d4272462') + version('1.16.0', sha256='0068ca4149a9f991d4c86a813ac73b4e2299c6a3fd53aba9e6ab276ef6f0ff9a') variant('netcdf', default=False, description='Enable netcdf encoding/decoding using netcdf library') diff --git a/var/spack/repos/builtin/packages/groff/package.py b/var/spack/repos/builtin/packages/groff/package.py index 1856a6c702c..7ec685b5a1b 100644 --- a/var/spack/repos/builtin/packages/groff/package.py +++ b/var/spack/repos/builtin/packages/groff/package.py @@ -27,7 +27,7 @@ class Groff(AutotoolsPackage): depends_on('sed', type='build') depends_on('ghostscript', when='+pdf') - version('1.22.3', 'cc825fa64bc7306a885f2fb2268d3ec5') + version('1.22.3', sha256='3a48a9d6c97750bfbd535feeb5be0111db6406ddb7bb79fc680809cda6d828a5') # https://savannah.gnu.org/bugs/index.php?43581 # TODO: figure out why this patch does not actually work for parallel diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 37a8a02ee2e..43cecbec810 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -30,15 +30,15 @@ class Gromacs(CMakePackage): version('2019', sha256='c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b') version('2018.4', sha256='6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891') version('2018.3', sha256='4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291') - version('2018.2', '7087462bb08393aec4ce3192fa4cd8df') - version('2018.1', '7ee393fa3c6b7ae351d47eae2adf980e') - version('2018', '6467ffb1575b8271548a13abfba6374c') - version('2016.5', 'f41807e5b2911ccb547a3fd11f105d47') - version('2016.4', '19c8b5c85f3ec62df79d2249a3c272f8') - version('2016.3', 'e9e3a41bd123b52fbcc6b32d09f8202b') - version('5.1.5', '831fe741bcd9f1612155dffc919885f2') - version('5.1.4', 'ba2e34d59b3982603b4935d650c08040') - version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98') + version('2018.2', sha256='4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857') + version('2018.1', sha256='4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd') + version('2018', sha256='deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9') + version('2016.5', sha256='57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c') + version('2016.4', sha256='4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264') + version('2016.3', sha256='7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27') + version('5.1.5', sha256='c25266abf07690ecad16ed3996899b1d489cbb1ef733a1befb3b5c75c91a703e') + version('5.1.4', sha256='0f3793d8f1f0be747cf9ebb0b588fb2b2b5dc5acc32c3046a7bee2d2c03437bc') + version('5.1.2', sha256='39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304') version('4.5.5', sha256='e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba') variant('mpi', default=True, description='Activate MPI support') diff --git a/var/spack/repos/builtin/packages/gsl/package.py b/var/spack/repos/builtin/packages/gsl/package.py index eaa85b7da0a..021bf26e919 100644 --- a/var/spack/repos/builtin/packages/gsl/package.py +++ b/var/spack/repos/builtin/packages/gsl/package.py @@ -18,9 +18,9 @@ class Gsl(AutotoolsPackage): url = "https://ftpmirror.gnu.org/gsl/gsl-2.3.tar.gz" version('2.5', sha256='0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d') - version('2.4', 'dba736f15404807834dc1c7b93e83b92') - version('2.3', '905fcbbb97bc552d1037e34d200931a0') - version('2.2.1', '3d90650b7cfe0a6f4b29c2d7b0f86458') - version('2.1', 'd8f70abafd3e9f0bae03c52d1f4e8de5') - version('2.0', 'ae44cdfed78ece40e73411b63a78c375') - version('1.16', 'e49a664db13d81c968415cd53f62bc8b') + version('2.4', sha256='4d46d07b946e7b31c19bbf33dda6204d7bedc2f5462a1bae1d4013426cd1ce9b') + version('2.3', sha256='562500b789cd599b3a4f88547a7a3280538ab2ff4939504c8b4ac4ca25feadfb') + version('2.2.1', sha256='13d23dc7b0824e1405f3f7e7d0776deee9b8f62c62860bf66e7852d402b8b024') + version('2.1', sha256='59ad06837397617f698975c494fe7b2b698739a59e2fcf830b776428938a0c66') + version('2.0', sha256='e361f0b19199b5e6c21922e9f16adf7eca8dd860842802424906d0f83485ca2d') + version('1.16', sha256='73bc2f51b90d2a780e6d266d43e487b3dbd78945dd0b04b14ca5980fe28d2f53') diff --git a/var/spack/repos/builtin/packages/gtkmm/package.py b/var/spack/repos/builtin/packages/gtkmm/package.py index 1484ef2f91d..13ac6107407 100644 --- a/var/spack/repos/builtin/packages/gtkmm/package.py +++ b/var/spack/repos/builtin/packages/gtkmm/package.py @@ -12,14 +12,14 @@ class Gtkmm(AutotoolsPackage): homepage = "https://www.gtkmm.org/en/" url = "https://ftp.acc.umu.se/pub/GNOME/sources/gtkmm/2.16/gtkmm-2.16.0.tar.gz" - version('2.19.7', '2afc018e5b15cde293cd2d21db9b6a55') - version('2.19.6', 'fb140e82e583620defe0d70bfe7eefd7') - version('2.19.4', '60006a23306487938dfe0e4b17e3fa46') - version('2.19.2', 'dc208575a24e8d5265af2fd59c08f3d8') - version('2.17.11', '2326ff83439aac83721ed4694acf14e5') - version('2.17.1', '19358644e5e620ad738658be2cb6d739') - version('2.16.0', 'de178c2a6f23eda0b6a8bfb0219e2e1c') - version('2.4.11', 'a339958bc4ab7f74201b312bd3562d46') + version('2.19.7', sha256='7cc8d26f9a0956092e61ecfbb029c5d6223cd7e49d4434653446ff190a990957') + version('2.19.6', sha256='d495d4012d49841a4f0a09584e002bc25ef55d7b2782660ecf7a58ed67357ad7') + version('2.19.4', sha256='ade220b0d395cb44215a69623af40a420281bc090ddaefc55350ad48e888fed2') + version('2.19.2', sha256='9c152f2d652344d9000756491c6b00bd394162f57f4302524db8535144b397a0') + version('2.17.11', sha256='0ec15d7aa14a0528352adf91aa612079590ba377aa15f47f7c8d37611ffbfbcd') + version('2.17.1', sha256='bd1369caeb28ffdc9e81b1c4dc846c265dd9533bed7958756b3ee4d14ffa1694') + version('2.16.0', sha256='7b2cccda794531ecfa65c01e57614ecba526153ad2a29d580c6e8df028d56ec4') + version('2.4.11', sha256='0754187a5bcf3795cd7c959de303e6a19a130b0c5927bff1504baa3524bee8c1') depends_on('glibmm') depends_on('atk') diff --git a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py index 65da75fcb64..e609cee178e 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py @@ -16,8 +16,8 @@ class GtkorvoAtl(CMakePackage): git = "https://github.com/GTkorvo/atl.git" version('develop', branch='master') - version('2.2', 'f0e3581e4b4c6943bf4b203685630564') - version('2.1', 'b2324ff041bccba127330a0e1b241978') + version('2.2', sha256='d88b6eaa3926e499317973bfb2ae469c584bb064da198217ea5fede6d919e160') + version('2.1', sha256='379b493ba867b76d76eabfe5bfeec85239606e821509c31e8eb93c2dc238e4a8') depends_on('gtkorvo-cercs-env') diff --git a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py index ea88f99a5ac..094ede18fd0 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py @@ -14,7 +14,7 @@ class GtkorvoCercsEnv(CMakePackage): git = "https://github.com/GTkorvo/cercs_env.git" version('develop', branch='master') - version('1.0', '08f0532d0c2f7bc9b53dfa7a1c40ea4d') + version('1.0', sha256='e4080a98c1af5003a038361c8bb343843665cac428101ac7d721bad8ba7d244e') def cmake_args(self): args = ["-DENABLE_TESTING=0", "-DENABLE_SHARED_STATIC=STATIC"] diff --git a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py index 5b2c53eefb1..effb7f8c1c6 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py @@ -17,8 +17,8 @@ class GtkorvoDill(CMakePackage): git = "https://github.com/GTkorvo/dill.git" version('develop', branch='master') - version('2.4', '6836673b24f395eaae044b8bb976511d') - version('2.1', '14c835e79b66c9acd2beee01d56e6200') + version('2.4', sha256='ed7745d13e8c6a556f324dcc0e48a807fc993bdd5bb1daa94c1df116cb7e81fa') + version('2.1', sha256='7671e1f3c25ac6a4ec2320cec2c342a2f668efb170e3dba186718ed17d2cf084') def cmake_args(self): args = [] diff --git a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py index aee2eea04bb..9f6c6b5f59f 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py @@ -16,5 +16,5 @@ class GtkorvoEnet(AutotoolsPackage): homepage = "http://www.github.com/GTkorvo/enet" url = "https://github.com/GTkorvo/enet/archive/v1.3.13.tar.gz" - version('1.3.14', '05272cac1a8cb0500995eeca310e7fac') - version('1.3.13', '3490f924a4d421e4832e45850e6ec142') + version('1.3.14', sha256='d1fda051bdee46ad8cce7c3bb36fb6b7a7a443945f27a280ac104753c29465b0') + version('1.3.13', sha256='ede6e4f03e4cb0c3d93044ace9e8c1818ef4d3ced4aaa70384155769b3c436dc') diff --git a/var/spack/repos/builtin/packages/gtkplus/package.py b/var/spack/repos/builtin/packages/gtkplus/package.py index 8e0bc0103fd..dcd3e365293 100644 --- a/var/spack/repos/builtin/packages/gtkplus/package.py +++ b/var/spack/repos/builtin/packages/gtkplus/package.py @@ -11,10 +11,10 @@ class Gtkplus(AutotoolsPackage): interfaces for applications.""" homepage = "http://www.gtk.org" url = "http://ftp.gnome.org/pub/gnome/sources/gtk+/2.24/gtk+-2.24.31.tar.xz" - version('3.20.10', 'e81da1af1c5c1fee87ba439770e17272fa5c06e64572939814da406859e56b70') - version('2.24.32', 'b6c8a93ddda5eabe3bfee1eb39636c9a03d2a56c7b62828b359bf197943c582e') - version('2.24.31', '68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658') - version('2.24.25', '38af1020cb8ff3d10dda2c8807f11e92af9d2fa4045de61c62eedb7fbc7ea5b3') + version('3.20.10', sha256='e81da1af1c5c1fee87ba439770e17272fa5c06e64572939814da406859e56b70') + version('2.24.32', sha256='b6c8a93ddda5eabe3bfee1eb39636c9a03d2a56c7b62828b359bf197943c582e') + version('2.24.31', sha256='68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658') + version('2.24.25', sha256='38af1020cb8ff3d10dda2c8807f11e92af9d2fa4045de61c62eedb7fbc7ea5b3') variant('cups', default='False', description='enable cups support') diff --git a/var/spack/repos/builtin/packages/gts/package.py b/var/spack/repos/builtin/packages/gts/package.py index c45b0d36065..c4b2beb8f83 100644 --- a/var/spack/repos/builtin/packages/gts/package.py +++ b/var/spack/repos/builtin/packages/gts/package.py @@ -24,6 +24,6 @@ class Gts(AutotoolsPackage): homepage = "http://gts.sourceforge.net/index.html" url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz" - version('121130', '023ebb6b13b8707534182a3ef0d12908') + version('121130', sha256='c23f72ab74bbf65599f8c0b599d6336fabe1ec2a09c19b70544eeefdc069b73b') depends_on('glib') diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py index da299ec50c1..ef4de4596cb 100644 --- a/var/spack/repos/builtin/packages/guidance/package.py +++ b/var/spack/repos/builtin/packages/guidance/package.py @@ -14,7 +14,7 @@ class Guidance(MakefilePackage): homepage = "http://guidance.tau.ac.il/ver2/" url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz" - version('2.02', 'aa6ae2168e8e0237ee56bc2ac81202cf') + version('2.02', sha256='825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844') depends_on('perl', type=('build', 'run')) depends_on('perl-bio-perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/guile/package.py b/var/spack/repos/builtin/packages/guile/package.py index 6d093942910..de15b1848d0 100644 --- a/var/spack/repos/builtin/packages/guile/package.py +++ b/var/spack/repos/builtin/packages/guile/package.py @@ -19,9 +19,9 @@ class Guile(AutotoolsPackage): version('2.2.3', sha256='87ee07caef33c97ddc74bf3c29ce7628cfac12061f573e4a29a3a1176754610a') version('2.2.2', sha256='3d9b94183b19f04dd4317da87beedafd1c947142f3d861ca1f0224e7a75127ee') version('2.2.1', sha256='f004b2a5e98017df80cd419773f12a77cfc7ba6069195f97d6702e3d6e487a14') - version('2.2.0', '0d5de8075b965f9ee5ea04399b60a3f9') - version('2.0.14', '333b6eec83e779935a45c818f712484e') - version('2.0.11', 'e532c68c6f17822561e3001136635ddd') + version('2.2.0', sha256='ef1e9544631f18029b113911350bffd5064955c208a975bfe0d27a4003d6d86b') + version('2.0.14', sha256='8aeb2f353881282fe01694cce76bb72f7ffdd296a12c7a1a39255c27b0dfe5f1') + version('2.0.11', sha256='e6786c934346fa2e38e46d8d81a622bb1c16d130153523f6129fcd79ef1fb040') variant('readline', default=True, description='Use the readline library') variant('threads', default=True, description='Use the thread interface') diff --git a/var/spack/repos/builtin/packages/h5part/package.py b/var/spack/repos/builtin/packages/h5part/package.py index 488f8a42e71..d08f37c82ca 100644 --- a/var/spack/repos/builtin/packages/h5part/package.py +++ b/var/spack/repos/builtin/packages/h5part/package.py @@ -13,7 +13,7 @@ class H5part(AutotoolsPackage): homepage = "http://vis.lbl.gov/Research/H5Part/" url = "https://codeforge.lbl.gov/frs/download.php/latestfile/18/H5Part-1.6.6.tar.gz" - version('1.6.6', '327c63d198e38a12565b74cffdf1f9d7') + version('1.6.6', sha256='10347e7535d1afbb08d51be5feb0ae008f73caf889df08e3f7dde717a99c7571') patch('mpiio.patch') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/h5utils/package.py b/var/spack/repos/builtin/packages/h5utils/package.py index f9b7dead4e8..5ffb6e98055 100644 --- a/var/spack/repos/builtin/packages/h5utils/package.py +++ b/var/spack/repos/builtin/packages/h5utils/package.py @@ -14,7 +14,7 @@ class H5utils(AutotoolsPackage): url = "http://ab-initio.mit.edu/h5utils/h5utils-1.12.1.tar.gz" list_url = "http://ab-initio.mit.edu/h5utils/old/" - version('1.12.1', '46a6869fee6e6bf87fbba9ab8a99930e') + version('1.12.1', sha256='7290290ca5d5d4451d757a70c86baaa70d23a28edb09c951b6b77c22b924a38d') variant('png', default=True, description='Enable PNG support') variant('vis5d', default=False, description='Enable Vis5d support') diff --git a/var/spack/repos/builtin/packages/halc/package.py b/var/spack/repos/builtin/packages/halc/package.py index 13752c53fcb..23545f48d5d 100644 --- a/var/spack/repos/builtin/packages/halc/package.py +++ b/var/spack/repos/builtin/packages/halc/package.py @@ -13,7 +13,7 @@ class Halc(MakefilePackage): homepage = "https://github.com/lanl001/halc" url = "https://github.com/lanl001/halc/archive/v1.1.tar.gz" - version('1.1', '4b289b366f6a5400ca481993aa68dd9c') + version('1.1', sha256='79675c3d6c40f567c2e1a5b5e7ec4fb150036582054f6ad079e06b73bd71c1ad') depends_on('blasr', type='run') depends_on('lordec', type='run') diff --git a/var/spack/repos/builtin/packages/haploview/package.py b/var/spack/repos/builtin/packages/haploview/package.py index 42e40fc55af..328b5e8205e 100644 --- a/var/spack/repos/builtin/packages/haploview/package.py +++ b/var/spack/repos/builtin/packages/haploview/package.py @@ -14,7 +14,7 @@ class Haploview(Package): homepage = "http://www.broadinstitute.org/haploview/haploview" url = "https://downloads.sourceforge.net/project/haploview/release/Haploview4.1.jar" - version('4.1', 'f7aa4accda5fad1be74c9c1969c6ee7d', expand=False) + version('4.1', sha256='b3ffe4c3d8bbab6af5eebf89a2dccdb185280088f70ae84c84be60f85f10201d', expand=False) depends_on('java', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py index a555ec1096f..deef607ec47 100644 --- a/var/spack/repos/builtin/packages/harfbuzz/package.py +++ b/var/spack/repos/builtin/packages/harfbuzz/package.py @@ -15,7 +15,7 @@ class Harfbuzz(AutotoolsPackage): version('2.1.3', sha256='613264460bb6814c3894e3953225c5357402915853a652d40b4230ce5faf0bee') version('1.9.0', sha256='11eca62bf0ac549b8d6be55f4e130946399939cdfe7a562fdaee711190248b00') version('1.4.6', sha256='21a78b81cd20cbffdb04b59ac7edfb410e42141869f637ae1d6778e74928d293') - version('0.9.37', 'bfe733250e34629a188d82e3b971bc1e') + version('0.9.37', sha256='255f3b3842dead16863d1d0c216643d97b80bfa087aaa8fc5926da24ac120207') depends_on("pkgconfig", type="build") depends_on("glib") diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py index 528cf6210e1..ef8be650843 100644 --- a/var/spack/repos/builtin/packages/hdf/package.py +++ b/var/spack/repos/builtin/packages/hdf/package.py @@ -16,9 +16,9 @@ class Hdf(AutotoolsPackage): list_depth = 2 version('4.2.14', sha256='2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a') - version('4.2.13', 'a6aa950b3fce5162b96496d8ea0b82bf') - version('4.2.12', '79fd1454c899c05e34a3da0456ab0c1c') - version('4.2.11', '063f9928f3a19cc21367b71c3b8bbf19') + version('4.2.13', sha256='be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483') + version('4.2.12', sha256='dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c') + version('4.2.11', sha256='c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24') variant('szip', default=False, description="Enable szip support") diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 6c482e8a3f8..715f57dd726 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -23,24 +23,24 @@ class Hdf5(AutotoolsPackage): version('develop', branch='develop') - version('1.10.5', '6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8') - version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') - version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39') - version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3') - version('1.10.1', '43a2f9466702fb1db31df98ae6677f15') - version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295') - version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199') + version('1.10.5', sha256='6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8') + version('1.10.4', sha256='8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') + version('1.10.3', sha256='b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39') + version('1.10.2', sha256='bfec1be8c366965a99812cf02ddc97e4b708c1754fccba5414d4adccdc073866') + version('1.10.1', sha256='048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172') + version('1.10.0-patch1', sha256='6e78cfe32a10e6e0629393cdfddf6cfa536571efdaf85f08e35326e1b4e9eff0') + version('1.10.0', sha256='81f6201aba5c30dced5dcd62f5d5477a2790fd5850e02ac514ca8bf3e2bb375a') - version('1.8.21', '87d8c82eba5cf766d97cd06c054f4639c1049c4adeaa3a79f77f8bd374f80f37') - version('1.8.19', '7f568e2464d4ab0a74d16b23956d900b') - version('1.8.18', 'dd2148b740713ca0295442ec683d7b1c') - version('1.8.17', '7d572f8f3b798a628b8245af0391a0ca') - version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618') - version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') - version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95') - version('1.8.13', 'c03426e9e77d7766944654280b467289') - version('1.8.12', 'd804802feb99b87fc668a90e6fa34411') - version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157') + version('1.8.21', sha256='87d8c82eba5cf766d97cd06c054f4639c1049c4adeaa3a79f77f8bd374f80f37') + version('1.8.19', sha256='a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38') + version('1.8.18', sha256='cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063') + version('1.8.17', sha256='d9cda297ee76ade9881c4208987939250d397bae6252d0ccb66fa7d24d67e263') + version('1.8.16', sha256='ed17178abd9928a7237f30370189ba767b9e39e0db45917c2ac4665eb9cb4771') + version('1.8.15', sha256='4e963216b7d32469596bc1321a8c3f6e0c278dcbbdb7be6414c63c081b34c275') + version('1.8.14', sha256='1dbefeeef7f591897c632b2b090db96bb8d35ad035beaa36bc39cb2bc67e0639') + version('1.8.13', sha256='82f6b38eec103b4fccfbf14892786e0c27a8135d3252d8601cf5bf20066d38c1') + version('1.8.12', sha256='b5cccea850096962b5fd9e96f22c4f47d2379224bb41130d9bc038bb6c37dfcb') + version('1.8.10', sha256='4813b79c5fb8701a625b9924b8203bc7154a77f9b826ad4e034144b4056a160a') variant('debug', default=False, description='Builds a debug version of the library') diff --git a/var/spack/repos/builtin/packages/help2man/package.py b/var/spack/repos/builtin/packages/help2man/package.py index 527e2ce6d6c..caafb79950b 100644 --- a/var/spack/repos/builtin/packages/help2man/package.py +++ b/var/spack/repos/builtin/packages/help2man/package.py @@ -14,7 +14,7 @@ class Help2man(AutotoolsPackage): url = "https://ftpmirror.gnu.org/help2man/help2man-1.47.4.tar.xz" version('1.47.8', sha256='528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc') - version('1.47.4', '544aca496a7d89de3e5d99e56a2f03d3') + version('1.47.4', sha256='d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753') depends_on('gettext', type='build') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/hepmc/package.py b/var/spack/repos/builtin/packages/hepmc/package.py index 5e2e2ee6e26..8a003e042a0 100644 --- a/var/spack/repos/builtin/packages/hepmc/package.py +++ b/var/spack/repos/builtin/packages/hepmc/package.py @@ -14,12 +14,12 @@ class Hepmc(CMakePackage): homepage = "http://hepmc.web.cern.ch/hepmc/" url = "http://hepmc.web.cern.ch/hepmc/releases/hepmc2.06.09.tgz" - version('3.0.0', '2212a5e8d693fbf726c28b43ebc6377a') - version('2.06.09', '52518437a64f6b4284e9acc2ecad6212') - version('2.06.08', 'a2e889114cafc4f60742029d69abd907') - version('2.06.07', '11d7035dccb0650b331f51520c6172e7') - version('2.06.06', '102e5503537a3ecd6ea6f466aa5bc4ae') - version('2.06.05', '2a4a2a945adf26474b8bdccf4f881d9c') + version('3.0.0', sha256='7ac3c939a857a5ad67bea1e77e3eb16e80d38cfdf825252ac57160634c26d9ec') + version('2.06.09', sha256='e0f8fddd38472c5615210894444686ac5d72df3be682f7d151b562b236d9b422') + version('2.06.08', sha256='8be6c1793e0a045f07ddb88bb64b46de7e66a52e75fb72b3f82f9a3e3ba8a8ce') + version('2.06.07', sha256='a0bdd6f36a3cc4cb59d6eb15cef9d46ce9b3739cae3324e81ebb2df6943e4594') + version('2.06.06', sha256='8cdff26c10783ed4248220a84a43b7e1f9b59cc2c9a29bd634d024ca469db125') + version('2.06.05', sha256='4c411077cc97522c03b74f973264b8d9fd2b6ccec0efc7ceced2645371c73618') depends_on('cmake@2.6:', type='build') diff --git a/var/spack/repos/builtin/packages/heppdt/package.py b/var/spack/repos/builtin/packages/heppdt/package.py index 442ef99586e..a9f4e1e3ff2 100644 --- a/var/spack/repos/builtin/packages/heppdt/package.py +++ b/var/spack/repos/builtin/packages/heppdt/package.py @@ -15,9 +15,9 @@ class Heppdt(AutotoolsPackage): homepage = "http://lcgapp.cern.ch/project/simu/HepPDT/" url = "http://lcgapp.cern.ch/project/simu/HepPDT/download/HepPDT-2.06.01.tar.gz" - version('3.04.01', 'a8e93c7603d844266b62d6f189f0ac7e') - version('3.04.00', '2d2cd7552d3e9539148febacc6287db2') - version('3.03.02', '0b85f1809bb8b0b28a46f23c718b2773') - version('3.03.01', 'd411f3bfdf9c4350d802241ba2629cc2') - version('3.03.00', 'cd84d0a0454be982dcd8c285e060a7b3') - version('2.06.01', '5688b4bdbd84b48ed5dd2545a3dc33c0') + version('3.04.01', sha256='2c1c39eb91295d3ded69e0d3f1a38b1cb55bc3f0cde37b725ffd5d722f63c0f6') + version('3.04.00', sha256='c5f0eefa19dbbae99f2b6a2ab1ad8fd5d5f844fbbbf96e62f0ddb68cc6a7d5f3') + version('3.03.02', sha256='409d940badbec672c139cb8972c88847b3f9a2476a336f4f7ee6924f8d08426c') + version('3.03.01', sha256='1aabb0add1a26dcb010f99bfb24e666a881cb03f796503220c93d3d4434b4e32') + version('3.03.00', sha256='c9fab0f7983234137d67e83d3e94e194856fc5f8994f11c6283194ce60010840') + version('2.06.01', sha256='12a1b6ffdd626603fa3b4d70f44f6e95a36f8f3b6d4fd614bac14880467a2c2e') diff --git a/var/spack/repos/builtin/packages/hic-pro/package.py b/var/spack/repos/builtin/packages/hic-pro/package.py index ced284672f8..c4fc45bdb18 100644 --- a/var/spack/repos/builtin/packages/hic-pro/package.py +++ b/var/spack/repos/builtin/packages/hic-pro/package.py @@ -14,7 +14,7 @@ class HicPro(MakefilePackage): homepage = "https://github.com/nservant/HiC-Pro" url = "https://github.com/nservant/HiC-Pro/archive/v2.10.0.tar.gz" - version('2.10.0', '6ae2213dcc984b722d1a1f65fcbb21a2') + version('2.10.0', sha256='df181ea5c57247caf6b25fd15dfbb03df597ff8c4f57599d88607648bb61f1b7') depends_on('bowtie2') depends_on('samtools') diff --git a/var/spack/repos/builtin/packages/highfive/package.py b/var/spack/repos/builtin/packages/highfive/package.py index cc82323311b..bd8aac37b44 100644 --- a/var/spack/repos/builtin/packages/highfive/package.py +++ b/var/spack/repos/builtin/packages/highfive/package.py @@ -13,10 +13,10 @@ class Highfive(CMakePackage): homepage = "https://github.com/BlueBrain/HighFive" url = "https://github.com/BlueBrain/HighFive/archive/v1.2.tar.gz" - version('1.5', '5e631c91d2ea7f3677e99d6bb6db8167') - version('1.2', '030728d53519c7e13b5a522d34240301') - version('1.1', '986f0bd18c5264709688a536c02d2b2a') - version('1.0', 'e44e548560ea92afdb244c223b7655b6') + version('1.5', sha256='f194bda482ab15efa7c577ecc4fb7ee519f6d4bf83470acdb3fb455c8accb407') + version('1.2', sha256='4d8f84ee1002e8fd6269b62c21d6232aea3d56ce4171609e39eb0171589aab31') + version('1.1', sha256='430fc312fc1961605ffadbfad82b9753a5e59482e9fbc64425fb2c184123d395') + version('1.0', sha256='d867fe73d00817f686d286f3c69a23731c962c3e2496ca1657ea7302cd0bb944') variant('boost', default=False, description='Support Boost') variant('mpi', default=True, description='Support MPI') diff --git a/var/spack/repos/builtin/packages/hisat2/package.py b/var/spack/repos/builtin/packages/hisat2/package.py index 3d881460d30..64c756a9e8e 100644 --- a/var/spack/repos/builtin/packages/hisat2/package.py +++ b/var/spack/repos/builtin/packages/hisat2/package.py @@ -17,7 +17,7 @@ class Hisat2(MakefilePackage): homepage = "http://ccb.jhu.edu/software/hisat2" url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zip" - version('2.1.0', '8b566d1b7e6c5801c8ae9824ed2da3d0') + version('2.1.0', sha256='89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781') def install(self, spec, prefix): install_tree('doc', prefix.doc) diff --git a/var/spack/repos/builtin/packages/hisea/package.py b/var/spack/repos/builtin/packages/hisea/package.py index 2f15cd392f6..f934edbee5b 100644 --- a/var/spack/repos/builtin/packages/hisea/package.py +++ b/var/spack/repos/builtin/packages/hisea/package.py @@ -14,7 +14,7 @@ class Hisea(MakefilePackage): homepage = "https://doi.org/10.1186/s12859-017-1953-9" url = "https://github.com/lucian-ilie/HISEA" - version('2017.12.26', '54211bdc33b7ce52a8f1e76845935eb8', + version('2017.12.26', sha256='3c6ddfb8490a327cc5f9e45f64cd4312abc6ef5719661ce8892db8a20a1e9c5e', url='https://github.com/lucian-ilie/HISEA/tarball/39e01e98caa0f2101da806ca59306296effe789c') depends_on('boost') diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py index c84fdcef759..197c58bc0d7 100644 --- a/var/spack/repos/builtin/packages/hmmer/package.py +++ b/var/spack/repos/builtin/packages/hmmer/package.py @@ -14,12 +14,12 @@ class Hmmer(Package): homepage = 'http://www.hmmer.org' url = 'http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz' - version('3.2.1', '4e0ad5ed45462d4e36807d21e6d82b69') - version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f') - version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588') - version('2.4i', 'dab234c87e026ac1de942450750acd20') - version('2.3.2', '5f073340c0cf761288f961a73821228a') - version('2.3.1', 'c724413e5761c630892506698a4716e2') + version('3.2.1', sha256='a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c') + version('3.1b2', sha256='dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536') + version('3.0', sha256='6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83') + version('2.4i', sha256='73cb85c2197017fa7a25482556ed250bdeed256974b99b0c25e02854e710a886') + version('2.3.2', sha256='d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4') + version('2.3.1', sha256='3956d53af8de5bb99eec18cba0628e86924c6543639d290293b6677a9224ea3f') variant('mpi', default=True, description='Compile with MPI') variant('gsl', default=False, description='Compile with GSL') diff --git a/var/spack/repos/builtin/packages/hpccg/package.py b/var/spack/repos/builtin/packages/hpccg/package.py index 8e25b9fd3f0..9fdf084e3aa 100644 --- a/var/spack/repos/builtin/packages/hpccg/package.py +++ b/var/spack/repos/builtin/packages/hpccg/package.py @@ -17,7 +17,7 @@ class Hpccg(MakefilePackage): tags = ['proxy-app'] - version('1.0', '2e99da1a89de5ef0844da5e6ffbf39dc') + version('1.0', sha256='5be1b8cc3246811bfc9d6d7072be29455777d61b585675512ae52043ea64cefc') variant('mpi', default=True, description='Build with MPI support') variant('openmp', default=True, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py index 64d9fafa048..18053151301 100644 --- a/var/spack/repos/builtin/packages/hpgmg/package.py +++ b/var/spack/repos/builtin/packages/hpgmg/package.py @@ -23,9 +23,9 @@ class Hpgmg(Package): tags = ['proxy-app'] version('develop', branch='master') - version('0.4', 'abdabfe09453487299500b5bd8da4e6dc3d88477199bcfa38ac41d0b3c780f6f') - version('a0a5510df23b', 'b9c50f25e541428d4735fb07344d1d0ed9fc821bdde918d8e0defa78c0d9b4f9') - version('0.3', '12a65da216fec91daea78594ae4b5a069c8f1a700f1ba21eed9f45a79a68c793') + version('0.4', sha256='abdabfe09453487299500b5bd8da4e6dc3d88477199bcfa38ac41d0b3c780f6f') + version('a0a5510df23b', sha256='b9c50f25e541428d4735fb07344d1d0ed9fc821bdde918d8e0defa78c0d9b4f9') + version('0.3', sha256='12a65da216fec91daea78594ae4b5a069c8f1a700f1ba21eed9f45a79a68c793') variant( 'fe', default=False, description='Build finite element solver') diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py index b25dac4be4f..22c9096e40e 100644 --- a/var/spack/repos/builtin/packages/hpl/package.py +++ b/var/spack/repos/builtin/packages/hpl/package.py @@ -20,7 +20,7 @@ class Hpl(AutotoolsPackage): # Note: HPL uses autotools starting with 2.3 version('2.3', sha256='32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830') - version('2.2', '0eb19e787c3dc8f4058db22c9e0c5320') + version('2.2', sha256='ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440') variant('openmp', default=False, description='Enable OpenMP support') diff --git a/var/spack/repos/builtin/packages/hpx/package.py b/var/spack/repos/builtin/packages/hpx/package.py index 9c5ce3a56e6..d3c6971cb70 100644 --- a/var/spack/repos/builtin/packages/hpx/package.py +++ b/var/spack/repos/builtin/packages/hpx/package.py @@ -18,7 +18,7 @@ class Hpx(CMakePackage, CudaPackage): version('1.2.0', sha256='20942314bd90064d9775f63b0e58a8ea146af5260a4c84d0854f9f968077c170') version('1.1.0', sha256='1f28bbe58d8f0da600d60c3a74a644d75ac777b20a018a5c1c6030a470e8a1c9') - version('1.0.0', '4983e7c6402417ec794d40343e36e417', url='http://stellar.cct.lsu.edu/files/hpx_1.0.0') + version('1.0.0', md5='4983e7c6402417ec794d40343e36e417', url='http://stellar.cct.lsu.edu/files/hpx_1.0.0') variant('cxxstd', default='17', diff --git a/var/spack/repos/builtin/packages/hsakmt/package.py b/var/spack/repos/builtin/packages/hsakmt/package.py index 8c938b76d9e..9e7064a90de 100644 --- a/var/spack/repos/builtin/packages/hsakmt/package.py +++ b/var/spack/repos/builtin/packages/hsakmt/package.py @@ -13,4 +13,4 @@ class Hsakmt(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/amd/hsakmt/" url = "https://www.x.org/archive/individual/lib/hsakmt-1.0.0.tar.gz" - version('1.0.0', '9beb20104e505300daf541266c4c3c3d') + version('1.0.0', sha256='3d46af85c27091937618f5e92f7446cff3e9e6378888645e6e238806461e5b77') diff --git a/var/spack/repos/builtin/packages/htop/package.py b/var/spack/repos/builtin/packages/htop/package.py index 63f33c466ac..f7da12491bc 100644 --- a/var/spack/repos/builtin/packages/htop/package.py +++ b/var/spack/repos/builtin/packages/htop/package.py @@ -14,8 +14,8 @@ class Htop(AutotoolsPackage): list_url = "https://hisham.hm/htop/releases" list_depth = 1 - version('2.2.0', '0d816b6beed31edc75babcfbf863ffa8') - version('2.0.2', '7d354d904bad591a931ad57e99fea84a') + version('2.2.0', sha256='d9d6826f10ce3887950d709b53ee1d8c1849a70fa38e91d5896ad8cbc6ba3c57') + version('2.0.2', sha256='179be9dccb80cee0c5e1a1f58c8f72ce7b2328ede30fb71dcdf336539be2f487') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py index 728dfc4cdd8..cfad4c78ce9 100644 --- a/var/spack/repos/builtin/packages/htslib/package.py +++ b/var/spack/repos/builtin/packages/htslib/package.py @@ -11,14 +11,14 @@ class Htslib(AutotoolsPackage): homepage = "https://github.com/samtools/htslib" - version('1.9', '2ac92c9c3eef9986345ac69a05dd4d24') - version('1.8', '54e9b3a04251fa59b1878f6b546b5c79') - version('1.7', 'd3cc7e080a9a8c4161d8f62b56d3b98d') - version('1.6', 'd6fd14e208aca7e08cbe9072233d0af9') + version('1.9', sha256='e04b877057e8b3b8425d957f057b42f0e8509173621d3eccaedd0da607d9929a') + version('1.8', sha256='c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1') + version('1.7', sha256='be3d4e25c256acdd41bebb8a7ad55e89bb18e2fc7fc336124b1e2c82ae8886c6') + version('1.6', sha256='9588be8be0c2390a87b7952d644e7a88bead2991b3468371347965f2e0504ccb') version('1.5', sha256='a02b515ea51d86352b089c63d778fb5e8b9d784937cf157e587189cb97ad922d') - version('1.4', '2a22ff382654c033c40e4ec3ea880050') - version('1.3.1', '16d78f90b72f29971b042e8da8be6843') - version('1.2', '64026d659c3b062cfb6ddc8a38e9779f') + version('1.4', sha256='5cfc8818ff45cd6e924c32fec2489cb28853af8867a7ee8e755c4187f5883350') + version('1.3.1', sha256='49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6') + version('1.2', sha256='125c01421d5131afb4c3fd2bc9c7da6f4f1cd9ab5fc285c076080b9aca24bffc') depends_on('zlib') depends_on('bzip2', when="@1.4:") diff --git a/var/spack/repos/builtin/packages/httpie/package.py b/var/spack/repos/builtin/packages/httpie/package.py index ceb3620e2fe..70fc8d764fe 100644 --- a/var/spack/repos/builtin/packages/httpie/package.py +++ b/var/spack/repos/builtin/packages/httpie/package.py @@ -12,8 +12,8 @@ class Httpie(PythonPackage): homepage = "https://httpie.org/" url = "https://pypi.io/packages/source/h/httpie/httpie-0.9.8.tar.gz" - version('0.9.9', '13ed0b79b65e793eb288e563db38b2a2') - version('0.9.8', 'e0d1af07d0959a2e081e7954797ce260') + version('0.9.9', sha256='f1202e6fa60367e2265284a53f35bfa5917119592c2ab08277efc7fffd744fcb') + version('0.9.8', sha256='515870b15231530f56fe2164190581748e8799b66ef0fe36ec9da3396f0df6e1') variant('socks', default=True, description='Enable SOCKS proxy support') diff --git a/var/spack/repos/builtin/packages/hub/package.py b/var/spack/repos/builtin/packages/hub/package.py index 3913ad115c0..aea764b448b 100644 --- a/var/spack/repos/builtin/packages/hub/package.py +++ b/var/spack/repos/builtin/packages/hub/package.py @@ -15,11 +15,11 @@ class Hub(Package): git = "https://github.com/github/hub.git" version('head', branch='master') - version('2.2.3', '6675992ddd16d186eac7ba4484d57f5b') - version('2.2.2', '7edc8f5b5d3c7c392ee191dd999596fc') - version('2.2.1', '889a31ee9d10ae9cb333480d8dbe881f') - version('2.2.0', 'eddce830a079b8480f104aa7496f46fe') - version('1.12.4', '4f2ebb14834c9981b04e40b0d1754717') + version('2.2.3', md5='6675992ddd16d186eac7ba4484d57f5b') + version('2.2.2', sha256='610572ee903aea1fa8622c16ab7ddef2bd1bfec9f4854447ab8e0fbdbe6a0cae') + version('2.2.1', sha256='9350aba6a8e3da9d26b7258a4020bf84491af69595f7484f922d75fc8b86dc10') + version('2.2.0', sha256='2da1351197eb5696c207f22c69a5422af052d74277b73d0b8661efb9ec1d0eb1') + version('1.12.4', sha256='b7fe404d7dc5f60554f088bec12de5e80229331430ea0ced46d5bf89ecae5117') extends("go") diff --git a/var/spack/repos/builtin/packages/hunspell/package.py b/var/spack/repos/builtin/packages/hunspell/package.py index 8ce6458b638..f127760dad5 100644 --- a/var/spack/repos/builtin/packages/hunspell/package.py +++ b/var/spack/repos/builtin/packages/hunspell/package.py @@ -13,7 +13,7 @@ class Hunspell(AutotoolsPackage): url = "https://github.com/hunspell/hunspell/archive/v1.6.0.tar.gz" version('1.7.0', sha256='57be4e03ae9dd62c3471f667a0d81a14513e314d4d92081292b90435944ff951') - version('1.6.0', '047c3feb121261b76dc16cdb62f54483') + version('1.6.0', sha256='512e7d2ee69dad0b35ca011076405e56e0f10963a02d4859dbcc4faf53ca68e2') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index 02fe2d7030a..05e5d006cba 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -29,21 +29,21 @@ class Hwloc(AutotoolsPackage): list_url = "http://www.open-mpi.org/software/hwloc/" list_depth = 2 - version('2.0.2', '71d1211eaa4b25ac7ad80cf326784e87') - version('2.0.1', '442b2482bb5b81983ed256522aadbf94') - version('2.0.0', '027e6928ae0b5b64c821d0a71a61cd82') + version('2.0.2', sha256='27dcfe42e3fb3422b72ce48b48bf601c0a3e46e850ee72d9bdd17b5863b6e42c') + version('2.0.1', sha256='f1156df22fc2365a31a3dc5f752c53aad49e34a5e22d75ed231cd97eaa437f9d') + version('2.0.0', sha256='a0d425a0fc7c7e3f2c92a272ffaffbd913005556b4443e1887d2e1718d902887') version('1.11.11', sha256='74329da3be1b25de8e98a712adb28b14e561889244bf3a8138afe91ab18e0b3a') version('1.11.10', sha256='0a2530b739d9ebf60c4c1e86adb5451a20d9e78f7798cf78d0147cc6df328aac') - version('1.11.9', '4d5f5da8b1d09731d82e865ecf3fa399') - version('1.11.8', 'a0fa1c9109a4d8b4b6568e62cc9b6e30') - version('1.11.7', '867a5266675e5bf1ef4ab66c459653f8') - version('1.11.6', 'b4e95eadd2fbdb6d40bbd96be6f03c84') - version('1.11.5', '8f5fe6a9be2eb478409ad5e640b2d3ba') - version('1.11.4', 'b6f23eb59074fd09fdd84905d50b103d') - version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f') - version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23') - version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc') - version('1.9', '1f9f9155682fe8946a97c08896109508') + version('1.11.9', sha256='85b978995b67db0b1a12dd1a73b09ef3d39f8e3cb09f8b9c60cf04633acce46c') + version('1.11.8', sha256='8af89b1164a330e36d18210360ea9bb305e19f9773d1c882855d261a13054ea8') + version('1.11.7', sha256='ac16bed9cdd3c63bca1fe1ac3de522a1376b1487c4fc85b7b19592e28fd98e26') + version('1.11.6', sha256='67963f15197e6b551539c4ed95a4f8882be9a16cf336300902004361cf89bdee') + version('1.11.5', sha256='da2c780fce9b5440a1a7d1caf78f637feff9181a9d1ca090278cae4bea71b3df') + version('1.11.4', sha256='1b6a58049c31ce36aff162cf4332998fd468486bd08fdfe0249a47437311512d') + version('1.11.3', sha256='03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0') + version('1.11.2', sha256='d11f091ed54c56c325ffca1083113a405fcd8a25d5888af64f5cd6cf587b7b0a') + version('1.11.1', sha256='b41f877d79b6026640943d57ef25311299378450f2995d507a5e633da711be61') + version('1.9', sha256='9fb572daef35a1c8608d1a6232a4a9f56846bab2854c50562dfb9a7be294f4e8') variant('nvml', default=False, description="Support NVML device discovery") variant('gl', default=False, description="Support GL device discovery") diff --git a/var/spack/repos/builtin/packages/hybpiper/package.py b/var/spack/repos/builtin/packages/hybpiper/package.py index 5b29670440f..86bab5b86a8 100644 --- a/var/spack/repos/builtin/packages/hybpiper/package.py +++ b/var/spack/repos/builtin/packages/hybpiper/package.py @@ -20,7 +20,7 @@ class Hybpiper(Package): git = "https://github.com/mossmatters/HybPiper/HybPiper.git" version('1.3.1', sha256='7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf') - version('1.2.0', '0ad78e9ca5e3f23ae0eb6236b07e1780') + version('1.2.0', sha256='34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57') depends_on('python@2.7:', type=('build', 'run')) depends_on('py-biopython', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py index 73028f370c8..4897f856eec 100644 --- a/var/spack/repos/builtin/packages/hydra/package.py +++ b/var/spack/repos/builtin/packages/hydra/package.py @@ -17,4 +17,4 @@ class Hydra(AutotoolsPackage): list_url = "http://www.mpich.org/static/downloads/" list_depth = 1 - version('3.2', '4d670916695bf7e3a869cc336a881b39') + version('3.2', sha256='f7a67ec91a773d95cbbd479a80e926d44bee1ff9fc70a8d1df075ea53ea33889') diff --git a/var/spack/repos/builtin/packages/hydrogen/package.py b/var/spack/repos/builtin/packages/hydrogen/package.py index 5c806f312bc..c77bae4ed10 100644 --- a/var/spack/repos/builtin/packages/hydrogen/package.py +++ b/var/spack/repos/builtin/packages/hydrogen/package.py @@ -20,7 +20,7 @@ class Hydrogen(CMakePackage): version('1.1.0', sha256='b4c12913acd01c72d31f4522266bfeb8df1d4d3b4aef02e07ccbc9a477894e71') version('1.0.1', sha256='27cf76e1ef1d58bd8f9b1e34081a14a682b7ff082fb5d1da56713e5e0040e528') version('1.0', sha256='d8a97de3133f2c6b6bb4b80d32b4a4cc25eb25e0df4f0cec0f8cb19bf34ece98') - version('0.99', 'b678433ab1d498da47acf3dc5e056c23') + version('0.99', md5='b678433ab1d498da47acf3dc5e056c23') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index fc5bf923c7d..3cd57ef6ba3 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -28,10 +28,10 @@ class Hypre(Package): version('2.14.0', sha256='705a0c67c68936bb011c50e7aa8d7d8b9693665a9709b584275ec3782e03ee8c') version('2.13.0', sha256='3979602689c3b6e491c7cf4b219cfe96df5a6cd69a5302ccaa8a95ab19064bad') version('2.12.1', sha256='824841a60b14167a0051b68fdb4e362e0207282348128c9d0ca0fd2c9848785c') - version('2.11.2', 'd507943a1a3ce5681c3308e2f3a6dd34') - version('2.11.1', '3f02ef8fd679239a6723f60b7f796519') - version('2.10.1', 'dc048c4cabb3cd549af72591474ad674') - version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') + version('2.11.2', sha256='25b6c1226411593f71bb5cf3891431afaa8c3fd487bdfe4faeeb55c6fdfb269e') + version('2.11.1', sha256='6bb2ff565ff694596d0e94d0a75f0c3a2cd6715b8b7652bc71feb8698554db93') + version('2.10.1', sha256='a4a9df645ebdc11e86221b794b276d1e17974887ead161d5050aaf0b43bb183a') + version('2.10.0b', sha256='b55dbdc692afe5a00490d1ea1c38dd908dae244f7bdd7faaf711680059824c11') version('xsdk-0.2.0', tag='xsdk-0.2.0', git='https://github.com/LLNL/hypre.git') # Versions 2.13.0 and later can be patched to build shared diff --git a/var/spack/repos/builtin/packages/i3/package.py b/var/spack/repos/builtin/packages/i3/package.py index 394ed1a68bf..32cc318921e 100644 --- a/var/spack/repos/builtin/packages/i3/package.py +++ b/var/spack/repos/builtin/packages/i3/package.py @@ -15,7 +15,7 @@ class I3(AutotoolsPackage): homepage = "https://i3wm.org/" url = "https://github.com/i3/i3/archive/4.14.1.tar.gz" - version('4.14.1', 'bdbb6d7bb5a647c8b7b53ed10de84cc5') + version('4.14.1', sha256='28d8102d656f17445a6e1523b12c1a730cc3925a520add1f75b56b9c842932f9') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index f30c58dba73..1e901220a35 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -14,7 +14,7 @@ class Ibmisc(CMakePackage): maintainers = ['citibeth'] - version('0.1.0', '18c63db3e466c5a6fc2db3f903d06ecb') + version('0.1.0', sha256='38481a8680aad4b40eca6723b2898b344cf0ef891ebc3581f5e99fbe420fa0d8') variant('everytrace', default=False, description='Report errors through Everytrace') diff --git a/var/spack/repos/builtin/packages/iceauth/package.py b/var/spack/repos/builtin/packages/iceauth/package.py index 74759219b79..2d16feb37c8 100644 --- a/var/spack/repos/builtin/packages/iceauth/package.py +++ b/var/spack/repos/builtin/packages/iceauth/package.py @@ -14,7 +14,7 @@ class Iceauth(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/iceauth" url = "https://www.x.org/archive/individual/app/iceauth-1.0.7.tar.gz" - version('1.0.7', '183e834ec8bd096ac084ad4acbc29f51') + version('1.0.7', sha256='6c9706cce276609876e768759ed4ee3b447cd17af4a61f9b5a374c7dda9696d8') depends_on('libice') diff --git a/var/spack/repos/builtin/packages/icedtea/package.py b/var/spack/repos/builtin/packages/icedtea/package.py index 90b06393db6..a62550b2c10 100644 --- a/var/spack/repos/builtin/packages/icedtea/package.py +++ b/var/spack/repos/builtin/packages/icedtea/package.py @@ -16,7 +16,7 @@ class Icedtea(AutotoolsPackage): homepage = "http://icedtea.classpath.org/wiki/Main_Page" url = "http://icedtea.wildebeest.org/download/source/icedtea-3.4.0.tar.gz" - version('3.4.0', 'eba66765b92794495e16b83f23640872') + version('3.4.0', sha256='2b606bbbf4ca5bcf2c8e811ea9060da30744860f3d63e1b3149fb5550a90b92b') variant('X', default=False, description="Build with GUI support.") variant('shenandoah', default=False, @@ -68,57 +68,39 @@ class Icedtea(AutotoolsPackage): force_autoreconf = True resource(name='corba', placement='corba_src', - sha512=('f0579608ab1342df231c4542dab1c40e648cda8e9780ea584fd476' - '79b07c93508cbfa85f0406d8aa8b9d528fc5bd99c9d41469568fbec' - '41a6456a13d914ac71c'), + sha256='47210b6c69dcc6193b9bf0a3d61b75b48f4fa56e8ca348e40200cfa14eca3fd1', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/corba.tar.xz', when='@3.4.0') resource(name='hotspot', placement='hotspot_src', - sha512=('29bc953d283f0a0a464fa150e2c4d71b0adaa29da67246843d230f3' - '70b5a20227fb40ef6a7e3b93f10b0cdec18b0cd2bbbceeaea3c9db4' - 'd64c158cc23babbad2'), + sha256='973d668f312b869184665def8abe4037dcd78562bf0dda40367102aca647fd76', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/hotspot.tar.xz', when='@3.4.0') resource(name='jaxp', placement='jaxp_src', - sha512=('ef3ed47815e6d15f40c5947fee1058c252ac673f70b6bf7c30505fa' - 'a12fa5cbab8168d816abe7791dc88acec457744883db4c0af23fb21' - '66bbb709e870685bcd'), + sha256='c74a8a27f1d2dfeaabfce3b5b46623e367fb0fbd5938a3aca8fcd23eb2ce1d53', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/jaxp.tar.xz', when='@3.4.0') resource(name='jaxws', placement='jaxws_src', - sha512=('867cac2919e715190596ae4f73fa42c6cba839ba48ae940adcef20a' - 'bfb23ffeeaa2501c4aedc214b3595bc4e2a4eea9fa7e7cac62a3420' - 'a11fb30a1f7edc9254'), + sha256='90642e9131f4c8922576305224278fcae72d8363956b76d4cdbf813027836cac', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/jaxws.tar.xz', when='@3.4.0') resource(name='jdk', placement='jdk_src', - sha512=('180d7b4435e465d68ed0b420b42dddc598c872075e225b8885ae183' - '3fa4ab5034ce5083c4dfba516a21b2d472321b37a01ba92793e17c7' - '8e9fddb1e254f12065'), + sha256='ec71e37b98b4baa6831c5cb30bcc1ab18cd95993744dbc4d37a28b2dc5049896', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/jdk.tar.xz', when='@3.4.0') resource(name='langtools', placement='langtools_src', - sha512=('0663f40b07de88cd7939557bf7fdb92077d7ca2132e369caefa82db' - '887261ea02102864d33ec0fef3b2c80dd366d25dbc1a95144139498' - 'be581dfabe913e4312'), + sha256='489799c6a86fbfb7da2f2c0ec48e44970a152ea38b97bb40cc04bc09155ab39f', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/langtools.tar.xz', when='@3.4.0') resource(name='openjdk', placement='openjdk_src', - sha512=('f3cca223bd39c0202dd1a65a38ca17024b6cb5c82d833946ec1b7d2' - '8d205833b4dd2dadde505a1c2384e3b28ff0d21a4f175e064b8ac82' - 'aa8a07508e53cdc722'), + sha256='f1eb8c8e45965adcaa1e9cc70df043a825d52409e96712d266167994ff88456d', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/openjdk.tar.xz', when='@3.4.0') resource(name='nashorn', placement='nashorn_src', - sha512=('79b5095bab447d1911696bc1e328fb72c08764c0139cab14a28c0f6' - 'c2e49a2d96bb06fbbb85523b2586672cb0f13709c3158823d5ac3f3' - 'fe3f0f88402d3cb246'), + sha256='3f3861e7268a3986fa8d5c940b85a0de1003f7ebb212df157a9b421ac621d6ae', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/nashorn.tar.xz', when='@3.4.0') resource(name='shenandoah', placement='shenandoah_src', - sha512=('0f085e87c63679314ef322b3f4b854792d46539d5530dd75a7fd45b' - '8b6d663f58469be2808ea5fb4bf31f6c5369cb78f28e1599f748e19' - '31ba7040136306eb20'), + sha256='61f7cc5896791ae564aa365cb3de80b16426b42f07e5734ebd30c4483fa2fd3a', url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/shenandoah.tar.xz', when='@3.4.0') diff --git a/var/spack/repos/builtin/packages/icet/package.py b/var/spack/repos/builtin/packages/icet/package.py index 750648b1020..6e708a77838 100644 --- a/var/spack/repos/builtin/packages/icet/package.py +++ b/var/spack/repos/builtin/packages/icet/package.py @@ -15,7 +15,7 @@ class Icet(CMakePackage): git = "https://gitlab.kitware.com/icet/icet.git" version('develop', branch='master') - version('2.1.1', '4f971c51105a64937460d482adca2a6c') + version('2.1.1', sha256='04cc5b7aa5b3ec95b255febdcfc2312e553ce3db5ca305526803d5737561ec32') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/ico/package.py b/var/spack/repos/builtin/packages/ico/package.py index 1b84700e83c..e79c8ba866b 100644 --- a/var/spack/repos/builtin/packages/ico/package.py +++ b/var/spack/repos/builtin/packages/ico/package.py @@ -15,7 +15,7 @@ class Ico(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/ico" url = "https://www.x.org/archive/individual/app/ico-1.0.4.tar.gz" - version('1.0.4', '8833b2da01a7f919b0db8e5a49184c0f') + version('1.0.4', sha256='eb8609c3b43dc2e575272f2702590525fe13229e022c4aff8b9a0cc2a3f3205d') depends_on('libx11@0.99.1:') diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py index b3ac585154a..9af9085ea61 100644 --- a/var/spack/repos/builtin/packages/icu4c/package.py +++ b/var/spack/repos/builtin/packages/icu4c/package.py @@ -16,10 +16,10 @@ class Icu4c(AutotoolsPackage): list_url = "http://download.icu-project.org/files/icu4c" list_depth = 2 - version('64.1', 'f150be2231c13bb45206d79e0242372b') - version('60.1', '3d164a2d1bcebd1464c6160ebb8315ef') - version('58.2', 'fac212b32b7ec7ab007a12dff1f3aea1') - version('57.1', '976734806026a4ef8bdd17937c8898b9') + version('64.1', sha256='92f1b7b9d51b396679c17f35a2112423361b8da3c1b9de00aa94fd768ae296e6') + version('60.1', sha256='f8f5a6c8fbf32c015a467972bdb1477dc5f5d5dfea908b6ed218715eeb5ee225') + version('58.2', sha256='2b0a4410153a9b20de0e20c7d8b66049a72aef244b53683d0d7521371683da0c') + version('57.1', sha256='ff8c67cb65949b1e7808f2359f2b80f722697048e90e7cfc382ec1fe229e9581') variant('cxxstd', default='11', diff --git a/var/spack/repos/builtin/packages/id3lib/package.py b/var/spack/repos/builtin/packages/id3lib/package.py index 278c09ed0b9..066dee1466f 100644 --- a/var/spack/repos/builtin/packages/id3lib/package.py +++ b/var/spack/repos/builtin/packages/id3lib/package.py @@ -12,7 +12,7 @@ class Id3lib(AutotoolsPackage): homepage = "http://id3lib.sourceforge.net/" url = "https://downloads.sourceforge.net/project/id3lib/id3lib/3.8.3/id3lib-3.8.3.tar.gz" - version('3.8.3', '19f27ddd2dda4b2d26a559a4f0f402a7') + version('3.8.3', sha256='2749cc3c0cd7280b299518b1ddf5a5bcfe2d1100614519b68702230e26c7d079') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/idba/package.py b/var/spack/repos/builtin/packages/idba/package.py index 2ec54b8256d..91bf23028f3 100644 --- a/var/spack/repos/builtin/packages/idba/package.py +++ b/var/spack/repos/builtin/packages/idba/package.py @@ -13,7 +13,7 @@ class Idba(AutotoolsPackage): homepage = "http://i.cs.hku.hk/~alse/hkubrg/projects/idba/" url = "https://github.com/loneknightpy/idba/archive/1.1.3.tar.gz" - version('1.1.3', '303d9b4af7a7498b56ac9698028b4e15') + version('1.1.3', sha256='6b1746a29884f4fa17b110d94d9ead677ab5557c084a93b16b6a043dbb148709') depends_on('m4', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/igraph/package.py b/var/spack/repos/builtin/packages/igraph/package.py index 7371d2969a5..67d3a0952f2 100644 --- a/var/spack/repos/builtin/packages/igraph/package.py +++ b/var/spack/repos/builtin/packages/igraph/package.py @@ -12,6 +12,6 @@ class Igraph(AutotoolsPackage): homepage = "http://igraph.org/" url = "https://github.com/igraph/igraph/releases/download/0.7.1/igraph-0.7.1.tar.gz" - version('0.7.1', '4f6e7c16b45fce8ed423516a9786e4e8') + version('0.7.1', sha256='d978030e27369bf698f3816ab70aa9141e9baf81c56cc4f55efbe5489b46b0df') depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/igvtools/package.py b/var/spack/repos/builtin/packages/igvtools/package.py index 829e794bdbc..15c81f42fb4 100644 --- a/var/spack/repos/builtin/packages/igvtools/package.py +++ b/var/spack/repos/builtin/packages/igvtools/package.py @@ -14,7 +14,7 @@ class Igvtools(Package): homepage = "https://software.broadinstitute.org/software/igv/home" url = "http://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip" - version('2.3.98', '17ed12a213cd9cdaeb2f2a5c56d84bc4') + version('2.3.98', sha256='07027c179f25960bab9919f255c0f8e08f0861861ac6dc02d92be8313e0316a4') depends_on('java@8:') diff --git a/var/spack/repos/builtin/packages/ilmbase/package.py b/var/spack/repos/builtin/packages/ilmbase/package.py index 77a3ffb17b5..3f16959e214 100644 --- a/var/spack/repos/builtin/packages/ilmbase/package.py +++ b/var/spack/repos/builtin/packages/ilmbase/package.py @@ -14,13 +14,13 @@ class Ilmbase(AutotoolsPackage): version('2.3.0', sha256='456978d1a978a5f823c7c675f3f36b0ae14dba36638aeaa3c4b0e784f12a3862') - version('2.2.0', 'b540db502c5fa42078249f43d18a4652', + version('2.2.0', sha256='ecf815b60695555c1fbc73679e84c7c9902f4e8faa6e8000d2f905b8b86cedc7', url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.2.0.tar.gz') - version('2.1.0', 'af1115f4d759c574ce84efcde9845d29', + version('2.1.0', md5='af1115f4d759c574ce84efcde9845d29', url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.1.0.tar.gz') - version('2.0.1', '74c0d0d2873960bd0dc1993f8e03f0ae', + version('2.0.1', sha256='19b03975fea4461f2eff91f5df138b301b3ea9709eccbda98447f372bf09735f', url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.0.1.tar.gz') - version('1.0.2', '26c133ee8ca48e1196fbfb3ffe292ab4', + version('1.0.2', sha256='2e5cda799ffdfca9b1a16bb120d49c74a39af1457ef22f968918c6200ba62e44', url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-1.0.2.tar.gz') - version('0.9.0', '4df45f8116cb7a013b286caf6da30a2e', + version('0.9.0', sha256='c134e47206d0e22ff0be96fa95391a13b635b6ad42668673e293f835fbd176b1', url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-0.9.0.tar.gz') diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/image-magick/package.py index 4754197fde1..2f9229c496d 100644 --- a/var/spack/repos/builtin/packages/image-magick/package.py +++ b/var/spack/repos/builtin/packages/image-magick/package.py @@ -13,9 +13,9 @@ class ImageMagick(AutotoolsPackage): homepage = "http://www.imagemagick.org" url = "https://github.com/ImageMagick/ImageMagick/archive/7.0.2-7.tar.gz" - version('7.0.5-9', '0bcde35180778a61367599e46ff40cb4') - version('7.0.2-7', 'c59cdc8df50e481b2bd1afe09ac24c08') - version('7.0.2-6', 'aa5689129c39a5146a3212bf5f26d478') + version('7.0.5-9', sha256='b85b269e0ed1628e88e840053823f8a33c314b2271f04762f43d33e9d0b4d264') + version('7.0.2-7', sha256='f2f18a97f861c1668befdaff0cc3aaafb2111847aab028a88b4c2cb017acfbaa') + version('7.0.2-6', sha256='7d49ca8030f895c683cae69c52d8edfc4876de651f5b8bfdbea907e222480bd3') depends_on('jpeg') depends_on('pango') diff --git a/var/spack/repos/builtin/packages/imake/package.py b/var/spack/repos/builtin/packages/imake/package.py index 4d4e55b90ab..6f451fa45bc 100644 --- a/var/spack/repos/builtin/packages/imake/package.py +++ b/var/spack/repos/builtin/packages/imake/package.py @@ -12,7 +12,7 @@ class Imake(AutotoolsPackage): homepage = "http://www.snake.net/software/imake-stuff/" url = "https://www.x.org/archive/individual/util/imake-1.0.7.tar.gz" - version('1.0.7', '186ca7b8ff0de8752f2a2d0426542363') + version('1.0.7', sha256='6bda266a07eb33445d513f1e3c82a61e4822ccb94d420643d58e1be5f881e5cb') depends_on('xproto', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/imp/package.py b/var/spack/repos/builtin/packages/imp/package.py index fd0bf588571..93c16165db5 100644 --- a/var/spack/repos/builtin/packages/imp/package.py +++ b/var/spack/repos/builtin/packages/imp/package.py @@ -12,7 +12,7 @@ class Imp(CMakePackage): homepage = "https://integrativemodeling.org" url = "https://github.com/salilab/imp/archive/2.8.0.tar.gz" - version('2.8.0', 'bc985d40dc63bb12e09d6d7403954645') + version('2.8.0', sha256='0b46b8988febd7cdfc5838849007f9a547493ed4b6c752fe54571467eeb1acd2') depends_on('python@2.7:') depends_on('swig') diff --git a/var/spack/repos/builtin/packages/impute2/package.py b/var/spack/repos/builtin/packages/impute2/package.py index 1703c161e90..91046caf261 100644 --- a/var/spack/repos/builtin/packages/impute2/package.py +++ b/var/spack/repos/builtin/packages/impute2/package.py @@ -13,7 +13,7 @@ class Impute2(Package): homepage = "https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#home" url = "https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_x86_64_dynamic.tgz" - version('2.3.2', '0e1bafb8f63eb5cf9ae02ab761af58aa') + version('2.3.2', sha256='da4f64ec75aa2787b8f234e5a7ac4503d464e55ef436a9cd3f4867a10f0c2867') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/infernal/package.py b/var/spack/repos/builtin/packages/infernal/package.py index 35fbfcb607e..39939ce0984 100644 --- a/var/spack/repos/builtin/packages/infernal/package.py +++ b/var/spack/repos/builtin/packages/infernal/package.py @@ -15,7 +15,7 @@ class Infernal(AutotoolsPackage): homepage = "http://eddylab.org/infernal/" url = "http://eddylab.org/infernal/infernal-1.1.2.tar.gz" - version('1.1.2', 'a73e6bbab0c4b79af2cc4c0aabb8accc') + version('1.1.2', sha256='ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b') variant('mpi', default=False, description='Enable MPI parallel support') diff --git a/var/spack/repos/builtin/packages/inputproto/package.py b/var/spack/repos/builtin/packages/inputproto/package.py index b4f09e03b8a..935627e5be1 100644 --- a/var/spack/repos/builtin/packages/inputproto/package.py +++ b/var/spack/repos/builtin/packages/inputproto/package.py @@ -15,7 +15,7 @@ class Inputproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/inputproto" url = "https://www.x.org/archive/individual/proto/inputproto-2.3.2.tar.gz" - version('2.3.2', '6450bad6f8d5ebe354b01b734d1fd7ca') + version('2.3.2', sha256='10eaadd531f38f7c92ab59ef0708ca195caf3164a75c4ed99f0c04f2913f6ef3') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/intel-daal/package.py b/var/spack/repos/builtin/packages/intel-daal/package.py index ec2d8518e37..69b6f11a0e6 100644 --- a/var/spack/repos/builtin/packages/intel-daal/package.py +++ b/var/spack/repos/builtin/packages/intel-daal/package.py @@ -11,34 +11,34 @@ class IntelDaal(IntelPackage): homepage = "https://software.intel.com/en-us/daal" - version('2019.3.199', '1f7d9cdecc1091b03f1ee6303fc7566179d1e3f1813a98ef7a6239f7d456b8ef', + version('2019.3.199', sha256='1f7d9cdecc1091b03f1ee6303fc7566179d1e3f1813a98ef7a6239f7d456b8ef', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15277/l_daal_2019.3.199.tgz") - version('2019.1.144', '1672afac568c93e185283cf7e044d511381092ebc95d7204c4dccb83cc493197', + version('2019.1.144', sha256='1672afac568c93e185283cf7e044d511381092ebc95d7204c4dccb83cc493197', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14869/l_daal_2019.1.144.tgz") - version('2019.0.117', 'd42fb6c3e8b31b1288049e89df37f2e8', + version('2019.0.117', sha256='85ac8e983bc9b9cc635e87cb4ec775ffd3695e44275d20fdaf53c19ed280d69f', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13577/l_daal_2019.0.117.tgz") # Doesn't appear to be a 2018.4 update yet - version('2018.3.222', 'e688825c563e357b7b626ece610d6a85', + version('2018.3.222', sha256='378fec529a36508dd97529037e1164ff98e0e062a9a47ede99ccf9e91493d1e2', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13007/l_daal_2018.3.222.tgz") - version('2018.2.199', 'd015ff34a87a18922736b5fba0d0b0e0', + version('2018.2.199', sha256='cee30299b3ffaea515f5a9609f4df0f644579c8a1ba2b61747b390f6caf85b14', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12727/l_daal_2018.2.199.tgz") - version('2018.1.163', '12a9586734a03a956095440161fd741a', + version('2018.1.163', sha256='ac96b5a6c137cda18817d9b3505975863f8f53347225ebb6ccdaaf4bdb8dc349', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_daal_2018.1.163.tgz") - version('2018.0.128', '5779e670f67c33cc1c6cdcdca5e4636e', + version('2018.0.128', sha256='d13a7cd1b6779971f2ba46797447de9409c98a4d2f0eb0dc9622d9d63ac8990f', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12072/l_daal_2018.0.128.tgz") - version('2017.4.239', 'b47e9b92d948ee312e8a98170a1c0640', + version('2017.4.239', sha256='cc4b608f59f3b2fafee16389102a763d27c46f6d136a6cfa89847418a8ea7460', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12148/l_daal_2017.4.239.tgz") - version('2017.3.196', '93221eaeb560917a129d42fb2cf02500', + version('2017.3.196', sha256='cfa863f342dd1c5fe8f1c7b6fd69589140370fc92742a19d82c8594e4e1e46ce', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11546/l_daal_2017.3.196.tgz") - version('2017.2.174', 'f067d5d7b0f70914fba1f78da0361065', + version('2017.2.174', sha256='5ee838b08d4cda7fc3e006e1deeed41671cbd7cfd11b64ec3b762c94dfc2b660', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11308/l_daal_2017.2.174.tgz") - version('2017.1.132', '56eef8cc45219f92a27de03ae914eba4', + version('2017.1.132', sha256='6281105d3947fc2860e67401ea0218198cc4753fd2d4b513528a89143248e4f3', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10983/l_daal_2017.1.132.tgz") - version('2017.0.098', 'b4eb234de12beff4a5cba4b81ea60673', + version('2017.0.098', sha256='a7064425653b4f5f0fe51e25358d267d8ae023179eece61e08da891b67d79fe5', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9664/l_daal_2017.0.098.tgz") - version('2016.3.210', 'ad747c0dd97dace4cad03cf2266cad28', + version('2016.3.210', sha256='367eaef21ea0143c11ae3fd56cd2a05315768c059e14caa15894bcf96853687c', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9099/l_daal_2016.3.210.tgz") - version('2016.2.181', 'aad2aa70e5599ebfe6f85b29d8719d46', + version('2016.2.181', sha256='afdb65768957784d28ac537b4933a86eb4193c68a636157caed17b29ccdbfacb', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8687/l_daal_2016.2.181.tgz") provides('daal') diff --git a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py index 5aff1cb4c7b..7404e8de704 100644 --- a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py +++ b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py @@ -20,7 +20,7 @@ class IntelGpuTools(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/app/intel-gpu-tools/" url = "https://www.x.org/archive/individual/app/intel-gpu-tools-1.16.tar.gz" - version('1.16', '3996f10fc86a28ec59e1cf7b227dad78') + version('1.16', sha256='4874e6e7704c8d315deaf5b44cc9467ea5e502c7f816470a4a28827fcb34643f') depends_on('libdrm@2.4.64:') depends_on('libpciaccess@0.10:', when=(sys.platform != 'darwin')) diff --git a/var/spack/repos/builtin/packages/intel-ipp/package.py b/var/spack/repos/builtin/packages/intel-ipp/package.py index cf6d8e08953..7055268bf9a 100644 --- a/var/spack/repos/builtin/packages/intel-ipp/package.py +++ b/var/spack/repos/builtin/packages/intel-ipp/package.py @@ -11,32 +11,32 @@ class IntelIpp(IntelPackage): homepage = "https://software.intel.com/en-us/intel-ipp" - version('2019.3.199', '02545383206c1ae4dd66bfa6a38e2e14480ba11932eeed632df8ab798aa15ccd', + version('2019.3.199', sha256='02545383206c1ae4dd66bfa6a38e2e14480ba11932eeed632df8ab798aa15ccd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15276/l_ipp_2019.3.199.tgz') - version('2019.1.144', '1eb7cd0fba74615aeafa4e314c645414497eb73f1705200c524fe78f00620db3', + version('2019.1.144', sha256='1eb7cd0fba74615aeafa4e314c645414497eb73f1705200c524fe78f00620db3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14887/l_ipp_2019.1.144.tgz') - version('2019.0.117', 'c96be6e138d32bf9b8abc789d25db71d', + version('2019.0.117', sha256='d552ba49fba58f0e94da2048176f21c5dfd490dca7c5ce666dfc2d18db7fd551', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13576/l_ipp_2019.0.117.tgz') - version('2018.4.274', 'bdc6082c65410c98ccf6daf239e0a6625d15ec5e0ddc1c0563aad42b6ba9063c', + version('2018.4.274', sha256='bdc6082c65410c98ccf6daf239e0a6625d15ec5e0ddc1c0563aad42b6ba9063c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13726/l_ipp_2018.4.274.tgz') - version('2018.3.222', '2ccc16ec002466e52f1e6e1bfe9b1149', + version('2018.3.222', sha256='bb783c5e6220e240f19136ae598cd1c1d647496495139ce680de58d3d5496934', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13006/l_ipp_2018.3.222.tgz') - version('2018.2.199', 'f87276b485d2f6ec070c1b41ac1ed871', + version('2018.2.199', sha256='55cb5c910b2c1e2bd798163fb5019b992b1259a0692e328bb9054778cf01562b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12726/l_ipp_2018.2.199.tgz') - version('2018.1.163', '183d4888f3d91f632b617fdd401f04ed', + version('2018.1.163', md5='183d4888f3d91f632b617fdd401f04ed', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_ipp_2018.1.163.tgz') - version('2018.0.128', 'e64190bc9041b52d9eed7e8ee91bf1de', + version('2018.0.128', sha256='da568ceec1b7acbcc8f666b73d4092788b037b1b03c0436974b82155056ed166', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12071/l_ipp_2018.0.128.tgz') - version('2017.3.196', '47e53bd1a2740041f4d0be7c36b61a18', + version('2017.3.196', sha256='50d49a1000a88a8a58bd610466e90ae28d07a70993a78cbbf85d44d27c4232b6', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11545/l_ipp_2017.3.196.tgz") - version('2017.2.174', '8ad7753ee30c5176c4931070334144bc', + version('2017.2.174', sha256='92f866c9dce8503d7e04223ec35f281cfeb0b81cf94208c3becb11aacfda7b99', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11307/l_ipp_2017.2.174.tgz") - version('2017.1.132', '9fbbaa402b8d16f4cb4be9aee2f557c2', + version('2017.1.132', sha256='2908bdeab3057d4ebcaa0b8ff5b00eb47425d35961a96f14780be68554d95376', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11031/l_ipp_2017.1.132.tgz") - version('2017.0.098', 'e7be757ebe351d9f9beed7efdc7b7118', + version('2017.0.098', sha256='7633d16e2578be64533892336c8a15c905139147b0f74eaf9f281358ad7cdcba', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9663/l_ipp_2017.0.098.tgz") # built from parallel_studio_xe_2016.3.067 - version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3', + version('9.0.3.210', sha256='8ce7bf17f4a0bbf8c441063de26be7f6e0f6179789e23f24eaa8b712632b3cdd', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9067/l_ipp_9.0.3.210.tgz") provides('ipp') diff --git a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py index d1d1973b0a4..ae5e10c2f0f 100644 --- a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py @@ -16,8 +16,8 @@ class IntelMklDnn(CMakePackage): version('1.0-pc2', sha256='fcc2d951f7170eade0cfdd0d8d1d58e3e7785bd326bca6555f3722f8cba71811') version('0.19', sha256='ba39da6adb263df05c4ca2a120295641fc97be75b588922e4274cb628dbe1dcd', preferred=True) version('0.18.1', sha256='fc7506701dfece9b03c0dc83d0cda9a44a5de17cdb54bc7e09168003f02dbb70') - version('0.11', 'a060a42753f633a146c3db699eeee666') - version('0.10', '3855ad02452a6906e3a9adc9cecef49c') - version('0.9', 'dfb89d8f9d0bce55e878df32544cb0ea') + version('0.11', sha256='4cb4a85b05fe42aa527fd70a048caddcba9361f6d3d7bea9f33d74524e206d7d') + version('0.10', sha256='59828764ae43f1151f77b8997012c52e0e757bc50af1196b86fce8934178c570') + version('0.9', sha256='8606a80851c45b0076f7d4047fbf774ce13d6b6d857cb2edf95c7e1fd4bca1c7') depends_on('intel-mkl') diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py index 2ed678df1f5..c56873ea3e7 100644 --- a/var/spack/repos/builtin/packages/intel-mkl/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl/package.py @@ -13,37 +13,37 @@ class IntelMkl(IntelPackage): homepage = "https://software.intel.com/en-us/intel-mkl" - version('2019.3.199', '06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f', + version('2019.3.199', sha256='06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/l_mkl_2019.3.199.tgz") - version('2019.1.144', '5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb', + version('2019.1.144', sha256='5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/l_mkl_2019.1.144.tgz") - version('2019.0.117', 'd9e1b6b96fbffd4b306c7e8291f141a2', + version('2019.0.117', sha256='4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/l_mkl_2019.0.117.tgz") - version('2018.4.274', '18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881', + version('2018.4.274', sha256='18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/l_mkl_2018.4.274.tgz") - version('2018.3.222', '3e63646a4306eff95e8d0aafd53a2983', + version('2018.3.222', sha256='108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/l_mkl_2018.3.222.tgz") - version('2018.2.199', 'fd31b656a8eb859c89495b9cc41230b4', + version('2018.2.199', sha256='e28d12173bef9e615b0ded2f95f59a42b3e9ad0afa713a79f8801da2bfb31936', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12725/l_mkl_2018.2.199.tgz") - version('2018.1.163', 'f1f7b6ddd7eb57dfe39bd4643446dc1c', + version('2018.1.163', sha256='f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mkl_2018.1.163.tgz") - version('2018.0.128', '0fa23779816a0f2ee23a396fc1af9978', + version('2018.0.128', sha256='c368baa40ca88057292512534d7fad59fa24aef06da038ea0248e7cd1e280cec', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12070/l_mkl_2018.0.128.tgz") - version('2017.4.239', '3066272dd0ad3da7961b3d782e1fab3b', + version('2017.4.239', sha256='dcac591ed1e95bd72357fd778edba215a7eab9c6993236373231cc16c200c92a', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12147/l_mkl_2017.4.239.tgz") - version('2017.3.196', '4a2eb4bee789391d9c07d7c348a80702', + version('2017.3.196', sha256='fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11544/l_mkl_2017.3.196.tgz") - version('2017.2.174', 'ef39a12dcbffe5f4a0ef141b8759208c', + version('2017.2.174', sha256='0b8a3fd6bc254c3c3d9d51acf047468c7f32bf0baff22aa1e064d16d9fea389f', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11306/l_mkl_2017.2.174.tgz") - version('2017.1.132', '7911c0f777c4cb04225bf4518088939e', + version('2017.1.132', sha256='8c6bbeac99326d59ef3afdc2a95308c317067efdaae50240d2f4a61f37622e69', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11024/l_mkl_2017.1.132.tgz") - version('2017.0.098', '3cdcb739ab5ab1e047eb130b9ffdd8d0', + version('2017.0.098', sha256='f2233e8e011f461d9c15a853edf7ed0ae8849aa665a1ec765c1ff196fd70c4d9', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9662/l_mkl_2017.0.098.tgz") # built from parallel_studio_xe_2016.3.x - version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34', + version('11.3.3.210', sha256='ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9068/l_mkl_11.3.3.210.tgz") # built from parallel_studio_xe_2016.2.062 - version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65', + version('11.3.2.181', sha256='bac04a07a1fe2ae4996a67d1439ee90c54f31305e8663d1ccfce043bed84fc27', url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8711/l_mkl_11.3.2.181.tgz") variant('shared', default=True, description='Builds shared library') diff --git a/var/spack/repos/builtin/packages/intel-mpi/package.py b/var/spack/repos/builtin/packages/intel-mpi/package.py index 1580a086b91..001e4be17f6 100644 --- a/var/spack/repos/builtin/packages/intel-mpi/package.py +++ b/var/spack/repos/builtin/packages/intel-mpi/package.py @@ -11,34 +11,34 @@ class IntelMpi(IntelPackage): homepage = "https://software.intel.com/en-us/intel-mpi-library" - version('2019.4.243', '233a8660b92ecffd89fedd09f408da6ee140f97338c293146c9c080a154c5fcd', + version('2019.4.243', sha256='233a8660b92ecffd89fedd09f408da6ee140f97338c293146c9c080a154c5fcd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15553/l_mpi_2019.4.243.tgz') - version('2019.3.199', '5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990', + version('2019.3.199', sha256='5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/l_mpi_2019.3.199.tgz') - version('2019.1.144', 'dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd', + version('2019.1.144', sha256='dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/l_mpi_2019.1.144.tgz') - version('2019.0.117', '8572d5fa1f26a7de8edc8b64653b0955', + version('2019.0.117', sha256='dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/l_mpi_2019.0.117.tgz') - version('2018.4.274', 'a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0', + version('2018.4.274', sha256='a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13741/l_mpi_2018.4.274.tgz') - version('2018.3.222', 'df92593818fadff63c57418669c6083b', + version('2018.3.222', sha256='5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13112/l_mpi_2018.3.222.tgz') - version('2018.2.199', '6ffeab59c83a8842537484d53e180520', + version('2018.2.199', sha256='0927f1bff90d10974433ba2892e3fd38e6fee5232ab056a9f9decf565e814460', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12748/l_mpi_2018.2.199.tgz') - version('2018.1.163', '437ce50224c5bbf98fd578a810c3e401', + version('2018.1.163', sha256='130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mpi_2018.1.163.tgz') - version('2018.0.128', '15b46fc6a3014595de897aa48d3a658b', + version('2018.0.128', sha256='debaf2cf80df06db9633dfab6aa82213b84a665a55ee2b0178403906b5090209', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12120/l_mpi_2018.0.128.tgz') - version('2017.4.239', '460a9ef1b3599d60b4d696e3f0f2a14d', + version('2017.4.239', sha256='5a1048d284dce8bc75b45789471c83c94b3c59f8f159cab43d783fc44302510b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12209/l_mpi_2017.4.239.tgz') - version('2017.3.196', '721ecd5f6afa385e038777e5b5361dfb', + version('2017.3.196', sha256='dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11595/l_mpi_2017.3.196.tgz') - version('2017.2.174', 'b6c2e62c3fb9b1558ede72ccf72cf1d6', + version('2017.2.174', sha256='106a4b362c13ddc6978715e50f5f81c58c1a4c70cd2d20a99e94947b7e733b88', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11334/l_mpi_2017.2.174.tgz') - version('2017.1.132', 'd5e941ac2bcf7c5576f85f6bcfee4c18', + version('2017.1.132', sha256='8d30a63674fe05f17b0a908a9f7d54403018bfed2de03c208380b171ab99be82', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11014/l_mpi_2017.1.132.tgz') # built from parallel_studio_xe_2016.3.068 - version('5.1.3.223', '4316e78533a932081b1a86368e890800', + version('5.1.3.223', sha256='544f4173b09609beba711fa3ba35567397ff3b8390e4f870a3307f819117dd9b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9278/l_mpi_p_5.1.3.223.tgz') provides('mpi') diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py index e4d9bd4d6c1..cb3658020b4 100644 --- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py +++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py @@ -20,98 +20,98 @@ class IntelParallelStudio(IntelPackage): # in the 'intel' package. # Cluster Edition (top tier; all components included) - version('cluster.2019.4', '32aee12de3b5ca14caf7578313c06b205795c67620f4a9606ea45696ee3b3d9e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15533/parallel_studio_xe_2019_update4_cluster_edition.tgz') - version('cluster.2019.3', 'b5b022366d6d1a98dbb63b60221c62bc951c9819653ad6f5142192e89f78cf63', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15268/parallel_studio_xe_2019_update3_cluster_edition.tgz') - version('cluster.2019.2', '8c526bdd95d1da454e5cada00f7a2353089b86d0c9df2088ca7f842fe3ff4cae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15088/parallel_studio_xe_2019_update2_cluster_edition.tgz') - version('cluster.2019.1', '3a1eb39f15615f7a2688426b9835e5e841e0c030f21dcfc899fe23e09bd2c645', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14850/parallel_studio_xe_2019_update1_cluster_edition.tgz') - version('cluster.2019.0', 'd4c249c5438c1a55640291efcc96418d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13589/parallel_studio_xe_2019_cluster_edition.tgz') + version('cluster.2019.4', sha256='32aee12de3b5ca14caf7578313c06b205795c67620f4a9606ea45696ee3b3d9e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15533/parallel_studio_xe_2019_update4_cluster_edition.tgz') + version('cluster.2019.3', sha256='b5b022366d6d1a98dbb63b60221c62bc951c9819653ad6f5142192e89f78cf63', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15268/parallel_studio_xe_2019_update3_cluster_edition.tgz') + version('cluster.2019.2', sha256='8c526bdd95d1da454e5cada00f7a2353089b86d0c9df2088ca7f842fe3ff4cae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15088/parallel_studio_xe_2019_update2_cluster_edition.tgz') + version('cluster.2019.1', sha256='3a1eb39f15615f7a2688426b9835e5e841e0c030f21dcfc899fe23e09bd2c645', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14850/parallel_studio_xe_2019_update1_cluster_edition.tgz') + version('cluster.2019.0', sha256='1096dd4139bdd4b3abbda69a17d1e229a606759f793f5b0ba0d39623928ee4a1', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13589/parallel_studio_xe_2019_cluster_edition.tgz') # - version('cluster.2018.4', '210a5904a860e11b861720e68416f91fd47a459e4500976853291fa8b0478566', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13717/parallel_studio_xe_2018_update4_cluster_edition.tgz') - version('cluster.2018.3', '7112837d20a100b895d9cd9ba9b6748d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12998/parallel_studio_xe_2018_update3_cluster_edition.tgz') - version('cluster.2018.2', '3b8d93a3fa10869dde024b739b96a9c4', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12717/parallel_studio_xe_2018_update2_cluster_edition.tgz') - version('cluster.2018.1', '9c007011e0e3fc72747b58756fbf01cd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12374/parallel_studio_xe_2018_update1_cluster_edition.tgz') - version('cluster.2018.0', 'fa9baeb83dd2e8e4a464e3db38f28d0f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12058/parallel_studio_xe_2018_cluster_edition.tgz') + version('cluster.2018.4', sha256='210a5904a860e11b861720e68416f91fd47a459e4500976853291fa8b0478566', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13717/parallel_studio_xe_2018_update4_cluster_edition.tgz') + version('cluster.2018.3', sha256='23c64b88cea5056eaeef7b4ae0f4c6a86485c97f5e41d6c8419cb00aa4929287', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12998/parallel_studio_xe_2018_update3_cluster_edition.tgz') + version('cluster.2018.2', sha256='550bc4758f7dd70e75830d329947532ad8b7cbb85225b8ec6db7e78a3f1d6d84', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12717/parallel_studio_xe_2018_update2_cluster_edition.tgz') + version('cluster.2018.1', sha256='f7a94e83248d2641eb7ae2c1abf681067203a5b4372619e039861b468744774c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12374/parallel_studio_xe_2018_update1_cluster_edition.tgz') + version('cluster.2018.0', sha256='526e5e71c420dc9b557b0bae2a81abb33eedb9b6a28ac94996ccbcf71cf53774', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12058/parallel_studio_xe_2018_cluster_edition.tgz') # - version('cluster.2017.7', '158461b000b31f0ef8169b6f0277bfb5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz') - version('cluster.2017.6', 'b0bbddeec3e78a84b967c9ca70dade77', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz') - version('cluster.2017.5', 'baeb8e584317fcdf1f60b8208bd4eab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz') - version('cluster.2017.4', '27398416078e1e4005afced3e9a6df7e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz') - version('cluster.2017.3', '691874735458d3e88fe0bcca4438b2a9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz') - version('cluster.2017.2', '70e54b33d940a1609ff1d35d3c56e3b3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz') - version('cluster.2017.1', '7f75a4a7e2c563be778c377f9d35a542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz') - version('cluster.2017.0', '34c98e3329d6ac57408b738ae1daaa01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz') + version('cluster.2017.7', sha256='133c3aa99841a4fe48149938a90f971467452a82f033be10cd9464ba810f6360', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz') + version('cluster.2017.6', sha256='d771b00d3658934c424f294170125dc58ae9b03639aa898a2f115d7a7482dd3a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz') + version('cluster.2017.5', sha256='36e496d1d1d7d7168cc3ba8f5bca9b52022339f30b62a87ed064b77a5cbccc09', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz') + version('cluster.2017.4', sha256='27d34625adfc635d767c136b5417a372f322fabe6701b651d858a8fe06d07f2d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz') + version('cluster.2017.3', sha256='856950c0493de3e8b4150e18f8821675c1cf75c2eea5ff0804f59eb301414bbe', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz') + version('cluster.2017.2', sha256='83a655f0c2969409758488d70d6719fb5ea81a84b6da3feb641ce67bb240bc8a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz') + version('cluster.2017.1', sha256='c808be744c98f7471c61258144859e8e8fc92771934281a16135803e941fd9b0', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz') + version('cluster.2017.0', sha256='f380a56a25cf17941eb691a640035e79f92516346500e0df80fbdd46c5c1b301', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz') # - version('cluster.2016.4', '16a641a06b156bb647c8a56e71f3bb33', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz') - version('cluster.2016.3', 'eda19bb0d0d19709197ede58f13443f3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz') - version('cluster.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz') - version('cluster.2016.1', '83b260ef3fcfd4e30afbeb7eb31b6b20', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz') - version('cluster.2016.0', '00b4de9727a906a3aff468c26dd3f89c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz') + version('cluster.2016.4', sha256='ea43c150ed6f9967bc781fe4253169a0447c69bac4fe2c563016a1ad2875ae23', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz') + version('cluster.2016.3', sha256='aa7c6f1a6603fae07c2b01409c12de0811aa5947eaa71dfb1fe9898076c2773e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz') + version('cluster.2016.2', sha256='280bf39c75d7f52f206759ca4d8b6334ab92d5970957b90f5aa286bb0aa8d65e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz') + version('cluster.2016.1', sha256='f5a3ab9fb581e19bf1bd966f7d40a11905e002a2bfae1c4a2140544288ca3e48', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz') + version('cluster.2016.0', sha256='fd4c32352fd78fc919601bedac5658ad5ac48efbc5700d9a8d42ed7d53bd8bb7', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz') # - version('cluster.2015.6', 'd460f362c30017b60f85da2e51ad25bf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz') - version('cluster.2015.1', '542b78c86beff9d7b01076a7be9c6ddc', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz') + version('cluster.2015.6', sha256='e604ed2bb45d227b151dd2898f3edd93526d58d1db1cb9d6b6f614907864f392', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz') + version('cluster.2015.1', sha256='84fdf48d1de20e1d580ba5d419a5bc1c55d217a4f5dc1807190ecffe0229a62b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz') # Professional Edition (middle tier; excluded: MPI/TAC/Cluster Checker) # # NB: Pre-2018 download packages for Professional are the same as for # Cluster; differences manifest only in the tokens present in the license # file delivered as part of the purchase. - version('professional.2019.4', '9b2818ea5739ade100841e99ce79ef7f4049a2513beb2ce20fc94706f1ba0231', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15534/parallel_studio_xe_2019_update4_professional_edition.tgz') - version('professional.2019.3', '92a8879106d0bdf1ecf4670cd97fbcdc67d78b13bdf484f2c516a533aa7a27f9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15269/parallel_studio_xe_2019_update3_professional_edition.tgz') - version('professional.2019.1', 'bc83ef5a728903359ae11a2b90ad7dae4ae61194afb28bb5bb419f6a6aea225d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14825/parallel_studio_xe_2019_update1_professional_edition.tgz') - version('professional.2019.0', '94b9714e353e5c4f58d38cb236e2f8911cbef31c4b42a148d60c988e926411e2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13578/parallel_studio_xe_2019_professional_edition.tgz') + version('professional.2019.4', sha256='9b2818ea5739ade100841e99ce79ef7f4049a2513beb2ce20fc94706f1ba0231', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15534/parallel_studio_xe_2019_update4_professional_edition.tgz') + version('professional.2019.3', sha256='92a8879106d0bdf1ecf4670cd97fbcdc67d78b13bdf484f2c516a533aa7a27f9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15269/parallel_studio_xe_2019_update3_professional_edition.tgz') + version('professional.2019.1', sha256='bc83ef5a728903359ae11a2b90ad7dae4ae61194afb28bb5bb419f6a6aea225d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14825/parallel_studio_xe_2019_update1_professional_edition.tgz') + version('professional.2019.0', sha256='94b9714e353e5c4f58d38cb236e2f8911cbef31c4b42a148d60c988e926411e2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13578/parallel_studio_xe_2019_professional_edition.tgz') # - version('professional.2018.4', '54ab4320da849108602096fa7a34aa21751068467e0d1584aa8f16352b77d323', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13718/parallel_studio_xe_2018_update4_professional_edition.tgz') - version('professional.2018.3', 'e0fb828de0a5f238f775b6122cc7e2c5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12999/parallel_studio_xe_2018_update3_professional_edition.tgz') - version('professional.2018.2', '91ed14aeb6157d60a0ec39929d0bc778', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12718/parallel_studio_xe_2018_update2_professional_edition.tgz') - version('professional.2018.1', '91669ff7afbfd07868a429a122c90357', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12375/parallel_studio_xe_2018_update1_professional_edition.tgz') - version('professional.2018.0', '9a233854e9218937bc5f46f02b3c7542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12062/parallel_studio_xe_2018_professional_edition.tgz') + version('professional.2018.4', sha256='54ab4320da849108602096fa7a34aa21751068467e0d1584aa8f16352b77d323', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13718/parallel_studio_xe_2018_update4_professional_edition.tgz') + version('professional.2018.3', sha256='3d8e72ccad31f243e43b72a925ad4a6908e2955682433898640ab783decf9960', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12999/parallel_studio_xe_2018_update3_professional_edition.tgz') + version('professional.2018.2', sha256='fc577b29fb2c687441d4faea14a6fb6da529fc78fcb778cbface59f40e128e02', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12718/parallel_studio_xe_2018_update2_professional_edition.tgz') + version('professional.2018.1', sha256='dd3e118069d87eebb614336732323b48172c8c8a653cde673a8ef02f7358e94d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12375/parallel_studio_xe_2018_update1_professional_edition.tgz') + version('professional.2018.0', sha256='72308ffa088391ea65726a79d7a73738206fbb1d8ed8563e3d06eab3120fb1a0', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12062/parallel_studio_xe_2018_professional_edition.tgz') # - version('professional.2017.7', '158461b000b31f0ef8169b6f0277bfb5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz') - version('professional.2017.6', 'b0bbddeec3e78a84b967c9ca70dade77', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz') - version('professional.2017.5', 'baeb8e584317fcdf1f60b8208bd4eab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz') - version('professional.2017.4', '27398416078e1e4005afced3e9a6df7e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz') - version('professional.2017.3', '691874735458d3e88fe0bcca4438b2a9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz') - version('professional.2017.2', '70e54b33d940a1609ff1d35d3c56e3b3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz') - version('professional.2017.1', '7f75a4a7e2c563be778c377f9d35a542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz') - version('professional.2017.0', '34c98e3329d6ac57408b738ae1daaa01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz') + version('professional.2017.7', sha256='133c3aa99841a4fe48149938a90f971467452a82f033be10cd9464ba810f6360', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz') + version('professional.2017.6', sha256='d771b00d3658934c424f294170125dc58ae9b03639aa898a2f115d7a7482dd3a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz') + version('professional.2017.5', sha256='36e496d1d1d7d7168cc3ba8f5bca9b52022339f30b62a87ed064b77a5cbccc09', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz') + version('professional.2017.4', sha256='27d34625adfc635d767c136b5417a372f322fabe6701b651d858a8fe06d07f2d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz') + version('professional.2017.3', sha256='856950c0493de3e8b4150e18f8821675c1cf75c2eea5ff0804f59eb301414bbe', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz') + version('professional.2017.2', sha256='83a655f0c2969409758488d70d6719fb5ea81a84b6da3feb641ce67bb240bc8a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz') + version('professional.2017.1', sha256='c808be744c98f7471c61258144859e8e8fc92771934281a16135803e941fd9b0', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz') + version('professional.2017.0', sha256='f380a56a25cf17941eb691a640035e79f92516346500e0df80fbdd46c5c1b301', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz') # - version('professional.2016.4', '16a641a06b156bb647c8a56e71f3bb33', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz') - version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz') - version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz') - version('professional.2016.1', '83b260ef3fcfd4e30afbeb7eb31b6b20', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz') - version('professional.2016.0', '00b4de9727a906a3aff468c26dd3f89c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz') + version('professional.2016.4', sha256='ea43c150ed6f9967bc781fe4253169a0447c69bac4fe2c563016a1ad2875ae23', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz') + version('professional.2016.3', sha256='aa7c6f1a6603fae07c2b01409c12de0811aa5947eaa71dfb1fe9898076c2773e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz') + version('professional.2016.2', sha256='280bf39c75d7f52f206759ca4d8b6334ab92d5970957b90f5aa286bb0aa8d65e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz') + version('professional.2016.1', sha256='f5a3ab9fb581e19bf1bd966f7d40a11905e002a2bfae1c4a2140544288ca3e48', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz') + version('professional.2016.0', sha256='fd4c32352fd78fc919601bedac5658ad5ac48efbc5700d9a8d42ed7d53bd8bb7', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz') # - version('professional.2015.6', 'd460f362c30017b60f85da2e51ad25bf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz') - version('professional.2015.1', '542b78c86beff9d7b01076a7be9c6ddc', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz') + version('professional.2015.6', sha256='e604ed2bb45d227b151dd2898f3edd93526d58d1db1cb9d6b6f614907864f392', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz') + version('professional.2015.1', sha256='84fdf48d1de20e1d580ba5d419a5bc1c55d217a4f5dc1807190ecffe0229a62b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz') # Composer Edition (basic tier; excluded: MPI/..., Advisor/Inspector/Vtune) - version('composer.2019.4', '1915993445323e1e78d6de73702a88fa3df2036109cde03d74ee38fef9f1abf2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/parallel_studio_xe_2019_update4_composer_edition.tgz') - version('composer.2019.3', '15373ac6df2a84e6dd9fa0eac8b5f07ab00cdbb67f494161fd0d4df7a71aff8e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15272/parallel_studio_xe_2019_update3_composer_edition.tgz') - version('composer.2019.1', 'db000cb2ebf411f6e91719db68a0c68b8d3f7d38ad7f2049ea5b2f1b5f006c25', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14832/parallel_studio_xe_2019_update1_composer_edition.tgz') - version('composer.2019.0', 'e1a29463038b063e01f694e2817c0fcf1a8e824e24f15a26ce85f20afa3f963a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13581/parallel_studio_xe_2019_composer_edition.tgz') + version('composer.2019.4', sha256='1915993445323e1e78d6de73702a88fa3df2036109cde03d74ee38fef9f1abf2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/parallel_studio_xe_2019_update4_composer_edition.tgz') + version('composer.2019.3', sha256='15373ac6df2a84e6dd9fa0eac8b5f07ab00cdbb67f494161fd0d4df7a71aff8e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15272/parallel_studio_xe_2019_update3_composer_edition.tgz') + version('composer.2019.1', sha256='db000cb2ebf411f6e91719db68a0c68b8d3f7d38ad7f2049ea5b2f1b5f006c25', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14832/parallel_studio_xe_2019_update1_composer_edition.tgz') + version('composer.2019.0', sha256='e1a29463038b063e01f694e2817c0fcf1a8e824e24f15a26ce85f20afa3f963a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13581/parallel_studio_xe_2019_composer_edition.tgz') # - version('composer.2018.4', '94aca8f091dff9535b02f022a37aef150b36925c8ef069335621496f8e4db267', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13722/parallel_studio_xe_2018_update4_composer_edition.tgz') - version('composer.2018.3', '234223cc470717c2095456d9f048d690', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz') - version('composer.2018.2', '76f820f53de4c1ff998229c983cf4f53', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz') - version('composer.2018.1', '28cb807126d713350f4aa6f9f167448a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz') - version('composer.2018.0', '31ba768fba6e7322957b03feaa3add28', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz') + version('composer.2018.4', sha256='94aca8f091dff9535b02f022a37aef150b36925c8ef069335621496f8e4db267', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13722/parallel_studio_xe_2018_update4_composer_edition.tgz') + version('composer.2018.3', sha256='f21f7759709a3d3e3390a8325fa89ac79b1fce8890c292e73b2ba3ec576ebd2b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz') + version('composer.2018.2', sha256='02d2a9fb10d9810f85dd77700215c4348d2e4475e814e4f086eb1442462667ff', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz') + version('composer.2018.1', sha256='db9aa417da185a03a63330c9d76ee8e88496ae6b771584d19003a29eedc7cab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz') + version('composer.2018.0', sha256='ecad64360fdaff2548a0ea250a396faf680077c5a83c3c3ce2c55f4f4270b904', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz') # - version('composer.2017.7', '4c02a4a29a8f2424f31baa23116a1001', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz') - version('composer.2017.6', 'd96cce0c3feef20091efde458f581a9f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz') - version('composer.2017.5', 'ede4ea9351fcf263103588ae0f130b4c2a79395529cdb698b0d6e866c4871f78', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12144/parallel_studio_xe_2017_update5_composer_edition.tgz') - version('composer.2017.4', 'd03d351809e182c481dc65e07376d9a2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz') - version('composer.2017.3', '52344df122c17ddff3687f84ceb21623', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz') - version('composer.2017.2', '2891ab1ece43eb61b6ab892f07c47f01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz') - version('composer.2017.1', '1f31976931ed8ec424ac7c3ef56f5e85', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz') - version('composer.2017.0', 'b67da0065a17a05f110ed1d15c3c6312', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz') + version('composer.2017.7', sha256='661e33b68e47bf335694d2255f5883955234e9085c8349783a5794eed2a937ad', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz') + version('composer.2017.6', sha256='771f50746fe130ea472394c42e25d2c7edae049ad809d2050945ef637becf65f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz') + version('composer.2017.5', sha256='ede4ea9351fcf263103588ae0f130b4c2a79395529cdb698b0d6e866c4871f78', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12144/parallel_studio_xe_2017_update5_composer_edition.tgz') + version('composer.2017.4', sha256='4304766f80206a27709be61641c16782fccf2b3fcf7285782cce921ddc9b10ff', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz') + version('composer.2017.3', sha256='3648578d7bba993ebb1da37c173979bfcfb47f26e7f4e17f257e78dea8fd96ab', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz') + version('composer.2017.2', sha256='abd26ab2a703e73ab93326984837818601c391782a6bce52da8b2a246798ad40', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz') + version('composer.2017.1', sha256='bc592abee829ba6e00a4f60961b486b80c15987ff1579d6560186407c84add6f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz') + version('composer.2017.0', sha256='d218db66a5bb57569bea00821ac95d4647eda7422bf8a178d1586b0fb314935a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz') # - version('composer.2016.4', '2bc9bfc9be9c1968a6e42efb4378f40e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz') - version('composer.2016.3', '3208eeabee951fc27579177b593cefe9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz') - version('composer.2016.2', '1133fb831312eb519f7da897fec223fa', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz') + version('composer.2016.4', sha256='17606c52cab6f5114223a2425923c8dd69f1858f5a3bdf280e0edea49ebd430d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz') + version('composer.2016.3', sha256='fcec90ba97533e4705077e0701813b5a3bcc197b010b03e96f83191a35c26acf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz') + version('composer.2016.2', sha256='6309ef8be1abba7737d3c1e17af64ca2620672b2da57afe2c3c643235f65b4c7', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz') # # Pre-2016, the only product was "Composer XE"; dir structure is different. - version('composer.2015.6', 'da9f8600c18d43d58fba0488844f79c9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz') - version('composer.2015.1', '85beae681ae56411a8e791a7c44a5c0a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz') + version('composer.2015.6', sha256='b1e09833469ca76a2834cd0a5bb5fea11ec9986da85abf4c6eed42cd96ec24cb', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz') + version('composer.2015.1', sha256='8a438fe20103e27bfda132955616d0c886aa6cfdd86dcd9764af5d937a8799d9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz') # Generic Variants variant('rpath', default=True, diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py index 7c3eb7d937f..4b646012611 100644 --- a/var/spack/repos/builtin/packages/intel-tbb/package.py +++ b/var/spack/repos/builtin/packages/intel-tbb/package.py @@ -22,30 +22,30 @@ class IntelTbb(Package): version('2019.3', sha256='b2244147bc8159cdd8f06a38afeb42f3237d3fc822555499d7ccfbd4b86f8ece') version('2019.2', sha256='1245aa394a92099e23ce2f60cdd50c90eb3ddcd61d86cae010ef2f1de61f32d9') version('2019.1', sha256='a4875c6b6853213083e52ecd303546bdf424568ec67cfc7e51d132a7c037c66a') - version('2019', '2119f1db2f905dc5b423482d7689b7d6') - version('2018.6', '9a0f78db4f72356068b00f29f54ee6bc') - version('2018.5', 'ff3ae09f8c23892fbc3008c39f78288f') - version('2018.4', '5e2e6ba0e25624a94331c945856551c2') - version('2018.3', 'cd2e136598ffa5c136f077ee85a35b4c') - version('2018.2', '0b8dfe30917a54e40828eeb0ed7562ae') - version('2018.1', 'b2f2fa09adf44a22f4024049907f774b') - version('2018', '7fb30d5ea2545f26ce02757d9ab05e6c') - version('2017.8', '7240f57f1aeea0e266a5e17ae68fdc16') - version('2017.7', '364f2a4b80e978f38a69cbf7c466b898') - version('2017.6', 'ec21254af4fc2a29574c272f501a3138') - version('2017.5', '85b41c64102c052e24d8a39f6193e599') - version('2017.4', '71526b2fef098515e212302d1455de7d') - version('2017.3', 'd7622eeaafeff8d271c7aa684bd82ddb') - version('2017.2', '9605cbea96998a10a186fc72c35cbd76') - version('2017.1', '6c0fe8aa7bc911a85e8e522e620511b3') - version('2017', '9e7f9ea684ecf84ac74dcd3c6012cfa6') - version('4.4.6', '20e15206f70c2651bfc964e451a443a0') - version('4.4.5', '531a67cd98f9b4ec8ece95c5f8193a83') - version('4.4.4', '61531b2e8684e06a621dcdca1a7a420e') - version('4.4.3', '8e3e39e1fdfb3f7c3a5ac8ec1afe186e') - version('4.4.2', 'e92b110e8eb238741b00e3789b39969e') - version('4.4.1', 'a02c9958f02c1b5f3626874219979ae8') - version('4.4', '1d512085221996eae6cec04e1a4cd3dd') + version('2019', sha256='4d149895826cea785cd3b9a14f4aa743b6ef0df520eca7ee27d438fdc3d73399') + version('2018.6', sha256='d3e5fbca3cc643d03bf332d576ff85e19aa774b483f148f95cd7d09958372109') + version('2018.5', sha256='c4c2896af527392496c5e01ef8579058a71b6eebbd695924cd138841c13f07be') + version('2018.4', sha256='d5604a04787c8a037d4944eeb89792e7c45f6a83c141b20df7ee89c2fb012ed1') + version('2018.3', sha256='23793c8645480148e9559df96b386b780f92194c80120acce79fcdaae0d81f45') + version('2018.2', sha256='78bb9bae474736d213342f01fe1a6d00c6939d5c75b367e2e43e7bf29a6d8eca') + version('2018.1', sha256='c6462217d4ecef2b44fce63cfdf31f9db4f6ff493869899d497a5aef68b05fc5') + version('2018', sha256='94f643f1edfaccb57d64b503c7c96f00dec64e8635c054bbaa33855d72c5822d') + version('2017.8', sha256='1b1357f280e750d42506212adad02f85ac07c9d3e3c0813104f9122ef350497f') + version('2017.7', sha256='78ad6ec9dd492b9dcc4753938b06716f7458506084adc138ced09aa0aa609b6b') + version('2017.6', sha256='40d5409a6fd7e214a21fd1949df422ba113fa78fde42a6aac40a2fba36e9bcdb') + version('2017.5', sha256='3122c87a35fde759567c8579ba36a36037c6df84c3f9c4df6c9e171f866f352f') + version('2017.4', sha256='ed4f0cfc4acec8a0cf253037e8c555dd32ebe1b80b34fb0e3b2bf54087932562') + version('2017.3', sha256='00a8b2798c498507572e24c2db7bf4896f05b760a38ed9ba566ffd348a7c6cef') + version('2017.2', sha256='85e44041d967ce8c70077dbb57941cfa1d351688855aec47eb14c74eb2075f28') + version('2017.1', sha256='a68bb7926fb9bee2a5f17b293c6d6aa33ccb089c3b321569bd4fe281cf65fa77') + version('2017', sha256='c49139279067df1260dae4f0fe7e4d485898ce45e5f7e314c37eb5da8a0c303a') + version('4.4.6', sha256='1d6b7e7db9141238c70984103f04280605dbcaa7fbcd049d332d2e73deed4f6d') + version('4.4.5', sha256='984308f9dd8a36ff274c124b6f7f7d0ff74d4b7ebdf06511af78e098b5b6e70f') + version('4.4.4', sha256='40e94c1adfd13308d207971629316ae9f76639b24f080bae8757c42d35778f10') + version('4.4.3', sha256='9acb1c4e71edc3d5004ab9f0ed2bbd697ecec28a4315bbd2be8c5365e8214b90') + version('4.4.2', sha256='3f6d7a32ac8b58469de7df3a2fcfe318793241ea39ce73aae1e637dbed833375') + version('4.4.1', sha256='d67c5860ba1116b320b0d60a0ce403b088dc19355ab32c28cdaa3e352609713a') + version('4.4', sha256='88e37f08ffcfaa24a2caf6c1a9084000cce689cc4b11edea7e89b20ab74ceceb') provides('tbb') diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py index 603ba4036f0..7a207dccdbd 100644 --- a/var/spack/repos/builtin/packages/intel/package.py +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -13,33 +13,33 @@ class Intel(IntelPackage): # Same as in ../intel-parallel-studio/package.py, Composer Edition, # but the version numbering in Spack differs. - version('19.0.4', '1915993445323e1e78d6de73702a88fa3df2036109cde03d74ee38fef9f1abf2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/parallel_studio_xe_2019_update4_composer_edition.tgz') - version('19.0.3', '15373ac6df2a84e6dd9fa0eac8b5f07ab00cdbb67f494161fd0d4df7a71aff8e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15272/parallel_studio_xe_2019_update3_composer_edition.tgz') - version('19.0.1', 'db000cb2ebf411f6e91719db68a0c68b8d3f7d38ad7f2049ea5b2f1b5f006c25', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14832/parallel_studio_xe_2019_update1_composer_edition.tgz') - version('19.0.0', 'e1a29463038b063e01f694e2817c0fcf1a8e824e24f15a26ce85f20afa3f963a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13581/parallel_studio_xe_2019_composer_edition.tgz') + version('19.0.4', sha256='1915993445323e1e78d6de73702a88fa3df2036109cde03d74ee38fef9f1abf2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/parallel_studio_xe_2019_update4_composer_edition.tgz') + version('19.0.3', sha256='15373ac6df2a84e6dd9fa0eac8b5f07ab00cdbb67f494161fd0d4df7a71aff8e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15272/parallel_studio_xe_2019_update3_composer_edition.tgz') + version('19.0.1', sha256='db000cb2ebf411f6e91719db68a0c68b8d3f7d38ad7f2049ea5b2f1b5f006c25', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14832/parallel_studio_xe_2019_update1_composer_edition.tgz') + version('19.0.0', sha256='e1a29463038b063e01f694e2817c0fcf1a8e824e24f15a26ce85f20afa3f963a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13581/parallel_studio_xe_2019_composer_edition.tgz') # - version('18.0.4', '94aca8f091dff9535b02f022a37aef150b36925c8ef069335621496f8e4db267', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13722/parallel_studio_xe_2018_update4_composer_edition.tgz') - version('18.0.3', '234223cc470717c2095456d9f048d690', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz') - version('18.0.2', '76f820f53de4c1ff998229c983cf4f53', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz') - version('18.0.1', '28cb807126d713350f4aa6f9f167448a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz') - version('18.0.0', '31ba768fba6e7322957b03feaa3add28', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz') + version('18.0.4', sha256='94aca8f091dff9535b02f022a37aef150b36925c8ef069335621496f8e4db267', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13722/parallel_studio_xe_2018_update4_composer_edition.tgz') + version('18.0.3', sha256='f21f7759709a3d3e3390a8325fa89ac79b1fce8890c292e73b2ba3ec576ebd2b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz') + version('18.0.2', sha256='02d2a9fb10d9810f85dd77700215c4348d2e4475e814e4f086eb1442462667ff', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz') + version('18.0.1', sha256='db9aa417da185a03a63330c9d76ee8e88496ae6b771584d19003a29eedc7cab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz') + version('18.0.0', sha256='ecad64360fdaff2548a0ea250a396faf680077c5a83c3c3ce2c55f4f4270b904', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz') # - version('17.0.7', '4c02a4a29a8f2424f31baa23116a1001', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz') - version('17.0.6', 'd96cce0c3feef20091efde458f581a9f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz') - version('17.0.5', 'ede4ea9351fcf263103588ae0f130b4c2a79395529cdb698b0d6e866c4871f78', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12144/parallel_studio_xe_2017_update5_composer_edition.tgz') - version('17.0.4', 'd03d351809e182c481dc65e07376d9a2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz') - version('17.0.3', '52344df122c17ddff3687f84ceb21623', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz') - version('17.0.2', '2891ab1ece43eb61b6ab892f07c47f01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz') - version('17.0.1', '1f31976931ed8ec424ac7c3ef56f5e85', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz') - version('17.0.0', 'b67da0065a17a05f110ed1d15c3c6312', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz') + version('17.0.7', sha256='661e33b68e47bf335694d2255f5883955234e9085c8349783a5794eed2a937ad', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz') + version('17.0.6', sha256='771f50746fe130ea472394c42e25d2c7edae049ad809d2050945ef637becf65f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz') + version('17.0.5', sha256='ede4ea9351fcf263103588ae0f130b4c2a79395529cdb698b0d6e866c4871f78', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12144/parallel_studio_xe_2017_update5_composer_edition.tgz') + version('17.0.4', sha256='4304766f80206a27709be61641c16782fccf2b3fcf7285782cce921ddc9b10ff', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz') + version('17.0.3', sha256='3648578d7bba993ebb1da37c173979bfcfb47f26e7f4e17f257e78dea8fd96ab', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz') + version('17.0.2', sha256='abd26ab2a703e73ab93326984837818601c391782a6bce52da8b2a246798ad40', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz') + version('17.0.1', sha256='bc592abee829ba6e00a4f60961b486b80c15987ff1579d6560186407c84add6f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz') + version('17.0.0', sha256='d218db66a5bb57569bea00821ac95d4647eda7422bf8a178d1586b0fb314935a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz') # - version('16.0.4', '2bc9bfc9be9c1968a6e42efb4378f40e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz') - version('16.0.3', '3208eeabee951fc27579177b593cefe9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz') - version('16.0.2', '1133fb831312eb519f7da897fec223fa', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz') + version('16.0.4', sha256='17606c52cab6f5114223a2425923c8dd69f1858f5a3bdf280e0edea49ebd430d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz') + version('16.0.3', sha256='fcec90ba97533e4705077e0701813b5a3bcc197b010b03e96f83191a35c26acf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz') + version('16.0.2', sha256='6309ef8be1abba7737d3c1e17af64ca2620672b2da57afe2c3c643235f65b4c7', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz') # # Grandfathered release; different directory structure. - version('15.0.6', 'da9f8600c18d43d58fba0488844f79c9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz') - version('15.0.1', '85beae681ae56411a8e791a7c44a5c0a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz') + version('15.0.6', sha256='b1e09833469ca76a2834cd0a5bb5fea11ec9986da85abf4c6eed42cd96ec24cb', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz') + version('15.0.1', sha256='8a438fe20103e27bfda132955616d0c886aa6cfdd86dcd9764af5d937a8799d9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz') variant('rpath', default=True, description='Add rpath to .cfg files') diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py index e7f6e5e8578..dd711f4beee 100644 --- a/var/spack/repos/builtin/packages/intltool/package.py +++ b/var/spack/repos/builtin/packages/intltool/package.py @@ -14,7 +14,7 @@ class Intltool(AutotoolsPackage): url = 'https://launchpad.net/intltool/trunk/0.51.0/+download/intltool-0.51.0.tar.gz' list_url = 'https://launchpad.net/intltool/+download' - version('0.51.0', '12e517cac2b57a0121cda351570f1e63') + version('0.51.0', sha256='67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd') # requires XML::Parser perl module depends_on('perl-xml-parser', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py index 3e37cbdb284..023945979dd 100644 --- a/var/spack/repos/builtin/packages/ior/package.py +++ b/var/spack/repos/builtin/packages/ior/package.py @@ -14,7 +14,7 @@ class Ior(AutotoolsPackage): url = "https://github.com/hpc/ior/archive/3.2.0.tar.gz" version('3.2.0', sha256='91a766fb9c34b5780705d0997b71b236a1120da46652763ba11d9a8c44251852') - version('3.0.1', '71150025e0bb6ea1761150f48b553065') + version('3.0.1', sha256='0cbefbcdb02fb13ba364e102f9e7cc2dcf761698533dac25de446a3a3e81390d') variant('hdf5', default=False, description='support IO with HDF5 backend') variant('ncmpi', default=False, description='support IO with NCMPI backend') diff --git a/var/spack/repos/builtin/packages/iozone/package.py b/var/spack/repos/builtin/packages/iozone/package.py index 54767aa4e61..f25519fb691 100644 --- a/var/spack/repos/builtin/packages/iozone/package.py +++ b/var/spack/repos/builtin/packages/iozone/package.py @@ -14,7 +14,7 @@ class Iozone(MakefilePackage): homepage = "http://www.iozone.org/" url = "http://www.iozone.org/src/current/iozone3_465.tar" - version('3_465', 'c924e5e46fb1cf8145f420e8e57eb954') + version('3_465', sha256='2e3d72916e7d7340a7c505fc0c3d28553fcc5ff2daf41d811368e55bd4e6a293') # TODO: Add support for other architectures as necessary build_targets = ['linux-AMD64'] diff --git a/var/spack/repos/builtin/packages/iperf2/package.py b/var/spack/repos/builtin/packages/iperf2/package.py index 57f684aadbf..e35aa9fe602 100644 --- a/var/spack/repos/builtin/packages/iperf2/package.py +++ b/var/spack/repos/builtin/packages/iperf2/package.py @@ -14,4 +14,4 @@ class Iperf2(AutotoolsPackage): homepage = "https://sourceforge.net/projects/iperf2" url = "https://downloads.sourceforge.net/project/iperf2/iperf-2.0.12.tar.gz" - version('2.0.12', 'e501e26b9289097086ce0c44a42b10bc') + version('2.0.12', sha256='367f651fb1264b13f6518e41b8a7e08ce3e41b2a1c80e99ff0347561eed32646') diff --git a/var/spack/repos/builtin/packages/iperf3/package.py b/var/spack/repos/builtin/packages/iperf3/package.py index 37e9207c0a7..5dee626d4e2 100644 --- a/var/spack/repos/builtin/packages/iperf3/package.py +++ b/var/spack/repos/builtin/packages/iperf3/package.py @@ -14,4 +14,4 @@ class Iperf3(AutotoolsPackage): homepage = "https://software.es.net/iperf/" url = "https://github.com/esnet/iperf/archive/3.6.tar.gz" - version('3.6', '5082ffc4141abc1bac7cbd59337ff409') + version('3.6', sha256='1ad23f70a8eb4b892a3cbb247cafa956e0f5c7d8b8601b1d9c8031c2a806f23f') diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py index 31175e0e57c..fd9c87fba1e 100644 --- a/var/spack/repos/builtin/packages/ipopt/package.py +++ b/var/spack/repos/builtin/packages/ipopt/package.py @@ -12,17 +12,17 @@ class Ipopt(AutotoolsPackage): homepage = "https://projects.coin-or.org/Ipopt" url = "http://www.coin-or.org/download/source/Ipopt/Ipopt-3.12.4.tgz" - version('3.12.10', 'e1a3ad09e41edbfe41948555ece0bdc78757a5ca764b6be5a9a127af2e202d2e') - version('3.12.9', '8ff3fe1a8560896fc5559839a87c2530cac4ed231b0806e487bfd3cf2d294ab8') - version('3.12.8', '62c6de314220851b8f4d6898b9ae8cf0a8f1e96b68429be1161f8550bb7ddb03') - version('3.12.7', '2a36e4a04717a8ed7012ac7d1253ae4ffbc1a8fd') - version('3.12.6', 'ed4072427fab786fcf6082fe7e6f6c2ed9b5e6f8') - version('3.12.5', '3f63ddfff517235ead17af6cceb426ca858dda37') - version('3.12.4', '12a8ecaff8dd90025ddea6c65b49cb03') - version('3.12.3', 'c560cbfa9cbf62acf8b485823c255a1b') - version('3.12.2', 'ec1e855257d7de09e122c446506fb00d') - version('3.12.1', 'ceaf895ce80c77778f2cab68ba9f17f3') - version('3.12.0', 'f7dfc3aa106a6711a85214de7595e827') + version('3.12.10', sha256='e1a3ad09e41edbfe41948555ece0bdc78757a5ca764b6be5a9a127af2e202d2e') + version('3.12.9', sha256='8ff3fe1a8560896fc5559839a87c2530cac4ed231b0806e487bfd3cf2d294ab8') + version('3.12.8', sha256='62c6de314220851b8f4d6898b9ae8cf0a8f1e96b68429be1161f8550bb7ddb03') + version('3.12.7', sha256='9c8b02149fa4f0cdf63e838ae68f86aa41a577d7f05932139eede9179f314861') + version('3.12.6', sha256='6aaa6bd862d54eba6fb966950fa6928ca01d66cf4cb842b2f41a7ebfa61eee2b') + version('3.12.5', sha256='53e7af6eefcb6de1f8e936c9c887c7bcb5a9fa4fcf7673a227f16de131147325') + version('3.12.4', sha256='292afd952c25ec9fe6225041683dcbd3cb76e15a128764671927dbaf881c2e89') + version('3.12.3', sha256='754fb9473bc683b59a53d2057ff852d0a8d56198bcdba2e2529ce299243fdaa5') + version('3.12.2', sha256='3903657788bff7d7743f8bb25c34ccf91c445e72a4710cb821c024107bd1b474') + version('3.12.1', sha256='d6c18f7c5bf486712b493167d27ec6e940ad376c5b903b97acc5a3ade1c0a3ef') + version('3.12.0', sha256='ed19e5e7174355e93c93c798b5056036e2fd2ec78cf0f3954876483f74fe618b') variant('coinhsl', default=False, description="Build with Coin Harwell Subroutine Libraries") diff --git a/var/spack/repos/builtin/packages/isaac-server/package.py b/var/spack/repos/builtin/packages/isaac-server/package.py index e712df2b298..df501484396 100644 --- a/var/spack/repos/builtin/packages/isaac-server/package.py +++ b/var/spack/repos/builtin/packages/isaac-server/package.py @@ -17,11 +17,11 @@ class IsaacServer(CMakePackage): version('develop', branch='dev') version('master', branch='master') - version('1.4.0', '3ad05c8fad4673366077204c5d39285f') - version('1.3.3', '7aeebaf0c5a77e2cb9bea066750e369b') - version('1.3.2', 'c557daa74de52fd79e734c9758fca38b') - version('1.3.1', '7fe075f9af68d05355eaba0e224f20ca') - version('1.3.0', 'c8a794da9bb998ef0e75449bfece1a12') + version('1.4.0', sha256='6cbd4cc54a22de5e5a3427e44141db6e7b80b33fe7a0c707390a113655bf344e') + version('1.3.3', sha256='92a972d05d315ad66546671c047b7edf8ed0e05d64d2b8d77ababb5bb9b93d8e') + version('1.3.2', sha256='e6eedc641de5b0a7c5ea5cda6b11e9b6d4a78dfac8be90302147b26d09859a68') + version('1.3.1', sha256='7dead8f3d5467cbd2cde8187e7b860a4ab7796348895d18291f97a76e28757cf') + version('1.3.0', sha256='fcf10f4738e7790ef6604e1e2cdd052a129ba4e53a439deaafa9fb2a70585574') # variant('gstreamer', default=False, description= \ # 'Support for RTP streams, e.g. to Twitch or Youtube') diff --git a/var/spack/repos/builtin/packages/isaac/package.py b/var/spack/repos/builtin/packages/isaac/package.py index c2d5d78cc01..0477aabf8e3 100644 --- a/var/spack/repos/builtin/packages/isaac/package.py +++ b/var/spack/repos/builtin/packages/isaac/package.py @@ -17,11 +17,11 @@ class Isaac(CMakePackage): version('develop', branch='dev') version('master', branch='master') - version('1.4.0', '3ad05c8fad4673366077204c5d39285f') - version('1.3.3', '7aeebaf0c5a77e2cb9bea066750e369b') - version('1.3.2', 'c557daa74de52fd79e734c9758fca38b') - version('1.3.1', '7fe075f9af68d05355eaba0e224f20ca') - version('1.3.0', 'c8a794da9bb998ef0e75449bfece1a12') + version('1.4.0', sha256='6cbd4cc54a22de5e5a3427e44141db6e7b80b33fe7a0c707390a113655bf344e') + version('1.3.3', sha256='92a972d05d315ad66546671c047b7edf8ed0e05d64d2b8d77ababb5bb9b93d8e') + version('1.3.2', sha256='e6eedc641de5b0a7c5ea5cda6b11e9b6d4a78dfac8be90302147b26d09859a68') + version('1.3.1', sha256='7dead8f3d5467cbd2cde8187e7b860a4ab7796348895d18291f97a76e28757cf') + version('1.3.0', sha256='fcf10f4738e7790ef6604e1e2cdd052a129ba4e53a439deaafa9fb2a70585574') variant('cuda', default=True, description='Generate CUDA kernels for Nvidia GPUs') diff --git a/var/spack/repos/builtin/packages/itstool/package.py b/var/spack/repos/builtin/packages/itstool/package.py index c81544ca2ee..18923479ffc 100644 --- a/var/spack/repos/builtin/packages/itstool/package.py +++ b/var/spack/repos/builtin/packages/itstool/package.py @@ -14,7 +14,7 @@ class Itstool(AutotoolsPackage): homepage = "http://itstool.org/" url = "http://files.itstool.org/itstool/itstool-2.0.2.tar.bz2" - version('2.0.2', 'd472d877a7bc49899a73d442085b2f93') - version('2.0.1', '40935cfb08228488bd45575e5f001a34') - version('2.0.0', 'd8c702c3e8961db83d04182c2aa4730b') - version('1.2.0', 'c0925f6869e33af8e7fe56848c129152') + version('2.0.2', sha256='bf909fb59b11a646681a8534d5700fec99be83bb2c57badf8c1844512227033a') + version('2.0.1', sha256='ec6b1b32403cbe338b6ac63c61ab1ecd361f539a6e41ef50eae56a4f577234d1') + version('2.0.0', sha256='14708111b11b4a70e240e3b404d7a58941e61dbb5caf7e18833294d654c09169') + version('1.2.0', sha256='46fed63fb89c72dbfc03097b4477084ff05ad6f171212d8f1f1546ea543978aa') diff --git a/var/spack/repos/builtin/packages/itsx/package.py b/var/spack/repos/builtin/packages/itsx/package.py index dd6eb61ff5a..fc31fee23ca 100644 --- a/var/spack/repos/builtin/packages/itsx/package.py +++ b/var/spack/repos/builtin/packages/itsx/package.py @@ -14,7 +14,7 @@ class Itsx(Package): homepage = "http://microbiology.se/software/itsx/" url = "http://microbiology.se/sw/ITSx_1.0.11.tar.gz" - version('1.0.11', '1bff12f1d5742f19be6ca585e9bf81fa') + version('1.0.11', sha256='8f4f76fc9c43b61f4dd4cd8dc4e495e9687943e15515396583f7a757651d435e') depends_on('perl', type=('build', 'run')) depends_on('hmmer') diff --git a/var/spack/repos/builtin/packages/jackcess/package.py b/var/spack/repos/builtin/packages/jackcess/package.py index e988df01a9a..64486fd3582 100644 --- a/var/spack/repos/builtin/packages/jackcess/package.py +++ b/var/spack/repos/builtin/packages/jackcess/package.py @@ -13,8 +13,8 @@ class Jackcess(Package): homepage = "http://jackcess.sourceforge.net/" url = "https://sourceforge.net/projects/jackcess/files/jackcess/2.1.12/jackcess-2.1.12.jar" - version('2.1.12', '7d051d8dd93f2fe7e5e86389ea380619', expand=False) - version('1.2.14.3', 'ef778421c1385ac9ab4aa7edfb954caa', expand=False, + version('2.1.12', sha256='347e666d8f6abf382a0e1a7597421911423f20cf71237225f9eb53626f377f22', expand=False) + version('1.2.14.3', sha256='a6fab0c4b5daf23dcf7fd309ee4ffc6df12ff982510c094e45442adf88712787', expand=False, url='https://sourceforge.net/projects/jackcess/files/jackcess/Older%20Releases/1.2.14.3/jackcess-1.2.14.3.jar') extends('jdk') diff --git a/var/spack/repos/builtin/packages/jags/package.py b/var/spack/repos/builtin/packages/jags/package.py index 42601898496..19768060625 100644 --- a/var/spack/repos/builtin/packages/jags/package.py +++ b/var/spack/repos/builtin/packages/jags/package.py @@ -16,8 +16,8 @@ class Jags(AutotoolsPackage): homepage = "http://mcmc-jags.sourceforge.net/" url = "https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Source/JAGS-4.2.0.tar.gz" - version('4.3.0', 'd88dff326603deee39ce7fa4234c5a43') - version('4.2.0', '9e521b3cfb23d3290a8c6bc0b79bf426') + version('4.3.0', sha256='8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc') + version('4.2.0', sha256='af3e9d2896d3e712f99e2a0c81091c6b08f096650af6aa9d0c631c0790409cf7') depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/jansson/package.py b/var/spack/repos/builtin/packages/jansson/package.py index 4ccabaa9941..5815d7aeba2 100644 --- a/var/spack/repos/builtin/packages/jansson/package.py +++ b/var/spack/repos/builtin/packages/jansson/package.py @@ -14,7 +14,7 @@ class Jansson(CMakePackage): url = "https://github.com/akheron/jansson/archive/v2.9.tar.gz" maintainers = ['ax3l'] - version('2.9', 'd2db25c437b359fc5a065ed938962237') + version('2.9', sha256='952fa714b399e71c1c3aa020e32e899f290c82126ca4d0d14cff5d10af457656') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/jasper/package.py b/var/spack/repos/builtin/packages/jasper/package.py index 166dec67699..f3a5819bd84 100644 --- a/var/spack/repos/builtin/packages/jasper/package.py +++ b/var/spack/repos/builtin/packages/jasper/package.py @@ -13,9 +13,9 @@ class Jasper(Package): url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz" list_url = homepage - version('2.0.14', '23561b51da8eb5d0dc85b91eff3d9a7f', + version('2.0.14', sha256='2a1f61e55afe8b4ce8115e1508c5d7cb314d56dfcc2dd323f90c072f88ccf57b', url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz") - version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754', + version('1.900.1', sha256='6b905a9c2aca2e275544212666eefc4eb44d95d0a57e4305457b407fe63f9494', url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip") variant('jpeg', default=True, description='Enable the use of the JPEG library') diff --git a/var/spack/repos/builtin/packages/jbigkit/package.py b/var/spack/repos/builtin/packages/jbigkit/package.py index 366a46e9ca2..b829a54132e 100644 --- a/var/spack/repos/builtin/packages/jbigkit/package.py +++ b/var/spack/repos/builtin/packages/jbigkit/package.py @@ -13,8 +13,8 @@ class Jbigkit(MakefilePackage): homepage = "http://www.cl.cam.ac.uk/~mgk25/jbigkit/" url = "http://www.cl.cam.ac.uk/~mgk25/jbigkit/download/jbigkit-2.1.tar.gz" - version('2.1', 'ebcf09bed9f14d7fa188d3bd57349522') - version('1.6', 'ce196e45f293d40ba76af3dc981ccfd7') + version('2.1', sha256='de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932') + version('1.6', sha256='d841b6d0723c1082450967f3ea500be01810a34ec4a97ad10985ae7071a6150b') build_directory = 'libjbig' diff --git a/var/spack/repos/builtin/packages/jchronoss/package.py b/var/spack/repos/builtin/packages/jchronoss/package.py index fbe3488f65f..ec631d52d34 100644 --- a/var/spack/repos/builtin/packages/jchronoss/package.py +++ b/var/spack/repos/builtin/packages/jchronoss/package.py @@ -14,10 +14,10 @@ class Jchronoss(CMakePackage): homepage = "http://jchronoss.hpcframework.com" url = "http://fs.paratools.com/mpc/contrib/apps/jchronoss/JCHRONOSS-1.2.tar.gz" - version('1.2', 'f083ca453537e4f60ad17d266bbab1f1') - version('1.1.1', '2d78a0998efec20e7726af19fff76a72') - version('1.1', 'a8ba0b21b18548874b8ab2a6ca6e1081') - version('1.0', '78d81e00248e21f4adea4a1ccfd6156b') + version('1.2', sha256='52a565a28c0b83b433065060863d29f2b3e4b05f4f26b7a5893a21a2c66d6eba') + version('1.1.1', sha256='5a11463b7295817f503c58dda1a82c0d3568bdee5e9d13d59e00d337ba84dc45') + version('1.1', sha256='e8230416c94fb58516a4b9293efd0a67edf4a37e82cfae2ced2c0af8b4615f22') + version('1.0', sha256='6a92d3cf2424fc7eaaeac9bfefe395596275e552ac5660eb4543e43679586f24') variant("realtime", default=False, description="Enable Real-Time support") variant("openmp", default=False, description="Enable OpenMP constructs") diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index 8109138b11e..461b0e6aa23 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -46,22 +46,22 @@ class Jdk(Package): url='http://download.oracle.com/otn-pub/java/jdk/11.0.1+13/90cf5d8f270a4347a95050320eef3fb7/jdk-11.0.1_linux-x64_bin.tar.gz') version('10.0.2_13', sha256='6633c20d53c50c20835364d0f3e172e0cbbce78fff81867488f22a6298fa372b', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/10.0.2+13/19aef61b38124481863b1413dce1855f/jdk-10.0.2_linux-x64_bin.tar.gz') - version('10.0.1_10', 'ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', curl_options=curl_options, + version('10.0.1_10', sha256='ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz') version('1.8.0_202', sha256='9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0', curl_options=curl_options, url='https://download.oracle.com/otn-pub/java/jdk/8u202-b08/1961070e4c9b4e26a04e7f5a083f551e/jdk-8u202-linux-x64.tar.gz') - version('1.8.0_181-b13', 'ef599e322eee42f6769991dd3e3b1a31', curl_options=curl_options, + version('1.8.0_181-b13', md5='ef599e322eee42f6769991dd3e3b1a31', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/8u181-b13/96a7b8442fe848ef90c96a2fad6ed6d1/jdk-8u181-linux-x64.tar.gz') - version('1.8.0_172-b11', 'eda2945e8c02b84adbf78f46c37b71c1', curl_options=curl_options, + version('1.8.0_172-b11', md5='eda2945e8c02b84adbf78f46c37b71c1', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/8u172-b11/a58eab1ec242421181065cdc37240b08/jdk-8u172-linux-x64.tar.gz') - version('1.8.0_141-b15', '8cf4c4e00744bfafc023d770cb65328c', curl_options=curl_options, + version('1.8.0_141-b15', sha256='041d5218fbea6cd7e81c8c15e51d0d32911573af2ed69e066787a8dc8a39ba4f', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz') - version('1.8.0_131-b11', '75b2cb2249710d822a60f83e28860053', curl_options=curl_options, + version('1.8.0_131-b11', sha256='62b215bdfb48bace523723cdbb2157c665e6a25429c73828a32f00e587301236', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz') - version('1.8.0_92-b14', '65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options) - version('1.8.0_73-b02', '1b0120970aa8bc182606a16bf848a686', curl_options=curl_options) - version('1.8.0_66-b17', '88f31f3d642c3287134297b8c10e61bf', curl_options=curl_options) - version('1.7.0_80-b0', '6152f8a7561acf795ca4701daa10a965', curl_options=curl_options) + version('1.8.0_92-b14', md5='65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options) + version('1.8.0_73-b02', md5='1b0120970aa8bc182606a16bf848a686', curl_options=curl_options) + version('1.8.0_66-b17', md5='88f31f3d642c3287134297b8c10e61bf', curl_options=curl_options) + version('1.7.0_80-b0', md5='6152f8a7561acf795ca4701daa10a965', curl_options=curl_options) provides('java') provides('java@12', when='@12.0:12.999') diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py index 662139c2c00..3063f456088 100644 --- a/var/spack/repos/builtin/packages/jellyfish/package.py +++ b/var/spack/repos/builtin/packages/jellyfish/package.py @@ -14,8 +14,8 @@ class Jellyfish(AutotoolsPackage): url = "https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz" list_url = "http://www.cbcb.umd.edu/software/jellyfish/" - version('2.2.7', 'f741192d9061f28e34cb67c86a1027ab') - version('1.1.11', 'dc994ea8b0896156500ea8c648f24846', + version('2.2.7', sha256='d80420b4924aa0119353a5b704f923863abc802e94efeb531593147c13e631a8') + version('1.1.11', sha256='496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2', url='http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py index 2fd801c2719..febc5290814 100644 --- a/var/spack/repos/builtin/packages/jemalloc/package.py +++ b/var/spack/repos/builtin/packages/jemalloc/package.py @@ -13,13 +13,13 @@ class Jemalloc(Package): url = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2" version('5.2.1', sha256='34330e5ce276099e2e8950d9335db5a875689a4c6a56751ef3b1d8c537f887f6') - version('4.5.0', 'a5624318fbf5bf653697306642683a11') - version('4.4.0', '81b59778e19696d99e2f7922820671b0') - version('4.3.1', 'f204c0ea1aef92fbb339dc640de338a6') - version('4.2.1', '094b0a7b8c77c464d0dc8f0643fd3901') - version('4.2.0', 'e6b5d5a1ea93a04207528d274efdd144') - version('4.1.0', 'c4e53c947905a533d5899e5cc3da1f94') - version('4.0.4', '687c5cc53b9a7ab711ccd680351ff988') + version('4.5.0', sha256='9409d85664b4f135b77518b0b118c549009dc10f6cba14557d170476611f6780') + version('4.4.0', sha256='a7aea63e9718d2f1adf81d87e3df3cb1b58deb86fc77bad5d702c4c59687b033') + version('4.3.1', sha256='f7bb183ad8056941791e0f075b802e8ff10bd6e2d904e682f87c8f6a510c278b') + version('4.2.1', sha256='5630650d5c1caab95d2f0898de4fe5ab8519dc680b04963b38bb425ef6a42d57') + version('4.2.0', sha256='b216ddaeb901697fe38bd30ea02d7505a4b60e8979092009f95cfda860d46acb') + version('4.1.0', sha256='fad06d714f72adb4265783bc169c6d98eeb032d57ba02d87d1dcb4a2d933ec8e') + version('4.0.4', sha256='3fda8d8d7fcd041aa0bebbecd45c46b28873cf37bd36c56bf44961b36d0f42d0') variant('stats', default=False, description='Enable heap statistics') variant('prof', default=False, description='Enable heap profiling') diff --git a/var/spack/repos/builtin/packages/jmol/package.py b/var/spack/repos/builtin/packages/jmol/package.py index ca191ac52ac..421199f70fe 100644 --- a/var/spack/repos/builtin/packages/jmol/package.py +++ b/var/spack/repos/builtin/packages/jmol/package.py @@ -13,7 +13,7 @@ class Jmol(Package): homepage = "http://jmol.sourceforge.net/" url = "https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.8/Jmol%2014.8.0/Jmol-14.8.0-binary.tar.gz" - version('14.8.0', '3c9f4004b9e617ea3ea0b78ab32397ea') + version('14.8.0', sha256='8ec45e8d289aa0762194ca71848edc7d736121ddc72276031a253a3651e6d588') depends_on('java', type='run') diff --git a/var/spack/repos/builtin/packages/jq/package.py b/var/spack/repos/builtin/packages/jq/package.py index 5fa827c5f55..a97c6c4b9ec 100644 --- a/var/spack/repos/builtin/packages/jq/package.py +++ b/var/spack/repos/builtin/packages/jq/package.py @@ -12,7 +12,7 @@ class Jq(AutotoolsPackage): homepage = "https://stedolan.github.io/jq/" url = "https://github.com/stedolan/jq/archive/jq-1.5.tar.gz" - version('1.5', 'c8070bd6ec275404f77db3d2e568c9a3') + version('1.5', sha256='d5667641d28c27d0c1e70de83e7f9bd8b2fed7fbf6a1d68731177d400a533c65') depends_on('oniguruma') depends_on('bison@3.0:', type='build') diff --git a/var/spack/repos/builtin/packages/json-c/package.py b/var/spack/repos/builtin/packages/json-c/package.py index 34053fc2baf..ff243c06c97 100644 --- a/var/spack/repos/builtin/packages/json-c/package.py +++ b/var/spack/repos/builtin/packages/json-c/package.py @@ -11,9 +11,9 @@ class JsonC(AutotoolsPackage): homepage = "https://github.com/json-c/json-c/wiki" url = "https://s3.amazonaws.com/json-c_releases/releases/json-c-0.12.1.tar.gz" - version('0.13.1', '04969ad59cc37bddd83741a08b98f350') - version('0.12.1', '55f7853f7d8cf664554ce3fa71bf1c7d') - version('0.11', 'aa02367d2f7a830bf1e3376f77881e98') + version('0.13.1', sha256='b87e608d4d3f7bfdd36ef78d56d53c74e66ab278d318b71e6002a369d36f4873') + version('0.12.1', sha256='2a136451a7932d80b7d197b10441e26e39428d67b1443ec43bbba824705e1123') + version('0.11', sha256='28dfc65145dc0d4df1dfe7701ac173c4e5f9347176c8983edbfac9149494448c') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/json-cwx/package.py b/var/spack/repos/builtin/packages/json-cwx/package.py index 11cd9d43bd8..db465dc5073 100644 --- a/var/spack/repos/builtin/packages/json-cwx/package.py +++ b/var/spack/repos/builtin/packages/json-cwx/package.py @@ -12,7 +12,7 @@ class JsonCwx(AutotoolsPackage): homepage = "https://github.com/LLNL/json-cwx" url = "https://github.com/LLNL/json-cwx/archive/0.12.tar.gz" - version('0.12', '8ba44ef7f463f004b4b14c6d8d85a2b70db977a4') + version('0.12', sha256='3bfae1f23eacba53ee130dbd1a6acf617af4627a9b4e4581d64b20a99b4e2b60') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/json-glib/package.py b/var/spack/repos/builtin/packages/json-glib/package.py index cc789bc652f..0647da6a9b0 100644 --- a/var/spack/repos/builtin/packages/json-glib/package.py +++ b/var/spack/repos/builtin/packages/json-glib/package.py @@ -13,6 +13,6 @@ class JsonGlib(AutotoolsPackage): homepage = "https://developer.gnome.org/json-glib" url = "https://ftp.gnome.org/pub/gnome/sources/json-glib/1.2/json-glib-1.2.8.tar.xz" - version('1.2.8', 'ff31e7d0594df44318e12facda3d086e') + version('1.2.8', sha256='fd55a9037d39e7a10f0db64309f5f0265fa32ec962bf85066087b83a2807f40a') depends_on('glib') diff --git a/var/spack/repos/builtin/packages/jsoncpp/package.py b/var/spack/repos/builtin/packages/jsoncpp/package.py index db71b8b2c6c..2fc27ad9741 100644 --- a/var/spack/repos/builtin/packages/jsoncpp/package.py +++ b/var/spack/repos/builtin/packages/jsoncpp/package.py @@ -26,7 +26,7 @@ class Jsoncpp(CMakePackage): version('1.7.6', sha256='07cf5d4f184394ec0a9aa657dd4c13ea682c52a1ab4da2fb176cb2d5501101e8') version('1.7.5', sha256='4338c6cab8af8dee6cdfd54e6218bd0533785f552c6162bb083f8dd28bf8fbbe') version('1.7.4', sha256='10dcd0677e80727e572a1e462193e51a5fde3e023b99e144b2ee1a469835f769') - version('1.7.3', 'aff6bfb5b81d9a28785429faa45839c5') + version('1.7.3', sha256='1cfcad14054039ba97c22531888796cb9369e6353f257aacaad34fda956ada53') variant('build_type', default='RelWithDebInfo', description='The build type to build', diff --git a/var/spack/repos/builtin/packages/judy/package.py b/var/spack/repos/builtin/packages/judy/package.py index 2a8cdb19b89..bec338b95b1 100644 --- a/var/spack/repos/builtin/packages/judy/package.py +++ b/var/spack/repos/builtin/packages/judy/package.py @@ -11,6 +11,6 @@ class Judy(AutotoolsPackage): homepage = "http://judy.sourceforge.net/" url = "http://downloads.sourceforge.net/project/judy/judy/Judy-1.0.5/Judy-1.0.5.tar.gz" - version('1.0.5', '115a0d26302676e962ae2f70ec484a54') + version('1.0.5', sha256='d2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb') parallel = False diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 26a023c0eb7..4a0e138c2cf 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -19,16 +19,16 @@ class Julia(Package): version('master', branch='master') version('1.1.1', sha256='3c5395dd3419ebb82d57bcc49dc729df3b225b9094e74376f8c649ee35ed79c2') version('1.0.0', sha256='1a2497977b1d43bb821a5b7475b4054b29938baae8170881c6b8dd4099d133f1') - version('0.6.2', '255d80bc8d56d5f059fe18f0798e32f6') + version('0.6.2', sha256='1e34c13091c9ddb47cf87a51566d94a06613f3db3c483b8f63b276e416dd621b') version('release-0.5', branch='release-0.5') - version('0.5.2', '8c3fff150a6f96cf0536fb3b4eaa5cbb') - version('0.5.1', 'bce119b98f274e0f07ce01498c463ad5') - version('0.5.0', 'b61385671ba74767ab452363c43131fb') + version('0.5.2', sha256='f5ef56d79ed55eacba9fe968bb175317be3f61668ef93e747d76607678cc01dd') + version('0.5.1', sha256='533b6427a1b01bd38ea0601f58a32d15bf403f491b8415e9ce4305b8bc83bb21') + version('0.5.0', sha256='732478536b6dccecbf56e541eef0aed04de0e6d63ae631b136e033dda2e418a9') version('release-0.4', branch='release-0.4') - version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078') - version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d') - version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6') - version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac') + version('0.4.7', md5='75a7a7dd882b7840829d8f165e9b9078') + version('0.4.6', sha256='4c23c9fc72398014bd39327c2f7efd3a301884567d4cb2a89105c984d4d633ba') + version('0.4.5', sha256='cbf361c23a77e7647040e8070371691083e92aa93c8a318afcc495ad1c3a71d9') + version('0.4.3', sha256='2b9df25a8f58df8e43038ec30bae195dfb160abdf925f3fa193b59d40e4113c5') # TODO: Split these out into jl-hdf5, jl-mpi packages etc. variant("cxx", default=False, description="Prepare for Julia Cxx package") diff --git a/var/spack/repos/builtin/packages/k8/package.py b/var/spack/repos/builtin/packages/k8/package.py index c560897cc27..d98c4eb8586 100644 --- a/var/spack/repos/builtin/packages/k8/package.py +++ b/var/spack/repos/builtin/packages/k8/package.py @@ -14,7 +14,7 @@ class K8(Package): homepage = "https://github.com/attractivechaos/k8" url = "https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2" - version('0.2.4', 'edc5579ff18842a2a59aa92ce8bab8b4') + version('0.2.4', sha256='da8a99c7f1ce7f0cb23ff07ce10510e770686b906d5431442a5439743c0b3c47') depends_on('zlib', type='run') diff --git a/var/spack/repos/builtin/packages/kahip/package.py b/var/spack/repos/builtin/packages/kahip/package.py index 5fb960fca18..8ff5626945c 100644 --- a/var/spack/repos/builtin/packages/kahip/package.py +++ b/var/spack/repos/builtin/packages/kahip/package.py @@ -27,7 +27,7 @@ class Kahip(SConsPackage): git = 'https://github.com/schulzchristian/KaHIP.git' version('develop', branch='master') - version('2.00', '0a66b0a604ad72cfb7e3dce00e2c9fdfac82b855') + version('2.00', sha256='1cc9e5b12fea559288d377e8b8b701af1b2b707de8e550d0bda18b36be29d21d') depends_on('argtable') depends_on('mpi') # Note: upstream package only tested on openmpi diff --git a/var/spack/repos/builtin/packages/kaiju/package.py b/var/spack/repos/builtin/packages/kaiju/package.py index ac5cc70258a..f5c24daf079 100644 --- a/var/spack/repos/builtin/packages/kaiju/package.py +++ b/var/spack/repos/builtin/packages/kaiju/package.py @@ -13,7 +13,7 @@ class Kaiju(MakefilePackage): homepage = "https://github.com/bioinformatics-centre/kaiju" url = "https://github.com/bioinformatics-centre/kaiju/archive/v1.6.2.zip" - version('1.6.2', '0bd85368954837aa31f3de8b87ea410b') + version('1.6.2', sha256='2685fed7e27ddeb26530fd60a4b388f2d5f3e29aaa79f8e2e6abcbac64075db8') build_directory = 'src' diff --git a/var/spack/repos/builtin/packages/kaks-calculator/package.py b/var/spack/repos/builtin/packages/kaks-calculator/package.py index 5e98caaee70..0d29aeb5edf 100644 --- a/var/spack/repos/builtin/packages/kaks-calculator/package.py +++ b/var/spack/repos/builtin/packages/kaks-calculator/package.py @@ -15,7 +15,7 @@ class KaksCalculator(MakefilePackage): homepage = "https://sourceforge.net/projects/kakscalculator2" url = "https://downloads.sourceforge.net/project/kakscalculator2/KaKs_Calculator2.0.tar.gz" - version('2.0', '956ec7bdb30fac7da3b5b2563151a85e') + version('2.0', sha256='e2df719a2fecc549d8ddc4e6d8f5cfa4b248282dca319c1928eaf886d68ec3c5') build_directory = 'src' diff --git a/var/spack/repos/builtin/packages/kallisto/package.py b/var/spack/repos/builtin/packages/kallisto/package.py index 25ed4c99801..9c13c773f39 100644 --- a/var/spack/repos/builtin/packages/kallisto/package.py +++ b/var/spack/repos/builtin/packages/kallisto/package.py @@ -13,7 +13,7 @@ class Kallisto(CMakePackage): homepage = "http://pachterlab.github.io/kallisto" url = "https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz" - version('0.43.1', '071e6bfb62be06fd76552298d4cf8144') + version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400') depends_on('zlib') depends_on('hdf5') diff --git a/var/spack/repos/builtin/packages/kbproto/package.py b/var/spack/repos/builtin/packages/kbproto/package.py index a787061e9a3..aa20174720b 100644 --- a/var/spack/repos/builtin/packages/kbproto/package.py +++ b/var/spack/repos/builtin/packages/kbproto/package.py @@ -15,7 +15,7 @@ class Kbproto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/kbproto" url = "https://www.x.org/archive/individual/proto/kbproto-1.0.7.tar.gz" - version('1.0.7', '19acc5f02ae80381e216f443134e0bbb') + version('1.0.7', sha256='828cb275b91268b1a3ea950d5c0c5eb076c678fdf005d517411f89cc8c3bb416') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py index 7e660fa31ac..1af0ea173ba 100644 --- a/var/spack/repos/builtin/packages/kdiff3/package.py +++ b/var/spack/repos/builtin/packages/kdiff3/package.py @@ -11,7 +11,7 @@ class Kdiff3(Package): homepage = "http://kdiff3.sourceforge.net/" url = "https://downloads.sourceforge.net/project/kdiff3/kdiff3/0.9.98/kdiff3-0.9.98.tar.gz" - version('0.9.98', 'b52f99f2cf2ea75ed5719315cbf77446') + version('0.9.98', sha256='802c1ababa02b403a5dca15955c01592997116a24909745016931537210fd668') depends_on("qt@:4.99,5.2.0:") diff --git a/var/spack/repos/builtin/packages/kmergenie/package.py b/var/spack/repos/builtin/packages/kmergenie/package.py index 87219d9caae..d242728ce41 100644 --- a/var/spack/repos/builtin/packages/kmergenie/package.py +++ b/var/spack/repos/builtin/packages/kmergenie/package.py @@ -13,7 +13,7 @@ class Kmergenie(MakefilePackage): homepage = "http://kmergenie.bx.psu.edu/" url = "http://kmergenie.bx.psu.edu/kmergenie-1.7044.tar.gz" - version('1.7044', '407209c8181f1631ecb79b0ca735d18f') + version('1.7044', sha256='46f2a08a2d7b1885414143e436829dd7e61fcc31ec4e429433e516a168d2978e') depends_on('python', type=('build', 'run')) depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/package.py b/var/spack/repos/builtin/packages/kokkos-kernels/package.py index 6694cc02d4e..7c3ea570473 100644 --- a/var/spack/repos/builtin/packages/kokkos-kernels/package.py +++ b/var/spack/repos/builtin/packages/kokkos-kernels/package.py @@ -13,9 +13,9 @@ class KokkosKernels(MakefilePackage): homepage = "https://github.com/kokkos/kokkos-kernels" url = "https://github.com/kokkos/kokkos-kernels/archive/2.7.00.tar.gz" - version('2.7.00', 'dfb21f26da9f1f976d84826a1510d91e') - version('2.6.00', 'ef8ba7509d82417dbc82a2f021886949') - version('2.5.00', '94f4bd78b36b9c53c18df3ccfd552041') + version('2.7.00', sha256='adf4af44eadbdfbeb9ec69dd5fae4e2852bd1fbe4a69213efd199e49f4098254') + version('2.6.00', sha256='14ebf806f66b9ca73949a478b8d959be7fa1165a640935760a724d7cc0a66335') + version('2.5.00', sha256='2c2289da3a41dafd97726e90507debafbb9f5e49ca5b0f5c8d1e044a5796f000') version('develop', git='https://github.com/kokkos/kokkos-kernels', branch='develop') diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py index f532a3cd3c2..e6b61c51b20 100644 --- a/var/spack/repos/builtin/packages/kokkos/package.py +++ b/var/spack/repos/builtin/packages/kokkos/package.py @@ -18,16 +18,16 @@ class Kokkos(Package): version('2.9.00', sha256='e0621197791ed3a381b4f02c78fa529f3cff3abb74d52157b4add17e8aa04bc4') version('2.8.00', sha256='1c72661f2d770517bff98837001b42b9c677d1df29f7493a1d7c008549aff630') version('2.7.24', sha256='a308a80ea1488f4c18884b828ce7ae9f5210b9a6b2f61b208d875084d8da8cb0') - version('2.7.00', 'b357f9374c1008754babb4495f95e392') - version('2.5.00', '2db83c56587cb83b772d0c81a3228a21') - version('2.04.11', 'd4849cee6eb9001d61c30f1d9fe74336') - version('2.04.04', '2c6d1c2569b91c9fcd4117296438e65c') - version('2.04.00', 'd99ac790ff5f29545d8eb53de90c0a85') - version('2.03.13', '3874a159a517384541ea5b52f85501ba') - version('2.03.05', '8727d783453f719eec392e10a36b49fd') - version('2.03.00', 'f205d659d4304747759fabfba32d43c3') - version('2.02.15', 'de41e38f452a50bb03363c519fe20769') - version('2.02.07', 'd5baeea70109249f7dca763074ffb202') + version('2.7.00', sha256='01595996e612ef7410aa42fa265a23101cfe1b6993fa9810ca844db5c89ad765') + version('2.5.00', sha256='ea232594bf746abb99ae2aafaeef5d07adc089968010a62a88aaa892106d9476') + version('2.04.11', sha256='f2680aee0169f6cbbec38410f9c80bf8a160435f6a07769c1e9112da8b9349a0') + version('2.04.04', sha256='5bac8ddc2fac9bc6e01dd40f92ca6cbbb346a25deca5be2fec71acf712d0d0c7') + version('2.04.00', sha256='b04658d368986df207662a7a37c1ad974c321447bc2c2b5b696d7e9ee4481f34') + version('2.03.13', sha256='002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056') + version('2.03.05', sha256='b18ddaa1496130ff3f675ea9ddbc6df9cdf378d53edf96df89e70ff189e10e1d') + version('2.03.00', sha256='722bea558d8986efee765ac912febb3c1ce289a8e9bdfef77cd0145df0ea8a3d') + version('2.02.15', sha256='6b4a7f189f0341f378f950f3c798f520d2e473b13435b137ff3b666e799a076d') + version('2.02.07', sha256='7b4ac81021d6868f4eb8e2a1cb92ba76bad9c3f197403b8b1eac0f11c983247c') variant('debug', default=False, description="Build debug version of Kokkos") diff --git a/var/spack/repos/builtin/packages/kraken/package.py b/var/spack/repos/builtin/packages/kraken/package.py index 82050d73e8b..b9982ec585d 100644 --- a/var/spack/repos/builtin/packages/kraken/package.py +++ b/var/spack/repos/builtin/packages/kraken/package.py @@ -15,7 +15,7 @@ class Kraken(Package): homepage = "https://ccb.jhu.edu/software/kraken/" url = "https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz" - version('1.0', 'e790d6b09662bbd810aa34517ef66586') + version('1.0', sha256='bade6d83233c26226d02bd427fe0a4d6cd6dc5c0300927e30d41e885a478c378') depends_on('perl', type=('build', 'run')) # Does NOT support JELLYFISH 2.0. Ver 1.1.11 is the last version of diff --git a/var/spack/repos/builtin/packages/krb5/package.py b/var/spack/repos/builtin/packages/krb5/package.py index 7c516445aa4..8e5e1256917 100644 --- a/var/spack/repos/builtin/packages/krb5/package.py +++ b/var/spack/repos/builtin/packages/krb5/package.py @@ -12,7 +12,7 @@ class Krb5(AutotoolsPackage): homepage = "https://kerberos.org" url = "https://kerberos.org/dist/krb5/1.16/krb5-1.16.1.tar.gz" - version('1.16.1', '848e9b80d6aaaa798e3f3df24b83c407') + version('1.16.1', sha256='214ffe394e3ad0c730564074ec44f1da119159d94281bbec541dc29168d21117') depends_on('bison', type='build') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/krims/package.py b/var/spack/repos/builtin/packages/krims/package.py index 3a08b61820a..36887a3bdca 100644 --- a/var/spack/repos/builtin/packages/krims/package.py +++ b/var/spack/repos/builtin/packages/krims/package.py @@ -19,7 +19,7 @@ class Krims(CMakePackage): # Versions # version("develop", branch="master") - version("0.2.1", "bf219656fd81c342a4782bad7d7beed0") + version("0.2.1", sha256="baac8de392e6c2a73a535f71596f51d4a80a08d9c0ecbf9a2d72d1d70dd17999") # # Variants diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py index affe0d2e9fd..801fdecaf1c 100644 --- a/var/spack/repos/builtin/packages/kripke/package.py +++ b/var/spack/repos/builtin/packages/kripke/package.py @@ -14,7 +14,7 @@ class Kripke(CMakePackage): url = "https://computing.llnl.gov/projects/co-design/download/kripke-openmp-1.1.tar.gz" tags = ['proxy-app'] - version('1.1', '7fe6f2b26ed983a6ce5495ab701f85bf') + version('1.1', sha256='232d74072fc7b848fa2adc8a1bc839ae8fb5f96d50224186601f55554a25f64a') variant('mpi', default=True, description='Build with MPI.') variant('openmp', default=True, description='Build with OpenMP enabled.') diff --git a/var/spack/repos/builtin/packages/laghos/package.py b/var/spack/repos/builtin/packages/laghos/package.py index 9ca8fc5cefe..16b9934c0d4 100644 --- a/var/spack/repos/builtin/packages/laghos/package.py +++ b/var/spack/repos/builtin/packages/laghos/package.py @@ -21,7 +21,7 @@ class Laghos(MakefilePackage): version('develop', branch='master') version('2.0', sha256='dd3632d5558889beec2cd3c49eb60f633f99e6d886ac868731610dd006c44c14') version('1.1', sha256='53b9bfe2af263c63eb4544ca1731dd26f40b73a0d2775a9883db51821bf23b7f') - version('1.0', '4c091e115883c79bed81c557ef16baff') + version('1.0', sha256='af50a126355a41c758fcda335a43fdb0a3cd97e608ba51c485afda3dd84a5b34') variant('metis', default=True, description='Enable/disable METIS support') diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py index a58b0993b8d..1b9e4c1fd82 100644 --- a/var/spack/repos/builtin/packages/lammps/package.py +++ b/var/spack/repos/builtin/packages/lammps/package.py @@ -34,11 +34,11 @@ class Lammps(CMakePackage): version('20180905', sha256='ee0df649e33a9bf4fe62e062452978731548a56b7487e8e1ce9403676217958d') version('20180831', sha256='6c604b3ebd0cef1a5b18730d2c2eb1e659b2db65c5b1ae6240b8a0b150e4dff3') version('20180822', sha256='9f8942ca3f8e81377ae88ccfd075da4e27d0dd677526085e1a807777c8324074') - version('20180629', '6d5941863ee25ad2227ff3b7577d5e7c') - version('20180316', '25bad35679583e0dd8cb8753665bb84b') - version('20180222', '4d0513e3183bd57721814d217fdaf957') - version('20170922', '4306071f919ec7e759bda195c26cfd9a') - version('20170901', '767e7f07289663f033474dfe974974e7') + version('20180629', sha256='1acf7d9b37b99f17563cd4c8bb00ec57bb2e29eb77c0603fd6871898de74763b') + version('20180316', sha256='a81f88c93e417ecb87cd5f5464c9a2570384a48ff13764051c5e846c3d1258c1') + version('20180222', sha256='374254d5131b7118b9ab0f0e27d20c3d13d96b03ed2b5224057f0c1065828694') + version('20170922', sha256='f0bf6eb530d528f4d261d0a261e5616cbb6e990156808b721e73234e463849d3') + version('20170901', sha256='5d88d4e92f4e0bb57c8ab30e0d20de556830af820223778b9967bec2184efd46') def url_for_version(self, version): vdate = dt.datetime.strptime(str(version), "%Y%m%d") diff --git a/var/spack/repos/builtin/packages/last/package.py b/var/spack/repos/builtin/packages/last/package.py index c79f8ca70f7..47c4275432b 100644 --- a/var/spack/repos/builtin/packages/last/package.py +++ b/var/spack/repos/builtin/packages/last/package.py @@ -14,7 +14,7 @@ class Last(MakefilePackage): homepage = "http://last.cbrc.jp/" url = "http://last.cbrc.jp/last-869.zip" - version('869', '12dced14418fb924a1b0604593274973') + version('869', sha256='6371a6282bc1bb02a5e5013cc463625f2ce3e7746ff2ea0bdf9fe6b15605a67c') def install(self, spec, prefix): make('install', 'prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/latte/package.py b/var/spack/repos/builtin/packages/latte/package.py index bf6e23784e6..9a0898b220a 100644 --- a/var/spack/repos/builtin/packages/latte/package.py +++ b/var/spack/repos/builtin/packages/latte/package.py @@ -17,10 +17,10 @@ class Latte(CMakePackage): tags = ['ecp', 'ecp-apps'] version('develop', branch='master') - version('1.2.1', '9a0690bf4e0e1cab057475a67052b0a8') - version('1.2.0', 'b9bf8f84a0e0cf7b0e278a1bc7751b3d') - version('1.1.1', 'ab11867ba6235189681cf6e50a50cc50') - version('1.0.1', 'd0b99edbcf7a19abe0a68a192d6f6234') + version('1.2.1', sha256='a21dda5ebdcefa56e9ff7296d74ef03f89c200d2e110a02af7a84612668bf702') + version('1.2.0', md5='b9bf8f84a0e0cf7b0e278a1bc7751b3d') + version('1.1.1', md5='ab11867ba6235189681cf6e50a50cc50') + version('1.0.1', md5='d0b99edbcf7a19abe0a68a192d6f6234') variant('mpi', default=True, description='Build with mpi') diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py index 51aee11b49b..b223387b96d 100644 --- a/var/spack/repos/builtin/packages/launchmon/package.py +++ b/var/spack/repos/builtin/packages/launchmon/package.py @@ -14,7 +14,7 @@ class Launchmon(AutotoolsPackage): git = "https://github.com/llnl/launchmon.git" version('master', branch='master') - version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a') + version('1.0.2', sha256='1d301ccccfe0873efcd66da87ed5e4d7bafc560b00aee396d8a9365f53b3a33a') depends_on('autoconf', type='build', when='@master') depends_on('automake', type='build', when='@master') diff --git a/var/spack/repos/builtin/packages/lazyten/package.py b/var/spack/repos/builtin/packages/lazyten/package.py index 7a0061a656a..8c782bedb0e 100644 --- a/var/spack/repos/builtin/packages/lazyten/package.py +++ b/var/spack/repos/builtin/packages/lazyten/package.py @@ -20,7 +20,7 @@ class Lazyten(CMakePackage): # Versions # version("develop", branch="master") - version('0.4.1', 'd06f7996144e1bf1b0aee82c2af36e83') + version('0.4.1', sha256='696d151382993c13d04516c77db3ea712a70e3cb449539b9e79abc78cf245ae4') # # Variants diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py index eed13ad7b44..cf39b3e5c1a 100644 --- a/var/spack/repos/builtin/packages/lbann/package.py +++ b/var/spack/repos/builtin/packages/lbann/package.py @@ -26,9 +26,9 @@ class Lbann(CMakePackage): version('0.96', sha256='97af78e9d3c405e963361d0db96ee5425ee0766fa52b43c75b8a5670d48e4b4a') version('0.95', sha256='d310b986948b5ee2bedec36383a7fe79403721c8dc2663a280676b4e431f83c2') version('0.94', sha256='567e99b488ebe6294933c98a212281bffd5220fc13a0a5cd8441f9a3761ceccf') - version('0.93', '1913a25a53d4025fa04c16f14afdaa55') - version('0.92', 'c0eb1595a7c74640e96f280beb497564') - version('0.91', '83b0ec9cd0b7625d41dfb06d2abd4134') + version('0.93', sha256='77bfd7fe52ee7495050f49bcdd0e353ba1730e3ad15042c678faa5eeed55fb8c') + version('0.92', sha256='9187c5bcbc562c2828fe619d53884ab80afb1bcd627a817edb935b80affe7b84') + version('0.91', sha256='b69f470829f434f266119a33695592f74802cff4b76b37022db00ab32de322f5') variant('gpu', default=False, description='Builds with support for GPUs via CUDA and cuDNN') variant('nccl', default=False, description='Builds with support for NCCL communication lib') diff --git a/var/spack/repos/builtin/packages/lbxproxy/package.py b/var/spack/repos/builtin/packages/lbxproxy/package.py index d2bf88a32b6..bde29ec23aa 100644 --- a/var/spack/repos/builtin/packages/lbxproxy/package.py +++ b/var/spack/repos/builtin/packages/lbxproxy/package.py @@ -19,7 +19,7 @@ class Lbxproxy(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/lbxproxy" url = "https://www.x.org/archive/individual/app/lbxproxy-1.0.3.tar.gz" - version('1.0.3', '50a2a1ae15e8edf7582f76bcdf6b8197') + version('1.0.3', sha256='db36251c9656c7da720f31e10df384f8946a9a5395915371b60d9423ad8f6a80') depends_on('libxext') depends_on('liblbxutil') diff --git a/var/spack/repos/builtin/packages/lcals/package.py b/var/spack/repos/builtin/packages/lcals/package.py index 58598e6eae5..ccdc9da1d10 100644 --- a/var/spack/repos/builtin/packages/lcals/package.py +++ b/var/spack/repos/builtin/packages/lcals/package.py @@ -21,7 +21,7 @@ class Lcals(MakefilePackage): tags = ['proxy-app'] - version('1.0.2', '40c65a88f1df1436a2f72b7d3c986a21') + version('1.0.2', sha256='a146590f7c1e9a9311ccf74dc0bef1fb19d77429db35a33c6725529fb1b0327e') variant( 'microarch', diff --git a/var/spack/repos/builtin/packages/lcms/package.py b/var/spack/repos/builtin/packages/lcms/package.py index 81e704736df..f4202717102 100644 --- a/var/spack/repos/builtin/packages/lcms/package.py +++ b/var/spack/repos/builtin/packages/lcms/package.py @@ -14,9 +14,9 @@ class Lcms(AutotoolsPackage): homepage = "http://www.littlecms.com" url = "http://downloads.sourceforge.net/project/lcms/lcms/2.9/lcms2-2.9.tar.gz" - version('2.9', '8de1b7724f578d2995c8fdfa35c3ad0e') - version('2.8', '87a5913f1a52464190bb655ad230539c') - version('2.6', 'f4c08d38ceade4a664ebff7228910a33') + version('2.9', sha256='48c6fdf98396fa245ed86e622028caf49b96fa22f3e5734f853f806fbc8e7d20') + version('2.8', sha256='66d02b229d2ea9474e62c2b6cd6720fde946155cd1d0d2bffdab829790a0fb22') + version('2.6', sha256='5172528839647c54c3da211837225e221be93e4733f5b5e9f57668f7107e14b1') depends_on('jpeg') depends_on('libtiff') diff --git a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py index a8e31107324..05291360f16 100644 --- a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py +++ b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py @@ -22,7 +22,7 @@ class LdcBootstrap(CMakePackage): url = "https://github.com/ldc-developers/ldc/releases/download/v0.17.4/ldc-0.17.4-src.tar.gz" # This is the last version that does not require a D compiler to bootstrap - version('0.17.4', '000e006426d6094fabd2a2bdab0ff0b7') + version('0.17.4', sha256='48428afde380415640f3db4e38529345f3c8485b1913717995547f907534c1c3') depends_on('llvm@3.7:') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/ldc/package.py b/var/spack/repos/builtin/packages/ldc/package.py index a1768d71b91..5a6cc8f0c62 100644 --- a/var/spack/repos/builtin/packages/ldc/package.py +++ b/var/spack/repos/builtin/packages/ldc/package.py @@ -19,7 +19,7 @@ class Ldc(CMakePackage): homepage = "https://dlang.org/" url = "https://github.com/ldc-developers/ldc/releases/download/v1.3.0/ldc-1.3.0-src.tar.gz" - version('1.3.0', '537d992a361b0fd0440b24a5145c9107') + version('1.3.0', sha256='efe31a639bcb44e1f5b752da21713376d9410a01279fecc8aab8572065a3050b') variant( 'shared', diff --git a/var/spack/repos/builtin/packages/legion/package.py b/var/spack/repos/builtin/packages/legion/package.py index 578db9a9a02..055b954c467 100644 --- a/var/spack/repos/builtin/packages/legion/package.py +++ b/var/spack/repos/builtin/packages/legion/package.py @@ -31,11 +31,11 @@ class Legion(CMakePackage): version('19.04.0', sha256='279bbc8dcdab4c75be570318989a9fc9821178143e9db9c3f62e58bf9070b5ac') version('18.12.0', sha256='71f2c409722975c0ad92f2caffcc9eaa9260f7035e2b55b731d819eb6a94016c') version('18.09.0', sha256='58c5a3072d2b5086225982563c23524692ca5758cbfda8d0f0a4f00ef17b3b8d') - version('18.05.0', 'ab5ac8cd4aa4c91e6187bf1333a031bf') - version('18.02.0', '14937b386100347b051a5fc514636353') - version('17.10.0', 'ebfc974dc82a9d7f3ba53242ecae62e1') - version('17.08.0', 'acc1ea8c564c4a382a015e0c9cf94574') - version('17.02.0', '31ac3004e2fb0996764362d2b6f6844a') + version('18.05.0', sha256='4c3cef548b3a459827e4c36b5963c06b6fcf0a4ca1800fbb0f73e6ba3b1cced4') + version('18.02.0', sha256='e08aeef98003593391a56f11a99d9d65af49647fe87a2a5e8837c8682a337a60') + version('17.10.0', sha256='af4f1e9215e57c4aac4805ae2bf53defe13eeaf192576bf5a702978f43171b1e') + version('17.08.0', sha256='20aabdb0fabb1e32aa713cd5fa406525093f8dad33fca5d23046408d42d3c7b3') + version('17.02.0', sha256='423d8699729b0e7fef663740e239aa722cca544f6bda8c9f782eaba4274bf60a') variant('mpi', default=True, description='Build on top of mpi conduit for mpi inoperability') diff --git a/var/spack/repos/builtin/packages/leveldb/package.py b/var/spack/repos/builtin/packages/leveldb/package.py index f8a453859c1..c3aeefa8f26 100644 --- a/var/spack/repos/builtin/packages/leveldb/package.py +++ b/var/spack/repos/builtin/packages/leveldb/package.py @@ -16,9 +16,9 @@ class Leveldb(CMakePackage): git = "https://github.com/google/leveldb.git" version('master', branch='master') - version('1.22', '55423cac9e3306f4a9502c738a001e4a339d1a38ffbee7572d4a07d5d63949b2') - version('1.20', '298b5bddf12c675d6345784261302252') - version('1.18', '73770de34a2a5ab34498d2e05b2b7fa0') + version('1.22', sha256='55423cac9e3306f4a9502c738a001e4a339d1a38ffbee7572d4a07d5d63949b2') + version('1.20', sha256='f5abe8b5b209c2f36560b75f32ce61412f39a2922f7045ae764a2c23335b6664') + version('1.18', sha256='4aa1a7479bc567b95a59ac6fb79eba49f61884d6fd400f20b7af147d54c5cee5') variant('shared', default=True, description='Build shared library') diff --git a/var/spack/repos/builtin/packages/lftp/package.py b/var/spack/repos/builtin/packages/lftp/package.py index 014cccdb5c0..d6f82960860 100644 --- a/var/spack/repos/builtin/packages/lftp/package.py +++ b/var/spack/repos/builtin/packages/lftp/package.py @@ -13,9 +13,9 @@ class Lftp(AutotoolsPackage): homepage = "http://lftp.yar.ru/" url = "http://lftp.yar.ru/ftp/lftp-4.7.7.tar.gz" - version('4.8.1', '419b27c016d968a0226b2e5df1454c22') - version('4.7.7', 'ddc71b3b11a1af465e829075ae14b3ff') - version('4.6.4', 'f84ecfc368b7afcc56fe7d3da2457d12') + version('4.8.1', sha256='6117866215cd889dab30ff73292cd1d35fe0e12a9af5cd76d093500d07ab65a3') + version('4.7.7', sha256='7bce216050094a1146ed05bed8fe5b3518224764ffe98884a848d44dc76fff8f') + version('4.6.4', sha256='791e783779d3d6b519d0c23155430b9785f2854023eb834c716f5ba78873b15a') depends_on('expat') depends_on('libiconv') diff --git a/var/spack/repos/builtin/packages/libaec/package.py b/var/spack/repos/builtin/packages/libaec/package.py index c2f184d245a..d79a6e8cecc 100644 --- a/var/spack/repos/builtin/packages/libaec/package.py +++ b/var/spack/repos/builtin/packages/libaec/package.py @@ -19,6 +19,6 @@ class Libaec(CMakePackage): provides('szip') - version('1.0.2', '13fb9dca01f95e2794010312c8fe345a') - version('1.0.1', '2180d2525d679a5f7950e7867b70e06b') - version('1.0.0', 'ebc0b4e47fa4e1bd5783c2b1c960fe94') + version('1.0.2', sha256='b9e5bbbc8bf9cbfd3b9b4ce38b3311f2c88d3d99f476edb35590eb0006aa1fc5') + version('1.0.1', sha256='3668eb4ed36724441e488a7aadc197426afef4b1e8bd139af6d3e36023906459') + version('1.0.0', sha256='849f08b08ddaaffe543d06d0ced5e4ee3e526b13a67c5f422d126b1c9cf1b546') diff --git a/var/spack/repos/builtin/packages/libaio/package.py b/var/spack/repos/builtin/packages/libaio/package.py index 638d57892d6..2e850e1cbc8 100644 --- a/var/spack/repos/builtin/packages/libaio/package.py +++ b/var/spack/repos/builtin/packages/libaio/package.py @@ -17,7 +17,7 @@ class Libaio(MakefilePackage): homepage = "http://lse.sourceforge.net/io/aio.html" url = "https://debian.inf.tu-dresden.de/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz" - version('0.3.110', '2a35602e43778383e2f4907a4ca39ab8') + version('0.3.110', sha256='e019028e631725729376250e32b473012f7cb68e1f7275bfc1bbcdd0f8745f7e') conflicts('platform=darwin', msg="libaio is a linux specific library") diff --git a/var/spack/repos/builtin/packages/libapplewm/package.py b/var/spack/repos/builtin/packages/libapplewm/package.py index 35bf16106f2..23b0e7d3249 100644 --- a/var/spack/repos/builtin/packages/libapplewm/package.py +++ b/var/spack/repos/builtin/packages/libapplewm/package.py @@ -14,7 +14,7 @@ class Libapplewm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libAppleWM" url = "https://www.x.org/archive/individual/lib/libAppleWM-1.4.1.tar.gz" - version('1.4.1', '52c587641eb57f00978d28d98d487af8') + version('1.4.1', sha256='d7fb098d65ad4d840f60e5c92de7f58f1725bd70d0d132755ea453462fd50049') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libarchive/package.py b/var/spack/repos/builtin/packages/libarchive/package.py index 0ce6a1da19d..1529cda25bd 100644 --- a/var/spack/repos/builtin/packages/libarchive/package.py +++ b/var/spack/repos/builtin/packages/libarchive/package.py @@ -13,11 +13,11 @@ class Libarchive(AutotoolsPackage): homepage = "http://www.libarchive.org" url = "http://www.libarchive.org/downloads/libarchive-3.1.2.tar.gz" - version('3.3.2', '4583bd6b2ebf7e0e8963d90879eb1b27') - version('3.2.1', 'afa257047d1941a565216edbf0171e72') - version('3.1.2', 'efad5a503f66329bb9d2f4308b5de98a') - version('3.1.1', '1f3d883daf7161a0065e42a15bbf168f') - version('3.1.0', '095a287bb1fd687ab50c85955692bf3a') + version('3.3.2', sha256='ed2dbd6954792b2c054ccf8ec4b330a54b85904a80cef477a1c74643ddafa0ce') + version('3.2.1', sha256='72ee1a4e3fd534525f13a0ba1aa7b05b203d186e0c6072a8a4738649d0b3cfd2') + version('3.1.2', sha256='eb87eacd8fe49e8d90c8fdc189813023ccc319c5e752b01fb6ad0cc7b2c53d5e') + version('3.1.1', sha256='4968f9a3f2405ec7e07d5f6e78b36f21bceee6196df0a795165f89774bbbc6d8') + version('3.1.0', sha256='64b15dfa623b323da8fc9c238b5bca962ec3b38dcdfd2ed86f5f509e578a3524') depends_on('zlib') depends_on('bzip2') diff --git a/var/spack/repos/builtin/packages/libassuan/package.py b/var/spack/repos/builtin/packages/libassuan/package.py index 34e6a48ed58..2ecccdbbab1 100644 --- a/var/spack/repos/builtin/packages/libassuan/package.py +++ b/var/spack/repos/builtin/packages/libassuan/package.py @@ -14,8 +14,8 @@ class Libassuan(AutotoolsPackage): url = "https://gnupg.org/ftp/gcrypt/libassuan/libassuan-2.4.5.tar.bz2" version('2.5.3', sha256='91bcb0403866b4e7c4bc1cc52ed4c364a9b5414b3994f718c70303f7f765e702') - version('2.4.5', '4f22bdb70d424cfb41b64fd73b7e1e45') - version('2.4.3', '8e01a7c72d3e5d154481230668e6eb5a') + version('2.4.5', sha256='fbfea5d1dbcdee34f2597b0afb3d8bb4eda96c924a1e01b01c2acde68b81625f') + version('2.4.3', sha256='22843a3bdb256f59be49842abf24da76700354293a066d82ade8134bb5aa2b71') depends_on('libgpg-error') diff --git a/var/spack/repos/builtin/packages/libatomic-ops/package.py b/var/spack/repos/builtin/packages/libatomic-ops/package.py index d0364023e22..bf88263e4cf 100644 --- a/var/spack/repos/builtin/packages/libatomic-ops/package.py +++ b/var/spack/repos/builtin/packages/libatomic-ops/package.py @@ -14,7 +14,7 @@ class LibatomicOps(AutotoolsPackage): url = "https://www.hboehm.info/gc/gc_source/libatomic_ops-7.6.6.tar.gz" version('7.6.6', sha256='99feabc5f54877f314db4fadeb109f0b3e1d1a54afb6b4b3dfba1e707e38e074') - version('7.4.4', '426d804baae12c372967a6d183e25af2') + version('7.4.4', sha256='bf210a600dd1becbf7936dd2914cf5f5d3356046904848dcfd27d0c8b12b6f8f') def configure_args(self): return ['--enable-shared'] diff --git a/var/spack/repos/builtin/packages/libbeagle/package.py b/var/spack/repos/builtin/packages/libbeagle/package.py index 32233a77480..0c21905a0a0 100644 --- a/var/spack/repos/builtin/packages/libbeagle/package.py +++ b/var/spack/repos/builtin/packages/libbeagle/package.py @@ -14,7 +14,7 @@ class Libbeagle(AutotoolsPackage, CudaPackage): url = "https://github.com/beagle-dev/beagle-lib/archive/v3.1.2.tar.gz" version('3.1.2', sha256='dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275') - version('2.1.2', '1107614e86f652f8ee45c1c92f2af3d4', + version('2.1.2', sha256='82ff13f4e7d7bffab6352e4551dfa13afabf82bff54ea5761d1fc1e78341d7de', url='https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/libbson/package.py b/var/spack/repos/builtin/packages/libbson/package.py index 48bcf00ae7f..ced955a5be4 100644 --- a/var/spack/repos/builtin/packages/libbson/package.py +++ b/var/spack/repos/builtin/packages/libbson/package.py @@ -15,13 +15,13 @@ class Libbson(AutotoolsPackage): maintainers = ['michaelkuhn'] - version('1.9.1', 'f91f59fc5a0cbba94d4d32dad1bd0cfd') - version('1.8.1', '42601455cf7f450b46f62c4e6115c440') - version('1.8.0', '8b3c64570eec721f951831958e707a5a') - version('1.7.0', 'e196ad77dd8458ebc1166e6135030b63') - version('1.6.3', 'b7bdb314197106fcfb4af105a582d343') - version('1.6.2', 'c128a2ae3e35295e1176465be60f19db') - version('1.6.1', '4d6779451bc5764a7d4982c01e7bd8c2') + version('1.9.1', sha256='236d9fcec0fe419c2201481081e497f49136eda2349b61cfede6233013bf7601') + version('1.8.1', sha256='9d18d14671b7890e27b2a5ce33a73a5ed5d33d39bba70209bae99c1dc7aa1ed4') + version('1.8.0', sha256='63dea744b265a2e17c7b5e289f7803c679721d98e2975ea7d56bc1e7b8586bc1') + version('1.7.0', sha256='442d89e89dfb43bba1f65080dc61fdcba01dcb23468b2842c1dbdd4acd6049d3') + version('1.6.3', sha256='e9e4012a9080bdc927b5060b126a2c82ca11e71ebe7f2152d079fa2ce461a7fb') + version('1.6.2', sha256='aad410123e4bd8a9804c3c3d79e03344e2df104872594dc2cf19605d492944ba') + version('1.6.1', sha256='5f160d44ea42ce9352a7a3607bc10d3b4b22d3271763aa3b3a12665e73e3a02d') depends_on('autoconf', type='build', when='@1.6.1') depends_on('automake', type='build', when='@1.6.1') diff --git a/var/spack/repos/builtin/packages/libcanberra/package.py b/var/spack/repos/builtin/packages/libcanberra/package.py index 9acd6073ace..06c340b3abc 100644 --- a/var/spack/repos/builtin/packages/libcanberra/package.py +++ b/var/spack/repos/builtin/packages/libcanberra/package.py @@ -14,7 +14,7 @@ class Libcanberra(AutotoolsPackage): homepage = "http://0pointer.de/lennart/projects/libcanberra/" url = "http://0pointer.de/lennart/projects/libcanberra/libcanberra-0.30.tar.xz" - version('0.30', '34cb7e4430afaf6f447c4ebdb9b42072') + version('0.30', sha256='c2b671e67e0c288a69fc33dc1b6f1b534d07882c2aceed37004bf48c601afa72') # TODO: Add variants and dependencies for the following audio support: # ALSA, OSS, PulseAudio, udev, GStreamer, null, GTK3+ , tdb diff --git a/var/spack/repos/builtin/packages/libcap/package.py b/var/spack/repos/builtin/packages/libcap/package.py index e72c5ab4de8..fedc9059ecb 100644 --- a/var/spack/repos/builtin/packages/libcap/package.py +++ b/var/spack/repos/builtin/packages/libcap/package.py @@ -15,7 +15,7 @@ class Libcap(MakefilePackage): homepage = "https://sites.google.com/site/fullycapable/" url = "https://www.kernel.org/pub/linux/libs/security/linux-privs/libcap2/libcap-2.25.tar.gz" - version('2.25', '4b18f7166a121138cca0cdd8ab64df4c') + version('2.25', sha256='4ca80dc6f9f23d14747e4b619fd9784434c570e24a7346f326c692784ed83a86') patch('libcap-fix-the-libcap-native-building-failure-on-CentOS-6.7.patch') diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py index 1451bbe52b7..8dc336c38d9 100644 --- a/var/spack/repos/builtin/packages/libcerf/package.py +++ b/var/spack/repos/builtin/packages/libcerf/package.py @@ -16,7 +16,7 @@ class Libcerf(AutotoolsPackage): homepage = "http://sourceforge.net/projects/libcerf" url = "http://downloads.sourceforge.net/project/libcerf/libcerf-1.3.tgz" - version('1.3', 'b3504c467204df71e62aeccf73a25612') + version('1.3', sha256='d7059e923d3f370c89fb4d19ed4f827d381bc3f0e36da5595a04aeaaf3e6a859') def configure_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/libcheck/package.py b/var/spack/repos/builtin/packages/libcheck/package.py index a2c4d683708..86886037f36 100644 --- a/var/spack/repos/builtin/packages/libcheck/package.py +++ b/var/spack/repos/builtin/packages/libcheck/package.py @@ -12,6 +12,6 @@ class Libcheck(CMakePackage): homepage = "https://libcheck.github.io/check/index.html" url = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz" - version('0.12.0', '31b17c6075820a434119592941186f70') - version('0.11.0', '9b90522b31f5628c2e0f55dda348e558') - version('0.10.0', '53c5e5c77d090e103a17f3ed7fd7d8b8') + version('0.12.0', sha256='464201098bee00e90f5c4bdfa94a5d3ead8d641f9025b560a27755a83b824234') + version('0.11.0', sha256='24f7a48aae6b74755bcbe964ce8bc7240f6ced2141f8d9cf480bc3b3de0d5616') + version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052') diff --git a/var/spack/repos/builtin/packages/libcircle/package.py b/var/spack/repos/builtin/packages/libcircle/package.py index 22c0236b5f3..fa8b5a33767 100644 --- a/var/spack/repos/builtin/packages/libcircle/package.py +++ b/var/spack/repos/builtin/packages/libcircle/package.py @@ -12,7 +12,7 @@ class Libcircle(AutotoolsPackage): homepage = "https://github.com/hpc/libcircle" - version('0.2.1-rc.1', '2b1369a5736457239f908abf88143ec2', + version('0.2.1-rc.1', sha256='5747f91cf4417023304dcc92fd07e3617ac712ca1eeb698880979bbca3f54865', url='https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/libconfig/package.py b/var/spack/repos/builtin/packages/libconfig/package.py index 1e2de612680..0a6caccf9ce 100644 --- a/var/spack/repos/builtin/packages/libconfig/package.py +++ b/var/spack/repos/builtin/packages/libconfig/package.py @@ -18,8 +18,8 @@ class Libconfig(AutotoolsPackage): sha256='d288e6ae817f4ef78df43cdb2647f768dc97899ee82fcc41f857e8eb9fd7fbdb') # there is currently a build error with version 1.6, see: # https://github.com/hyperrealm/libconfig/issues/47 - # version('1.6', '2ccd24b6a2ee39f7ff8a3badfafb6539') - version('1.5', 'e92a91c2ddf3bf77bea0f5ed7f09e492') + # version('1.6', md5='2ccd24b6a2ee39f7ff8a3badfafb6539') + version('1.5', sha256='cae5c02361d8a9b2bb26946c64f089d2e5e599972f386203fbc48975c0d885c8') depends_on('m4', type=('build')) depends_on('autoconf', type=('build')) diff --git a/var/spack/repos/builtin/packages/libcroco/package.py b/var/spack/repos/builtin/packages/libcroco/package.py index cdb4c8dc2fe..d2cee04546e 100644 --- a/var/spack/repos/builtin/packages/libcroco/package.py +++ b/var/spack/repos/builtin/packages/libcroco/package.py @@ -12,7 +12,7 @@ class Libcroco(AutotoolsPackage): homepage = "https://developer.gnome.org/libcroco" url = "http://ftp.gnome.org/pub/gnome/sources/libcroco/0.6/libcroco-0.6.12.tar.xz" - version('0.6.12', 'bc0984fce078ba2ce29f9500c6b9ddce') + version('0.6.12', sha256='ddc4b5546c9fb4280a5017e2707fbd4839034ed1aba5b7d4372212f34f84f860') depends_on('glib') depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/libctl/package.py b/var/spack/repos/builtin/packages/libctl/package.py index bf44fdf157e..fba9e33f471 100644 --- a/var/spack/repos/builtin/packages/libctl/package.py +++ b/var/spack/repos/builtin/packages/libctl/package.py @@ -14,7 +14,7 @@ class Libctl(AutotoolsPackage): url = "http://ab-initio.mit.edu/libctl/libctl-3.2.2.tar.gz" list_url = "http://ab-initio.mit.edu/libctl/old" - version('3.2.2', '5fd7634dc9ae8e7fa70a68473b9cbb68') + version('3.2.2', sha256='8abd8b58bc60e84e16d25b56f71020e0cb24d75b28bc5db86d50028197c7efbc') depends_on('guile') diff --git a/var/spack/repos/builtin/packages/libdivsufsort/package.py b/var/spack/repos/builtin/packages/libdivsufsort/package.py index fa711e91531..c06de91bfad 100644 --- a/var/spack/repos/builtin/packages/libdivsufsort/package.py +++ b/var/spack/repos/builtin/packages/libdivsufsort/package.py @@ -13,4 +13,4 @@ class Libdivsufsort(CMakePackage): homepage = "https://github.com/y-256/libdivsufsort" url = "https://github.com/y-256/libdivsufsort/archive/2.0.1.tar.gz" - version('2.0.1', 'a75c6be4715d3d659936f3a1ab8cb5c0') + version('2.0.1', sha256='9164cb6044dcb6e430555721e3318d5a8f38871c2da9fd9256665746a69351e0') diff --git a/var/spack/repos/builtin/packages/libdmx/package.py b/var/spack/repos/builtin/packages/libdmx/package.py index fb6d69ecc75..7c802a75f7c 100644 --- a/var/spack/repos/builtin/packages/libdmx/package.py +++ b/var/spack/repos/builtin/packages/libdmx/package.py @@ -13,7 +13,7 @@ class Libdmx(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libdmx" url = "https://www.x.org/archive/individual/lib/libdmx-1.1.3.tar.gz" - version('1.1.3', 'eed755e7cdb161e05f70e955f2b0ef4d') + version('1.1.3', sha256='c4b24d7e13e5a67ead7a18f0b4cc9b7b5363c9d04cd01b83b5122ff92b3b4996') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py index 1beb25689bd..a765ba7ef90 100644 --- a/var/spack/repos/builtin/packages/libdrm/package.py +++ b/var/spack/repos/builtin/packages/libdrm/package.py @@ -14,11 +14,11 @@ class Libdrm(Package): homepage = "http://dri.freedesktop.org/libdrm/" url = "http://dri.freedesktop.org/libdrm/libdrm-2.4.59.tar.gz" - version('2.4.81', 'dc575dd661a082390e9f1366ca5734b0') - version('2.4.75', '743c16109d91a2539dfc9cc56130d695') - version('2.4.70', 'a8c275bce5f3d71a5ca25e8fb60df084') - version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6') - version('2.4.33', '86e4e3debe7087d5404461e0032231c8') + version('2.4.81', sha256='64036c5e0668fdc2b820dcc0ebab712f44fd2c2147d23dc5a6e003b19f0d3e9f') + version('2.4.75', sha256='a411bff814b4336c8908dcbd045cd89fdc7afedc75b795d897d462e467cbb01d') + version('2.4.70', sha256='73615b9c1c4852e5ce045efa19c866e8df98e396b2443bf859eea05574ecb64f') + version('2.4.59', sha256='ed9d03a92c2d80e6310cc350db3430620f1659ae084a07c6824cee7bc81ae8fa') + version('2.4.33', sha256='bd2a8fecf28616f2157ca33ede691c139cc294ed2d0c4244b62ca7d22e98e5a4') depends_on('pkgconfig', type='build') depends_on('libpciaccess@0.10:', when=(sys.platform != 'darwin')) diff --git a/var/spack/repos/builtin/packages/libdwarf/package.py b/var/spack/repos/builtin/packages/libdwarf/package.py index 45a7c211899..f7667524d81 100644 --- a/var/spack/repos/builtin/packages/libdwarf/package.py +++ b/var/spack/repos/builtin/packages/libdwarf/package.py @@ -27,11 +27,11 @@ class Libdwarf(Package): url = "http://www.prevanders.net/libdwarf-20160507.tar.gz" list_url = homepage - version('20180129', 'c5e90fad4640f0d713ae8b986031f959') - version('20160507', 'ae32d6f9ece5daf05e2d4b14822ea811') - version('20130729', '4cc5e48693f7b93b7aa0261e63c0e21d') - version('20130207', '64b42692e947d5180e162e46c689dfbf') - version('20130126', 'ded74a5e90edb5a12aac3c29d260c5db') + version('20180129', sha256='8bd91b57064b0c14ade5a009d3a1ce819f1b6ec0e189fc876eb8f42a8720d8a6') + version('20160507', sha256='12ae39376e3915bf8fa92555989f3ad5f2f4f332b590a628541ce68987b337af') + version('20130729', sha256='b6455d8616baf2883e2af91f006d6cbd583128fdfff46e3d1fae460bc223bb7b') + version('20130207', sha256='5cb81459f0a1f6a2a10ef4635faddc2fa5e1a9e36901018c017759e491e708b8') + version('20130126', sha256='c23c847935f8612f4fcdcfa0b3311f1553dcbd95bb683d3d5e030440201192fe') depends_on("elfutils@0.163", when='@20160507', type='link') depends_on("elf", type='link') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py index c4b068ec2d4..78016430640 100644 --- a/var/spack/repos/builtin/packages/libedit/package.py +++ b/var/spack/repos/builtin/packages/libedit/package.py @@ -11,9 +11,9 @@ class Libedit(AutotoolsPackage): homepage = "http://thrysoee.dk/editline/" url = "http://thrysoee.dk/editline/libedit-20170329-3.1.tar.gz" - version('3.1-20170329', 'c57a0690e62ef523c083598730272cfd') - version('3.1-20160903', '0467d27684c453a351fbcefebbcb16a3') - version('3.1-20150325', '43cdb5df3061d78b5e9d59109871b4f6') + version('3.1-20170329', sha256='91f2d90fbd2a048ff6dad7131d9a39e690fd8a8fd982a353f1333dd4017dd4be') + version('3.1-20160903', sha256='0ccbd2e7d46097f136fcb1aaa0d5bc24e23bb73f57d25bee5a852a683eaa7567') + version('3.1-20150325', sha256='c88a5e4af83c5f40dda8455886ac98923a9c33125699742603a88a0253fcc8c5') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index e2c36cb7721..b6395b0b275 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -21,8 +21,8 @@ class Libelf(AutotoolsPackage): homepage = "https://directory.fsf.org/wiki/Libelf" url = "https://fossies.org/linux/misc/old/libelf-0.8.13.tar.gz" - version('0.8.13', '4136d7b4c04df68b686570afa26988ac') - # version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7') + version('0.8.13', sha256='591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d') + # version('0.8.12', md5='e21f8273d9f5f6d43a59878dc274fec7') provides('elf@0') diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py index 30bd081a634..40ae9ea67c2 100644 --- a/var/spack/repos/builtin/packages/libemos/package.py +++ b/var/spack/repos/builtin/packages/libemos/package.py @@ -14,11 +14,11 @@ class Libemos(CMakePackage): url = "https://software.ecmwf.int/wiki/download/attachments/3473472/libemos-4.4.2-Source.tar.gz" list_url = "https://software.ecmwf.int/wiki/display/EMOS/Releases" - version('4.5.1', 'eec1ef4de841df3c68c08fa94d7939ff') - version('4.5.0', '0ad8962a73e3ca90a8094561adc81276') - version('4.4.9', '24d098cd062d443a544fe17727726285') - version('4.4.7', '395dcf21cf06872f772fb6b73d8e67b9') - version('4.4.2', 'f15a9aff0f40861f3f046c9088197376') + version('4.5.1', sha256='c982d9fd7dcd15c3a4d1e1115b90430928b660e17f73f7d4e360dd9f87f68c46') + version('4.5.0', sha256='debe474603224c318f8ed4a1c209a4d1416807c594c3faa196059b2228824393') + version('4.4.9', sha256='61af7dfcd37875b4f834e2e4371922ec529a8c03879c52e8fb911b35e4c0d413') + version('4.4.7', sha256='669fb070c1ce655812882140a92b100233f065829868d9374bad2fcbb6b356e5') + version('4.4.2', sha256='e2d20ad71e3beb398916f98a35a3c56ee0141d5bc9b3adff15095ff3b6dccea8') variant('grib', default='eccodes', values=('eccodes', 'grib-api'), description='Specify GRIB backend') diff --git a/var/spack/repos/builtin/packages/libepoxy/package.py b/var/spack/repos/builtin/packages/libepoxy/package.py index 965d7612f20..56fdb9887b4 100644 --- a/var/spack/repos/builtin/packages/libepoxy/package.py +++ b/var/spack/repos/builtin/packages/libepoxy/package.py @@ -13,8 +13,8 @@ class Libepoxy(AutotoolsPackage): url = "https://github.com/anholt/libepoxy/releases/download/1.4.3/libepoxy-1.4.3.tar.xz" list_url = "https://github.com/anholt/libepoxy/releases" - version('1.4.3', 'af4c3ce0fb1143bdc4e43f85695a9bed') - version('1.3.1', '96f6620a9b005a503e7b44b0b528287d') + version('1.4.3', sha256='0b808a06c9685a62fca34b680abb8bc7fb2fda074478e329b063c1f872b826f6') + version('1.3.1', md5='96f6620a9b005a503e7b44b0b528287d') depends_on('pkgconfig', type='build') depends_on('meson') diff --git a/var/spack/repos/builtin/packages/libev/package.py b/var/spack/repos/builtin/packages/libev/package.py index 1ca8170db39..dfdea698131 100644 --- a/var/spack/repos/builtin/packages/libev/package.py +++ b/var/spack/repos/builtin/packages/libev/package.py @@ -16,7 +16,7 @@ class Libev(AutotoolsPackage): list_url = "http://dist.schmorp.de/libev/Attic/" version('develop', branch='master') - version('4.24', '94459a5a22db041dec6f98424d6efe54') + version('4.24', sha256='973593d3479abdf657674a55afe5f78624b0e440614e2b8cb3a07f16d4d7f821') depends_on('autoconf', type='build', when='@develop') depends_on('automake', type='build', when='@develop') diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py index b417c9ca0dd..dc658bb1f35 100644 --- a/var/spack/repos/builtin/packages/libevent/package.py +++ b/var/spack/repos/builtin/packages/libevent/package.py @@ -18,18 +18,18 @@ class Libevent(AutotoolsPackage): url = "https://github.com/libevent/libevent/releases/download/release-2.1.8-stable/libevent-2.1.8-stable.tar.gz" list_url = "http://libevent.org/old-releases.html" - version('2.1.8', '965cc5a8bb46ce4199a47e9b2c9e1cae3b137e8356ffdad6d94d3b9069b71dc2') - version('2.0.22', '71c2c49f0adadacfdbe6332a372c38cf9c8b7895bb73dabeaa53cdcc1d4e1fa3') - version('2.0.21', 'b2405cc9ebf264aa47ff615d9de527a2') - version('2.0.20', '94270cdee32c0cd0aa9f4ee6ede27e8e') - version('2.0.19', '91111579769f46055b0a438f5cc59572') - version('2.0.18', 'aa1ce9bc0dee7b8084f6855765f2c86a') - version('2.0.17', 'dad64aaaaff16b5fbec25160c06fee9a') - version('2.0.16', '899efcffccdb3d5111419df76e7dc8df') - version('2.0.15', '2643abe7ba242df15c08b2cc14ec8759') - version('2.0.14', 'cac0f379da35d3b98f83ac16fcfe1df4') - version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc') - version('2.0.12', '42986228baf95e325778ed328a93e070') + version('2.1.8', sha256='965cc5a8bb46ce4199a47e9b2c9e1cae3b137e8356ffdad6d94d3b9069b71dc2') + version('2.0.22', sha256='71c2c49f0adadacfdbe6332a372c38cf9c8b7895bb73dabeaa53cdcc1d4e1fa3') + version('2.0.21', sha256='22a530a8a5ba1cb9c080cba033206b17dacd21437762155c6d30ee6469f574f5') + version('2.0.20', sha256='10698a0e6abb3ca00b1c9e8cfddc66933bcc4c9c78b5600a7064c4c3ef9c6a24') + version('2.0.19', sha256='1591fb411a67876a514a33df54b85417b31e01800284bcc6894fc410c3eaea21') + version('2.0.18', sha256='44ed97277715b24ef3b36e93d8c1d39ae80c29c7723793911e22dc6e0c3c4acb') + version('2.0.17', sha256='51735d1241f9f6d2d6465d8abc76f7511764f6de7d81026120c629612296faa6') + version('2.0.16', sha256='a578c7bcaf3bab1cc7924bd4d219f2ea621ab8c51dfc4f886e234b6ef4d38295') + version('2.0.15', sha256='ab535bae9af788c8711a8d138c4cae0722f22a1a4ac4d8084abc7b0e0468bc5c') + version('2.0.14', sha256='3c97a72cddd5bff63450efe7c646e15ad08dec32d5223b69cb10c2dc305812da') + version('2.0.13', sha256='e2cc3b9f03e68ff878919b1cd031a210ba9ff376283d895161afcbc25aca00a9') + version('2.0.12', sha256='ac0283f72e0f881e93ac3ae9497a20c78bd075c6c12506ad10e821aa1c29e5ab') variant('openssl', default=True, description="Build with encryption enabled at the libevent level.") diff --git a/var/spack/repos/builtin/packages/libevpath/package.py b/var/spack/repos/builtin/packages/libevpath/package.py index c4f766d3de1..c34936b66fa 100644 --- a/var/spack/repos/builtin/packages/libevpath/package.py +++ b/var/spack/repos/builtin/packages/libevpath/package.py @@ -18,11 +18,11 @@ class Libevpath(CMakePackage): git = "https://github.com/GTkorvo/evpath.git" version('develop', branch='master') - version('4.4.0', 'd8630eb358ec90ae2d188e0e6c74022a') - version('4.2.4', '757ce010a6b7564dc62d3c79edd861d5') - version('4.2.1', 'f928dc0dee41668afc91634c7051ce1a') - version('4.1.2', '1a187f55431c991ae7040e3ff041d75c') - version('4.1.1', '65a8db820f396ff2926e3d31908d123d') + version('4.4.0', sha256='c8d20d33c84d8d826493f453760eceb792d601734ff61238662c16fa6243dc29') + version('4.2.4', sha256='070698a068798e2e34dd73debb936cf275af23987a4cb0d06aa3e50c481042ff') + version('4.2.1', sha256='c745946f2ecff65bfc80978c2038c37c3803076064cfd29ea3023d671c950770') + version('4.1.2', sha256='2c0d5acc0e1c5aadd32d7147d2f0ce26220e3870e21c7d5429372d8f881e519e') + version('4.1.1', sha256='cfc9587f98c1f057eb25712855d14311fd91d6284151eee7bd8936c4ff7ee001') variant('enet_transport', default=False, description='Build an ENET transport for EVpath') diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py index 6cb06f3c01f..ede7f53f668 100644 --- a/var/spack/repos/builtin/packages/libfabric/package.py +++ b/var/spack/repos/builtin/packages/libfabric/package.py @@ -22,11 +22,11 @@ class Libfabric(AutotoolsPackage): version('1.7.1', sha256='312e62c57f79b7274f89c41823932c00b15f1cc8de9c1f8dce17cd7fdae66fa1') version('1.7.0', sha256='9d7059e2ef48341f967f2a20ee215bc50f9079b32aad485f654098f83040e4be') version('1.6.2', sha256='b1a9cf8c47189a1c918f8b5710d05cb50df6b47a1c9b2ba51d927e97503b4df0') - version('1.6.1', 'ff78dc9fcbf273a119c737a4e1df46d1') - version('1.6.0', '91d63ab3c0b9724a4db660019f928cab') - version('1.5.3', '1fe07e972fe487c6a3e44c0fb68b49a2') - version('1.5.0', 'fda3e9b31ebe184f5157288d059672d6') - version('1.4.2', '2009c8e0817060fb99606ddbf6c5ccf8') + version('1.6.1', sha256='ac85f18bbf09226e868d72771ecba39cfdb7915aab3aeb855c95f8be7817f8bc') + version('1.6.0', sha256='cd7d4543cf706820e4a33003457eff97336b5160f35d0e8b001aea18b5470423') + version('1.5.3', sha256='770e505185074b4c66a0c33ac2155670142746a71a6299c286f6d5cd220cbff8') + version('1.5.0', sha256='f62709e70fab6abea719402da854f3c6ab60369be6b1e31e4f77554c7454da28') + version('1.4.2', sha256='858e30d92b69ee5e47ac10a8ac0c731b491d75a6e28267a128f3d6eb43f940a1') fabrics = ('psm', 'psm2', diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py index 9ed9563a54c..9d0377e28da 100644 --- a/var/spack/repos/builtin/packages/libffi/package.py +++ b/var/spack/repos/builtin/packages/libffi/package.py @@ -13,9 +13,9 @@ class Libffi(AutotoolsPackage): run time.""" homepage = "https://sourceware.org/libffi/" - version('3.2.1', '83b89587607e3eb65c70d361f13bab43', + version('3.2.1', sha256='d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37', url="https://www.mirrorservice.org/sites/sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") - # version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = + # version('3.1', md5='f5898b29bbfd70502831a212d9249d10',url = # "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug # $(lib64) instead of ${lib64} in libffi.pc diff --git a/var/spack/repos/builtin/packages/libffs/package.py b/var/spack/repos/builtin/packages/libffs/package.py index 9b7ba209ae4..9958c4c0805 100644 --- a/var/spack/repos/builtin/packages/libffs/package.py +++ b/var/spack/repos/builtin/packages/libffs/package.py @@ -19,9 +19,9 @@ class Libffs(CMakePackage): git = "https://github.com/GTkorvo/ffs.git" version('develop', branch='master') - version('1.5', 'c41c5f5f448b627740deecd695b7bbf8') - version('1.1.1', 'aa1c8ad5cf35e8cf76735e3a60891509') - version('1.1', '561c6b3abc53e12b3c01192e8ef2ffbc') + version('1.5', sha256='e1f3df42eb36fa35c5445887d679e26b7e3c9be697a07cd38e4ae824dbcd8ef8') + version('1.1.1', sha256='9c3a82b3357e6ac255b65d4f45003dd270dea3ec0cd7a2aa40b59b3eab4bdb83') + version('1.1', sha256='008fd87c5a6cb216cd757b4dc04057fc987b39b7a367623eb4cf0fd32a9fd81e') depends_on('flex', type='build', when='@:1.4') depends_on('bison', type='build', when='@:1.4') diff --git a/var/spack/repos/builtin/packages/libfontenc/package.py b/var/spack/repos/builtin/packages/libfontenc/package.py index bf7db0a1cbf..9c841abe50a 100644 --- a/var/spack/repos/builtin/packages/libfontenc/package.py +++ b/var/spack/repos/builtin/packages/libfontenc/package.py @@ -12,7 +12,7 @@ class Libfontenc(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libfontenc" url = "https://www.x.org/archive/individual/lib/libfontenc-1.1.3.tar.gz" - version('1.1.3', '0ffa28542aa7d246299b1f7211cdb768') + version('1.1.3', sha256='6fba26760ca8d5045f2b52ddf641c12cedc19ee30939c6478162b7db8b6220fb') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/libfs/package.py b/var/spack/repos/builtin/packages/libfs/package.py index 5fa291521f2..681fe929d29 100644 --- a/var/spack/repos/builtin/packages/libfs/package.py +++ b/var/spack/repos/builtin/packages/libfs/package.py @@ -15,7 +15,7 @@ class Libfs(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libFS" url = "https://www.x.org/archive/individual/lib/libFS-1.0.7.tar.gz" - version('1.0.7', 'd8c1246f5b3d0e7ccf2190d3bf2ecb73') + version('1.0.7', sha256='91bf1c5ce4115b7dbf4e314fdbee54052708e8f7b6a2ec6e82c309bcbe40ef3d') depends_on('xproto@7.0.17:', type='build') depends_on('fontsproto', type='build') diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py index 0b10421b096..46ba7ab7039 100644 --- a/var/spack/repos/builtin/packages/libgcrypt/package.py +++ b/var/spack/repos/builtin/packages/libgcrypt/package.py @@ -16,8 +16,8 @@ class Libgcrypt(AutotoolsPackage): url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.8.1.tar.bz2" version('1.8.4', sha256='f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227') - version('1.8.1', 'b21817f9d850064d2177285f1073ec55') - version('1.7.6', '54e180679a7ae4d090f8689ca32b654c') - version('1.6.2', 'b54395a93cb1e57619943c082da09d5f') + version('1.8.1', sha256='7a2875f8b1ae0301732e878c0cca2c9664ff09ef71408f085c50e332656a78b3') + version('1.7.6', sha256='626aafee84af9d2ce253d2c143dc1c0902dda045780cc241f39970fc60be05bc') + version('1.6.2', sha256='de084492a6b38cdb27b67eaf749ceba76bf7029f63a9c0c3c1b05c88c9885c4c') depends_on("libgpg-error") diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index 1b9553e565a..eb6d6800742 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -21,9 +21,9 @@ class Libgd(AutotoolsPackage): homepage = "https://github.com/libgd/libgd" url = 'https://github.com/libgd/libgd/releases/download/gd-2.2.4/libgd-2.2.4.tar.gz' - version('2.2.4', '0a3c307b5075edbe1883543dd1153c02') - version('2.2.3', 'a67bd15fa33d4aac0a1c7904aed19f49') - version('2.1.1', 'e91a1a99903e460e7ba00a794e72cc1e') + version('2.2.4', sha256='487a650aa614217ed08ab1bd1aa5d282f9d379cfd95c756aed0b43406381be65') + version('2.2.3', md5='a67bd15fa33d4aac0a1c7904aed19f49') + version('2.1.1', md5='e91a1a99903e460e7ba00a794e72cc1e') # Build dependencies depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py index 040d5c6e688..d788b09a04e 100644 --- a/var/spack/repos/builtin/packages/libgit2/package.py +++ b/var/spack/repos/builtin/packages/libgit2/package.py @@ -16,8 +16,8 @@ class Libgit2(CMakePackage): homepage = "https://libgit2.github.com/" url = "https://github.com/libgit2/libgit2/archive/v0.24.2.tar.gz" - version('0.26.0', '6ea75a8a5745a7b2a14d3ed94486e761') - version('0.24.2', '735661b5b73e3c120d13e2bae21e49b3') + version('0.26.0', sha256='6a62393e0ceb37d02fe0d5707713f504e7acac9006ef33da1e88960bd78b6eac') + version('0.24.2', md5='735661b5b73e3c120d13e2bae21e49b3') depends_on('cmake@2.8:', type='build') depends_on('libssh2') diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py index 3da61b52dbf..848f4760f45 100644 --- a/var/spack/repos/builtin/packages/libgpg-error/package.py +++ b/var/spack/repos/builtin/packages/libgpg-error/package.py @@ -16,6 +16,6 @@ class LibgpgError(AutotoolsPackage): url = "https://gnupg.org/ftp/gcrypt/libgpg-error/libgpg-error-1.27.tar.bz2" version('1.36', sha256='babd98437208c163175c29453f8681094bcaf92968a15cafb1a276076b33c97c') - version('1.27', '5217ef3e76a7275a2a3b569a12ddc989') - version('1.21', 'ab0b5aba6d0a185b41d07bda804fd8b2') - version('1.18', '12312802d2065774b787cbfc22cc04e9') + version('1.27', sha256='4f93aac6fecb7da2b92871bb9ee33032be6a87b174f54abf8ddf0911a22d29d2') + version('1.21', sha256='b7dbdb3cad63a740e9f0c632a1da32d4afdb694ec86c8625c98ea0691713b84d') + version('1.18', sha256='9ff1d6e61d4cef7c1d0607ceef6d40dc33f3da7a3094170c3718c00153d80810') diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py index 2e935f0f1a2..017d20048df 100644 --- a/var/spack/repos/builtin/packages/libgpuarray/package.py +++ b/var/spack/repos/builtin/packages/libgpuarray/package.py @@ -14,16 +14,16 @@ class Libgpuarray(CMakePackage): homepage = "http://deeplearning.net/software/libgpuarray/" url = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz" - version('0.7.5', '2534011464555c3e99d14231db965c20') - version('0.7.4', '19f57cd381175162048c8154f5251546') - version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d') - version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e') - version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb') - version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e') - version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0') - version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4') - version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2') - version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b') + version('0.7.5', sha256='39c4d2e743848be43c8819c736e089ae51b11aa446cc6ee05af945c2dfd63420') + version('0.7.4', md5='19f57cd381175162048c8154f5251546') + version('0.7.3', md5='cb44aeb8482330974abdb36b0a477e5d') + version('0.7.2', sha256='ef11ee6f8d62d53831277fd3dcab662aa770a5b5de2d30fe3018c4af959204da') + version('0.7.1', sha256='4d0f9dd63b0595a8c04d8cee91b2619847c033b011c71d776caa784322382ed6') + version('0.7.0', sha256='afe7907435dcbf78b3ea9b9f6c97e5a0d4a219a7170f5025ca0db1c289bb88df') + version('0.6.9', sha256='689716feecb4e495f4d383ec1518cf3ba70a2a642a903cc445b6b6ffc119bc25') + version('0.6.2', sha256='04756c6270c0ce3b91a9bf01be38c4fc743f5356acc18d9f807198021677bcc8') + version('0.6.1', sha256='b2466311e0e3bacdf7a586bba0263f6d232bf9f8d785e91ddb447653741e6ea5') + version('0.6.0', sha256='a58a0624e894475a4955aaea25e82261c69b4d22c8f15ec07041a4ba176d35af') depends_on('cuda') depends_on('cmake@3:', type='build') diff --git a/var/spack/repos/builtin/packages/libgridxc/package.py b/var/spack/repos/builtin/packages/libgridxc/package.py index d20015623f0..3de369473ee 100644 --- a/var/spack/repos/builtin/packages/libgridxc/package.py +++ b/var/spack/repos/builtin/packages/libgridxc/package.py @@ -13,7 +13,7 @@ class Libgridxc(Package): homepage = "https://launchpad.net/libgridxc" url = "https://launchpad.net/libgridxc/trunk/0.7/+download/libgridxc-0.7.6.tgz" - version('0.7.6', 'a593f845d7565a168f1cf515a0a89879') + version('0.7.6', sha256='ecf88ea68b9dbbdae3e86c8d598aee63b134f2f2d0e879fdedc06544b8267b91') phases = ['configure', 'install'] diff --git a/var/spack/repos/builtin/packages/libgtextutils/package.py b/var/spack/repos/builtin/packages/libgtextutils/package.py index d4da2730d0c..2d8fdb0c34e 100644 --- a/var/spack/repos/builtin/packages/libgtextutils/package.py +++ b/var/spack/repos/builtin/packages/libgtextutils/package.py @@ -13,4 +13,4 @@ class Libgtextutils(AutotoolsPackage): url = "https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz" patch('text_line_reader.patch') - version('0.7', '593c7c62e3c76ec49f5736eed4f96806') + version('0.7', sha256='792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a') diff --git a/var/spack/repos/builtin/packages/libharu/package.py b/var/spack/repos/builtin/packages/libharu/package.py index 0487c1c5911..e2ccc199022 100644 --- a/var/spack/repos/builtin/packages/libharu/package.py +++ b/var/spack/repos/builtin/packages/libharu/package.py @@ -18,8 +18,8 @@ class Libharu(AutotoolsPackage): git = "https://github.com/libharu/libharu.git" version('master', branch='master') - version('2.3.0', '4f916aa49c3069b3a10850013c507460') - version('2.2.0', 'b65a6fc33a0bdad89bec6b7def101f01') + version('2.3.0', sha256='8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2') + version('2.2.0', sha256='5e63246d2da0272a9dbe5963fd827c7efa6e29d97a2d047c0d4c5f0b780f10b5') depends_on('libtool', type=('build')) depends_on('autoconf', type=('build')) diff --git a/var/spack/repos/builtin/packages/libiberty/package.py b/var/spack/repos/builtin/packages/libiberty/package.py index 5a8507407f6..cd4895db6d6 100644 --- a/var/spack/repos/builtin/packages/libiberty/package.py +++ b/var/spack/repos/builtin/packages/libiberty/package.py @@ -18,10 +18,10 @@ class Libiberty(AutotoolsPackage): homepage = "https://www.gnu.org/software/binutils/" url = "https://ftpmirror.gnu.org/binutils/binutils-2.31.1.tar.xz" - version('2.31.1', '5b7c9d4ce96f507d95c1b9a255e52418') - version('2.30', 'ffc476dd46c96f932875d1b2e27e929f') - version('2.29.1', 'acc9cd826edb9954ac7cecb81c727793') - version('2.28.1', 'a3bf359889e4b299fce1f4cb919dc7b6') + version('2.31.1', sha256='5d20086ecf5752cc7d9134246e9588fa201740d540f7eb84d795b1f7a93bca86') + version('2.30', sha256='6e46b8aeae2f727a36f0bd9505e405768a72218f1796f0d09757d45209871ae6') + version('2.29.1', sha256='e7010a46969f9d3e53b650a518663f98a5dde3c3ae21b7d71e5e6803bc36b577') + version('2.28.1', sha256='16328a906e55a3c633854beec8e9e255a639b366436470b4f6245eb0d2fde942') variant('pic', default=False, description='Compile with position independent code.') diff --git a/var/spack/repos/builtin/packages/libice/package.py b/var/spack/repos/builtin/packages/libice/package.py index 04cb2b5182f..3f18de3153f 100644 --- a/var/spack/repos/builtin/packages/libice/package.py +++ b/var/spack/repos/builtin/packages/libice/package.py @@ -12,7 +12,7 @@ class Libice(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libICE" url = "https://www.x.org/archive/individual/lib/libICE-1.0.9.tar.gz" - version('1.0.9', '95812d61df8139c7cacc1325a26d5e37') + version('1.0.9', sha256='7812a824a66dd654c830d21982749b3b563d9c2dfe0b88b203cefc14a891edc0') depends_on('xproto', type='build') depends_on('xtrans', type='build') diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py index 9aeb1ec7b03..a1e76e48940 100644 --- a/var/spack/repos/builtin/packages/libiconv/package.py +++ b/var/spack/repos/builtin/packages/libiconv/package.py @@ -14,8 +14,8 @@ class Libiconv(AutotoolsPackage): url = "https://ftpmirror.gnu.org/libiconv/libiconv-1.16.tar.gz" version('1.16', sha256='e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04') - version('1.15', 'ace8b5f2db42f7b3b3057585e80d9808') - version('1.14', 'e34509b1623cec449dfeb73d7ce9c6c6') + version('1.15', sha256='ccf536620a45458d26ba83887a983b96827001e92a13847b45e4925cc8913178') + version('1.14', sha256='72b24ded17d687193c3366d0ebe7cde1e6b18f0df8c55438ac95be39e8a30613') # We cannot set up a warning for gets(), since gets() is not part # of C11 any more and thus might not exist. diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py index 039b77052b2..f7e31f475b0 100644 --- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py +++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py @@ -16,10 +16,10 @@ class LibjpegTurbo(Package): url = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/2.0.2.tar.gz" version('2.0.2', sha256='b45255bd476c19c7c6b198c07c0487e8b8536373b82f2b38346b32b4fa7bb942') - version('1.5.90', '85f7f9c377b70cbf48e61726097d4efa') - version('1.5.3', '5b7549d440b86c98a517355c102d155e') - version('1.5.0', 'eff98ac84de05eafc65ae96caa6e23e9') - version('1.3.1', '5e4bc19c3cb602bcab1296b9bee5124c') + version('1.5.90', sha256='cb948ade92561d8626fd7866a4a7ba3b952f9759ea3dd642927bc687470f60b7') + version('1.5.3', sha256='1a17020f859cb12711175a67eab5c71fc1904e04b587046218e36106e07eabde') + version('1.5.0', sha256='232280e1c9c3e6a1de95fe99be2f7f9c0362ee08f3e3e48d50ee83b9a2ed955b') + version('1.3.1', sha256='5008aeeac303ea9159a0ec3ccff295434f4e63b05aed4a684c9964d497304524') provides('jpeg') diff --git a/var/spack/repos/builtin/packages/libjpeg/package.py b/var/spack/repos/builtin/packages/libjpeg/package.py index b61a3d96556..c457bcb7ba4 100644 --- a/var/spack/repos/builtin/packages/libjpeg/package.py +++ b/var/spack/repos/builtin/packages/libjpeg/package.py @@ -14,9 +14,9 @@ class Libjpeg(AutotoolsPackage): homepage = "http://www.ijg.org" url = "http://www.ijg.org/files/jpegsrc.v9c.tar.gz" - version('9c', '93c62597eeef81a84d988bccbda1e990') - version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb') - version('9a', '3353992aecaee1805ef4109aadd433e7') + version('9c', sha256='650250979303a649e21f87b5ccd02672af1ea6954b911342ea491f351ceb7122') + version('9b', sha256='240fd398da741669bf3c90366f58452ea59041cacc741a489b99f2f6a0bad052') + version('9a', sha256='3a753ea48d917945dd54a2d97de388aa06ca2eb1066cbfdc6652036349fe05a7') provides('jpeg') diff --git a/var/spack/repos/builtin/packages/libksba/package.py b/var/spack/repos/builtin/packages/libksba/package.py index 896c371cd35..23d0c1509f7 100644 --- a/var/spack/repos/builtin/packages/libksba/package.py +++ b/var/spack/repos/builtin/packages/libksba/package.py @@ -13,7 +13,7 @@ class Libksba(AutotoolsPackage): homepage = "https://gnupg.org/software/libksba/index.html" url = "https://gnupg.org/ftp/gcrypt/libksba/libksba-1.3.5.tar.bz2" - version('1.3.5', '8302a3e263a7c630aa7dea7d341f07a2') + version('1.3.5', sha256='41444fd7a6ff73a79ad9728f985e71c9ba8cd3e5e53358e70d5f066d35c1a340') depends_on('libgpg-error') diff --git a/var/spack/repos/builtin/packages/liblbxutil/package.py b/var/spack/repos/builtin/packages/liblbxutil/package.py index f9e4da68c9e..9b6d9f71c96 100644 --- a/var/spack/repos/builtin/packages/liblbxutil/package.py +++ b/var/spack/repos/builtin/packages/liblbxutil/package.py @@ -12,7 +12,7 @@ class Liblbxutil(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/liblbxutil" url = "https://www.x.org/archive/individual/lib/liblbxutil-1.1.0.tar.gz" - version('1.1.0', '2735cd23625d4cc870ec4eb7ca272788') + version('1.1.0', sha256='285c1bc688cc71ec089e9284f2566d1780cc5d90816e9997890af8689f386951') depends_on('xextproto@7.0.99.1:', type='build') depends_on('xproto', type='build') diff --git a/var/spack/repos/builtin/packages/liblockfile/package.py b/var/spack/repos/builtin/packages/liblockfile/package.py index 49d545a8550..e25d335ef2e 100644 --- a/var/spack/repos/builtin/packages/liblockfile/package.py +++ b/var/spack/repos/builtin/packages/liblockfile/package.py @@ -12,7 +12,7 @@ class Liblockfile(AutotoolsPackage): homepage = "https://github.com/miquels/liblockfile" url = "https://github.com/miquels/liblockfile/archive/v1.14.tar.gz" - version('1.14', '24ce9dbb34d7f508a52a91f762746ce3') + version('1.14', sha256='be85dba347889d9b65cbd361a611e6b88e044fdca9c98e5139d5fbc9ba37ccc8') patch('install_as_nonroot.patch') diff --git a/var/spack/repos/builtin/packages/libmatheval/package.py b/var/spack/repos/builtin/packages/libmatheval/package.py index e5825d95bc8..5cfab6000dc 100644 --- a/var/spack/repos/builtin/packages/libmatheval/package.py +++ b/var/spack/repos/builtin/packages/libmatheval/package.py @@ -17,7 +17,7 @@ class Libmatheval(AutotoolsPackage): homepage = "https://www.gnu.org/software/libmatheval/" url = "https://ftpmirror.gnu.org/libmatheval/libmatheval-1.1.11.tar.gz" - version('1.1.11', '595420ea60f6ddd75623847f46ca45c4') + version('1.1.11', sha256='474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab') # Only needed for unit tests, but configure crashes without it depends_on('guile', type='build') diff --git a/var/spack/repos/builtin/packages/libmaxminddb/package.py b/var/spack/repos/builtin/packages/libmaxminddb/package.py index 36f6c051d78..8c34e62281b 100644 --- a/var/spack/repos/builtin/packages/libmaxminddb/package.py +++ b/var/spack/repos/builtin/packages/libmaxminddb/package.py @@ -12,7 +12,7 @@ class Libmaxminddb(AutotoolsPackage): homepage = "https://github.com/maxmind/libmaxminddb" url = "https://github.com/maxmind/libmaxminddb/releases/download/1.3.2/libmaxminddb-1.3.2.tar.gz" - version('1.3.2', '67a861965b30d045bf29a2126bcc05ed') + version('1.3.2', sha256='e6f881aa6bd8cfa154a44d965450620df1f714c6dc9dd9971ad98f6e04f6c0f0') def configure_args(self): args = ['--disable-debug', diff --git a/var/spack/repos/builtin/packages/libmesh/package.py b/var/spack/repos/builtin/packages/libmesh/package.py index 5968ff890bb..0990d25a2f6 100644 --- a/var/spack/repos/builtin/packages/libmesh/package.py +++ b/var/spack/repos/builtin/packages/libmesh/package.py @@ -22,7 +22,7 @@ class Libmesh(AutotoolsPackage): version('1.3.1', sha256='638cf30d05c249315760f16cbae4804964db8857a04d5e640f37617bef17ab0f') version('1.3.0', sha256='a8cc2cd44f42b960989dba10fa438b04af5798c46db0b4ec3ed29591b8359786') version('1.2.1', sha256='11c22c7d96874a17de6b8c74caa45d6745d40bf3610e88b2bd28fd3381f5ba70') - version('1.0.0', 'cb464fc63ea0b71b1e69fa3f5d4f93a4') + version('1.0.0', sha256='8909b0354e147fa50d176caa63ef22b02326d49250e964be23532d89432e727f') # support for libraries that are only available through the bundled copies: # TODO libMesh 1.2.1 gained the ability to specify a path to capnproto diff --git a/var/spack/repos/builtin/packages/libmng/package.py b/var/spack/repos/builtin/packages/libmng/package.py index 6ba14908221..6b35fd44492 100644 --- a/var/spack/repos/builtin/packages/libmng/package.py +++ b/var/spack/repos/builtin/packages/libmng/package.py @@ -13,8 +13,8 @@ class Libmng(AutotoolsPackage): homepage = "http://sourceforge.net/projects/libmng/" url = "http://downloads.sourceforge.net/project/libmng/libmng-devel/2.0.3/libmng-2.0.3.tar.gz" - version('2.0.3', '7e9a12ba2a99dff7e736902ea07383d4') - version('2.0.2', '1ffefaed4aac98475ee6267422cbca55') + version('2.0.3', sha256='cf112a1fb02f5b1c0fce5cab11ea8243852c139e669c44014125874b14b7dfaa') + version('2.0.2', sha256='4908797bb3541fb5cd8fffbe0b1513ed163509f2a4d57a78b26a96f8d1dd05a2') depends_on("jpeg") depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/libmongoc/package.py b/var/spack/repos/builtin/packages/libmongoc/package.py index 56575382904..0d3110a803e 100644 --- a/var/spack/repos/builtin/packages/libmongoc/package.py +++ b/var/spack/repos/builtin/packages/libmongoc/package.py @@ -17,13 +17,13 @@ class Libmongoc(AutotoolsPackage): version('1.9.5', sha256='4a4bd0b0375450250a3da50c050b84b9ba8950ce32e16555714e75ebae0b8019') version('1.9.4', sha256='910c2f1b2e3df4d0ea39c2f242160028f90fcb8201f05339a730ec4ba70811fb') version('1.9.3', sha256='c2c94ef63aaa09efabcbadc4ac3c8740faa102266bdd2559d550f1955b824398') - version('1.9.1', '86f98ace1a5f073eea6875a96761b198') - version('1.8.1', '52d54a4107a2da20c1a1b28bc1ff9d44') - version('1.8.0', '8c271a16ff30f6d4f5e134f699f7360f') - version('1.7.0', '21acf3584e92631422bc91e9e3cf4f76') - version('1.6.3', '0193610cf1d98aae7008f272a1000972') - version('1.6.2', 'aac86df153282cda1e4905cca181631a') - version('1.6.1', '826946de9a15f7f453aefecdc76b1c0d') + version('1.9.1', sha256='91951444d34581deeaff46cc2985c68805754f618a20ac369b761ce9b621c4cd') + version('1.8.1', sha256='87d87b7581018cde7edff85f522d43d9c0a226df26fa53b77ca1613a3aca8233') + version('1.8.0', sha256='1b53883b4cbf08e7d77ad7ab7a02deca90b1719c67f9ad132b47e60d0206ea4e') + version('1.7.0', sha256='48a0dbd44fef2124b51cf501f06be269b1a39452303b880b37473a6030c6e023') + version('1.6.3', sha256='82df03de117a3ccf563b9eccfd2e5365df8f215a36dea7446d439969033ced7b') + version('1.6.2', sha256='7ec27e9be4da2bf9e4b316374f8c29f816f0a0f019b984411777e9681e17f70e') + version('1.6.1', sha256='1bdfb27944c6da8e56da209a5d56efac70df1f8c4ca4498b46f75bf3f9360898') variant('ssl', default=True, description='Enable SSL support.') variant('snappy', default=True, description='Enable Snappy support.') diff --git a/var/spack/repos/builtin/packages/libnbc/package.py b/var/spack/repos/builtin/packages/libnbc/package.py index 3a521b5660e..1f9f6183dd9 100644 --- a/var/spack/repos/builtin/packages/libnbc/package.py +++ b/var/spack/repos/builtin/packages/libnbc/package.py @@ -15,6 +15,6 @@ class Libnbc(AutotoolsPackage): homepage = "http://unixer.de/research/nbcoll/libnbc/" url = "http://unixer.de/research/nbcoll/libnbc/libNBC-1.1.1.tar.gz" - version('1.1.1', 'ece5c94992591a9fa934a90e5dbe50ce') + version('1.1.1', sha256='63aa5f75f84c191da0688cb551ebd0e9e46928edfba350b2a534eb0c704dd9c3') depends_on("mpi") diff --git a/var/spack/repos/builtin/packages/libnl/package.py b/var/spack/repos/builtin/packages/libnl/package.py index 9fef1a8c0ff..d976a504ecc 100644 --- a/var/spack/repos/builtin/packages/libnl/package.py +++ b/var/spack/repos/builtin/packages/libnl/package.py @@ -13,8 +13,8 @@ class Libnl(AutotoolsPackage): homepage = "https://www.infradead.org/~tgr/libnl/" url = "https://github.com/thom311/libnl/releases/download/libnl3_3_0/libnl-3.3.0.tar.gz" - version('3.3.0', 'ab3ef137cad95bdda5ff0ffa5175dfa5') - version('3.2.25', '03f74d0cd5037cadc8cdfa313bbd195c') + version('3.3.0', sha256='705468b5ae4cd1eb099d2d1c476d6a3abe519bc2810becf12fb1e32de1e074e4') + version('3.2.25', md5='03f74d0cd5037cadc8cdfa313bbd195c') depends_on('bison', type='build') depends_on('flex', type='build') diff --git a/var/spack/repos/builtin/packages/libnova/package.py b/var/spack/repos/builtin/packages/libnova/package.py index 927eaa4eb51..e28014c49cf 100644 --- a/var/spack/repos/builtin/packages/libnova/package.py +++ b/var/spack/repos/builtin/packages/libnova/package.py @@ -13,7 +13,7 @@ class Libnova(AutotoolsPackage): homepage = "http://libnova.sourceforge.net" url = "https://sourceforge.net/projects/libnova/files/libnova/v%200.15.0/libnova-0.15.0.tar.gz/download" - version('0.15.0', '756fdb55745cb78511f83a62c25f3be4') + version('0.15.0', sha256='7c5aa33e45a3e7118d77df05af7341e61784284f1e8d0d965307f1663f415bb1') depends_on('m4') depends_on('autoconf') diff --git a/var/spack/repos/builtin/packages/libnrm/package.py b/var/spack/repos/builtin/packages/libnrm/package.py index a1ecddccf3e..ad79170f9e2 100644 --- a/var/spack/repos/builtin/packages/libnrm/package.py +++ b/var/spack/repos/builtin/packages/libnrm/package.py @@ -12,7 +12,7 @@ class Libnrm(AutotoolsPackage): homepage = "https://xgitlab.cels.anl.gov/argo/libnrm" url = "https://www.mcs.anl.gov/research/projects/argo/downloads/libnrm-0.1.0.tar.gz" - version('0.1.0', '9261a55e58fd6350d9382dd09001cfd4') + version('0.1.0', sha256='f849ada384025fa41251acc2a43aa335e0cb1b9cd1c8ab8b9d1808a036ae551e') depends_on('m4', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/libogg/package.py b/var/spack/repos/builtin/packages/libogg/package.py index 13410cc54f7..f4d463993b2 100644 --- a/var/spack/repos/builtin/packages/libogg/package.py +++ b/var/spack/repos/builtin/packages/libogg/package.py @@ -13,4 +13,4 @@ class Libogg(AutotoolsPackage): homepage = "https://www.xiph.org/ogg/" url = "http://downloads.xiph.org/releases/ogg/libogg-1.3.2.tar.gz" - version('1.3.2', 'b72e1a1dbadff3248e4ed62a4177e937') + version('1.3.2', sha256='e19ee34711d7af328cb26287f4137e70630e7261b17cbe3cd41011d73a654692') diff --git a/var/spack/repos/builtin/packages/liboldx/package.py b/var/spack/repos/builtin/packages/liboldx/package.py index 4080d67e157..a7b1a169414 100644 --- a/var/spack/repos/builtin/packages/liboldx/package.py +++ b/var/spack/repos/builtin/packages/liboldx/package.py @@ -12,7 +12,7 @@ class Liboldx(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/liboldX/" url = "https://www.x.org/archive/individual/lib/liboldX-1.0.1.tar.gz" - version('1.0.1', 'ea7c4b6a19bf2d04100e2580abf83fae') + version('1.0.1', sha256='74322dbf04df69787485eb24b16e12783dfc3454befaf18482ead51bd7b55dc8') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/libpcap/package.py b/var/spack/repos/builtin/packages/libpcap/package.py index a3d500eb1e7..37a5b1f7fd6 100644 --- a/var/spack/repos/builtin/packages/libpcap/package.py +++ b/var/spack/repos/builtin/packages/libpcap/package.py @@ -12,7 +12,7 @@ class Libpcap(AutotoolsPackage): list_url = "http://www.tcpdump.org/release/" url = "http://www.tcpdump.org/release/libpcap-1.8.1.tar.gz" - version('1.8.1', '3d48f9cd171ff12b0efd9134b52f1447') + version('1.8.1', sha256='673dbc69fdc3f5a86fb5759ab19899039a8e5e6c631749e48dcd9c6f0c83541e') depends_on('flex', type='build') depends_on('bison', type='build') diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py index fd331b15247..14ee76f0b94 100644 --- a/var/spack/repos/builtin/packages/libpciaccess/package.py +++ b/var/spack/repos/builtin/packages/libpciaccess/package.py @@ -12,8 +12,8 @@ class Libpciaccess(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/" url = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.5.tar.gz" - version('0.13.5', '81468664fde96d1df2c3216fdf3c4a20') - version('0.13.4', 'cc1fad87da60682af1d5fa43a5da45a4') + version('0.13.5', sha256='fe26ec788732b4ef60b550f2d3fa51c605d27f646e18ecec878f061807a3526e') + version('0.13.4', sha256='74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f') depends_on('libtool', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/libpfm4/package.py b/var/spack/repos/builtin/packages/libpfm4/package.py index e8801e1fcf8..a4ff0358e25 100644 --- a/var/spack/repos/builtin/packages/libpfm4/package.py +++ b/var/spack/repos/builtin/packages/libpfm4/package.py @@ -14,9 +14,9 @@ class Libpfm4(MakefilePackage): homepage = "http://perfmon2.sourceforge.net" url = "https://downloads.sourceforge.net/project/perfmon2/libpfm4/libpfm-4.8.0.tar.gz" - version('4.10.1', 'd8f66cb9bfa7e1434434e0de6409db5b') - version('4.9.0', '42ad4a2e5b8e1f015310db8535739c73') - version('4.8.0', '730383896db92e12fb2cc10f2d41dd43') + version('4.10.1', sha256='c61c575378b5c17ccfc5806761e4038828610de76e2e34fac9f7fa73ba844b49') + version('4.9.0', sha256='db0fbe8ee28fd9beeb5d3e80b7cb3b104debcf6a9fcf5cb8b882f0662c79e4e2') + version('4.8.0', sha256='9193787a73201b4254e3669243fd71d15a9550486920861912090a09f366cf68') # Fails to build libpfm4 with intel compiler version 16 and 17 conflicts('%intel@16:17') diff --git a/var/spack/repos/builtin/packages/libpipeline/package.py b/var/spack/repos/builtin/packages/libpipeline/package.py index 353ec0a59df..35e90956fa6 100644 --- a/var/spack/repos/builtin/packages/libpipeline/package.py +++ b/var/spack/repos/builtin/packages/libpipeline/package.py @@ -13,7 +13,7 @@ class Libpipeline(AutotoolsPackage): homepage = "http://libpipeline.nongnu.org/" url = "http://git.savannah.nongnu.org/cgit/libpipeline.git/snapshot/libpipeline-1.4.2.tar.gz" - version('1.4.2', '30cec7bcd6fee723adea6a54389f3da2') + version('1.4.2', sha256='ac8b103b281ff63129c4fa6a8cc40bb5863e3a4266343d6e3bb5788de1ede488') depends_on('pkgconfig', type='build') depends_on('check', type='test') diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index 4d62fff6c6b..d9547786000 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -14,10 +14,10 @@ class Libpng(AutotoolsPackage): list_url = "https://sourceforge.net/projects/libpng/files/" list_depth = 2 - version('1.6.34', '03fbc5134830240104e96d3cda648e71') - version('1.6.29', '68553080685f812d1dd7a6b8215c37d8') - version('1.6.28', '897ccec1ebfb0922e83c2bfaa1be8748') - version('1.6.27', '58698519e9f6126c1caeefc28dbcbd5f') + version('1.6.34', sha256='574623a4901a9969080ab4a2df9437026c8a87150dfd5c235e28c94b212964a7') + version('1.6.29', sha256='e30bf36cd5882e017c23a5c6a79a9aa1a744dd5841bb45ff7035ec6e3b3096b8') + version('1.6.28', sha256='b6cec903e74e9fdd7b5bbcde0ab2415dd12f2f9e84d9e4d9ddd2ba26a41623b2') + version('1.6.27', sha256='c9d164ec247f426a525a7b89936694aefbc91fb7a50182b198898b8fc91174b4') # From http://www.libpng.org/pub/png/libpng.html (2017-01-04) # Virtually all libpng versions through 1.6.26, 1.5.27, # 1.4.19, 1.2.56, and 1.0.66, respectively, have a @@ -31,7 +31,7 @@ class Libpng(AutotoolsPackage): # December 2016. # Required for qt@3 - version('1.2.57', 'dfcda3603e29dcc11870c48f838ef75b') + version('1.2.57', sha256='09ec37869fc5b130f5eb06ffb9bf949796e8d2d78e0788f78ab1c78624c6e9da') depends_on('zlib@1.0.4:') # 1.2.5 or later recommended diff --git a/var/spack/repos/builtin/packages/libpsl/package.py b/var/spack/repos/builtin/packages/libpsl/package.py index 5daff9fd1b6..a8c430a3dd3 100644 --- a/var/spack/repos/builtin/packages/libpsl/package.py +++ b/var/spack/repos/builtin/packages/libpsl/package.py @@ -12,7 +12,7 @@ class Libpsl(AutotoolsPackage): homepage = "https://github.com/rockdaboot/libpsl" url = "https://github.com/rockdaboot/libpsl/releases/download/libpsl-0.17.0/libpsl-0.17.0.tar.gz" - version('0.17.0', 'fed13f33d0d6dc13ef24de255630bfcb') + version('0.17.0', sha256='025729d6a26ffd53cb54b4d86196f62c01d1813a4360c627546c6eb60ce3dd4b') depends_on('icu4c') diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py index 57c851fe9c5..3bc0471622b 100644 --- a/var/spack/repos/builtin/packages/libpthread-stubs/package.py +++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py @@ -13,5 +13,5 @@ class LibpthreadStubs(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/libpthread-stubs-0.4.tar.gz" - version('0.4', '7d2734e604a3e2f6f665c420b835ab62') - version('0.3', 'a09d928c4af54fe5436002345ef71138') + version('0.4', sha256='50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9') + version('0.3', sha256='3031f466cf0b06de6b3ccbf2019d15c4fcf75229b7d226a711bc1885b3a82cde') diff --git a/var/spack/repos/builtin/packages/libquo/package.py b/var/spack/repos/builtin/packages/libquo/package.py index 5b04ecab806..770bf2329f6 100644 --- a/var/spack/repos/builtin/packages/libquo/package.py +++ b/var/spack/repos/builtin/packages/libquo/package.py @@ -17,8 +17,8 @@ class Libquo(AutotoolsPackage): git = "https://github.com/lanl/libquo.git" version('develop', branch='master') - version('1.3', '1a1fb83d2c9e99ef5d5fcd71037ef8e8') - version('1.2.9', '85907cfbdb8b1e57fc5fcf3bced7cfa8') + version('1.3', sha256='61b0beff15eae4be94b5d3cbcbf7bf757659604465709ed01827cbba45efcf90') + version('1.2.9', sha256='0a64bea8f52f9eecd89e4ab82fde1c5bd271f3866c612da0ce7f38049409429b') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/libsigcpp/package.py b/var/spack/repos/builtin/packages/libsigcpp/package.py index 53be14ea317..500fba16d2f 100644 --- a/var/spack/repos/builtin/packages/libsigcpp/package.py +++ b/var/spack/repos/builtin/packages/libsigcpp/package.py @@ -15,9 +15,9 @@ class Libsigcpp(AutotoolsPackage): list_depth = 1 version('2.99.12', sha256='d902ae277f5baf2d56025586e2153cc2f158472e382723c67f49049f7c6690a8') - version('2.9.3', '0e5630fd0557ee80b5e5cbbcebaa2594') - version('2.1.1', '5ae4d6da9a408c90e86c776673c38972') - version('2.0.3', '57c6887dd46ce0bd312a4823589db5d8') + version('2.9.3', sha256='0bf9b301ad6198c550986c51150a646df198e8d1d235270c16486b0dda30097f') + version('2.1.1', sha256='7a2bd0b521544b31051c476205a0e74ace53771ec1a939bfec3c297b50c9fd78') + version('2.0.3', sha256='6ee6d5f164d8a34da33d2251cdb348b4f5769bf993ed8a6d4055bd47562f94a2') def url_for_version(self, version): """Handle version-based custom URLs.""" diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py index 63f8de66c85..f8afacc8a35 100644 --- a/var/spack/repos/builtin/packages/libsigsegv/package.py +++ b/var/spack/repos/builtin/packages/libsigsegv/package.py @@ -13,8 +13,8 @@ class Libsigsegv(AutotoolsPackage): url = "https://ftpmirror.gnu.org/libsigsegv/libsigsegv-2.12.tar.gz" version('2.12', sha256='3ae1af359eebaa4ffc5896a1aee3568c052c99879316a1ab57f8fe1789c390b6') - version('2.11', 'a812d9481f6097f705599b218eea349f') - version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f') + version('2.11', sha256='dd7c2eb2ef6c47189406d562c1dc0f96f2fc808036834d596075d58377e37a18') + version('2.10', sha256='8460a4a3dd4954c3d96d7a4f5dd5bc4d9b76f5754196aa245287553b26d2199a') patch('patch.new_config_guess', when='@2.10') diff --git a/var/spack/repos/builtin/packages/libsm/package.py b/var/spack/repos/builtin/packages/libsm/package.py index 809d12bb964..7ab37b7e518 100644 --- a/var/spack/repos/builtin/packages/libsm/package.py +++ b/var/spack/repos/builtin/packages/libsm/package.py @@ -12,7 +12,7 @@ class Libsm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libSM" url = "https://www.x.org/archive/individual/lib/libSM-1.2.2.tar.gz" - version('1.2.2', '18e5084ed9500b1b47719fd1758f0ec8') + version('1.2.2', sha256='14bb7c669ce2b8ff712fbdbf48120e3742a77edcd5e025d6b3325ed30cf120f4') depends_on('libice@1.0.5:') diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py index 75949142fd0..00371cfc3e7 100644 --- a/var/spack/repos/builtin/packages/libsodium/package.py +++ b/var/spack/repos/builtin/packages/libsodium/package.py @@ -13,18 +13,18 @@ class Libsodium(AutotoolsPackage): url = "https://download.libsodium.org/libsodium/releases/libsodium-1.0.13.tar.gz" list_url = "https://download.libsodium.org/libsodium/releases/old" - version('1.0.17', '0f71e2680187a1558b5461e6879342c5') - version('1.0.16', '37b18839e57e7a62834231395c8e962b') - version('1.0.15', '070373e73a0b10bd96f412e1732ebc42') - version('1.0.13', 'f38aac160a4bd05f06f743863e54e499') - version('1.0.12', 'c308e3faa724b630b86cc0aaf887a5d4') - version('1.0.11', 'b58928d035064b2a46fb564937b83540') - version('1.0.10', 'ea89dcbbda0b2b6ff6a1c476231870dd') - version('1.0.3', 'b3bcc98e34d3250f55ae196822307fab') - version('1.0.2', 'dc40eb23e293448c6fc908757738003f') - version('1.0.1', '9a221b49fba7281ceaaf5e278d0f4430') - version('1.0.0', '3093dabe4e038d09f0d150cef064b2f7') - version('0.7.1', 'c224fe3923d1dcfe418c65c8a7246316') + version('1.0.17', sha256='0cc3dae33e642cc187b5ceb467e0ad0e1b51dcba577de1190e9ffa17766ac2b1') + version('1.0.16', sha256='eeadc7e1e1bcef09680fb4837d448fbdf57224978f865ac1c16745868fbd0533') + version('1.0.15', sha256='fb6a9e879a2f674592e4328c5d9f79f082405ee4bb05cb6e679b90afe9e178f4') + version('1.0.13', sha256='9c13accb1a9e59ab3affde0e60ef9a2149ed4d6e8f99c93c7a5b97499ee323fd') + version('1.0.12', md5='c308e3faa724b630b86cc0aaf887a5d4') + version('1.0.11', md5='b58928d035064b2a46fb564937b83540') + version('1.0.10', md5='ea89dcbbda0b2b6ff6a1c476231870dd') + version('1.0.3', sha256='cbcfc63cc90c05d18a20f229a62c7e7054a73731d0aa858c0517152c549b1288') + version('1.0.2', sha256='961d8f10047f545ae658bcc73b8ab0bf2c312ac945968dd579d87c768e5baa19') + version('1.0.1', sha256='c3090887a4ef9e2d63af1c1e77f5d5a0656fadb5105ebb9fb66a302210cb3af5') + version('1.0.0', sha256='ced1fe3d2066953fea94f307a92f8ae41bf0643739a44309cbe43aa881dbc9a5') + version('0.7.1', sha256='ef46bbb5bac263ef6d3fc00ccc11d4690aea83643412919fe15369b9870280a7') def url_for_version(self, version): url = 'https://download.libsodium.org/libsodium/releases/' diff --git a/var/spack/repos/builtin/packages/libspatialindex/package.py b/var/spack/repos/builtin/packages/libspatialindex/package.py index c41e23930a4..110f6d52e31 100644 --- a/var/spack/repos/builtin/packages/libspatialindex/package.py +++ b/var/spack/repos/builtin/packages/libspatialindex/package.py @@ -12,4 +12,4 @@ class Libspatialindex(CMakePackage): homepage = "https://libspatialindex.org/" url = "https://github.com/libspatialindex/libspatialindex/tarball/1.8.5" - version('1.8.5', 'a95d8159714dbda9a274792cd273d298') + version('1.8.5', sha256='271f0d1425c527fd7d8b4be45b27e9383b244047b5918225877105616e7c0ad2') diff --git a/var/spack/repos/builtin/packages/libsplash/package.py b/var/spack/repos/builtin/packages/libsplash/package.py index b02686c8a99..1db0534b0a7 100644 --- a/var/spack/repos/builtin/packages/libsplash/package.py +++ b/var/spack/repos/builtin/packages/libsplash/package.py @@ -22,12 +22,12 @@ class Libsplash(CMakePackage): version('develop', branch='dev') version('master', branch='master') - version('1.7.0', '22dea94734fe4f4c5f4e875ce70900d3') - version('1.6.0', 'c05bce95abfe1ae4cd9d9817acf58d94') - version('1.5.0', 'c1efec4c20334242c8a3b6bfdc0207e3') - version('1.4.0', '2de37bcef6fafa1960391bf44b1b50e0') - version('1.3.1', '524580ba088d97253d03b4611772f37c') - version('1.2.4', '3fccb314293d22966beb7afd83b746d0') + version('1.7.0', sha256='51ab17c54233a8be86d7c5d59c755fb63a4a197315a510e5c49b20b070ebab73') + version('1.6.0', sha256='4d068de85504dfafb11bbaf6f2725a442c1f611e7cf962a924931a6220dad0f4') + version('1.5.0', sha256='a94547c416cee64bffd06736f61dd4e134f98a3da24117d52ee9f997c36d6b8d') + version('1.4.0', sha256='b86f2af15e5a05df30d4791c4ddb99a1db7b727d51b84706525fe247cfc70c78') + version('1.3.1', sha256='6ad04261e6d377a59b209f345af56405b37830f0dcfac28770b63091bff59383') + version('1.2.4', sha256='f5c4f792fee5609ede6a7d2fee5fa5799d3b68e8cdc23001a3aba390394d2f36') variant('mpi', default=True, description='Enable parallel I/O (one-file aggregation) support') diff --git a/var/spack/repos/builtin/packages/libssh/package.py b/var/spack/repos/builtin/packages/libssh/package.py index f3f65694330..597b528975a 100644 --- a/var/spack/repos/builtin/packages/libssh/package.py +++ b/var/spack/repos/builtin/packages/libssh/package.py @@ -12,8 +12,8 @@ class Libssh(CMakePackage): homepage = "https://www.libssh.org" url = "https://www.libssh.org/files/0.8/libssh-0.8.5.tar.xz" - version('0.8.5', '07d2c431240fc88f6b06bcb36ae267f9afeedce2e32f6c42f8844b205ab5a335') - version('0.7.5', 'd3fc864208bf607ad87cdee836894feb') + version('0.8.5', sha256='07d2c431240fc88f6b06bcb36ae267f9afeedce2e32f6c42f8844b205ab5a335') + version('0.7.5', sha256='54e86dd5dc20e5367e58f3caab337ce37675f863f80df85b6b1614966a337095') depends_on('openssl@:1.0', when='@:0.7') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/libssh2/package.py b/var/spack/repos/builtin/packages/libssh2/package.py index 0418365c6e4..9f198d3cf69 100644 --- a/var/spack/repos/builtin/packages/libssh2/package.py +++ b/var/spack/repos/builtin/packages/libssh2/package.py @@ -12,9 +12,9 @@ class Libssh2(CMakePackage): homepage = "https://www.libssh2.org/" url = "https://www.libssh2.org/download/libssh2-1.7.0.tar.gz" - version('1.8.0', '3d1147cae66e2959ea5441b183de1b1c') - version('1.7.0', 'b01662a210e94cccf2f76094db7dac5c') - version('1.4.3', '071004c60c5d6f90354ad1b701013a0b') # CentOS7 + version('1.8.0', sha256='39f34e2f6835f4b992cafe8625073a88e5a28ba78f83e8099610a7b3af4676d4') + version('1.7.0', sha256='e4561fd43a50539a8c2ceb37841691baf03ecb7daf043766da1b112e4280d584') + version('1.4.3', sha256='eac6f85f9df9db2e6386906a6227eb2cd7b3245739561cad7d6dc1d5d021b96d') # CentOS7 variant('shared', default=True, description="Build shared libraries") diff --git a/var/spack/repos/builtin/packages/libsvm/package.py b/var/spack/repos/builtin/packages/libsvm/package.py index 100c466be25..ee49566e9f6 100644 --- a/var/spack/repos/builtin/packages/libsvm/package.py +++ b/var/spack/repos/builtin/packages/libsvm/package.py @@ -13,7 +13,7 @@ class Libsvm(MakefilePackage): homepage = "https://www.csie.ntu.edu.tw/~cjlin/libsvm/" url = "https://github.com/cjlin1/libsvm/archive/v322.tar.gz" - version('322', 'd9617d29efad013573f63ca9a517f490') + version('322', sha256='a3469436f795bb3f8b1e65ea761e14e5599ec7ee941c001d771c07b7da318ac6') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/libszip/package.py b/var/spack/repos/builtin/packages/libszip/package.py index b1b0c70c49e..2c9bcc639a5 100644 --- a/var/spack/repos/builtin/packages/libszip/package.py +++ b/var/spack/repos/builtin/packages/libszip/package.py @@ -21,8 +21,8 @@ class Libszip(AutotoolsPackage): provides('szip') - version('2.1.1', '5addbf2a5b1bf928b92c47286e921f72') - version('2.1', '902f831bcefb69c6b635374424acbead') + version('2.1.1', sha256='21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412') + version('2.1', sha256='a816d95d5662e8279625abdbea7d0e62157d7d1f028020b1075500bf483ed5ef') def configure_args(self): return [ diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py index 9bdeba5555c..173edc8f115 100644 --- a/var/spack/repos/builtin/packages/libtermkey/package.py +++ b/var/spack/repos/builtin/packages/libtermkey/package.py @@ -11,11 +11,11 @@ class Libtermkey(Package): homepage = "http://www.leonerd.org.uk/code/libtermkey/" url = "http://www.leonerd.org.uk/code/libtermkey/libtermkey-0.18.tar.gz" - version('0.18', '3be2e3e5a851a49cc5e8567ac108b520') - version('0.17', '20edb99e0d95ec1690fe90e6a555ae6d') - version('0.16', '7a24b675aaeb142d30db28e7554987d4') - version('0.15b', '27689756e6c86c56ae454f2ac259bc3d') - version('0.14', 'e08ce30f440f9715c459060e0e048978') + version('0.18', sha256='239746de41c845af52bb3c14055558f743292dd6c24ac26c2d6567a5a6093926') + version('0.17', sha256='68949364ed5eaad857b3dea10071cde74b00b9f236dfbb702169f246c3cef389') + version('0.16', sha256='6c8136efa5d0b3277014a5d4519ea81190079c82656b7db1655a1bd147326a70') + version('0.15b', sha256='6825422c6297e4f81b2c48962b4512585ca8a50bf31f24b3234a1be71a9d7a6e') + version('0.14', sha256='3d114d4509499b80a583ea39cd35f18268aacf4a7bbf56c142cd032632005c79') depends_on('libtool', type='build') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py index f7b7b617124..9694e9269a3 100644 --- a/var/spack/repos/builtin/packages/libtiff/package.py +++ b/var/spack/repos/builtin/packages/libtiff/package.py @@ -13,12 +13,12 @@ class Libtiff(AutotoolsPackage): url = "http://download.osgeo.org/libtiff/tiff-4.0.10.tar.gz" version('4.0.10', sha256='2c52d11ccaf767457db0c46795d9c7d1a8d8f76f68b0b800a3dfe45786b996e4') - version('4.0.9', '54bad211279cc93eb4fca31ba9bfdc79') - version('4.0.8', '2a7d1c1318416ddf36d5f6fa4600069b') - version('4.0.7', '77ae928d2c6b7fb46a21c3a29325157b') - version('4.0.6', 'd1d2e940dea0b5ad435f21f03d96dd72') - version('4.0.3', '051c1068e6a0627f461948c365290410') - version('3.9.7', '626102f448ba441d42e3212538ad67d2') + version('4.0.9', sha256='6e7bdeec2c310734e734d19aae3a71ebe37a4d842e0e23dbb1b8921c0026cfcd') + version('4.0.8', sha256='59d7a5a8ccd92059913f246877db95a2918e6c04fb9d43fd74e5c3390dac2910') + version('4.0.7', sha256='9f43a2cfb9589e5cecaa66e16bf87f814c945f22df7ba600d63aac4632c4f019') + version('4.0.6', sha256='4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c') + version('4.0.3', md5='051c1068e6a0627f461948c365290410') + version('3.9.7', sha256='f5d64dd4ce61c55f5e9f6dc3920fbe5a41e02c2e607da7117a35eb5c320cef6a') depends_on('jpeg') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index 7823fa4bb44..bbad95e5735 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -14,8 +14,8 @@ class Libtool(AutotoolsPackage): version('develop', git='https://git.savannah.gnu.org/git/libtool.git', branch='master', submodules=True) - version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e') - version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50') + version('2.4.6', sha256='e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3') + version('2.4.2', sha256='b38de44862a987293cd3d8dfae1c409d514b6c4e794ebc93648febf9afc38918') depends_on('m4@1.4.6:', type='build') depends_on('autoconf', type='build', when='@2.4.2,develop') diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py index 8f450417999..86f03a10a6c 100644 --- a/var/spack/repos/builtin/packages/libunistring/package.py +++ b/var/spack/repos/builtin/packages/libunistring/package.py @@ -16,8 +16,8 @@ class Libunistring(AutotoolsPackage): version('0.9.10', sha256='eb8fb2c3e4b6e2d336608377050892b54c3c983b646c561836550863003c05d7') version('0.9.9', sha256='a4d993ecfce16cf503ff7579f5da64619cee66226fb3b998dafb706190d9a833') version('0.9.8', sha256='7b9338cf52706facb2e18587dceda2fbc4a2a3519efa1e15a3f2a68193942f80') - version('0.9.7', '82e0545363d111bfdfec2ddbfe62ffd3') - version('0.9.6', 'cb09c398020c27edac10ca590e9e9ef3') + version('0.9.7', sha256='2e3764512aaf2ce598af5a38818c0ea23dedf1ff5460070d1b6cee5c3336e797') + version('0.9.6', sha256='2df42eae46743e3f91201bf5c100041540a7704e8b9abfd57c972b2d544de41b') depends_on('libiconv') diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py index c226b344f69..e729b7c20db 100644 --- a/var/spack/repos/builtin/packages/libunwind/package.py +++ b/var/spack/repos/builtin/packages/libunwind/package.py @@ -16,9 +16,9 @@ class Libunwind(AutotoolsPackage): version('develop', branch='master') version('2018.10.12', commit='f551e16213c52169af8bda554e4051b756a169cc') - version('1.3-rc1', 'f09b670de5db6430a3de666e6aed60e3') - version('1.2.1', '06ba9e60d92fd6f55cd9dadb084df19e', preferred=True) - version('1.1', 'fb4ea2f6fbbe45bf032cd36e586883ce') + version('1.3-rc1', sha256='e40f49dcbfdea3f4d15fa555fe68958e69a3f410aacf1ec46fd86aeced699773') + version('1.2.1', sha256='3f3ecb90e28cbe53fba7a4a27ccce7aad188d3210bb1964a923a731a27a75acb', preferred=True) + version('1.1', sha256='9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a') variant('xz', default=False, description='Support xz (lzma) compressed symbol tables.') diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py index d2cb9cc5a11..140cd7f93fe 100644 --- a/var/spack/repos/builtin/packages/libuuid/package.py +++ b/var/spack/repos/builtin/packages/libuuid/package.py @@ -12,4 +12,4 @@ class Libuuid(AutotoolsPackage): homepage = "http://sourceforge.net/projects/libuuid/" url = "http://downloads.sourceforge.net/project/libuuid/libuuid-1.0.3.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Flibuuid%2F&ts=1433881396&use_mirror=iweb" - version('1.0.3', 'd44d866d06286c08ba0846aba1086d68') + version('1.0.3', sha256='46af3275291091009ad7f1b899de3d0cea0252737550e7919d17237997db5644') diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py index 61e9da43391..57662913e56 100644 --- a/var/spack/repos/builtin/packages/libuv/package.py +++ b/var/spack/repos/builtin/packages/libuv/package.py @@ -11,9 +11,9 @@ class Libuv(AutotoolsPackage): homepage = "http://libuv.org" url = "https://github.com/libuv/libuv/archive/v1.9.0.tar.gz" - version('1.25.0', '31a1873ebceacae42573bac8ec5da687') - version('1.10.0', 'f7a12f3a8ee021c20cfbc9af4cc5b793') - version('1.9.0', '14737f9c76123a19a290dabb7d1cd04c') + version('1.25.0', sha256='ce3036d444c3fb4f9a9e2994bec1f4fa07872b01456998b422ce918fdc55c254') + version('1.10.0', sha256='50f4ed57d65af4ab634e2cbdd90c49213020e15b4d77d3631feb633cbba9239f') + version('1.9.0', sha256='f8b8272a0d80138b709d38fad2baf771899eed61e7f9578d17898b07a1a2a5eb') depends_on('automake', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/libvdwxc/package.py b/var/spack/repos/builtin/packages/libvdwxc/package.py index aece4ec0bc9..cec8e06002f 100644 --- a/var/spack/repos/builtin/packages/libvdwxc/package.py +++ b/var/spack/repos/builtin/packages/libvdwxc/package.py @@ -14,7 +14,7 @@ class Libvdwxc(AutotoolsPackage): homepage = "https://libvdwxc.gitlab.io/libvdwxc/" url = "https://launchpad.net/libvdwxc/stable/0.4.0/+download/libvdwxc-0.4.0.tar.gz" - version("0.4.0", "68196798d69d593b62ea9f482468db66") + version("0.4.0", sha256="3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33") variant("mpi", default=True, description="Enable MPI support") variant("pfft", default=False, description="Enable support for PFFT") diff --git a/var/spack/repos/builtin/packages/libvorbis/package.py b/var/spack/repos/builtin/packages/libvorbis/package.py index 7b1ffd7652d..6f6de52b460 100644 --- a/var/spack/repos/builtin/packages/libvorbis/package.py +++ b/var/spack/repos/builtin/packages/libvorbis/package.py @@ -15,7 +15,7 @@ class Libvorbis(AutotoolsPackage): homepage = "https://xiph.org/vorbis/" url = "http://downloads.xiph.org/releases/vorbis/libvorbis-1.3.5.tar.gz" - version('1.3.5', '7220e089f3be3412a2317d6fde9e3944') + version('1.3.5', sha256='6efbcecdd3e5dfbf090341b485da9d176eb250d893e3eb378c428a2db38301ce') depends_on('libogg') diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py index 6784fa04829..95c5b819ede 100644 --- a/var/spack/repos/builtin/packages/libvterm/package.py +++ b/var/spack/repos/builtin/packages/libvterm/package.py @@ -11,7 +11,7 @@ class Libvterm(Package): homepage = "http://www.leonerd.org.uk/code/libvterm/" url = "http://www.leonerd.org.uk/code/libvterm/libvterm-0+bzr681.tar.gz" - version('681', '7a4325a7350b7092245c04e8ee185ac3') + version('681', sha256='abea46d1b0b831dec2af5d582319635cece63d260f8298d9ccce7c1c2e62a6e8') depends_on('libtool', type='build') diff --git a/var/spack/repos/builtin/packages/libwebsockets/package.py b/var/spack/repos/builtin/packages/libwebsockets/package.py index 5484b5128f3..b49aea6f036 100644 --- a/var/spack/repos/builtin/packages/libwebsockets/package.py +++ b/var/spack/repos/builtin/packages/libwebsockets/package.py @@ -13,11 +13,11 @@ class Libwebsockets(CMakePackage): url = "https://github.com/warmcat/libwebsockets/archive/v2.1.0.tar.gz" maintainers = ['ax3l'] - version('2.2.1', '1f641cde2ab3687db3d553f68fe0f620') - version('2.1.1', '674684ffb90d4a0bcf7a075eb7b90192') - version('2.1.0', '4df3be57dee43aeebd54a3ed56568f50') - version('2.0.3', 'a025156d606d90579e65d53ccd062a94') - version('1.7.9', '7b3692ead5ae00fd0e1d56c080170f07') + version('2.2.1', sha256='e7f9eaef258e003c9ada0803a9a5636757a5bc0a58927858834fb38a87d18ad2') + version('2.1.1', sha256='96183cbdfcd6e6a3d9465e854a924b7bfde6c8c6d3384d6159ad797c2e823b4d') + version('2.1.0', sha256='bcc96aaa609daae4d3f7ab1ee480126709ef4f6a8bf9c85de40aae48e38cce66') + version('2.0.3', sha256='cf0e91b564c879ab98844385c98e7c9e298cbb969dbc251a3f18a47feb94342c') + version('1.7.9', sha256='86a5105881ea2cb206f8795483d294e9509055decf60436bcc1e746262416438') depends_on('zlib') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/libwindowswm/package.py b/var/spack/repos/builtin/packages/libwindowswm/package.py index 3d777301a43..3d38b280958 100644 --- a/var/spack/repos/builtin/packages/libwindowswm/package.py +++ b/var/spack/repos/builtin/packages/libwindowswm/package.py @@ -17,7 +17,7 @@ class Libwindowswm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libWindowsWM" url = "https://www.x.org/archive/individual/lib/libWindowsWM-1.0.1.tar.gz" - version('1.0.1', 'f260e124706ff6209c566689528667c6') + version('1.0.1', sha256='94f9c0add3bad38ebd84bc43d854207c4deaaa74fb15339276e022546124b98a') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libx11/package.py b/var/spack/repos/builtin/packages/libx11/package.py index d4a58183a51..5c1a7f21f33 100644 --- a/var/spack/repos/builtin/packages/libx11/package.py +++ b/var/spack/repos/builtin/packages/libx11/package.py @@ -13,8 +13,8 @@ class Libx11(AutotoolsPackage): url = "https://www.x.org/archive/individual/lib/libX11-1.6.7.tar.gz" version('1.6.7', sha256='f62ab88c2a87b55e1dc338726a55bb6ed8048084fe6a3294a7ae324ca45159d1') - version('1.6.5', '300b5831916ffcc375468431d856917e') - version('1.6.3', '7d16653fe7c36209799175bb3dc1ae46') + version('1.6.5', sha256='3abce972ba62620611fab5b404dafb852da3da54e7c287831c30863011d28fb3') + version('1.6.3', sha256='0b03b9d22f4c9e59b4ba498f294e297f013cae27050dfa0f3496640200db5376') depends_on('libxcb@1.1.92:') diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py index 4cc9e84bd4a..a9ffe42930b 100644 --- a/var/spack/repos/builtin/packages/libxau/package.py +++ b/var/spack/repos/builtin/packages/libxau/package.py @@ -14,7 +14,7 @@ class Libxau(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libXau/" url = "https://www.x.org/archive/individual/lib/libXau-1.0.8.tar.gz" - version('1.0.8', 'a85cd601d82bc79c0daa280917572e20') + version('1.0.8', sha256='c343b4ef66d66a6b3e0e27aa46b37ad5cab0f11a5c565eafb4a1c7590bc71d7b') depends_on('xproto', type=('build', 'link')) depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/libxaw/package.py b/var/spack/repos/builtin/packages/libxaw/package.py index 709615564d1..068e9ec7956 100644 --- a/var/spack/repos/builtin/packages/libxaw/package.py +++ b/var/spack/repos/builtin/packages/libxaw/package.py @@ -13,8 +13,8 @@ class Libxaw(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXaw" url = "https://www.x.org/archive/individual/lib/libXaw-1.0.13.tar.gz" - version('1.0.13', '6c522476024df5872cddc5f1562fb656') - version('1.0.12', 'a1dd3ced7cefe99b2db8a5d390cf5fe9') + version('1.0.13', sha256='7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694') + version('1.0.12', sha256='e32abc68d759ffb643f842329838f8b6c157e31023cc91059aabf730e7222ad2') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxaw3d/package.py b/var/spack/repos/builtin/packages/libxaw3d/package.py index e0c5b4104d6..61bba5ca6d2 100644 --- a/var/spack/repos/builtin/packages/libxaw3d/package.py +++ b/var/spack/repos/builtin/packages/libxaw3d/package.py @@ -13,7 +13,7 @@ class Libxaw3d(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXaw3d" url = "https://www.x.org/archive/individual/lib/libXaw3d-1.6.2.tar.gz" - version('1.6.2', 'e51e00b734853e555ae9b367d213de45') + version('1.6.2', sha256='847dab01aeac1448916e3b4edb4425594b3ac2896562d9c7141aa4ac6c898ba9') depends_on('libx11') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index ea1c8c97860..b1e4eea2a66 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -15,10 +15,10 @@ class Libxcb(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/libxcb-1.13.tar.gz" - version('1.13', '3ba7fe0a7d60650bfb73fbf623aa57cc') - version('1.12', '95eee7c28798e16ba5443f188b27a476') - version('1.11.1', '118623c15a96b08622603a71d8789bf3') - version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb') + version('1.13', sha256='0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb') + version('1.12', sha256='092f147149d8a6410647a848378aaae749304d5b73e028ccb8306aa8a9e26f06') + version('1.11.1', sha256='660312d5e64d0a5800262488042c1707a0261fa01a759bad265b1b75dd4844dd') + version('1.11', sha256='4b351e1dc95eb0a1c25fa63611a6f4cf033cb63e20997c4874c80bbd1876d0b4') depends_on('libpthread-stubs') depends_on('libxau@0.99.2:') diff --git a/var/spack/repos/builtin/packages/libxcomposite/package.py b/var/spack/repos/builtin/packages/libxcomposite/package.py index 282341c4acd..b9ce5083dbb 100644 --- a/var/spack/repos/builtin/packages/libxcomposite/package.py +++ b/var/spack/repos/builtin/packages/libxcomposite/package.py @@ -13,7 +13,7 @@ class Libxcomposite(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXcomposite" url = "https://www.x.org/archive/individual/lib/libXcomposite-0.4.4.tar.gz" - version('0.4.4', 'af860b1554a423735d831e6f29ac1ef5') + version('0.4.4', sha256='83c04649819c6f52cda1b0ce8bcdcc48ad8618428ad803fb07f20b802f1bdad1') depends_on('libx11') depends_on('libxfixes') diff --git a/var/spack/repos/builtin/packages/libxcursor/package.py b/var/spack/repos/builtin/packages/libxcursor/package.py index e53b6fb8c2e..6b906ad0518 100644 --- a/var/spack/repos/builtin/packages/libxcursor/package.py +++ b/var/spack/repos/builtin/packages/libxcursor/package.py @@ -12,7 +12,7 @@ class Libxcursor(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXcursor" url = "https://www.x.org/archive/individual/lib/libXcursor-1.1.14.tar.gz" - version('1.1.14', '39c8423de190d64f1c52fbc00022e52c') + version('1.1.14', sha256='be0954faf274969ffa6d95b9606b9c0cfee28c13b6fc014f15606a0c8b05c17b') depends_on('libxrender@0.8.2:') depends_on('libxfixes') diff --git a/var/spack/repos/builtin/packages/libxdamage/package.py b/var/spack/repos/builtin/packages/libxdamage/package.py index a9cdb93b5ec..fedfee9efba 100644 --- a/var/spack/repos/builtin/packages/libxdamage/package.py +++ b/var/spack/repos/builtin/packages/libxdamage/package.py @@ -12,7 +12,7 @@ class Libxdamage(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXdamage" url = "https://www.x.org/archive/individual/lib/libXdamage-1.1.4.tar.gz" - version('1.1.4', '95867778da012623815214769007c0d7') + version('1.1.4', sha256='4bb3e9d917f5f593df2277d452926ee6ad96de7b7cd1017cbcf4579fe5d3442b') depends_on('libxfixes') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/libxdmcp/package.py b/var/spack/repos/builtin/packages/libxdmcp/package.py index fe1bdfa8d70..bf9a0c8993a 100644 --- a/var/spack/repos/builtin/packages/libxdmcp/package.py +++ b/var/spack/repos/builtin/packages/libxdmcp/package.py @@ -12,7 +12,7 @@ class Libxdmcp(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXdmcp" url = "https://www.x.org/archive/individual/lib/libXdmcp-1.1.2.tar.gz" - version('1.1.2', 'ab0d6a38f0344a05d698ec7d48cfa5a8') + version('1.1.2', sha256='6f7c7e491a23035a26284d247779174dedc67e34e93cc3548b648ffdb6fc57c0') depends_on('xproto', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/libxevie/package.py b/var/spack/repos/builtin/packages/libxevie/package.py index e638afb5108..c8e86f558ae 100644 --- a/var/spack/repos/builtin/packages/libxevie/package.py +++ b/var/spack/repos/builtin/packages/libxevie/package.py @@ -12,7 +12,7 @@ class Libxevie(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXevie" url = "https://www.x.org/archive/individual/lib/libXevie-1.0.3.tar.gz" - version('1.0.3', '100e6485cabfe6e788e09c110ca680d8') + version('1.0.3', sha256='3759bb1f7fdade13ed99bfc05c0717bc42ce3f187e7da4eef80beddf5e461258') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxext/package.py b/var/spack/repos/builtin/packages/libxext/package.py index cd744f1b585..03986f088e3 100644 --- a/var/spack/repos/builtin/packages/libxext/package.py +++ b/var/spack/repos/builtin/packages/libxext/package.py @@ -12,7 +12,7 @@ class Libxext(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXext" url = "https://www.x.org/archive/individual/lib/libXext-1.3.3.tar.gz" - version('1.3.3', '93f5ec084c998efbfb0befed22f9b57f') + version('1.3.3', sha256='eb0b88050491fef4716da4b06a4d92b4fc9e76f880d6310b2157df604342cfe5') depends_on('libx11@1.6:') diff --git a/var/spack/repos/builtin/packages/libxfixes/package.py b/var/spack/repos/builtin/packages/libxfixes/package.py index 2c64096a3f3..93671b41e81 100644 --- a/var/spack/repos/builtin/packages/libxfixes/package.py +++ b/var/spack/repos/builtin/packages/libxfixes/package.py @@ -13,7 +13,7 @@ class Libxfixes(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXfixes" url = "https://www.x.org/archive/individual/lib/libXfixes-5.0.2.tar.gz" - version('5.0.2', '3636e59f8f5fa2e469d556d49f30e98d') + version('5.0.2', sha256='ad8df1ecf3324512b80ed12a9ca07556e561b14256d94216e67a68345b23c981') depends_on('libx11@1.6:') diff --git a/var/spack/repos/builtin/packages/libxfont/package.py b/var/spack/repos/builtin/packages/libxfont/package.py index e663651bd39..0a3c9e48820 100644 --- a/var/spack/repos/builtin/packages/libxfont/package.py +++ b/var/spack/repos/builtin/packages/libxfont/package.py @@ -17,7 +17,7 @@ class Libxfont(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXfont" url = "https://www.x.org/archive/individual/lib/libXfont-1.5.2.tar.gz" - version('1.5.2', 'e8c616db0e59df4614980915e79bb05e') + version('1.5.2', sha256='a7350c75171d03d06ae0d623e42240356d6d3e1ac7dfe606639bf20f0d653c93') depends_on('libfontenc') depends_on('freetype') diff --git a/var/spack/repos/builtin/packages/libxfont2/package.py b/var/spack/repos/builtin/packages/libxfont2/package.py index b2b7582d61c..4678212baa7 100644 --- a/var/spack/repos/builtin/packages/libxfont2/package.py +++ b/var/spack/repos/builtin/packages/libxfont2/package.py @@ -17,7 +17,7 @@ class Libxfont2(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXfont" url = "https://www.x.org/archive/individual/lib/libXfont2-2.0.1.tar.gz" - version('2.0.1', '6ae5ae1f9fb1213b04f14a802a1d721c') + version('2.0.1', sha256='381b6b385a69343df48a082523c856aed9042fbbc8ee0a6342fb502e4321230a') depends_on('libfontenc') depends_on('freetype') diff --git a/var/spack/repos/builtin/packages/libxfontcache/package.py b/var/spack/repos/builtin/packages/libxfontcache/package.py index 00d7453ca23..1d8c14d9000 100644 --- a/var/spack/repos/builtin/packages/libxfontcache/package.py +++ b/var/spack/repos/builtin/packages/libxfontcache/package.py @@ -12,7 +12,7 @@ class Libxfontcache(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXfontcache" url = "https://www.x.org/archive/individual/lib/libXfontcache-1.0.5.tar.gz" - version('1.0.5', '5030fc9c7f16dbb52f92a8ba2c574f5c') + version('1.0.5', sha256='fdba75307a0983d2566554e0e9effa7079551f1b7b46e8de642d067998619659') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxft/package.py b/var/spack/repos/builtin/packages/libxft/package.py index a4f36433f5f..9ab8687de54 100644 --- a/var/spack/repos/builtin/packages/libxft/package.py +++ b/var/spack/repos/builtin/packages/libxft/package.py @@ -16,7 +16,7 @@ class Libxft(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXft" url = "https://www.x.org/archive/individual/lib/libXft-2.3.2.tar.gz" - version('2.3.2', '3a2c1ce2641817dace55cd2bfe10b0f0') + version('2.3.2', sha256='26cdddcc70b187833cbe9dc54df1864ba4c03a7175b2ca9276de9f05dce74507') depends_on('freetype@2.1.6:') depends_on('fontconfig@2.5.92:') diff --git a/var/spack/repos/builtin/packages/libxi/package.py b/var/spack/repos/builtin/packages/libxi/package.py index 0b42dda8165..037a0e36a2f 100644 --- a/var/spack/repos/builtin/packages/libxi/package.py +++ b/var/spack/repos/builtin/packages/libxi/package.py @@ -12,7 +12,7 @@ class Libxi(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXi" url = "https://www.x.org/archive/individual/lib/libXi-1.7.6.tar.gz" - version('1.7.6', 'f3828f9d7893068f6f6f10fe15b31afa') + version('1.7.6', sha256='4e88fa7decd287e58140ea72238f8d54e4791de302938c83695fc0c9ac102b7e') depends_on('pkgconfig', type='build') depends_on('libx11@1.6:') diff --git a/var/spack/repos/builtin/packages/libxinerama/package.py b/var/spack/repos/builtin/packages/libxinerama/package.py index 490818a1064..bfc12e81365 100644 --- a/var/spack/repos/builtin/packages/libxinerama/package.py +++ b/var/spack/repos/builtin/packages/libxinerama/package.py @@ -12,7 +12,7 @@ class Libxinerama(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXinerama" url = "https://www.x.org/archive/individual/lib/libXinerama-1.1.3.tar.gz" - version('1.1.3', '7224a1baa9733a54053550a3fb4be118') + version('1.1.3', sha256='0ba243222ae5aba4c6a3d7a394c32c8b69220a6872dbb00b7abae8753aca9a44') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxkbfile/package.py b/var/spack/repos/builtin/packages/libxkbfile/package.py index 0734b60d62c..a91198e05ac 100644 --- a/var/spack/repos/builtin/packages/libxkbfile/package.py +++ b/var/spack/repos/builtin/packages/libxkbfile/package.py @@ -12,7 +12,7 @@ class Libxkbfile(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libxkbfile" url = "https://www.x.org/archive/individual/lib/libxkbfile-1.0.9.tar.gz" - version('1.0.9', '5aab87eba67f37dd910a19be5c1129ee') + version('1.0.9', sha256='95df50570f38e720fb79976f603761ae6eff761613eb56f258c3cb6bab4fd5e3') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/libxkbui/package.py b/var/spack/repos/builtin/packages/libxkbui/package.py index b9eecbdbb02..7fd81908a0a 100644 --- a/var/spack/repos/builtin/packages/libxkbui/package.py +++ b/var/spack/repos/builtin/packages/libxkbui/package.py @@ -12,7 +12,7 @@ class Libxkbui(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libxkbui/" url = "https://www.x.org/archive/individual/lib/libxkbui-1.0.2.tar.gz" - version('1.0.2', 'a6210171defde64d9e8bcf6a6f6074b0') + version('1.0.2', sha256='196ab4867f3754caae34e51a663cbce26b4af819db3960f1fc4fb42c6a3c535d') depends_on('libx11') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py index e95b7101bc4..b7a6381f305 100644 --- a/var/spack/repos/builtin/packages/libxml2/package.py +++ b/var/spack/repos/builtin/packages/libxml2/package.py @@ -15,10 +15,10 @@ class Libxml2(AutotoolsPackage): url = "http://xmlsoft.org/sources/libxml2-2.9.8.tar.gz" version('2.9.9', sha256='94fb70890143e3c6549f265cee93ec064c80a84c42ad0f23e85ee1fd6540a871') - version('2.9.8', 'b786e353e2aa1b872d70d5d1ca0c740d') - version('2.9.4', 'ae249165c173b1ff386ee8ad676815f5') - version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788') - version('2.7.8', '8127a65e8c3b08856093099b52599c86') + version('2.9.8', sha256='0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732') + version('2.9.4', sha256='ffb911191e509b966deb55de705387f14156e1a56b21824357cdf0053233633c') + version('2.9.2', sha256='5178c30b151d044aefb1b08bf54c3003a0ac55c59c866763997529d60770d5bc') + version('2.7.8', sha256='cda23bc9ebd26474ca8f3d67e7d1c4a1f1e7106364b690d822e009fdc3c417ec') variant('python', default=False, description='Enable Python support') diff --git a/var/spack/repos/builtin/packages/libxmu/package.py b/var/spack/repos/builtin/packages/libxmu/package.py index 35dd69c015f..cf825ec74a6 100644 --- a/var/spack/repos/builtin/packages/libxmu/package.py +++ b/var/spack/repos/builtin/packages/libxmu/package.py @@ -15,7 +15,7 @@ class Libxmu(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXmu" url = "https://www.x.org/archive/individual/lib/libXmu-1.1.2.tar.gz" - version('1.1.2', 'd5be323b02e6851607205c8e941b4e61') + version('1.1.2', sha256='e5fd4bacef068f9509b8226017205040e38d3fba8d2de55037200e7176c13dba') depends_on('libxt') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxp/package.py b/var/spack/repos/builtin/packages/libxp/package.py index a42681c063e..7a4d194a953 100644 --- a/var/spack/repos/builtin/packages/libxp/package.py +++ b/var/spack/repos/builtin/packages/libxp/package.py @@ -12,7 +12,7 @@ class Libxp(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXp" url = "https://www.x.org/archive/individual/lib/libXp-1.0.3.tar.gz" - version('1.0.3', '1157da663b28e110f440ce64cede6e18') + version('1.0.3', sha256='f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c') depends_on('libx11@1.6:') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxpm/package.py b/var/spack/repos/builtin/packages/libxpm/package.py index 24a49f04363..542052d4ddf 100644 --- a/var/spack/repos/builtin/packages/libxpm/package.py +++ b/var/spack/repos/builtin/packages/libxpm/package.py @@ -12,12 +12,12 @@ class Libxpm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXpm" url = "https://www.x.org/archive//individual/lib/libXpm-3.5.12.tar.gz" - version('3.5.12', 'b286c884b11b5a0b4371175c5327141f') - version('3.5.11', '7c67c878ee048206b070bc0b24154f04') - version('3.5.10', 'a70507638d74541bf30a771f1e5938bb') - version('3.5.9', 'd6d4b0f76248a6b346eb42dfcdaa72a6') - version('3.5.8', '2d81d6633e67ac5562e2fbee126b2897') - version('3.5.7', '7bbc8f112f7143ed6961a58ce4e14558') + version('3.5.12', sha256='2523acc780eac01db5163267b36f5b94374bfb0de26fc0b5a7bee76649fd8501') + version('3.5.11', sha256='53ddf924441b7ed2de994d4934358c13d9abf4828b1b16e1255ade5032b31df7') + version('3.5.10', sha256='f73f06928a140fd2090c439d1d55c6682095044495af6bf886f8e66cf21baee5') + version('3.5.9', sha256='23beb930e27bc7df33cb0f6dbffc703852297c311b7e20146ff82e9a51f3e358') + version('3.5.8', sha256='06472c7fdd175ea54c84162a428be19c154e7dda03d8bf91beee7f1d104669a6') + version('3.5.7', sha256='422fbb311c4fe6ef337e937eb3adc8617a4320bd3e00fce06850d4360829b3ae') depends_on('gettext') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/libxpresent/package.py b/var/spack/repos/builtin/packages/libxpresent/package.py index a285c3dc703..0acfcd44dee 100644 --- a/var/spack/repos/builtin/packages/libxpresent/package.py +++ b/var/spack/repos/builtin/packages/libxpresent/package.py @@ -13,7 +13,7 @@ class Libxpresent(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libXpresent/" url = "https://www.x.org/archive/individual/lib/libXpresent-1.0.0.tar.gz" - version('1.0.0', '2f543a595c3e6a519e2e38d079002958') + version('1.0.0', sha256='92f1bdfb67ae2ffcdb25ad72c02cac5e4912dc9bc792858240df1d7f105946fa') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/libxprintapputil/package.py b/var/spack/repos/builtin/packages/libxprintapputil/package.py index 998eea3381c..5d145ee0241 100644 --- a/var/spack/repos/builtin/packages/libxprintapputil/package.py +++ b/var/spack/repos/builtin/packages/libxprintapputil/package.py @@ -12,7 +12,7 @@ class Libxprintapputil(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libXprintAppUtil/" url = "https://www.x.org/archive/individual/lib/libXprintAppUtil-1.0.1.tar.gz" - version('1.0.1', '3adb71fa34a2d4e75d8b840310318f76') + version('1.0.1', sha256='5af3939ffe15508b942bc1e325a29a95b1c85e8900a5f65a896101e63048bbf7') depends_on('libx11') depends_on('libxp') diff --git a/var/spack/repos/builtin/packages/libxprintutil/package.py b/var/spack/repos/builtin/packages/libxprintutil/package.py index 11bb33106c4..2f13cc0964b 100644 --- a/var/spack/repos/builtin/packages/libxprintutil/package.py +++ b/var/spack/repos/builtin/packages/libxprintutil/package.py @@ -12,7 +12,7 @@ class Libxprintutil(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libXprintUtil/" url = "https://www.x.org/archive/individual/lib/libXprintUtil-1.0.1.tar.gz" - version('1.0.1', '2f02e812f3e419534ced6fcb5860825f') + version('1.0.1', sha256='220924216f98ef8f7aa4cff33629edb1171ad10f8ea302a1eb85055545d4d195') depends_on('libx11') depends_on('libxp') diff --git a/var/spack/repos/builtin/packages/libxrandr/package.py b/var/spack/repos/builtin/packages/libxrandr/package.py index 1fd7b8d9787..85fdb0ab94b 100644 --- a/var/spack/repos/builtin/packages/libxrandr/package.py +++ b/var/spack/repos/builtin/packages/libxrandr/package.py @@ -12,7 +12,7 @@ class Libxrandr(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXrandr" url = "https://www.x.org/archive/individual/lib/libXrandr-1.5.0.tar.gz" - version('1.5.0', 'e2fafff575b94ba0b15983eb4df93656') + version('1.5.0', sha256='1b594a149e6b124aab7149446f2fd886461e2935eca8dca43fe83a70cf8ec451') depends_on('libx11@1.6:') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxrender/package.py b/var/spack/repos/builtin/packages/libxrender/package.py index d6020f9f4cd..db2da986c64 100644 --- a/var/spack/repos/builtin/packages/libxrender/package.py +++ b/var/spack/repos/builtin/packages/libxrender/package.py @@ -12,8 +12,8 @@ class Libxrender(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXrender" url = "https://www.x.org/archive/individual/lib/libXrender-0.9.10.tar.gz" - version('0.9.10', '98a14fc11aee08b4a1769426ab4b23a3') - version('0.9.9', '0c797c4f2a7b782896bc223e6dac4333') + version('0.9.10', sha256='770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf') + version('0.9.9', sha256='beeac64ff8d225f775019eb7c688782dee9f4cc7b412a65538f8dde7be4e90fe') depends_on('libx11@1.6:') diff --git a/var/spack/repos/builtin/packages/libxres/package.py b/var/spack/repos/builtin/packages/libxres/package.py index e201015aa2e..d90d81b615c 100644 --- a/var/spack/repos/builtin/packages/libxres/package.py +++ b/var/spack/repos/builtin/packages/libxres/package.py @@ -12,7 +12,7 @@ class Libxres(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXRes" url = "https://www.x.org/archive/individual/lib/libXres-1.0.7.tar.gz" - version('1.0.7', '7fad9ab34201bb4adffcbf0cd7e87a89') + version('1.0.7', sha256='488c9fa14b38f794d1f019fe62e6b06514a39f1a7538e55ece8faf22482fefcd') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxscrnsaver/package.py b/var/spack/repos/builtin/packages/libxscrnsaver/package.py index 94971939936..176b0186d82 100644 --- a/var/spack/repos/builtin/packages/libxscrnsaver/package.py +++ b/var/spack/repos/builtin/packages/libxscrnsaver/package.py @@ -12,7 +12,7 @@ class Libxscrnsaver(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXScrnSaver" url = "https://www.x.org/archive/individual/lib/libXScrnSaver-1.2.2.tar.gz" - version('1.2.2', '79227e7d8c0dad27654c526de3d6fef3') + version('1.2.2', sha256='e12ba814d44f7b58534c0d8521e2d4574f7bf2787da405de4341c3b9f4cc8d96') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxshmfence/package.py b/var/spack/repos/builtin/packages/libxshmfence/package.py index f7e7b20363f..a81380ac291 100644 --- a/var/spack/repos/builtin/packages/libxshmfence/package.py +++ b/var/spack/repos/builtin/packages/libxshmfence/package.py @@ -16,8 +16,8 @@ class Libxshmfence(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libxshmfence/" url = "https://www.x.org/archive/individual/lib/libxshmfence-1.3.tar.bz2" - version('1.3', '42dda8016943dc12aff2c03a036e0937') - version('1.2', '66662e76899112c0f99e22f2fc775a7e') + version('1.3', sha256='b884300d26a14961a076fbebc762a39831cb75f92bed5ccf9836345b459220c7') + version('1.2', sha256='d21b2d1fd78c1efbe1f2c16dae1cb23f8fd231dcf891465b8debe636a9054b0c') depends_on('xproto', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py index de359fa8103..e68fab7e557 100644 --- a/var/spack/repos/builtin/packages/libxslt/package.py +++ b/var/spack/repos/builtin/packages/libxslt/package.py @@ -18,9 +18,9 @@ class Libxslt(AutotoolsPackage): version('1.1.33', sha256='8e36605144409df979cab43d835002f63988f3dc94d5d3537c12796db90e38c8') version('1.1.32', sha256='526ecd0abaf4a7789041622c3950c0e7f2c4c8835471515fd77eec684a355460') - version('1.1.29', 'a129d3c44c022de3b9dcf6d6f288d72e') - version('1.1.28', '9667bf6f9310b957254fdcf6596600b7') - version('1.1.26', 'e61d0364a30146aaa3001296f853b2b9') + version('1.1.29', sha256='b5976e3857837e7617b29f2249ebb5eeac34e249208d31f1fbf7a6ba7a4090ce') + version('1.1.28', sha256='5fc7151a57b89c03d7b825df5a0fae0a8d5f05674c0e7cf2937ecec4d54a028c') + version('1.1.26', sha256='55dd52b42861f8a02989d701ef716d6280bfa02971e967c285016f99c66e3db1') variant('crypto', default=True, description='Build libexslt with crypto support') variant('python', default=False, description='Build Python bindings') diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py index c56317f0777..a6cd5ccc680 100644 --- a/var/spack/repos/builtin/packages/libxsmm/package.py +++ b/var/spack/repos/builtin/packages/libxsmm/package.py @@ -18,33 +18,33 @@ class Libxsmm(MakefilePackage): git = 'https://github.com/hfp/libxsmm.git' version('develop', branch='master') - version('1.13', '47c034e169820a9633770eece0e0fdd8d4a744e09b81da2af8c2608a4625811e') - version('1.12.1', '3687fb98da00ba92cd50b5f0d18b39912c7886dad3856843573aee0cb34e9791') - version('1.12', '37432fae4404ca12d8c5a205bfec7f9326c2d607d9ec37680f42dae60b52382a') - version('1.11', '5fc1972471cd8e2b8b64ea017590193739fc88d9818e3d086621e5c08e86ea35') - version('1.10', '2904f7983719fd5c5af081121c1d028d45b10b854aec9a9e67996a0602631abc') - version('1.9', 'cd8532021352b4a0290d209f7f9bfd7c2411e08286a893af3577a43457287bfa') - version('1.8.3', '08ed4a67731d07c739fa83c426a06a5a8fe576bc273da4bab84eb0d1f4405011') - version('1.8.2', '252ab73e437f5fcc87268df1ac130ffe6eb41e4281d9d3a3eaa7d591a85a612f') - version('1.8.1', '2ade869c3f42f23b5263c7d594aa3c7e5e61ac6a3afcaf5d6e42899d2a7986ce') - version('1.8', '0330201afb5525d0950ec861fec9dd75eb40a03845ebe03d2c635cf8bfc14fea') - version('1.7.1', '9d3f63ce3eed62f04e4036de6f2be2ce0ff07781ca571af6e0bf85b077edf17a') - version('1.7', '2eea65624a697e74b939511cd2a686b4c957e90c99be168fe134d96771e811ad') - version('1.6.6', '7c048a48e17f7f14a475be7b83e6e941289e03debb42ce9e02a06353412f9f2a') - version('1.6.5', '5231419a8e13e7a6d286cf25d32a3aa75c443a625e5ea57024d36468bc3d5936') - version('1.6.4', '3788bf1cdb60f119f8a04ed7ed96861322e539ce2d2ea977f00431d6b2b80beb') - version('1.6.3', 'afad4f75ec5959bc3b18b741f3f16864f699c8b763598d01faf6af029dded48c') - version('1.6.2', 'c1ad21dee1239c9c2422b2dd2dc83e7a364909fc82ff9bd6ce7d9c73ee4569de') - version('1.6.1', '1dd81077b186300122dc8a8f1872c21fd2bd9b88286ab9f068cc7b62fa7593a7') - version('1.6', 'c2a56f8cdc2ab03a6477ef98dbaa00917674fda59caa2824a1a29f78d2255ba5') - version('1.5.2', 'a037b7335932921960d687ef3d49b50ee38a83e0c8ad237bc20d3f4a0523f7d3') - version('1.5.1', '9e2a400e63b6fb2d4954e53536090eb8eb6f0ca25d0f34dd3a4f166802aa3d54') - version('1.5', 'c52568c5e0e8dc9d8fcf869a716d73598e52f71c3d83af5a4c0b3be81403b423') - version('1.4.4', 'bf4a0fff05cf721e11cb6cdb74f3d27dd0fa67ccc024055f2d9dd5dbd928c7c0') - version('1.4.3', '5033c33038ba4a75c675387aeb7c86b629e43ffc0a40df0b78e4ed52e4b5bd90') - version('1.4.2', '9c89391635be96759486a245365793bc4593859e6d7957b37c39a29f9b4f95eb') - version('1.4.1', 'c19be118694c9b4e9a61ef4205b1e1a7e0c400c07f9bce65ae430d2dc2be5fe1') - version('1.4', 'cf483a370d802bd8800c06a12d14d2b4406a745c8a0b2c8722ccc992d0cd72dd') + version('1.13', sha256='47c034e169820a9633770eece0e0fdd8d4a744e09b81da2af8c2608a4625811e') + version('1.12.1', sha256='3687fb98da00ba92cd50b5f0d18b39912c7886dad3856843573aee0cb34e9791') + version('1.12', sha256='37432fae4404ca12d8c5a205bfec7f9326c2d607d9ec37680f42dae60b52382a') + version('1.11', sha256='5fc1972471cd8e2b8b64ea017590193739fc88d9818e3d086621e5c08e86ea35') + version('1.10', sha256='2904f7983719fd5c5af081121c1d028d45b10b854aec9a9e67996a0602631abc') + version('1.9', sha256='cd8532021352b4a0290d209f7f9bfd7c2411e08286a893af3577a43457287bfa') + version('1.8.3', sha256='08ed4a67731d07c739fa83c426a06a5a8fe576bc273da4bab84eb0d1f4405011') + version('1.8.2', sha256='252ab73e437f5fcc87268df1ac130ffe6eb41e4281d9d3a3eaa7d591a85a612f') + version('1.8.1', sha256='2ade869c3f42f23b5263c7d594aa3c7e5e61ac6a3afcaf5d6e42899d2a7986ce') + version('1.8', sha256='0330201afb5525d0950ec861fec9dd75eb40a03845ebe03d2c635cf8bfc14fea') + version('1.7.1', sha256='9d3f63ce3eed62f04e4036de6f2be2ce0ff07781ca571af6e0bf85b077edf17a') + version('1.7', sha256='2eea65624a697e74b939511cd2a686b4c957e90c99be168fe134d96771e811ad') + version('1.6.6', sha256='7c048a48e17f7f14a475be7b83e6e941289e03debb42ce9e02a06353412f9f2a') + version('1.6.5', sha256='5231419a8e13e7a6d286cf25d32a3aa75c443a625e5ea57024d36468bc3d5936') + version('1.6.4', sha256='3788bf1cdb60f119f8a04ed7ed96861322e539ce2d2ea977f00431d6b2b80beb') + version('1.6.3', sha256='afad4f75ec5959bc3b18b741f3f16864f699c8b763598d01faf6af029dded48c') + version('1.6.2', sha256='c1ad21dee1239c9c2422b2dd2dc83e7a364909fc82ff9bd6ce7d9c73ee4569de') + version('1.6.1', sha256='1dd81077b186300122dc8a8f1872c21fd2bd9b88286ab9f068cc7b62fa7593a7') + version('1.6', sha256='c2a56f8cdc2ab03a6477ef98dbaa00917674fda59caa2824a1a29f78d2255ba5') + version('1.5.2', sha256='a037b7335932921960d687ef3d49b50ee38a83e0c8ad237bc20d3f4a0523f7d3') + version('1.5.1', sha256='9e2a400e63b6fb2d4954e53536090eb8eb6f0ca25d0f34dd3a4f166802aa3d54') + version('1.5', sha256='c52568c5e0e8dc9d8fcf869a716d73598e52f71c3d83af5a4c0b3be81403b423') + version('1.4.4', sha256='bf4a0fff05cf721e11cb6cdb74f3d27dd0fa67ccc024055f2d9dd5dbd928c7c0') + version('1.4.3', sha256='5033c33038ba4a75c675387aeb7c86b629e43ffc0a40df0b78e4ed52e4b5bd90') + version('1.4.2', sha256='9c89391635be96759486a245365793bc4593859e6d7957b37c39a29f9b4f95eb') + version('1.4.1', sha256='c19be118694c9b4e9a61ef4205b1e1a7e0c400c07f9bce65ae430d2dc2be5fe1') + version('1.4', sha256='cf483a370d802bd8800c06a12d14d2b4406a745c8a0b2c8722ccc992d0cd72dd') variant('shared', default=False, description='With shared libraries (and static libraries).') diff --git a/var/spack/repos/builtin/packages/libxstream/package.py b/var/spack/repos/builtin/packages/libxstream/package.py index e754450ece4..7ab9e5e674d 100644 --- a/var/spack/repos/builtin/packages/libxstream/package.py +++ b/var/spack/repos/builtin/packages/libxstream/package.py @@ -14,7 +14,7 @@ class Libxstream(Package): homepage = 'https://github.com/hfp/libxstream' url = 'https://github.com/hfp/libxstream/archive/0.9.0.tar.gz' - version('0.9.0', 'fd74b7cf5f145ff4925d91be2809571c') + version('0.9.0', sha256='03365f23b337533b8e5a049a24bc5a91c0f1539dd042ca5312abccc8f713b473') def patch(self): kwargs = {'ignore_absent': False, 'backup': True, 'string': True} diff --git a/var/spack/repos/builtin/packages/libxt/package.py b/var/spack/repos/builtin/packages/libxt/package.py index e74e958c28b..88d579c6085 100644 --- a/var/spack/repos/builtin/packages/libxt/package.py +++ b/var/spack/repos/builtin/packages/libxt/package.py @@ -12,7 +12,7 @@ class Libxt(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXt" url = "https://www.x.org/archive/individual/lib/libXt-1.1.5.tar.gz" - version('1.1.5', '77d317fbc508dd6adefb59d57a663032') + version('1.1.5', sha256='b59bee38a9935565fa49dc1bfe84cb30173e2e07e1dcdf801430d4b54eb0caa3') depends_on('libsm') depends_on('libice') diff --git a/var/spack/repos/builtin/packages/libxtrap/package.py b/var/spack/repos/builtin/packages/libxtrap/package.py index 6be6ac464f8..320b674d912 100644 --- a/var/spack/repos/builtin/packages/libxtrap/package.py +++ b/var/spack/repos/builtin/packages/libxtrap/package.py @@ -21,7 +21,7 @@ class Libxtrap(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXTrap" url = "https://www.x.org/archive/individual/lib/libXTrap-1.0.1.tar.gz" - version('1.0.1', 'fde266b82ee14da3e4f4f81c9584c1ea') + version('1.0.1', sha256='db748e299dcc9af68428795b898a4a96cf806f79b75786781136503e4fce5e17') depends_on('libx11') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/libxtst/package.py b/var/spack/repos/builtin/packages/libxtst/package.py index 89dfa84bc28..6ba8cc824fc 100644 --- a/var/spack/repos/builtin/packages/libxtst/package.py +++ b/var/spack/repos/builtin/packages/libxtst/package.py @@ -21,7 +21,7 @@ class Libxtst(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXtst" url = "https://www.x.org/archive/individual/lib/libXtst-1.2.2.tar.gz" - version('1.2.2', 'efef3b1e44bd8074a601c0c5ce0788f4') + version('1.2.2', sha256='221838960c7b9058cd6795c1c3ee8e25bae1c68106be314bc3036a4f26be0e6c') depends_on('libx11') depends_on('libxext@1.0.99.4:') diff --git a/var/spack/repos/builtin/packages/libxv/package.py b/var/spack/repos/builtin/packages/libxv/package.py index 9de268cf1c2..b0d5209b8ba 100644 --- a/var/spack/repos/builtin/packages/libxv/package.py +++ b/var/spack/repos/builtin/packages/libxv/package.py @@ -13,7 +13,7 @@ class Libxv(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXv" url = "https://www.x.org/archive/individual/lib/libXv-1.0.10.tar.gz" - version('1.0.10', 'e7182673b4bbe3ca00ac932e22edc038') + version('1.0.10', sha256='89a664928b625558268de81c633e300948b3752b0593453d7815f8775bab5293') depends_on('libx11@1.6:') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxvmc/package.py b/var/spack/repos/builtin/packages/libxvmc/package.py index ae192906c8d..4d2fa167040 100644 --- a/var/spack/repos/builtin/packages/libxvmc/package.py +++ b/var/spack/repos/builtin/packages/libxvmc/package.py @@ -12,7 +12,7 @@ class Libxvmc(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/lib/libXvMC" url = "https://www.x.org/archive/individual/lib/libXvMC-1.0.9.tar.gz" - version('1.0.9', 'a28c0780373537f4774565309b31a69e') + version('1.0.9', sha256='090f087fe65b30b3edfb996c79ff6cf299e473fb25e955fff1c4e9cb624da2c2') depends_on('libx11@1.6:') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxxf86dga/package.py b/var/spack/repos/builtin/packages/libxxf86dga/package.py index 04f42bd0888..6160033167d 100644 --- a/var/spack/repos/builtin/packages/libxxf86dga/package.py +++ b/var/spack/repos/builtin/packages/libxxf86dga/package.py @@ -12,7 +12,7 @@ class Libxxf86dga(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXxf86dga" url = "https://www.x.org/archive/individual/lib/libXxf86dga-1.1.4.tar.gz" - version('1.1.4', '8ed1c8674e730e8d333dfe4b9f2097d9') + version('1.1.4', sha256='e6361620a15ceba666901ca8423e8be0c6ed0271a7088742009160349173766b') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxxf86misc/package.py b/var/spack/repos/builtin/packages/libxxf86misc/package.py index 3e558cca3ad..64ccd738ec0 100644 --- a/var/spack/repos/builtin/packages/libxxf86misc/package.py +++ b/var/spack/repos/builtin/packages/libxxf86misc/package.py @@ -12,7 +12,7 @@ class Libxxf86misc(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXxf86misc" url = "https://www.x.org/archive/individual/lib/libXxf86misc-1.0.3.tar.gz" - version('1.0.3', 'c8d8743e146bcd2aa9856117ac5ef6c0') + version('1.0.3', sha256='358f692f793af00f6ef4c7a8566c1bcaeeea37e417337db3f519522cc1df3946') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libxxf86vm/package.py b/var/spack/repos/builtin/packages/libxxf86vm/package.py index 892d8319b48..1a332f3153f 100644 --- a/var/spack/repos/builtin/packages/libxxf86vm/package.py +++ b/var/spack/repos/builtin/packages/libxxf86vm/package.py @@ -12,7 +12,7 @@ class Libxxf86vm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libXxf86vm" url = "https://www.x.org/archive/individual/lib/libXxf86vm-1.1.4.tar.gz" - version('1.1.4', '675bd0c521472628d5796602f625ef51') + version('1.1.4', sha256='5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99') depends_on('libx11@1.6:') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/libyogrt/package.py b/var/spack/repos/builtin/packages/libyogrt/package.py index e74f982c5e2..c7445c0499a 100644 --- a/var/spack/repos/builtin/packages/libyogrt/package.py +++ b/var/spack/repos/builtin/packages/libyogrt/package.py @@ -17,11 +17,11 @@ class Libyogrt(AutotoolsPackage): version('1.22', sha256='38e7d1ea3fa030f0169197aa96cde9f01caa595a590764ef1cb2ae07379cb711') version('1.21', sha256='5f8f0942d35ee4e418273e478e632210b3fa648dcb6a2e6a92c6ba4213cdc362') version('1.20-7', sha256='735e9d6fa572e239ccc73e11c84b4583338b24df0fa91c48e8bc038d882003f7') - version('1.20-6', '478f27512842cc5f2b74a0c22b851f60') - version('1.20-5', 'd0fa6526fcd1f56ddb3d93f602ec72f7') - version('1.20-4', '092bea10de22c505ce92aa07001decbb') - version('1.20-3', 'd0507717009a5f8e2009e3b63594738f') - version('1.20-2', '780bda03268324f6b5f72631fff6e6cb') + version('1.20-6', sha256='ba5a2e202f995cf7ae3bf87b451943733e760ede02ca172f712cbf2eea693222') + version('1.20-5', sha256='1e41bc656abffb121145264bc898421c3f355d3be35f1711b7b5e3ffe7effdd9') + version('1.20-4', sha256='0858a729068b272d4047d79f6a5187cdbd427bdfec64db4e143524b4789a06c5') + version('1.20-3', sha256='61a8f28f452aef0e09d700dbaaffd91ae3855f7ac221c7ebe478a028df635e31') + version('1.20-2', sha256='bf22a82ab3bfede780be3fb6c132cc354234f8d57d3cccd58fe594f074ed7f95') # libyogrt supports the following schedulers: # lcrm, lsf, moab, slurm, AIX+slurm diff --git a/var/spack/repos/builtin/packages/libzip/package.py b/var/spack/repos/builtin/packages/libzip/package.py index 66773b2bf0d..16a9bf3976a 100644 --- a/var/spack/repos/builtin/packages/libzip/package.py +++ b/var/spack/repos/builtin/packages/libzip/package.py @@ -13,6 +13,6 @@ class Libzip(AutotoolsPackage): homepage = "https://nih.at/libzip/index.html" url = "https://nih.at/libzip/libzip-1.2.0.tar.gz" - version('1.2.0', '5c3372ab3a7897295bfefb27f745cf69') + version('1.2.0', sha256='6cf9840e427db96ebf3936665430bab204c9ebbd0120c326459077ed9c907d9f') depends_on('zlib@1.1.2:') diff --git a/var/spack/repos/builtin/packages/liggghts/package.py b/var/spack/repos/builtin/packages/liggghts/package.py index 936252f268b..324439c05fd 100644 --- a/var/spack/repos/builtin/packages/liggghts/package.py +++ b/var/spack/repos/builtin/packages/liggghts/package.py @@ -16,7 +16,7 @@ class Liggghts(MakefilePackage): url = 'https://github.com/CFDEMproject/LIGGGHTS-PUBLIC/archive/3.8.0.tar.gz' git = 'git@github.com:CFDEMproject/LIGGGHTS-PUBLIC.git' - version('3.8.0', 'dabd019e0ea0260ebb96df2cc4703e14d77498e6') + version('3.8.0', sha256='9cb2e6596f584463ac2f80e3ff7b9588b7e3638c44324635b6329df87b90ab03') variant('mpi', default=True, description='Enable MPI support') variant('jpeg', default=True, description='Enable JPEG support') diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py index 2f7f43b8e7c..411a6f8fe66 100644 --- a/var/spack/repos/builtin/packages/likwid/package.py +++ b/var/spack/repos/builtin/packages/likwid/package.py @@ -19,11 +19,11 @@ class Likwid(Package): homepage = "https://github.com/RRZE-HPC/likwid" url = "https://github.com/RRZE-HPC/likwid/archive/4.1.2.tar.gz" - version('4.3.4', '37bdcd20630ef3694435065a6c8a14fa') - version('4.3.3', '70ff0d1238989010842644db792f4910') - version('4.3.2', '2cf00e220dfe22c8d9b6e44f7534e11d') - version('4.3.1', 'ff28250f622185688bf5e2e0975368ea') - version('4.3.0', '7f8f6981d7d341fce2621554323f8c8b') + version('4.3.4', sha256='5c0d1c66b25dac8292a02232f06454067f031a238f010c62f40ef913c6609a83') + version('4.3.3', sha256='a681378cd66c1679ca840fb5fac3136bfec93c01b3d78cc1d00a641db325a9a3') + version('4.3.2', sha256='fd39529854b8952e7530da1684835aa43ac6ce2169f5ebd1fb2a481f6fb288ac') + version('4.3.1', sha256='4b40a96717da54514274d166f9b71928545468091c939c1d74109733279eaeb1') + version('4.3.0', sha256='86fc5f82c80fcff1a643394627839ec79f1ca2bcfad30000eb7018da592588b4') patch('https://github.com/RRZE-HPC/likwid/commit/d2d0ef333b5e0997d7c80fc6ac1a473b5e47d084.patch', sha256='636cbf40669261fdb36379d67253be2b731cfa7b6d610d232767d72fbdf08bc0', when='@4.3.4') diff --git a/var/spack/repos/builtin/packages/linux-headers/package.py b/var/spack/repos/builtin/packages/linux-headers/package.py index 338ff7abeee..6b0133dd75f 100644 --- a/var/spack/repos/builtin/packages/linux-headers/package.py +++ b/var/spack/repos/builtin/packages/linux-headers/package.py @@ -14,7 +14,7 @@ class LinuxHeaders(Package): list_url = "https://www.kernel.org/pub/linux/kernel" list_depth = 2 - version('4.9.10', 'ce5ab2a86c9b880617e36e84aa2deb6c') + version('4.9.10', sha256='bd6e05476fd8d9ea4945e11598d87bc97806bbc8d03556abbaaf809707661525') def setup_environment(self, spack_env, run_env): # This variable is used in the Makefile. If it is defined on the diff --git a/var/spack/repos/builtin/packages/listres/package.py b/var/spack/repos/builtin/packages/listres/package.py index 1574fa071d8..25742deaab1 100644 --- a/var/spack/repos/builtin/packages/listres/package.py +++ b/var/spack/repos/builtin/packages/listres/package.py @@ -13,7 +13,7 @@ class Listres(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/listres" url = "https://www.x.org/archive/individual/app/listres-1.0.3.tar.gz" - version('1.0.3', '77cafc32e8e02cca2d4453e73e0c0e7d') + version('1.0.3', sha256='87d5698b8aa4d841e45e6556932c9914210cbd8b10003d664b31185b087981be') depends_on('libxaw') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index be385873f67..b79798eb534 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -21,7 +21,7 @@ class Llvm(CMakePackage): family = 'compiler' # Used by lmod # currently required by mesa package - version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', + version('3.0', sha256='519eb11d3499ce99c6ffdb8718651fc91425ed7690eac91c8d6853474f7c0477', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # NOTE: The debug version of LLVM is an order of magnitude larger than @@ -182,302 +182,302 @@ class Llvm(CMakePackage): }, { 'version': '9.0.0', - 'md5': '0fd4283ff485dffb71a4f1cc8fd3fc72', + 'sha256': 'd6a0565cf21f22e9b4353b2eb92622e8365000a9e90a16b09b56f8157eabfe84', 'resources': { - 'compiler-rt': 'c92b8a1aed654463962d77445ebee10b', - 'openmp': 'aea2a701d5d62605bf82cfc2bb57cd0f', - 'polly': '5cd3222a5d7f96cf789dd0bdba14d0fc', - 'libcxx': '3b26e4c37aac2650b594668437a57966', - 'libcxxabi': 'bd8799cc69c7660c7a4729019fbfe286', - 'cfe': '0df6971e2f99b1e99e7bfb533e4067af', - 'clang-tools-extra': '6d1b6e8a9c24ccf98b6ed4f63dbb6356', - 'lldb': '963b43e591d9501965e932fc4218d1a0', - 'lld': 'aa70e956ddbe0c7bff029b8358ff6c44', - 'libunwind': 'ea60ad42e59193ae99bf239d69dfa086' + 'compiler-rt': '56e4cd96dd1d8c346b07b4d6b255f976570c6f2389697347a6c3dcb9e820d10e', + 'openmp': '9979eb1133066376cc0be29d1682bc0b0e7fb541075b391061679111ae4d3b5b', + 'polly': 'a4fa92283de725399323d07f18995911158c1c5838703f37862db815f513d433', + 'libcxx': '3c4162972b5d3204ba47ac384aa456855a17b5e97422723d4758251acf1ed28c', + 'libcxxabi': '675041783565c906ac2f7f8b2bc5c40f14d871ecfa8ade34855aa18de95530e9', + 'cfe': '7ba81eef7c22ca5da688fdf9d88c20934d2d6b40bfe150ffd338900890aa4610', + 'clang-tools-extra': 'ea1c86ce352992d7b6f6649bc622f6a2707b9f8b7153e9f9181a35c76aa3ac10', + 'lldb': '1e4c2f6a1f153f4b8afa2470d2e99dab493034c1ba8b7ffbbd7600de016d0794', + 'lld': '31c6748b235d09723fb73fea0c816ed5a3fab0f96b66f8fbc546a0fcc8688f91', + 'libunwind': '976a8d09e1424fb843210eecec00a506b956e6c31adda3b0d199e945be0d0db2' } }, { 'version': '8.0.0', - 'md5': '74818f431563603515a62be1ee69a142', + 'sha256': '8872be1b12c61450cacc82b3d153eab02be2546ef34fa3580ed14137bb26224c', 'resources': { - 'compiler-rt': '547893456e22c75d16189a13881bc866', - 'openmp': 'b6f9bf1df85fe4b0ab9d273adcef6f6d', - 'polly': '7643bba808becabf35785fbacc413ee5', - 'libcxx': '214211a34baee2292fb79e868697a1aa', - 'libcxxabi': 'aa8fab49faa65ebf0322d42520630df2', - 'cfe': '988b59cdb372c5a4f44ae4c39df3de73', - 'clang-tools-extra': 'acd22ccbd06bfc0054027fe2644af1e0', - 'lldb': '9d319ed0f02a026242a85399938afed2', - 'lld': 'c09fb102d4537a0c37a2e8e36a1dc6d2', - 'libunwind': 'be6b89b5887c5c78dd67cb4e8520d41f' + 'compiler-rt': 'b435c7474f459e71b2831f1a4e3f1d21203cb9c0172e94e9d9b69f50354f21b1', + 'openmp': 'f7b1705d2f16c4fc23d6531f67d2dd6fb78a077dd346b02fed64f4b8df65c9d5', + 'polly': 'e3f5a3d6794ef8233af302c45ceb464b74cdc369c1ac735b6b381b21e4d89df4', + 'libcxx': 'c2902675e7c84324fb2c1e45489220f250ede016cc3117186785d9dc291f9de2', + 'libcxxabi': 'c2d6de9629f7c072ac20ada776374e9e3168142f20a46cdb9d6df973922b07cd', + 'cfe': '084c115aab0084e63b23eee8c233abb6739c399e29966eaeccfc6e088e0b736b', + 'clang-tools-extra': '4f00122be408a7482f2004bcf215720d2b88cf8dc78b824abb225da8ad359d4b', + 'lldb': '49918b9f09816554a20ac44c5f85a32dc0a7a00759b3259e78064d674eac0373', + 'lld': '9caec8ec922e32ffa130f0fb08e4c5a242d7e68ce757631e425e9eba2e1a6e37', + 'libunwind': 'ff243a669c9cef2e2537e4f697d6fb47764ea91949016f2d643cb5d8286df660' } }, { 'version': '7.0.1', - 'md5': '79f1256f97d52a054da8660706deb5f6', + 'sha256': 'a38dfc4db47102ec79dcc2aa61e93722c5f6f06f0a961073bd84b78fb949419b', 'resources': { - 'compiler-rt': '697b70141ae7cc854e4fbde1a07b7287', - 'openmp': 'd7d05ac0109df51a47099cba08cb43ec', - 'polly': '287d7391438b5285265fede3b08e1e29', - 'libcxx': 'aa9202ebb2aef2078fccfa24b3b1eed1', - 'libcxxabi': 'c82a187e95744d15c040108bc2b8868f', - 'cfe': '8583c9fb2af0ce61a7154fd9125363c1', - 'clang-tools-extra': 'f0a94f63cc3d717f8f6662e0bf9c7330', - 'lldb': '9ea3dc5cb9a1d9e390652d42ef1ccf41', - 'lld': '9162cde32887cd33facead766645ef1f', - 'libunwind': 'fe8c801dd79e087a6fa8d039390a47d0' + 'compiler-rt': '782edfc119ee172f169c91dd79f2c964fb6b248bd9b73523149030ed505bbe18', + 'openmp': 'bf16b78a678da67d68405214ec7ee59d86a15f599855806192a75dcfca9b0d0c', + 'polly': '1bf146842a09336b9c88d2d76c2d117484e5fad78786821718653d1a9d57fb71', + 'libcxx': '020002618b319dc2a8ba1f2cba88b8cc6a209005ed8ad29f9de0c562c6ebb9f1', + 'libcxxabi': '8168903a157ca7ab8423d3b974eaa497230b1564ceb57260be2bd14412e8ded8', + 'cfe': 'a45b62dde5d7d5fdcdfa876b0af92f164d434b06e9e89b5d0b1cbc65dfe3f418', + 'clang-tools-extra': '4c93c7d2bb07923a8b272da3ef7914438080aeb693725f4fc5c19cd0e2613bed', + 'lldb': '76b46be75b412a3d22f0d26279306ae7e274fe4d7988a2184c529c38a6a76982', + 'lld': '8869aab2dd2d8e00d69943352d3166d159d7eae2615f66a684f4a0999fc74031', + 'libunwind': '89c852991dfd9279dbca9d5ac10b53c67ad7d0f54bbab7156e9f057a978b5912' } }, { 'version': '7.0.0', - 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'md5': '0c1ee3597d75280dee603bae9cbf5cc2', + 'sha256': 'f60dc158bfda6822de167e87275848969f0558b3134892ff54fced87e4667b94', 'resources': { - 'compiler-rt': 'e3bc4eb7ba8c39a6fe90d6c988927f3c', - 'openmp': '65dd5863b9b270960a96817e9152b123', - 'libcxx': '22214c90697636ef960a49aef7c1823a', - 'libcxxabi': '17518e361e4e228f193dd91e8ef54ba2', - 'cfe': 'ff862793682f714bb7862325b9c06e20', - 'clang-tools-extra': '3ebc1dc41659fcec3db1b47d81575e06', - 'lldb': '51e5eb552f777b950bb0ff326e60d5f0', - 'lld': '7143cc4fa88851a9f9b9a03621fbb387', + 'compiler-rt': '0f2ff37d80a64575fecd8cf0d5c50f7ac1f837ddf700d1855412bb7547431d87', + 'openmp': '9d9640e7fc76ef531b5e919d79ee241cb35aa599fd1cac97c52ca49c97778f8e', + 'libcxx': '52f3d452f48209c9df1792158fdbd7f3e98ed9bca8ebb51fcd524f67437c8b81', + 'libcxxabi': '6fb48ce5a514686b9b75e73e59869f782ed374a86d71be8423372e4b3329b09b', + 'cfe': 'ae9180466a23acb426d12444d866b266ff2289b266064d362462e44f8d4699f3', + 'clang-tools-extra': '6a0ec627d398f501ddf347060f7a2ccea4802b2494f1d4fd7bda3e0442d04feb', + 'lldb': '940dc96b64919b7dbf32c37e0e1d1fc88cc18e1d4b3acf1e7dfe5a46eb6523a9', + 'lld': '43f553c115563600577764262f1f2fac3740f0c639750f81e125963c90030b33', } }, { 'version': '3.5.1', - 'md5': '2d3d8004f38852aa679e5945b8ce0b14', + 'sha256': 'bf3275d2d7890015c8d8f5e6f4f882f8cf3bf51967297ebe74111d6d8b53be15', 'resources': { - 'compiler-rt': 'd626cfb8a9712cb92b820798ab5bc1f8', - 'openmp': '121ddb10167d7fc38b1f7e4b029cf059', - 'libcxx': '406f09b1dab529f3f7879f4d548329d2', - 'libcxxabi': 'b22c707e8d474a99865ad3c521c3d464', - 'cfe': '93f9532f8f7e6f1d8e5c1116907051cb', - 'clang-tools-extra': 'f13f31ed3038acadc6fa63fef812a246', - 'lldb': 'cc5ea8a414c62c33e760517f8929a204', - 'lld': '173be02b7ff4e5e31fbb0a591a03d7a3', + 'compiler-rt': 'adf4b526f33e681aff5961f0821f5b514d3fc375410008842640b56a2e6a837a', + 'openmp': '43ea73eeac3045127cf01b496d714b559e42311043480682049e8fea243eac55', + 'libcxx': 'a16d0ae0c0cf2c8cebb94fafcb907022cd4f8579ebac99a4c9919990a37ad475', + 'libcxxabi': '7ff14fdce0ed7bfcc532c627c7a2dc7876dd8a3d788b2aa201d3bbdc443d06a3', + 'cfe': '6773f3f9cf815631cc7e779ec134ddd228dc8e9a250e1ea3a910610c59eb8f5c', + 'clang-tools-extra': 'e8d011250389cfc36eb51557ca25ae66ab08173e8d53536a0747356105d72906', + 'lldb': 'e8b948c6c85cd61bd9a48361959401b9c631fa257c0118db26697c5d57460e13', + 'lld': 'f29f684723effd204b6fe96edb1bf2f66f0f81297230bc92b8cc514f7a24236f', } }, ] @@ -551,12 +551,12 @@ class Llvm(CMakePackage): resources[rname].get('variant', "")), placement=resources[rname].get('placement', None)) else: - version(release['version'], release['md5'], url=llvm_url % release) + version(release['version'], release['sha256'], url=llvm_url % release) - for rname, md5 in release['resources'].items(): + for rname, sha256 in release['resources'].items(): resource(name=rname, url=resources[rname]['url'] % release, - md5=md5, + sha256=sha256, destination=resources[rname]['destination'], when='@%s%s' % (release['version'], resources[rname].get('variant', "")), diff --git a/var/spack/repos/builtin/packages/lm-sensors/package.py b/var/spack/repos/builtin/packages/lm-sensors/package.py index 7e623099be3..39e2f2b75db 100644 --- a/var/spack/repos/builtin/packages/lm-sensors/package.py +++ b/var/spack/repos/builtin/packages/lm-sensors/package.py @@ -14,16 +14,16 @@ class LmSensors(MakefilePackage): url = "https://github.com/groeck/lm-sensors/archive/V3-4-0.tar.gz" maintainers = ['G-Ragghianti'] - version('3-4-0', '1e9f117cbfa11be1955adc96df71eadb') - version('3-3-5', '42dcbc32c61133f5dbcdfd7ef8d0ee3c') - version('3-3-4', 'b2bee2bc0b2dedc92b8ef60b719b87a3') - version('3-3-3', 'e9be751b91c619cef3fd1ccfc22d0ded') - version('3-3-2', 'd580e0cf872768c2670ab0721b1dedc9') - version('3-3-1', 'e03c761365dd89ebc04913166018281b') - version('3-3-0', '97f22cb084420aee88f765df084b8cd0') - version('3-2-0', '07cd13fecb0e0ea19ddf97ec797ee222') - version('3-1-2', '4031e02c566992e6a6fd87af018c457e') - version('3-1-1', '2a62fb3789972756ff2ad2d3ad3f016c') + version('3-4-0', sha256='e334c1c2b06f7290e3e66bdae330a5d36054701ffd47a5dde7a06f9a7402cb4e') + version('3-3-5', sha256='e3802f80785c54822027a8c187b10066ba685ec5e997fd02c1d29761ea9c83d4') + version('3-3-4', sha256='1c586684b39292b5fabaf5a2701241885ea6483e5e15265e1f501e1b639fdd86') + version('3-3-3', sha256='f1c1078afc712693f003989446b59d817794ed7eb733b401c83ed6b1d7d45b73') + version('3-3-2', sha256='927f841e42afb16b35a313a02825122d3a5be59d4b6c567fd90caf23eeda30a8') + version('3-3-1', sha256='769b8649e4da2739c07c9a1b2975a8efe6aa9b69cd65fe350ccccbafd4821d95') + version('3-3-0', sha256='35ed28640cb2cd1492c4d6620a7c6b8dd2fa44fbb603d5f4d867311e8f56dd37') + version('3-2-0', sha256='ff54bee654f9f317224489fa64aeb659425d58ac3d031fe019c2c072ba19ee9a') + version('3-1-2', sha256='a587f4f37c0f32ac48575338013ee443a0152d87543e8e702db6161ec0ca1161') + version('3-1-1', sha256='22b5ab0bab853c34298ff617efb292c5dde7b254596b31ce4c6e90b1d1cf8ad8') depends_on('bison', type='build') depends_on('flex', type='build') diff --git a/var/spack/repos/builtin/packages/lmdb/package.py b/var/spack/repos/builtin/packages/lmdb/package.py index e24b0d612b6..3d45b223707 100644 --- a/var/spack/repos/builtin/packages/lmdb/package.py +++ b/var/spack/repos/builtin/packages/lmdb/package.py @@ -15,9 +15,9 @@ class Lmdb(MakefilePackage): homepage = "https://lmdb.tech/" url = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.21.tar.gz" - version('0.9.22', 'f3927859882eb608868c8c31586bb7eb84562a40a6bf5cc3e13b6b564641ea28') - version('0.9.21', '41a4f7b63212a00e53fabd8159008201') - version('0.9.16', '0de89730b8f3f5711c2b3a4ba517b648') + version('0.9.22', sha256='f3927859882eb608868c8c31586bb7eb84562a40a6bf5cc3e13b6b564641ea28') + version('0.9.21', sha256='1187b635a4cc415bb6972bba346121f81edd996e99b8f0816151d4090f90b559') + version('0.9.16', sha256='49d7b40949f2ced9bc8b23ea6a89e75471a1c9126537a8b268c318a00b84322b') build_directory = 'libraries/liblmdb' diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index ad4ccf9b466..3596ae4362c 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -23,21 +23,21 @@ class Lmod(AutotoolsPackage): version('8.0.9', sha256='9813c22ae4dd21eb3dc480f6ce307156512092b4bca954bf8aacc15944f23673') version('7.8.15', sha256='00a257f5073d656adc73045997c28f323b7a4f6d901f1c57b7db2b0cd6bee6e6') version('7.8', sha256='40388380a36a00c3ce929a9f88c8fffc93deeabf87a7c3f8864a82acad38c3ba') - version('7.7.29', 'bd3f171995e6863505e8a958d158ced1') - version('7.7.13', 'e1d222fa04148707dceb08c82d7e9fa5') - version('7.7', '8ac594401716c6d1b40cac22bc1030ca') - version('7.6.14', '60726c991038b6337fbb27b6a333a2d4') - version('7.4.11', '70c55ba0ba3877b6d8df536ee7ea6d49') - version('7.4.10', 'a13e36d6196747fded7987ef3dcfb605') - version('7.4.9', 'd8ffab81ddca2491fe13e2ac0a4fd320') - version('7.4.8', '3b22932437cc29ce546ec887885355e7') - version('7.4.5', 'fc34029c60dd9782c3d011c2b93fd266') - version('7.4.1', '59b2558ee50877f2cf49ed37d7b09fea') - version('7.3', '70180ec2ea1fae53aa83350523f6b2b3') - version('6.4.5', '14f6c58dbc0a5a75574d795eac2c1e3c') - version('6.4.1', '7978ba777c8aa41a4d8c05fec5f780f4') - version('6.3.7', '0fa4d5a24c41cae03776f781aa2dedc1') - version('6.0.1', '91abf52fe5033bd419ffe2842ebe7af9') + version('7.7.29', sha256='269235d07d8ea387a2578f90bb64cf8ad16b4f28dcce196b293eb48cf1f71fb4') + version('7.7.13', sha256='6145f075e5d49e12fcf0e75bb38afb27f205d23ba3496c1ff6c8b2cbaa9908be') + version('7.7', sha256='090118fcecedbce5515cca8b77297f082686583aa06ca811b9703cd828f10e0a') + version('7.6.14', sha256='f628ed2272bb26671d2c478afef2ddd88dce324748032bfe8d6f6c7747f00162') + version('7.4.11', sha256='54c3629f6e455a4767dfb775e1b0ca46b8f217dcc0966bf0227c0ea11e0e0d62') + version('7.4.10', sha256='7b37936ddbc574f03eb08579f1d1bb5fa8c476b55ee070dc3c432d96970e6562') + version('7.4.9', sha256='5aee6cc9cf0b27327c8b4f5fdfb9aa079d90aed685ee7853cbcc49c32b48a5d9') + version('7.4.8', sha256='a634989dcd34b0ad7bee95ca535765b7de886d9f9ef78cad5976122356d71169') + version('7.4.5', sha256='a4af6dcd3d9b209cc10467e6ce77301c0ec517437b70cfc567a3180030c4f404') + version('7.4.1', sha256='1d407c68a5a8c1ae9870a12303ba81d2a92b68f66ac7dd704ccffb65bfb873d9') + version('7.3', sha256='624e8ffb7527b380dc248cf7ddf36beecb91c762d840be447bc9a55bf8cd26c2') + version('6.4.5', sha256='741744a2837c9d92fceeccfebdc8e07ce4f4b7e56f67b214d317955bbd8786b7') + version('6.4.1', sha256='a260b4e42269a80b517c066ba8484658362ea095e80767a2376bbe33d9b070a5') + version('6.3.7', sha256='55ddb52cbdc0e2e389b3405229336df9aabfa582c874f5df2559ea264e2ee4ae') + version('6.0.1', md5='91abf52fe5033bd419ffe2842ebe7af9') depends_on('lua@5.1:') depends_on('lua-luaposix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/lndir/package.py b/var/spack/repos/builtin/packages/lndir/package.py index 8b3f5ab3683..41184c46a7d 100644 --- a/var/spack/repos/builtin/packages/lndir/package.py +++ b/var/spack/repos/builtin/packages/lndir/package.py @@ -13,7 +13,7 @@ class Lndir(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/util/lndir" url = "https://www.x.org/archive/individual/util/lndir-1.0.3.tar.gz" - version('1.0.3', '7173b2e4832658d319c2980a7c834205') + version('1.0.3', sha256='95b2d26fb3cbe702f828146c7a4c7c48001d2da52b062580227b7b68180be902') depends_on('xproto@7.0.17:', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/log4cplus/package.py b/var/spack/repos/builtin/packages/log4cplus/package.py index ab218ec24ef..3313570d81c 100644 --- a/var/spack/repos/builtin/packages/log4cplus/package.py +++ b/var/spack/repos/builtin/packages/log4cplus/package.py @@ -14,6 +14,6 @@ class Log4cplus(CMakePackage): homepage = "https://sourceforge.net/projects/log4cplus/" url = "https://download.sourceforge.net/project/log4cplus/log4cplus-stable/2.0.1/log4cplus-2.0.1.tar.bz2" - version('2.0.1', 'ec01c03241ebd31127a44d1880830d8f') - version('1.2.1', 'e4e6c38b065b70b5d6efc238a5106bc9') - version('1.2.0', 'e250f0f431c0723f8b625323e7b6465d') + version('2.0.1', sha256='43baa7dec3db1ecc97dd9ecf3b50220439d2c7041d15860c36aa1d48dcf480b5') + version('1.2.1', sha256='ada80be050033d7636beb894eb54de5575ceca95a5572e9437b0fc4ed7d877c4') + version('1.2.0', md5='e250f0f431c0723f8b625323e7b6465d') diff --git a/var/spack/repos/builtin/packages/log4cxx/package.py b/var/spack/repos/builtin/packages/log4cxx/package.py index 9155408b627..a8507a7c41c 100644 --- a/var/spack/repos/builtin/packages/log4cxx/package.py +++ b/var/spack/repos/builtin/packages/log4cxx/package.py @@ -12,7 +12,7 @@ class Log4cxx(AutotoolsPackage): homepage = "https://logging.apache.org/log4cxx/latest_stable/" url = "http://mirror.netcologne.de/apache.org/logging/log4cxx/0.10.0/apache-log4cxx-0.10.0.tar.gz" - version('0.10.0', 'b30ffb8da3665178e68940ff7a61084c') + version('0.10.0', sha256='0de0396220a9566a580166e66b39674cb40efd2176f52ad2c65486c99c920c8c') depends_on('apr-util') depends_on('apr') diff --git a/var/spack/repos/builtin/packages/loki/package.py b/var/spack/repos/builtin/packages/loki/package.py index b6a04daa362..f88eeb1db5c 100644 --- a/var/spack/repos/builtin/packages/loki/package.py +++ b/var/spack/repos/builtin/packages/loki/package.py @@ -13,7 +13,7 @@ class Loki(MakefilePackage): homepage = "http://loki-lib.sourceforge.net" url = "https://downloads.sourceforge.net/project/loki-lib/Loki/Loki%200.1.7/loki-0.1.7.tar.bz2" - version('0.1.7', '33a24bcbb99fa2ec8fcbbab65649f3f6') + version('0.1.7', sha256='07553754f6be2738559947db69b0718512665bf4a34015fa3a875b6eb1111198') variant('shared', default=True, description="Build shared libraries") diff --git a/var/spack/repos/builtin/packages/lordec/package.py b/var/spack/repos/builtin/packages/lordec/package.py index f80ef1ee1d9..012a01fde77 100644 --- a/var/spack/repos/builtin/packages/lordec/package.py +++ b/var/spack/repos/builtin/packages/lordec/package.py @@ -14,7 +14,7 @@ class Lordec(MakefilePackage): homepage = "http://www.atgc-montpellier.fr/lordec/" url = "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz" - version('0.8', 'd5a57db681d1cd31c516aa780ce53f9d') + version('0.8', sha256='3894a7c57649a3545b598f92a48d55eda66d729ab51606b00470c50611b12823') depends_on('boost') depends_on('cmake@3.1.0:', type='build') diff --git a/var/spack/repos/builtin/packages/lrslib/package.py b/var/spack/repos/builtin/packages/lrslib/package.py index b10f5a30942..a27b74f7693 100644 --- a/var/spack/repos/builtin/packages/lrslib/package.py +++ b/var/spack/repos/builtin/packages/lrslib/package.py @@ -14,11 +14,11 @@ class Lrslib(Package): homepage = "http://cgm.cs.mcgill.ca/~avis/C/lrs.html" url = "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/lrslib-062.tar.gz" - version('6.2', 'be5da7b3b90cc2be628dcade90c5d1b9') - version('6.1', '0b3687c8693cd7d1f234a3f65e147551') - version('6.0', 'd600a2e62969ad03f7ab2f85f1b3709c') - version('5.1', 'cca323eee8bf76f598a13d7bf67cc13d') - version('4.3', '86dd9a45d20a3a0069f77e61be5b46ad') + version('6.2', sha256='adf92f9c7e70c001340b9c28f414208d49c581df46b550f56ab9a360348e4f09') + version('6.1', sha256='6d5b30ee67e1fdcd6bf03e14717616f18912d59b3707f6d53f9c594c1674ec45') + version('6.0', sha256='1a569786ecd89ef4f2ddee5ebc32e321f0339505be40f4ffbd2daa95fed1c505') + version('5.1', sha256='500893df61631944bac14a76c6e13fc08e6e729727443fa5480b2510de0db635') + version('4.3', sha256='04fc1916ea122b3f2446968d2739717aa2c6c94b21fba1f2c627fd17fcf7a963') # Note: lrslib can also be built with Boost, and probably without gmp diff --git a/var/spack/repos/builtin/packages/lrzip/package.py b/var/spack/repos/builtin/packages/lrzip/package.py index b9599c3c3bd..de2375622a0 100644 --- a/var/spack/repos/builtin/packages/lrzip/package.py +++ b/var/spack/repos/builtin/packages/lrzip/package.py @@ -19,10 +19,10 @@ class Lrzip(Package): git = 'https://github.com/ckolivas/lrzip.git' version('master', branch='master') - version('0.630', '3ca7f1d1365aa105089d1fbfc6b0924a') - version('0.621', '1f07227b39ae81a98934411e8611e341') - version('0.616', 'd40bdb046d0807ef602e36b1e9782cc0') - version('0.615', 'f1c01e7f3de07f54d916b61c989dfaf2') + version('0.630', sha256='7b9bf6415fb2294a8e83a5a1c6a8d7da17a19f4730567c8fa16e3016d79250a6') + version('0.621', sha256='4bf93c1df076b6e6a57f32c0c4b7790b4d25d724c259394e1d32b680c0657121') + version('0.616', sha256='6ef50bfec15d7585e5b085067c9fe91a87246ccd14a3165acd08b147bba26a2e') + version('0.615', sha256='45bc3e09a9c467c9331499e4e7919ea97d0824d24a1f2c3ec9548bb2b9d14898') # depends_on('coreutils') depends_on('lzo') diff --git a/var/spack/repos/builtin/packages/ltrace/package.py b/var/spack/repos/builtin/packages/ltrace/package.py index af0004cb0d8..bad6faa5c80 100644 --- a/var/spack/repos/builtin/packages/ltrace/package.py +++ b/var/spack/repos/builtin/packages/ltrace/package.py @@ -14,6 +14,6 @@ class Ltrace(AutotoolsPackage): homepage = "https://www.ltrace.org" url = "https://www.ltrace.org/ltrace_0.7.3.orig.tar.bz2" - version('0.7.3', 'b3dd199af8f18637f7d4ef97fdfb9d14') + version('0.7.3', sha256='0e6f8c077471b544c06def7192d983861ad2f8688dd5504beae62f0c5f5b9503') conflicts('platform=darwin', msg='ltrace runs only on Linux.') diff --git a/var/spack/repos/builtin/packages/lua-bitlib/package.py b/var/spack/repos/builtin/packages/lua-bitlib/package.py index e8e99e60398..ca5d20764f0 100644 --- a/var/spack/repos/builtin/packages/lua-bitlib/package.py +++ b/var/spack/repos/builtin/packages/lua-bitlib/package.py @@ -14,7 +14,7 @@ class LuaBitlib(Package): homepage = "http://luaforge.net/projects/bitlib" url = "https://luarocks.org/bitlib-23-2.src.rock" - version('23', '9fee36a6e512c54bf6364dfe97d1d871', + version('23', sha256='fe226edc2808162e67418e6b2c98befc0ed25a489ecffc6974fa153f951c0c34', url="https://luarocks.org/bitlib-23-2.src.rock", expand=False) diff --git a/var/spack/repos/builtin/packages/lua-jit/package.py b/var/spack/repos/builtin/packages/lua-jit/package.py index e8cda54ade3..a0f8e2b88d0 100644 --- a/var/spack/repos/builtin/packages/lua-jit/package.py +++ b/var/spack/repos/builtin/packages/lua-jit/package.py @@ -12,7 +12,7 @@ class LuaJit(Package): homepage = "http://www.luajit.org" url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz" - version('2.0.4', 'dd9c38307f2223a504cbfb96e477eca0') + version('2.0.4', sha256='620fa4eb12375021bef6e4f237cbd2dd5d49e56beb414bee052c746beef1807d') def install(self, spec, prefix): # Linking with the C++ compiler is a dirty hack to deal with the fact diff --git a/var/spack/repos/builtin/packages/lua-lpeg/package.py b/var/spack/repos/builtin/packages/lua-lpeg/package.py index e5e06895161..8d6d35d1ff4 100644 --- a/var/spack/repos/builtin/packages/lua-lpeg/package.py +++ b/var/spack/repos/builtin/packages/lua-lpeg/package.py @@ -13,7 +13,7 @@ class LuaLpeg(Package): homepage = "http://www.inf.puc-rio.br/~roberto/lpeg/" url = "https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock" - version('0.12.1', 'b5778bfee67761fcbe7a2d23cb889ea8', + version('0.12.1', sha256='3962e8d695d0f9095c9453f2a42f9f1a89fb94db9b0c3bf22934c1e8a3b0ef5a', url='https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock', expand=False) diff --git a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py index 82638bc5e9d..b549486b3b1 100644 --- a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py +++ b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py @@ -20,7 +20,7 @@ class LuaLuafilesystem(Package): url = 'https://github.com/keplerproject/luafilesystem/archive/v1_6_3.tar.gz' version('1_7_0_2', sha256='23b4883aeb4fb90b2d0f338659f33a631f9df7a7e67c54115775a77d4ac3cc59') - version('1_6_3', 'bed11874cfded8b4beed7dd054127b24') + version('1_6_3', sha256='11c7b1fc2e560c0a521246b84e6257138d97dddde5a19e405714dbabcb9436ca') # The version constraint here comes from this post: # diff --git a/var/spack/repos/builtin/packages/lua-luaposix/package.py b/var/spack/repos/builtin/packages/lua-luaposix/package.py index e544f24c550..08c64b189c1 100644 --- a/var/spack/repos/builtin/packages/lua-luaposix/package.py +++ b/var/spack/repos/builtin/packages/lua-luaposix/package.py @@ -12,7 +12,7 @@ class LuaLuaposix(Package): homepage = "https://github.com/luaposix/luaposix/" url = "https://github.com/luaposix/luaposix/archive/release-v33.4.0.tar.gz" - version('33.4.0', 'b36ff049095f28752caeb0b46144516c') + version('33.4.0', sha256='e66262f5b7fe1c32c65f17a5ef5ffb31c4d1877019b4870a5d373e2ab6526a21') extends("lua") diff --git a/var/spack/repos/builtin/packages/lua-mpack/package.py b/var/spack/repos/builtin/packages/lua-mpack/package.py index 55e644ef1a6..777ff19e18a 100644 --- a/var/spack/repos/builtin/packages/lua-mpack/package.py +++ b/var/spack/repos/builtin/packages/lua-mpack/package.py @@ -15,7 +15,7 @@ class LuaMpack(Package): depends_on('msgpack-c') - version('1.0.0-0', '9a7bd842753194124830bc7426e78c1b', + version('1.0.0-0', sha256='9068d9d3f407c72a7ea18bc270b0fa90aad60a2f3099fa23d5902dd71ea4cd5f', url='https://luarocks.org/manifests/tarruda/mpack-1.0.6-0.src.rock', expand=False) diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index 238676c8dfd..91528a6e2ad 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -14,18 +14,18 @@ class Lua(Package): url = "http://www.lua.org/ftp/lua-5.3.4.tar.gz" version('5.3.5', sha256='0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac') - version('5.3.4', '53a9c68bcc0eda58bdc2095ad5cdfc63') - version('5.3.2', '33278c2ab5ee3c1a875be8d55c1ca2a1') - version('5.3.1', '797adacada8d85761c079390ff1d9961') - version('5.3.0', 'a1b0a7e92d0c85bbff7a8d27bf29f8af') - version('5.2.4', '913fdb32207046b273fdb17aad70be13') - version('5.2.3', 'dc7f94ec6ff15c985d2d6ad0f1b35654') - version('5.2.2', 'efbb645e897eae37cad4344ce8b0a614') - version('5.2.1', 'ae08f641b45d737d12d30291a5e5f6e3') - version('5.2.0', 'f1ea831f397214bae8a265995ab1a93e') - version('5.1.5', '2e115fe26e435e33b0d5c022e4490567') - version('5.1.4', 'd0870f2de55d59c1c8419f36e8fac150') - version('5.1.3', 'a70a8dfaa150e047866dc01a46272599') + version('5.3.4', sha256='f681aa518233bc407e23acf0f5887c884f17436f000d453b2491a9f11a52400c') + version('5.3.2', sha256='c740c7bb23a936944e1cc63b7c3c5351a8976d7867c5252c8854f7b2af9da68f') + version('5.3.1', sha256='072767aad6cc2e62044a66e8562f51770d941e972dc1e4068ba719cd8bffac17') + version('5.3.0', sha256='ae4a5eb2d660515eb191bfe3e061f2b8ffe94dce73d32cfd0de090ddcc0ddb01') + version('5.2.4', sha256='b9e2e4aad6789b3b63a056d442f7b39f0ecfca3ae0f1fc0ae4e9614401b69f4b') + version('5.2.3', sha256='13c2fb97961381f7d06d5b5cea55b743c163800896fd5c5e2356201d3619002d') + version('5.2.2', sha256='3fd67de3f5ed133bf312906082fa524545c6b9e1b952e8215ffbd27113f49f00') + version('5.2.1', sha256='64304da87976133196f9e4c15250b70f444467b6ed80d7cfd7b3b982b5177be5') + version('5.2.0', sha256='cabe379465aa8e388988073d59b69e76ba0025429d2c1da80821a252cdf6be0d') + version('5.1.5', sha256='2640fc56a795f29d28ef15e13c34a47e223960b0240e8cb0a82d9b0738695333') + version('5.1.4', sha256='b038e225eaf2a5b57c9bcc35cd13aa8c6c8288ef493d52970c9545074098af3a') + version('5.1.3', sha256='6b5df2edaa5e02bf1a2d85e1442b2e329493b30b0c0780f77199d24f087d296d') extendable = True @@ -38,7 +38,7 @@ class Lua(Package): name="luarocks", url="https://keplerproject.github.io/luarocks/releases/" "luarocks-2.3.0.tar.gz", - md5="a38126684cf42b7d0e7a3c7cf485defb", + sha256="68e38feeb66052e29ad1935a71b875194ed8b9c67c2223af5f4d4e3e2464ed97", destination="luarocks", placement='luarocks') diff --git a/var/spack/repos/builtin/packages/luit/package.py b/var/spack/repos/builtin/packages/luit/package.py index badeb7b4bde..6770ed81535 100644 --- a/var/spack/repos/builtin/packages/luit/package.py +++ b/var/spack/repos/builtin/packages/luit/package.py @@ -15,7 +15,7 @@ class Luit(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/luit" url = "https://www.x.org/archive/individual/app/luit-1.1.1.tar.gz" - version('1.1.1', '04128a52f68c05129f709196819ddad3') + version('1.1.1', sha256='87b0be0bd01f3b857a53e6625bdd31cef18418c95394b7f4387f8ecef78e45da') depends_on('libfontenc') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/lumpy-sv/package.py b/var/spack/repos/builtin/packages/lumpy-sv/package.py index 737ecce2992..442fe91553f 100644 --- a/var/spack/repos/builtin/packages/lumpy-sv/package.py +++ b/var/spack/repos/builtin/packages/lumpy-sv/package.py @@ -12,7 +12,7 @@ class LumpySv(MakefilePackage): homepage = "https://github.com/arq5x/lumpy-sv" url = "https://github.com/arq5x/lumpy-sv/archive/0.2.13.tar.gz" - version('0.2.13', '36929d29fc3a171d3abbe1d93f9f3b50') + version('0.2.13', sha256='3672b86ef0190ebe520648a6140077ee9f15b0549cb233dca18036e63bbf6375') depends_on('htslib') diff --git a/var/spack/repos/builtin/packages/lwgrp/package.py b/var/spack/repos/builtin/packages/lwgrp/package.py index 0d431b32a20..72ee0a0e6ac 100644 --- a/var/spack/repos/builtin/packages/lwgrp/package.py +++ b/var/spack/repos/builtin/packages/lwgrp/package.py @@ -13,6 +13,6 @@ class Lwgrp(AutotoolsPackage): homepage = "https://github.com/hpc/lwgrp" url = "https://github.com/hpc/lwgrp/releases/download/v1.0.2/lwgrp-1.0.2.tar.gz" - version('1.0.2', 'ab7ba3bdd8534a651da5076f47f27d8a') + version('1.0.2', sha256='c9d4233946e40f01efd0b4644fd9224becec51b9b5f8cbf45f5bac3129b5b536') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/lz4/package.py b/var/spack/repos/builtin/packages/lz4/package.py index 973def6138c..0f01a59743b 100644 --- a/var/spack/repos/builtin/packages/lz4/package.py +++ b/var/spack/repos/builtin/packages/lz4/package.py @@ -16,11 +16,11 @@ class Lz4(Package): homepage = "http://lz4.github.io/lz4/" url = "https://github.com/lz4/lz4/archive/v1.7.5.tar.gz" - version('1.9.0', 'f8b6d5662fa534bd61227d313535721ae41a68c9d84058b7b7d86e143572dcfb') - version('1.8.3', '33af5936ac06536805f9745e0b6d61da606a1f8b4cc5c04dd3cbaca3b9b4fc43') - version('1.8.1.2', '343538e69ba752a386c669b1a28111e2') - version('1.7.5', 'c9610c5ce97eb431dddddf0073d919b9') - version('1.3.1', '42b09fab42331da9d3fb33bd5c560de9') + version('1.9.0', sha256='f8b6d5662fa534bd61227d313535721ae41a68c9d84058b7b7d86e143572dcfb') + version('1.8.3', sha256='33af5936ac06536805f9745e0b6d61da606a1f8b4cc5c04dd3cbaca3b9b4fc43') + version('1.8.1.2', sha256='12f3a9e776a923275b2dc78ae138b4967ad6280863b77ff733028ce89b8123f9') + version('1.7.5', sha256='0190cacd63022ccb86f44fa5041dc6c3804407ad61550ca21c382827319e7e7e') + version('1.3.1', sha256='9d4d00614d6b9dec3114b33d1224b6262b99ace24434c53487a0c8fd0b18cfed') depends_on('valgrind', type='test') diff --git a/var/spack/repos/builtin/packages/lzma/package.py b/var/spack/repos/builtin/packages/lzma/package.py index e33b6c8fb05..7cc8b376b33 100644 --- a/var/spack/repos/builtin/packages/lzma/package.py +++ b/var/spack/repos/builtin/packages/lzma/package.py @@ -19,4 +19,4 @@ class Lzma(AutotoolsPackage): homepage = "http://tukaani.org/lzma/" url = "http://tukaani.org/lzma/lzma-4.32.7.tar.gz" - version('4.32.7', '2a748b77a2f8c3cbc322dbd0b4c9d06a') + version('4.32.7', sha256='9f337a8c51e5ded198d1032f5087ba3fe438f2a54e9df419e513a151775b032c') diff --git a/var/spack/repos/builtin/packages/lzo/package.py b/var/spack/repos/builtin/packages/lzo/package.py index d67bd87aaa6..0d2c1e78567 100644 --- a/var/spack/repos/builtin/packages/lzo/package.py +++ b/var/spack/repos/builtin/packages/lzo/package.py @@ -13,11 +13,11 @@ class Lzo(AutotoolsPackage): url = 'http://www.oberhumer.com/opensource/lzo/download/lzo-2.09.tar.gz' version('2.10', sha256='c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072') - version('2.09', 'c7ffc9a103afe2d1bba0b015e7aa887f') - version('2.08', 'fcec64c26a0f4f4901468f360029678f') - version('2.07', '4011935e95171e78ad4894f7335c982a') - version('2.06', '95380bd4081f85ef08c5209f4107e9f8') - version('2.05', 'c67cda5fa191bab761c7cb06fe091e36') + version('2.09', sha256='f294a7ced313063c057c504257f437c8335c41bfeed23531ee4e6a2b87bcb34c') + version('2.08', sha256='ac1b3e4dee46febe9fd28737eb7f5692d3232ef1a01da10444394c3d47536614') + version('2.07', sha256='9298ccf43f856ef00643d110042b2fefe694b569c161aef0c6f8e4ada590e6d4') + version('2.06', sha256='ff79e6f836d62d3f86ef6ce893ed65d07e638ef4d3cb952963471b4234d43e73') + version('2.05', sha256='449f98186d76ba252cd17ff1241ca2a96b7f62e0d3e4766f88730dab0ea5f333') def configure_args(self): return [ diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py index c86fcbefdb7..7b440e845e9 100644 --- a/var/spack/repos/builtin/packages/m4/package.py +++ b/var/spack/repos/builtin/packages/m4/package.py @@ -12,8 +12,8 @@ class M4(AutotoolsPackage): homepage = "https://www.gnu.org/software/m4/m4.html" url = "https://ftpmirror.gnu.org/m4/m4-1.4.18.tar.gz" - version('1.4.18', 'a077779db287adf4e12a035029002d28') - version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76') + version('1.4.18', sha256='ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab') + version('1.4.17', sha256='3ce725133ee552b8b4baca7837fb772940b25e81b2a9dc92537aeaf733538c9e') patch('gnulib-pgi.patch', when='@1.4.18') patch('pgi.patch', when='@1.4.17') diff --git a/var/spack/repos/builtin/packages/macsio/package.py b/var/spack/repos/builtin/packages/macsio/package.py index bde149ec71e..c343e75cba3 100644 --- a/var/spack/repos/builtin/packages/macsio/package.py +++ b/var/spack/repos/builtin/packages/macsio/package.py @@ -18,7 +18,7 @@ class Macsio(CMakePackage): version('develop', branch='master') version('1.1', sha256='a86249b0f10647c0b631773db69568388094605ec1a0af149d9e61e95e6961ec') - version('1.0', '90e8e00ea84af2a47bee387ad331dbde') + version('1.0', md5='90e8e00ea84af2a47bee387ad331dbde') variant('mpi', default=True, description="Build MPI plugin") variant('silo', default=True, description="Build with SILO plugin") diff --git a/var/spack/repos/builtin/packages/mad-numdiff/package.py b/var/spack/repos/builtin/packages/mad-numdiff/package.py index 4b462d7c436..afa13c5cd05 100644 --- a/var/spack/repos/builtin/packages/mad-numdiff/package.py +++ b/var/spack/repos/builtin/packages/mad-numdiff/package.py @@ -15,4 +15,4 @@ class MadNumdiff(CMakePackage): git = "https://github.com/quinoacomputing/ndiff.git" version('develop', branch='master') - version('20150724', '7723c0f2499aea8fd960377c5bed28d8') + version('20150724', sha256='33130b48416f8dcb6402acbcb8906cdec35b7242fe2f3ad49b7d7c063d75377b') diff --git a/var/spack/repos/builtin/packages/mafft/package.py b/var/spack/repos/builtin/packages/mafft/package.py index 1f08e4de9b9..886e491d0bc 100644 --- a/var/spack/repos/builtin/packages/mafft/package.py +++ b/var/spack/repos/builtin/packages/mafft/package.py @@ -16,7 +16,7 @@ class Mafft(Package): url = "http://mafft.cbrc.jp/alignment/software/mafft-7.221-with-extensions-src.tgz" version('7.407', sha256='1840b51a0b93f40b4d6076af996ee46396428d8dbaf7ba1d847abff9cb1463e5') - version('7.221', 'b1aad911e51024d631722a2e061ba215') + version('7.221', sha256='0bc78111966d9b00ddfa14fa217fa5bb0c593a558674a13f02dca7bcd51f7fcf') def install(self, spec, prefix): with working_dir('core'): diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py index ecc303391b9..d2f3a99003f 100644 --- a/var/spack/repos/builtin/packages/magics/package.py +++ b/var/spack/repos/builtin/packages/magics/package.py @@ -19,14 +19,14 @@ class Magics(CMakePackage): # The policy on which minor releases remain available and which get deleted # after a newer version becomes available is unclear. version('4.1.0', sha256='e56fb1bf82d57957a61a76284ad22024f4a7c3c989f6f796e57dfd45d88400c0') - version('2.34.3', 'b4180bc4114ffd723b80728947f50c17') - version('2.34.1', '1ecc5cc20cb0c3f2f0b9171626f09d53') - version('2.33.0', '8d513fd2244f2974b3517a8b30dd51f6') - version('2.32.0', 'e17956fffce9ea826cf994f8d275e0f5') - version('2.31.0', '3564dca9e1b4af096fd631906f5e6c89') - version('2.29.6', '56d2c31ca75162e5e86ef75d355e87f1') - version('2.29.4', '91c561f413316fb665b3bb563f3878d1') - version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709') + version('2.34.3', sha256='38487562e83c0470f94d9c7fb9418cbadf92f1e643033237baba2abdc77e6238') + version('2.34.1', sha256='8df27f8f262ebc32a61f8696df15a7b4a6e4203b2a8e53fe7aa13caa1c4e3fa4') + version('2.33.0', sha256='32d3079749f89988715a8c3df01b712d9b989b7fd242828ec09563e47c5a3e82') + version('2.32.0', sha256='233b046c93b84be60ac8011212668de35c2693d89fffcaad333b42b8c4ffad06') + version('2.31.0', sha256='13c314661bb154499a87db9063238d6ecebad0d4fec37b0f3d90fe34aa37eec6') + version('2.29.6', sha256='88cfa5e2bd823c4669a3d2fe0349f14545e810333c1b4d031ce74a7a5218a2db') + version('2.29.4', sha256='82bdb4f7e38776776d2155a82d0acaa017402365a043731708345ac4ac00198f') + version('2.29.0', sha256='4c5067c4630e831bf81d15454476ff0d050c488b768f6a10272aad62ce8d0f92') # The patch reorders includes and adds namespaces where necessary to # resolve ambiguity of invocations of isnan and isinf functions. The diff --git a/var/spack/repos/builtin/packages/makedepend/package.py b/var/spack/repos/builtin/packages/makedepend/package.py index 58e7e12cc88..42c38a0deec 100644 --- a/var/spack/repos/builtin/packages/makedepend/package.py +++ b/var/spack/repos/builtin/packages/makedepend/package.py @@ -12,7 +12,7 @@ class Makedepend(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/util/makedepend" url = "https://www.x.org/archive/individual/util/makedepend-1.0.5.tar.gz" - version('1.0.5', 'efb2d7c7e22840947863efaedc175747') + version('1.0.5', sha256='503903d41fb5badb73cb70d7b3740c8b30fe1cc68c504d3b6a85e6644c4e5004') depends_on('xproto@7.0.17:', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/mallocmc/package.py b/var/spack/repos/builtin/packages/mallocmc/package.py index 707ce978dd8..667267a9696 100644 --- a/var/spack/repos/builtin/packages/mallocmc/package.py +++ b/var/spack/repos/builtin/packages/mallocmc/package.py @@ -26,11 +26,11 @@ class Mallocmc(CMakePackage): version('develop', branch='dev') version('master', branch='master') - version('2.2.0crp', '3e5c5fc963d1a9abc829ff701504e54c') - version('2.1.0crp', 'd2bd2644012b64a246048575e9a9051c') - version('2.0.1crp', '1f674d5d1ae05446d9a4e4b65465dca0') - version('2.0.0crp', '2c63c3ea2a882f29962c67b095d8f7a8') - version('1.0.2crp', '8f5edf07daa527261e52bc61be340ae6') + version('2.2.0crp', sha256='1b500ee7fcea45a67a81fc0e1c294b4b0c413cd1f76168522f35ade7d44be9b6') + version('2.1.0crp', sha256='973c606624cf4e049518d0366d72fb164fa837ab0068c7a44df7e567b95ef9bf') + version('2.0.1crp', sha256='85873355814be22310e22e214e4d8e9798aaab9001c19da8ec9dd29c04603e9e') + version('2.0.0crp', sha256='1a6b5b4f9a890d4389703cb853868cc31a97457bfea3b62d6b3ae31e56d7bbd9') + version('1.0.2crp', sha256='696c5bb7e90a75937a2479c40e7cfddcc876f8fc634dca04b61d132ab1243f12') depends_on('cmake@2.8.12.2:', type='build') depends_on('boost@1.48.0:', type='link') diff --git a/var/spack/repos/builtin/packages/man-db/package.py b/var/spack/repos/builtin/packages/man-db/package.py index bef52da8fed..44e75d7eda0 100644 --- a/var/spack/repos/builtin/packages/man-db/package.py +++ b/var/spack/repos/builtin/packages/man-db/package.py @@ -15,7 +15,7 @@ class ManDb(AutotoolsPackage): homepage = "http://www.nongnu.org/man-db/" url = "http://git.savannah.nongnu.org/cgit/man-db.git/snapshot/man-db-2.7.6.1.tar.gz" - version('2.7.6.1', '312761baade811db2b956af3432c285e') + version('2.7.6.1', sha256='dd913662e341fc01e6721878b6cbe1001886cc3bfa6632b095937bba3238c779') depends_on('autoconf') depends_on('automake') diff --git a/var/spack/repos/builtin/packages/manta/package.py b/var/spack/repos/builtin/packages/manta/package.py index 0922e3f0352..52dc3b2e9bf 100644 --- a/var/spack/repos/builtin/packages/manta/package.py +++ b/var/spack/repos/builtin/packages/manta/package.py @@ -14,10 +14,10 @@ class Manta(CMakePackage): version('1.6.0', sha256='c846d61b02483265c09d58bd85dacf5326a94f38179b5ae4f70694be96e1368f') version('1.5.0', sha256='9aa1a59c9cb8d2dd33724a42959c9398aff7840c5bf3c895d2483a8093b3d2dc') - version('1.4.0', '582d10f3bc56aecfa5c24931af3742b4') - version('1.3.2', '83f43fe1a12605c1e9803d1020b24bd1') - version('1.3.1', 'e315caff775878872ee300ed34e8adae') - version('1.3.0', '1243e2bb58ca7c9d69bbfbe528f492ec') + version('1.4.0', sha256='4f8f827485e3ad9a12318bfcbf62fa622263378767514eb938bc02ad5ad74f10') + version('1.3.2', sha256='eb346d1a44aff1180732dcd03864b89efc1245652e1993107fb60da4ad739f79') + version('1.3.1', sha256='9ba943623088e552a4b45bccea48125a0553905f4cc7ea86a9de567e155a5888') + version('1.3.0', sha256='3db4b5475c33e3aeeb5435969c74364af9d2d77dd3bcf8dc70bf44a851e450dd') depends_on('boost@1.58.0:', type='build') depends_on('cmake@2.8.12:', type='build') diff --git a/var/spack/repos/builtin/packages/maq/package.py b/var/spack/repos/builtin/packages/maq/package.py index f2c6149c14e..fbb5b3feaa3 100644 --- a/var/spack/repos/builtin/packages/maq/package.py +++ b/var/spack/repos/builtin/packages/maq/package.py @@ -14,7 +14,7 @@ class Maq(AutotoolsPackage): url = "https://downloads.sourceforge.net/project/maq/maq/0.7.1/maq-0.7.1.tar.bz2" list_url = "https://sourceforge.net/projects/maq/files/maq/" - version('0.7.1', '51130f6c8257c133719adacdd1433f35') - version('0.5.0', '854e2bee32d5237236d4c68c0ed7c52d') + version('0.7.1', sha256='e1671e0408b0895f5ab943839ee8f28747cf5f55dc64032c7469b133202b6de2') + version('0.5.0', sha256='c292c19baf291b2415b460d687d43a71ece00a7d178cc5984bc8fc30cfce2dfb') conflicts('%gcc@4.7.0:', when='@0.7.1') diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py index c094da88651..42019809c7e 100644 --- a/var/spack/repos/builtin/packages/mariadb/package.py +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -21,11 +21,11 @@ class Mariadb(CMakePackage): url = "http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-10.2.8/source/mariadb-10.2.8.tar.gz" version('10.4.7', sha256='c8e6a6d0bb4f22c416ed675d24682a3ecfa383c5283efee70c8edf131374d817') - version('10.2.8', 'f93cbd5bfde3c0d082994764ff7db580') - version('10.1.23', '1a7392cc05c7c249acd4495022719ca8') - version('5.5.56', '8bc7772fea3e11b0bc1a09d2278e2e32') - version('10.1.14', '294925531e0fd2f0461e3894496a5adc') - version('5.5.49', '67b5a499a5f158b2a586e6e3bfb4f304') + version('10.2.8', sha256='8dd250fe79f085e26f52ac448fbdb7af2a161f735fae3aed210680b9f2492393') + version('10.1.23', sha256='54d8114e24bfa5e3ebdc7d69e071ad1471912847ea481b227d204f9d644300bf') + version('5.5.56', sha256='950c3422cb262b16ce133caadbc342219f50f9b45dcc71b8db78fc376a971726') + version('10.1.14', sha256='18e71974a059a268a3f28281599607344d548714ade823d575576121f76ada13') + version('5.5.49', sha256='2c82f2af71b88a7940d5ff647498ed78922c92e88004942caa213131e20f4706') variant('nonblocking', default=True, description='Allow non blocking ' 'operations in the mariadb client library.') diff --git a/var/spack/repos/builtin/packages/maven/package.py b/var/spack/repos/builtin/packages/maven/package.py index 0163c40464c..c4108c6e2f2 100644 --- a/var/spack/repos/builtin/packages/maven/package.py +++ b/var/spack/repos/builtin/packages/maven/package.py @@ -12,8 +12,8 @@ class Maven(Package): homepage = "https://maven.apache.org/index.html" url = "https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.3.9/apache-maven-3.3.9-bin.tar.gz" - version('3.5.0', '35c39251d2af99b6624d40d801f6ff02') - version('3.3.9', '516923b3955b6035ba6b0a5b031fbd8b') + version('3.5.0', sha256='beb91419245395bd69a4a6edad5ca3ec1a8b64e41457672dc687c173a495f034') + version('3.3.9', sha256='6e3e9c949ab4695a204f74038717aa7b2689b1be94875899ac1b3fe42800ff82') depends_on('java') diff --git a/var/spack/repos/builtin/packages/maverick/package.py b/var/spack/repos/builtin/packages/maverick/package.py index ce1989b2e41..539dc1a4114 100644 --- a/var/spack/repos/builtin/packages/maverick/package.py +++ b/var/spack/repos/builtin/packages/maverick/package.py @@ -13,7 +13,7 @@ class Maverick(MakefilePackage): homepage = "https://github.com/bobverity/MavericK" url = "https://github.com/bobverity/MavericK/archive/v1.0.4.tar.gz" - version('1.0.4', '0c17c9a73fd0ac0aef17339173ddedc2') + version('1.0.4', sha256='d4634c1b3f09cec9eb60d72348e2f479d74220ecbdebd940bb18b480db8df8cb') conflicts('%gcc@:6.0') conflicts('%cce') diff --git a/var/spack/repos/builtin/packages/mawk/package.py b/var/spack/repos/builtin/packages/mawk/package.py index 89b3a9faba4..24a79c02143 100644 --- a/var/spack/repos/builtin/packages/mawk/package.py +++ b/var/spack/repos/builtin/packages/mawk/package.py @@ -13,6 +13,6 @@ class Mawk(AutotoolsPackage): url = "http://invisible-mirror.net/archives/mawk/mawk-1.3.4.tgz" version('1.3.4-20171017', sha256='db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b') - version('1.3.4', 'b1d27324ae80302452d0fa0c98447b65') + version('1.3.4', sha256='2f2ab8831c441a5793ad333193c888c9ba29c900f009aa23c9fffc100c405925') provides('awk') diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py index 690eba08134..e5104eeb249 100644 --- a/var/spack/repos/builtin/packages/mbedtls/package.py +++ b/var/spack/repos/builtin/packages/mbedtls/package.py @@ -16,14 +16,14 @@ class Mbedtls(CMakePackage): homepage = "https://tls.mbed.org" url = "https://github.com/ARMmbed/mbedtls/archive/mbedtls-2.2.1.tar.gz" - version('2.16.1', 'daf0d40f3016c34eb42d1e4b3b52be047e976d566aba8668977723c829af72f3') - version('2.7.10', '42b19b30b86a798bdb69c5da2f8bbd7d72ffede9a35b888ab986a29480f9dc3e') - version('2.3.0', '98158e1160a0825a3e8db38881a177a0') - version('2.2.1', '73a38f96898d6d03e32f55dd9f9a67be') - version('2.2.0', 'eaf4586c1ef93ae872e606b6c1203942') - version('2.1.4', '40cdf67b6c6d92c9cbcfd552d39ea3ae') - version('2.1.3', '7eb4cf1dfa68578a2c8dbd0b6fa752dd') - version('1.3.16', '4144d7320c691f721aeb9e67a1bc38e0') + version('2.16.1', sha256='daf0d40f3016c34eb42d1e4b3b52be047e976d566aba8668977723c829af72f3') + version('2.7.10', sha256='42b19b30b86a798bdb69c5da2f8bbd7d72ffede9a35b888ab986a29480f9dc3e') + version('2.3.0', sha256='1614ee70be99a18ca8298148308fb725aad4ad31c569438bb51655a4999b14f9') + version('2.2.1', sha256='32819c62c20e8740a11b49daa5d09ac6f179edf120a87ac559cd63120b66b699') + version('2.2.0', sha256='75494361e412444b38ebb9c908b7e17a5fb582eb9c3fadb2fe9b21e96f1bf8cb') + version('2.1.4', sha256='a0ee4d3dd135baf67a3cf5ad9e70d67575561704325d6c93d8f087181f4db338') + version('2.1.3', sha256='94da4618d5a518b99f7914a5e348be436e3571113d9a9978d130725a1fc7bfac') + version('1.3.16', sha256='0c2666222b66cf09c4630fa60a715aafd7decb1a09933b75c0c540b0625ac5df') variant('build_type', default='Release', description='The build type to build', diff --git a/var/spack/repos/builtin/packages/mc/package.py b/var/spack/repos/builtin/packages/mc/package.py index a15f0d5eda2..e67d10069dc 100644 --- a/var/spack/repos/builtin/packages/mc/package.py +++ b/var/spack/repos/builtin/packages/mc/package.py @@ -13,8 +13,8 @@ class Mc(AutotoolsPackage): url = "http://ftp.midnight-commander.org/mc-4.8.20.tar.bz2" version('4.8.23', sha256='238c4552545dcf3065359bd50753abbb150c1b22ec5a36eaa02c82808293267d') - version('4.8.21', '251d9f0ef9309ef3eea0fdc4c12b8b61149e5056bef1b2de2ccc7f015d973444') - version('4.8.20', 'dcfc7aa613c62291a0f71f6b698d8267') + version('4.8.21', sha256='251d9f0ef9309ef3eea0fdc4c12b8b61149e5056bef1b2de2ccc7f015d973444') + version('4.8.20', sha256='2d85daaa6ab26e524946df4823ac2f69802bc16bc967781b5e28d5b86fc3b979') depends_on('ncurses') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/mcl/package.py b/var/spack/repos/builtin/packages/mcl/package.py index 4ab795b62a5..29372c73f47 100644 --- a/var/spack/repos/builtin/packages/mcl/package.py +++ b/var/spack/repos/builtin/packages/mcl/package.py @@ -14,4 +14,4 @@ class Mcl(AutotoolsPackage): homepage = "https://www.micans.org/mcl/index.html" url = "https://www.micans.org/mcl/src/mcl-14-137.tar.gz" - version('14-137', 'bc8740456cf51019d0a9ac5eba665bb5') + version('14-137', sha256='b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497') diff --git a/var/spack/repos/builtin/packages/med/package.py b/var/spack/repos/builtin/packages/med/package.py index 4f4ee1aa04c..55d6be7b03f 100644 --- a/var/spack/repos/builtin/packages/med/package.py +++ b/var/spack/repos/builtin/packages/med/package.py @@ -15,7 +15,7 @@ class Med(CMakePackage): maintainers = ['likask'] - version('3.2.0', 'eb61df92f0624feb6328f517cd756a23') + version('3.2.0', sha256='d52e9a1bdd10f31aa154c34a5799b48d4266dc6b4a5ee05a9ceda525f2c6c138') variant('api23', default=True, description='Enable API2.3') diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py index 8683687cce3..2620b62f480 100644 --- a/var/spack/repos/builtin/packages/meep/package.py +++ b/var/spack/repos/builtin/packages/meep/package.py @@ -14,9 +14,9 @@ class Meep(AutotoolsPackage): url = "http://ab-initio.mit.edu/meep/meep-1.3.tar.gz" list_url = "http://ab-initio.mit.edu/meep/old" - version('1.3', '18a5b9e18008627a0411087e0bb60db5') - version('1.2.1', '9be2e743c3a832ae922de9d955d016c5') - version('1.1.1', '415e0cd312b6caa22b5dd612490e1ccf') + version('1.3', sha256='564c1ff1b413a3487cf81048a45deabfdac4243a1a37ce743f4fcf0c055fd438') + version('1.2.1', sha256='f1f0683e5688d231f7dd1863939677148fc27a6744c03510e030c85d6c518ea5') + version('1.1.1', sha256='7a97b5555da1f9ea2ec6eed5c45bd97bcd6ddbd54bdfc181f46c696dffc169f2') variant('blas', default=True, description='Enable BLAS support') variant('lapack', default=True, description='Enable LAPACK support') diff --git a/var/spack/repos/builtin/packages/megahit/package.py b/var/spack/repos/builtin/packages/megahit/package.py index 216bae616fa..cc69790f654 100644 --- a/var/spack/repos/builtin/packages/megahit/package.py +++ b/var/spack/repos/builtin/packages/megahit/package.py @@ -14,7 +14,7 @@ class Megahit(MakefilePackage): url = "https://github.com/voutcn/megahit/archive/v1.1.3.tar.gz" version('1.1.4', sha256='ecd64c8bfa516ef6b19f9b2961ede281ec814db836f1a91953c213c944e1575f') - version('1.1.3', '2962a781a22c0884fa97b95f740ed2fe') + version('1.1.3', sha256='b6eefdee075aaf7a8f9090e2e8b08b770caff90aa43a255e0e220d82ce71c492') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py index 1714c4a65c3..1fa70113395 100644 --- a/var/spack/repos/builtin/packages/memaxes/package.py +++ b/var/spack/repos/builtin/packages/memaxes/package.py @@ -11,7 +11,7 @@ class Memaxes(Package): homepage = "https://github.com/llnl/MemAxes" - version('0.5', '5874f3fda9fd2d313c0ff9684f915ab5', + version('0.5', sha256='9858f0f675b50e347d0b88545558e5d6b4333347c762b15d399b8d8004d7b68b', url='https://github.com/llnl/MemAxes/archive/v0.5.tar.gz') depends_on('cmake@2.8.9:', type='build') diff --git a/var/spack/repos/builtin/packages/meme/package.py b/var/spack/repos/builtin/packages/meme/package.py index f323a5b2399..a045e6d1ee8 100644 --- a/var/spack/repos/builtin/packages/meme/package.py +++ b/var/spack/repos/builtin/packages/meme/package.py @@ -14,8 +14,8 @@ class Meme(AutotoolsPackage): homepage = "http://meme-suite.org" url = "http://meme-suite.org/meme-software/4.11.4/meme_4.11.4.tar.gz" - version('4.12.0', '40d282cc33f7dedb06b24b9f34ac15c1') - version('4.11.4', '371f513f82fa0888205748e333003897') + version('4.12.0', sha256='49ff80f842b59d328588acfcd1d15bf94c55fed661d22b0f95f37430cc363a06') + version('4.11.4', sha256='3e869ff57e327a9c8615dbef784e3f1095f7f7a0120cecd55efe10c3f2ee8eb3') variant('mpi', default=True, description='Enable MPI support') variant('image-magick', default=False, description='Enable image-magick for png output') diff --git a/var/spack/repos/builtin/packages/memkind/package.py b/var/spack/repos/builtin/packages/memkind/package.py index 2c2fcb740be..95b0714a7ac 100644 --- a/var/spack/repos/builtin/packages/memkind/package.py +++ b/var/spack/repos/builtin/packages/memkind/package.py @@ -23,7 +23,7 @@ class Memkind(AutotoolsPackage): homepage = "https://github.com/memkind/memkind" url = "https://github.com/memkind/memkind/archive/v1.7.0.tar.gz" - version('1.7.0', 'bfbbb9226d40fd12ae1822a8be4c9207') + version('1.7.0', sha256='5048eaaa1bc484203c685a019f3f428ab6c9b1cf94ef6d264e299bc0127ec572') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py index 8e44be55967..271e8756ad2 100644 --- a/var/spack/repos/builtin/packages/meraculous/package.py +++ b/var/spack/repos/builtin/packages/meraculous/package.py @@ -15,7 +15,7 @@ class Meraculous(CMakePackage): git = "https://bitbucket.org/berkeleylab/genomics-meraculous2.git" version('2.2.5.1', branch='release-2.2.5.1') - version('2.2.4', '349feb6cb178643a46e4b092c87bad3a') + version('2.2.4', sha256='3b4b8848232be902af9ebc77b38b83bcc531f12120115be089bdd6371ad2bf5b') depends_on('perl', type=('build', 'run')) depends_on('boost@1.5.0:') diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py index 988e5c54679..5b7ec7bdd31 100644 --- a/var/spack/repos/builtin/packages/mercurial/package.py +++ b/var/spack/repos/builtin/packages/mercurial/package.py @@ -22,14 +22,14 @@ class Mercurial(PythonPackage): version('5.1.1', sha256='35fc8ba5e0379c1b3affa2757e83fb0509e8ac314cbd9f1fd133cf265d16e49f') version('4.9.1', sha256='1bdd21bb87d1e05fb5cd395d488d0e0cc2f2f90ce0fd248e31a03595da5ccb47') - version('4.4.1', '37974a416d1d9525e1375c92025b16d9') - version('4.1.2', '934c99808bdc8385e074b902d59b0d93') - version('3.9.1', '3759dd10edb8c1a6dfb8ff0ce82658ce') - version('3.9', 'e2b355da744e94747daae3a5339d28a0') - version('3.8.4', 'cec2c3db688cb87142809089c6ae13e9') - version('3.8.3', '97aced7018614eeccc9621a3dea35fda') - version('3.8.2', 'c38daa0cbe264fc621dc3bb05933b0b3') - version('3.8.1', '172a8c588adca12308c2aca16608d7f4') + version('4.4.1', sha256='8f2a5512d6cc2ffb08988aef639330a2f0378e4ac3ee0e1fbbdb64d9fff56246') + version('4.1.2', sha256='09415253fb409a77e19b9951532a3c22c4e07e74bab80652527064617daab194') + version('3.9.1', sha256='625e4fc7e85ec2278c2828bdc547fce74091b3bbe4d9eeeba2d61af51195df74') + version('3.9', sha256='834f25dcff44994198fb8a7ba161a6e24204dbd63c8e6270577e06e6cedbdabc') + version('3.8.4', sha256='4b2e3ef19d34fa1d781cb7425506a05d4b6b1172bab69d6ea78874175fdf3da6') + version('3.8.3', sha256='f84556cdf9a331984261549d9d08143ab9da33d7c03f0aa323b0ee52d0782a4c') + version('3.8.2', sha256='cb78b16956140625266a8a6d1fadc7c868969d994086e1ec60279a66bf20bffd') + version('3.8.1', sha256='face1f058de5530b56b0dfd3b4d0b23d89590c588605c06f3d18b79e8c30d594') depends_on('python@2.6:2.8', when='@:4.2.99') depends_on('python@2.7:2.8,3.5:3.5.999,3.6.2:', when='@4.3:') diff --git a/var/spack/repos/builtin/packages/mesa-glu/package.py b/var/spack/repos/builtin/packages/mesa-glu/package.py index db29da92b2e..9e8412414a6 100644 --- a/var/spack/repos/builtin/packages/mesa-glu/package.py +++ b/var/spack/repos/builtin/packages/mesa-glu/package.py @@ -12,7 +12,7 @@ class MesaGlu(AutotoolsPackage): homepage = "https://www.mesa3d.org" url = "https://www.mesa3d.org/archive/glu/glu-9.0.0.tar.gz" - version('9.0.0', 'bbc57d4fe3bd3fb095bdbef6fcb977c4') + version('9.0.0', sha256='4387476a1933f36fec1531178ea204057bbeb04cc2d8396c9ea32720a1f7e264') depends_on('gl@3:') diff --git a/var/spack/repos/builtin/packages/meshkit/package.py b/var/spack/repos/builtin/packages/meshkit/package.py index 59f39246ae5..52291056533 100644 --- a/var/spack/repos/builtin/packages/meshkit/package.py +++ b/var/spack/repos/builtin/packages/meshkit/package.py @@ -16,7 +16,7 @@ class Meshkit(AutotoolsPackage): homepage = "http://sigma.mcs.anl.gov/meshkit-library" url = "http://ftp.mcs.anl.gov/pub/fathom/meshkit-1.5.0.tar.gz" - version('1.5.0', '90b52416598ef65525ce4457a50ffe68') + version('1.5.0', sha256='6a4c119af191e24ef40644acb7cfbe967af0678ac3412f38a943fb28d661cac7') variant("mpi", default=True, description='enable mpi support') variant("netgen", default=False, description='enable netgen support') diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py index eb0067f982d..9e0da3b9f06 100644 --- a/var/spack/repos/builtin/packages/meson/package.py +++ b/var/spack/repos/builtin/packages/meson/package.py @@ -16,9 +16,9 @@ class Meson(PythonPackage): version('0.49.1', sha256='a944e7f25a2bc8e4ba3502ab5835d8a8b8f2530415c9d6fcffb53e0abaea2ced') version('0.49.0', sha256='11bc959e7173e714e4a4e85dd2bd9d0149b0a51c8ba82d5f44cc63735f603c74') - version('0.42.0', '9e26bf154ca439b78b1b9366c8a89437') - version('0.41.2', 'aa9c69ced965e47f5c75a9257ee91ce3') - version('0.41.1', 'c6d285b35cfd7acc8517124d417efbdc') + version('0.42.0', sha256='6c318a2da3859326a37f8a380e3c50e97aaabff6990067218dffffea674ed76f') + version('0.41.2', sha256='2daf448d3f2479d60e30617451f09bf02d26304dd1bd12ee1de936a53e42c7a4') + version('0.41.1', sha256='a48901f02ffeb9ff5cf5361d71b1fca202f9cd72998043ad011fc5de0294cf8b') variant('ninjabuild', default=True) diff --git a/var/spack/repos/builtin/packages/mesquite/package.py b/var/spack/repos/builtin/packages/mesquite/package.py index cd0056ca8e3..199065e5851 100644 --- a/var/spack/repos/builtin/packages/mesquite/package.py +++ b/var/spack/repos/builtin/packages/mesquite/package.py @@ -18,9 +18,9 @@ class Mesquite(AutotoolsPackage): homepage = "https://software.sandia.gov/mesquite" url = "https://software.sandia.gov/mesquite/mesquite-2.3.0.tar.gz" - version('2.99', '92b94167981bb8fcd59b0f0f18fbab64') - version('2.3.0', 'f64948b5210d5ccffaa9a2482447b322') - version('2.2.0', '41360c363e541aff7dc10024c90072d3') + version('2.99', sha256='7d834dbcc3132d903dbecb59337dc5b47505b7fb579b68f1ce66e5df87106954') + version('2.3.0', sha256='4ab4ceadfa596e16c00dbb0e8b830a9112fa1b73291ca07633ec379a39b8bb28') + version('2.2.0', sha256='3d48322c3e148431ee1af155d6bb94dfeef15795da1f46996c112df27778a4a2') variant('mpi', default=True, description='Enable MPI parallel support') diff --git a/var/spack/repos/builtin/packages/metabat/package.py b/var/spack/repos/builtin/packages/metabat/package.py index 12623f528e1..fc9f22d225d 100644 --- a/var/spack/repos/builtin/packages/metabat/package.py +++ b/var/spack/repos/builtin/packages/metabat/package.py @@ -13,7 +13,7 @@ class Metabat(SConsPackage): homepage = "https://bitbucket.org/berkeleylab/metabat" url = "https://bitbucket.org/berkeleylab/metabat/get/v2.12.1.tar.gz" - version('2.12.1', 'c032f47a8b24e58a5a9fefe52cb6e0f8') + version('2.12.1', sha256='e3aca0656f56f815135521360dc56667ec26af25143c3a31d645fef1a96abbc2') version('2.11.2', sha256='9baf81b385e503e71792706237c308a21ff9177a3211c79057dcecf8434e9a67') depends_on('boost@1.55.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index d5aae891904..4e64f43b400 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -21,9 +21,9 @@ class Metis(Package): url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz" list_url = "http://glaros.dtc.umn.edu/gkhome/fsroot/sw/metis/OLD" - version('5.1.0', '5465e67079419a69e0116de24fce58fe') - version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5') - version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10') + version('5.1.0', sha256='76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2') + version('5.0.2', sha256='f79790676ca2ce3dfa9d5e2d74801e91d92415664ede2c2fc18fc49d4a161981') + version('4.0.3', sha256='5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55') variant('shared', default=True, description='Enables the build of shared libraries.') variant('gdb', default=False, description='Enables gdb support (version 5+).') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 7ec3fae7e0d..bb27e6927f2 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -49,27 +49,27 @@ class Mfem(Package): version('3.4.1-laghos-v2.0', tag='laghos-v2.0') version('3.4.0', - '4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05', + sha256='4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05', url='https://bit.ly/mfem-3-4', extension='.tar.gz', preferred=True) version('3.3.2', - 'b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce', + sha256='b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce', url='https://goo.gl/Kd7Jk8', extension='.tar.gz') # Tagged development version used by the laghos package: version('3.3.1-laghos-v1.0', tag='laghos-v1.0') version('3.3', - 'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b', + sha256='b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b', url='http://goo.gl/Vrpsns', extension='.tar.gz') version('3.2', - '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340', + sha256='2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340', url='http://goo.gl/Y9T75B', extension='.tar.gz') version('3.1', - '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', + sha256='841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', url='http://goo.gl/xrScXn', extension='.tar.gz') variant('static', default=True, diff --git a/var/spack/repos/builtin/packages/microbiomeutil/package.py b/var/spack/repos/builtin/packages/microbiomeutil/package.py index 8be2ad7fa8e..d536c139892 100644 --- a/var/spack/repos/builtin/packages/microbiomeutil/package.py +++ b/var/spack/repos/builtin/packages/microbiomeutil/package.py @@ -12,7 +12,7 @@ class Microbiomeutil(MakefilePackage): homepage = "http://microbiomeutil.sourceforge.net/" url = "https://downloads.sourceforge.net/project/microbiomeutil/microbiomeutil-r20110519.tgz" - version('20110519', '11eaac4b0468c05297ba88ec27bd4b56') + version('20110519', sha256='9233de80ea57bfb9e9371cbe7e3bfad2d4a51168fddaf60fa144c4046c80d823') depends_on('perl', type=('build', 'run')) depends_on('blast-plus') diff --git a/var/spack/repos/builtin/packages/minced/package.py b/var/spack/repos/builtin/packages/minced/package.py index ce9019d5e9e..18418b15ebf 100644 --- a/var/spack/repos/builtin/packages/minced/package.py +++ b/var/spack/repos/builtin/packages/minced/package.py @@ -16,7 +16,7 @@ class Minced(Package): url = "https://github.com/ctSkennerton/minced/archive/0.2.0.tar.gz" version('0.3.2', sha256='334aee43292d0b657c4849f818ddfb3ac7811eb505502bf24a01d66719084b44') - version('0.2.0', '32544f5a523f10fece6a127699e11245') + version('0.2.0', sha256='e1ca61e0307e6a2a2480bc0a1291a2c677110f34c3247d4773fdba7e95a6b573') version('0.1.6', sha256='035e343591b4595c571e17b0b3f526a01a23c3a47ebafb66f20ba667b29b3ed7') depends_on('java', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/miniamr/package.py b/var/spack/repos/builtin/packages/miniamr/package.py index ef1f7a20b86..d0d2d445f44 100644 --- a/var/spack/repos/builtin/packages/miniamr/package.py +++ b/var/spack/repos/builtin/packages/miniamr/package.py @@ -22,7 +22,7 @@ class Miniamr(MakefilePackage): version('1.4.3', sha256='4c3fbc1662ae3e139669fb3844134486a7488a0b6e085c3b24bebcc8d12d3ac6') version('1.4.2', sha256='d2347e0e22a8e79aa0dc3316b67dd7c40dded39d82f6e068e6fb8c9f0766566b') version('1.4.1', sha256='dd8e8d9fd0768cb4f2c5d7fe6989dfa6bb95a8461f04deaccdbb50b0dd51e97a') - version('1.4.0', '3aab0247047a94e343709cf2e51cc46e') + version('1.4.0', sha256='f0b959c90416288c5ab51ed86b6ba49bc8a319006c2a74a070c94133267edc6f') variant('mpi', default=True, description='Build with MPI support') diff --git a/var/spack/repos/builtin/packages/miniconda2/package.py b/var/spack/repos/builtin/packages/miniconda2/package.py index 0d33a5b77f5..e79d94528fd 100644 --- a/var/spack/repos/builtin/packages/miniconda2/package.py +++ b/var/spack/repos/builtin/packages/miniconda2/package.py @@ -15,10 +15,10 @@ class Miniconda2(Package): version('4.6.14', sha256='3e20425afa1a2a4c45ee30bd168b90ca30a3fdf8598b61cb68432886aadc6f4d', expand=False) version('4.5.11', sha256='0e23e8d0a1a14445f78960a66b363b464b889ee3b0e3f275b7ffb836df1cb0c6', expand=False) - version('4.5.4', '8a1c02f6941d8778f8afad7328265cf5', expand=False) - version('4.3.30', 'bd1655b4b313f7b2a1f2e15b7b925d03', expand=False) - version('4.3.14', '8cb075cf5462480980ef2373ad9fad38', expand=False) - version('4.3.11', 'd573980fe3b5cdf80485add2466463f5', expand=False) + version('4.5.4', sha256='77d95c99996495b9e44db3c3b7d7981143d32d5e9a58709c51d35bf695fda67d', expand=False) + version('4.3.30', sha256='0891000ca28359e63aa77e613c01f7a88855dedfc0ddc8be31829f3139318cf3', expand=False) + version('4.3.14', sha256='2dc629843be954fc747f08ffbcb973b5473f6818464b82a00260c38f687e02f1', expand=False) + version('4.3.11', sha256='fbc77646cc62e39f4aa5dd1dda1c94cc4e0bc3be580b10aa2ca2ae0013456a87', expand=False) def install(self, spec, prefix): # peel the name of the script out of the pathname of the diff --git a/var/spack/repos/builtin/packages/miniconda3/package.py b/var/spack/repos/builtin/packages/miniconda3/package.py index 28febf23d7c..3ad1f81b635 100644 --- a/var/spack/repos/builtin/packages/miniconda3/package.py +++ b/var/spack/repos/builtin/packages/miniconda3/package.py @@ -15,10 +15,10 @@ class Miniconda3(Package): version('4.6.14', sha256='0d6b23895a91294a4924bd685a3a1f48e35a17970a073cd2f684ffe2c31fc4be', expand=False) version('4.5.11', sha256='ea4594241e13a2671c5b158b3b813f0794fe58d514795fbf72a1aad24db918cf', expand=False) - version('4.5.4', 'a946ea1d0c4a642ddf0c3a26a18bb16d', expand=False) - version('4.3.30', '0b80a152332a4ce5250f3c09589c7a81', expand=False) - version('4.3.14', 'fc6fc37479e3e3fcf3f9ba52cae98991', expand=False) - version('4.3.11', '1924c8d9ec0abf09005aa03425e9ab1a', expand=False) + version('4.5.4', sha256='80ecc86f8c2f131c5170e43df489514f80e3971dd105c075935470bbf2476dea', expand=False) + version('4.3.30', sha256='66c822dfe76636b4cc2ae5604816e0e723aa01620f50087f06410ecf5bfdf38c', expand=False) + version('4.3.14', sha256='902f31a46b4a05477a9862485be5f84af761a444f8813345ff8dad8f6d3bccb2', expand=False) + version('4.3.11', sha256='b9fe70ce7b6fa8df05abfb56995959b897d0365299f5046063bc236843474fb8', expand=False) def install(self, spec, prefix): # peel the name of the script out of the pathname of the diff --git a/var/spack/repos/builtin/packages/minife/package.py b/var/spack/repos/builtin/packages/minife/package.py index 13d4d0153ff..c72b8cce484 100644 --- a/var/spack/repos/builtin/packages/minife/package.py +++ b/var/spack/repos/builtin/packages/minife/package.py @@ -16,7 +16,7 @@ class Minife(MakefilePackage): tags = ['proxy-app', 'ecp-proxy-app'] - version('2.1.0', '930a6b99c09722428a6f4d795b506a62') + version('2.1.0', sha256='59f4c56d73d2a758cba86939db2d36e12705282cb4174ce78223d984527f5d15') variant('build', default='ref', description='Type of Parallelism', values=('ref', 'openmp_ref', 'qthreads', 'kokkos')) diff --git a/var/spack/repos/builtin/packages/minighost/package.py b/var/spack/repos/builtin/packages/minighost/package.py index 6109a10e350..3af09fa8de4 100644 --- a/var/spack/repos/builtin/packages/minighost/package.py +++ b/var/spack/repos/builtin/packages/minighost/package.py @@ -20,7 +20,7 @@ class Minighost(MakefilePackage): tags = ['proxy-app'] - version('1.0.1', '2a4ac4383e9be00f87b6067c3cfe6463') + version('1.0.1', sha256='713f305559d892923cde0ad3cbc53c7cefc52a684f65275ccc9fb0b1d049cccc') variant('mpi', default=True, description='Enable MPI Support') diff --git a/var/spack/repos/builtin/packages/minigmg/package.py b/var/spack/repos/builtin/packages/minigmg/package.py index 2f96bf2c3b4..c1e4eece40a 100644 --- a/var/spack/repos/builtin/packages/minigmg/package.py +++ b/var/spack/repos/builtin/packages/minigmg/package.py @@ -25,7 +25,7 @@ class Minigmg(Package): homepage = "http://crd.lbl.gov/departments/computer-science/PAR/research/previous-projects/miniGMG/" url = "http://crd.lbl.gov/assets/Uploads/FTG/Projects/miniGMG/miniGMG.tar.gz" - version('master', '975a2a118403fc0024b5e04cef280e95') + version('master', sha256='1c2d27496a881f655f5e849d6a7a132625e535739f82575991c511cc2cf899ac') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py index 9682c1c6d6b..0159123cb55 100644 --- a/var/spack/repos/builtin/packages/minimap2/package.py +++ b/var/spack/repos/builtin/packages/minimap2/package.py @@ -14,9 +14,9 @@ class Minimap2(PythonPackage): homepage = "https://github.com/lh3/minimap2" url = "https://github.com/lh3/minimap2/releases/download/v2.2/minimap2-2.2.tar.bz2" - version('2.14', '9088b785bb0c33488ca3a27c8994648ce21a8be54cb117f5ecee26343facd03b') - version('2.10', '52b36f726ec00bfca4a2ffc23036d1a2b5f96f0aae5a92fd826be6680c481c20') - version('2.2', '5b68e094f4fa3dfbd9b37d5b654b7715') + version('2.14', sha256='9088b785bb0c33488ca3a27c8994648ce21a8be54cb117f5ecee26343facd03b') + version('2.10', sha256='52b36f726ec00bfca4a2ffc23036d1a2b5f96f0aae5a92fd826be6680c481c20') + version('2.2', sha256='7e8683aa74c4454a8cfe3821f405c4439082e24c152b4b834fdb56a117ecaed9') conflicts('target=aarch64:', when='@:2.10') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/minimd/package.py b/var/spack/repos/builtin/packages/minimd/package.py index b673d0bcd36..4ecaf1412dd 100644 --- a/var/spack/repos/builtin/packages/minimd/package.py +++ b/var/spack/repos/builtin/packages/minimd/package.py @@ -20,7 +20,7 @@ class Minimd(MakefilePackage): tags = ['proxy-app'] - version('1.2', '893ef1ca5062e32b43a8d11bcfe1a056') + version('1.2', sha256='2874d35b12a15f9e92137e6f2060c1150cff75f8a7b88b255daf130087e5901e') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/miniqmc/package.py b/var/spack/repos/builtin/packages/miniqmc/package.py index ece657cda0d..0da43dbfbf7 100644 --- a/var/spack/repos/builtin/packages/miniqmc/package.py +++ b/var/spack/repos/builtin/packages/miniqmc/package.py @@ -16,7 +16,7 @@ class Miniqmc(CMakePackage): version('0.4.0', sha256='41ddb5de6dcc85404344c80dc7538aedf5e1f1eb0f2a67ebac069209f7dd11e4') version('0.3.0', sha256='3ba494ba1055df91e157cb426d1fbe4192aa3f04b019277d9e571d057664d5a9') - version('0.2.0', 'b96bacaf48b8e9c0de05d04a95066bc1') + version('0.2.0', sha256='cdf6fc6df6ccc1e034c62f937c040bfd6a4e65a0974b95f6884edd004ae36ee4') tags = ['proxy-app', 'ecp-proxy-app'] diff --git a/var/spack/repos/builtin/packages/minisign/package.py b/var/spack/repos/builtin/packages/minisign/package.py old mode 100755 new mode 100644 index e1b2c114936..34d07d075ec --- a/var/spack/repos/builtin/packages/minisign/package.py +++ b/var/spack/repos/builtin/packages/minisign/package.py @@ -12,6 +12,6 @@ class Minisign(CMakePackage): homepage = "https://jedisct1.github.io/minisign/" url = "https://github.com/jedisct1/minisign/archive/0.7.tar.gz" - version('0.7', 'd634202555c4f499e8ef9d6848d6f4ca') + version('0.7', sha256='0c9f25ae647b6ba38cf7e6aea1da4e8fb20e1bc64ef0c679da737a38c8ad43ef') depends_on('libsodium') diff --git a/var/spack/repos/builtin/packages/minismac2d/package.py b/var/spack/repos/builtin/packages/minismac2d/package.py index 32f682d2f31..ded2ad08f2e 100644 --- a/var/spack/repos/builtin/packages/minismac2d/package.py +++ b/var/spack/repos/builtin/packages/minismac2d/package.py @@ -18,7 +18,7 @@ class Minismac2d(MakefilePackage): tags = ['proxy-app'] - version('2.0', '1bb1a52cea21bc9162bf7a71a6ddf37d') + version('2.0', sha256='ec01b74c06a2c0386efbbb61b14305327342a08fb92bf52e76f60a2063adf065') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/minitri/package.py b/var/spack/repos/builtin/packages/minitri/package.py index 3fb0184dfc5..fb2e5cb176a 100644 --- a/var/spack/repos/builtin/packages/minitri/package.py +++ b/var/spack/repos/builtin/packages/minitri/package.py @@ -12,7 +12,7 @@ class Minitri(MakefilePackage): homepage = "https://github.com/Mantevo/miniTri" url = "https://github.com/Mantevo/miniTri/archive/v1.0.tar.gz" - version('1.0', '947e296ca408275232f47724267a85ce') + version('1.0', sha256='e340dbb04b7c182804ebf6f5a946a392f1c68b7f798885c091c3f0d8aaa844ce') variant('mpi', default=True, description='Build with MPI support') diff --git a/var/spack/repos/builtin/packages/minixyce/package.py b/var/spack/repos/builtin/packages/minixyce/package.py index 7c914df1a04..b45761d1faa 100644 --- a/var/spack/repos/builtin/packages/minixyce/package.py +++ b/var/spack/repos/builtin/packages/minixyce/package.py @@ -17,7 +17,7 @@ class Minixyce(MakefilePackage): tags = ['proxy-app'] - version('1.0', '6fc0e5a561af0b8ff581d9f704194133') + version('1.0', sha256='40e3b4ed5c65cb1d210e828460e99b755cac922a7e27e70c687d5bb6ed19a21b') variant('mpi', default=True, description='Build with MPI Support') diff --git a/var/spack/repos/builtin/packages/minuit/package.py b/var/spack/repos/builtin/packages/minuit/package.py index 87104326fcb..7f38a88cb9c 100644 --- a/var/spack/repos/builtin/packages/minuit/package.py +++ b/var/spack/repos/builtin/packages/minuit/package.py @@ -13,26 +13,26 @@ class Minuit(AutotoolsPackage): url = "http://www.cern.ch/mathlibs/sw/5_34_14/Minuit2/Minuit2-5.34.14.tar.gz" list_url = "https://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/release/download.html" - version('5.34.14', '7fc00378a2ed1f731b719d4837d62d6a') - version('5.28.00', '536a1d29e5cc9bd4499d17d665021370') - version('5.27.02', 'b54673f2b9b62a8ff4e6937a2ed8fda5') - version('5.24.00', '9a915e56bee1e8986a719aa80e7b05d6') - version('5.22.00', '2cbc34907bfe202c7a779e9713355846') - version('5.21.06', 'b431ed129abb6c5020fd58d53cb8d27c') - version('5.20.00', '3083d31e3764de45d477d082d60f2c29') - version('5.18.00', 'a8764e7213fe811e56d5b6e5f3a91f5e') - version('5.16.00', '6ea5feca06fca365d324bcfe16db7f08') - version('5.14.00', 'b7452867b01c76cd115c696336c202d2') - version('5.12.00', '36726b8c6fcddf4f0837c900461a1d3c') - version('5.10.00', 'dfc7afc0add70deaca105ff549f5a786') - version('5.08.00', '1cc8da07c4a247c877f39acf8d76ba02') - version('1.7.9', '10fd518fc778317fdadbc4ef6f7ce8e4') - version('1.7.6', '6a9a8341557de154274caff810686364') - version('1.7.1', 'd202a1cf58662e9833f2967b4dc8808e') - version('1.6.3', '955f560d0fb17bd7f081eddd7080fad6') - version('1.6.0', '6992d70fc8fded50be49b6b358b58507') - version('1.5.2', '31a0698febe59edd70aa001c4d7a56f8') - version('1.5.0', 'bc502c66af071fcdc0a2ae45a8740c75') + version('5.34.14', sha256='2ca9a283bbc315064c0a322bc4cb74c7e8fd51f9494f7856e5159d0a0aa8c356') + version('5.28.00', sha256='c3d380b021f4f8e21cde9b73f7019a2aa94c4fcaf5af3f30151ef5f7bfcb23cb') + version('5.27.02', sha256='262e2a014f17dd54535b71efc69d1ee6318e6109a57dbe376b416247a031ad5e') + version('5.24.00', sha256='2e4df8de85eab97484424d1c10128c489948f0dbab4779c36195aa1a42d4b2c2') + version('5.22.00', sha256='9a64698e8c38a1ac88c98a023f423611f3a157fd9f63bf13671211d3c7a9d7c4') + version('5.21.06', sha256='4c12b35993c8ecf644043d3d876afb5537a702eb24771f57dbe55d5ea6f49d92') + version('5.20.00', sha256='c5afbfcf25cb4fb95f773f6611a46ec4f293ad2f3c3a3cd75f79ea5e226f62e4') + version('5.18.00', sha256='57f0a6079677d45f89ac7d1105bbcb28fe6f22609856f3225c582ff5209ada7e') + version('5.16.00', sha256='db840e4983de0cea9fa1e861cd3c373c5effd969ad88849b1dd0894f80a02717') + version('5.14.00', sha256='d38fc8477124b07ebf38fa3fe9f16e7fa070aefe700fce15454b2e749f89db8d') + version('5.12.00', sha256='c206033a723888a0a079fd0de05027460d99dca1d2b4eeb0ad0e7b60cea86236') + version('5.10.00', sha256='4f51eb73b0eed527cc2c6f860cc6e2a5d86bb84f37f3c6d8ca469ce6c1ae96c4') + version('5.08.00', sha256='cf5f2858f40933928738b4d204651dfdfdca8431111bb8b7300b3b43b9b5fa30') + version('1.7.9', sha256='a7b7fdf89267fe272ae336725c9f4b98e5ccc67ab666e34284a64ec977ee0e07') + version('1.7.6', sha256='1141e885eec53a0fa859581c160dee522876c65fc7396255ab9a0388622aedd8') + version('1.7.1', sha256='fe7255974969a7e329dd3ed2b934f502c80a6f74ffb85a311ea56a325cd7ca06') + version('1.6.3', sha256='17851717cd7e99c705bf3546641572064ef9485653c5741698ff760d34af7271') + version('1.6.0', sha256='d12259f53ed9957215c3cef11e2d0dce755f627bb3506172f25dcd7ce9950a24') + version('1.5.2', sha256='b0ed8d7d0071b1e8daa5a5dc4c05d522731617a5430a288b932edc331869c063') + version('1.5.0', sha256='b5fffdc1d06a2b4ffd6dad5fdd30d127ea354a789aaa9f25f33cf7c539898b7f') def url_for_version(self, version): if version > Version('5.0.0'): diff --git a/var/spack/repos/builtin/packages/mira/package.py b/var/spack/repos/builtin/packages/mira/package.py index d39479d8d43..a4c9b7d4a7f 100644 --- a/var/spack/repos/builtin/packages/mira/package.py +++ b/var/spack/repos/builtin/packages/mira/package.py @@ -13,7 +13,7 @@ class Mira(AutotoolsPackage): homepage = "http://sourceforge.net/projects/mira-assembler/" url = "https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2" - version('4.0.2', '1921b426910653a34a6dbb37346f28ea') + version('4.0.2', sha256='a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80') depends_on('boost@1.46:') depends_on('expat@2.0.1:') diff --git a/var/spack/repos/builtin/packages/mirdeep2/package.py b/var/spack/repos/builtin/packages/mirdeep2/package.py index 4fde162ae92..3de2fccf6b1 100644 --- a/var/spack/repos/builtin/packages/mirdeep2/package.py +++ b/var/spack/repos/builtin/packages/mirdeep2/package.py @@ -15,7 +15,7 @@ class Mirdeep2(Package): homepage = "https://www.mdc-berlin.de/8551903/en/" url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip" - version('0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483') + version('0.0.8', sha256='eeb24ee1b0e76b49ee2f542da3ee7d46d163c80b152709e963492b79f4fca1b8') depends_on('perl', type=('build', 'run')) depends_on('perl-pdf-api2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/mitofates/package.py b/var/spack/repos/builtin/packages/mitofates/package.py index 161c9dba860..e6140808b28 100644 --- a/var/spack/repos/builtin/packages/mitofates/package.py +++ b/var/spack/repos/builtin/packages/mitofates/package.py @@ -14,7 +14,7 @@ class Mitofates(Package): homepage = "http://mitf.cbrc.jp/MitoFates/cgi-bin/top.cgi" url = "http://mitf.cbrc.jp/MitoFates/program/MitoFates_1.2.tar.gz" - version('1.2', 'aaac42a8e8c7318a4abde9df3a4b72d1') + version('1.2', sha256='fafc93d8d619fe993ce747782d31ab9a89b248cd4f817e0242e4ceb5e33cf0a7') depends_on('libsvm') depends_on('perl', type='run') diff --git a/var/spack/repos/builtin/packages/mitos/package.py b/var/spack/repos/builtin/packages/mitos/package.py index 07eb0fbc6e9..414a074f473 100644 --- a/var/spack/repos/builtin/packages/mitos/package.py +++ b/var/spack/repos/builtin/packages/mitos/package.py @@ -15,7 +15,7 @@ class Mitos(CMakePackage): git = "https://github.com/llnl/Mitos.git" version('0.9.2', commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d') - version('0.9.1', 'c6cb57f3cae54f5157affd97ef7ef79e') + version('0.9.1', sha256='67abe227d2f9b4d2f235031b526d3ceb2c4792ad98772b1b1d5af0d227a795fc') depends_on('dyninst@8.2.1:') depends_on('hwloc') diff --git a/var/spack/repos/builtin/packages/mkfontdir/package.py b/var/spack/repos/builtin/packages/mkfontdir/package.py index f9f2a7afd12..fcf0b08e93e 100644 --- a/var/spack/repos/builtin/packages/mkfontdir/package.py +++ b/var/spack/repos/builtin/packages/mkfontdir/package.py @@ -14,7 +14,7 @@ class Mkfontdir(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/mkfontdir" url = "https://www.x.org/archive/individual/app/mkfontdir-1.0.7.tar.gz" - version('1.0.7', '52a5bc129f3f3ac54e7115608cec3cdc') + version('1.0.7', sha256='bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7') depends_on('mkfontscale', type='run') diff --git a/var/spack/repos/builtin/packages/mkfontscale/package.py b/var/spack/repos/builtin/packages/mkfontscale/package.py index 2d944ceb47b..3a78857e0b5 100644 --- a/var/spack/repos/builtin/packages/mkfontscale/package.py +++ b/var/spack/repos/builtin/packages/mkfontscale/package.py @@ -13,7 +13,7 @@ class Mkfontscale(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/mkfontscale" url = "https://www.x.org/archive/individual/app/mkfontscale-1.1.2.tar.gz" - version('1.1.2', 'fab4e1598b8948c124ec7a9f06d30e5b') + version('1.1.2', sha256='8bba59e60fbc4cb082092cf6b67e810b47b4fe64fbc77dbea1d7e7d55312b2e4') depends_on('libfontenc') depends_on('freetype') diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py index 5e116bd91bd..6ab1311309c 100644 --- a/var/spack/repos/builtin/packages/moab/package.py +++ b/var/spack/repos/builtin/packages/moab/package.py @@ -26,11 +26,11 @@ class Moab(AutotoolsPackage): # of MoAB to 5.0.2 set to current head of the master branch. version('5.0.2', commit='01d05b1805236ef44da36f67eb2701095f2e33c7') version('5.0.1', commit='6cc12bd4ae3fa7c9ad81c595e4d38fa84f0884be') - version('5.0.0', '1840ca02366f4d3237d44af63e239e3b') - version('4.9.2', '540931a604c180bbd3c1bb3ee8c51dd0') - version('4.9.1', '19cc2189fa266181ad9109b18d0b2ab8') - version('4.9.0', '40695d0a159040683cfa05586ad4a7c2') - version('4.8.2', '1dddd10f162fce3cfffaedc48f6f467d') + version('5.0.0', sha256='df5d5eb8c0d0dbb046de2e60aa611f276cbf007c9226c44a24ed19c570244e64') + version('4.9.2', sha256='26611b8cc24f6b7df52eb4ecbd31523d61523da0524b5a2d066a7656e2e82ac5') + version('4.9.1', sha256='b26cee46c096157323cafe047ad58616e16ebdb1e06caf6878673817cb4410cf') + version('4.9.0', sha256='267a7c05da847e4ea856db2c649a5484fb7bdc132ab56721ca50ee69a7389f4d') + version('4.8.2', sha256='b105cff42930058dc14eabb9a25e979df7289b175732fe319d2494e83e09e968') variant('mpi', default=True, description='enable mpi support') variant('hdf5', default=True, diff --git a/var/spack/repos/builtin/packages/modern-wheel/package.py b/var/spack/repos/builtin/packages/modern-wheel/package.py index 14b7a4b43ee..03e70290d86 100644 --- a/var/spack/repos/builtin/packages/modern-wheel/package.py +++ b/var/spack/repos/builtin/packages/modern-wheel/package.py @@ -15,9 +15,9 @@ class ModernWheel(CMakePackage): homepage = "https://github.com/alalazo/modern_wheel" url = "https://github.com/alalazo/modern_wheel/archive/1.2.tar.gz" - version('1.2', 'dc440099c52b6af3b8ddff6fd7730aff') - version('1.1', '289455239ad19497b7db55aacb299ca8') - version('1.0', '503dc3e7da2b422c4295e4afcba09dfb') + version('1.2', sha256='48612f698d7159f0eb10d93ddc3e2682b06a54d3a836ff227636be3261aed15e') + version('1.1', sha256='d8ba4891257b96108e9b9406a556f8ced3b71ce85c3fcdca6bfd9cc37bf010a3') + version('1.0', sha256='b90a1e29af0b67dfa4c07f9c19b2d04fa78cd878b29a9c42bc766dabd6cb1b90') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/mono/package.py b/var/spack/repos/builtin/packages/mono/package.py index 3928e7c1d42..69f0542deb1 100644 --- a/var/spack/repos/builtin/packages/mono/package.py +++ b/var/spack/repos/builtin/packages/mono/package.py @@ -33,10 +33,10 @@ class Mono(AutotoolsPackage): version('5.14.0.177', sha256='d4f5fa2e8188d66fbc8054f4145711e45c1faa6d070e63600efab93d1d189498') version('5.12.0.309', sha256='7c4738c91187bfcea7b40f9e7a4bf3a0e4f54fdc0f4472612f84803e8bed368f') version('5.10.1.57', sha256='76cbd8545db6adc5a1738c343d957a7015c95e1439c461ea4f2bd56bd6337ab4') - version('5.4.1.7', '28a82df5d0b7854b387d4f21d852ac70') - version('5.4.0.167', '103c7a737632046a9e9a0b039d752ee1') - version('5.0.1.1', '17692c7a797f95ee6f9a0987fda3d486') - version('4.8.0.524', 'baeed5b8139a85ad7e291d402a4bcccb') + version('5.4.1.7', sha256='543d9ec2ccebad9bb8425b22e10271f13d9512487c0e1578eeccdb1b8dc6a055') + version('5.4.0.167', sha256='c2afe51b0fb074936a8e7eaee805c352f37cbf1093bb41c5345078f77d913ce0') + version('5.0.1.1', sha256='48d6ae71d593cd01bf0f499de569359d45856cda325575e1bacb5fabaa7e9718') + version('4.8.0.524', sha256='ca02614cfc9fe65e310631cd611d7b07d1ff205ce193006d4be0f9919c26bdcf') def patch(self): if '+patch-folder-path' in self.spec: diff --git a/var/spack/repos/builtin/packages/mosh/package.py b/var/spack/repos/builtin/packages/mosh/package.py index 3c80db086bb..69ce155c8a8 100644 --- a/var/spack/repos/builtin/packages/mosh/package.py +++ b/var/spack/repos/builtin/packages/mosh/package.py @@ -16,9 +16,9 @@ class Mosh(AutotoolsPackage): homepage = "https://mosh.org/" url = "https://mosh.org/mosh-1.2.6.tar.gz" - version('1.3.2', '5122f4d2b973ab7c38dcdac8c35cb61e') - version('1.3.0', 'd961276995936953bf2d5a794068b076') - version('1.2.6', 'bb4e24795bb135a754558176a981ee9e') + version('1.3.2', sha256='da600573dfa827d88ce114e0fed30210689381bbdcff543c931e4d6a2e851216') + version('1.3.0', sha256='320e12f461e55d71566597976bd9440ba6c5265fa68fbf614c6f1c8401f93376') + version('1.2.6', sha256='7e82b7fbfcc698c70f5843bb960dadb8e7bd7ac1d4d2151c9d979372ea850e85') depends_on('protobuf') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/mothur/package.py b/var/spack/repos/builtin/packages/mothur/package.py index bd9fdea25a7..26235cb9a08 100644 --- a/var/spack/repos/builtin/packages/mothur/package.py +++ b/var/spack/repos/builtin/packages/mothur/package.py @@ -14,8 +14,8 @@ class Mothur(MakefilePackage): homepage = "https://github.com/mothur/mothur" url = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz" - version('1.40.5', 'd57847849fdb961c3f66c9b9fdf3057b') - version('1.39.5', '1f826ea4420e6822fc0db002c5940b92') + version('1.40.5', sha256='a0fbdfa68b966d7adc4560e3787506a0dad8b47b4b996c2663cd6c0b416d101a') + version('1.39.5', sha256='9f1cd691e9631a2ab7647b19eb59cd21ea643f29b22cde73d7f343372dfee342') depends_on('boost') depends_on('readline') diff --git a/var/spack/repos/builtin/packages/motif/package.py b/var/spack/repos/builtin/packages/motif/package.py index 87327968744..b15302c64c9 100644 --- a/var/spack/repos/builtin/packages/motif/package.py +++ b/var/spack/repos/builtin/packages/motif/package.py @@ -14,7 +14,7 @@ class Motif(AutotoolsPackage): homepage = "http://motif.ics.com/" url = "http://cfhcable.dl.sourceforge.net/project/motif/Motif%202.3.8%20Source%20Code/motif-2.3.8.tar.gz" - version('2.3.8', '7572140bb52ba21ec2f0c85b2605e2b1') + version('2.3.8', sha256='859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7') depends_on("flex") depends_on("libx11") diff --git a/var/spack/repos/builtin/packages/mount-point-attributes/package.py b/var/spack/repos/builtin/packages/mount-point-attributes/package.py index ea29c077c97..990cdd1b46f 100644 --- a/var/spack/repos/builtin/packages/mount-point-attributes/package.py +++ b/var/spack/repos/builtin/packages/mount-point-attributes/package.py @@ -13,7 +13,7 @@ class MountPointAttributes(AutotoolsPackage): homepage = "https://github.com/LLNL/MountPointAttributes" url = 'https://github.com/LLNL/MountPointAttributes/files/2270601/mountpointattr-1.1.tar.gz' - version('1.1', 'c9f0e7f5a3e16b9a022e5948712ecb2a') + version('1.1', sha256='bff84c75c47b74ea09b6cff949dd699b185ddba0463cb1ff39ab138003c96e02') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/mozjs/package.py b/var/spack/repos/builtin/packages/mozjs/package.py index fecf08292b2..bff5708a0f6 100644 --- a/var/spack/repos/builtin/packages/mozjs/package.py +++ b/var/spack/repos/builtin/packages/mozjs/package.py @@ -13,11 +13,11 @@ class Mozjs(AutotoolsPackage): homepage = "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/SpiderMonkey" - version('24.2.0', '5db79c10e049a2dc117a6e6a3bc78a8e', + version('24.2.0', sha256='e62f3f331ddd90df1e238c09d61a505c516fe9fd8c5c95336611d191d18437d8', url="http://ftp.mozilla.org/pub/js/mozjs-24.2.0.tar.bz2") - version('17.0.0', '20b6f8f1140ef6e47daa3b16965c9202', + version('17.0.0', sha256='321e964fe9386785d3bf80870640f2fa1c683e32fe988eeb201b04471c172fba', url="http://ftp.mozilla.org/pub/js/mozjs17.0.0.tar.gz") - version('1.8.5', 'a4574365938222adca0a6bd33329cb32', + version('1.8.5', sha256='5d12f7e1f5b4a99436685d97b9b7b75f094d33580227aa998c406bbae6f2a687', url="http://ftp.mozilla.org/pub/js/js185-1.0.0.tar.gz") depends_on('perl@5.6:', type='build') diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py index 216d8a2abd9..a8d3a30ab92 100644 --- a/var/spack/repos/builtin/packages/mpc/package.py +++ b/var/spack/repos/builtin/packages/mpc/package.py @@ -15,9 +15,9 @@ class Mpc(AutotoolsPackage): url = "https://ftpmirror.gnu.org/mpc/mpc-1.1.0.tar.gz" list_url = "http://www.multiprecision.org/mpc/download.html" - version('1.1.0', '4125404e41e482ec68282a2e687f6c73') - version('1.0.3', 'd6a1d5f8ddea3abd2cc3e98f58352d26') - version('1.0.2', '68fadff3358fb3e7976c7a398a0af4c3') + version('1.1.0', sha256='6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e') + version('1.0.3', sha256='617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3') + version('1.0.2', sha256='b561f54d8a479cee3bc891ee52735f18ff86712ba30f036f8b8537bae380c488') # Could also be built against mpir instead depends_on('gmp@4.3.2:') diff --git a/var/spack/repos/builtin/packages/mpe2/package.py b/var/spack/repos/builtin/packages/mpe2/package.py index 5b317761195..e185e42c0b6 100644 --- a/var/spack/repos/builtin/packages/mpe2/package.py +++ b/var/spack/repos/builtin/packages/mpe2/package.py @@ -12,7 +12,7 @@ class Mpe2(AutotoolsPackage): homepage = "http://www.mcs.anl.gov/research/projects/perfvis/software/MPE/" url = "http://ftp.mcs.anl.gov/pub/mpi/mpe/mpe2-1.3.0.tar.gz" - version('1.3.0', '67bf0c7b2e573df3ba0d2059a96c2f7b') + version('1.3.0', sha256='0faf32f9adab6fd882be30be913089ebf75272f8b5e4a012bb20c54abc21c0be') patch('mpe2.patch') diff --git a/var/spack/repos/builtin/packages/mpest/package.py b/var/spack/repos/builtin/packages/mpest/package.py index 09174e79fdc..e1ecca84f94 100644 --- a/var/spack/repos/builtin/packages/mpest/package.py +++ b/var/spack/repos/builtin/packages/mpest/package.py @@ -13,7 +13,7 @@ class Mpest(MakefilePackage): homepage = "http://faculty.franklin.uga.edu/lliu/content/mp-est" url = "https://faculty.franklin.uga.edu/lliu/sites/faculty.franklin.uga.edu.lliu/files/mpest_1.5.zip" - version('1.5', 'f176d5301aa26567918664e5e30027d1') + version('1.5', sha256='536895120fc34b19b0740c7fef6467b74c284ae4f1f29c9f5fc5c633f30e4916') @property def build_directory(self): diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py index e0fd6885d3a..97436ccaf18 100644 --- a/var/spack/repos/builtin/packages/mpfr/package.py +++ b/var/spack/repos/builtin/packages/mpfr/package.py @@ -14,13 +14,13 @@ class Mpfr(AutotoolsPackage): url = "https://ftpmirror.gnu.org/mpfr/mpfr-4.0.2.tar.bz2" version('4.0.2', sha256='c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc') - version('4.0.1', '8c21d8ac7460493b2b9f3ef3cc610454') - version('4.0.0', 'ef619f3bb68039e35c4a219e06be72d0') - version('3.1.6', '320c28198def956aeacdb240b46b8969') - version('3.1.5', 'b1d23a55588e3b2a13e3be66bc69fd8d') - version('3.1.4', 'b8a2f6b0e68bef46e53da2ac439e1cf4') - version('3.1.3', '5fdfa3cfa5c86514ee4a241a1affa138') - version('3.1.2', 'ee2c3ac63bf0c2359bf08fc3ee094c19') + version('4.0.1', sha256='a4d97610ba8579d380b384b225187c250ef88cfe1d5e7226b89519374209b86b') + version('4.0.0', sha256='6aa31fbf3bd1f9f95bcfa241590a9d11cb0f874e2bb93b99c9e2de8eaea6d5fd') + version('3.1.6', sha256='cf4f4b2d80abb79e820e78c8077b6725bbbb4e8f41896783c899087be0e94068') + version('3.1.5', sha256='ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658') + version('3.1.4', sha256='d3103a80cdad2407ed581f3618c4bed04e0c92d1cf771a65ead662cc397f7775') + version('3.1.3', sha256='f63bb459157cacd223caac545cb816bcdb5a0de28b809e7748b82e9eb89b0afd') + version('3.1.2', sha256='79c73f60af010a30a5c27a955a1d2d01ba095b72537dab0ecaad57f5a7bb1b6b') # mpir is a drop-in replacement for gmp depends_on('gmp@4.1:') # 4.2.3 or higher is recommended diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpibash/package.py index e06c3d054bc..174109f6d9d 100644 --- a/var/spack/repos/builtin/packages/mpibash/package.py +++ b/var/spack/repos/builtin/packages/mpibash/package.py @@ -12,7 +12,7 @@ class Mpibash(AutotoolsPackage): homepage = "https://github.com/lanl/MPI-Bash" url = "https://github.com/lanl/MPI-Bash/releases/download/v1.2/mpibash-1.2.tar.gz" - version('1.2', 'b81001fb234ed79c4e5bf2f7efee3529') + version('1.2', sha256='5c2faaa74464111205dbae4799bd89c2425810ec3708d004237b42d620c8be57') depends_on('bash@4.4:') # uses MPI_Exscan which is in MPI-1.2 and later diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 230974294c9..5b92fbafee4 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -19,16 +19,16 @@ class Mpich(AutotoolsPackage): list_depth = 1 version('develop', submodules=True) - version('3.3.1', 'fe551ef29c8eea8978f679484441ed8bb1d943f6ad25b63c235d4b9243d551e5') - version('3.3', '574af413dc0dc7fbb929a761822beb06') - version('3.2.1', 'e175452f4d61646a52c73031683fc375') - version('3.2', 'f414cfa77099cd1fa1a5ae4e22db508a') - version('3.1.4', '2ab544607986486562e076b83937bba2') - version('3.1.3', '93cb17f91ac758cbf9174ecb03563778') - version('3.1.2', '7fbf4b81dcb74b07ae85939d1ceee7f1') - version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7') - version('3.1', '5643dd176499bfb7d25079aaff25f2ec') - version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') + version('3.3.1', sha256='fe551ef29c8eea8978f679484441ed8bb1d943f6ad25b63c235d4b9243d551e5') + version('3.3', sha256='329ee02fe6c3d101b6b30a7b6fb97ddf6e82b28844306771fa9dd8845108fa0b') + version('3.2.1', sha256='5db53bf2edfaa2238eb6a0a5bc3d2c2ccbfbb1badd79b664a1a919d2ce2330f1') + version('3.2', sha256='0778679a6b693d7b7caff37ff9d2856dc2bfc51318bf8373859bfa74253da3dc') + version('3.1.4', sha256='f68b5330e94306c00ca5a1c0e8e275c7f53517d01d6c524d51ce9359d240466b') + version('3.1.3', sha256='afb690aa828467721e9d9ab233fe00c68cae2b7b930d744cb5f7f3eb08c8602c') + version('3.1.2', sha256='37c3ba2d3cd3f4ea239497d9d34bd57a663a34e2ea25099c2cbef118c9156587') + version('3.1.1', sha256='455ccfaf4ec724d2cf5d8bff1f3d26a958ad196121e7ea26504fd3018757652d') + version('3.1', sha256='fcf96dbddb504a64d33833dc455be3dda1e71c7b3df411dfcf9df066d7c32c39') + version('3.0.4', sha256='cf638c85660300af48b6f776e5ecd35b5378d5905ec5d34c3da7a27da0acf0b3') variant('hydra', default=True, description='Build the hydra process manager') variant('romio', default=True, description='Enable ROMIO MPI I/O implementation') diff --git a/var/spack/repos/builtin/packages/mpifileutils/package.py b/var/spack/repos/builtin/packages/mpifileutils/package.py index 54f7bd90551..e547a38a7a6 100644 --- a/var/spack/repos/builtin/packages/mpifileutils/package.py +++ b/var/spack/repos/builtin/packages/mpifileutils/package.py @@ -23,10 +23,10 @@ class Mpifileutils(Package): version('develop', branch='master') version('0.9.1', sha256='15a22450f86b15e7dc4730950b880fda3ef6f59ac82af0b268674d272aa61c69') version('0.9', sha256='1b8250af01aae91c985ca5d61521bfaa4564e46efa15cee65cd0f82cf5a2bcfb') - version('0.8.1', 'acbd5b5c15919a67392509614bb7871e') - version('0.8', '1082600e7ac4e6b2c13d91bbec40cffb') - version('0.7', 'c081f7f72c4521dddccdcf9e087c5a2b') - version('0.6', '620bcc4966907481f1b1a965b28fc9bf') + version('0.8.1', md5='acbd5b5c15919a67392509614bb7871e') + version('0.8', md5='1082600e7ac4e6b2c13d91bbec40cffb') + version('0.7', md5='c081f7f72c4521dddccdcf9e087c5a2b') + version('0.6', md5='620bcc4966907481f1b1a965b28fc9bf') conflicts('platform=darwin') diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py index c710ed1ed17..4f4d5c006d1 100644 --- a/var/spack/repos/builtin/packages/mpip/package.py +++ b/var/spack/repos/builtin/packages/mpip/package.py @@ -12,7 +12,7 @@ class Mpip(AutotoolsPackage): homepage = "http://mpip.sourceforge.net/" url = "http://downloads.sourceforge.net/project/mpip/mpiP/mpiP-3.4.1/mpiP-3.4.1.tar.gz" - version("3.4.1", "1168adc83777ac31d6ebd385823aabbd") + version("3.4.1", sha256="688bf37d73211e6a915f9fc59c358282a266d166c0a10af07a38a01a473296f0") depends_on("elf") depends_on("libdwarf") diff --git a/var/spack/repos/builtin/packages/mpir/package.py b/var/spack/repos/builtin/packages/mpir/package.py index f662e75fbdc..06b6db7e272 100644 --- a/var/spack/repos/builtin/packages/mpir/package.py +++ b/var/spack/repos/builtin/packages/mpir/package.py @@ -14,8 +14,8 @@ class Mpir(Package): git = "https://github.com/wbhart/mpir.git" version('develop', branch='master') - version('2.7.0', '985b5d57bd0e74c74125ee885b9c8f71') - version('2.6.0', 'ec17d6a7e026114ceb734b2466aa0a91') + version('2.7.0', sha256='2d0174aaccff918766215df00420f12929a6c376ab4e558af31f57c55193bcb7') + version('2.6.0', sha256='dedb336098d41d4e298909586cf351003bcd7aad9317e801f3e4c4838f6d7691') # This setting allows mpir to act as a drop-in replacement for gmp variant('gmp_compat', default=False, diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py index 3169341a948..6cdbef3130f 100644 --- a/var/spack/repos/builtin/packages/mrnet/package.py +++ b/var/spack/repos/builtin/packages/mrnet/package.py @@ -16,9 +16,9 @@ class Mrnet(AutotoolsPackage): version('5.0.1-3', branch='master') version('5.0.1-2', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9') - version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd') - version('4.1.0', '5a248298b395b329e2371bf25366115c') - version('4.0.0', 'd00301c078cba57ef68613be32ceea2f') + version('5.0.1', sha256='df0bab4c4c462d0c32df4fd97bf2546f32439f31ca96b54ebbbadd33dd6bc107') + version('4.1.0', sha256='94758191ac46a9dbfea931a8e61167fe7e8a5f880caa418305c44f1d12af5e45') + version('4.0.0', sha256='7207c6d493b3f17c386667cfefa81364c96b9c8b831c67442d218d77813c5d38') variant('cti', default=False, description="Build the MRNet with the CTI startup option") diff --git a/var/spack/repos/builtin/packages/mscgen/package.py b/var/spack/repos/builtin/packages/mscgen/package.py index b56ba0933a7..34a3d921b40 100644 --- a/var/spack/repos/builtin/packages/mscgen/package.py +++ b/var/spack/repos/builtin/packages/mscgen/package.py @@ -15,7 +15,7 @@ class Mscgen(AutotoolsPackage): homepage = "http://www.mcternan.me.uk/mscgen/" url = "http://www.mcternan.me.uk/mscgen/software/mscgen-src-0.20.tar.gz" - version('0.20', '65c90fb5150d7176b65b793f0faa7377') + version('0.20', sha256='3c3481ae0599e1c2d30b7ed54ab45249127533ab2f20e768a0ae58d8551ddc23') depends_on('flex') depends_on('bison') diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py index 16b1eee71fa..114c760a3f5 100644 --- a/var/spack/repos/builtin/packages/msgpack-c/package.py +++ b/var/spack/repos/builtin/packages/msgpack-c/package.py @@ -11,8 +11,8 @@ class MsgpackC(CMakePackage): homepage = "http://www.msgpack.org" url = "https://github.com/msgpack/msgpack-c/archive/cpp-3.0.1.tar.gz" - version('3.0.1', 'a79f05f0dc5637c161805d6c0e9bfbe7') - version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0') + version('3.0.1', sha256='1b834ab0b5b41da1dbfb96dd4a673f6de7e79dbd7f212f45a553ff9cc54abf3b') + version('1.4.1', sha256='74324d696f9abb75d8a7cd5e77add5062592b7eac386c8102de78a6cc5309886') depends_on('cmake@2.8.12:', type='build') depends_on('googletest', type='test') diff --git a/var/spack/repos/builtin/packages/multitail/package.py b/var/spack/repos/builtin/packages/multitail/package.py index 0f6cd8a46bd..ab35455be1c 100644 --- a/var/spack/repos/builtin/packages/multitail/package.py +++ b/var/spack/repos/builtin/packages/multitail/package.py @@ -13,7 +13,7 @@ class Multitail(MakefilePackage): homepage = "https://www.vanheusden.com/multitail/index.php" url = "https://www.vanheusden.com/multitail/multitail-6.4.2.tgz" - version('6.4.2', 'a0959f7b2385061080712afd8ae6e33d') + version('6.4.2', sha256='af1d5458a78ad3b747c5eeb135b19bdca281ce414cefdc6ea0cff6d913caa1fd') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/multiverso/package.py b/var/spack/repos/builtin/packages/multiverso/package.py index 444a8ceaf88..c38696dba98 100644 --- a/var/spack/repos/builtin/packages/multiverso/package.py +++ b/var/spack/repos/builtin/packages/multiverso/package.py @@ -16,7 +16,7 @@ class Multiverso(CMakePackage): version('master', branch='master') version('143187', commit='143187575d1cfa410100037b8aea2e767e0af637') - version('0.2', '483ca7524fea14a311389e421f2bc098') + version('0.2', sha256='40e86543968faa2fe203cf0b004a4c7905303db0c860efe4ce4e1f27e46394fc') depends_on('mpi') depends_on('boost') diff --git a/var/spack/repos/builtin/packages/mummer/package.py b/var/spack/repos/builtin/packages/mummer/package.py index b70599f4a6d..7b8a3ca51e0 100644 --- a/var/spack/repos/builtin/packages/mummer/package.py +++ b/var/spack/repos/builtin/packages/mummer/package.py @@ -12,7 +12,7 @@ class Mummer(Package): homepage = "http://mummer.sourceforge.net/" url = "https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download" - version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2') + version('3.23', sha256='1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f') depends_on('gnuplot') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 9b1928c69c5..48e8cca29e7 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -15,13 +15,13 @@ class Mumps(Package): homepage = "http://mumps.enseeiht.fr" url = "http://mumps.enseeiht.fr/MUMPS_5.0.1.tar.gz" - version('5.2.0', '41f2c7cb20d69599fb47e2ad6f628f3798c429f49e72e757e70722680f70853f') - version('5.1.2', 'eb345cda145da9aea01b851d17e54e7eef08e16bfa148100ac1f7f046cd42ae9') - version('5.1.1', 'f15c6b5dd8c71b1241004cd19818259d') - version('5.0.2', '591bcb2c205dcb0283872608cdf04927') + version('5.2.0', sha256='41f2c7cb20d69599fb47e2ad6f628f3798c429f49e72e757e70722680f70853f') + version('5.1.2', sha256='eb345cda145da9aea01b851d17e54e7eef08e16bfa148100ac1f7f046cd42ae9') + version('5.1.1', sha256='a2a1f89c470f2b66e9982953cbd047d429a002fab9975400cef7190d01084a06') + version('5.0.2', sha256='77292b204942640256097a3da482c2abcd1e0d5a74ecd1d4bab0f5ef6e60fe45') # Alternate location if main server is down. - # version('5.0.1', 'b477573fdcc87babe861f62316833db0', url='http://pkgs.fedoraproject.org/repo/pkgs/MUMPS/MUMPS_5.0.1.tar.gz/md5/b477573fdcc87babe861f62316833db0/MUMPS_5.0.1.tar.gz') - version('5.0.1', 'b477573fdcc87babe861f62316833db0') + # version('5.0.1', sha256='50355b2e67873e2239b4998a46f2bbf83f70cdad6517730ab287ae3aae9340a0', url='http://pkgs.fedoraproject.org/repo/pkgs/MUMPS/MUMPS_5.0.1.tar.gz/md5/b477573fdcc87babe861f62316833db0/MUMPS_5.0.1.tar.gz') + version('5.0.1', sha256='50355b2e67873e2239b4998a46f2bbf83f70cdad6517730ab287ae3aae9340a0') variant('mpi', default=True, description='Compile MUMPS with MPI support') diff --git a/var/spack/repos/builtin/packages/munge/package.py b/var/spack/repos/builtin/packages/munge/package.py index bfd37b4af9b..d56768d29fd 100644 --- a/var/spack/repos/builtin/packages/munge/package.py +++ b/var/spack/repos/builtin/packages/munge/package.py @@ -11,9 +11,9 @@ class Munge(AutotoolsPackage): """ MUNGE Uid 'N' Gid Emporium """ homepage = "https://code.google.com/p/munge/" url = "https://github.com/dun/munge/releases/download/munge-0.5.13/munge-0.5.13.tar.xz" - version('0.5.13', '9204f34aac7f0cc50880196f4a8f5f33') - version('0.5.12', '84ffef069af93caea4b4c06f183b99c0') - version('0.5.11', 'bd8fca8d5f4c1fcbef1816482d49ee01', + version('0.5.13', sha256='99753dfd06a4f063c36f3fb0eb1964f394feb649937d94c4734d85b7964144da') + version('0.5.12', sha256='e972e3c3e947995a99e023f5758047db16cfe2f0c2c9ca76399dc1511fa71be8') + version('0.5.11', sha256='8e075614f81cb0a6df21a0aafdc825498611a04429d0876f074fc828739351a5', url='https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py index d7538178487..46a066d393e 100644 --- a/var/spack/repos/builtin/packages/muparser/package.py +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -11,10 +11,10 @@ class Muparser(Package): homepage = "http://muparser.beltoforion.de/" url = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz" - version('2.2.6.1', '410d29b4c58d1cdc2fc9ed1c1c7f67fe') + version('2.2.6.1', sha256='d2562853d972b6ddb07af47ce8a1cdeeb8bb3fa9e8da308746de391db67897b3') # 2.2.6 presents itself as 2.2.5, don't add it to Spack - # version('2.2.6', 'f197b2815ca0422b2091788a78f2dc8a') - version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7') + # version('2.2.6', md5='f197b2815ca0422b2091788a78f2dc8a') + version('2.2.5', sha256='0666ef55da72c3e356ca85b6a0084d56b05dd740c3c21d26d372085aa2c6e708') # Replace std::auto_ptr by std::unique_ptr # https://github.com/beltoforion/muparser/pull/46 diff --git a/var/spack/repos/builtin/packages/muscle/package.py b/var/spack/repos/builtin/packages/muscle/package.py index 114aef8e31a..f1d5a71a16a 100644 --- a/var/spack/repos/builtin/packages/muscle/package.py +++ b/var/spack/repos/builtin/packages/muscle/package.py @@ -14,7 +14,7 @@ class Muscle(MakefilePackage): homepage = "http://drive5.com/muscle/" url = "http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz" - version('3.8.1551', '1b7c9661f275a82d3cf708f923736bf8') + version('3.8.1551', sha256='c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e') def edit(self, spec, prefix): makefile = FileFilter('Makefile') diff --git a/var/spack/repos/builtin/packages/muse/package.py b/var/spack/repos/builtin/packages/muse/package.py index eb4685a2f65..7481435bd23 100644 --- a/var/spack/repos/builtin/packages/muse/package.py +++ b/var/spack/repos/builtin/packages/muse/package.py @@ -12,7 +12,7 @@ class Muse(MakefilePackage): homepage = "http://bioinformatics.mdanderson.org/main/MuSE" url = "https://github.com/danielfan/MuSE/archive/v1.0-rc.tar.gz" - version('1.0-rc', 'c63fdb48c041f6f9545879f1a7e4da58') + version('1.0-rc', sha256='b48b8be0044a2249bdc0b625fe0192c65089c598bbd1b1142902dfa81e804023') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py index 8aa8265b95b..a2a733e9666 100644 --- a/var/spack/repos/builtin/packages/muster/package.py +++ b/var/spack/repos/builtin/packages/muster/package.py @@ -16,8 +16,8 @@ class Muster(CMakePackage): homepage = "https://github.com/llnl/muster" url = "https://github.com/llnl/muster/archive/v1.0.tar.gz" - version('1.0.1', 'd709787db7e080447afb6571ac17723c') - version('1.0', '2eec6979a4a36d3a65a792d12969be16') + version('1.0.1', sha256='71e2fcdd7abf7ae5cc648a5f310e1c5369e4889718eab2a045e747c590d2dd71') + version('1.0', sha256='370a670419e391494fcca0294882ee5f83c5d8af94ca91ac4182235332bd56d6') depends_on('boost') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/mutationpp/package.py b/var/spack/repos/builtin/packages/mutationpp/package.py index 3a9191c22f4..26eabdf8c11 100644 --- a/var/spack/repos/builtin/packages/mutationpp/package.py +++ b/var/spack/repos/builtin/packages/mutationpp/package.py @@ -17,8 +17,8 @@ class Mutationpp(CMakePackage): homepage = "https://github.com/mutationpp/Mutationpp" url = "https://github.com/mutationpp/Mutationpp/archive/v0.3.1.tar.gz" - version('1.0.0', '928df99accd1a02706a57246edeef8ebbf3bd91bb40492258ee18b810a7e0194') - version('0.3.1', 'a6da2816e145ac9fcfbd8920595b7f65ce7bc8df0bec572b32647720758cbe69') + version('1.0.0', sha256='928df99accd1a02706a57246edeef8ebbf3bd91bb40492258ee18b810a7e0194') + version('0.3.1', sha256='a6da2816e145ac9fcfbd8920595b7f65ce7bc8df0bec572b32647720758cbe69') variant('fortran', default=True, description='Enable Fortran interface') variant('data', default=True, description='Install default model data') diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index 8ca06ed8c5a..e0d4aff45ff 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -17,12 +17,12 @@ class Mvapich2(AutotoolsPackage): # Prefer the latest stable release version('2.3.1', sha256='314e12829f75f3ed83cd4779a972572d1787aac6543a3d024ea7c6080e0ee3bf', preferred=True) version('2.3', sha256='01d5fb592454ddd9ecc17e91c8983b6aea0e7559aa38f410b111c8ef385b50dd') - version('2.3rc2', '6fcf22fe2a16023b462ef57614daa357') - version('2.3rc1', '386d79ae36b2136d203826465ad8b6cc') - version('2.3a', '87c3fbf8a755b53806fa9ecb21453445') - version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e') - version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6') - version('2.0', '9fbb68a4111a8b6338e476dc657388b4') + version('2.3rc2', sha256='dc3801f879a54358d17002a56afd45186e2e83edc5b8367b5c317e282eb6d6bf') + version('2.3rc1', sha256='607d309c864a6d57f5fa78fe6dd02368919736b8be0f4ddb938aba303ef9c45c') + version('2.3a', sha256='7f0bc94265de9f66af567a263b1be6ef01755f7f6aedd25303d640cc4d8b1cff') + version('2.2', sha256='791a6fc2b23de63b430b3e598bf05b1b25b82ba8bf7e0622fc81ba593b3bb131') + version('2.1', sha256='49f3225ad17d2f3b6b127236a0abdc979ca8a3efb8d47ab4b6cd4f5252d05d29') + version('2.0', md5='9fbb68a4111a8b6338e476dc657388b4') provides('mpi') provides('mpi@:3.0') diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py index 73ddd197ee9..718284c0fc1 100644 --- a/var/spack/repos/builtin/packages/mxml/package.py +++ b/var/spack/repos/builtin/packages/mxml/package.py @@ -15,12 +15,12 @@ class Mxml(AutotoolsPackage): homepage = "http://michaelrsweet.github.io/mxml/" url = "https://github.com/michaelrsweet/mxml/releases/download/release-2.10/mxml-2.10.tar.gz" - version('2.10', '8804c961a24500a95690ef287d150abe') - version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19') - version('2.8', 'd85ee6d30de053581242c4a86e79a5d2') - version('2.7', '76f2ae49bf0f5745d5cb5d9507774dc9') - version('2.6', '68977789ae64985dddbd1a1a1652642e') - version('2.5', 'f706377fba630b39fa02fd63642b17e5') + version('2.10', sha256='267ff58b64ddc767170d71dab0c729c06f45e1df9a9b6f75180b564f09767891') + version('2.9', sha256='cded54653c584b24c4a78a7fa1b3b4377d49ac4f451ddf170ebbc8161d85ff92') + version('2.8', sha256='0c9369f91a718d82e32cb007c0bd41b6642822c9a0ffe1d10eccbdea9a3011d5') + version('2.7', md5='76f2ae49bf0f5745d5cb5d9507774dc9') + version('2.6', md5='68977789ae64985dddbd1a1a1652642e') + version('2.5', md5='f706377fba630b39fa02fd63642b17e5') def url_for_version(self, version): if version <= Version('2.7'): diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py index 9495bbc74d3..db5946e59ce 100644 --- a/var/spack/repos/builtin/packages/mxnet/package.py +++ b/var/spack/repos/builtin/packages/mxnet/package.py @@ -13,13 +13,13 @@ class Mxnet(MakefilePackage): homepage = "http://mxnet.io" url = "https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz" - version('1.3.0', 'c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2', + version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2', url='https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz') - version('0.10.0.post2', '7819d511cf4a6efad681e6662fa966e4', + version('0.10.0.post2', md5='7819d511cf4a6efad681e6662fa966e4', url="https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz") - version('0.10.0.post1', '16d540f407cd22285555b3ab22040032', + version('0.10.0.post1', md5='16d540f407cd22285555b3ab22040032', url="https://github.com/apache/incubator-mxnet/archive/v0.10.0.post1.tar.gz") - version('0.10.0', '2d0c83c33eda729932d620cca3078826', + version('0.10.0', md5='2d0c83c33eda729932d620cca3078826', url="https://github.com/apache/incubator-mxnet/archive/v0.10.0.tar.gz") variant('cuda', default=False, description='Enable CUDA support') diff --git a/var/spack/repos/builtin/packages/mysql/package.py b/var/spack/repos/builtin/packages/mysql/package.py index 9c5656ad974..ec5d7d183da 100644 --- a/var/spack/repos/builtin/packages/mysql/package.py +++ b/var/spack/repos/builtin/packages/mysql/package.py @@ -18,12 +18,12 @@ class Mysql(CMakePackage): version('8.0.14', sha256='bc53f4c914fb39650289700d144529121d71f38399d2d24a0f5c76e5a8abd204') version('8.0.13', sha256='d85eb7f98b6aa3e2c6fe38263bf40b22acb444a4ce1f4668473e9e59fb98d62e') version('8.0.12', sha256='69f16e20834dbc60cb28d6df7351deda323330b9de685d22415f135bcedd1b20') - version('8.0.11', '38d5a5c1a1eeed1129fec3a999aa5efd') + version('8.0.11', sha256='3bde3e30d5d4afcedfc6db9eed5c984237ac7db9480a9cc3bddc026d50700bf9') version('5.7.26', sha256='5f01d579a20199e06fcbc28f0801c3cb545a54a2863ed8634f17fe526480b9f1') version('5.7.25', sha256='53751c6243806103114567c1a8b6a3ec27f23c0e132f377a13ce1eb56c63723f') version('5.7.24', sha256='05bf0c92c6a97cf85b67fff1ac83ca7b3467aea2bf306374d727fa4f18431f87') version('5.7.23', sha256='0730f2d5520bfac359e9272da6c989d0006682eacfdc086a139886c0741f6c65') - version('5.7.22', '269935a8b72dcba2c774d8d63a8bd1dd') + version('5.7.22', sha256='4eb8405b0a9acb0381eae94c1741b2850dfc6467742b24b676e62b566409cff2') version('5.7.21', sha256='fa205079c27a39c24f3485e7498dd0906a6e0b379b4f99ebc0ec38a9ec5b09b7') version('5.7.20', sha256='5397549bb7c238f396c123db2df4cad2191b11adf8986de7fe63bff8e2786487') version('5.7.19', sha256='3e51e76f93179ca7b165a7008a6cc14d56195b3aef35d26d3ac194333d291eb1') diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py index 19a085ab571..267f7062d0d 100644 --- a/var/spack/repos/builtin/packages/nag/package.py +++ b/var/spack/repos/builtin/packages/nag/package.py @@ -11,9 +11,9 @@ class Nag(Package): """The NAG Fortran Compiler.""" homepage = "http://www.nag.com/nagware/np.asp" - version('6.2', '8b119cc3296969bbd68b781f625de272') - version('6.1', '9b3cc0f8703c79f6231ae12359535119') - version('6.0', '3fa1e7f7b51ef8a23e6c687cdcad9f96') + version('6.2', md5='8b119cc3296969bbd68b781f625de272') + version('6.1', sha256='32580e0004e6798abf1fa52f0070281b28abeb0da2387530a4cc41218e813c7c') + version('6.0', md5='3fa1e7f7b51ef8a23e6c687cdcad9f96') # Licensing license_required = True diff --git a/var/spack/repos/builtin/packages/nanoflann/package.py b/var/spack/repos/builtin/packages/nanoflann/package.py index d2fe6f642b8..371df53487e 100644 --- a/var/spack/repos/builtin/packages/nanoflann/package.py +++ b/var/spack/repos/builtin/packages/nanoflann/package.py @@ -13,7 +13,7 @@ class Nanoflann(CMakePackage): homepage = "https://github.com/jlblancoc/nanoflann" url = "https://github.com/jlblancoc/nanoflann/archive/v1.2.3.tar.gz" - version('1.2.3', '92a0f44a631c41aa06f9716c51dcdb11') + version('1.2.3', sha256='5ef4dfb23872379fe9eb306aabd19c9df4cae852b72a923af01aea5e8d7a59c3') def patch(self): filter_file('-mtune=native', '', 'CMakeLists.txt') diff --git a/var/spack/repos/builtin/packages/nanopb/package.py b/var/spack/repos/builtin/packages/nanopb/package.py index 275832f4397..75726c37e4a 100644 --- a/var/spack/repos/builtin/packages/nanopb/package.py +++ b/var/spack/repos/builtin/packages/nanopb/package.py @@ -13,7 +13,7 @@ class Nanopb(CMakePackage): homepage = "https://jpa.kapsi.fi/nanopb/" url = "https://github.com/nanopb/nanopb/archive/0.3.9.1.tar.gz" - version('0.3.9.1', '08d71b315819626366b0303f8658fc68') + version('0.3.9.1', sha256='b22d1f86d4adb2aa0436a277c4a59a5adfc467cafeb9bf405c27ef136599bbb3') depends_on('protobuf', type=('build')) depends_on('py-protobuf', type=('build')) diff --git a/var/spack/repos/builtin/packages/nasm/package.py b/var/spack/repos/builtin/packages/nasm/package.py index 0000db97652..aa64098be3a 100644 --- a/var/spack/repos/builtin/packages/nasm/package.py +++ b/var/spack/repos/builtin/packages/nasm/package.py @@ -16,8 +16,8 @@ class Nasm(AutotoolsPackage): list_depth = 1 version('2.14.02', sha256='e24ade3e928f7253aa8c14aa44726d1edf3f98643f87c9d72ec1df44b26be8f5') - version('2.13.03', 'd5ca2ad7121ccbae69dd606b1038532c') - version('2.11.06', '2b958e9f5d200641e6fc9564977aecc5') + version('2.13.03', sha256='812ecfb0dcbc5bd409aaa8f61c7de94c5b8752a7b00c632883d15b2ed6452573') + version('2.11.06', sha256='90f60d95a15b8a54bf34d87b9be53da89ee3d6213ea739fb2305846f4585868a') # Fix compilation with GCC 8 # https://bugzilla.nasm.us/show_bug.cgi?id=3392461 diff --git a/var/spack/repos/builtin/packages/nauty/package.py b/var/spack/repos/builtin/packages/nauty/package.py index a38296c5078..444629efd73 100644 --- a/var/spack/repos/builtin/packages/nauty/package.py +++ b/var/spack/repos/builtin/packages/nauty/package.py @@ -14,7 +14,7 @@ class Nauty(AutotoolsPackage): homepage = "http://pallini.di.uniroma1.it/index.html" url = "http://pallini.di.uniroma1.it/nauty26r7.tar.gz" - version('2.6r7', 'b2b18e03ea7698db3fbe06c5d76ad8fe') + version('2.6r7', sha256='97b5648de17645895cbd56a9a0b3e23cf01f5332c476d013ea459f1a0363cdc6') # Debian/ Fedora patches for @2.6r7: urls_for_patches = { diff --git a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py index 392e05b0d12..74e755d6104 100644 --- a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py +++ b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py @@ -13,7 +13,7 @@ class NcbiMagicblast(AutotoolsPackage): homepage = "https://ncbi.github.io/magicblast/" url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-src.tar.gz" - version('1.3.0', '2615b919c1fe1bf7dc3d816392ab4420') + version('1.3.0', sha256='47b9b65d595b5cb0c4fef22bc7f7c038fb8d4a0accdbe560d7232820575aff67') depends_on('lmdb') configure_directory = 'c++' diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py index b23f6161633..66c24739c31 100644 --- a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py +++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py @@ -12,7 +12,7 @@ class NcbiRmblastn(AutotoolsPackage): homepage = "http://www.repeatmasker.org/RMBlast.html" url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-src.tar.gz" - version('2.9.0', 'e6a44564e6278c445826ec2720f104b4') + version('2.9.0', sha256='a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257') patch('isb-2.9.0+-rmblast-p1.patch', when="@2.9.0") configure_directory = 'c++' diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py index b0a0bb3063d..39dc3e8761f 100644 --- a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py +++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py @@ -14,9 +14,9 @@ class NcbiToolkit(AutotoolsPackage): homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/" url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--22_0_0.tar.gz" - version('22_0_0', 'e352d25b24c3a2d087c2cf3cedf6ea95', + version('22_0_0', sha256='ef39429bbc7f13c44c0d327432d9cfb430f9f20d10d825e6b2c4ddd7ccce457f', url='ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/Mar_28_2019/ncbi_cxx--22_0_0.tar.gz') - version('21_0_0', '14e021e08b1a78ac9cde98d0cab92098', + version('21_0_0', sha256='48cc3ae24ca63d1ab1be148e7525e8c5b9f4eaa5eb36d172800784b640a84a4f', url='ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2018/Apr_2_2018/ncbi_cxx--21_0_0.tar.gz') variant('debug', default=False, diff --git a/var/spack/repos/builtin/packages/nccl/package.py b/var/spack/repos/builtin/packages/nccl/package.py index 9f5d976adbc..caef4bdb314 100644 --- a/var/spack/repos/builtin/packages/nccl/package.py +++ b/var/spack/repos/builtin/packages/nccl/package.py @@ -17,8 +17,8 @@ class Nccl(MakefilePackage): version('2.4.2-1', sha256='e3dd04b22eb541394bd818e5f78ac23a09cc549690d5d55d6fccc1a36155385a') version('2.3.7-1', sha256='e6eff80d9d2db13c61f8452e1400ca2f098d2dfe42857cb23413ce081c5b9e9b') version('2.3.5-5', sha256='bac9950b4d3980c25baa8e3e4541d2dfb4d21edf32ad3b89022d04920357142f') - version('1.3.4-1', '5b9ce7fbdce0fde68e0f66318e6ff422') - version('1.3.0-1', 'f6fb1d56913a7d212ca0c300e76f01fb') + version('1.3.4-1', sha256='11e4eb44555bb28b9cbad973dacb4640b82710c9769e719afc2013b63ffaf884') + version('1.3.0-1', sha256='53f36151061907bdcafad1c26c1d9370a0a8400f561a83704a5138213ba51003') depends_on('cuda') diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py index 13b87e5fcc3..6bf5fdb1b40 100644 --- a/var/spack/repos/builtin/packages/nccmp/package.py +++ b/var/spack/repos/builtin/packages/nccmp/package.py @@ -11,7 +11,7 @@ class Nccmp(Package): homepage = "http://nccmp.sourceforge.net/" url = "http://downloads.sourceforge.net/project/nccmp/nccmp-1.8.2.0.tar.gz" - version('1.8.2.0', '81e6286d4413825aec4327e61a28a580') + version('1.8.2.0', sha256='7f5dad4e8670568a71f79d2bcebb08d95b875506d3d5faefafe1a8b3afa14f18') depends_on('netcdf') diff --git a/var/spack/repos/builtin/packages/ncdu/package.py b/var/spack/repos/builtin/packages/ncdu/package.py index 98b17d91fd6..56989300693 100644 --- a/var/spack/repos/builtin/packages/ncdu/package.py +++ b/var/spack/repos/builtin/packages/ncdu/package.py @@ -19,11 +19,11 @@ class Ncdu(Package): version('1.13', sha256='f4d9285c38292c2de05e444d0ba271cbfe1a705eee37c2b23ea7c448ab37255a') version('1.12', sha256='820e4e4747a2a2ec7a2e9f06d2f5a353516362c22496a10a9834f871b877499a') - version('1.11', '9e44240a5356b029f05f0e70a63c4d12') - version('1.10', '7535decc8d54eca811493e82d4bfab2d') - version('1.9', '93258079db897d28bb8890e2db89b1fb') - version('1.8', '94d7a821f8a0d7ba8ef3dd926226f7d5') - version('1.7', '172047c29d232724cc62e773e82e592a') + version('1.11', sha256='d0aea772e47463c281007f279a9041252155a2b2349b18adb9055075e141bb7b') + version('1.10', sha256='f5994a4848dbbca480d39729b021f057700f14ef72c0d739bbd82d862f2f0c67') + version('1.9', sha256='ea7349544a9da77764293d84e52862110ab49ee29b949158bc4bab908d3dd3a5') + version('1.8', sha256='42aaf0418c05e725b39b220166a9c604a9c54c0fbf7692c9c119b36d0ed5d099') + version('1.7', sha256='70dfe10b4c0843050ee17ab27b7ad4d65714682f117079b85d779f83431fb333') depends_on("ncurses") diff --git a/var/spack/repos/builtin/packages/ncftp/package.py b/var/spack/repos/builtin/packages/ncftp/package.py index b2779e4bd5c..01593e419fd 100644 --- a/var/spack/repos/builtin/packages/ncftp/package.py +++ b/var/spack/repos/builtin/packages/ncftp/package.py @@ -13,6 +13,6 @@ class Ncftp(AutotoolsPackage): homepage = "http://www.ncftp.com/" url = "ftp://ftp.ncftp.com/ncftp/ncftp-3.2.6-src.tar.gz" - version('3.2.6', 'e7cce57ef6274d4c7433ffe28ffe0a71') + version('3.2.6', sha256='129e5954850290da98af012559e6743de193de0012e972ff939df9b604f81c23') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py index bbf84b8cd00..c3940136c43 100644 --- a/var/spack/repos/builtin/packages/ncl/package.py +++ b/var/spack/repos/builtin/packages/ncl/package.py @@ -19,9 +19,9 @@ class Ncl(Package): url = "https://github.com/NCAR/ncl/archive/6.4.0.tar.gz" - version('6.6.2', 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e') - version('6.5.0', '133446f3302eddf237db56bf349e1ebf228240a7320699acc339a3d7ee414591') - version('6.4.0', 'd891452cda7bb25afad9b6c876c73986') + version('6.6.2', sha256='cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e') + version('6.5.0', sha256='133446f3302eddf237db56bf349e1ebf228240a7320699acc339a3d7ee414591') + version('6.4.0', sha256='0962ae1a1d716b182b3b27069b4afe66bf436c64c312ddfcf5f34d4ec60153c8') patch('spack_ncl.patch') # Make ncl compile with hdf5 1.10 (upstream as of 6.5.0) @@ -89,7 +89,7 @@ class Ncl(Package): resource( name='triangle', url='http://www.netlib.org/voronoi/triangle.zip', - md5='10aff8d7950f5e0e2fb6dd2e340be2c9', + sha256='1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480', placement='triangle_src', when='+triangle') diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py index 4ab74fd19f1..951d6f59741 100644 --- a/var/spack/repos/builtin/packages/nco/package.py +++ b/var/spack/repos/builtin/packages/nco/package.py @@ -13,15 +13,15 @@ class Nco(AutotoolsPackage): homepage = "http://nco.sourceforge.net/" url = "https://github.com/nco/nco/archive/4.6.7.tar.gz" - version('4.7.9', '048f6298bceb40913c3ae433f875dea1e9129b1c86019128e7271d08f274a879') - version('4.6.7', 'b04c92aa715d3fad3ebebd1fd178ce32') - version('4.6.6', 'df6fa47aaf6e41adfc0631912a7a341f') - version('4.6.5', '2afd34a6bb5ff6c7ed39cf40c917b6e4') - version('4.6.4', '22f4e779d0011a9c0db90fda416c8e45') - version('4.6.3', '0e1d6616c65ed3a30c54cc776da4f987') - version('4.6.2', 'b7471acf0cc100343392f4171fb56113') - version('4.6.1', 'ef43cc989229c2790a9094bd84728fd8') - version('4.5.5', '9f1f1cb149ad6407c5a03c20122223ce') + version('4.7.9', sha256='048f6298bceb40913c3ae433f875dea1e9129b1c86019128e7271d08f274a879') + version('4.6.7', sha256='2fe2dabf14a60bface694307cbe719df57103682b715348e9d77bfe8d31487f3') + version('4.6.6', sha256='079d83f800b73d9b12b8de1634a88c2cbe40a639aaf7bc056cd2e836c6047697') + version('4.6.5', sha256='d5b18c9ada25d062a539e2995be445db39e8021c56cd4b20c88485cb2452c7ae') + version('4.6.4', sha256='1c2ab906fc81f91bf8aff3e6da27ae7a4c89821c5836d787188fff5262418062') + version('4.6.3', sha256='414ccb349ed25cb37b669fb87f9e2e4ca8d58c2f45538feda199bf895b982bf8') + version('4.6.2', sha256='cec82e35d47a6bbf8ab9301d5ff4cf08051f489b49e8529ebf780380f2c21ed3') + version('4.6.1', sha256='7433fe5901f48eb5170f24c6d53b484161e1c63884d9350600070573baf8b8b0') + version('4.5.5', sha256='bc6f5b976fdfbdec51f2ebefa158fa54672442c2fd5f042ba884f9f32c2ad666') # https://github.com/nco/nco/issues/43 patch('NUL-0-NULL.patch', when='@:4.6.7') diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index 7d599893e1f..2e77799233f 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -20,9 +20,9 @@ class Ncurses(AutotoolsPackage): # URL must remain http:// so Spack can bootstrap curl url = "http://ftpmirror.gnu.org/ncurses/ncurses-6.1.tar.gz" - version('6.1', '98c889aaf8d23910d2b92d65be2e737a') - version('6.0', 'ee13d052e1ead260d7c28071f46eefb1') - version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1') + version('6.1', sha256='aa057eeeb4a14d470101eff4597d5833dcef5965331be3528c08d99cebaa0d17') + version('6.0', sha256='f551c24b30ce8bfb6e96d9f59b42fbea30fa3a6123384172f9e7284bcf647260') + version('5.9', sha256='9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b') variant('symlinks', default=False, description='Enables symlinks. Needed on AFS filesystem.') diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py index e78139a7894..3f1d6f4d8cc 100644 --- a/var/spack/repos/builtin/packages/ncview/package.py +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -11,7 +11,7 @@ class Ncview(AutotoolsPackage): homepage = "http://meteora.ucsd.edu/~pierce/ncview_home_page.html" url = "ftp://cirrus.ucsd.edu/pub/ncview/ncview-2.1.7.tar.gz" - version('2.1.7', 'debd6ca61410aac3514e53122ab2ba07') + version('2.1.7', sha256='a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82') depends_on('netcdf') depends_on('udunits2') diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py index 7c190a06bd8..c2071af64d5 100644 --- a/var/spack/repos/builtin/packages/ndiff/package.py +++ b/var/spack/repos/builtin/packages/ndiff/package.py @@ -18,8 +18,8 @@ class Ndiff(Package): homepage = "http://ftp.math.utah.edu/pub/ndiff/" url = "http://ftp.math.utah.edu/pub/ndiff/ndiff-2.00.tar.gz" - version('2.00', '885548b4dc26e72c5455bebb5ba6c16d') - version('1.00', 'f41ffe5d12f36cd36b6311acf46eccdc') + version('2.00', sha256='f2bbd9a2c8ada7f4161b5e76ac5ebf9a2862cab099933167fe604b88f000ec2c') + version('1.00', sha256='d4be3ab38e4b87da8d689fe47413e01a7bfdf8c8627bfb673aac37953a463a92') def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/nek5000/package.py b/var/spack/repos/builtin/packages/nek5000/package.py index 99d533b606b..e2dfa2333b9 100644 --- a/var/spack/repos/builtin/packages/nek5000/package.py +++ b/var/spack/repos/builtin/packages/nek5000/package.py @@ -20,7 +20,7 @@ class Nek5000(Package): 'spectral-elements', 'fluid', 'ecp', 'ecp-apps'] version('develop', branch='master') - version('17.0', '6a13bfad2ce023897010dd88f54a0a87') + version('17.0', sha256='298d83ffd9f695ee7cf565cb445be33b02775eb9c2e9f0f74d91d89fe722e114') # MPI, Profiling and Visit variants variant('mpi', default=True, description='Build with MPI.') diff --git a/var/spack/repos/builtin/packages/nektools/package.py b/var/spack/repos/builtin/packages/nektools/package.py index 43dd014b0a2..61ea5b297ed 100644 --- a/var/spack/repos/builtin/packages/nektools/package.py +++ b/var/spack/repos/builtin/packages/nektools/package.py @@ -29,7 +29,7 @@ class Nektools(Package): 'spectral-elements', 'fluid', 'ecp', 'ecp-apps'] version('develop', branch='master') - version('17.0', '6a13bfad2ce023897010dd88f54a0a87') + version('17.0', sha256='298d83ffd9f695ee7cf565cb445be33b02775eb9c2e9f0f74d91d89fe722e114') # Variant for MAXNEL, we need to read this from user variant( diff --git a/var/spack/repos/builtin/packages/neovim/package.py b/var/spack/repos/builtin/packages/neovim/package.py index db398f5a2a9..205607d4a64 100644 --- a/var/spack/repos/builtin/packages/neovim/package.py +++ b/var/spack/repos/builtin/packages/neovim/package.py @@ -14,11 +14,11 @@ class Neovim(CMakePackage): url = "https://github.com/neovim/neovim/archive/v0.3.4.tar.gz" version('0.3.4', sha256='a641108bdebfaf319844ed46b1bf35d6f7c30ef5aeadeb29ba06e19c3274bc0e') - version('0.3.1', '5405bced1c929ebc245c75409cd6c7ef') - version('0.3.0', 'e5fdb2025757c337c17449c296eddf5b') - version('0.2.2', '44b69f8ace88b646ec890670f1e462c4') - version('0.2.1', 'f4271f22d2a46fa18dace42849c56a98') - version('0.2.0', '9af7f61f9f0b1a2891147a479d185aa2') + version('0.3.1', sha256='bc5e392d4c076407906ccecbc283e1a44b7832c2f486cad81aa04cc29973ad22') + version('0.3.0', sha256='f7acb61b16d3f521907d99c486b7a9f1e505e8b2a18c9ef69a6d7f18f29f74b8') + version('0.2.2', sha256='a838ee07cc9a2ef8ade1b31a2a4f2d5e9339e244ade68e64556c1f4b40ccc5ed') + version('0.2.1', sha256='9e2c068a8994c9023a5f84cde9eb7188d3c85996a7e42e611e3cd0996e345dd3') + version('0.2.0', sha256='72e263f9d23fe60403d53a52d4c95026b0be428c1b9c02b80ab55166ea3f62b5') depends_on('lua@5.1:5.2') depends_on('lua-lpeg') diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py index 3d610eb7ca3..94bb28412f8 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -15,7 +15,7 @@ class NetcdfCxx(AutotoolsPackage): homepage = "http://www.unidata.ucar.edu/software/netcdf" url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz" - version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c') + version('4.2', sha256='95ed6ab49a0ee001255eac4e44aacb5ca4ea96ba850c08337a3e4c9a0872ccd1') depends_on('netcdf') diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index 463652b4c90..1eb3508b30e 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -12,8 +12,8 @@ class NetcdfCxx4(AutotoolsPackage): homepage = "http://www.unidata.ucar.edu/software/netcdf" url = "https://www.github.com/unidata/netcdf-cxx4/tarball/v4.3.0" - version('4.3.0', '0dde8b9763eecdafbd69d076e687337e') - version('4.2.1', 'd019853802092cf686254aaba165fc81') + version('4.3.0', sha256='f4766d5a19c91093be80ddd2eaf1fbbd8d203854cc69fc73d2ad293b099ac799') + version('4.2.1', md5='d019853802092cf686254aaba165fc81') # Usually the configure automatically inserts the pic flags, but we can # force its usage with this variant. diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py index 52c6a6d7ed3..ddfa2295f8e 100644 --- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -12,9 +12,9 @@ class NetcdfFortran(AutotoolsPackage): homepage = "http://www.unidata.ucar.edu/software/netcdf" url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz" - version('4.4.5', 'edb51c7320a9024b419b7a87e05fa79a') - version('4.4.4', 'e855c789cd72e1b8bc1354366bf6ac72') - version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e') + version('4.4.5', sha256='2467536ce29daea348c736476aa8e684c075d2f6cab12f3361885cb6905717b8') + version('4.4.4', sha256='b2d395175f8d283e68c8be516e231a96b191ade67ad0caafaf7fa01b1e6b5d75') + version('4.4.3', sha256='330373aa163d5931e475b5e83da5c1ad041e855185f24e6a8b85d73b48d6cda9') variant('pic', default=True, description='Produce position-independent code (for shared libs)') diff --git a/var/spack/repos/builtin/packages/netgauge/package.py b/var/spack/repos/builtin/packages/netgauge/package.py index 7ee55cfddad..1d4eee11e56 100644 --- a/var/spack/repos/builtin/packages/netgauge/package.py +++ b/var/spack/repos/builtin/packages/netgauge/package.py @@ -15,6 +15,6 @@ class Netgauge(AutotoolsPackage): homepage = "http://unixer.de/research/netgauge/" url = "http://unixer.de/research/netgauge/netgauge-2.4.6.tar.gz" - version('2.4.6', 'e0e040ec6452e93ca21ccc54deac1d7f') + version('2.4.6', sha256='dc9398e4e042efec70881f2c7074ff18cc5b74bc5ffc4b8a4aaf813b39f83444') depends_on("mpi") diff --git a/var/spack/repos/builtin/packages/netgen/package.py b/var/spack/repos/builtin/packages/netgen/package.py index 8e7723f3ba2..767ccec819a 100644 --- a/var/spack/repos/builtin/packages/netgen/package.py +++ b/var/spack/repos/builtin/packages/netgen/package.py @@ -17,7 +17,7 @@ class Netgen(AutotoolsPackage): homepage = "https://ngsolve.org/" url = "https://sourceforge.net/projects/netgen-mesher/files/netgen-mesher/5.3/netgen-5.3.1.tar.gz" - version('5.3.1', 'afd5a9b0b1296c242a9c554f06af6510') + version('5.3.1', sha256='cb97f79d8f4d55c00506ab334867285cde10873c8a8dc783522b47d2bc128bf9') variant("mpi", default=True, description='enable mpi support') variant("oce", default=False, description='enable oce geometry kernel') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 5a768c5142f..a4205e733f0 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -17,17 +17,17 @@ class NetlibLapack(CMakePackage): homepage = "http://www.netlib.org/lapack/" url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" - version('3.8.0', '96591affdbf58c450d45c1daa540dbd2', + version('3.8.0', sha256='deb22cc4a6120bff72621155a9917f485f96ef8319ac074a7afbc68aab88bcf6', url='http://www.netlib.org/lapack/lapack-3.8.0.tar.gz') - version('3.7.1', 'dcdeeed73de152c4643ccc5b1aeb453c') - version('3.7.0', '697bb8d67c7d336a0f339cc9dd0fa72f') - version('3.6.1', '421b2cb72e15f237e144428f9c460ee0') - version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101') - version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') - version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478') - version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55') - version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70') - version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') + version('3.7.1', sha256='f6c53fd9f56932f3ddb3d5e24c1c07e4cd9b3b08e7f89de9c867125eecc9a1c8') + version('3.7.0', sha256='ed967e4307e986474ab02eb810eed1d1adc73f5e1e3bc78fb009f6fe766db3be') + version('3.6.1', sha256='888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de') + version('3.6.0', sha256='a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3') + version('3.5.0', sha256='9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352') + version('3.4.2', sha256='60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0') + version('3.4.1', sha256='93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f') + version('3.4.0', sha256='a7139ef97004d0e3c4c30f1c52d508fd7ae84b5fbaf0dd8e792c167dc306c3e9') + version('3.3.1', sha256='56821ab51c29369a34e5085728f92c549a9aa926f26acf7eeac87b61eed329e4') variant('shared', default=True, description="Build shared library version") variant('external-blas', default=False, diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 3d4014b16ef..bd05e73d4b7 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -15,9 +15,9 @@ class NetlibScalapack(CMakePackage): homepage = "http://www.netlib.org/scalapack/" url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz" - version('2.0.2', '2f75e600a2ba155ed9ce974a1c4b536f') - version('2.0.1', '17b8cde589ea0423afe1ec43e7499161') - version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe') + version('2.0.2', sha256='0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c') + version('2.0.1', sha256='a9b34278d4e10b40cbe084c6d87d09af8845e874250719bfbbc497b2a88bfde1') + version('2.0.0', sha256='e51fbd9c3ef3a0dbd81385b868e2355900148eea689bf915c5383d72daf73114') # versions before 2.0.0 are not using cmake and requires blacs as # a separated package diff --git a/var/spack/repos/builtin/packages/netlib-xblas/package.py b/var/spack/repos/builtin/packages/netlib-xblas/package.py index fb97e797f93..330d0306557 100644 --- a/var/spack/repos/builtin/packages/netlib-xblas/package.py +++ b/var/spack/repos/builtin/packages/netlib-xblas/package.py @@ -23,7 +23,7 @@ class NetlibXblas(AutotoolsPackage): homepage = "http://www.netlib.org/xblas" url = "http://www.netlib.org/xblas/xblas.tar.gz" - version('1.0.248', '990c680fb5e446bb86c10936e4cd7f88') + version('1.0.248', sha256='b5fe7c71c2da1ed9bcdc5784a12c5fa9fb417577513fe8a38de5de0007f7aaa1') variant('fortran', default=True, description='Build Fortran interfaces') diff --git a/var/spack/repos/builtin/packages/nettle/package.py b/var/spack/repos/builtin/packages/nettle/package.py index 32f7c424e66..8776e850aea 100644 --- a/var/spack/repos/builtin/packages/nettle/package.py +++ b/var/spack/repos/builtin/packages/nettle/package.py @@ -14,11 +14,11 @@ class Nettle(AutotoolsPackage): url = "https://ftpmirror.gnu.org/nettle/nettle-3.3.tar.gz" version('3.4.1', sha256='f941cf1535cd5d1819be5ccae5babef01f6db611f9b5a777bae9c7604b8a92ad') - version('3.4', 'dc0f13028264992f58e67b4e8915f53d') - version('3.3', '10f969f78a463704ae73529978148dbe') - version('3.2', 'afb15b4764ebf1b4e6d06c62bd4d29e4') - version('2.7.1', '003d5147911317931dd453520eb234a5') - version('2.7', '2caa1bd667c35db71becb93c5d89737f') + version('3.4', sha256='ae7a42df026550b85daca8389b6a60ba6313b0567f374392e54918588a411e94') + version('3.3', sha256='46942627d5d0ca11720fec18d81fc38f7ef837ea4197c1f630e71ce0d470b11e') + version('3.2', sha256='ea4283def236413edab5a4cf9cf32adf540c8df1b9b67641cfc2302fca849d97') + version('2.7.1', sha256='bc71ebd43435537d767799e414fce88e521b7278d48c860651216e1fc6555b40') + version('2.7', sha256='c294ea133c05382cc2effb1734d49f4abeb1ad8515543a333de49a11422cd4d6') depends_on('gmp') depends_on('m4', type='build') diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py index 8ddf04f998c..86fcf5ac844 100644 --- a/var/spack/repos/builtin/packages/neuron/package.py +++ b/var/spack/repos/builtin/packages/neuron/package.py @@ -22,10 +22,10 @@ class Neuron(Package): git = "https://github.com/nrnhines/nrn.git" version('develop', branch='master') - version('7.5', 'fb72c841374dfacbb6c2168ff57bfae9') - version('7.4', '2c0bbee8a9e55d60fa26336f4ab7acbf') - version('7.3', '993e539cb8bf102ca52e9fefd644ab61') - version('7.2', '5486709b6366add932e3a6d141c4f7ad') + version('7.5', sha256='67642216a969fdc844da1bd56643edeed5e9f9ab8c2a3049dcbcbcccba29c336') + version('7.4', sha256='1403ba16b2b329d2376f4bf007d96e6bf2992fa850f137f1068ad5b22b432de6') + version('7.3', sha256='71cff5962966c5cd5d685d90569598a17b4b579d342126b31e2d431128cc8832') + version('7.2', sha256='c777d73a58ff17a073e8ea25f140cb603b8b5f0df3c361388af7175e44d85b0e') variant('mpi', default=True, description='Enable MPI parallelism') variant('python', default=True, description='Enable python') diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py index 0330cdf2731..c763aceb8ee 100644 --- a/var/spack/repos/builtin/packages/nextflow/package.py +++ b/var/spack/repos/builtin/packages/nextflow/package.py @@ -12,12 +12,12 @@ class Nextflow(Package): homepage = "http://www.nextflow.io" url = "https://github.com/nextflow-io/nextflow/releases/download/v0.24.1/nextflow" - version('0.25.6', '29d739b6caf8ceb5aa9997310ee8d0e7', expand=False) - version('0.24.1', '80ec8c4fe8e766e0bdd1371a50410d1d', expand=False) - version('0.23.3', '71fb69275b6788af1c6f1165f40d362e', expand=False) - version('0.21.0', '38e5e335cb33f05ba358e1f883c8386c', expand=False) - version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a', expand=False) - version('0.17.3', '5df00105fb1ce6fd0ba019ae735d9617', expand=False) + version('0.25.6', sha256='9498806596c96ba87396194fa6f1d7d1cdb739990f83e7e89d1d055366c5a943', expand=False) + version('0.24.1', sha256='0bfde5335b385e3cff99bf4aab619e583de5dc0849767240f675037a2e7c1d83', expand=False) + version('0.23.3', sha256='ffe1c314962ff97ebf47b0567883e152522acfbf6fd5800200b1a7a0ca2896d2', expand=False) + version('0.21.0', sha256='076089079479da0d91fe1ad7aad06816164ecbcf17f73c55e795b1db8462b28d', expand=False) + version('0.20.1', sha256='02635f3371f76a10e12f7366508c90bacf532ab7c23ae03c895317a150a39bd4', expand=False) + version('0.17.3', sha256='05563ee1474fbef22f65fa3080792dcb08d218dd1b1561c517ebff4346559dbe', expand=False) depends_on('java') diff --git a/var/spack/repos/builtin/packages/nfft/package.py b/var/spack/repos/builtin/packages/nfft/package.py index 9009111ea8e..0b60277cb43 100644 --- a/var/spack/repos/builtin/packages/nfft/package.py +++ b/var/spack/repos/builtin/packages/nfft/package.py @@ -14,8 +14,8 @@ class Nfft(AutotoolsPackage): homepage = "https://www-user.tu-chemnitz.de/~potts/nfft" url = "https://github.com/NFFT/nfft/releases/download/3.4.1/nfft-3.4.1.tar.gz" - version('3.4.1', '9c2ad6cf86fe4a7bc0de8d2d92b101f4') - version('3.3.2', '13e48b923501ed6feb5130c3be115fc8') + version('3.4.1', sha256='1cf6060eec0afabbbba323929d8222397a77fa8661ca74927932499db26b4aaf') + version('3.3.2', sha256='9dcebd905a82c4f0a339d0d5e666b68c507169d9173b66d5ac588aae5d50b57c') depends_on('fftw') diff --git a/var/spack/repos/builtin/packages/nghttp2/package.py b/var/spack/repos/builtin/packages/nghttp2/package.py index 1ac0ee9beb2..9f39e163d43 100644 --- a/var/spack/repos/builtin/packages/nghttp2/package.py +++ b/var/spack/repos/builtin/packages/nghttp2/package.py @@ -13,7 +13,7 @@ class Nghttp2(AutotoolsPackage): homepage = "https://nghttp2.org/" url = "https://github.com/nghttp2/nghttp2/releases/download/v1.26.0/nghttp2-1.26.0.tar.gz" - version('1.26.0', '83fa813b22bacbc6ea80dfb24847569f') + version('1.26.0', sha256='daf7c0ca363efa25b2cbb1e4bd925ac4287b664c3d1465f6a390359daa3f0cf1') depends_on('python@2.7:', type=('build', 'run')) depends_on('py-cython@0.19:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/nginx/package.py b/var/spack/repos/builtin/packages/nginx/package.py index dcd0bf8228a..32d7142a9ea 100644 --- a/var/spack/repos/builtin/packages/nginx/package.py +++ b/var/spack/repos/builtin/packages/nginx/package.py @@ -14,9 +14,9 @@ class Nginx(AutotoolsPackage): homepage = "https://nginx.org/en/" url = "https://nginx.org/download/nginx-1.12.0.tar.gz" - version('1.15.6', 'a3d8c67c2035808c7c0d475fffe263db8c353b11521aa7ade468b780ed826cc6') - version('1.13.8', 'df4be9294365782dc1349ca33ce8c4ac') - version('1.12.0', '995eb0a140455cf0cfc497e5bd7f94b3') + version('1.15.6', sha256='a3d8c67c2035808c7c0d475fffe263db8c353b11521aa7ade468b780ed826cc6') + version('1.13.8', sha256='8410b6c31ff59a763abf7e5a5316e7629f5a5033c95a3a0ebde727f9ec8464c5') + version('1.12.0', sha256='b4222e26fdb620a8d3c3a3a8b955e08b713672e1bc5198d1e4f462308a795b30') depends_on('openssl') depends_on('pcre') diff --git a/var/spack/repos/builtin/packages/ngmlr/package.py b/var/spack/repos/builtin/packages/ngmlr/package.py index 72033007a66..182643c08b7 100644 --- a/var/spack/repos/builtin/packages/ngmlr/package.py +++ b/var/spack/repos/builtin/packages/ngmlr/package.py @@ -14,6 +14,6 @@ class Ngmlr(CMakePackage): homepage = "https://github.com/philres/ngmlr" url = "https://github.com/philres/ngmlr/archive/v0.2.5.tar.gz" - version('0.2.5', '1b2b1aaeb6a3accc8b9f3e5c29e77037') + version('0.2.5', sha256='719944a35cc7ff9c321eedbf3385a7375ce2301f609b3fd7be0a850cabbb028b') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/ninja-fortran/package.py b/var/spack/repos/builtin/packages/ninja-fortran/package.py index 022db64fbae..4c6deda2a00 100644 --- a/var/spack/repos/builtin/packages/ninja-fortran/package.py +++ b/var/spack/repos/builtin/packages/ninja-fortran/package.py @@ -15,15 +15,15 @@ class NinjaFortran(Package): # Each version is a fork off of a specific commit of ninja # Hashes don't sort properly, so added "artificial" tweak-level version # number prior to the hashes for sorting puposes - version('1.9.0.2.g99df1', 'f0892b1c8fd2984e8f47e9e1fcb9ce32') - version('1.9.0.1.g5b44b', 'f7c2e718801c1fd097a728530559e0d4') - version('1.9.0.0.gad558', 'cb93ffb5871225e2b813eb9c34b3096d') - version('1.8.2.2.g81279', '0e29d0c441dcbd9b9ee9291c3a8dfbdd') - version('1.8.2.1.g3bbbe', 'de6257118f2e3ac7fa1abca1e7c70afa') - version('1.8.2.0.g972a7', '8ace90ad0c5657022d10ba063783a652') - version('1.7.2.1.gaad58', 'eb51b042b9dbaf8ecd79a6fb24de1320') - version('1.7.2.0.gcc0ea', '3982f508c415c0abaca34cb5e92e711a') - version('1.7.1.0.g7ca7f', '187a8d15c1e20e5e9b00c5c3f227ca8a') + version('1.9.0.2.g99df1', sha256='b7bc3d91e906b92d2e0887639e8ed6b0c45b28e339dda2dbb66c1388c86a9fcf') + version('1.9.0.1.g5b44b', sha256='449359a402c3adccd37f6fece19ce7d7cda586e837fdf50eb7d53597b7f1ce90') + version('1.9.0.0.gad558', sha256='ab486a3ccfb38636bfa61fefb976ddf9a7652f4bf12495a77718b35cc3db61ee') + version('1.8.2.2.g81279', sha256='744a13475ace2c0ff8c8edaf95eb73edf3daf8805e4060b60d18ad4f55bb98aa') + version('1.8.2.1.g3bbbe', sha256='121c432cec32c8aea730a71a256a81442ac8446c6f0e7652ea3121da9e0d482d') + version('1.8.2.0.g972a7', sha256='127db130cb1c711ac4a5bb93d2f2665d304cff5206283332b50bc8ba2eb70d2e') + version('1.7.2.1.gaad58', sha256='fac971edef78fc9f52e47365facb88c5c1c85d6d9c15f4356a1b97352c9ae5f8') + version('1.7.2.0.gcc0ea', sha256='6afa570fa9300833f76e56fa5b01f5a3b7d8a7108f6ad368b067a003d25ef18b') + version('1.7.1.0.g7ca7f', sha256='53472d0c3cf9c1cff7e991699710878be55d21a1c229956dea6a2c3e44edee80') depends_on('python', type='build') diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py index c7da7c19334..51f0a45f435 100644 --- a/var/spack/repos/builtin/packages/ninja/package.py +++ b/var/spack/repos/builtin/packages/ninja/package.py @@ -18,9 +18,9 @@ class Ninja(Package): version('kitware', branch='features-for-fortran') version('1.9.0', sha256='5d7ec75828f8d3fd1a0c2f31b5b0cea780cdfe1031359228c428c1a48bfcd5b9') - version('1.8.2', '5fdb04461cc7f5d02536b3bfc0300166') - version('1.7.2', '7b482218757acbaeac4d4d54a3cd94e1') - version('1.6.0', '254133059f2da79d8727f654d7198f43') + version('1.8.2', sha256='86b8700c3d0880c2b44c2ff67ce42774aaf8c28cbf57725cb881569288c1c6f4') + version('1.7.2', sha256='2edda0a5421ace3cf428309211270772dd35a91af60c96f93f90df6bc41b16d9') + version('1.6.0', sha256='b43e88fb068fe4d92a3dfd9eb4d19755dae5c33415db2e9b7b61b4659009cde7') depends_on('python', type='build') diff --git a/var/spack/repos/builtin/packages/nlopt/package.py b/var/spack/repos/builtin/packages/nlopt/package.py index 9c09f46a87e..417e7f5cd6e 100644 --- a/var/spack/repos/builtin/packages/nlopt/package.py +++ b/var/spack/repos/builtin/packages/nlopt/package.py @@ -17,7 +17,7 @@ class Nlopt(CMakePackage): git = "https://github.com/stevengj/nlopt.git" version('develop', branch='master') - version('2.5.0', 'ada08c648bf9b52faf8729412ff6dd6d') + version('2.5.0', sha256='c6dd7a5701fff8ad5ebb45a3dc8e757e61d52658de3918e38bab233e7fd3b4ae') variant('shared', default=True, description='Enables the build of shared libraries') variant('python', default=True, description='Build python wrappers') diff --git a/var/spack/repos/builtin/packages/nmap/package.py b/var/spack/repos/builtin/packages/nmap/package.py index 3f9cdc4650b..8bedd76b743 100644 --- a/var/spack/repos/builtin/packages/nmap/package.py +++ b/var/spack/repos/builtin/packages/nmap/package.py @@ -14,6 +14,6 @@ class Nmap(AutotoolsPackage): homepage = "https://nmap.org" url = "https://nmap.org/dist/nmap-7.70.tar.bz2" - version('7.70', '84eb6fbe788e0d4918c2b1e39421bf79') - version('7.31', 'f2f6660142a777862342a58cc54258ea') - version('7.30', '8d86797d5c9e56de571f9630c0e6b5f8') + version('7.70', sha256='847b068955f792f4cc247593aca6dc3dc4aae12976169873247488de147a6e18') + version('7.31', sha256='cb9f4e03c0771c709cd47dc8fc6ac3421eadbdd313f0aae52276829290583842') + version('7.30', sha256='ba38a042ec67e315d903d28a4976b74999da94c646667c0c63f31e587d6d8d0f') diff --git a/var/spack/repos/builtin/packages/node-js/package.py b/var/spack/repos/builtin/packages/node-js/package.py index ccd932f1dec..93dd232143b 100644 --- a/var/spack/repos/builtin/packages/node-js/package.py +++ b/var/spack/repos/builtin/packages/node-js/package.py @@ -15,12 +15,12 @@ class NodeJs(Package): homepage = "https://nodejs.org/" url = "https://nodejs.org/download/release/v6.3.0/node-v6.3.0.tar.gz" - version('11.1.0', '3f53b5ac25b2d36ad538267083c0e603d9236867a936c22a9116d95fa10c60d5') - version('10.13.0', 'aa06825fff375ece7c0d881ae0de5d402a857e8cabff9b4a50f2f0b7b44906be') - version('8.9.1', '7482b2523f72000d1b6060c38945026b') - version('7.1.0', '1db5df2cb025f9c70e83d9cf21c4266a') - version('6.3.0', '8c14e5c89d66d4d060c91b3ba15dfd31') - version('6.2.2', '1120e8bf191fdaee42206d031935210d') + version('11.1.0', sha256='3f53b5ac25b2d36ad538267083c0e603d9236867a936c22a9116d95fa10c60d5') + version('10.13.0', sha256='aa06825fff375ece7c0d881ae0de5d402a857e8cabff9b4a50f2f0b7b44906be') + version('8.9.1', sha256='32491b7fcc4696b2cdead45c47e52ad16bbed8f78885d32e873952fee0f971e1') + version('7.1.0', sha256='595e7e2a37d1e0573044a90077bb12c0f750e5d8851899ffa74038238da9a983') + version('6.3.0', sha256='4ed7a99985f8afee337cc22d5fef61b495ab4238dfff3750ac9019e87fc6aae6') + version('6.2.2', sha256='b6baee57a0ede496c7c7765001f7495ad74c8dfe8c34f1a6fb2cd5d8d526ffce') # variant('bash-completion', default=False, description='Build with bash-completion support for npm') # NOQA: ignore=E501 variant('debug', default=False, description='Include debugger support') diff --git a/var/spack/repos/builtin/packages/notmuch/package.py b/var/spack/repos/builtin/packages/notmuch/package.py index a3c0f414be7..676a275f4c2 100644 --- a/var/spack/repos/builtin/packages/notmuch/package.py +++ b/var/spack/repos/builtin/packages/notmuch/package.py @@ -15,7 +15,7 @@ class Notmuch(AutotoolsPackage): homepage = "https://notmuchmail.org/" url = "https://notmuchmail.org/releases/notmuch-0.23.7.tar.gz" - version('0.23.7', '1ad339b6d0c03548140434c7bcdf0624') + version('0.23.7', sha256='f11bb10d71945f6c3f16d23117afc70810aa485878e66bb4bf43cc3f08038913') depends_on('zlib') depends_on('talloc') diff --git a/var/spack/repos/builtin/packages/npb/package.py b/var/spack/repos/builtin/packages/npb/package.py index 9922b94ac12..1f6499f09d0 100644 --- a/var/spack/repos/builtin/packages/npb/package.py +++ b/var/spack/repos/builtin/packages/npb/package.py @@ -31,7 +31,7 @@ class Npb(MakefilePackage): homepage = "https://www.nas.nasa.gov/publications/npb.html" url = "https://www.nas.nasa.gov/assets/npb/NPB3.3.1.tar.gz" - version('3.3.1', '8e5ec2c819480759725df67833619911') + version('3.3.1', sha256='4a8ea679b1df69f583c544c47198b3c26a50ec2bb6f8f69aef66c04c9a747d2d') # Valid Benchmark Names valid_names = ( diff --git a/var/spack/repos/builtin/packages/npm/package.py b/var/spack/repos/builtin/packages/npm/package.py index 8a7b17f13d1..76cc11703d7 100644 --- a/var/spack/repos/builtin/packages/npm/package.py +++ b/var/spack/repos/builtin/packages/npm/package.py @@ -14,8 +14,8 @@ class Npm(AutotoolsPackage): # base http://www.npmjs.com/ url = "https://registry.npmjs.org/npm/-/npm-3.10.5.tgz" - version('3.10.9', 'ec1eb22b466ce87cdd0b90182acce07f') - version('3.10.5', '46002413f4a71de9b0da5b506bf1d992') + version('3.10.9', sha256='fb0871b1aebf4b74717a72289fade356aedca83ee54e7386e38cb51874501dd6') + version('3.10.5', sha256='ff019769e186152098841c1fa6325e5a79f7903a45f13bd0046a4dc8e63f845f') depends_on('node-js', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/npth/package.py b/var/spack/repos/builtin/packages/npth/package.py index 59375b959f0..5d2a6e95d14 100644 --- a/var/spack/repos/builtin/packages/npth/package.py +++ b/var/spack/repos/builtin/packages/npth/package.py @@ -13,5 +13,5 @@ class Npth(AutotoolsPackage): homepage = "https://gnupg.org/software/npth/index.html" url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.5.tar.bz2" - version('1.5', '9ba2dc4302d2f32c66737c43ed191b1b') - version('1.4', '76cef5542e0db6a339cf960641ed86f8') + version('1.5', sha256='294a690c1f537b92ed829d867bee537e46be93fbd60b16c04630fbbfcd9db3c2') + version('1.4', sha256='8915141836a3169a502d65c1ebd785fcc6d406cae5ee84474272ebf2fa96f1f2') diff --git a/var/spack/repos/builtin/packages/nrm/package.py b/var/spack/repos/builtin/packages/nrm/package.py index bc4af79457b..b15bc113231 100644 --- a/var/spack/repos/builtin/packages/nrm/package.py +++ b/var/spack/repos/builtin/packages/nrm/package.py @@ -11,7 +11,7 @@ class Nrm(PythonPackage): homepage = "https://xgitlab.cels.anl.gov/argo/nrm" url = "https://www.mcs.anl.gov/research/projects/argo/downloads/nrm-0.1.0.tar.gz" - version('0.1.0', '2135baf658355480b515c0989d019758') + version('0.1.0', sha256='911a848042fa50ed216c818e0667bcd3e4219687eb5a35476b7313abe12106dc') depends_on('py-setuptools', type=('build')) diff --git a/var/spack/repos/builtin/packages/nspr/package.py b/var/spack/repos/builtin/packages/nspr/package.py index 390ecf43430..83acbb01bca 100644 --- a/var/spack/repos/builtin/packages/nspr/package.py +++ b/var/spack/repos/builtin/packages/nspr/package.py @@ -13,7 +13,7 @@ class Nspr(AutotoolsPackage): homepage = "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR" url = "http://ftp.mozilla.org/pub/nspr/releases/v4.13.1/src/nspr-4.13.1.tar.gz" - version('4.13.1', '9c44298a6fc478b3c0a4e98f4f9981ed') + version('4.13.1', sha256='5e4c1751339a76e7c772c0c04747488d7f8c98980b434dc846977e43117833ab') depends_on('perl', type='build') diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py index 12ea39aae04..3518a5545f8 100644 --- a/var/spack/repos/builtin/packages/numdiff/package.py +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -14,8 +14,8 @@ class Numdiff(AutotoolsPackage): homepage = 'https://www.nongnu.org/numdiff' url = 'http://nongnu.askapache.com/numdiff/numdiff-5.8.1.tar.gz' - version('5.9.0', '794461a7285d8b9b1f2c4a8149889ea6') - version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') + version('5.9.0', sha256='87284a117944723eebbf077f857a0a114d818f8b5b54d289d59e73581194f5ef') + version('5.8.1', sha256='99aebaadf63325f5658411c09c6dde60d2990c5f9a24a51a6851cb574a4af503') variant('nls', default=False, description="Enable Natural Language Support") diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py index d354a087e81..3c5b7556efa 100644 --- a/var/spack/repos/builtin/packages/nwchem/package.py +++ b/var/spack/repos/builtin/packages/nwchem/package.py @@ -16,11 +16,11 @@ class Nwchem(Package): tags = ['ecp', 'ecp-apps'] - version('6.8.1', '6eccddc6db11886aa6f152626efc600c', + version('6.8.1', sha256='fd20f9ca1b410270a815e77e052ec23552f828526cd252709f798f589b2a6431', url='https://github.com/nwchemgit/nwchem/releases/download/6.8.1-release/nwchem-6.8.1-release.revision-v6.8-133-ge032219-srconly.2018-06-14.tar.bz2') - version('6.8', '50b18116319f4c15d1cb7eaa1b433006', + version('6.8', sha256='8401d9f4cce2f653a38639df61260b06be580ff0e1b8d77ed3262da159b372a6', url='https://github.com/nwchemgit/nwchem/archive/v6.8-release.tar.gz') - version('6.6', 'c581001c004ea5e5dfacb783385825e3', + version('6.6', md5='c581001c004ea5e5dfacb783385825e3', url='http://www.nwchem-sw.org/images/Nwchem-6.6.revision27746-src.2015-10-20.tar.gz') depends_on('blas') diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 5282a601d2a..a285a5e025a 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -16,15 +16,15 @@ class Oce(Package): homepage = "https://github.com/tpaviot/oce" url = "https://github.com/tpaviot/oce/archive/OCE-0.18.tar.gz" - version('0.18.3', '1686393c8493bbbb2f3f242330b33cba') - version('0.18.2', '6dfd68e459e2c62387579888a867281f') - version('0.18.1', '2a7597f4243ee1f03245aeeb02d00956') - version('0.18', '226e45e77c16a4a6e127c71fefcd171410703960ae75c7ecc7eb68895446a993') - version('0.17.2', 'bf2226be4cd192606af677cf178088e5') - version('0.17.1', '36c67b87093c675698b483454258af91') - version('0.17', 'f1a89395c4b0d199bea3db62b85f818d') - version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') - version('0.16', '7a4b4df5a104d75a537e25e7dd387eca') + version('0.18.3', sha256='c553d6a7bf52f790abc3b6bb7a1e91a65947e92a426bb1a88a11960c31f0966c') + version('0.18.2', sha256='dc21ddea678a500ad87c773e9a502ed7a71768cf83d9af0bd4c43294186a7fef') + version('0.18.1', sha256='1acf5da4bffa3592ca9f3535af9b927b79fcfeadcb81e9963e89aec192929a6c') + version('0.18', sha256='226e45e77c16a4a6e127c71fefcd171410703960ae75c7ecc7eb68895446a993') + version('0.17.2', sha256='8d9995360cd531cbd4a7aa4ca5ed969f08ec7c7a37755e2f3d4ef832c1b2f56e') + version('0.17.1', sha256='b1ff0cb8cf31339bbb30ac7ed2415d376b9b75810279d2f497e115f08c090928') + version('0.17', sha256='9ab0dc2a2d125b46cef458b56c6d171dfe2218d825860d616c5ab17994b8f74d') + version('0.16.1', sha256='d31030c8da4a1b33f767d0d59895a995c8eabc8fc65cbe0558734f6021ea2f57') + version('0.16', sha256='841fe4337a5a4e733e36a2efc4fe60a4e6e8974917028df05d47a02f59787515') variant('tbb', default=True, description='Build with Intel Threading Building Blocks') diff --git a/var/spack/repos/builtin/packages/oclint/package.py b/var/spack/repos/builtin/packages/oclint/package.py index b6f3f740b45..645e7090d45 100644 --- a/var/spack/repos/builtin/packages/oclint/package.py +++ b/var/spack/repos/builtin/packages/oclint/package.py @@ -16,7 +16,7 @@ class Oclint(Package): homepage = "http://oclint.org/" url = "https://github.com/oclint/oclint/archive/v0.13.tar.gz" - version('0.13', '1d0e605eb7815ac15e6a2a82327d2dd8') + version('0.13', sha256='a0fd188673863e6357d6585b9bb9c3affe737df134b9383a1a5ed021d09ed848') depends_on('python', type=('build')) depends_on('py-argparse', type=('build')) diff --git a/var/spack/repos/builtin/packages/oclock/package.py b/var/spack/repos/builtin/packages/oclock/package.py index d0bf374e085..816bb57f465 100644 --- a/var/spack/repos/builtin/packages/oclock/package.py +++ b/var/spack/repos/builtin/packages/oclock/package.py @@ -13,7 +13,7 @@ class Oclock(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/oclock" url = "https://www.x.org/archive/individual/app/oclock-1.0.3.tar.gz" - version('1.0.3', 'f25b05d987ef8ed6dd5a887c82eace62') + version('1.0.3', sha256='6628d1abe1612b87db9d0170cbe7f1cf4205cd764274f648c3c1bdb745bff877') depends_on('libx11') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/octave-optim/package.py b/var/spack/repos/builtin/packages/octave-optim/package.py index 6258767e9d9..bb63bfe4291 100644 --- a/var/spack/repos/builtin/packages/octave-optim/package.py +++ b/var/spack/repos/builtin/packages/octave-optim/package.py @@ -12,7 +12,7 @@ class OctaveOptim(OctavePackage): homepage = "https://octave.sourceforge.io/optim/" url = "https://downloads.sourceforge.net/octave/optim-1.5.2.tar.gz" - version('1.5.2', 'd3d77982869ea7c1807b13b24e044d44') + version('1.5.2', sha256='7b36033c5581559dc3e7616f97d402bc44dde0dfd74c0e3afdf47d452a76dddf') depends_on('octave-struct@1.0.12:') extends('octave@3.6.0:') diff --git a/var/spack/repos/builtin/packages/octave-splines/package.py b/var/spack/repos/builtin/packages/octave-splines/package.py index 1922c495d8e..efa0893144f 100644 --- a/var/spack/repos/builtin/packages/octave-splines/package.py +++ b/var/spack/repos/builtin/packages/octave-splines/package.py @@ -12,5 +12,5 @@ class OctaveSplines(OctavePackage): homepage = "http://octave.sourceforge.net/splines/index.html" url = "http://downloads.sourceforge.net/octave/splines-1.3.1.tar.gz" - version('1.3.1', 'f9665d780c37aa6a6e17d1f424c49bdeedb89d1192319a4e39c08784122d18f9') + version('1.3.1', sha256='f9665d780c37aa6a6e17d1f424c49bdeedb89d1192319a4e39c08784122d18f9') extends('octave@3.6.0:') diff --git a/var/spack/repos/builtin/packages/octave-struct/package.py b/var/spack/repos/builtin/packages/octave-struct/package.py index 75ca81450c0..a8f679f06e1 100644 --- a/var/spack/repos/builtin/packages/octave-struct/package.py +++ b/var/spack/repos/builtin/packages/octave-struct/package.py @@ -12,5 +12,5 @@ class OctaveStruct(OctavePackage): homepage = "https://octave.sourceforge.io/struct/" url = "https://downloads.sourceforge.net/octave/struct-1.0.14.tar.gz" - version('1.0.14', '3589d5eb8000f18426e2178587eb82f4') + version('1.0.14', sha256='ad4e17687bc24650f032757271b20b70fe32c35513d4dd9ab1e549919df36b47') extends('octave@2.9.7:') diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 03480968af3..cdfa076c73b 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -19,13 +19,13 @@ class Octave(AutotoolsPackage): extendable = True - version('4.4.1', '09fbd0f212f4ef21e53f1d9c41cf30ce3d7f9450fb44911601e21ed64c67ae97') - version('4.4.0', '72f846379fcec7e813d46adcbacd069d72c4f4d8f6003bcd92c3513aafcd6e96') - version('4.2.2', '77b84395d8e7728a1ab223058fe5e92dc38c03bc13f7358e6533aab36f76726e') - version('4.2.1', '80c28f6398576b50faca0e602defb9598d6f7308b0903724442c2a35a605333b') - version('4.2.0', '443ba73782f3531c94bcf016f2f0362a58e186ddb8269af7dcce973562795567') - version('4.0.2', 'c2a5cacc6e4c52f924739cdf22c2c687') - version('4.0.0', 'a69f8320a4f20a8480c1b278b1adb799') + version('4.4.1', sha256='09fbd0f212f4ef21e53f1d9c41cf30ce3d7f9450fb44911601e21ed64c67ae97') + version('4.4.0', sha256='72f846379fcec7e813d46adcbacd069d72c4f4d8f6003bcd92c3513aafcd6e96') + version('4.2.2', sha256='77b84395d8e7728a1ab223058fe5e92dc38c03bc13f7358e6533aab36f76726e') + version('4.2.1', sha256='80c28f6398576b50faca0e602defb9598d6f7308b0903724442c2a35a605333b') + version('4.2.0', sha256='443ba73782f3531c94bcf016f2f0362a58e186ddb8269af7dcce973562795567') + version('4.0.2', sha256='39cd8fd36c218fc00adace28d74a6c7c9c6faab7113a5ba3c4372324c755bdc1') + version('4.0.0', sha256='4c7ee0957f5dd877e3feb9dfe07ad5f39b311f9373932f0d2a289dc97cca3280') # patches # see https://savannah.gnu.org/bugs/?50234 diff --git a/var/spack/repos/builtin/packages/ompss/package.py b/var/spack/repos/builtin/packages/ompss/package.py index 5f80bff6ab3..be79dc958e2 100644 --- a/var/spack/repos/builtin/packages/ompss/package.py +++ b/var/spack/repos/builtin/packages/ompss/package.py @@ -23,7 +23,7 @@ class Ompss(Package): url = "http://pm.bsc.es/sites/default/files/ftp/ompss/releases/ompss-14.10.tar.gz" list_url = 'http://pm.bsc.es/ompss-downloads' - version('14.10', '404d161265748f2f96bb35fd8c7e79ee') + version('14.10', sha256='5b38d3e6ce108e7ca73a2599bc698d75ea9f6d90a3be0349faf6d61022e62a38') # all dependencies are optional, really depends_on("mpi") diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py index 9b2018526c5..fa23d0fd3c6 100644 --- a/var/spack/repos/builtin/packages/ompt-openmp/package.py +++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py @@ -16,7 +16,7 @@ class OmptOpenmp(CMakePackage): homepage = "https://github.com/OpenMPToolsInterface/LLVM-openmp" url = "http://github.com/khuck/LLVM-openmp/archive/v0.1.tar.gz" - version('0.1', '59d6933a2e9b7d1423fb9c7c77d5663f') + version('0.1', sha256='a35dd2a83777fce54386d54cea8d2df9b5f34309d66fbc1d1757d55f6048c7a7') depends_on('cmake@2.8:', type='build') diff --git a/var/spack/repos/builtin/packages/oniguruma/package.py b/var/spack/repos/builtin/packages/oniguruma/package.py index b28eb9462cb..9d9ccecdecc 100644 --- a/var/spack/repos/builtin/packages/oniguruma/package.py +++ b/var/spack/repos/builtin/packages/oniguruma/package.py @@ -12,4 +12,4 @@ class Oniguruma(AutotoolsPackage): homepage = "https://github.com/kkos/oniguruma" url = "https://github.com/kkos/oniguruma/releases/download/v6.1.3/onig-6.1.3.tar.gz" - version('6.1.3', '2d105d352c3f852d662414f639e7e859') + version('6.1.3', sha256='480c850cd7c7f2fcaad0942b4a488e2af01fbb8e65375d34908f558b432725cf') diff --git a/var/spack/repos/builtin/packages/ont-albacore/package.py b/var/spack/repos/builtin/packages/ont-albacore/package.py index 3f0c6e611de..be11466ad28 100644 --- a/var/spack/repos/builtin/packages/ont-albacore/package.py +++ b/var/spack/repos/builtin/packages/ont-albacore/package.py @@ -16,10 +16,10 @@ class OntAlbacore(Package): homepage = "https://nanoporetech.com" url = "https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.3.1-cp35-cp35m-manylinux1_x86_64.whl" - version('2.3.1', '0e85ad176e691252344c4c4b673c4b68', expand=False) - version('2.1.2', '1e60cfb95628829f2a61a85247f1b6af', expand=False) - version('1.2.4', '559640bec4693af12e4d923e8d77adf6', expand=False) - version('1.1.0', 'fab4502ea1bad99d813aa2629e03e83d', expand=False) + version('2.3.1', sha256='dc1af11b0f38b26d071e5389c2b4595c496319c987401754e1853de42467a7d1', expand=False) + version('2.1.2', md5='1e60cfb95628829f2a61a85247f1b6af', expand=False) + version('1.2.4', md5='559640bec4693af12e4d923e8d77adf6', expand=False) + version('1.1.0', md5='fab4502ea1bad99d813aa2629e03e83d', expand=False) extends('python') depends_on('python@3.5.0:3.5.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/opa-psm2/package.py b/var/spack/repos/builtin/packages/opa-psm2/package.py index 32f4a8c0a3e..29e573e5bb0 100644 --- a/var/spack/repos/builtin/packages/opa-psm2/package.py +++ b/var/spack/repos/builtin/packages/opa-psm2/package.py @@ -14,13 +14,13 @@ class OpaPsm2(MakefilePackage): version('11.2.77', sha256='5cc33d1e19d871a5861efe0bb897526f404b4bf2b88ac58bb277db96ac5ecb54') version('11.2.68', sha256='42e16a14fc8c90b50855dcea46af3315bee32fb1ae89d83060f9b2ebdce1ec26') - version('10.3-37', '9bfca04f29b937b3856f893e1f8b1b60') - version('10.3-17', 'e7263eb449939cb87612e2c7623ca21c') - version('10.3-10', '59d36b49eb126f980f3272a9d66a8e98') - version('10.3-8', '07bc5cb2a6bf1189a29cbea836843db2') - version('10.2-260', '71df31b5776be64ff243417ac88eec66') - version('10.2-235', '23539f725a597bf2d35aac47a793a37b') - version('10.2-175', 'c542b8641ad573f08f61d0a6a70f4013') + version('10.3-37', sha256='43e46f6fb345db67bb45b48e2b2bb05f590f7ccbc3ee337b33312043b46946b9') + version('10.3-17', sha256='17704cd4d9aeffb0d90d4ead3ad6f637bcd4cf030880e2cb2de192235859779e') + version('10.3-10', sha256='08d2821aa84645b93b2617dae355fcac5b690e42873c4946f2e91fa25e5a7372') + version('10.3-8', sha256='9ec4c2891dc3214e90f09df4d2f49b993c029279ba5d2a4306349d0ba273099e') + version('10.2-260', sha256='825913e6a8848508eb65fa2ca97546943a90ef0c9e16dbdd543bc75b45aa51d7') + version('10.2-235', sha256='052031ab87abadc2c11971e6aa53be363b38d58a496a6e54a820ca5bcd6545a5') + version('10.2-175', sha256='61b694191eca66e15e7ae1659bfacb10813e569d4e27182a88fb00b5661fb365') variant('avx2', default=True, description='Enable AVX2 instructions') diff --git a/var/spack/repos/builtin/packages/opam/package.py b/var/spack/repos/builtin/packages/opam/package.py index 33f7b788417..bc32c26e525 100644 --- a/var/spack/repos/builtin/packages/opam/package.py +++ b/var/spack/repos/builtin/packages/opam/package.py @@ -16,8 +16,8 @@ class Opam(AutotoolsPackage): homepage = "https://opam.ocaml.org/" url = "https://github.com/ocaml/opam/releases/download/1.2.2/opam-full-1.2.2.tar.gz" - version('1.2.2', '7d348c2898795e9f325fb80eaaf5eae8') - version('1.2.1', '04e8823a099ab631943952e4c2ab18fc') + version('1.2.2', sha256='15e617179251041f4bf3910257bbb8398db987d863dd3cfc288bdd958de58f00') + version('1.2.1', sha256='f210ece7a2def34b486c9ccfb75de8febd64487b2ea4a14a7fa0358f37eacc3b') depends_on('ocaml') # Not a strict dependency, but recommended diff --git a/var/spack/repos/builtin/packages/opari2/package.py b/var/spack/repos/builtin/packages/opari2/package.py index aed17037c48..ec0f6df5a10 100644 --- a/var/spack/repos/builtin/packages/opari2/package.py +++ b/var/spack/repos/builtin/packages/opari2/package.py @@ -20,13 +20,13 @@ class Opari2(AutotoolsPackage): homepage = "http://www.vi-hps.org/projects/score-p" url = "https://www.vi-hps.org/cms/upload/packages/opari2/opari2-2.0.4.tar.gz" - version('2.0.5', '9034dd7596ac2176401090fd5ced45d0ab9a9404444ff767f093ccce68114ef5') - version('2.0.4', 'f69e324792f66780b473daf2b3c81f58ee8188adc72b6fe0dacf43d4c1a0a131') - version('2.0.3', 'f34674718ffdb098a48732a1eb9c1aa2') - version('2.0.1', '74af78f1f27b8caaa4271e0b97fb0fba') - version('2.0', '72350dbdb6139f2e68a5055a4f0ba16c') - version('1.1.4', '245d3d11147a06de77909b0805f530c0') - version('1.1.2', '9a262c7ca05ff0ab5f7775ae96f3539e') + version('2.0.5', sha256='9034dd7596ac2176401090fd5ced45d0ab9a9404444ff767f093ccce68114ef5') + version('2.0.4', sha256='f69e324792f66780b473daf2b3c81f58ee8188adc72b6fe0dacf43d4c1a0a131') + version('2.0.3', sha256='7e2efcfbc99152ee6e31454ef4fb747f77165691539d5d2c1df2abc4612de86c') + version('2.0.1', sha256='f49d74d7533f428a4701cd561eba8a69f60615332e81b66f01ef1c9b7ee54666') + version('2.0', sha256='0c4e575be05627cd001d692204f10caef37b2f3d1ec825f98cbe1bfa4232b0b7') + version('1.1.4', sha256='b80c04fe876faaa4ee9a0654486ecbeba516b27fc14a90d20c6384e81060cffe') + version('1.1.2', sha256='8405c2903730d94c828724b3a5f8889653553fb8567045a6c54ac0816237835d') def configure_args(self): return ["--enable-shared"] diff --git a/var/spack/repos/builtin/packages/openbabel/package.py b/var/spack/repos/builtin/packages/openbabel/package.py index 90a5def63ed..68fbff7fde0 100644 --- a/var/spack/repos/builtin/packages/openbabel/package.py +++ b/var/spack/repos/builtin/packages/openbabel/package.py @@ -15,7 +15,7 @@ class Openbabel(CMakePackage): homepage = "http://openbabel.org/wiki/Main_Page" url = "https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/openbabel-2.4.1.tar.gz" - version('2.4.1', 'd9defcd7830b0592fece4fe54a137b99') + version('2.4.1', sha256='204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc') variant('python', default=True, description='Build Python bindings') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 7dfa98efd88..d0655b793c5 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -25,13 +25,13 @@ class Openblas(MakefilePackage): version('0.3.3', sha256='49d88f4494ae780e3d7fa51769c00d982d7cdb73e696054ac3baa81d42f13bab') version('0.3.2', sha256='e8ba64f6b103c511ae13736100347deb7121ba9b41ba82052b1a018a65c0cb15') version('0.3.1', sha256='1f5e956f35f3acdd3c74516e955d797a320c2e0135e31d838cbdb3ea94d0eb33') - version('0.3.0', '42cde2c1059a8a12227f1e6551c8dbd2') - version('0.2.20', '48637eb29f5b492b91459175dcc574b1') - version('0.2.19', '28c998054fd377279741c6f0b9ea7941') - version('0.2.18', '805e7f660877d588ea7e3792cda2ee65') - version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1') - version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') - version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') + version('0.3.0', sha256='cf51543709abe364d8ecfb5c09a2b533d2b725ea1a66f203509b21a8e9d8f1a1') + version('0.2.20', sha256='5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394') + version('0.2.19', sha256='9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557') + version('0.2.18', sha256='7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112') + version('0.2.17', sha256='0fe836dfee219ff4cadcc3567fb2223d9e0da5f60c7382711fb9e2c35ecf0dbf') + version('0.2.16', sha256='766f350d0a4be614812d535cead8c816fc3ad3b9afcd93167ea5e4df9d61869b') + version('0.2.15', sha256='73c40ace5978282224e5e122a41c8388c5a19e65a6f2329c2b7c0b61bacc9044') variant( 'shared', diff --git a/var/spack/repos/builtin/packages/opencoarrays/package.py b/var/spack/repos/builtin/packages/opencoarrays/package.py index 4dc7eada921..9cd2b31cb64 100644 --- a/var/spack/repos/builtin/packages/opencoarrays/package.py +++ b/var/spack/repos/builtin/packages/opencoarrays/package.py @@ -17,13 +17,13 @@ class Opencoarrays(CMakePackage): homepage = "http://www.opencoarrays.org/" url = "https://github.com/sourceryinstitute/OpenCoarrays/releases/download/2.2.0/OpenCoarrays-2.2.0.tar.gz" - version('2.7.1', 'd74ee914f94de1c396b96bbad2cf43d68f29fcc87460fcc0db6582e6ae691588') - version('2.2.0', '9311547a85a21853111f1e8555ceab4593731c6fd9edb64cfb9588805f9d1a0d') - version('1.8.10', '9ba1670647db4d986634abf743abfd6a') - version('1.8.4', '7c9eaffc3a0b5748d0d840e52ec9d4ad') - version('1.8.0', 'ca78d1507b2a118c75128c6c2e093e27') - version('1.7.4', '85ba87def461e3ff5a164de2e6482930') - version('1.6.2', '5a4da993794f3e04ea7855a6678981ba') + version('2.7.1', sha256='d74ee914f94de1c396b96bbad2cf43d68f29fcc87460fcc0db6582e6ae691588') + version('2.2.0', sha256='9311547a85a21853111f1e8555ceab4593731c6fd9edb64cfb9588805f9d1a0d') + version('1.8.10', sha256='69b61d2d3b171a294702efbddc8a602824e35a3c49ee394b41d7fb887001501a') + version('1.8.4', sha256='0cde7b114fa6d2d5eac55ace4f709e3b5eb7c7a33b81ddcaa3aaf01b2f486c0c') + version('1.8.0', sha256='96f5a9c37f7bb587eacd44bc8789924d20c8e56dbbc51fad57e73d9f7a3768b5') + version('1.7.4', sha256='1929dee793ce8f09e3b183e2b07c3e0008580cc76b460b1f7f7c066ad6672e14') + version('1.6.2', sha256='7855d42a01babc233a070cc87282b5f8ffd538a7c87ec5119605d4d7c6d7f67e') variant('build_type', default='RelWithDebInfo', description='The build type to build', diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py index f6bf5634952..bf74f644181 100644 --- a/var/spack/repos/builtin/packages/opencv/package.py +++ b/var/spack/repos/builtin/packages/opencv/package.py @@ -34,19 +34,19 @@ class Opencv(CMakePackage): version('3.4.6', sha256='e7d311ff97f376b8ee85112e2b536dbf4bdf1233673500175ed7cf21a0089f6d') version('3.4.5', sha256='0c57d9dd6d30cbffe68a09b03f4bebe773ee44dc8ff5cd6eaeb7f4d5ef3b428e') version('3.4.4', sha256='a35b00a71d77b484f73ec485c65fe56c7a6fa48acd5ce55c197aef2e13c78746') - version('3.4.3', '712896f5815938c014c199dde142d508') - version('3.4.1', 'a0b7a47899e67b3490ea31edc4f6e8e6') - version('3.4.0', '170732dc760e5f7ddeccbe53ba5d16a6') - version('3.3.1', 'b1ed9aea030bb5bd9df28524d97de84c') - version('3.3.0', '98a4e4c6f23ec725e808a891dc11eec4') - version('3.2.0', '1ea44a1d98c126ad40079d8eb914a72e') - version('3.1.0', 'a0669e22172dfc3225835b180744c9f0') - version('2.4.13.2', 'fe52791ce523681a67036def4c25261b') - version('2.4.13.1', 'f6d354500d5013e60dc0fc44b07a63d1') - version('2.4.13', '8feb45a71adad89b8017a777477c3eff') - version('2.4.12.3', '2496a4a4caf8fecfbfc294fbe6a814b0') - version('2.4.12.2', 'bc0c60c2ea1cf4078deef99569912fc7') - version('2.4.12.1', '7192f51434710904b5e3594872b897c3') + version('3.4.3', sha256='4eef85759d5450b183459ff216b4c0fa43e87a4f6aa92c8af649f89336f002ec') + version('3.4.1', sha256='f1b87684d75496a1054405ae3ee0b6573acaf3dad39eaf4f1d66fdd7e03dc852') + version('3.4.0', sha256='678cc3d2d1b3464b512b084a8cca1fad7de207c7abdf2caa1fed636c13e916da') + version('3.3.1', sha256='5dca3bb0d661af311e25a72b04a7e4c22c47c1aa86eb73e70063cd378a2aa6ee') + version('3.3.0', sha256='8bb312b9d9fd17336dc1f8b3ac82f021ca50e2034afc866098866176d985adc6') + version('3.2.0', sha256='9541efbf68f298f45914b4e837490647f4d5e472b4c0c04414a787d116a702b2') + version('3.1.0', sha256='f3b160b9213dd17aa15ddd45f6fb06017fe205359dbd1f7219aad59c98899f15') + version('2.4.13.2', sha256='4b00c110e6c54943cbbb7cf0d35c5bc148133ab2095ee4aaa0ac0a4f67c58080') + version('2.4.13.1', sha256='0d5ce5e0973e3a745f927d1ee097aaf909aae59f787be6d27a03d639e2d96bd7') + version('2.4.13', sha256='94ebcca61c30034d5fb16feab8ec12c8a868f5162d20a9f0396f0f5f6d8bbbff') + version('2.4.12.3', sha256='a4cbcd2d470860b0cf1f8faf504619c18a8ac38fd414c5a88ed3e94c963aa750') + version('2.4.12.2', sha256='150a165eb14a5ea74fb94dcc16ac7d668a6ff20a4449df2570734a2abaab9c0e') + version('2.4.12.1', sha256='c1564771f79304a2597ae4f74f44032021e3a46657e4a117060c08f5ed05ad83') # Standard variants variant('shared', default=True, diff --git a/var/spack/repos/builtin/packages/openexr/package.py b/var/spack/repos/builtin/packages/openexr/package.py index 6eee078e3de..c5d2188405b 100644 --- a/var/spack/repos/builtin/packages/openexr/package.py +++ b/var/spack/repos/builtin/packages/openexr/package.py @@ -15,21 +15,21 @@ class Openexr(Package): # New versions should come from github now version('2.3.0', sha256='fd6cb3a87f8c1a233be17b94c74799e6241d50fc5efd4df75c7a4b9cf4e25ea6') - version('2.2.0', 'b64e931c82aa3790329c21418373db4e', + version('2.2.0', sha256='36a012f6c43213f840ce29a8b182700f6cf6b214bea0d5735594136b44914231', url="http://download.savannah.nongnu.org/releases/openexr/openexr-2.2.0.tar.gz") - version('2.1.0', '33735d37d2ee01c6d8fbd0df94fb8b43', + version('2.1.0', sha256='54486b454073c1dcb5ae9892cf0f730ffefe62f38176325281505093fd218a14', url="http://download.savannah.nongnu.org/releases/openexr/openexr-2.1.0.tar.gz") - version('2.0.1', '4387e6050d2faa65dd5215618ff2ddce', + version('2.0.1', sha256='b9924d2f9d57376ff99234209231ad97a47f5cfebd18a5d0570db6d1a220685a', url="http://download.savannah.nongnu.org/releases/openexr/openexr-2.0.1.tar.gz") - version('1.7.0', '27113284f7d26a58f853c346e0851d7a', + version('1.7.0', sha256='b68a2164d01bd028d15bd96af2704634a344e291dc7cc2019a662045d8c52ca4', url="http://download.savannah.nongnu.org/releases/openexr/openexr-1.7.0.tar.gz") - version('1.6.1', '11951f164f9c872b183df75e66de145a', + version('1.6.1', sha256='c616906ab958de9c37bb86ca7547cfedbdfbad5e1ca2a4ab98983c9afa6a5950', url="http://download.savannah.nongnu.org/releases/openexr/openexr-1.6.1.tar.gz") - version('1.5.0', '55342d2256ab3ae99da16f16b2e12ce9', + version('1.5.0', sha256='5a745eee4b8ab94cd16f85528c2debfebe6aa1ba23f5b8fc7933d4aa5c3c3416', url="http://download.savannah.nongnu.org/releases/openexr/openexr-1.5.0.tar.gz") - version('1.4.0a', 'd0a4b9a930c766fa51561b05fb204afe', + version('1.4.0a', sha256='5d8a7327bd28eeb5d3064640d8eb32c3cd8c5a15999c70b0afa9f8af851936d1', url="http://download.savannah.nongnu.org/releases/openexr/openexr-1.4.0a.tar.gz") - version('1.3.2', '1522fe69135016c52eb88fc7d8514409', + version('1.3.2', sha256='fa08ad904bf89e2968078d25d1d9817f5bc17f372d1bafabf82e8f08ca2adc20', url="http://download.savannah.nongnu.org/releases/openexr/openexr-1.3.2.tar.gz") variant('debug', default=False, diff --git a/var/spack/repos/builtin/packages/openfoam-org/package.py b/var/spack/repos/builtin/packages/openfoam-org/package.py index 1bdec401815..363cc32f055 100644 --- a/var/spack/repos/builtin/packages/openfoam-org/package.py +++ b/var/spack/repos/builtin/packages/openfoam-org/package.py @@ -62,11 +62,11 @@ class OpenfoamOrg(Package): git = "https://github.com/OpenFOAM/OpenFOAM-dev.git" version('develop', branch='master') - version('5.0', 'cd8c5bdd3ff39c34f61747c8e55f59d1', + version('5.0', sha256='9057d6a8bb9fa18802881feba215215699065e0b3c5cdd0c0e84cb29c9916c89', url=baseurl + '/OpenFOAM-5.x/archive/version-5.0.tar.gz') - version('4.1', 'afd7d8e66e7db0ffaf519b14f1a8e1d4', + version('4.1', sha256='2de18de64e7abdb1b649ad8e9d2d58b77a2b188fb5bcb6f7c2a038282081fd31', url=baseurl + '/OpenFOAM-4.x/archive/version-4.1.tar.gz') - version('2.4.0', 'ad7d8b7b0753655b2b6fd9e92eefa92a', + version('2.4.0', sha256='9529aa7441b64210c400c019dcb2e0410fcfd62a6f62d23b6c5994c4753c4465', url=baseurl + '/OpenFOAM-2.4.x/archive/version-2.4.0.tar.gz') variant('int64', default=False, diff --git a/var/spack/repos/builtin/packages/openfoam/package.py b/var/spack/repos/builtin/packages/openfoam/package.py index a2c82cf0540..d0d6dac390c 100644 --- a/var/spack/repos/builtin/packages/openfoam/package.py +++ b/var/spack/repos/builtin/packages/openfoam/package.py @@ -264,13 +264,13 @@ class Openfoam(Package): list_depth = 2 version('develop', branch='develop', submodules='True') - version('1906', 'ab7017e262c0c0fceec55c31e2153180') - version('1812_190531', 'a4b416838a8a76fdec22706a33c96de3') - version('1812', '6a315687b3601eeece7ff7c7aed3d9a5') - version('1806', 'bb244a3bde7048a03edfccffc46c763f') - version('1712', '6ad92df051f4d52c7d0ec34f4b8eb3bc') - version('1706', '630d30770f7b54d6809efbf94b7d7c8f') - version('1612', 'ca02c491369150ab127cbb88ec60fbdf') + version('1906', sha256='15e38c2dc659b63753a0dd3dff913222cc46d6a40089a1b76973dd741145f61a') + version('1812_190531', sha256='51f0ef49a199edf3cd94e2ccfc7330e54e93c8e4ddb29ee66fe3e6b443583b34') + version('1812', sha256='d4d23d913419c6a364b1fe91509c1fadb5661bdf2eedb8fe9a8a005924eb2032') + version('1806', sha256='6951aab6405294fe59cec90b0a4e425f5403043191cda02ebaaa890ce1fcc819') + version('1712', sha256='4d22caa25d638d4c59bb93ee4dec51e8f71724f9f507eeb4162f771ebe885d21') + version('1706', sha256='7779048bb53798d9a5bd2b2be0bf302c5fd3dff98e29249d6e0ef7eeb83db79a') + version('1612', sha256='2909c43506a68e1f23efd0ca6186a6948ae0fc8fe1e39c78cc23ef0d69f3569d') variant('float32', default=False, description='Use single-precision') diff --git a/var/spack/repos/builtin/packages/openfst/package.py b/var/spack/repos/builtin/packages/openfst/package.py index 27b32e4c8f6..d699657f744 100644 --- a/var/spack/repos/builtin/packages/openfst/package.py +++ b/var/spack/repos/builtin/packages/openfst/package.py @@ -16,17 +16,17 @@ class Openfst(AutotoolsPackage): url = "http://www.openfst.org/twiki/pub/FST/FstDownload/openfst-1.6.1.tar.gz" list_url = "http://www.openfst.org/twiki/bin/view/FST/FstDownload" - version('1.6.1', '1173066ed987072183b950b54bdc9315') - version('1.6.0', '2b7bcfde6b629857dc5f9ad7edd6ece9') - version('1.5.4', 'e52bd59ec9d9edde0c1268a382662741') - version('1.5.3', 'f04e580b5bc574571854304c9656a3e2') - version('1.5.2', 'e9d43874f7cadf791394caab3925eee4') - version('1.5.1', '8869e44c5a4af65409ae78b9f482b40e') - version('1.5.0', 'a24fee5ffe28744c6fb7b1a49e0006c4') - version('1.4.1-patch', 'ca8f1730b9b9b281e515611fa9ae23c0', + version('1.6.1', sha256='5245af8ebccb96208eec2dfe3b3a81143d3565a4d41220bff299287fb3333f7d') + version('1.6.0', sha256='c03467951631af3f74a6f33ffd50f04285bc4562f79127afd95785120379d293') + version('1.5.4', sha256='acc115aaaa33de53de62dae44120ab368fabaea06f52606b77714081ecd32657') + version('1.5.3', sha256='9b09e457aeab87f613508b92a0f9f820140c9e18d05584e3f1ae384396b5dcbd') + version('1.5.2', sha256='944b9ae654d62345f51b9c2f728eee2751af32f90caeb35283bb7a5262d19cf2') + version('1.5.1', sha256='6593edb401d047d942365437be012d974990609b6eb89814d1c6422a4161771e') + version('1.5.0', sha256='01c2b810295a942fede5b711bd04bdc9677855c846fedcc999c792604e02177b') + version('1.4.1-patch', sha256='e671bf6bd4425a1fed4e7543a024201b74869bfdd029bdf9d10c53a3c2818277', url='http://www.openfst.org/twiki/pub/FST/FstDownload/openfst-1.4.1.tar.gz') - version('1.4.1', 'ca8f1730b9b9b281e515611fa9ae23c0') - version('1.4.0', '662367ec91084ffab48ee9b5716de39c') + version('1.4.1', sha256='e671bf6bd4425a1fed4e7543a024201b74869bfdd029bdf9d10c53a3c2818277') + version('1.4.0', sha256='eb557f37560438f03912b4e43335c4c9e72aa486d4f2046127131185eb88f17a') conflicts('%intel@16:') conflicts('%gcc@6:') diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py index 43684c54bd1..d4617b00284 100644 --- a/var/spack/repos/builtin/packages/openjpeg/package.py +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -20,15 +20,15 @@ class Openjpeg(CMakePackage): url = 'https://github.com/uclouvain/openjpeg/archive/v2.3.1.tar.gz' version('2.3.1', sha256='63f5a4713ecafc86de51bfad89cc07bb788e9bba24ebbf0c4ca637621aadb6a9') - version('2.3.0', '6a1f8aaa1fe55d2088e3a9c942e0f698') - version('2.2.0', '269bb0b175476f3addcc0d03bd9a97b6') - version('2.1.2', '40a7bfdcc66280b3c1402a0eb1a27624') - version('2.1.1', '0cc4b2aee0a9b6e9e21b7abcd201a3ec') - version('2.1.0', '3e1c451c087f8462955426da38aa3b3d') - version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5') - version('2.0.0', 'cdf266530fee8af87454f15feb619609') - version('1.5.2', '545f98923430369a6b046ef3632ef95c') - version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') + version('2.3.0', sha256='3dc787c1bb6023ba846c2a0d9b1f6e179f1cd255172bde9eb75b01f1e6c7d71a') + version('2.2.0', sha256='6fddbce5a618e910e03ad00d66e7fcd09cc6ee307ce69932666d54c73b7c6e7b') + version('2.1.2', sha256='4ce77b6ef538ef090d9bde1d5eeff8b3069ab56c4906f083475517c2c023dfa7') + version('2.1.1', sha256='82c27f47fc7219e2ed5537ac69545bf15ed8c6ba8e6e1e529f89f7356506dbaa') + version('2.1.0', sha256='4afc996cd5e0d16360d71c58216950bcb4ce29a3272360eb29cadb1c8bce4efc') + version('2.0.1', sha256='f184d402a218359184fd162075bb5246a68165b9776678185b6a379c49093816') + version('2.0.0', sha256='5480f801a9f88af1a456145e41f3adede1dfae425bbac66a19c7eeeba94a1249') + version('1.5.2', sha256='3734e95edd0bef6e056815591755efd822228dc3cd866894e00a2c929026b16d') + version('1.5.1', sha256='6a42fcc23cb179f69a1e94429089e5a5926aee1ffe582a0a6bd91299d297e61a') # The problem with install name of the library on MacOs was fixed starting # version 2.1.1: https://github.com/uclouvain/openjpeg/commit/b9a247b559e62e55f5561624cf4a19aee3c8afdc diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index ef5a788c5e5..b5ddba63556 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -82,7 +82,7 @@ class Openmpi(AutotoolsPackage): # Still supported version('4.0.0', sha256='2f0b8a36cfeb7354b45dda3c5425ef8393c9b04115570b615213faaa3f97366b') # libmpi.so.40.20.0 - version('3.1.4', preferred=True, sha256='957b5547bc61fd53d08af0713d0eaa5cd6ee3d58') # libmpi.so.40.10.4 + version('3.1.4', preferred=True, sha256='17a69e0054db530c7dc119f75bd07d079efa147cf94bf27e590905864fe379d6') # libmpi.so.40.10.4 version('3.1.3', sha256='8be04307c00f51401d3fb9d837321781ea7c79f2a5a4a2e5d4eaedc874087ab6') # libmpi.so.40.10.3 version('3.1.2', sha256='c654ed847f34a278c52a15c98add40402b4a90f0c540779f1ae6c489af8a76c5') # libmpi.so.40.10.2 version('3.1.1', sha256='3f11b648dd18a8b878d057e9777f2c43bf78297751ad77ae2cef6db0fe80c77c') # libmpi.so.40.10.1 @@ -108,81 +108,81 @@ class Openmpi(AutotoolsPackage): version('2.0.1', sha256='fed74f4ae619b7ebcc18150bb5bdb65e273e14a8c094e78a3fea0df59b9ff8ff') # libmpi.so.20.0.1 version('2.0.0', sha256='08b64cf8e3e5f50a50b4e5655f2b83b54653787bd549b72607d9312be44c18e0') # libmpi.so.20.0.0 - version('1.10.7', 'c87c613f9acb1a4eee21fa1ac8042579') # libmpi.so.12.0.7 - version('1.10.6', '2e65008c1867b1f47c32f9f814d41706') # libmpi.so.12.0.6 - version('1.10.5', 'd32ba9530a869d9c1eae930882ea1834') # libmpi.so.12.0.5 - version('1.10.4', '9d2375835c5bc5c184ecdeb76c7c78ac') # libmpi.so.12.0.4 - version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b') # libmpi.so.12.0.3 - version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c') # libmpi.so.12.0.2 - version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e') # libmpi.so.12.0.1 - version('1.10.0', '280cf952de68369cebaca886c5ce0304') # libmpi.so.12.0.0 + version('1.10.7', sha256='a089ece151fec974905caa35b0a59039b227bdea4e7933069e94bee4ed0e5a90') # libmpi.so.12.0.7 + version('1.10.6', sha256='65606184a084a0eda6102b01e5a36a8f02d3195d15e91eabbb63e898bd110354') # libmpi.so.12.0.6 + version('1.10.5', sha256='a95fa355ed3a905c7c187bc452529a9578e2d6bae2559d8197544ab4227b759e') # libmpi.so.12.0.5 + version('1.10.4', sha256='fb3c0c4c77896185013b6091b306d29ba592eb40d8395533da5c8bc300d922db') # libmpi.so.12.0.4 + version('1.10.3', sha256='7484bb664312082fd12edc2445b42362089b53b17fb5fce12efd4fe452cc254d') # libmpi.so.12.0.3 + version('1.10.2', sha256='8846e7e69a203db8f50af90fa037f0ba47e3f32e4c9ccdae2db22898fd4d1f59') # libmpi.so.12.0.2 + version('1.10.1', sha256='7919ecde15962bab2e26d01d5f5f4ead6696bbcacb504b8560f2e3a152bfe492') # libmpi.so.12.0.1 + version('1.10.0', sha256='26b432ce8dcbad250a9787402f2c999ecb6c25695b00c9c6ee05a306c78b6490') # libmpi.so.12.0.0 - version('1.8.8', '0dab8e602372da1425e9242ae37faf8c') # libmpi.so.1.6.3 - version('1.8.7', '2485ed6fa0fab9bb5b4e7a9f63718630') # libmpi.so.1.6.2 - version('1.8.6', 'eb569e7dc97eeaa5b1876cccf114f377') # libmpi.so.1.6.1 - version('1.8.5', '93e958914ff0e4d9634d668d2d48c793') # libmpi.so.1.6.0 - version('1.8.4', '93b7ea2c4ebae76947f942579608ae4a') # libmpi.so.1.6.0 - version('1.8.3', '2067d00853e0c33d498153fc7d268d2b') # libmpi.so.1.6.0 - version('1.8.2', '339a9fc199563bacbb359875ce8c9e20') # libmpi.so.1.5.2 - version('1.8.1', '0e12c24a28a605f681ff9a19a1aca2f1') # libmpi.so.1.5.0 - version('1.8', '5999cfb177a50c480b5d0bced379aff1') # libmpi.so.1.5.0 + version('1.8.8', sha256='a28382d1e6a36f4073412dc00836ff2524e42b674da9caf6ca7377baad790b94') # libmpi.so.1.6.3 + version('1.8.7', sha256='da629e9bd820a379cfafe15f842ee9b628d7451856085ccc23ee75ab3e1b48c7') # libmpi.so.1.6.2 + version('1.8.6', sha256='b9fe3bdfb86bd42cc53448e17f11278531b989b05ff9513bc88ba1a523f14e87') # libmpi.so.1.6.1 + version('1.8.5', sha256='4cea06a9eddfa718b09b8240d934b14ca71670c2dc6e6251a585ce948a93fbc4') # libmpi.so.1.6.0 + version('1.8.4', sha256='23158d916e92c80e2924016b746a93913ba7fae9fff51bf68d5c2a0ae39a2f8a') # libmpi.so.1.6.0 + version('1.8.3', sha256='2ef02dab61febeb74714ff80d508c00b05defc635b391ed2c8dcc1791fbc88b3') # libmpi.so.1.6.0 + version('1.8.2', sha256='ab70770faf1bac15ef44301fe2186b02f857646545492dd7331404e364a7d131') # libmpi.so.1.5.2 + version('1.8.1', sha256='171427ebc007943265f33265ec32e15e786763952e2bfa2eac95e3e192c1e18f') # libmpi.so.1.5.0 + version('1.8', sha256='35d5db86f49c0c64573b2eaf6d51c94ed8a06a9bb23dda475e602288f05e4ecf') # libmpi.so.1.5.0 - version('1.7.5', '321ab81147ac69a5bbca72652fb3b468') # libmpi.so.1.4.0 - version('1.7.4', '4aea4fb00f8956dd56ccf50e5784e03f') # libmpi.so.1.3.0 - version('1.7.3', '7d0779f73c43eb1d098ad037d60649bc') # libmpi.so.1.2.0 - version('1.7.2', 'b897b92100bd13b367e651df483421d5') # libmpi.so.1.1.2 - version('1.7.1', 'f25b446a9dcbbd6a105a99d926d34441') # libmpi.so.1.1.1 - version('1.7', 'c0e3c4b3bfcd8b8bbd027f6f4c164acb') # libmpi.so.1.1.0 + version('1.7.5', sha256='cb3eef6880537d341d5d098511d390ec853716a6ec94007c03a0d1491b2ac8f2') # libmpi.so.1.4.0 + version('1.7.4', sha256='ff8e31046c5bacfc6202d67f2479731ccd8542cdd628583ae75874000975f45c') # libmpi.so.1.3.0 + version('1.7.3', sha256='438d96c178dbf5a1bc92fa1d238a8225d87b64af26ce2a07789faaf312117e45') # libmpi.so.1.2.0 + version('1.7.2', sha256='82a1c477dcadad2032ab24d9be9e39c1042865965841911f072c49aa3544fd85') # libmpi.so.1.1.2 + version('1.7.1', sha256='554583008fa34ecdfaca22e46917cc3457a69cba08c29ebbf53eef4f4b8be171') # libmpi.so.1.1.1 + version('1.7', sha256='542e44aaef6546798c0d39c0fd849e9fbcd04a762f0ab100638499643253a513') # libmpi.so.1.1.0 - version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475') # libmpi.so.1.0.8 - version('1.6.4', '62119579ab92b2592cd96b6a9d2a8cc3') # libmpi.so.1.0.7 - version('1.6.3', 'eedb73155a7a40b0b07718494298fb25') # libmpi.so.1.0.6 - version('1.6.2', '219754715a8e40beb468bbc8f0b3251a') # libmpi.so.1.0.3 - version('1.6.1', '33d2782c20ff6be79130a703b85da8f0') # libmpi.so.1.0.3 - version('1.6', 'dd6f5bd4b3cb14d93bbf530e50e46e60') # libmpi.so.1.0.3 + version('1.6.5', sha256='fe37bab89b5ef234e0ac82dc798282c2ab08900bf564a1ec27239d3f1ad1fc85') # libmpi.so.1.0.8 + version('1.6.4', sha256='40cb113a27d76e1e915897661579f413564c032dc6e703073e6a03faba8093fa') # libmpi.so.1.0.7 + version('1.6.3', sha256='0c30cfec0e420870630fdc101ffd82f7eccc90276bc4e182f8282a2448668798') # libmpi.so.1.0.6 + version('1.6.2', sha256='5cc7744c6cc4ec2c04bc76c8b12717c4011822a2bd7236f2ea511f09579a714a') # libmpi.so.1.0.3 + version('1.6.1', sha256='077240dd1ab10f0caf26931e585db73848e9815c7119b993f91d269da5901e3a') # libmpi.so.1.0.3 + version('1.6', sha256='6e0d8b336543fb9ab78c97d364484923167857d30b266dfde1ccf60f356b9e0e') # libmpi.so.1.0.3 # Ancient - version('1.5.5', 'f882fd61ff89db856bfd8f0dfa42e1bd') # libmpi.so.1.0.3 - version('1.5.4', '51153d794c49ce6d275dba2793ab0c68') # libmpi.so.1.0.2 - version('1.5.3', '0eb8ec2aa05c74a4bc7602b01847131e') # libmpi.so.1.0.1 - version('1.5.2', 'faaee6a2777bf607d7fa1297c0b3a9ed') # libmpi.so.1.0.1 - version('1.5.1', '3f9409f5d3b617c04dea48ba8fbd703a') # libmpi.so.1.0.0 - version('1.5', '86bf5f9ef7337231abbca3350b31f112') # libmpi.so.1.0.0 + version('1.5.5', sha256='660e6e49315185f88a87b6eae3d292b81774eab7b29a9b058b10eb35d892ff23') # libmpi.so.1.0.3 + version('1.5.4', sha256='81126a95a51b8af4bb0ad28790f852c30d22d989713ec30ad22e9e0a79587ef6') # libmpi.so.1.0.2 + version('1.5.3', sha256='70745806cdbe9b945d47d9fa058f99e072328e41e40c0ced6dd75220885c5263') # libmpi.so.1.0.1 + version('1.5.2', sha256='7123b781a9fd21cc79870e7fe01e9c0d3f36935c444922661e24af523b116ab1') # libmpi.so.1.0.1 + version('1.5.1', sha256='c28bb0bd367ceeec08f739d815988fca54fc4818762e6abcaa6cfedd6fd52274') # libmpi.so.1.0.0 + version('1.5', sha256='1882b1414a94917ec26b3733bf59da6b6db82bf65b5affd7f0fcbd96efaca506') # libmpi.so.1.0.0 - version('1.4.5', '84ddd2772f46d35da79e1db8a274c99d') # libmpi.so.0.0.4 - version('1.4.4', 'e58a1ea7b8af62453aaa0ddaee5f26a0') # libmpi.so.0.0.3 - version('1.4.3', 'd2ead141c43b915343f5c5a18f3b5016') # libmpi.so.0.0.2 - version('1.4.2', '53b26fa2586aedaf73cf40effbfcc2f3') # libmpi.so.0.0.2 - version('1.4.1', '28a820c85e02973809df881fdeddd15e') # libmpi.so.0.0.1 - version('1.4', '9786ec0698afed9498ce43dc3978a435') # libmpi.so.0.0.1 + version('1.4.5', sha256='a3857bc69b7d5258cf7fc1ed1581d9ac69110f5c17976b949cb7ec789aae462d') # libmpi.so.0.0.4 + version('1.4.4', sha256='9ad125304a89232d5b04da251f463fdbd8dcd997450084ba4227e7f7a095c3ed') # libmpi.so.0.0.3 + version('1.4.3', sha256='220b72b1c7ee35469ff74b4cfdbec457158ac6894635143a33e9178aa3981015') # libmpi.so.0.0.2 + version('1.4.2', sha256='19129e3d51860ad0a7497ede11563908ba99c76b3a51a4d0b8801f7e2db6cd80') # libmpi.so.0.0.2 + version('1.4.1', sha256='d4d71d7c670d710d2d283ea60af50d6c315318a4c35ec576bedfd0f3b7b8c218') # libmpi.so.0.0.1 + version('1.4', sha256='fa55edef1bd8af256e459d4d9782516c6998b9d4698eda097d5df33ae499858e') # libmpi.so.0.0.1 - version('1.3.4', '978c29f3b671856daa0fc67459b73e01') # libmpi.so.0.0.1 - version('1.3.3', 'f6cdc9c195daa8571b2e509e952d6755') # libmpi.so.0.0.0 - version('1.3.2', '75781dc31255cd841701c065e239d994') # libmpi.so.0.0.0 - version('1.3.1', 'd759523b0752139872c534714d641d64') # libmpi.so.0.0.0 - version('1.3', 'efbba7d652d1e430d456f65d7a2e339b') # libmpi.so.0.0.0 + version('1.3.4', sha256='fbfe4b99b0c98f81a4d871d02f874f84ea66efcbb098f6ad84ebd19353b681fc') # libmpi.so.0.0.1 + version('1.3.3', sha256='e1425853282da9237f5b41330207e54da1dc803a2e19a93dacc3eca1d083e422') # libmpi.so.0.0.0 + version('1.3.2', sha256='c93ed90962d879a2923bed17171ed9217036ee1279ffab0925ea7eead26105d8') # libmpi.so.0.0.0 + version('1.3.1', sha256='22d18919ddc5f49d55d7d63e2abfcdac34aa0234427e861e296a630c6c11632c') # libmpi.so.0.0.0 + version('1.3', sha256='864706d88d28b586a045461a828962c108f5912671071bc3ef0ca187f115e47b') # libmpi.so.0.0.0 - version('1.2.9', '78c2aebbb746610ed12bdedcc2b6ec0e') # libmpi.so.0.0.0 - version('1.2.8', '7f2d5af02101c5f01173f4f6de296549') # libmpi.so.0.0.0 - version('1.2.7', 'b5ae3059fba71eba4a89a2923da8223f') # libmpi.so.0.0.0 - version('1.2.6', 'f126793b68e71f5ec4a192c40675af2d') # libmpi.so.0.0.0 - version('1.2.5', 'c6e82aab6cdcd425bf29217e8317d7dc') # libmpi.so.0.0.0 - version('1.2.4', '311b38c597f54d8d6b277225ef458666') # libmpi.so.0.0.0 - version('1.2.3', 'ae980bb00f9686934a1143701cc041e4') # libmpi.so.0.0.0 - version('1.2.2', '7f553317e388c4efe479e908b66f910d') # libmpi.so.0.0.0 - version('1.2.1', 'ceaa42891edba2324a94fdd0b87e46ca') # libmpi.so.0.0.0 - version('1.2', '37e8d4edad54a8d8c3127fbef87ebda1') # libmpi.so.0.0.0 + version('1.2.9', sha256='0eb36abe09ba7bf6f7a70255974e5d0a273f7f32d0e23419862c6dcc986f1dff') # libmpi.so.0.0.0 + version('1.2.8', sha256='75b286cb3b1bf6528a7e64ee019369e0601b8acb5c3c167a987f755d1e41c95c') # libmpi.so.0.0.0 + version('1.2.7', sha256='d66c7f0bb11494023451651d0e61afaef9d2199ed9a91ed08f0dedeb51541c36') # libmpi.so.0.0.0 + version('1.2.6', sha256='e5b27af5a153a257b1562a97bbf7164629161033934558cefd8e1e644a9f73d3') # libmpi.so.0.0.0 + version('1.2.5', sha256='3c3aed872c17165131c77bd7a12fe8aec776cb23da946b7d12840db93ab79322') # libmpi.so.0.0.0 + version('1.2.4', sha256='594a3a0af69cc7895e0d8f9add776a44bf9ed389794323d0b1b45e181a97e538') # libmpi.so.0.0.0 + version('1.2.3', sha256='f936ca3a197e5b2d1a233b7d546adf07898127683b03c4b37cf31ae22a6f69bb') # libmpi.so.0.0.0 + version('1.2.2', sha256='aa763e0e6a6f5fdff8f9d3fc988a4ba0ed902132d292c85aef392cc65bb524e6') # libmpi.so.0.0.0 + version('1.2.1', sha256='a94731d84fb998df33960e0b57ea5661d35e7c7cd9d03d900f0b6a5a72e4546c') # libmpi.so.0.0.0 + version('1.2', sha256='ba0bfa3dec2ead38a3ed682ca36a0448617b8e29191ab3f48c9d0d24d87d14c0') # libmpi.so.0.0.0 - version('1.1.5', '6aada92896a1830ece6d3ba1e66a17fa') # libmpi.so.0.0.0 - version('1.1.4', '28940b182156478fa442397b0c9660e1') # libmpi.so.0.0.0 - version('1.1.3', 'bbaa7fe9d556212d877d872544a31569') # libmpi.so.0.0.0 - version('1.1.2', '53877ec8bca5f6e505496b6b94b1d850') # libmpi.so.0.0.0 - version('1.1.1', '498b9322ae0ad512026a008a30c7e0b5') # libmpi.so.0.0.0 - version('1.1', '821af8bbb7a8e85ec707cb4c3b6bcbf6') # libmpi.so.0.0.0 + version('1.1.5', sha256='913deaedf3498bd5d06299238ec4d048eb7af9c3afd8e32c12f4257c8b698a91') # libmpi.so.0.0.0 + version('1.1.4', sha256='21c37f85df7e959f17cc7cb5571d8db2a94ed2763e3e96e5d052aff2725c1d18') # libmpi.so.0.0.0 + version('1.1.3', sha256='c33f8f5e65cfe872173616cca27ae8dc6d93ea66e0708118b9229128aecc174f') # libmpi.so.0.0.0 + version('1.1.2', sha256='3bd8d9fe40b356be7f9c3d336013d3865f8ca6a79b3c6e7ef28784f6c3a2b8e6') # libmpi.so.0.0.0 + version('1.1.1', sha256='dc31aaec986c4ce436dbf31e73275ed1a9391432dcad7609de8d0d3a78d2c700') # libmpi.so.0.0.0 + version('1.1', sha256='ebe14801d2caeeaf47b0e437b43f73668b711f4d3fcff50a0d665d4bd4ea9531') # libmpi.so.0.0.0 - version('1.0.2', 'fd32861d643f9fe539a01d0d5b836f41') # libmpi.so.0.0.0 - version('1.0.1', '8abccca5cdddc81a6d9d9e22b3bb6db9') # libmpi.so.0.0.0 - version('1.0', 'f5dcb5d3a98f2e5a9c2a0caaef54d806') # libmpi.so.0.0.0 + version('1.0.2', sha256='ccd1074d7dd9566b73812d9882c84e446a8f4c77b6f471d386d3e3b9467767b8') # libmpi.so.0.0.0 + version('1.0.1', sha256='f801b7c8ea6c485ac0709a628a479aeafa718a205ed6bc0cf2c684bc0cc73253') # libmpi.so.0.0.0 + version('1.0', sha256='cf75e56852caebe90231d295806ac3441f37dc6d9ad17b1381791ebb78e21564') # libmpi.so.0.0.0 patch('ad_lustre_rwcontig_open_source.patch', when="@1.6.5") patch('llnl-platforms.patch', when="@1.6.5") diff --git a/var/spack/repos/builtin/packages/opennurbs/package.py b/var/spack/repos/builtin/packages/opennurbs/package.py index 81ab620c384..0ea61fa36f5 100644 --- a/var/spack/repos/builtin/packages/opennurbs/package.py +++ b/var/spack/repos/builtin/packages/opennurbs/package.py @@ -19,7 +19,7 @@ class Opennurbs(Package): version('develop', branch='develop') - version('percept', '59163fd085a24c7a4c2170c70bb60fea', + version('percept', sha256='d12a8f14f0b27d286fb7a75ab3c4e300f77d1fbb028326d1c8d28e4641605538', url='https://github.com/PerceptTools/percept/raw/master/build-cmake/opennurbs-percept.tar.gz') variant('shared', default=True, diff --git a/var/spack/repos/builtin/packages/openslide/package.py b/var/spack/repos/builtin/packages/openslide/package.py index f3f45255793..b3cb4d55f2b 100644 --- a/var/spack/repos/builtin/packages/openslide/package.py +++ b/var/spack/repos/builtin/packages/openslide/package.py @@ -12,7 +12,7 @@ class Openslide(AutotoolsPackage): homepage = "http://openslide.org/" url = "https://github.com/openslide/openslide/releases/download/v3.4.1/openslide-3.4.1.tar.xz" - version('3.4.1', 'ad9fa84775ed6b505d6f50bf6420c6bf') + version('3.4.1', sha256='9938034dba7f48fadc90a2cdf8cfe94c5613b04098d1348a5ff19da95b990564') depends_on('openjpeg') depends_on('jpeg') diff --git a/var/spack/repos/builtin/packages/openssh/package.py b/var/spack/repos/builtin/packages/openssh/package.py index 1487760be53..59252cc833f 100644 --- a/var/spack/repos/builtin/packages/openssh/package.py +++ b/var/spack/repos/builtin/packages/openssh/package.py @@ -18,18 +18,18 @@ class Openssh(AutotoolsPackage): homepage = "https://www.openssh.com/" url = "https://mirrors.sonic.net/pub/OpenBSD/OpenSSH/portable/openssh-7.6p1.tar.gz" - version('7.9p1', '6b4b3ba2253d84ed3771c8050728d597c91cfce898713beb7b64a305b6f11aad') - version('7.6p1', '06a88699018e5fef13d4655abfed1f63') - version('7.5p1', '652fdc7d8392f112bef11cacf7e69e23') - version('7.4p1', 'b2db2a83caf66a208bb78d6d287cdaa3') - version('7.3p1', 'dfadd9f035d38ce5d58a3bf130b86d08') - version('7.2p2', '13009a9156510d8f27e752659075cced') - version('7.1p2', '4d8547670e2a220d5ef805ad9e47acf2') - version('7.0p1', '831883f251ac34f0ab9c812acc24ee69') - version('6.9p1', '0b161c44fc31fbc6b76a6f8ae639f16f') - version('6.8p1', '08f72de6751acfbd0892b5f003922701') - version('6.7p1', '3246aa79317b1d23cae783a3bf8275d6') - version('6.6p1', '3e9800e6bca1fbac0eea4d41baa7f239') + version('7.9p1', sha256='6b4b3ba2253d84ed3771c8050728d597c91cfce898713beb7b64a305b6f11aad') + version('7.6p1', sha256='a323caeeddfe145baaa0db16e98d784b1fbc7dd436a6bf1f479dfd5cd1d21723') + version('7.5p1', sha256='9846e3c5fab9f0547400b4d2c017992f914222b3fd1f8eee6c7dc6bc5e59f9f0') + version('7.4p1', sha256='1b1fc4a14e2024293181924ed24872e6f2e06293f3e8926a376b8aec481f19d1') + version('7.3p1', sha256='3ffb989a6dcaa69594c3b550d4855a5a2e1718ccdde7f5e36387b424220fbecc') + version('7.2p2', sha256='a72781d1a043876a224ff1b0032daa4094d87565a68528759c1c2cab5482548c') + version('7.1p2', sha256='dd75f024dcf21e06a0d6421d582690bf987a1f6323e32ad6619392f3bfde6bbd') + version('7.0p1', sha256='fd5932493a19f4c81153d812ee4e042b49bbd3b759ab3d9344abecc2bc1485e5') + version('6.9p1', sha256='6e074df538f357d440be6cf93dc581a21f22d39e236f217fcd8eacbb6c896cfe') + version('6.8p1', sha256='3ff64ce73ee124480b5bf767b9830d7d3c03bbcb6abe716b78f0192c37ce160e') + version('6.7p1', sha256='b2f8394eae858dabbdef7dac10b99aec00c95462753e80342e530bbb6f725507') + version('6.6p1', sha256='48c1f0664b4534875038004cc4f3555b8329c2a81c1df48db5c517800de203bb') depends_on('openssl@:1.0', when='@:7.7p1') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index d3ebcc5d183..4c3a93c3256 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -37,10 +37,10 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package version('1.1.0k', sha256='efa4965f4f773574d6cbda1cf874dbbe455ab1c0d4f906115f867d30444470b1') version('1.1.0j', sha256='31bec6c203ce1a8e93d5994f4ed304c63ccf07676118b6634edded12ad1b3246') version('1.1.0i', sha256='ebbfc844a8c8cc0ea5dc10b86c9ce97f401837f3fa08c17b2cdadc118253cf99') - version('1.1.0g', 'ba5f1b8b835b88cadbce9b35ed9531a6') - version('1.1.0e', '51c42d152122e474754aea96f66928c6') - version('1.1.0d', '711ce3cd5f53a99c0e12a7d5804f0f63') - version('1.1.0c', '601e8191f72b18192a937ecf1a800f3f') + version('1.1.0g', sha256='de4d501267da39310905cb6dc8c6121f7a2cad45a7707f76df828fe1b85073af') + version('1.1.0e', sha256='57be8618979d80c910728cfc99369bf97b2a1abd8f366ab6ebdee8975ad3874c') + version('1.1.0d', sha256='7d5ebb9e89756545c156ff9c13cf2aa6214193b010a468a3bc789c3c28fe60df') + version('1.1.0c', sha256='fc436441a2e05752d31b4e46115eb89709a28aef96d4fe786abe92409b2fd6f5') # Our previous LTS version (1.0.2 series) will continue to be supported # until 31st December 2019 (security fixes only during the last year of @@ -49,24 +49,24 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package version('1.0.2s', sha256='cabd5c9492825ce5bd23f3c3aeed6a97f8142f606d893df216411f07d1abab96') version('1.0.2r', sha256='ae51d08bba8a83958e894946f15303ff894d75c2b8bbd44a852b64e3fe11d0d6') version('1.0.2p', sha256='50a98e07b1a89eb8f6a99477f262df71c6fa7bef77df4dc83025a2845c827d00') - version('1.0.2o', '44279b8557c3247cbe324e2322ecd114') - version('1.0.2n', '13bdc1b1d1ff39b6fd42a255e74676a4') - version('1.0.2m', '10e9e37f492094b9ef296f68f24a7666') - version('1.0.2k', 'f965fc0bf01bf882b31314b61391ae65') - version('1.0.2j', '96322138f0b69e61b7212bc53d5e912b') - version('1.0.2i', '678374e63f8df456a697d3e5e5a931fb') - version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0') - version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa') - version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d') - version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5') - version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a') + version('1.0.2o', sha256='ec3f5c9714ba0fd45cb4e087301eb1336c317e0d20b575a125050470e8089e4d') + version('1.0.2n', sha256='370babb75f278c39e0c50e8c4e7493bc0f18db6867478341a832a982fd15a8fe') + version('1.0.2m', sha256='8c6ff15ec6b319b50788f42c7abc2890c08ba5a1cdcd3810eb9092deada37b0f') + version('1.0.2k', sha256='6b3977c61f2aedf0f96367dcfb5c6e578cf37e7b8d913b4ecb6643c3cb88d8c0') + version('1.0.2j', sha256='e7aff292be21c259c6af26469c7a9b3ba26e9abaaffd325e3dccc9785256c431') + version('1.0.2i', sha256='9287487d11c9545b6efb287cdb70535d4e9b284dd10d51441d9b9963d000de6f') + version('1.0.2h', sha256='1d4007e53aad94a5b2002fe045ee7bb0b3d98f1a47f8b2bc851dcd1c74332919') + version('1.0.2g', sha256='b784b1b3907ce39abf4098702dade6365522a253ad1552e267a9a0e89594aa33') + version('1.0.2f', sha256='932b4ee4def2b434f85435d9e3e19ca8ba99ce9a065a61524b429a9d5e9b2e9c') + version('1.0.2e', sha256='e23ccafdb75cfcde782da0151731aa2185195ac745eea3846133f2e05c0e0bff') + version('1.0.2d', sha256='671c36487785628a703374c652ad2cebea45fa920ae5681515df25d9f2c9a8c8') # The 1.0.1 version is now out of support and should not be used. - version('1.0.1u', '130bb19745db2a5a09f22ccbbf7e69d0') - version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1') - version('1.0.1r', '1abd905e079542ccae948af37e393d28') - version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') - version('1.0.1e', '66bf6f10f060d561929de96f9dfe5b8c') + version('1.0.1u', sha256='4312b4ca1215b6f2c97007503d80db80d5157f76f8f7d3febbe6b4c56ff26739') + version('1.0.1t', sha256='4a6ee491a2fdb22e519c76fdc2a628bb3cec12762cd456861d207996c8a07088') + version('1.0.1r', sha256='784bd8d355ed01ce98b812f873f8b2313da61df7c7b5677fcf2e57b0863a3346') + version('1.0.1h', sha256='9d1c8a9836aa63e2c6adb684186cbd4371c9e9dcc01d6e3bb447abf2d4d3d093') + version('1.0.1e', sha256='f74f15e8c8ff11aa3d5bb5f276d202ec18d7246e95f961db76054199c69c1ae3') variant('systemcerts', default=True, description='Use system certificates') diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py index 9c9ed311eef..13d2c3ef971 100644 --- a/var/spack/repos/builtin/packages/opium/package.py +++ b/var/spack/repos/builtin/packages/opium/package.py @@ -12,7 +12,7 @@ class Opium(Package): homepage = "https://opium.sourceforge.net/index.html" url = "https://downloads.sourceforge.net/project/opium/opium/opium-v3.8/opium-v3.8-src.tgz" - version('3.8', 'f710c0f869e70352b4a510c31e13bf9f') + version('3.8', sha256='edee6606519330aecaee436ee8cfb0a33788b5677861d59e38aba936e87d5ad3') depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/opus/package.py b/var/spack/repos/builtin/packages/opus/package.py index 0159adad9d1..7efac2e296d 100644 --- a/var/spack/repos/builtin/packages/opus/package.py +++ b/var/spack/repos/builtin/packages/opus/package.py @@ -12,25 +12,25 @@ class Opus(AutotoolsPackage): homepage = "http://opus-codec.org/" url = "http://downloads.xiph.org/releases/opus/opus-1.1.4.tar.gz" - version('1.1.4', 'a2c09d995d0885665ff83b5df2505a5f') - version('1.1.3', '32bbb6b557fe1b6066adc0ae1f08b629') - version('1.1.2', '1f08a661bc72930187893a07f3741a91') - version('1.1.1', 'cfb354d4c65217ca32a762f8ab15f2ac') - version('1.1', 'c5a8cf7c0b066759542bc4ca46817ac6') - version('1.0.3', '86eedbd3c5a0171d2437850435e6edff') - version('1.0.2', 'c503ad05a59ddb44deab96204401be03') - version('1.0.1', 'bbac19996957b404a1139816e2f357f5') - version('1.0.0', 'ec3ff0a16d9ad8c31a8856d13d97b155') - version('0.9.14', 'c7161b247a8437ae6b0f11dd872e69e8') - version('0.9.10', 'afbda2fd20dc08e6075db0f60297a137') - version('0.9.9', '0c18f0aac37f1ed955f5d694ddd88000') - version('0.9.8', '76c1876eae9169dee808ff4710d847cf') - version('0.9.7', '49834324ab618105cf112e161770b422') - version('0.9.6', '030556bcaebb241505f8577e92abe6d4') - version('0.9.5', '6bec090fd28996da0336e165b153ebd8') - version('0.9.3', '934226d4f572d01c5848bd70538248f5') - version('0.9.2', '8b9047956c4a781e05d3ac8565cd28f5') - version('0.9.1', 'f58214e530928aa3db1dec217d5dfcd4') - version('0.9.0', '8a729db587430392e64280a499e9d061') + version('1.1.4', sha256='9122b6b380081dd2665189f97bfd777f04f92dc3ab6698eea1dbb27ad59d8692') + version('1.1.3', sha256='58b6fe802e7e30182e95d0cde890c0ace40b6f125cffc50635f0ad2eef69b633') + version('1.1.2', sha256='0e290078e31211baa7b5886bcc8ab6bc048b9fc83882532da4a1a45e58e907fd') + version('1.1.1', sha256='9b84ff56bd7720d5554103c557664efac2b8b18acc4bbcc234cb881ab9a3371e') + version('1.1', sha256='b9727015a58affcf3db527322bf8c4d2fcf39f5f6b8f15dbceca20206cbe1d95') + version('1.0.3', sha256='191a089c92dbc403de6980463dd3604b65beb12d283c607e246c8076363cb49c') + version('1.0.2', sha256='da615edbee5d019c1833071d69a4782c19f178cf9ca1401375036ecef25cd78a') + version('1.0.1', sha256='80fa5c3caf2ac0fd68f8a22cce1564fc46b368c773a17554887d0066fe1841ef') + version('1.0.0', sha256='9250fcc74472d45c1e14745542ec9c8d09982538aefed56962495614be3e0d2d') + version('0.9.14', sha256='b1cad6846a8f819a141009fe3f8f10c946e8eff7e9c2339cd517bb136cc59eae') + version('0.9.10', sha256='4e379a98ba95bbbfe9087ef10fdd05c8ac9060b6d695f587ea82a7b43a0df4fe') + version('0.9.9', sha256='2f62359f09151fa3b242040dc9b4c5b6bda15557c5daea59c8420f1a2ff328b7') + version('0.9.8', sha256='4aa30d2e0652ffb4a7a22cc8a29c4ce78267626f560a2d9213b1d2d4e618cf36') + version('0.9.7', sha256='1b69772c31c5cbaa43d1dfa5b1c495fc29712e8e0ff69d6f8ad46459e5c6715f') + version('0.9.6', sha256='3bfaeb25f4b4a625a0bc994d6fc6f6776a05193f60099e0a99f7530c6b256309') + version('0.9.5', sha256='53801066fa97329768e7b871fd1495740269ec46802e1c9051aa7e78c6edee5b') + version('0.9.3', sha256='d916e34c18a396eb7dffc47af754f441af52a290b761e20db9aedb65928c699e') + version('0.9.2', sha256='6e85c1b57e1d7b7dfe2928bf92586b96b73a9067e054ede45bd8e6d24bd30582') + version('0.9.1', sha256='206221afc47b87496588013bd4523e1e9f556336c0813f4372773fc536dd4293') + version('0.9.0', sha256='b2f75c4ac5ab837845eb028413fae2a28754bfb0a6d76416e2af1441ef447649') depends_on('libvorbis') diff --git a/var/spack/repos/builtin/packages/orfm/package.py b/var/spack/repos/builtin/packages/orfm/package.py index 68c992e8a80..0d55ca42432 100644 --- a/var/spack/repos/builtin/packages/orfm/package.py +++ b/var/spack/repos/builtin/packages/orfm/package.py @@ -15,6 +15,6 @@ class Orfm(AutotoolsPackage): homepage = "https://github.com/wwood/OrfM" url = "https://github.com/wwood/OrfM/releases/download/v0.7.1/orfm-0.7.1.tar.gz" - version('0.7.1', 'fcf18283a028cea2af90663a76a73a2a') + version('0.7.1', sha256='19f39c72bcc48127b757613c5eef4abae95ee6c82dccf96b041db527b27f319a') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/orthofinder/package.py b/var/spack/repos/builtin/packages/orthofinder/package.py index e854bcf5f6f..bb16a134c5f 100644 --- a/var/spack/repos/builtin/packages/orthofinder/package.py +++ b/var/spack/repos/builtin/packages/orthofinder/package.py @@ -20,7 +20,7 @@ class Orthofinder(Package): homepage = "https://github.com/davidemms/OrthoFinder" url = "https://github.com/davidemms/OrthoFinder/releases/download/2.2.0/OrthoFinder-2.2.0.tar.gz" - version('2.2.0', '4ff585e1eb148fc694a219296fbdd431') + version('2.2.0', sha256='7314f3fdfb24d84aa5b9ee27ce9f670df314889c12b8100e4e476c2d21a1c8e7') depends_on('blast-plus', type='run') depends_on('mcl', type='run') diff --git a/var/spack/repos/builtin/packages/orthomcl/package.py b/var/spack/repos/builtin/packages/orthomcl/package.py index 65c66c43916..1d939688997 100644 --- a/var/spack/repos/builtin/packages/orthomcl/package.py +++ b/var/spack/repos/builtin/packages/orthomcl/package.py @@ -13,7 +13,7 @@ class Orthomcl(Package): homepage = "http://orthomcl.org/orthomcl/" url = "http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz" - version('2.0.9', '2e0202ed4e36a753752c3567edb9bba9') + version('2.0.9', sha256='5f96d23ff255778535c4926d75b19f059db0c01be1ac599289d2431115d68640') depends_on('perl', type=('build', 'run')) depends_on('blast-plus') diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py index 3bc61a2a257..333287c80a0 100644 --- a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py @@ -17,10 +17,10 @@ class OsuMicroBenchmarks(AutotoolsPackage): homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/" url = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.tar.gz" - version('5.6.1', '0d2389d93ec2a0be60f21b0aecd14345') - version('5.5', 'bcb970d5a1f3424e2c7302ff60611008') - version('5.4', '7e7551879b944d71b7cc60d476d5403b') - version('5.3', '42e22b931d451e8bec31a7424e4adfc2') + version('5.6.1', sha256='943c426a653a6c56200193d747755efaa4c4e6f23b3571b0e3ef81ecd21b1063') + version('5.5', sha256='1e5a4ae5ef2b03143a815b21fefc23373c1b079cc163c2fa1ed1e0c9b83c28ad') + version('5.4', sha256='e1ca762e13a07205a59b59ad85e85ce0f826b70f76fd555ce5568efb1f2a8f33') + version('5.3', sha256='d7b3ad4bee48ac32f5bef39650a88f8f2c23a3050b17130c63966283edced89b') variant('cuda', default=False, description="Enable CUDA support") diff --git a/var/spack/repos/builtin/packages/otf/package.py b/var/spack/repos/builtin/packages/otf/package.py index 092a08be395..eeab4e105ed 100644 --- a/var/spack/repos/builtin/packages/otf/package.py +++ b/var/spack/repos/builtin/packages/otf/package.py @@ -14,7 +14,7 @@ class Otf(AutotoolsPackage): homepage = "http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/otf/index_html/document_view?set_language=en" url = "http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz" - version('1.12.5salmon', 'bf260198633277031330e3356dcb4eec') + version('1.12.5salmon', sha256='0a8427360dedb38e8ddca30f14d95f826420c550337c5a79dbb754904e194088') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py index f163c02dcc0..1feae614d63 100644 --- a/var/spack/repos/builtin/packages/otf2/package.py +++ b/var/spack/repos/builtin/packages/otf2/package.py @@ -15,14 +15,14 @@ class Otf2(AutotoolsPackage): homepage = "http://www.vi-hps.org/projects/score-p" url = "https://www.vi-hps.org/cms/upload/packages/otf2/otf2-2.1.1.tar.gz" - version('2.2', 'd0519af93839dc778eddca2ce1447b1ee23002c41e60beac41ea7fe43117172d') - version('2.1.1', 'e51ad0d8ca374d25f47426746ca629e7') - version('2.1', 'e2994e53d9b7c2cbd0c4f564d638751e') - version('2.0', '5b546188b25bc1c4e285e06dddf75dfc') - version('1.5.1', '16a9df46e0da78e374f5d12c8cdc1109') - version('1.4', 'a23c42e936eb9209c4e08b61c3cf5092') - version('1.3.1', 'd0ffc4e858455ace4f596f910e68c9f2') - version('1.2.1', '8fb3e11fb7489896596ae2c7c83d7fc8') + version('2.2', sha256='d0519af93839dc778eddca2ce1447b1ee23002c41e60beac41ea7fe43117172d') + version('2.1.1', sha256='01591b42e76f396869ffc84672f4eaa90ee8ec2a8939755d9c0b5b8ecdcf47d3') + version('2.1', sha256='8ad38ea0461099e34f00f2947af4409ce9b9c379e14c3f449ba162e51ac4cad3') + version('2.0', sha256='bafe0ac08e0a13e71568e5774dc83bd305d907159b4ceeb53d2e9f6e29462754') + version('1.5.1', sha256='a4dc9f6c99376030b43a4c7b1ee77cfb530b03928ea688c6d1a380b3f4e8e488') + version('1.4', sha256='fb5fe169003c01e40848e224f09c440014e9872e84d2ca02ce7fffdd3f879a2f') + version('1.3.1', sha256='c4605ace845d89fb1a19223137b92cc503b01e3db5eda8c9e0715d0cfcf2e4b9') + version('1.2.1', sha256='1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4') def configure_args(self): return [ diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index 039c82485ff..9eda813a1a8 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -15,8 +15,8 @@ class P4est(AutotoolsPackage): maintainers = ['davydden'] version('2.2', sha256='1549cbeba29bee2c35e7cc50a90a04961da5f23b6eada9c8047f511b90a8e438') - version('2.0', 'c522c5b69896aab39aa5a81399372a19a6b03fc6200d2d5d677d9a22fe31029a') - version('1.1', '37ba7f4410958cfb38a2140339dbf64f') + version('2.0', sha256='c522c5b69896aab39aa5a81399372a19a6b03fc6200d2d5d677d9a22fe31029a') + version('1.1', sha256='0b5327a35f0c869bf920b8cab5f20caa4eb55692eaaf1f451d5de30285b25139') variant('mpi', default=True, description='Enable MPI') variant('openmp', default=False, description='Enable OpenMP') diff --git a/var/spack/repos/builtin/packages/p7zip/package.py b/var/spack/repos/builtin/packages/p7zip/package.py index 7fc8fe91a76..160cf825654 100644 --- a/var/spack/repos/builtin/packages/p7zip/package.py +++ b/var/spack/repos/builtin/packages/p7zip/package.py @@ -12,7 +12,7 @@ class P7zip(MakefilePackage): homepage = "http://p7zip.sourceforge.net" url = "https://downloads.sourceforge.net/project/p7zip/p7zip/16.02/p7zip_16.02_src_all.tar.bz2" - version('16.02', 'a0128d661cfe7cc8c121e73519c54fbf') + version('16.02', sha256='5eb20ac0e2944f6cb9c2d51dd6c4518941c185347d4089ea89087ffdd6e2341f') # all3 includes 7z, 7za, and 7zr build_targets = ['all3'] diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py index 43bcf71db01..7cc1496b53a 100644 --- a/var/spack/repos/builtin/packages/pagit/package.py +++ b/var/spack/repos/builtin/packages/pagit/package.py @@ -13,7 +13,7 @@ class Pagit(Package): homepage = "http://www.sanger.ac.uk/science/tools/pagit" url = "ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz" - version('1.01', '2c4e8512c8c02073146b50b328962e9d') + version('1.01', sha256='8069c1d236804cf4ea782495adcc50d18561ef466af06b21946b980b3c37ad55') depends_on('java', type=('build', 'run')) depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/pagmo/package.py b/var/spack/repos/builtin/packages/pagmo/package.py index 920947334b1..11a8b922a8b 100644 --- a/var/spack/repos/builtin/packages/pagmo/package.py +++ b/var/spack/repos/builtin/packages/pagmo/package.py @@ -19,7 +19,7 @@ class Pagmo(CMakePackage): homepage = "https://esa.github.io/pagmo/" url = "https://github.com/esa/pagmo/archive/1.1.7.tar.gz" - version('1.1.7', '57ee65a5871ae36ab97087af5199cb89') + version('1.1.7', sha256='6d8fab89ef9d5d5f30f148225bf9b84b2e5a38997f3d68b85547840e9fd95172') variant('examples', default=False, description='Build examples') variant('cxx', default=True, description='Build the C++ interface') diff --git a/var/spack/repos/builtin/packages/panda/package.py b/var/spack/repos/builtin/packages/panda/package.py index dc16779e228..e607f12627a 100644 --- a/var/spack/repos/builtin/packages/panda/package.py +++ b/var/spack/repos/builtin/packages/panda/package.py @@ -12,7 +12,7 @@ class Panda(CMakePackage): homepage = "http://comopt.ifi.uni-heidelberg.de/software/PANDA/index.html" url = "http://comopt.ifi.uni-heidelberg.de/software/PANDA/downloads/panda-2016-03-07.tar" - version('2016-03-07', 'b06dc312ee56e13eefea9c915b70fcef') + version('2016-03-07', sha256='9fae1544626db417ade7318d26bc43c8af04151b9f7679b6d742dba598762037') # Note: Panda can also be built without MPI support diff --git a/var/spack/repos/builtin/packages/pandaseq/package.py b/var/spack/repos/builtin/packages/pandaseq/package.py index 650c0aab4b9..4ad9060d562 100644 --- a/var/spack/repos/builtin/packages/pandaseq/package.py +++ b/var/spack/repos/builtin/packages/pandaseq/package.py @@ -14,8 +14,8 @@ class Pandaseq(AutotoolsPackage): homepage = "https://github.com/neufeld/pandaseq" url = "https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz" - version('2.11', 'a8ae0e938bac592fc07dfa668147d80b') - version('2.10', '5b5b04c9b693a999f10a9c9bd643f068') + version('2.11', sha256='6e3e35d88c95f57d612d559e093656404c1d48c341a8baa6bef7bb0f09fc8f82') + version('2.10', sha256='93cd34fc26a7357e14e386b9c9ba9b28361cf4da7cf62562dc8501e220f9a561') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py index 8facdc1b0a4..35fd629b548 100644 --- a/var/spack/repos/builtin/packages/pango/package.py +++ b/var/spack/repos/builtin/packages/pango/package.py @@ -16,10 +16,10 @@ class Pango(AutotoolsPackage): list_url = "http://ftp.gnome.org/pub/gnome/sources/pango/" list_depth = 1 - version('1.41.0', '1f76ef95953dc58ee5d6a53e5f1cb6db913f3e0eb489713ee9266695cae580ba') - version('1.40.3', 'abba8b5ce728520c3a0f1535eab19eac3c14aeef7faa5aded90017ceac2711d3') - version('1.40.1', 'e27af54172c72b3ac6be53c9a4c67053e16c905e02addcf3a603ceb2005c1a40') - version('1.36.8', '18dbb51b8ae12bae0ab7a958e7cf3317c9acfc8a1e1103ec2f147164a0fc2d07') + version('1.41.0', sha256='1f76ef95953dc58ee5d6a53e5f1cb6db913f3e0eb489713ee9266695cae580ba') + version('1.40.3', sha256='abba8b5ce728520c3a0f1535eab19eac3c14aeef7faa5aded90017ceac2711d3') + version('1.40.1', sha256='e27af54172c72b3ac6be53c9a4c67053e16c905e02addcf3a603ceb2005c1a40') + version('1.36.8', sha256='18dbb51b8ae12bae0ab7a958e7cf3317c9acfc8a1e1103ec2f147164a0fc2d07') variant('X', default=False, description="Enable an X toolkit") diff --git a/var/spack/repos/builtin/packages/pangomm/package.py b/var/spack/repos/builtin/packages/pangomm/package.py index 42b5b5721cf..0fec54ba4ee 100644 --- a/var/spack/repos/builtin/packages/pangomm/package.py +++ b/var/spack/repos/builtin/packages/pangomm/package.py @@ -12,8 +12,8 @@ class Pangomm(AutotoolsPackage): homepage = "http://www.pango.org/" url = "https://ftp.gnome.org/pub/GNOME/sources/pangomm/2.14/pangomm-2.14.1.tar.gz" - version('2.14.1', '607a404291d9eeb895f1df3d08f531d7') - version('2.14.0', '897d8c56cec4a9c297a426eb0fc2af91') + version('2.14.1', sha256='2ea6cee273cca1aae2ee5a5dac0c416b4dc354e46debb51f20c6eeba828f5ed5') + version('2.14.0', sha256='baa3b231c9498fb1140254e3feb4eb93c638f07e6e26ae0e36c3699ec14d80fd') depends_on('pango') depends_on('glibmm') diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 9379d4f2865..7f863fa7f65 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -22,13 +22,13 @@ class Papi(Package): homepage = "http://icl.cs.utk.edu/papi/index.html" url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" - version('5.7.0', 'd1a3bb848e292c805bc9f29e09c27870e2ff4cda6c2fba3b7da8b4bba6547589') - version('5.6.0', 'fdd075860b2bc4b8de8b8b5c3abf594a') - version('5.5.1', '86a8a6f3d0f34cd83251da3514aae15d') - version('5.5.0', '5e1244a04ca031d4cc29b46ce3dd05b5') - version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412') - version('5.4.1', '9134a99219c79767a11463a76b0b01a2') - version('5.3.0', '367961dd0ab426e5ae367c2713924ffb') + version('5.7.0', sha256='d1a3bb848e292c805bc9f29e09c27870e2ff4cda6c2fba3b7da8b4bba6547589') + version('5.6.0', sha256='49b7293f9ca2d74d6d80bd06b5c4be303663123267b4ac0884cbcae4c914dc47') + version('5.5.1', sha256='49dc2c2323f6164c4a7e81b799ed690ee73158671205e71501f849391dd2c2d4') + version('5.5.0', sha256='3ea15e6cc2354017335b659c1635409ddab1414e70573aa4df91fd892e99f98d') + version('5.4.3', sha256='3aefd581e274f0a103f001f1ffd1009019b297c637e97f4b8c5fc13fa5a1e675') + version('5.4.1', sha256='e131c1449786fe870322a949e44f974a5963824f683232e653fb570cc65d4e87') + version('5.3.0', sha256='99f2f36398b370e75d100b4a189d5bc0ac4f5dd66df44d441f88fd32e1421524') # Does not build with newer versions of gcc, see # https://bitbucket.org/icl/papi/issues/46/cannot-compile-on-arch-linux diff --git a/var/spack/repos/builtin/packages/papyrus/package.py b/var/spack/repos/builtin/packages/papyrus/package.py index d3e14d9f4ed..4a5119deb0e 100644 --- a/var/spack/repos/builtin/packages/papyrus/package.py +++ b/var/spack/repos/builtin/packages/papyrus/package.py @@ -14,6 +14,6 @@ class Papyrus(CMakePackage): git = "https://code.ornl.gov/eck/papyrus.git" version('develop', branch='master') - version('1.0.0', 'fe0fca073c3604110f0507f375d71e64') + version('1.0.0', sha256='5d57c0bcc80de48951e42460785783b882087a5714195599d773a6eabde5c4c4') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/parallel/package.py b/var/spack/repos/builtin/packages/parallel/package.py index d926c08112d..596bb814e35 100644 --- a/var/spack/repos/builtin/packages/parallel/package.py +++ b/var/spack/repos/builtin/packages/parallel/package.py @@ -16,10 +16,10 @@ class Parallel(AutotoolsPackage): url = "https://ftpmirror.gnu.org/parallel/parallel-20170122.tar.bz2" version('20190222', sha256='86b1badc56ee2de1483107c2adf634604fd72789c91f65e40138d21425906b1c') - version('20170322', '4fe1b8d2e3974d26c77f0b514988214d') - version('20170122', 'c9f0ec01463dc75dbbf292fd8be5f1eb') - version('20160422', '24621f684130472694333709bd4454cb') - version('20160322', '4e81e0d36902ab4c4e969ee6f35e6e57') + version('20170322', sha256='f8f810040088bf3c52897a2ee0c0c71bd8d097e755312364b946f107ae3553f6') + version('20170122', sha256='417e83d9de2fe518a976fcff5a96bffe41421c2a57713cd5272cc89d1072aaa6') + version('20160422', sha256='065a8f471266361218a9eb45c5f8ab995d73b181cc1180600ee08cc768c9ac42') + version('20160322', sha256='6430f649ec07243645c955e8d6bee6da1df2e699b1e49b185946d1ab38731b08') def check(self): # The Makefile has a 'test' target, but it does not work diff --git a/var/spack/repos/builtin/packages/paraver/package.py b/var/spack/repos/builtin/packages/paraver/package.py index 7cc4c70d9ac..8bcfc5952cc 100644 --- a/var/spack/repos/builtin/packages/paraver/package.py +++ b/var/spack/repos/builtin/packages/paraver/package.py @@ -17,8 +17,8 @@ class Paraver(Package): # NOTE: Paraver provides only latest version for download. # Don't keep/add older versions. - version('4.6.3', '7940a2651f56712c4e8a21138b4bf16c') - version('4.6.2', '3f5b3e207d98b2c44101f1ff5685aa55') + version('4.6.3', sha256='ac6025eec5419e1060967eab71dfd123e585be5b5f3ac3241085895dbeca255a') + version('4.6.2', sha256='74b85bf9e6570001d372b376b58643526e349b1d2f1e7633ca38bb0800ecf929') depends_on("boost") # depends_on("extrae") diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index fc6d0e99c29..938004b97c7 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -22,16 +22,16 @@ class Paraview(CMakePackage, CudaPackage): version('develop', branch='master', submodules=True) version('5.6.2', sha256='1f3710b77c58a46891808dbe23dc59a1259d9c6b7bb123aaaeaa6ddf2be882ea') version('5.6.0', sha256='cb8c4d752ad9805c74b4a08f8ae6e83402c3f11e38b274dba171b99bb6ac2460') - version('5.5.2', '7eb93c31a1e5deb7098c3b4275e53a4a') - version('5.5.1', 'a7d92a45837b67c3371006cc45163277') - version('5.5.0', 'a8f2f41edadffdcc89b37fdc9aa7f005') - version('5.4.1', '4030c70477ec5a85aa72d6fc86a30753') - version('5.4.0', 'b92847605bac9036414b644f33cb7163') - version('5.3.0', '68fbbbe733aa607ec13d1db1ab5eba71') - version('5.2.0', '4570d1a2a183026adb65b73c7125b8b0') - version('5.1.2', '44fb32fc8988fcdfbc216c9e40c3e925') - version('5.0.1', 'fdf206113369746e2276b95b257d2c9b') - version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378') + version('5.5.2', sha256='64561f34c4402b88f3cb20a956842394dde5838efd7ebb301157a837114a0e2d') + version('5.5.1', sha256='a6e67a95a7a5711a2b5f95f38ccbff4912262b3e1b1af7d6b9afe8185aa85c0d') + version('5.5.0', sha256='1b619e326ff574de808732ca9a7447e4cd14e94ae6568f55b6581896cd569dff') + version('5.4.1', sha256='390d0f5dc66bf432e202a39b1f34193af4bf8aad2355338fa5e2778ea07a80e4') + version('5.4.0', sha256='f488d84a53b1286d2ee1967e386626c8ad05a6fe4e6cbdaa8d5e042f519f94a9') + version('5.3.0', sha256='046631bbf00775edc927314a3db207509666c9c6aadc7079e5159440fd2f88a0') + version('5.2.0', sha256='894e42ef8475bb49e4e7e64f4ee2c37c714facd18bfbb1d6de7f69676b062c96') + version('5.1.2', sha256='ff02b7307a256b7c6e8ad900dee5796297494df7f9a0804fe801eb2f66e6a187') + version('5.0.1', sha256='caddec83ec284162a2cbc46877b0e5a9d2cca59fb4ab0ea35b0948d2492950bb') + version('4.4.0', sha256='c2dc334a89df24ce5233b81b74740fc9f10bc181cd604109fd13f6ad2381fc73') variant('plugins', default=True, description='Install include files for plugins support') diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index 884608e066d..bf487a80f22 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -17,8 +17,8 @@ class Parmetis(CMakePackage): url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz' list_url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD' - version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628') - version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce') + version('4.0.3', sha256='f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f') + version('4.0.2', sha256='5acbb700f457d3bda7d4bb944b559d7f21f075bb6fa4c33f42c261019ef2f0b2') variant('shared', default=True, description='Enables the build of shared libraries.') variant('gdb', default=False, description='Enables gdb support.') diff --git a/var/spack/repos/builtin/packages/parquet/package.py b/var/spack/repos/builtin/packages/parquet/package.py index dc092a6c8b7..ac130b359fd 100644 --- a/var/spack/repos/builtin/packages/parquet/package.py +++ b/var/spack/repos/builtin/packages/parquet/package.py @@ -13,7 +13,7 @@ class Parquet(CMakePackage): homepage = "https://github.com/apache/parquet-cpp" url = "https://github.com/apache/parquet-cpp/archive/apache-parquet-cpp-1.4.0.tar.gz" - version('1.4.0', '3a3659e65052ef5a76fb88e4922283b9') + version('1.4.0', sha256='52899be6c9dc49a14976d4ad84597243696c3fa2882e5c802b56e912bfbcc7ce') depends_on('arrow') depends_on('boost') diff --git a/var/spack/repos/builtin/packages/parsplice/package.py b/var/spack/repos/builtin/packages/parsplice/package.py index b96db056ac6..6301f6ea5e9 100644 --- a/var/spack/repos/builtin/packages/parsplice/package.py +++ b/var/spack/repos/builtin/packages/parsplice/package.py @@ -18,7 +18,7 @@ class Parsplice(CMakePackage): version('develop', branch='master') version('multisplice', branch='multisplice') - version('1.1', '3a72340d49d731a076e8942f2ae2f4e9') + version('1.1', sha256='a011c4d14f66e7cdbc151cc74b5d40dfeae19ceea033ef48185d8f3b1bc2f86b') depends_on("cmake@3.1:", type='build') depends_on("berkeley-db") diff --git a/var/spack/repos/builtin/packages/partitionfinder/package.py b/var/spack/repos/builtin/packages/partitionfinder/package.py index 930492c04fd..e8109825051 100644 --- a/var/spack/repos/builtin/packages/partitionfinder/package.py +++ b/var/spack/repos/builtin/packages/partitionfinder/package.py @@ -14,7 +14,7 @@ class Partitionfinder(Package): homepage = "https://github.com/brettc/partitionfinder" url = "https://github.com/brettc/partitionfinder/archive/v2.1.1.tar.gz" - version('2.1.1', 'b1b6539f93146c69b967cf92459ae28a') + version('2.1.1', sha256='ccf3718996ee6ca496909b4b97d2b075028e0543eba3bc47a8c14b689c84e061') depends_on('python@2.7.10:2.999', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/patch/package.py b/var/spack/repos/builtin/packages/patch/package.py index 7fe2c6cf02e..d67d564280f 100644 --- a/var/spack/repos/builtin/packages/patch/package.py +++ b/var/spack/repos/builtin/packages/patch/package.py @@ -15,7 +15,7 @@ class Patch(AutotoolsPackage): homepage = "http://savannah.gnu.org/projects/patch/" url = "https://ftpmirror.gnu.org/patch/patch-2.7.6.tar.xz" - version('2.7.6', '78ad9937e4caadcba1526ef1853730d5') - version('2.7.5', 'e3da7940431633fb65a01b91d3b7a27a') + version('2.7.6', sha256='ac610bda97abe0d9f6b7c963255a11dcb196c25e337c61f94e4778d632f1d8fd') + version('2.7.5', sha256='fd95153655d6b95567e623843a0e77b81612d502ecf78a489a4aed7867caa299') build_directory = 'spack-build' diff --git a/var/spack/repos/builtin/packages/patchelf/package.py b/var/spack/repos/builtin/packages/patchelf/package.py index 80291ad3627..73328f3c01a 100644 --- a/var/spack/repos/builtin/packages/patchelf/package.py +++ b/var/spack/repos/builtin/packages/patchelf/package.py @@ -16,5 +16,5 @@ class Patchelf(AutotoolsPackage): list_url = "http://nixos.org/releases/patchelf/" list_depth = 1 - version('0.9', '3c265508526760f233620f35d79c79fc') - version('0.8', '407b229e6a681ffb0e2cdd5915cb2d01') + version('0.9', sha256='f2aa40a6148cb3b0ca807a1bf836b081793e55ec9e5540a5356d800132be7e0a') + version('0.8', sha256='14af06a2da688d577d64ff8dac065bb8903bbffbe01d30c62df7af9bf4ce72fe') diff --git a/var/spack/repos/builtin/packages/pathfinder/package.py b/var/spack/repos/builtin/packages/pathfinder/package.py index 4f4d7bc9d7c..3f5bf368e2f 100644 --- a/var/spack/repos/builtin/packages/pathfinder/package.py +++ b/var/spack/repos/builtin/packages/pathfinder/package.py @@ -15,7 +15,7 @@ class Pathfinder(MakefilePackage): tags = ['proxy-app'] - version('1.0.0', '374269e8d42c305eda3e392444e22dde') + version('1.0.0', sha256='e002ff7df1ee9a6ee8a892fc208e047e2daf4215ff0d77e7ddc6b09d0506be16') build_targets = ['--directory=PathFinder_ref', 'CC=cc'] diff --git a/var/spack/repos/builtin/packages/pax-utils/package.py b/var/spack/repos/builtin/packages/pax-utils/package.py index c46f80fc7a1..85013e69dae 100644 --- a/var/spack/repos/builtin/packages/pax-utils/package.py +++ b/var/spack/repos/builtin/packages/pax-utils/package.py @@ -13,4 +13,4 @@ class PaxUtils(AutotoolsPackage): homepage = "https://wiki.gentoo.org/index.php?title=Project:Hardened/PaX_Utilities" url = "https://dev.gentoo.org/~vapier/dist/pax-utils-1.2.2.tar.xz" - version('1.2.2', 'a580468318f0ff42edf4a8cd314cc942') + version('1.2.2', sha256='7f4a7f8db6b4743adde7582fa48992ad01776796fcde030683732f56221337d9') diff --git a/var/spack/repos/builtin/packages/pbbam/package.py b/var/spack/repos/builtin/packages/pbbam/package.py index e432db7b536..97486e1606d 100644 --- a/var/spack/repos/builtin/packages/pbbam/package.py +++ b/var/spack/repos/builtin/packages/pbbam/package.py @@ -15,7 +15,7 @@ class Pbbam(CMakePackage): homepage = "https://github.com/PacificBiosciences/pbbam" url = "https://github.com/PacificBiosciences/pbbam/archive/0.18.0.tar.gz" - version('0.18.0', 'abbb687b1e7ea08916c26da828e11384') + version('0.18.0', sha256='45286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a') depends_on('zlib') depends_on('boost@1.55.0:') diff --git a/var/spack/repos/builtin/packages/pcma/package.py b/var/spack/repos/builtin/packages/pcma/package.py index ad0ca82af79..baaf935f909 100644 --- a/var/spack/repos/builtin/packages/pcma/package.py +++ b/var/spack/repos/builtin/packages/pcma/package.py @@ -13,7 +13,7 @@ class Pcma(MakefilePackage): homepage = "http://prodata.swmed.edu/pcma/pcma.php" url = "http://prodata.swmed.edu/download/pub/PCMA/pcma.tar.gz" - version('2.0', 'e78449b2f6b0e90348a0a6747d266f9b') + version('2.0', sha256='4b92d412126d393baa3ede501cafe9606ada9a66af6217d56befd6ec2e0c01ba') def edit(self, spec, prefix): makefile = FileFilter('makefile') diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py index 952181361cb..f2a4e494a5d 100644 --- a/var/spack/repos/builtin/packages/pcre/package.py +++ b/var/spack/repos/builtin/packages/pcre/package.py @@ -14,11 +14,11 @@ class Pcre(AutotoolsPackage): homepage = "http://www.pcre.org" url = "https://ftp.pcre.org/pub/pcre/pcre-8.42.tar.bz2" - version('8.42', '085b6aa253e0f91cae70b3cdbe8c1ac2') - version('8.41', 'c160d22723b1670447341b08c58981c1') - version('8.40', '41a842bf7dcecd6634219336e2167d1d') - version('8.39', 'e3fca7650a0556a2647821679d81f585') - version('8.38', '00aabbfe56d5a48b270f999b508c5ad2') + version('8.42', sha256='2cd04b7c887808be030254e8d77de11d3fe9d4505c39d4b15d2664ffe8bf9301') + version('8.41', sha256='e62c7eac5ae7c0e7286db61ff82912e1c0b7a0c13706616e94a7dd729321b530') + version('8.40', sha256='00e27a29ead4267e3de8111fcaa59b132d0533cdfdbdddf4b0604279acbcf4f4') + version('8.39', sha256='b858099f82483031ee02092711689e7245586ada49e534a06e678b8ea9549e8b') + version('8.38', sha256='b9e02d36e23024d6c02a2e5b25204b3a4fa6ade43e0a5f869f254f49535079df') patch('intel.patch', when='@8.38') diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py index f29708b26bf..abe62d70fdf 100644 --- a/var/spack/repos/builtin/packages/pcre2/package.py +++ b/var/spack/repos/builtin/packages/pcre2/package.py @@ -14,8 +14,8 @@ class Pcre2(AutotoolsPackage): homepage = "http://www.pcre.org""" url = "https://ftp.pcre.org/pub/pcre/pcre2-10.31.tar.bz2" - version('10.31', 'e0b91c891a3c49050f7fd15de33d0ba4') - version('10.20', 'dcd027c57ecfdc8a6c3af9d0acf5e3f7') + version('10.31', sha256='e07d538704aa65e477b6a392b32ff9fc5edf75ab9a40ddfc876186c4ff4d68ac') + version('10.20', sha256='332e287101c9e9567d1ed55391b338b32f1f72c5b5ee7cc81ef2274a53ad487a') variant('multibyte', default=True, description='Enable support for 16 and 32 bit characters.') diff --git a/var/spack/repos/builtin/packages/pdf2svg/package.py b/var/spack/repos/builtin/packages/pdf2svg/package.py index 49b2abefd0f..00f242f6715 100644 --- a/var/spack/repos/builtin/packages/pdf2svg/package.py +++ b/var/spack/repos/builtin/packages/pdf2svg/package.py @@ -12,8 +12,8 @@ class Pdf2svg(AutotoolsPackage): homepage = "http://www.cityinthesky.co.uk/opensource/pdf2svg" url = "https://github.com/dawbarton/pdf2svg/archive/v0.2.3.tar.gz" - version('0.2.3', 'd398b3b1c1979f554596238a44f12123') - version('0.2.2', 'f7e0d2213f9e1422cee9421e18f72553') + version('0.2.3', sha256='4fb186070b3e7d33a51821e3307dce57300a062570d028feccd4e628d50dea8a') + version('0.2.2', sha256='e5f1d9b78821e44cd85379fb07f38a42f00bb2bde3743b95301ff8c0a5ae229a') depends_on('pkgconfig@0.9.0:', type='build') depends_on('cairo@1.2.6:') diff --git a/var/spack/repos/builtin/packages/pdftk/package.py b/var/spack/repos/builtin/packages/pdftk/package.py index 98bdfbd2877..8f06385f148 100644 --- a/var/spack/repos/builtin/packages/pdftk/package.py +++ b/var/spack/repos/builtin/packages/pdftk/package.py @@ -20,7 +20,7 @@ class Pdftk(MakefilePackage): maintainers = ['citibeth'] - version('2.02', '6534365fd6727724f288a556ede33faa') + version('2.02', sha256='118f6a25fd3acaafb58824dce6f97cdc07e56050e666b90e4c4ef426ea37b8c1') depends_on('eclipse-gcj-parser', type='build') diff --git a/var/spack/repos/builtin/packages/pdsh/package.py b/var/spack/repos/builtin/packages/pdsh/package.py index bc74c3dce1e..8b58fb595d1 100644 --- a/var/spack/repos/builtin/packages/pdsh/package.py +++ b/var/spack/repos/builtin/packages/pdsh/package.py @@ -14,7 +14,7 @@ class Pdsh(AutotoolsPackage): homepage = "https://github.com/grondo/pdsh" url = "https://github.com/grondo/pdsh/archive/pdsh-2.31.tar.gz" - version('2.31', 'cab34b0ca78f3cf596fd648b265223ed') + version('2.31', sha256='0ee066ce395703285cf4f6cf00b54b7097d12457a4b1c146bc6f33d8ba73caa7') variant('ssh', default=True, description="Build with ssh module") diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py index 1f312dc1607..dd4c1110da7 100644 --- a/var/spack/repos/builtin/packages/pdt/package.py +++ b/var/spack/repos/builtin/packages/pdt/package.py @@ -19,16 +19,16 @@ class Pdt(AutotoolsPackage): homepage = "https://www.cs.uoregon.edu/research/pdt/home.php" url = "http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdtoolkit-3.25.1.tar.gz" - version('3.25.1', 'a248b1d6874390dcb30feea16a26e0ef') - version('3.25', '2cad41fcabf4c79cab8780d3b87f7bb4') - version('3.24', 'b8fa5189e5602276ce225ba497b617e4') - version('3.23', 'd61e7a631a27b00e58def52950230a2c') - version('3.22.1', 'b56b9b3e621161c7fd9e4908b944840d') - version('3.22', '982d667617802962a1f7fe6c4c31184f') - version('3.21', '3092ca0d8833b69992c17e63ae66c263') - version('3.20', 'c3edabe202926abe04552e33cd39672d') - version('3.19', '5c5e1e6607086aa13bf4b1b9befc5864') - version('3.18.1', 'e401534f5c476c3e77f05b7f73b6c4f2') + version('3.25.1', sha256='0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97') + version('3.25', sha256='1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be') + version('3.24', sha256='4a2bb31f3f7f2e52ed49d9b7189ade05170a4386ef76771280a06e8b3ca97ab2') + version('3.23', sha256='c17fca2f9126e10b4922b54e737a39c081b2dcf99bf20062c203247e05ecb850') + version('3.22.1', sha256='215a3684bfe0df8ca673b09ee1efcdb5388ab5f45130dd67a00ef1041bfb5818') + version('3.22', sha256='3a539c04b6d1b7b77b31999a7936717dfccda138b318756e306415e3af17dd8b') + version('3.21', sha256='582f14347b4dd7a6f9bc2f41b3b62a6b40079c0a3127109c2c0c953e3c922401') + version('3.20', sha256='561c3559fba7c3d053df3b98f75f3c2087c64a6d51204b40825a1737677f780b') + version('3.19', sha256='d57234077e2e999f2acf9860ea84369a4694b50cc17fa6728e5255dc5f4a2160') + version('3.18.1', sha256='d06c2d1793fadebf169752511e5046d7e02cf3fead6135a35c34b1fee6d6d3b2') def patch(self): if self.spec.satisfies('%clang'): diff --git a/var/spack/repos/builtin/packages/pegtl/package.py b/var/spack/repos/builtin/packages/pegtl/package.py index c93f8ee8db6..749b1dbd2c7 100644 --- a/var/spack/repos/builtin/packages/pegtl/package.py +++ b/var/spack/repos/builtin/packages/pegtl/package.py @@ -19,5 +19,5 @@ class Pegtl(CMakePackage): git = "https://github.com/taocpp/PEGTL.git" version('develop', branch='master') - version('2.1.4', 'e5288b6968e6e910287fce93dc5557bf') - version('2.0.0', 'c772828e7188459338a920c21f9896db') + version('2.1.4', sha256='d990dccc07b4d9ba548326d11c5c5e34fa88b34fe113cb5377da03dda29f23f2') + version('2.0.0', sha256='5aae0505077e051cae4d855c38049cc6cf71103a6cc8d0ddef01a576e8a60cc0') diff --git a/var/spack/repos/builtin/packages/pennant/package.py b/var/spack/repos/builtin/packages/pennant/package.py index c23ab981f08..372db4559f0 100644 --- a/var/spack/repos/builtin/packages/pennant/package.py +++ b/var/spack/repos/builtin/packages/pennant/package.py @@ -18,12 +18,12 @@ class Pennant(MakefilePackage): url = "https://github.com/lanl/PENNANT/archive/pennant_v0.9.tar.gz" tags = ['proxy-app'] - version('0.9', '4f21ba3836b2721436277308c2e33f45') - version('0.8', 'a1afff4914fef8140c3024a02d7c993c') - version('0.7', 'd642a030d5388f65f799504803794a4e') - version('0.6', '8ab2d4b47ec9870643bfe6f262cd47a4') - version('0.5', '534547878c698b9926e2886c74e10831') - version('0.4', '0f67d8da0a92bd42d92a4823d3e4dbe1') + version('0.9', sha256='5fc07e64c246f8b1b552595a0868ba0042b7a2410aa844e7b510bc31e2512dd8') + version('0.8', sha256='b07226b377c0e22c0f9a631be07ab28793c6d9a337a7a6eed2c7d4dc79f93f18') + version('0.7', sha256='a6b7e76f7e68a693fd12ec338eaeb59430db9f12b69279b24f78724882684ae4') + version('0.6', sha256='0b317c19d6af96fe0544afb19ea503449c9f57869b9ad788f654ebec316341f4') + version('0.5', sha256='21ef5889731fad0075f9dab8ffa97af8fd8ff87f6a5fe6434916b6e28cf64e43') + version('0.4', sha256='65b81b92ed6fdbe407310948dd76ffb48cca155ee05c1f990a649faf81b45bb0') variant('mpi', default=True, description='Build with MPI support') variant('openmp', default=True, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py index 28cd2ef2d83..f44c8452b56 100644 --- a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py +++ b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py @@ -12,4 +12,4 @@ class PerlAlgorithmDiff(PerlPackage): homepage = "http://search.cpan.org/~tyemq/Algorithm-Diff-1.1903/lib/Algorithm/Diff.pm" url = "http://search.cpan.org/CPAN/authors/id/T/TY/TYEMQ/Algorithm-Diff-1.1903.tar.gz" - version('1.1903', '0e8add21a641b8d66436df0c2024bf3b') + version('1.1903', sha256='30e84ac4b31d40b66293f7b1221331c5a50561a39d580d85004d9c1fff991751') diff --git a/var/spack/repos/builtin/packages/perl-app-cmd/package.py b/var/spack/repos/builtin/packages/perl-app-cmd/package.py index 1469038cea8..faef6535e35 100644 --- a/var/spack/repos/builtin/packages/perl-app-cmd/package.py +++ b/var/spack/repos/builtin/packages/perl-app-cmd/package.py @@ -12,4 +12,4 @@ class PerlAppCmd(PerlPackage): homepage = "http://search.cpan.org/~rjbs/App-Cmd/lib/App/Cmd.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/App-Cmd-0.331.tar.gz" - version('0.331', 'b43c07d7b4d4e2a6baf32aa92cd00b93') + version('0.331', sha256='4a5d3df0006bd278880d01f4957aaa652a8f91fe8f66e93adf70fba0c3ecb680') diff --git a/var/spack/repos/builtin/packages/perl-array-utils/package.py b/var/spack/repos/builtin/packages/perl-array-utils/package.py index d8c19c49d43..6216eeea2ea 100644 --- a/var/spack/repos/builtin/packages/perl-array-utils/package.py +++ b/var/spack/repos/builtin/packages/perl-array-utils/package.py @@ -12,4 +12,4 @@ class PerlArrayUtils(PerlPackage): homepage = "http://search.cpan.org/~zmij/Array-Utils/Utils.pm" url = "http://search.cpan.org/CPAN/authors/id/Z/ZM/ZMIJ/Array/Array-Utils-0.5.tar.gz" - version('0.5', 'ac15e6dce2c7c9d1855ecab9eb00aee6') + version('0.5', sha256='89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770') diff --git a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py index ff17101d4c4..3ffa56d0a4a 100644 --- a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py +++ b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py @@ -12,6 +12,6 @@ class PerlBHooksEndofscope(PerlPackage): homepage = "http://search.cpan.org/~ether/B-Hooks-EndOfScope-0.21/lib/B/Hooks/EndOfScope.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/B-Hooks-EndOfScope-0.21.tar.gz" - version('0.21', 'df9dacbf55a01d7a444b1ebc616435ae') + version('0.21', sha256='90f3580880f1d68b843c142cc86f58bead1f3e03634c63868ac9eba5eedae02c') depends_on('perl-sub-exporter-progressive', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bio-perl/package.py index 05294029015..a8680d8b2e9 100644 --- a/var/spack/repos/builtin/packages/perl-bio-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-bio-perl/package.py @@ -36,7 +36,7 @@ class PerlBioPerl(PerlPackage): url = "https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.6.tar.gz" version('1.7.6', sha256='df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d') - version('1.7.2', 'a912c92b56d009198f1786b4cf560d5c', + version('1.7.2', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1', url="http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz") # According to cpandeps.grinnz.com Module-Build is both a build and run diff --git a/var/spack/repos/builtin/packages/perl-bit-vector/package.py b/var/spack/repos/builtin/packages/perl-bit-vector/package.py index 221facee21f..380d79191c5 100644 --- a/var/spack/repos/builtin/packages/perl-bit-vector/package.py +++ b/var/spack/repos/builtin/packages/perl-bit-vector/package.py @@ -12,6 +12,6 @@ class PerlBitVector(PerlPackage): homepage = "http://search.cpan.org/~stbey/Bit-Vector-7.4/Vector.pod" url = "http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/Bit-Vector-7.4.tar.gz" - version('7.4', 'bf67f144e5be5327ed79d4c69e6e0086') + version('7.4', sha256='3c6daa671fecfbc35f92a9385b563d65f50dfc6bdc8b4805f9ef46c0d035a926') depends_on('perl-carp-clan', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-cairo/package.py b/var/spack/repos/builtin/packages/perl-cairo/package.py index f1ec5dfd4a8..3b4ebe9dc9b 100644 --- a/var/spack/repos/builtin/packages/perl-cairo/package.py +++ b/var/spack/repos/builtin/packages/perl-cairo/package.py @@ -12,7 +12,7 @@ class PerlCairo(PerlPackage): homepage = "http://search.cpan.org/~xaoc/Cairo/lib/Cairo.pm" url = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/Cairo-1.106.tar.gz" - version('1.106', '47ca0ae0f5b9bc4c16a27627ff48bd8b') + version('1.106', sha256='e64803018bc7cba49e73e258547f5378cc4249797beafec524852140f49c45c4') depends_on('cairo') depends_on('perl-extutils-depends') diff --git a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py index 1686925caf2..041ee0903ad 100644 --- a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py @@ -12,4 +12,4 @@ class PerlCaptureTiny(PerlPackage): homepage = "http://search.cpan.org/~dagolden/Capture-Tiny-0.46/lib/Capture/Tiny.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/Capture-Tiny-0.46.tar.gz" - version('0.46', 'd718af07729d26a793949ca6ba2580a7') + version('0.46', sha256='5d7a6a830cf7f2b2960bf8b8afaac16a537ede64f3023827acea5bd24ca77015') diff --git a/var/spack/repos/builtin/packages/perl-carp-clan/package.py b/var/spack/repos/builtin/packages/perl-carp-clan/package.py index 4f30ebe4666..19b046d2bde 100644 --- a/var/spack/repos/builtin/packages/perl-carp-clan/package.py +++ b/var/spack/repos/builtin/packages/perl-carp-clan/package.py @@ -12,7 +12,7 @@ class PerlCarpClan(PerlPackage): homepage = "http://search.cpan.org/~kentnl/Carp-Clan-6.06/lib/Carp/Clan.pod" url = "http://search.cpan.org/CPAN/authors/id/K/KE/KENTNL/Carp-Clan-6.06.tar.gz" - version('6.06', 'c562a35c48f43665fab735cdc7fe3cb2') + version('6.06', sha256='ea4ac8f611354756d43cb369880032901e9cc4cc7e0bebb7b647186dac00c9d4') depends_on('perl-test-exception', type=('build', 'run')) depends_on('perl-sub-uplevel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py index 1ee2d6354b0..d5e8c7e3924 100644 --- a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py +++ b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py @@ -12,4 +12,4 @@ class PerlClassDataInheritable(PerlPackage): homepage = "http://search.cpan.org/~tmtm/Class-Data-Inheritable-0.08/lib/Class/Data/Inheritable.pm" url = "http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/Class-Data-Inheritable-0.08.tar.gz" - version('0.08', 'fc0fe65926eb8fb932743559feb54eb9') + version('0.08', sha256='9967feceea15227e442ec818723163eb6d73b8947e31f16ab806f6e2391af14a') diff --git a/var/spack/repos/builtin/packages/perl-class-inspector/package.py b/var/spack/repos/builtin/packages/perl-class-inspector/package.py index 2497dd05dd2..5f04cf5b25b 100644 --- a/var/spack/repos/builtin/packages/perl-class-inspector/package.py +++ b/var/spack/repos/builtin/packages/perl-class-inspector/package.py @@ -12,4 +12,4 @@ class PerlClassInspector(PerlPackage): homepage = "http://search.cpan.org/~plicease/Class-Inspector-1.32/lib/Class/Inspector.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/Class-Inspector-1.32.tar.gz" - version('1.32', 'db471d6ecf47fa054726553319b7c34f') + version('1.32', sha256='cefadc8b5338e43e570bc43f583e7c98d535c17b196bcf9084bb41d561cc0535') diff --git a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py index c25e00f08f0..7133d8bd12b 100644 --- a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py +++ b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py @@ -13,6 +13,6 @@ class PerlClassLoadXs(PerlPackage): homepage = "http://search.cpan.org/~ether/Class-Load-XS-0.10/lib/Class/Load/XS.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Class-Load-XS-0.10.tar.gz" - version('0.10', '2c15488b5b28afadbb5315e44a721e05') + version('0.10', sha256='5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1') depends_on('perl-class-load', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-class-load/package.py b/var/spack/repos/builtin/packages/perl-class-load/package.py index 0efc8ea157a..3e7ef53f9e3 100644 --- a/var/spack/repos/builtin/packages/perl-class-load/package.py +++ b/var/spack/repos/builtin/packages/perl-class-load/package.py @@ -12,4 +12,4 @@ class PerlClassLoad(PerlPackage): homepage = "http://search.cpan.org/~ether/Class-Load-0.24/lib/Class/Load.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Class-Load-0.24.tar.gz" - version('0.24', 'daf8aeedf4d19ed6d3f75cd3e720116d') + version('0.24', sha256='0bb983da46c146534fc77a556d6e40d925142f2eb43103534025ee545265ca36') diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py index 22de18bc17b..56cd8605f30 100644 --- a/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py +++ b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py @@ -12,7 +12,7 @@ class PerlCompressRawBzip2(PerlPackage): homepage = "http://search.cpan.org/~pmqs/Compress-Raw-Bzip2-2.081/lib/Compress/Raw/Bzip2.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PM/PMQS/Compress-Raw-Bzip2-2.081.tar.gz" - version('2.081', '25fa9c9cc4fd3250b65b91694f9eac2e') + version('2.081', sha256='8692b5c9db91954408e24e805fbfda222879da80d89d9410791421e3e5bc3520') depends_on('bzip2') depends_on('perl-extutils-makemaker', type='build') diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py index 197566773b1..8fdbd023e67 100644 --- a/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py +++ b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py @@ -12,7 +12,7 @@ class PerlCompressRawZlib(PerlPackage): homepage = "http://search.cpan.org/~pmqs/Compress-Raw-Zlib-2.081/lib/Compress/Raw/Zlib.pm" url = "https://cpan.metacpan.org/authors/id/P/PM/PMQS/Compress-Raw-Zlib-2.081.tar.gz" - version('2.081', 'a22d23bb4f8ce92a41ace1dff29f2bd1') + version('2.081', sha256='e156de345bd224bbdabfcab0eeb3f678a3099a4e86c9d1b6771d880b55aa3a1b') depends_on('zlib') depends_on('perl-extutils-makemaker', type='build') diff --git a/var/spack/repos/builtin/packages/perl-contextual-return/package.py b/var/spack/repos/builtin/packages/perl-contextual-return/package.py index 1cf5087f3e4..3330a5175a4 100644 --- a/var/spack/repos/builtin/packages/perl-contextual-return/package.py +++ b/var/spack/repos/builtin/packages/perl-contextual-return/package.py @@ -12,6 +12,6 @@ class PerlContextualReturn(PerlPackage): homepage = "http://search.cpan.org/~dconway/Contextual-Return/lib/Contextual/Return.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/Contextual-Return-0.004014.tar.gz" - version('0.004014', '5cb31f1637c17af6a8e5b852d820af79') + version('0.004014', sha256='09fe1415e16e49a69e13c0ef6e6a4a3fd8b856f389d3f3e624d7ab3b71719f78') depends_on('perl-want') diff --git a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py index 99e11161378..79bdc6cd0c2 100644 --- a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py +++ b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py @@ -13,6 +13,6 @@ class PerlCpanMetaCheck(PerlPackage): homepage = "http://search.cpan.org/~leont/CPAN-Meta-Check-0.014/lib/CPAN/Meta/Check.pm" url = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/CPAN-Meta-Check-0.014.tar.gz" - version('0.014', 'ccd4448a7b08e1e3ef6f475030b282c9') + version('0.014', sha256='28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f') depends_on('perl-test-deep', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-data-dumper/package.py b/var/spack/repos/builtin/packages/perl-data-dumper/package.py index d596c7e010b..3fc0dca758b 100644 --- a/var/spack/repos/builtin/packages/perl-data-dumper/package.py +++ b/var/spack/repos/builtin/packages/perl-data-dumper/package.py @@ -12,4 +12,4 @@ class PerlDataDumper(PerlPackage): homepage = "http://search.cpan.org/dist/Data-Dumper/Dumper.pm" url = "https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX/Data-Dumper-2.173.tar.gz" - version('2.173', '5e57ded19aff069f3f05dfb5e5ca1e1d') + version('2.173', sha256='697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa') diff --git a/var/spack/repos/builtin/packages/perl-data-optlist/package.py b/var/spack/repos/builtin/packages/perl-data-optlist/package.py index 319f74a1506..11e35734105 100644 --- a/var/spack/repos/builtin/packages/perl-data-optlist/package.py +++ b/var/spack/repos/builtin/packages/perl-data-optlist/package.py @@ -12,6 +12,6 @@ class PerlDataOptlist(PerlPackage): homepage = "http://search.cpan.org/~rjbs/Data-OptList-0.110/lib/Data/OptList.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Data-OptList-0.110.tar.gz" - version('0.110', 'f9236c9ea5607134ad8a2b3dc901c4c5') + version('0.110', sha256='366117cb2966473f2559f2f4575ff6ae69e84c69a0f30a0773e1b51a457ef5c3') depends_on('perl-sub-install', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-data-stag/package.py b/var/spack/repos/builtin/packages/perl-data-stag/package.py index 4f068327502..eae912d6798 100644 --- a/var/spack/repos/builtin/packages/perl-data-stag/package.py +++ b/var/spack/repos/builtin/packages/perl-data-stag/package.py @@ -12,6 +12,6 @@ class PerlDataStag(PerlPackage): homepage = "http://search.cpan.org/~cmungall/Data-Stag-0.14/Data/Stag.pm" url = "http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/Data-Stag-0.14.tar.gz" - version('0.14', 'f803acf74f1bfccc118aeac5483ee871') + version('0.14', sha256='4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59') depends_on('perl-io-string', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py index 0e04cc8d04b..fa56bfc8a64 100644 --- a/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py +++ b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py @@ -12,7 +12,7 @@ class PerlDbdMysql(PerlPackage): homepage = "http://search.cpan.org/~michielb/DBD-mysql-4.043/lib/DBD/mysql.pm" url = "http://search.cpan.org/CPAN/authors/id/M/MI/MICHIELB/DBD-mysql-4.043.tar.gz" - version('4.043', '4a00dd7f1c057931147c65dfc4901c36') + version('4.043', sha256='629f865e8317f52602b2f2efd2b688002903d2e4bbcba5427cb6188b043d6f99') depends_on('perl-test-deep', type=('build', 'run')) depends_on('perl-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-dbfile/package.py index 99f986ab2ee..c56d98f8426 100644 --- a/var/spack/repos/builtin/packages/perl-dbfile/package.py +++ b/var/spack/repos/builtin/packages/perl-dbfile/package.py @@ -17,6 +17,6 @@ class PerlDbfile(PerlPackage): homepage = "https://metacpan.org/pod/DB_File" url = "https://cpan.metacpan.org/authors/id/P/PM/PMQS/DB_File-1.840.tar.gz" - version('1.840', '8a2e98d457a216840ac893913c24141e') + version('1.840', sha256='b7864707fad0f2d1488c748c4fa08f1fb8bcfd3da247c36909fd42f20bfab2c4') depends_on('perl-extutils-makemaker', type='build') diff --git a/var/spack/repos/builtin/packages/perl-dbi/package.py b/var/spack/repos/builtin/packages/perl-dbi/package.py index 5cb10543014..e2024c71b16 100644 --- a/var/spack/repos/builtin/packages/perl-dbi/package.py +++ b/var/spack/repos/builtin/packages/perl-dbi/package.py @@ -14,4 +14,4 @@ class PerlDbi(PerlPackage): homepage = "https://dbi.perl.org/" url = "http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBI-1.636.tar.gz" - version('1.636', '60f291e5f015550dde71d1858dfe93ba') + version('1.636', sha256='8f7ddce97c04b4b7a000e65e5d05f679c964d62c8b02c94c1a7d815bb2dd676c') diff --git a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py index 20ee0d5ddc0..6b90cfb6ae6 100644 --- a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py @@ -12,4 +12,4 @@ class PerlDevelCycle(PerlPackage): homepage = "http://search.cpan.org/~lds/Devel-Cycle-1.12/lib/Devel/Cycle.pm" url = "http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Devel-Cycle-1.12.tar.gz" - version('1.12', '3d9a963da87b17398fab9acbef63f277') + version('1.12', sha256='fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2') diff --git a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py index 1c16e60c9fe..e5c76cfec84 100644 --- a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py @@ -12,4 +12,4 @@ class PerlDevelGlobaldestruction(PerlPackage): homepage = "http://search.cpan.org/~haarg/Devel-GlobalDestruction-0.14/lib/Devel/GlobalDestruction.pm" url = "http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/Devel-GlobalDestruction-0.14.tar.gz" - version('0.14', '24221ba322cf2dc46a1fc99b53e2380b') + version('0.14', sha256='34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab') diff --git a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py index b4ae12395ab..5c8f30a268e 100644 --- a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py @@ -12,7 +12,7 @@ class PerlDevelOverloadinfo(PerlPackage): homepage = "http://search.cpan.org/~ilmari/Devel-OverloadInfo-0.004/lib/Devel/OverloadInfo.pm" url = "http://search.cpan.org/CPAN/authors/id/I/IL/ILMARI/Devel-OverloadInfo-0.004.tar.gz" - version('0.005', '607b65dfe9fdb47df780f3b22dcb7917') - version('0.004', '97a27e31858b073daba54121d57be705') + version('0.005', sha256='8bfde2ffa47c9946f8adc8cfc445c2f97b8d1cdd678111bee9f444e82f7aa6e7') + version('0.004', sha256='83e88450064b0b0bbfd520cc9d7997fc7bed14ae257894eeadda28dc3e94937d') depends_on('perl-mro-compat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py index 6687e642a51..d5629f22836 100644 --- a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py @@ -12,4 +12,4 @@ class PerlDevelStacktrace(PerlPackage): homepage = "http://search.cpan.org/~drolsky/Devel-StackTrace-2.02/lib/Devel/StackTrace.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Devel-StackTrace-2.02.tar.gz" - version('2.02', 'bcc49dc2744d1fae906de0de3df07cca') + version('2.02', sha256='cbbd96db0ecf194ed140198090eaea0e327d9a378a4aa15f9a34b3138a91931f') diff --git a/var/spack/repos/builtin/packages/perl-digest-md5/package.py b/var/spack/repos/builtin/packages/perl-digest-md5/package.py index 921a5593779..ee90d905565 100644 --- a/var/spack/repos/builtin/packages/perl-digest-md5/package.py +++ b/var/spack/repos/builtin/packages/perl-digest-md5/package.py @@ -12,4 +12,4 @@ class PerlDigestMd5(PerlPackage): homepage = "http://search.cpan.org/dist/Digest-MD5/MD5.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Digest-MD5-2.55.tar.gz" - version('2.55', '601519b826ca14c233f13a4578b967ef') + version('2.55', sha256='03b198a2d14425d951e5e50a885d3818c3162c8fe4c21e18d7798a9a179d0e3c') diff --git a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py index 34e042b4988..a1984ef6a0d 100644 --- a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py +++ b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py @@ -12,4 +12,4 @@ class PerlDistCheckconflicts(PerlPackage): homepage = "http://search.cpan.org/~doy/Dist-CheckConflicts-0.11/lib/Dist/CheckConflicts.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DO/DOY/Dist-CheckConflicts-0.11.tar.gz" - version('0.11', 'c8725a92b9169708b0f63036812070f2') + version('0.11', sha256='ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4') diff --git a/var/spack/repos/builtin/packages/perl-encode-locale/package.py b/var/spack/repos/builtin/packages/perl-encode-locale/package.py index 8e91b2fd4d9..aa7b098174a 100644 --- a/var/spack/repos/builtin/packages/perl-encode-locale/package.py +++ b/var/spack/repos/builtin/packages/perl-encode-locale/package.py @@ -12,4 +12,4 @@ class PerlEncodeLocale(PerlPackage): homepage = "http://search.cpan.org/~gaas/Encode-Locale-1.05/lib/Encode/Locale.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Encode-Locale-1.05.tar.gz" - version('1.05', 'fcfdb8e4ee34bcf62aed429b4a23db27') + version('1.05', sha256='176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1') diff --git a/var/spack/repos/builtin/packages/perl-eval-closure/package.py b/var/spack/repos/builtin/packages/perl-eval-closure/package.py index b093b81cdc5..3e3ce2bed28 100644 --- a/var/spack/repos/builtin/packages/perl-eval-closure/package.py +++ b/var/spack/repos/builtin/packages/perl-eval-closure/package.py @@ -12,4 +12,4 @@ class PerlEvalClosure(PerlPackage): homepage = "http://search.cpan.org/~doy/Eval-Closure-0.14/lib/Eval/Closure.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DO/DOY/Eval-Closure-0.14.tar.gz" - version('0.14', 'ceeb1fc579ac9af981fa6b600538c285') + version('0.14', sha256='ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad') diff --git a/var/spack/repos/builtin/packages/perl-exception-class/package.py b/var/spack/repos/builtin/packages/perl-exception-class/package.py index a8e9877f7d2..6df79cbc54a 100644 --- a/var/spack/repos/builtin/packages/perl-exception-class/package.py +++ b/var/spack/repos/builtin/packages/perl-exception-class/package.py @@ -12,7 +12,7 @@ class PerlExceptionClass(PerlPackage): homepage = "http://search.cpan.org/~drolsky/Exception-Class-1.43/lib/Exception/Class.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Exception-Class-1.43.tar.gz" - version('1.43', 'ff3fa5c26fa417b68d1f2d0a14cce7f1') + version('1.43', sha256='ff3b4b3f706e84aaa87ab0dee5cec6bd7a8fc9f72cf76d115212541fa0a13760') depends_on('perl-devel-stacktrace', type=('build', 'run')) depends_on('perl-class-data-inheritable', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py index 2307a3c5c8a..993544506e1 100644 --- a/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py @@ -13,4 +13,4 @@ class PerlExporterTiny(PerlPackage): homepage = "http://search.cpan.org/~tobyink/Exporter-Tiny/lib/Exporter/Tiny.pm" url = "http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK/Exporter-Tiny-1.000000.tar.gz" - version('1.000000', '0d413747bdcf880f9ec62de8801ccf5e') + version('1.000000', sha256='ffdd77d57de099e8f64dd942ef12a00a3f4313c2531f342339eeed2d366ad078') diff --git a/var/spack/repos/builtin/packages/perl-extutils-depends/package.py b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py index 70a2b83688c..3034f2e3cbd 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-depends/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py @@ -12,4 +12,4 @@ class PerlExtutilsDepends(PerlPackage): homepage = "http://search.cpan.org/~xaoc/ExtUtils-Depends/lib/ExtUtils/Depends.pm" url = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-Depends-0.405.tar.gz" - version('0.405', 'caefbca2f173d0cea3f5ac26b6c08a2c') + version('0.405', sha256='8ad6401ad7559b03ceda1fe4b191c95f417bdec7c542a984761a4656715a8a2c') diff --git a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py index 7545d18c8de..d1b40ef0435 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py @@ -14,6 +14,6 @@ class PerlExtutilsMakemaker(PerlPackage): homepage = "https://github.com/Perl-Toolchain-Gang/ExtUtils-MakeMaker" url = "http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/ExtUtils-MakeMaker-7.24.tar.gz" - version('7.24', '15c67ba2ea2c9e20a3d976b738adb113') + version('7.24', sha256='416abc97c3bb2cc72bef28852522f2859de53e37bf3d0ae8b292067d78755e69') depends_on('perl@5.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py index 08cf9e3582f..e6ce7863e84 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py @@ -12,6 +12,6 @@ class PerlExtutilsPkgconfig(PerlPackage): homepage = "http://search.cpan.org/~xaoc/ExtUtils-PkgConfig-1.16/lib/ExtUtils/PkgConfig.pm" url = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz" - version('1.16', 'b86318f2b6ac6af3ee985299e1e38fe5') + version('1.16', sha256='bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e') depends_on('pkgconfig', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py index d8e789e2ffd..b7971013c9b 100644 --- a/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py +++ b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py @@ -12,5 +12,5 @@ class PerlFileCopyRecursive(PerlPackage): homepage = "http://search.cpan.org/~dmuey/File-Copy-Recursive-0.38/Recursive.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DM/DMUEY/File-Copy-Recursive-0.38.tar.gz" - version('0.40', '659c634f248885c4b3876b15baf56c79') - version('0.38', 'e76dc75ab456510d67c6c3a95183f72f') + version('0.40', sha256='e8b8923b930ef7bcb59d4a97456d0e149b8487597cd1550f836451d936ce55a1') + version('0.38', sha256='84ccbddf3894a88a2c2b6be68ff6ef8960037803bb36aa228b31944cfdf6deeb') diff --git a/var/spack/repos/builtin/packages/perl-file-listing/package.py b/var/spack/repos/builtin/packages/perl-file-listing/package.py index 9e81d6cdad1..89eaabc0c84 100644 --- a/var/spack/repos/builtin/packages/perl-file-listing/package.py +++ b/var/spack/repos/builtin/packages/perl-file-listing/package.py @@ -12,6 +12,6 @@ class PerlFileListing(PerlPackage): homepage = "http://search.cpan.org/~gaas/File-Listing-6.04/lib/File/Listing.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/File-Listing-6.04.tar.gz" - version('6.04', '83f636b477741f3a014585bb9cc079a6') + version('6.04', sha256='1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5') depends_on('perl-http-date', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-file-pushd/package.py b/var/spack/repos/builtin/packages/perl-file-pushd/package.py index bcf356bcebd..b0e8b998f36 100644 --- a/var/spack/repos/builtin/packages/perl-file-pushd/package.py +++ b/var/spack/repos/builtin/packages/perl-file-pushd/package.py @@ -12,4 +12,4 @@ class PerlFilePushd(PerlPackage): homepage = "http://search.cpan.org/~dagolden/File-pushd-1.014/lib/File/pushd.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/File-pushd-1.014.tar.gz" - version('1.014', '09c03001fb653c35663842191e315f5f') + version('1.014', sha256='b5ab37ffe3acbec53efb7c77b4423a2c79afa30a48298e751b9ebee3fdc6340b') diff --git a/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py index de174887b46..227e4a4889d 100644 --- a/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py +++ b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py @@ -12,6 +12,6 @@ class PerlFileSharedirInstall(PerlPackage): homepage = "http://search.cpan.org/~ether/File-ShareDir-Install-0.11/lib/File/ShareDir/Install.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/File-ShareDir-Install-0.11.tar.gz" - version('0.11', '61107e6ce6eee42bf29525b1a4d029e0') + version('0.11', sha256='32bf8772e9fea60866074b27ff31ab5bc3f88972d61915e84cbbb98455e00cc8') depends_on('perl-module-build', type='build') diff --git a/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py index 3b3d8ec65ff..0596513ca54 100644 --- a/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py @@ -12,4 +12,4 @@ class PerlFileSlurpTiny(PerlPackage): homepage = "http://search.cpan.org/~leont/File-Slurp-Tiny-0.004/lib/File/Slurp/Tiny.pm" url = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/File-Slurp-Tiny-0.004.tar.gz" - version('0.004', '7575b81543281ea57cdb7e5eb3f73264') + version('0.004', sha256='452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e') diff --git a/var/spack/repos/builtin/packages/perl-file-slurper/package.py b/var/spack/repos/builtin/packages/perl-file-slurper/package.py index ca9ef2a9988..b792a441ea6 100644 --- a/var/spack/repos/builtin/packages/perl-file-slurper/package.py +++ b/var/spack/repos/builtin/packages/perl-file-slurper/package.py @@ -12,4 +12,4 @@ class PerlFileSlurper(PerlPackage): homepage = "http://search.cpan.org/~leont/File-Slurper/lib/File/Slurper.pm" url = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/File-Slurper-0.011.tar.gz" - version('0.011', 'e0482d3d5a0522e39132ba54af9f1ce3') + version('0.011', sha256='f6494844b9759b3d1dd8fc4ffa790f8e6e493c4eb58e88831a51e085f2e76010') diff --git a/var/spack/repos/builtin/packages/perl-file-which/package.py b/var/spack/repos/builtin/packages/perl-file-which/package.py index ed338a65068..4ba1404103f 100644 --- a/var/spack/repos/builtin/packages/perl-file-which/package.py +++ b/var/spack/repos/builtin/packages/perl-file-which/package.py @@ -12,4 +12,4 @@ class PerlFileWhich(PerlPackage): homepage = "http://cpansearch.perl.org/src/PLICEASE/File-Which-1.22/lib/File/Which.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/File-Which-1.22.tar.gz" - version('1.22', 'face60fafd220dc83fa581ef6f96d480') + version('1.22', sha256='e8a8ffcf96868c6879e82645db4ff9ef00c2d8a286fed21971e7280f52cf0dd4') diff --git a/var/spack/repos/builtin/packages/perl-font-ttf/package.py b/var/spack/repos/builtin/packages/perl-font-ttf/package.py index eed1a8b504e..7d995027e1d 100644 --- a/var/spack/repos/builtin/packages/perl-font-ttf/package.py +++ b/var/spack/repos/builtin/packages/perl-font-ttf/package.py @@ -12,4 +12,4 @@ class PerlFontTtf(PerlPackage): homepage = "http://search.cpan.org/~bhallissy/Font-TTF-1.06/lib/Font/TTF.pm" url = "http://search.cpan.org/CPAN/authors/id/B/BH/BHALLISSY/Font-TTF-1.06.tar.gz" - version('1.06', '241b59310ad4450e6e050d5e790f1b21') + version('1.06', sha256='4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293') diff --git a/var/spack/repos/builtin/packages/perl-gd-graph/package.py b/var/spack/repos/builtin/packages/perl-gd-graph/package.py index 985a5677c71..a4c83eefc4b 100644 --- a/var/spack/repos/builtin/packages/perl-gd-graph/package.py +++ b/var/spack/repos/builtin/packages/perl-gd-graph/package.py @@ -12,7 +12,7 @@ class PerlGdGraph(PerlPackage): homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm" url = "http://search.cpan.org/CPAN/authors/id/B/BW/BWARFIELD/GDGraph-1.4308.tar.gz" - version('1.4308', 'fcdd34d5e09ae917b5d264887734b3b1') + version('1.4308', sha256='75b3c7e280431404ed096c6e120d552cc39052a8610787149515e94b9ba237cb') depends_on('perl-capture-tiny', type=('build', 'run')) depends_on('perl-test-exception', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-gd-text/package.py b/var/spack/repos/builtin/packages/perl-gd-text/package.py index e6ebf2dbaa2..1988eeaf708 100644 --- a/var/spack/repos/builtin/packages/perl-gd-text/package.py +++ b/var/spack/repos/builtin/packages/perl-gd-text/package.py @@ -12,6 +12,6 @@ class PerlGdText(PerlPackage): homepage = "http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm" url = "http://search.cpan.org/CPAN/authors/id/M/MV/MVERB/GDTextUtil-0.86.tar.gz" - version('0.86', '941ad06eadc86b47f3a32da405665c41') + version('0.86', sha256='886ecbf85cfe94f4135ee5689c4847a9ae783ecb99e6759e12c734f2dd6116bc') depends_on('perl-gd', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-gd/package.py b/var/spack/repos/builtin/packages/perl-gd/package.py index 2f34f39f729..ffedf63d8c8 100644 --- a/var/spack/repos/builtin/packages/perl-gd/package.py +++ b/var/spack/repos/builtin/packages/perl-gd/package.py @@ -12,7 +12,7 @@ class PerlGd(PerlPackage): homepage = "http://search.cpan.org/~lds/GD-2.53/GD.pm" url = "http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GD-2.53.tar.gz" - version('2.53', 'd2c9b18123bcaff8672eb50f2eb37ed3') + version('2.53', sha256='d05d01fe95e581adb3468cf05ab5d405db7497c0fb3ec7ecf23d023705fab7aa') depends_on('perl-module-build', type='build') depends_on('perl-extutils-makemaker', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py index 7cc6a6fd122..05559cccf54 100644 --- a/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py +++ b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py @@ -12,4 +12,4 @@ class PerlGraphReadwrite(PerlPackage): homepage = "http://search.cpan.org/~neilb/Graph-ReadWrite/lib/Graph/Writer/Dot.pm" url = "http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/Graph-ReadWrite-2.09.tar.gz" - version('2.09', '5cd9191eadd2fe8fe8bb431575434f67') + version('2.09', sha256='b01ef06ce922eea12d5ce614d63ddc5f3ee7ad0d05f9577051d3f87a89799a4a') diff --git a/var/spack/repos/builtin/packages/perl-graph/package.py b/var/spack/repos/builtin/packages/perl-graph/package.py index e3122124355..67a6c31ebf0 100644 --- a/var/spack/repos/builtin/packages/perl-graph/package.py +++ b/var/spack/repos/builtin/packages/perl-graph/package.py @@ -12,6 +12,6 @@ class PerlGraph(PerlPackage): homepage = "http://search.cpan.org/~jhi/Graph/lib/Graph.pod" url = "http://search.cpan.org/CPAN/authors/id/J/JH/JHI/Graph-0.9704.tar.gz" - version('0.9704', '1ab4e49420e56eeb1bc81d842aa8f3af') + version('0.9704', sha256='325e8eb07be2d09a909e450c13d3a42dcb2a2e96cc3ac780fe4572a0d80b2a25') depends_on('perl@5.6.0:') diff --git a/var/spack/repos/builtin/packages/perl-html-parser/package.py b/var/spack/repos/builtin/packages/perl-html-parser/package.py index 76d31fd745a..8fab2f83c60 100644 --- a/var/spack/repos/builtin/packages/perl-html-parser/package.py +++ b/var/spack/repos/builtin/packages/perl-html-parser/package.py @@ -12,6 +12,6 @@ class PerlHtmlParser(PerlPackage): homepage = "http://search.cpan.org/~gaas/HTML-Parser-3.72/Parser.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTML-Parser-3.72.tar.gz" - version('3.72', 'eb7505e5f626913350df9dd4a03d54a8') + version('3.72', sha256='ec28c7e1d9e67c45eca197077f7cdc41ead1bb4c538c7f02a3296a4bb92f608b') depends_on('perl-html-tagset', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-html-tagset/package.py b/var/spack/repos/builtin/packages/perl-html-tagset/package.py index 9236ca5eaf7..d7a67697cd7 100644 --- a/var/spack/repos/builtin/packages/perl-html-tagset/package.py +++ b/var/spack/repos/builtin/packages/perl-html-tagset/package.py @@ -12,4 +12,4 @@ class PerlHtmlTagset(PerlPackage): homepage = "http://search.cpan.org/~petdance/HTML-Tagset-3.20/Tagset.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PE/PETDANCE/HTML-Tagset-3.20.tar.gz" - version('3.20', 'd2bfa18fe1904df7f683e96611e87437') + version('3.20', sha256='adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2') diff --git a/var/spack/repos/builtin/packages/perl-http-cookies/package.py b/var/spack/repos/builtin/packages/perl-http-cookies/package.py index 3ace2589248..fc383c709be 100644 --- a/var/spack/repos/builtin/packages/perl-http-cookies/package.py +++ b/var/spack/repos/builtin/packages/perl-http-cookies/package.py @@ -12,7 +12,7 @@ class PerlHttpCookies(PerlPackage): homepage = "http://search.cpan.org/~oalders/HTTP-Cookies-6.04/lib/HTTP/Cookies.pm" url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/HTTP-Cookies-6.04.tar.gz" - version('6.04', '7bf1e277bd5c886bc18d21eb8423b65f') + version('6.04', sha256='0cc7f079079dcad8293fea36875ef58dd1bfd75ce1a6c244cd73ed9523eb13d4') depends_on('perl-uri', type=('build', 'run')) depends_on('perl-http-message', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-http-daemon/package.py b/var/spack/repos/builtin/packages/perl-http-daemon/package.py index 5bebdb4ec57..eac9e93f024 100644 --- a/var/spack/repos/builtin/packages/perl-http-daemon/package.py +++ b/var/spack/repos/builtin/packages/perl-http-daemon/package.py @@ -12,7 +12,7 @@ class PerlHttpDaemon(PerlPackage): homepage = "http://search.cpan.org/~gaas/HTTP-Daemon-6.01/lib/HTTP/Daemon.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Daemon-6.01.tar.gz" - version('6.01', 'ed0ae02d25d7f1e89456d4d69732adc2') + version('6.01', sha256='43fd867742701a3f9fcc7bd59838ab72c6490c0ebaf66901068ec6997514adc2') depends_on('perl-lwp-mediatypes', type=('build', 'run')) depends_on('perl-http-message', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-http-date/package.py b/var/spack/repos/builtin/packages/perl-http-date/package.py index f9be7e4f4e9..6f5491d2579 100644 --- a/var/spack/repos/builtin/packages/perl-http-date/package.py +++ b/var/spack/repos/builtin/packages/perl-http-date/package.py @@ -12,4 +12,4 @@ class PerlHttpDate(PerlPackage): homepage = "http://search.cpan.org/~gaas/HTTP-Date-6.02/lib/HTTP/Date.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Date-6.02.tar.gz" - version('6.02', '52b7a0d5982d61be1edb217751d7daba') + version('6.02', sha256='e8b9941da0f9f0c9c01068401a5e81341f0e3707d1c754f8e11f42a7e629e333') diff --git a/var/spack/repos/builtin/packages/perl-http-message/package.py b/var/spack/repos/builtin/packages/perl-http-message/package.py index cc627037276..57b3127177a 100644 --- a/var/spack/repos/builtin/packages/perl-http-message/package.py +++ b/var/spack/repos/builtin/packages/perl-http-message/package.py @@ -12,7 +12,7 @@ class PerlHttpMessage(PerlPackage): homepage = "http://search.cpan.org/~oalders/HTTP-Message-6.13/lib/HTTP/Status.pm" url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/HTTP-Message-6.13.tar.gz" - version('6.13', '4c1b7c6ee114c1cff69379ec9651d9ac') + version('6.13', sha256='f25f38428de851e5661e72f124476494852eb30812358b07f1c3a289f6f5eded') depends_on('perl-lwp-mediatypes', type=('build', 'run')) depends_on('perl-encode-locale', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-http-negotiate/package.py b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py index 78fa6a6f5d3..6e3b7cd5a18 100644 --- a/var/spack/repos/builtin/packages/perl-http-negotiate/package.py +++ b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py @@ -12,6 +12,6 @@ class PerlHttpNegotiate(PerlPackage): homepage = "http://search.cpan.org/~gaas/HTTP-Negotiate-6.01/lib/HTTP/Negotiate.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Negotiate-6.01.tar.gz" - version('6.01', '1236195250e264d7436e7bb02031671b') + version('6.01', sha256='1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016') depends_on('perl-http-message', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-inline-c/package.py b/var/spack/repos/builtin/packages/perl-inline-c/package.py index 6c123ee9a2e..dfcd457c6e4 100644 --- a/var/spack/repos/builtin/packages/perl-inline-c/package.py +++ b/var/spack/repos/builtin/packages/perl-inline-c/package.py @@ -12,7 +12,7 @@ class PerlInlineC(PerlPackage): homepage = "http://search.cpan.org/~tinita/Inline-C-0.78/lib/Inline/C.pod" url = "http://search.cpan.org/CPAN/authors/id/T/TI/TINITA/Inline-C-0.78.tar.gz" - version('0.78', '710a454b5337b1cbf3f2ae5c8c45b413') + version('0.78', sha256='9a7804d85c01a386073d2176582b0262b6374c5c0341049da3ef84c6f53efbc7') depends_on('perl-yaml-libyaml', type=('build', 'run')) depends_on('perl-parse-recdescent', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-inline/package.py b/var/spack/repos/builtin/packages/perl-inline/package.py index bed10b651f5..baa0d78621f 100644 --- a/var/spack/repos/builtin/packages/perl-inline/package.py +++ b/var/spack/repos/builtin/packages/perl-inline/package.py @@ -12,6 +12,6 @@ class PerlInline(PerlPackage): homepage = "http://search.cpan.org/~ingy/Inline-0.80/lib/Inline.pod" url = "http://search.cpan.org/CPAN/authors/id/I/IN/INGY/Inline-0.80.tar.gz" - version('0.80', '510bbac46e727bcaf240b7feac2646c9') + version('0.80', sha256='7e2bd984b1ebd43e336b937896463f2c6cb682c956cbd2c311a464363d2ccef6') depends_on('perl-test-warn', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-intervaltree/package.py index cf4ec1a65b3..5f875cdd6ec 100644 --- a/var/spack/repos/builtin/packages/perl-intervaltree/package.py +++ b/var/spack/repos/builtin/packages/perl-intervaltree/package.py @@ -13,6 +13,6 @@ class PerlIntervaltree(PerlPackage): homepage = "https://metacpan.org/release/Set-IntervalTree" url = "https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/Set-IntervalTree-0.10.tar.gz" - version('0.10', '42efe9369f1b30e7fd04e10c07226b06') + version('0.10', sha256='e3bd9ccf0d074b5f879eef1ed88254983697bf83d02744fce62150ee46553ebc') depends_on('perl-extutils-makemaker', type='build') diff --git a/var/spack/repos/builtin/packages/perl-io-compress/package.py b/var/spack/repos/builtin/packages/perl-io-compress/package.py index d4c0993fdcf..eec1245daa3 100644 --- a/var/spack/repos/builtin/packages/perl-io-compress/package.py +++ b/var/spack/repos/builtin/packages/perl-io-compress/package.py @@ -13,7 +13,7 @@ class PerlIoCompress(PerlPackage): homepage = "http://search.cpan.org/~pmqs/IO-Compress-2.070/lib/IO/Uncompress/AnyUncompress.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PM/PMQS/IO-Compress-2.081.tar.gz" - version('2.081', '379932c1b9428b873ed7ad3c1db15872') + version('2.081', sha256='5211c775544dc8c511af08edfb1c0c22734daa2789149c2a88d68e17b43546d9') depends_on('perl-compress-raw-zlib', type='run') depends_on('perl-compress-raw-bzip2', type='run') diff --git a/var/spack/repos/builtin/packages/perl-io-html/package.py b/var/spack/repos/builtin/packages/perl-io-html/package.py index 9f18ffcbd45..8809663b760 100644 --- a/var/spack/repos/builtin/packages/perl-io-html/package.py +++ b/var/spack/repos/builtin/packages/perl-io-html/package.py @@ -12,4 +12,4 @@ class PerlIoHtml(PerlPackage): homepage = "http://search.cpan.org/~cjm/IO-HTML-1.001/lib/IO/HTML.pm" url = "http://search.cpan.org/CPAN/authors/id/C/CJ/CJM/IO-HTML-1.001.tar.gz" - version('1.001', '3f8958718844dc96b9f6946f21d70d22') + version('1.001', sha256='ea78d2d743794adc028bc9589538eb867174b4e165d7d8b5f63486e6b828e7e0') diff --git a/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py index 77afc6ff4b7..215eb239da8 100644 --- a/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py +++ b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py @@ -12,4 +12,4 @@ class PerlIoSessiondata(PerlPackage): homepage = "http://search.cpan.org/~phred/IO-SessionData-1.03/" url = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/IO-SessionData-1.03.tar.gz" - version('1.03', '790f9e05465c774cf9a6299500463104') + version('1.03', sha256='64a4712a3edbb3fd10230db296c29c8c66f066adfbc0c3df6a48258fef392ddd') diff --git a/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py index 0c1e687bafb..88dc0008a1d 100644 --- a/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py +++ b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py @@ -13,7 +13,7 @@ class PerlIoSocketSsl(PerlPackage): homepage = "http://search.cpan.org/~sullr/IO-Socket-SSL-2.052/lib/IO/Socket/SSL.pod" url = "http://search.cpan.org/CPAN/authors/id/S/SU/SULLR/IO-Socket-SSL-2.052.tar.gz" - version('2.052', '26c9bcdfb4ba8763ef89264f21326a48') + version('2.052', sha256='e4897a9b17cb18a3c44aa683980d52cef534cdfcb8063d6877c879bfa2f26673') depends_on('perl-net-ssleay', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-io-string/package.py b/var/spack/repos/builtin/packages/perl-io-string/package.py index a2028875c0d..a117b578fe4 100644 --- a/var/spack/repos/builtin/packages/perl-io-string/package.py +++ b/var/spack/repos/builtin/packages/perl-io-string/package.py @@ -12,4 +12,4 @@ class PerlIoString(PerlPackage): homepage = "http://search.cpan.org/~gaas/IO-String-1.08/String.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/IO-String-1.08.tar.gz" - version('1.08', '250e5424f290299fc3d6b5d1e9da3835') + version('1.08', sha256='2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0') diff --git a/var/spack/repos/builtin/packages/perl-json/package.py b/var/spack/repos/builtin/packages/perl-json/package.py index 6b0019933bf..a62663777af 100644 --- a/var/spack/repos/builtin/packages/perl-json/package.py +++ b/var/spack/repos/builtin/packages/perl-json/package.py @@ -12,4 +12,4 @@ class PerlJson(PerlPackage): homepage = "http://search.cpan.org/~ishigaki/JSON/lib/JSON.pm" url = "http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/JSON-2.97001.tar.gz" - version('2.97001', '693d6ff167496362f8ec6c3c5b8ba5ee') + version('2.97001', sha256='e277d9385633574923f48c297e1b8acad3170c69fa590e31fa466040fc6f8f5a') diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py index ea2ef1f6f48..63a36a0e65e 100644 --- a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py @@ -15,7 +15,7 @@ class PerlLibwwwPerl(PerlPackage): homepage = "https://github.com/libwww-perl/libwww-perl" url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz" - version('6.33', '2e15c1c789ac9036c99d094e47e3da23') + version('6.33', sha256='97417386f11f007ae129fe155b82fd8969473ce396a971a664c8ae6850c69b99') depends_on('perl-encode-locale', type=('build', 'run')) depends_on('perl-file-listing', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py index fd60e656681..17ae5cce701 100644 --- a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py +++ b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py @@ -12,7 +12,7 @@ class PerlListMoreutils(PerlPackage): homepage = "http://search.cpan.org/~rehsack/List-MoreUtils/lib/List/MoreUtils.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/List-MoreUtils-0.428.tar.gz" - version('0.428', '493032a211cdff1fcf45f59ebd680407') + version('0.428', sha256='713e0945d5f16e62d81d5f3da2b6a7b14a4ce439f6d3a7de74df1fd166476cc2') depends_on('perl-exporter-tiny', type=('build', 'run')) depends_on('perl-list-moreutils-xs', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py index 43e10929963..ef7faad32c0 100644 --- a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py +++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py @@ -12,4 +12,4 @@ class PerlLogLog4perl(PerlPackage): homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm" url = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz" - version('146', '500abbd978ed326cfe5367dc4f9f3be2') + version('146', sha256='a361e483095795753b97f8a506b40c24c753cf73828bb8697665499ef8596402') diff --git a/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py index 571bf7d2e9c..a3fa8365b81 100644 --- a/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py +++ b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py @@ -12,4 +12,4 @@ class PerlLwpMediatypes(PerlPackage): homepage = "http://search.cpan.org/~gaas/LWP-MediaTypes-6.02/lib/LWP/MediaTypes.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/LWP-MediaTypes-6.02.tar.gz" - version('6.02', '8c5f25fb64b974d22aff424476ba13c9') + version('6.02', sha256='18790b0cc5f0a51468495c3847b16738f785a2d460403595001e0b932e5db676') diff --git a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py index 838b85e7976..0974a00bc7a 100644 --- a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py +++ b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py @@ -12,7 +12,7 @@ class PerlLwpProtocolHttps(PerlPackage): homepage = "http://search.cpan.org/~gaas/LWP-Protocol-https-6.04/lib/LWP/Protocol/https.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/LWP-Protocol-https-6.04.tar.gz" - version('6.04', '1b422a7d3b5fed1eb4d748fdc9fd79a4') + version('6.04', sha256='1ef67750ee363525cf729b59afde805ac4dc80eaf8d36ca01082a4d78a7af629') depends_on('perl-test-requiresinternet', type=('build', 'run')) depends_on('perl-io-socket-ssl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-lwp/package.py b/var/spack/repos/builtin/packages/perl-lwp/package.py index 54471984958..4cbe00854e0 100644 --- a/var/spack/repos/builtin/packages/perl-lwp/package.py +++ b/var/spack/repos/builtin/packages/perl-lwp/package.py @@ -12,7 +12,7 @@ class PerlLwp(PerlPackage): homepage = "http://search.cpan.org/~oalders/libwww-perl-6.29/lib/LWP.pm" url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.29.tar.gz" - version('6.29', 'efec8d563ffd3652333356aa722c2b56') + version('6.29', sha256='4c6f2697999d2d0e6436b584116b12b30dc39990ec0622751c1a6cec2c0e6662') depends_on('perl-test-requiresinternet', type=('build', 'run')) depends_on('perl-http-message', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-math-cdf/package.py b/var/spack/repos/builtin/packages/perl-math-cdf/package.py index 4274f6f36fd..d53b4149555 100644 --- a/var/spack/repos/builtin/packages/perl-math-cdf/package.py +++ b/var/spack/repos/builtin/packages/perl-math-cdf/package.py @@ -13,4 +13,4 @@ class PerlMathCdf(PerlPackage): homepage = "http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm" url = "http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/Math-CDF-0.1.tar.gz" - version('0.1', '7866c7b6b9d27f0ce4b7637334478ab7') + version('0.1', sha256='7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565') diff --git a/var/spack/repos/builtin/packages/perl-math-cephes/package.py b/var/spack/repos/builtin/packages/perl-math-cephes/package.py index e8cf44af1d3..3550414a027 100644 --- a/var/spack/repos/builtin/packages/perl-math-cephes/package.py +++ b/var/spack/repos/builtin/packages/perl-math-cephes/package.py @@ -13,4 +13,4 @@ class PerlMathCephes(PerlPackage): homepage = "http://search.cpan.org/~shlomif/Math-Cephes/lib/Math/Cephes.pod" url = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Math-Cephes-0.5305.tar.gz" - version('0.5305', '30922dd213783aaaf91a47626f6a1853') + version('0.5305', sha256='561a800a4822e748d2befc366baa4b21e879a40cc00c22293c7b8736caeb83a1') diff --git a/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py index e6cc2acbc17..697289b2b95 100644 --- a/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py +++ b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py @@ -13,6 +13,6 @@ class PerlMathMatrixreal(PerlPackage): homepage = "http://search.cpan.org/~leto/Math-MatrixReal/lib/Math/MatrixReal.pm" url = "http://search.cpan.org/CPAN/authors/id/L/LE/LETO/Math-MatrixReal-2.13.tar.gz" - version('2.13', 'cf9d6ff71f2df075559ea752104ca199') + version('2.13', sha256='4f9fa1a46dd34d2225de461d9a4ed86932cdd821c121fa501a15a6d4302fb4b2') depends_on('perl-module-build', type='build') diff --git a/var/spack/repos/builtin/packages/perl-module-build/package.py b/var/spack/repos/builtin/packages/perl-module-build/package.py index c2aaa0e1686..bb54259cc64 100644 --- a/var/spack/repos/builtin/packages/perl-module-build/package.py +++ b/var/spack/repos/builtin/packages/perl-module-build/package.py @@ -20,4 +20,4 @@ class PerlModuleBuild(PerlPackage): url = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/Module-Build-0.4224.tar.gz" version('0.4224', sha256='a6ca15d78244a7b50fdbf27f85c85f4035aa799ce7dd018a0d98b358ef7bc782') - version('0.4220', '9df204e188462a4410d496f316c2c531') + version('0.4220', sha256='fb1207c7e799366f7a8adda3f135bf8141c4d6068505650d4db2b2d3ce34b5a2') diff --git a/var/spack/repos/builtin/packages/perl-module-implementation/package.py b/var/spack/repos/builtin/packages/perl-module-implementation/package.py index b9fddc9e9ac..ef802b6b110 100644 --- a/var/spack/repos/builtin/packages/perl-module-implementation/package.py +++ b/var/spack/repos/builtin/packages/perl-module-implementation/package.py @@ -13,7 +13,7 @@ class PerlModuleImplementation(PerlPackage): homepage = "http://search.cpan.org/~drolsky/Module-Implementation/lib/Module/Implementation.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Module-Implementation-0.09.tar.gz" - version('0.09', '52e3fe0ca6b1eff0488d59b7aacc0667') + version('0.09', sha256='c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d') depends_on('perl-module-runtime', type=('build', 'run')) depends_on('perl-test-fatal', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py index 669879070d2..c86a6a641a9 100644 --- a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py +++ b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py @@ -12,4 +12,4 @@ class PerlModuleRuntimeConflicts(PerlPackage): homepage = "http://search.cpan.org/~ether/Module-Runtime-Conflicts-0.003/lib/Module/Runtime/Conflicts.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Module-Runtime-Conflicts-0.003.tar.gz" - version('0.003', '67aaf699072063cc00c5b6afd4c67a6f') + version('0.003', sha256='707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875') diff --git a/var/spack/repos/builtin/packages/perl-module-runtime/package.py b/var/spack/repos/builtin/packages/perl-module-runtime/package.py index f73456535b7..b7f172aa519 100644 --- a/var/spack/repos/builtin/packages/perl-module-runtime/package.py +++ b/var/spack/repos/builtin/packages/perl-module-runtime/package.py @@ -12,6 +12,6 @@ class PerlModuleRuntime(PerlPackage): homepage = "http://search.cpan.org/~zefram/Module-Runtime/lib/Module/Runtime.pm" url = "http://search.cpan.org/CPAN/authors/id/Z/ZE/ZEFRAM/Module-Runtime-0.016.tar.gz" - version('0.016', 'd3d47222fa2e3dfcb4526f6cc8437b20') + version('0.016', sha256='68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024') depends_on('perl-module-build', type='build') diff --git a/var/spack/repos/builtin/packages/perl-moose/package.py b/var/spack/repos/builtin/packages/perl-moose/package.py index aa660ed0f43..11dbe467f87 100644 --- a/var/spack/repos/builtin/packages/perl-moose/package.py +++ b/var/spack/repos/builtin/packages/perl-moose/package.py @@ -12,10 +12,10 @@ class PerlMoose(PerlPackage): homepage = "http://search.cpan.org/~ether/Moose-2.2006/lib/Moose.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Moose-2.2006.tar.gz" - version('2.2010', '636238ac384818ee1e92eff6b9ecc50a') - version('2.2009', '5527b1a5abc29b5c57fc488447e76ccd') - version('2.2007', 'de487ae226003f7e7f22c0fd8f0074e6') - version('2.2006', '929c6b3877a6054ef617cf7ef1e220b5') + version('2.2010', sha256='af0905b69f18c27de1177c9bc7778ee495d4ec91be1f223e8ca8333af4de08c5') + version('2.2009', sha256='63ba8a5e27dbcbdbac2cd8f4162fff50a31e9829d8955a196a5898240c02d194') + version('2.2007', sha256='bc75a320b55ba26ac9e60e11a77b3471066cb615bf7097537ed22e20df88afe8') + version('2.2006', sha256='a4e00ab25cc41bebc5e7a11d71375fb5e64b56d5f91159afee225d698e06392b') depends_on('perl-cpan-meta-check', type=('build', 'run')) depends_on('perl-test-cleannamespaces', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py index f4ffdb1ab57..c5a4e0c5d6d 100644 --- a/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py +++ b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py @@ -12,4 +12,4 @@ class PerlMozillaCa(PerlPackage): homepage = "http://search.cpan.org/~abh/Mozilla-CA-20160104/lib/Mozilla/CA.pm" url = "http://search.cpan.org/CPAN/authors/id/A/AB/ABH/Mozilla-CA-20160104.tar.gz" - version('20160104', '1b91edb15953a8188f011ab5ff433300') + version('20160104', sha256='27a7069a243162b65ada4194ff9d21b6ebc304af723eb5d3972fb74c11b03f2a') diff --git a/var/spack/repos/builtin/packages/perl-mro-compat/package.py b/var/spack/repos/builtin/packages/perl-mro-compat/package.py index 6c3b430b5d1..fa25854b434 100644 --- a/var/spack/repos/builtin/packages/perl-mro-compat/package.py +++ b/var/spack/repos/builtin/packages/perl-mro-compat/package.py @@ -12,4 +12,4 @@ class PerlMroCompat(PerlPackage): homepage = "http://search.cpan.org/~haarg/MRO-Compat-0.13/lib/MRO/Compat.pm" url = "http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/MRO-Compat-0.13.tar.gz" - version('0.13', 'd2e603e8ae9dc6934162d190eb085385') + version('0.13', sha256='8a2c3b6ccc19328d5579d02a7d91285e2afd85d801f49d423a8eb16f323da4f8') diff --git a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py index 46631581e4e..749313e7568 100644 --- a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py +++ b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py @@ -12,6 +12,6 @@ class PerlNamespaceClean(PerlPackage): homepage = "http://search.cpan.org/~ribasushi/namespace-clean-0.27/lib/namespace/clean.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/namespace-clean-0.27.tar.gz" - version('0.27', 'cba97f39ef7e594bd8489b4fdcddb662') + version('0.27', sha256='8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d') depends_on('perl-b-hooks-endofscope', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-net-http/package.py b/var/spack/repos/builtin/packages/perl-net-http/package.py index 94c72f2a36c..0d7667bd8a5 100644 --- a/var/spack/repos/builtin/packages/perl-net-http/package.py +++ b/var/spack/repos/builtin/packages/perl-net-http/package.py @@ -12,6 +12,6 @@ class PerlNetHttp(PerlPackage): homepage = "http://search.cpan.org/~oalders/Net-HTTP-6.17/lib/Net/HTTP.pm" url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/Net-HTTP-6.17.tar.gz" - version('6.17', '068fa02fd3c8a5b63316025b5a24844c') + version('6.17', sha256='1e8624b1618dc6f7f605f5545643ebb9b833930f4d7485d4124aa2f2f26d1611') depends_on('perl-uri', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py index 6a467bc418e..c1c0dc2f334 100644 --- a/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py +++ b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py @@ -12,4 +12,4 @@ class PerlNetScpExpect(PerlPackage): homepage = "http://search.cpan.org/~rybskej/Net-SCP-Expect/Expect.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/Net-SCP-Expect-0.16.tar.gz" - version('0.16', 'a3d8f5e6a34ba3df8527aea098f64a58') + version('0.16', sha256='97586e0ee0d61c987a7efaaffbfa551b95c426b3ef3625e046dc456fe9170591') diff --git a/var/spack/repos/builtin/packages/perl-net-ssleay/package.py b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py index 2ea0a6a0a67..58f4d237f39 100644 --- a/var/spack/repos/builtin/packages/perl-net-ssleay/package.py +++ b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py @@ -13,8 +13,8 @@ class PerlNetSsleay(PerlPackage): homepage = "http://search.cpan.org/~mikem/Net-SSLeay-1.82/lib/Net/SSLeay.pod" url = "http://search.cpan.org/CPAN/authors/id/M/MI/MIKEM/Net-SSLeay-1.82.tar.gz" - version('1.85', '9d8188b9fb1cae3bd791979c20554925d5e94a138d00414f1a6814549927b0c8') - version('1.82', '2170469d929d5173bacffd0cb2d7fafa') + version('1.85', sha256='9d8188b9fb1cae3bd791979c20554925d5e94a138d00414f1a6814549927b0c8') + version('1.82', sha256='5895c519c9986a5e5af88e3b8884bbdc70e709ee829dc6abb9f53155c347c7e5') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py index 955db1e91a9..4213a1bc0f9 100644 --- a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py +++ b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py @@ -12,4 +12,4 @@ class PerlPackageDeprecationmanager(PerlPackage): homepage = "http://search.cpan.org/~drolsky/Package-DeprecationManager-0.17/lib/Package/DeprecationManager.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Package-DeprecationManager-0.17.tar.gz" - version('0.17', '7b46e92aaae3047ede3c67c1714ab88e') + version('0.17', sha256='1d743ada482b5c9871d894966e87d4c20edc96931bb949fb2638b000ddd6684b') diff --git a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py index d2c4bd5183b..a607a40accb 100644 --- a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py +++ b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py @@ -12,4 +12,4 @@ class PerlPackageStashXs(PerlPackage): homepage = "http://search.cpan.org/~doy/Package-Stash-XS-0.28/lib/Package/Stash/XS.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DO/DOY/Package-Stash-XS-0.28.tar.gz" - version('0.28', '9664356ec3be02626cbd3081ec246b70') + version('0.28', sha256='23d8c5c25768ef1dc0ce53b975796762df0d6e244445d06e48d794886c32d486') diff --git a/var/spack/repos/builtin/packages/perl-package-stash/package.py b/var/spack/repos/builtin/packages/perl-package-stash/package.py index 89886997865..600315fc244 100644 --- a/var/spack/repos/builtin/packages/perl-package-stash/package.py +++ b/var/spack/repos/builtin/packages/perl-package-stash/package.py @@ -12,7 +12,7 @@ class PerlPackageStash(PerlPackage): homepage = "http://search.cpan.org/~doy/Package-Stash-0.37/lib/Package/Stash.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DO/DOY/Package-Stash-0.37.tar.gz" - version('0.37', '7e47a8261312e1cf3d12bd2007916b66') + version('0.37', sha256='06ab05388f9130cd377c0e1d3e3bafeed6ef6a1e22104571a9e1d7bfac787b2c') depends_on('perl-test-requires', type=('build', 'run')) depends_on('perl-test-fatal', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-padwalker/package.py b/var/spack/repos/builtin/packages/perl-padwalker/package.py index 3e1f4ea02b9..03bb145f791 100644 --- a/var/spack/repos/builtin/packages/perl-padwalker/package.py +++ b/var/spack/repos/builtin/packages/perl-padwalker/package.py @@ -12,4 +12,4 @@ class PerlPadwalker(PerlPackage): homepage = "http://search.cpan.org/~robin/PadWalker-2.2/PadWalker.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/PadWalker-2.2.tar.gz" - version('2.2', '6bcc741f77b1831a893b2a22c785e31a') + version('2.2', sha256='fc1df2084522e29e892da393f3719d2c1be0da022fdd89cff4b814167aecfea3') diff --git a/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py index ef132c5d4cf..9277b3b2f35 100644 --- a/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py +++ b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py @@ -12,4 +12,4 @@ class PerlParallelForkmanager(PerlPackage): homepage = "http://search.cpan.org/~yanick/Parallel-ForkManager/lib/Parallel/ForkManager.pm" url = "http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz" - version('1.19', '0e7137dd4b6948e1633b3b9ebe3b87e1') + version('1.19', sha256='f1de2e9875eeb77d65f80338905dedd522f3913822502982f805aa71cde5a472') diff --git a/var/spack/repos/builtin/packages/perl-params-util/package.py b/var/spack/repos/builtin/packages/perl-params-util/package.py index cd8465d9ce9..49899534497 100644 --- a/var/spack/repos/builtin/packages/perl-params-util/package.py +++ b/var/spack/repos/builtin/packages/perl-params-util/package.py @@ -12,4 +12,4 @@ class PerlParamsUtil(PerlPackage): homepage = "http://search.cpan.org/~adamk/Params-Util-1.07/lib/Params/Util.pm" url = "http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/Params-Util-1.07.tar.gz" - version('1.07', '02db120c0eef87aae1830cc62bdec37b') + version('1.07', sha256='30f1ec3f2cf9ff66ae96f973333f23c5f558915bb6266881eac7423f52d7c76c') diff --git a/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py index ccdc2a3a374..3c5d3ae7fdd 100644 --- a/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py +++ b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py @@ -12,6 +12,6 @@ class PerlParseRecdescent(PerlPackage): homepage = "http://search.cpan.org/~jtbraun/Parse-RecDescent-1.967015/lib/Parse/RecDescent.pm" url = "http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/Parse-RecDescent-1.967015.tar.gz" - version('1.967015', '7a36d45d62a9b68603edcdbd276006cc') + version('1.967015', sha256='1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37') depends_on('perl-module-build', type='build') diff --git a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py index 425900e34c8..200d2c02e18 100644 --- a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py +++ b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py @@ -12,7 +12,7 @@ class PerlPdfApi2(PerlPackage): homepage = "http://search.cpan.org/~ssimms/PDF-API2-2.033/lib/PDF/API2.pm" url = "http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/PDF-API2-2.033.tar.gz" - version('2.033', '4223a38add42741f996bd67d5f2f8e5b') + version('2.033', sha256='9c0866ec1a3053f73afaca5f5cdbe6925903b4ce606f4bf4ac317731a69d27a0') depends_on('perl-test-exception', type=('build', 'run')) depends_on('perl-test-memory-cycle', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-pegex/package.py b/var/spack/repos/builtin/packages/perl-pegex/package.py index 85ade374947..96fb751d1ca 100644 --- a/var/spack/repos/builtin/packages/perl-pegex/package.py +++ b/var/spack/repos/builtin/packages/perl-pegex/package.py @@ -12,7 +12,7 @@ class PerlPegex(PerlPackage): homepage = "http://search.cpan.org/~ingy/Pegex-0.64/lib/Pegex.pod" url = "http://search.cpan.org/CPAN/authors/id/I/IN/INGY/Pegex-0.64.tar.gz" - version('0.64', 'db86d4f1ddc36c4c7860ce060e77976f') + version('0.64', sha256='27e00264bdafb9c2109212b9654542032617fecf7b7814915d2bdac198f067cd') depends_on('perl-file-sharedir-install', type=('build', 'run')) depends_on('perl-yaml-libyaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py index b35768d01be..32e1fe7a913 100644 --- a/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py +++ b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py @@ -12,6 +12,6 @@ class PerlPerl6Slurp(PerlPackage): homepage = "http://search.cpan.org/~dconway/Perl6-Slurp-0.051005/lib/Perl6/Slurp.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/Perl6-Slurp-0.051005.tar.gz" - version('0.051005', '6095c8df495c7983f36996ed78c5ead7') + version('0.051005', sha256='0e0ceb30495ecf64dc6cacd12113d604871104c0cfe153487b8d68bc9393d78f') depends_on('perl@5.8:5.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py index d7f68d420b2..e70ca307209 100644 --- a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py +++ b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py @@ -12,8 +12,8 @@ class PerlPerlioGzip(PerlPackage): homepage = "http://search.cpan.org/~nwclark/PerlIO-gzip/gzip.pm" url = "http://search.cpan.org/CPAN/authors/id/N/NW/NWCLARK/PerlIO-gzip-0.19.tar.gz" - version('0.20', '0393eae5d0b23df6cf40ed44af7d711c') - version('0.19', 'dbcfc1450f6b593b65048b8ced061c98') + version('0.20', sha256='4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5') + version('0.19', sha256='d2e9351d58b8a93c86811e25a898ee651fc393a157413652bf42f9aada2eb284') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py index 57ff1b7f959..24b8bde83ab 100644 --- a/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py +++ b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py @@ -12,4 +12,4 @@ class PerlPerlioUtf8Strict(PerlPackage): homepage = "http://search.cpan.org/~leont/PerlIO-utf8_strict/lib/PerlIO/utf8_strict.pm" url = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/PerlIO-utf8_strict-0.002.tar.gz" - version('0.002', '2e5b13efe6dfd7748e44e47f6dedb1da') + version('0.002', sha256='6e3163f8a2f1d276c975f21789d7a07843586d69e3e6156ffb67ef6680ceb75f') diff --git a/var/spack/repos/builtin/packages/perl-soap-lite/package.py b/var/spack/repos/builtin/packages/perl-soap-lite/package.py index b05c1adcee3..78563d69cad 100644 --- a/var/spack/repos/builtin/packages/perl-soap-lite/package.py +++ b/var/spack/repos/builtin/packages/perl-soap-lite/package.py @@ -12,7 +12,7 @@ class PerlSoapLite(PerlPackage): homepage = "http://search.cpan.org/~phred/SOAP-Lite-1.20/lib/SOAP/Lite.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/SOAP-Lite-1.22.tar.gz" - version('1.22', '86c31341311498a08c6309e62168f655') + version('1.22', sha256='92f492f8722cb3002cd1dce11238cee5599bb5bd451a062966df45223d33693a') depends_on('perl-io-sessiondata', type=('build', 'run')) depends_on('perl-lwp-protocol-https', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py index 25612d49d2d..0860ab9e3d4 100644 --- a/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py +++ b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py @@ -12,4 +12,4 @@ class PerlStatisticsDescriptive(PerlPackage): homepage = "http://search.cpan.org/~shlomif/Statistics-Descriptive-3.0612/lib/Statistics/Descriptive.pm" url = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0612.tar.gz" - version('3.0612', 'e38cfbc1e3962d099b62a14a57a175f1') + version('3.0612', sha256='772413148e5e00efb32f277c4254aa78b9112490a896208dcd0025813afdbf7a') diff --git a/var/spack/repos/builtin/packages/perl-statistics-pca/package.py b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py index 3641edfe7ed..7e2ffea5112 100644 --- a/var/spack/repos/builtin/packages/perl-statistics-pca/package.py +++ b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py @@ -12,7 +12,7 @@ class PerlStatisticsPca(PerlPackage): homepage = "http://search.cpan.org/~dsth/Statistics-PCA/lib/Statistics/PCA.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DS/DSTH/Statistics-PCA-0.0.1.tar.gz" - version('0.0.1', '6e0e05fe13f6becea525b973a0c29001') + version('0.0.1', sha256='f8adb10b00232123d103a5b49161ad46370f47fe0f752e5462a4dc15f9d46bc4') depends_on('perl-module-build', type='build') depends_on('perl-contextual-return', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py index e5e9e898f6c..86136fc0d83 100644 --- a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py @@ -12,4 +12,4 @@ class PerlSubExporterProgressive(PerlPackage): homepage = "http://search.cpan.org/~frew/Sub-Exporter-Progressive-0.001013/lib/Sub/Exporter/Progressive.pm" url = "http://search.cpan.org/CPAN/authors/id/F/FR/FREW/Sub-Exporter-Progressive-0.001013.tar.gz" - version('0.001013', '72cf6acdd2a0a8b105821a4db98e4ebe') + version('0.001013', sha256='d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056') diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py index 2a26414d81b..a9b8966efc8 100644 --- a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py @@ -12,7 +12,7 @@ class PerlSubExporter(PerlPackage): homepage = "http://search.cpan.org/~rjbs/Sub-Exporter-0.987/lib/Sub/Exporter.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Sub-Exporter-0.987.tar.gz" - version('0.987', '5332d269a7ba387773fcd140b72a0ed2') + version('0.987', sha256='543cb2e803ab913d44272c7da6a70bb62c19e467f3b12aaac4c9523259b083d6') depends_on('perl-params-util', type=('build', 'run')) depends_on('perl-data-optlist', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-sub-identify/package.py b/var/spack/repos/builtin/packages/perl-sub-identify/package.py index 614d6a78200..945ea81a062 100644 --- a/var/spack/repos/builtin/packages/perl-sub-identify/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-identify/package.py @@ -12,4 +12,4 @@ class PerlSubIdentify(PerlPackage): homepage = "http://search.cpan.org/~rgarcia/Sub-Identify-0.14/lib/Sub/Identify.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RG/RGARCIA/Sub-Identify-0.14.tar.gz" - version('0.14', '014f19e72698b6a2cbcb54adc9691825') + version('0.14', sha256='068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f') diff --git a/var/spack/repos/builtin/packages/perl-sub-install/package.py b/var/spack/repos/builtin/packages/perl-sub-install/package.py index 7c250ff0ba9..c6b99426d7c 100644 --- a/var/spack/repos/builtin/packages/perl-sub-install/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-install/package.py @@ -12,4 +12,4 @@ class PerlSubInstall(PerlPackage): homepage = "http://search.cpan.org/~rjbs/Sub-Install-0.928/lib/Sub/Install.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Sub-Install-0.928.tar.gz" - version('0.928', 'e1ce4f9cb6b2f6b8778b036c31afa5ab') + version('0.928', sha256='61e567a7679588887b7b86d427bc476ea6d77fffe7e0d17d640f89007d98ef0f') diff --git a/var/spack/repos/builtin/packages/perl-sub-name/package.py b/var/spack/repos/builtin/packages/perl-sub-name/package.py index bab16426384..4eaeb16cbe0 100644 --- a/var/spack/repos/builtin/packages/perl-sub-name/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-name/package.py @@ -12,4 +12,4 @@ class PerlSubName(PerlPackage): homepage = "http://search.cpan.org/~ether/Sub-Name-0.21/lib/Sub/Name.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Sub-Name-0.21.tar.gz" - version('0.21', '7e7a181e30b3249d0b81585f55e36621') + version('0.21', sha256='bd32e9dee07047c10ae474c9f17d458b6e9885a6db69474c7a494ccc34c27117') diff --git a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py index 3a1f53556a3..4c8d6ff6e4d 100644 --- a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py @@ -12,4 +12,4 @@ class PerlSubUplevel(PerlPackage): homepage = "http://search.cpan.org/~dagolden/Sub-Uplevel-0.2800/lib/Sub/Uplevel.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz" - version('0.2800', '6c6a174861fd160e8d5871a86df00baf') + version('0.2800', sha256='b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293') diff --git a/var/spack/repos/builtin/packages/perl-svg/package.py b/var/spack/repos/builtin/packages/perl-svg/package.py index 9d5fd0bb450..290d1ef9ef8 100644 --- a/var/spack/repos/builtin/packages/perl-svg/package.py +++ b/var/spack/repos/builtin/packages/perl-svg/package.py @@ -13,4 +13,4 @@ class PerlSvg(PerlPackage): homepage = "http://search.cpan.org/~manwar/SVG-2.78/lib/SVG.pm" url = "http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/SVG-2.78.tar.gz" - version('2.78', 'b247c216ab11fae24533d0ce556e2e75') + version('2.78', sha256='a665c1f18c0529f3da0f4b631976eb47e0f71f6d6784ef3f44d32fd76643d6bb') diff --git a/var/spack/repos/builtin/packages/perl-swissknife/package.py b/var/spack/repos/builtin/packages/perl-swissknife/package.py index 694e481a609..91c5a6024c3 100644 --- a/var/spack/repos/builtin/packages/perl-swissknife/package.py +++ b/var/spack/repos/builtin/packages/perl-swissknife/package.py @@ -12,6 +12,6 @@ class PerlSwissknife(PerlPackage): homepage = "http://swissknife.sourceforge.net" url = "https://downloads.sourceforge.net/project/swissknife/swissknife/1.75/Swissknife_1.75.tar.gz" - version('1.75', '09d008cb1d1d211ae4eb9f087c213edf') + version('1.75', sha256='3d9af0d71366c90698488f6dae54118e6a4dba087b3c33d1bfa8245663cba53a') depends_on('perl-module-build', type='build') diff --git a/var/spack/repos/builtin/packages/perl-task-weaken/package.py b/var/spack/repos/builtin/packages/perl-task-weaken/package.py index 42a740945e4..5c3e680f94f 100644 --- a/var/spack/repos/builtin/packages/perl-task-weaken/package.py +++ b/var/spack/repos/builtin/packages/perl-task-weaken/package.py @@ -12,4 +12,4 @@ class PerlTaskWeaken(PerlPackage): homepage = "http://search.cpan.org/~adamk/Task-Weaken-1.04/lib/Task/Weaken.pm" url = "http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/Task-Weaken-1.04.tar.gz" - version('1.04', 'affd0c395515bb95d29968404d7fe6de') + version('1.04', sha256='67e271c55900fe7889584f911daa946e177bb60c8af44c32f4584b87766af3c4') diff --git a/var/spack/repos/builtin/packages/perl-term-readkey/package.py b/var/spack/repos/builtin/packages/perl-term-readkey/package.py index 93317e3bf78..0e89420d336 100644 --- a/var/spack/repos/builtin/packages/perl-term-readkey/package.py +++ b/var/spack/repos/builtin/packages/perl-term-readkey/package.py @@ -19,4 +19,4 @@ class PerlTermReadkey(PerlPackage): url = "http://www.cpan.org/authors/id/J/JS/JSTOWE/TermReadKey-2.37.tar.gz" version('2.38', sha256='5a645878dc570ac33661581fbb090ff24ebce17d43ea53fd22e105a856a47290') - version('2.37', 'e8ea15c16333ac4f8d146d702e83cc0c') + version('2.37', sha256='4a9383cf2e0e0194668fe2bd546e894ffad41d556b41d2f2f577c8db682db241') diff --git a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py index db3b2e88014..29aa07bbccd 100644 --- a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py +++ b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py @@ -13,7 +13,7 @@ class PerlTestCleannamespaces(PerlPackage): homepage = "http://search.cpan.org/~ether/Test-CleanNamespaces-0.22/lib/Test/CleanNamespaces.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.22.tar.gz" - version('0.22', '8c48bb0427f2077edce57c50491468ec') + version('0.22', sha256='862a221994dd413b2f350450f22c96f57cac78784b1aca1a8fc763fc5449aaca') depends_on('perl-sub-exporter', type=('build', 'run')) depends_on('perl-module-runtime', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-test-deep/package.py b/var/spack/repos/builtin/packages/perl-test-deep/package.py index 919e741399b..9d5cf6a6bf0 100644 --- a/var/spack/repos/builtin/packages/perl-test-deep/package.py +++ b/var/spack/repos/builtin/packages/perl-test-deep/package.py @@ -12,4 +12,4 @@ class PerlTestDeep(PerlPackage): homepage = "http://search.cpan.org/~rjbs/Test-Deep-1.127/lib/Test/Deep.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Test-Deep-1.127.tar.gz" - version('1.127', 'eeafe5795ba20ba051a1423f4fa86dd6') + version('1.127', sha256='b78cfc59c41ba91f47281e2c1d2bfc4b3b1b42bfb76b4378bc88cc37b7af7268') diff --git a/var/spack/repos/builtin/packages/perl-test-differences/package.py b/var/spack/repos/builtin/packages/perl-test-differences/package.py index edeedb973c2..e53aa7f4066 100644 --- a/var/spack/repos/builtin/packages/perl-test-differences/package.py +++ b/var/spack/repos/builtin/packages/perl-test-differences/package.py @@ -12,7 +12,7 @@ class PerlTestDifferences(PerlPackage): homepage = "http://search.cpan.org/~dcantrell/Test-Differences-0.64/lib/Test/Differences.pm" url = "http://search.cpan.org/CPAN/authors/id/D/DC/DCANTRELL/Test-Differences-0.64.tar.gz" - version('0.64', 'ecfda620fe133e36a6e392d94ab8424d') + version('0.64', sha256='9f459dd9c2302a0a73e2f5528a0ce7d09d6766f073187ae2c69e603adf2eb276') depends_on('perl-module-build', type='build') depends_on('perl-capture-tiny', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-test-exception/package.py b/var/spack/repos/builtin/packages/perl-test-exception/package.py index 8bbf9268188..12374856e9e 100644 --- a/var/spack/repos/builtin/packages/perl-test-exception/package.py +++ b/var/spack/repos/builtin/packages/perl-test-exception/package.py @@ -12,6 +12,6 @@ class PerlTestException(PerlPackage): homepage = "http://search.cpan.org/~exodist/Test-Exception-0.43/lib/Test/Exception.pm" url = "http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/Test-Exception-0.43.tar.gz" - version('0.43', '572d355026fb0b87fc2b8c64b83cada0') + version('0.43', sha256='156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533') depends_on('perl-sub-uplevel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-test-fatal/package.py b/var/spack/repos/builtin/packages/perl-test-fatal/package.py index 140e9370c2c..9582184f0ee 100644 --- a/var/spack/repos/builtin/packages/perl-test-fatal/package.py +++ b/var/spack/repos/builtin/packages/perl-test-fatal/package.py @@ -12,6 +12,6 @@ class PerlTestFatal(PerlPackage): homepage = "http://search.cpan.org/~rjbs/Test-Fatal-0.014/lib/Test/Fatal.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Test-Fatal-0.014.tar.gz" - version('0.014', '7954f6d2e3607be10c0fbd69063a3d1b') + version('0.014', sha256='bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0') depends_on('perl-try-tiny', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py index 63012e3cb82..514bfc8fea1 100644 --- a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py +++ b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py @@ -12,7 +12,7 @@ class PerlTestMemoryCycle(PerlPackage): homepage = "http://search.cpan.org/~petdance/Test-Memory-Cycle-1.06/Cycle.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PE/PETDANCE/Test-Memory-Cycle-1.06.tar.gz" - version('1.06', '397e709ba33d3883b5fb2bc49e3a70b0') + version('1.06', sha256='9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202') depends_on('perl-padwalker', type=('build', 'run')) depends_on('perl-devel-cycle', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-test-most/package.py b/var/spack/repos/builtin/packages/perl-test-most/package.py index 2974f970f7e..609414d870b 100644 --- a/var/spack/repos/builtin/packages/perl-test-most/package.py +++ b/var/spack/repos/builtin/packages/perl-test-most/package.py @@ -12,7 +12,7 @@ class PerlTestMost(PerlPackage): homepage = "http://search.cpan.org/~ovid/Test-Most-0.35/lib/Test/Most.pm" url = "http://search.cpan.org/CPAN/authors/id/O/OV/OVID/Test-Most-0.35.tar.gz" - version('0.35', '03dbabd34d6f40af8bd47f5fbb0c6989') + version('0.35', sha256='9897a6f4d751598d2ed1047e01c1554b01d0f8c96c45e7e845229782bf6f657f') depends_on('perl-exception-class', type=('build', 'run')) depends_on('perl-test-differences', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-test-needs/package.py b/var/spack/repos/builtin/packages/perl-test-needs/package.py index 3160a18dd5b..5696ea096da 100644 --- a/var/spack/repos/builtin/packages/perl-test-needs/package.py +++ b/var/spack/repos/builtin/packages/perl-test-needs/package.py @@ -12,4 +12,4 @@ class PerlTestNeeds(PerlPackage): homepage = "http://search.cpan.org/~haarg/Test-Needs-0.002005/lib/Test/Needs.pm" url = "http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/Test-Needs-0.002005.tar.gz" - version('0.002005', '356634a56c99282e8059f290f5d534c8') + version('0.002005', sha256='5a4f33983586edacdbe00a3b429a9834190140190dab28d0f873c394eb7df399') diff --git a/var/spack/repos/builtin/packages/perl-test-requires/package.py b/var/spack/repos/builtin/packages/perl-test-requires/package.py index 77611c5f556..4246cdb4097 100644 --- a/var/spack/repos/builtin/packages/perl-test-requires/package.py +++ b/var/spack/repos/builtin/packages/perl-test-requires/package.py @@ -12,4 +12,4 @@ class PerlTestRequires(PerlPackage): homepage = "http://search.cpan.org/~tokuhirom/Test-Requires-0.10/lib/Test/Requires.pm" url = "http://search.cpan.org/CPAN/authors/id/T/TO/TOKUHIROM/Test-Requires-0.10.tar.gz" - version('0.10', '0d5da779609d0c8fa6f796b45ff8c6f3') + version('0.10', sha256='2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5') diff --git a/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py index 0e984bcbb79..d583bdc6afd 100644 --- a/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py +++ b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py @@ -12,4 +12,4 @@ class PerlTestRequiresinternet(PerlPackage): homepage = "http://search.cpan.org/~mallen/Test-RequiresInternet-0.05/lib/Test/RequiresInternet.pm" url = "http://search.cpan.org/CPAN/authors/id/M/MA/MALLEN/Test-RequiresInternet-0.05.tar.gz" - version('0.05', '0ba9f1cff4cf90ed2618c2eddfd525d8') + version('0.05', sha256='bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e') diff --git a/var/spack/repos/builtin/packages/perl-test-warn/package.py b/var/spack/repos/builtin/packages/perl-test-warn/package.py index aae67b9862d..c2dc2693840 100644 --- a/var/spack/repos/builtin/packages/perl-test-warn/package.py +++ b/var/spack/repos/builtin/packages/perl-test-warn/package.py @@ -12,4 +12,4 @@ class PerlTestWarn(PerlPackage): homepage = "http://search.cpan.org/~chorny/Test-Warn-0.30/Warn.pm" url = "http://search.cpan.org/CPAN/authors/id/C/CH/CHORNY/Test-Warn-0.30.tar.gz" - version('0.30', '8306b998a96d2cc69266b5248d550472') + version('0.30', sha256='8197555b94189d919349a03f7058f83861f145af9bee59f505bfe47562144e41') diff --git a/var/spack/repos/builtin/packages/perl-test-warnings/package.py b/var/spack/repos/builtin/packages/perl-test-warnings/package.py index 1c0f89a8f14..2193dc1f52b 100644 --- a/var/spack/repos/builtin/packages/perl-test-warnings/package.py +++ b/var/spack/repos/builtin/packages/perl-test-warnings/package.py @@ -12,4 +12,4 @@ class PerlTestWarnings(PerlPackage): homepage = "http://deps.cpantesters.org/?module=Test%3A%3ACleanNamespaces;perl=latest" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Test-Warnings-0.026.tar.gz" - version('0.026', '1a379f7eac4c89155d98e652459593a7') + version('0.026', sha256='ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08') diff --git a/var/spack/repos/builtin/packages/perl-text-csv/package.py b/var/spack/repos/builtin/packages/perl-text-csv/package.py index abe4c70e6e9..9616677c83b 100644 --- a/var/spack/repos/builtin/packages/perl-text-csv/package.py +++ b/var/spack/repos/builtin/packages/perl-text-csv/package.py @@ -12,4 +12,4 @@ class PerlTextCsv(PerlPackage): homepage = "http://search.cpan.org/~ishigaki/Text-CSV/lib/Text/CSV.pm" url = "http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/Text-CSV-1.95.tar.gz" - version('1.95', '1e076b4b1f8ba6a5003bf93f3c437a9e') + version('1.95', sha256='7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61') diff --git a/var/spack/repos/builtin/packages/perl-text-diff/package.py b/var/spack/repos/builtin/packages/perl-text-diff/package.py index 4c7c3597391..5ef6589a515 100644 --- a/var/spack/repos/builtin/packages/perl-text-diff/package.py +++ b/var/spack/repos/builtin/packages/perl-text-diff/package.py @@ -12,6 +12,6 @@ class PerlTextDiff(PerlPackage): homepage = "http://search.cpan.org/~neilb/Text-Diff-1.45/lib/Text/Diff.pm" url = "http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/Text-Diff-1.45.tar.gz" - version('1.45', 'edf57b6189f7651a6be454062a4e6d9c') + version('1.45', sha256='e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04') depends_on('perl-algorithm-diff', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-text-simpletable/package.py b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py index 74ed28e396a..444d27c0d99 100644 --- a/var/spack/repos/builtin/packages/perl-text-simpletable/package.py +++ b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py @@ -12,4 +12,4 @@ class PerlTextSimpletable(PerlPackage): homepage = "http://search.cpan.org/~mramberg/Text-SimpleTable/lib/Text/SimpleTable.pm" url = "http://search.cpan.org/CPAN/authors/id/M/MR/MRAMBERG/Text-SimpleTable-2.04.tar.gz" - version('2.04', '550136523c8da37b616988f9a5f58d59') + version('2.04', sha256='8d82f3140b1453b962956b7855ba288d435e7f656c3c40ced4e3e8e359ab5293') diff --git a/var/spack/repos/builtin/packages/perl-text-soundex/package.py b/var/spack/repos/builtin/packages/perl-text-soundex/package.py index 17788088161..ade3ce0d6ec 100644 --- a/var/spack/repos/builtin/packages/perl-text-soundex/package.py +++ b/var/spack/repos/builtin/packages/perl-text-soundex/package.py @@ -15,4 +15,4 @@ class PerlTextSoundex(PerlPackage): homepage = "http://search.cpan.org/~rjbs/Text-Soundex-3.05/Soundex.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Text-Soundex-3.05.tar.gz" - version('3.05', 'cb40ded7a5d27aa3a411d274d6ec18ae') + version('3.05', sha256='f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed') diff --git a/var/spack/repos/builtin/packages/perl-text-unidecode/package.py b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py index 20d10dc06d9..ebc31b7e004 100644 --- a/var/spack/repos/builtin/packages/perl-text-unidecode/package.py +++ b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py @@ -12,4 +12,4 @@ class PerlTextUnidecode(PerlPackage): homepage = "http://search.cpan.org/~sburke/Text-Unidecode/lib/Text/Unidecode.pm" url = "http://search.cpan.org/CPAN/authors/id/S/SB/SBURKE/Text-Unidecode-1.30.tar.gz" - version('1.30', '31cca8505bd74ed9d8036cdc84c808ca') + version('1.30', sha256='6c24f14ddc1d20e26161c207b73ca184eed2ef57f08b5fb2ee196e6e2e88b1c6') diff --git a/var/spack/repos/builtin/packages/perl-time-hires/package.py b/var/spack/repos/builtin/packages/perl-time-hires/package.py index e18a04c29c9..0e98a781113 100644 --- a/var/spack/repos/builtin/packages/perl-time-hires/package.py +++ b/var/spack/repos/builtin/packages/perl-time-hires/package.py @@ -12,4 +12,4 @@ class PerlTimeHires(PerlPackage): homepage = "http://search.cpan.org/~jhi/Time-HiRes-1.9746/HiRes.pm" url = "http://search.cpan.org/CPAN/authors/id/J/JH/JHI/Time-HiRes-1.9746.tar.gz" - version('1.9746', '728dc2c2715313a056792191d7d0726c') + version('1.9746', sha256='89408c81bb827bc908c98eec50071e6e1158f38fa462865ecc3dc03aebf5f596') diff --git a/var/spack/repos/builtin/packages/perl-time-piece/package.py b/var/spack/repos/builtin/packages/perl-time-piece/package.py index 1137dbea150..fae533f4d22 100644 --- a/var/spack/repos/builtin/packages/perl-time-piece/package.py +++ b/var/spack/repos/builtin/packages/perl-time-piece/package.py @@ -12,4 +12,4 @@ class PerlTimePiece(PerlPackage): homepage = "http://search.cpan.org/~esaym/Time-Piece/Piece.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ES/ESAYM/Time-Piece-1.3203.tar.gz" - version('1.3203', '515c1306f123a00116a95335cf543501') + version('1.3203', sha256='6971faf6476e4f715a5b5336f0a97317f36e7880fcca6c4db7c3e38e764a6f41') diff --git a/var/spack/repos/builtin/packages/perl-try-tiny/package.py b/var/spack/repos/builtin/packages/perl-try-tiny/package.py index 41ffa14148a..67c655970fe 100644 --- a/var/spack/repos/builtin/packages/perl-try-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-try-tiny/package.py @@ -12,4 +12,4 @@ class PerlTryTiny(PerlPackage): homepage = "http://search.cpan.org/~ether/Try-Tiny-0.28/lib/Try/Tiny.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Try-Tiny-0.28.tar.gz" - version('0.28', 'e2f8af601a62981aab30df15a6f47475') + version('0.28', sha256='f1d166be8aa19942c4504c9111dade7aacb981bc5b3a2a5c5f6019646db8c146') diff --git a/var/spack/repos/builtin/packages/perl-uri/package.py b/var/spack/repos/builtin/packages/perl-uri/package.py index ddcb5ed5cfb..d9c42fd7d9a 100644 --- a/var/spack/repos/builtin/packages/perl-uri/package.py +++ b/var/spack/repos/builtin/packages/perl-uri/package.py @@ -12,7 +12,7 @@ class PerlUri(PerlPackage): homepage = "http://search.cpan.org/~ether/URI-1.72/lib/URI.pm" url = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/URI-1.72.tar.gz" - version('1.72', 'cd56d81ed429efaa97e7f3ff08851b48') - version('1.71', '247c3da29a794f72730e01aa5a715daf') + version('1.72', sha256='35f14431d4b300de4be1163b0b5332de2d7fbda4f05ff1ed198a8e9330d40a32') + version('1.71', sha256='9c8eca0d7f39e74bbc14706293e653b699238eeb1a7690cc9c136fb8c2644115') depends_on('perl-test-needs', type=('build', 'test')) diff --git a/var/spack/repos/builtin/packages/perl-version/package.py b/var/spack/repos/builtin/packages/perl-version/package.py index e6d5eade223..a1413c0c373 100644 --- a/var/spack/repos/builtin/packages/perl-version/package.py +++ b/var/spack/repos/builtin/packages/perl-version/package.py @@ -12,6 +12,6 @@ class PerlVersion(PerlPackage): homepage = "http://search.cpan.org/~bdfoy/Perl-Version-1.013/lib/Perl/Version.pm" url = "http://search.cpan.org/CPAN/authors/id/B/BD/BDFOY/Perl-Version-1.013_03.tar.gz" - version('1.013_03', 'b2c94c8b33ccfa1635c760fcfa1c5358') + version('1.013_03', sha256='6b5978f598dcdf8a304500c1b7bcdce967ca05e7b38673cebfdb4237531c2ff9') depends_on('perl-file-slurp-tiny', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-want/package.py b/var/spack/repos/builtin/packages/perl-want/package.py index f8196b1d7a7..4255901836c 100644 --- a/var/spack/repos/builtin/packages/perl-want/package.py +++ b/var/spack/repos/builtin/packages/perl-want/package.py @@ -12,4 +12,4 @@ class PerlWant(PerlPackage): homepage = "search.cpan.org/~robin/Want/Want.pm" url = "http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/Want-0.29.tar.gz" - version('0.29', '33b2dae5db59781b9a0434fa1db04aab') + version('0.29', sha256='b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7') diff --git a/var/spack/repos/builtin/packages/perl-www-robotrules/package.py b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py index 3b9e266493e..720a2aa158a 100644 --- a/var/spack/repos/builtin/packages/perl-www-robotrules/package.py +++ b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py @@ -12,6 +12,6 @@ class PerlWwwRobotrules(PerlPackage): homepage = "http://deps.cpantesters.org/?module=WWW%3A%3ARobotRules;perl=latest" url = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/WWW-RobotRules-6.02.tar.gz" - version('6.02', 'b7186e8b8b3701e70c22abf430742403') + version('6.02', sha256='46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e') depends_on('perl-uri', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py index 14f25373f26..57b4406be72 100644 --- a/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py @@ -12,6 +12,6 @@ class PerlXmlParserLite(PerlPackage): homepage = "http://search.cpan.org/~phred/XML-Parser-Lite-0.721/lib/XML/Parser/Lite.pm" url = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/XML-Parser-Lite-0.721.tar.gz" - version('0.721', 'ad8a87b9bf413aa540c7cb724d650808') + version('0.721', sha256='5862a36ecab9db9aad021839c847e8d2f4ab5a7796c61d0fb069bb69cf7908ba') depends_on('perl-test-requires', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-parser/package.py b/var/spack/repos/builtin/packages/perl-xml-parser/package.py index b1407fe9a80..9730132af00 100644 --- a/var/spack/repos/builtin/packages/perl-xml-parser/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-parser/package.py @@ -13,7 +13,7 @@ class PerlXmlParser(PerlPackage): homepage = "http://search.cpan.org/perldoc/XML::Parser" url = "http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.44.tar.gz" - version('2.44', 'af4813fe3952362451201ced6fbce379') + version('2.44', sha256='1ae9d07ee9c35326b3d9aad56eae71a6730a73a116b9fe9e8a4758b7cc033216') depends_on('expat') depends_on('perl-libwww-perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-simple/package.py b/var/spack/repos/builtin/packages/perl-xml-simple/package.py index 3925a46d7dc..709fde6b3e4 100644 --- a/var/spack/repos/builtin/packages/perl-xml-simple/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-simple/package.py @@ -12,6 +12,6 @@ class PerlXmlSimple(PerlPackage): homepage = "http://search.cpan.org/~grantm/XML-Simple/lib/XML/Simple.pm" url = "http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/XML-Simple-2.24.tar.gz" - version('2.24', '1cd2e8e3421160c42277523d5b2f4dd2') + version('2.24', sha256='9a14819fd17c75fbb90adcec0446ceab356cab0ccaff870f2e1659205dc2424f') depends_on('perl-xml-parser', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py index 6068c36c117..b5df47fb81c 100644 --- a/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py +++ b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py @@ -12,4 +12,4 @@ class PerlYamlLibyaml(PerlPackage): homepage = "http://search.cpan.org/~tinita/YAML-LibYAML/" url = "http://search.cpan.org/CPAN/authors/id/T/TI/TINITA/YAML-LibYAML-0.67.tar.gz" - version('0.67', '5a787150db680e3ab3f753f2e54640ab') + version('0.67', sha256='e65a22abc912a46a10abddf3b88d806757f44f164ab3167c8f0ff6aa30648187') diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py index 715ed9732db..45239576da6 100644 --- a/var/spack/repos/builtin/packages/perl/package.py +++ b/var/spack/repos/builtin/packages/perl/package.py @@ -38,16 +38,16 @@ class Perl(Package): # Perl doesn't use Autotools, it should subclass Package # End of life releases version('5.28.0', sha256='7e929f64d4cb0e9d1159d4a59fc89394e27fa1f7004d0836ca0d514685406ea8') - version('5.26.2', 'dc0fea097f3992a8cd53f8ac0810d523') - version('5.24.1', '765ef511b5b87a164e2531403ee16b3c') - version('5.22.4', '31a71821682e02378fcdadeed85688b8') - version('5.22.3', 'aa4f236dc2fc6f88b871436b8d0fda95') - version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b') - version('5.22.1', '19295bbb775a3c36123161b9bf4892f1') - version('5.22.0', 'e32cb6a8dda0084f2a43dac76318d68d') - version('5.20.3', 'd647d0ea5a7a8194c34759ab9f2610cd') - version('5.18.4', '1f9334ff730adc05acd3dd7130d295db') - version('5.16.3', 'eb5c40f2575df6c155bc99e3fe0a9d82') + version('5.26.2', sha256='572f9cea625d6062f8a63b5cee9d3ee840800a001d2bb201a41b9a177ab7f70d') + version('5.24.1', sha256='e6c185c9b09bdb3f1b13f678999050c639859a7ef39c8cad418448075f5918af') + version('5.22.4', sha256='ba9ef57c2b709f2dad9c5f6acf3111d9dfac309c484801e0152edbca89ed61fa') + version('5.22.3', sha256='1b351fb4df7e62ec3c8b2a9f516103595b2601291f659fef1bbe3917e8410083') + version('5.22.2', sha256='81ad196385aa168cb8bd785031850e808c583ed18a7901d33e02d4f70ada83c2') + version('5.22.1', sha256='2b475d0849d54c4250e9cba4241b7b7291cffb45dfd083b677ca7b5d38118f27') + version('5.22.0', sha256='0c690807f5426bbd1db038e833a917ff00b988bf03cbf2447fa9ffdb34a2ab3c') + version('5.20.3', sha256='3524e3a76b71650ab2f794fd68e45c366ec375786d2ad2dca767da424bbb9b4a') + version('5.18.4', sha256='01a4e11a9a34616396c4a77b3cef51f76a297e1a2c2c490ae6138bf0351eb29f') + version('5.16.3', sha256='69cf08dca0565cec2c5c6c2f24b87f986220462556376275e5431cc2204dedb6') extendable = True @@ -78,7 +78,7 @@ class Perl(Package): # Perl doesn't use Autotools, it should subclass Package resource( name="cpanm", url="http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7042.tar.gz", - md5="e87f55fbcb3c13a4754500c18e89219f", + sha256="9da50e155df72bce55cb69f51f1dbb4b62d23740fb99f6178bb27f22ebdf8a46", destination="cpanm", placement="cpanm" ) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 78e72b3db72..72f331b1369 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -24,39 +24,39 @@ class Petsc(Package): version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') - version('3.12.0', 'ba9ecf69783c7ebf05bd1c91dd1d4b38bf09b7a2d5f9a774aa6bb46deff7cb14') - version('3.11.4', '319cb5a875a692a67fe5b1b90009ba8f182e21921ae645d38106544aff20c3c1') - version('3.11.3', '199ad9650a9f58603b49e7fff7cd003ceb03aa231e5d37d0bf0496c6348eca81') - version('3.11.2', '4d244dd7d1565d6534e776445fcf6977a6ee2a8bb2be4a36ac1e0fc1f9ad9cfa') - version('3.11.1', 'cb627f99f7ce1540ebbbf338189f89a5f1ecf3ab3b5b0e357f9e46c209f1fb23') - version('3.11.0', 'b3bed2a9263193c84138052a1b92d47299c3490dd24d1d0bf79fb884e71e678a') - version('3.10.5', '3a81c8406410e0ffa8a3e9f8efcdf2e683cc40613c9bb5cb378a6498f595803e') - version('3.10.4', '6c836df84caa9ae683ae401d3f94eb9471353156fec6db602bf2e857e4ec339f') - version('3.10.3', 'cd106babbae091604fee40c258737c84dec048949be779eaef5a745df3dc8de4') - version('3.10.2', '63ed950653ae9b8d19daea47e24c0338') - version('3.10.1', '2d0d5a9bd8112a4147a2a23f7f62a906') - version('3.10.0', '0240c2ce8c54e47b3531a743ee844d41') - version('3.9.4', 'c98eb67573efb2f91c6f239368259e44') - version('3.9.3', '7b71d705f66f9961cb0e2da3f9da79a1') - version('3.9.2', '8bedc0cd8c8603d54bfd99a6e8f77b3d') - version('3.9.1', 'd3a229a188dbeef9b3f29b9a63622fad') - version('3.9.0', '34b8a81814ca050a96d58e53a2f0ac7a') - version('3.8.4', 'd7767fe2919536aa393eb22841899306') - version('3.8.3', '322cbcf2a0f7b7bad562643b05d66f11') - version('3.8.2', '00666e1c4cbfa8dd6eebf91ff8180f79') - version('3.8.1', '3ed75c1147800fc156fe1f1e515a68a7') - version('3.8.0', '02680f1f78a0d4c5a9de80a366793eb8') - version('3.7.7', 'c2cfb76677d32839810c4cf51a2f9cf5') - version('3.7.6', '977aa84b85aa3146c695592cd0a11057') - version('3.7.5', 'f00f6e6a3bac39052350dd47194b58a3') - version('3.7.4', 'aaf94fa54ef83022c14091f10866eedf') - version('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34') - version('3.6.4', '7632da2375a3df35b8891c9526dbdde7') - version('3.6.3', '91dd3522de5a5ef039ff8f50800db606') - version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f') - version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13') - version('3.5.1', 'a557e029711ebf425544e117ffa44d8f') - version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d') + version('3.12.0', sha256='ba9ecf69783c7ebf05bd1c91dd1d4b38bf09b7a2d5f9a774aa6bb46deff7cb14') + version('3.11.4', sha256='319cb5a875a692a67fe5b1b90009ba8f182e21921ae645d38106544aff20c3c1') + version('3.11.3', sha256='199ad9650a9f58603b49e7fff7cd003ceb03aa231e5d37d0bf0496c6348eca81') + version('3.11.2', sha256='4d244dd7d1565d6534e776445fcf6977a6ee2a8bb2be4a36ac1e0fc1f9ad9cfa') + version('3.11.1', sha256='cb627f99f7ce1540ebbbf338189f89a5f1ecf3ab3b5b0e357f9e46c209f1fb23') + version('3.11.0', sha256='b3bed2a9263193c84138052a1b92d47299c3490dd24d1d0bf79fb884e71e678a') + version('3.10.5', sha256='3a81c8406410e0ffa8a3e9f8efcdf2e683cc40613c9bb5cb378a6498f595803e') + version('3.10.4', sha256='6c836df84caa9ae683ae401d3f94eb9471353156fec6db602bf2e857e4ec339f') + version('3.10.3', sha256='cd106babbae091604fee40c258737c84dec048949be779eaef5a745df3dc8de4') + version('3.10.2', sha256='9d3381bcf9c63abe6521b21a88efc70f8e893293503cff497971d0d9c1ec68cc') + version('3.10.1', sha256='b6e64ce062113ee0e2e2a6cfffb4d33c085ec91d5bc3afeb33781074aa5a22a5') + version('3.10.0', sha256='6ebacc010397ea47649495e8363cd7d7d86b876e6df07c6f6ccfa48b22fa555c') + version('3.9.4', sha256='ecc647c9b1ef565a2c113936454c65632eedc1626e0fc99b5a36accb91195a63') + version('3.9.3', sha256='6c7f2c7a28433385d74d647b4934aaeea3c1b3053b207973c9497639b6ebf7c8') + version('3.9.2', sha256='ab396ae5dbfff808df1b5648f5ce30f3021ec70faec3d5cd63df324d416ac6ac') + version('3.9.1', sha256='742e838a35d278693e956ed1ca4592c1d663451f6beea0694bf334aeb67681e8') + version('3.9.0', sha256='dcbcab1f321667be1c6e5f8e7b4ee8670bb09e372e51f1ea6471464519d54b2d') + version('3.8.4', sha256='9f78dc4dd4c58433fa18d3dd3a9029e39a83e4e4b64f845a029dd9fed44bc4c7') + version('3.8.3', sha256='01f9c3ed937eafac6c9e006510b61c7cd07197115ec40c429fc835f346ca3eac') + version('3.8.2', sha256='42690508d408e31fb98be738ac097bc869be14c5bfe08dda2184243283ceb16a') + version('3.8.1', sha256='9b48a9e72d304046923667d2ab1f201778cc56242928a374ff9e074843a334ff') + version('3.8.0', sha256='1e1b4d90ccbf98dc5759a956ac9a771310a6690f1cbb37b31502b29568262d7e') + version('3.7.7', sha256='40fd3bc76998e056c4097704c08f28eb89bf3b93164dc9e69abab393f43bf6f0') + version('3.7.6', sha256='3c8ee051349587d45baa7910c54ce8e0a571592e3b40f3054a7b7f986919d449') + version('3.7.5', sha256='493ab0b6c1b3fe68e71d990eff87c84f499f680e6d2c0c394e78646a82ed4be3') + version('3.7.4', sha256='54b804f924ea5be3b6718b4d4e98f8ccb9d1bd6bbbd1e9c0f18c4a90ddf5db18') + version('3.7.2', sha256='36681dd0df97e0d5cd182d902e89f527eb8f441f05271159dac5340acb4cf0ec') + version('3.6.4', sha256='eb09925a139b52b4dd5a071b3da4fe2165f1d6e8f71d410479603c9976c940f0') + version('3.6.3', sha256='776e2644e4003653c56a44a6f7c02c41427af26f7c5cd9bec3aa84ed90223245') + version('3.5.3', sha256='68e6a42f5ec75bad87f74d4df8f55ad63f0c4d996f162da6713cb3d6f566830d') + version('3.5.2', sha256='1a8f09af654afab787c732e7b2f5d0c1d856777398148351565389d38d30935e') + version('3.5.1', sha256='199af205f62dcc572728600670c7d4c8cb0d4efc4172c26f02b895d9dd1df245') + version('3.4.4', sha256='fa73b99caf70c416a967234f5476cdb1d2c014610ee0619e48f54d8d309631b7') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py index 71afe495a8c..632e6818272 100644 --- a/var/spack/repos/builtin/packages/pexsi/package.py +++ b/var/spack/repos/builtin/packages/pexsi/package.py @@ -26,10 +26,10 @@ class Pexsi(MakefilePackage): homepage = 'https://math.berkeley.edu/~linlin/pexsi/index.html' url = 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz' - # version('1.0', '4600b03e235935fe623acf500df0edfa') - version('0.10.2', '012f6800098671ec39c2ed7b38935e27') - version('0.9.2', '0ce491a3a922d271c4edf9b20aa93076') - version('0.9.0', '0c1a2de891ba1445dfc184b2fa270ed8') + # version('1.0', md5='4600b03e235935fe623acf500df0edfa') + version('0.10.2', sha256='8714c71b76542e096211b537a9cb1ffb2c28f53eea4f5a92f94cc1ca1e7b499f') + version('0.9.2', sha256='9dc0fb66fc52c2b68e8fe485bbf4354ab0d9a548a4eaf7211eb4174c51bcf1de') + version('0.9.0', sha256='e5efe0c129013392cdac3234e37f1f4fea641c139b1fbea47618b4b839d05029') depends_on('parmetis') depends_on('superlu-dist@3.3:3.999', when='@:0.9.0') diff --git a/var/spack/repos/builtin/packages/pfft/package.py b/var/spack/repos/builtin/packages/pfft/package.py index af203778643..61a14682cfa 100644 --- a/var/spack/repos/builtin/packages/pfft/package.py +++ b/var/spack/repos/builtin/packages/pfft/package.py @@ -15,7 +15,7 @@ class Pfft(AutotoolsPackage): homepage = "https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en" url = "https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/pfft-1.0.8-alpha.tar.gz" - version('1.0.8-alpha', '46457fbe8e38d02ff87d439b63dc0709') + version('1.0.8-alpha', sha256='6c43960ad72fcff7e49b87c604c5f471fb5890f1bd11ce750ab52f035e7c5317') depends_on('fftw+mpi+pfft_patches') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/pgdspider/package.py b/var/spack/repos/builtin/packages/pgdspider/package.py index fcc192635a6..e8bb15987b2 100644 --- a/var/spack/repos/builtin/packages/pgdspider/package.py +++ b/var/spack/repos/builtin/packages/pgdspider/package.py @@ -14,7 +14,7 @@ class Pgdspider(Package): homepage = "http://www.cmpg.unibe.ch/software/PGDSpider" url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_2.1.1.2.zip" - version('2.1.1.2', '170e5b4a002277ff66866486da920693') + version('2.1.1.2', sha256='a630ef9f3ef0c36be0d613867c5293378d77b52396ac701bc7b9ec5d3ba7f2e1') depends_on('java', type=('build', 'run')) depends_on('bcftools') diff --git a/var/spack/repos/builtin/packages/pgmath/package.py b/var/spack/repos/builtin/packages/pgmath/package.py index 5586df07c6c..bd554890a0c 100644 --- a/var/spack/repos/builtin/packages/pgmath/package.py +++ b/var/spack/repos/builtin/packages/pgmath/package.py @@ -15,8 +15,8 @@ class Pgmath(CMakePackage): git = "https://github.com/flang-compiler/flang.git" version('develop', branch='master') - version('20180921', '4440ed5fdc390e4b7a085fb77b44ac54') - version('20180612', '62284e26214eaaff261a922c67f6878c') + version('20180921', sha256='f33bd1f054e474f1e8a204bb6f78d42f8f6ecf7a894fdddc3999f7c272350784') + version('20180612', sha256='6af858bea013548e091371a97726ac784edbd4ff876222575eaae48a3c2920ed') depends_on("awk", type="build") conflicts("%gcc@:7.1.9999") diff --git a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py index 2e3bd872adb..8811cc34917 100644 --- a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py +++ b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py @@ -13,7 +13,7 @@ class Phantompeakqualtools(RPackage): homepage = "https://github.com/kundajelab/phantompeakqualtools" url = "https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz" - version('1.2', 'e94943a42132b9ff2886f006ab34c121') + version('1.2', sha256='86cbcca80b65f150b1cdbea673d8a47caba88c2db6b3b567a80f2c797c9a1668') depends_on('awk') depends_on('samtools') diff --git a/var/spack/repos/builtin/packages/phast/package.py b/var/spack/repos/builtin/packages/phast/package.py index 3b7c315ca7c..1d98d353cab 100644 --- a/var/spack/repos/builtin/packages/phast/package.py +++ b/var/spack/repos/builtin/packages/phast/package.py @@ -13,7 +13,7 @@ class Phast(MakefilePackage): homepage = "http://compgen.cshl.edu/phast/index.php" url = "https://github.com/CshlSiepelLab/phast/archive/v1.4.tar.gz" - version('1.4', '2bc0412ba58ea1f08ba5e12fad43b4c7') + version('1.4', sha256='287c77599c51256a3adbd62ed217cb6d6a547fcec2c29262e9d61fa32ed92b99') # phast cannot build with clapack using external blas depends_on('clapack~external-blas') diff --git a/var/spack/repos/builtin/packages/phist/package.py b/var/spack/repos/builtin/packages/phist/package.py index 67b0d9e3471..344a0911134 100644 --- a/var/spack/repos/builtin/packages/phist/package.py +++ b/var/spack/repos/builtin/packages/phist/package.py @@ -32,8 +32,8 @@ class Phist(CMakePackage): version('1.7.3', sha256='ab2d853c9ba13bcd3069fcc61c359cb412466a2e4b22ebbd2f5263cffa685126') version('1.7.2', sha256='29b504d78b5efd57b87d2ca6e20bc8a32b1ba55b40f5a5b7189cc0d28e43bcc0') version('1.6.1', sha256='4ed4869f24f920a494aeae0f7d1d94fe9efce55ebe0d298a5948c9603e07994d') - version('1.6.0', '751f855230d6227b972b5ab7bce2c65f') - version('1.4.3', 'af3300378d4282366d148e38c3a3199a') + version('1.6.0', sha256='667a967b37d248242c275226c96efc447ef73a2b15f241c6a588d570d7fac07b') + version('1.4.3', sha256='9cc1c7ba7f7a04e94f4497da14199e4631a0d02d0e4187f3e16f4c242dc777c1') variant(name='kernel_lib', default='builtin', description='select the kernel library (backend) for phist', diff --git a/var/spack/repos/builtin/packages/phylip/package.py b/var/spack/repos/builtin/packages/phylip/package.py index d655c0da9db..53454ab8967 100644 --- a/var/spack/repos/builtin/packages/phylip/package.py +++ b/var/spack/repos/builtin/packages/phylip/package.py @@ -13,8 +13,8 @@ class Phylip(Package): homepage = "http://evolution.genetics.washington.edu/phylip/" url = "http://evolution.gs.washington.edu/phylip/download/phylip-3.697.tar.gz" - version('3.697', '0e83d17fb4d668213603c86bc21d9012') - version('3.696', 'dbe5abc26f6089ead3dba41c2db526ee') + version('3.697', sha256='9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1') + version('3.696', md5='dbe5abc26f6089ead3dba41c2db526ee') def install(self, spec, prefix): with working_dir('src'): diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py index 98d311b4e58..d7fdbdb3f2c 100644 --- a/var/spack/repos/builtin/packages/picard/package.py +++ b/var/spack/repos/builtin/packages/picard/package.py @@ -23,20 +23,20 @@ class Picard(Package): # that it was a .zip file with multiple .jar and .so files version('2.20.8', sha256='aff92d618ee9e6bafc1ab4fbfa89fc557a0dbe596ae4b92fe3bf93ebf95c7105', expand=False) version('2.19.0', sha256='f97fc3f7a73b55cceea8b6a6488efcf1b2fbf8cad61d88645704ddd45a8c5950', expand=False) - version('2.18.3', '181b1b0731fd35f0d8bd44677d8787e9', expand=False) - version('2.18.0', '20045ff141e4a67512365f0b6bbd8229', expand=False) - version('2.17.0', '72cc527f1e4ca6a799ae0117af60b54e', expand=False) - version('2.16.0', 'fed8928b03bb36e355656f349e579083', expand=False) - version('2.15.0', '3f5751630b1a3449edda47a0712a64e4', expand=False) - version('2.13.2', '3d7b33fd1f43ad2129e6ec7883af56f5', expand=False) - version('2.10.0', '96f3c11b1c9be9fc8088bc1b7b9f7538', expand=False) - version('2.9.4', '5ce72af4d5efd02fba7084dcfbb3c7b3', expand=False) - version('2.9.3', '3a33c231bcf3a61870c3d44b3b183924', expand=False) - version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False) - version('2.9.0', 'b711d492f16dfe0084d33e684dca2202', expand=False) - version('2.8.3', '4a181f55d378cd61d0b127a40dfd5016', expand=False) - version('2.6.0', '91f35f22977d9692ce2718270077dc50', expand=False) - version('1.140', '308f95516d94c1f3273a4e7e2b315ec2') + version('2.18.3', sha256='0e0fc45d9a822ee9fa562b3bb8f1525a439e4cd541429a1a4ca4646f37189b70', expand=False) + version('2.18.0', sha256='c4c64b39ab47968e4afcaf1a30223445ee5082eab31a03eee240e54c2e9e1dce', expand=False) + version('2.17.0', sha256='ffea8bf90e850919c0833e9dcc16847d40090a1ef733c583a710a3282b925998', expand=False) + version('2.16.0', sha256='01cf3c930d2b4841960497491512d327bf669c1ed2e753152e1e651a27288c2d', expand=False) + version('2.15.0', sha256='dc3ff74c704954a10796b390738078617bb0b0fef15731e9d268ed3b26c6a285', expand=False) + version('2.13.2', sha256='db7749f649e8423053fb971e6af5fb8a9a1a797cb1f20fef1100edf9f82f6f94', expand=False) + version('2.10.0', sha256='e256d5e43656b7d8be454201a7056dce543fe9cbeb30329a0d8c22d28e655775', expand=False) + version('2.9.4', sha256='0ecee9272bd289d902cc18053010f0364d1696e7518ac92419a99b2f0a1cf689', expand=False) + version('2.9.3', sha256='6cca26ce5094b25a82e1a8d646920d584c6db5f009476196dc285be6522e00ce', expand=False) + version('2.9.2', sha256='05714b9743a7685a43c94a93f5d03aa4070d3ab6e20151801301916d3e546eb7', expand=False) + version('2.9.0', sha256='9a57f6bd9086ea0f5f1a6d9d819459854cb883bb8093795c916538ed9dd5de64', expand=False) + version('2.8.3', sha256='97a4b6c8927c8cb5f3450630c9b39bf210ced8c271f198119118ce1c24b8b0f6', expand=False) + version('2.6.0', sha256='671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b', expand=False) + version('1.140', sha256='0d27287217413db6b846284c617d502eaa578662dcb054a7017083eab9c54438') depends_on('java@8:', type='run') diff --git a/var/spack/repos/builtin/packages/pigz/package.py b/var/spack/repos/builtin/packages/pigz/package.py index 9534be42db0..fdcf42e8a78 100644 --- a/var/spack/repos/builtin/packages/pigz/package.py +++ b/var/spack/repos/builtin/packages/pigz/package.py @@ -13,8 +13,8 @@ class Pigz(MakefilePackage): homepage = "http://zlib.net/pigz/" url = "https://github.com/madler/pigz/archive/v2.3.4.tar.gz" - version('2.4', '3c8a601db141d3013ef9fe5f2daaf73f') - version('2.3.4', 'c109057050b15edf3eb9bb4d0805235e') + version('2.4', sha256='e228e7d18b34c4ece8d596eb6eee97bde533c6beedbb728d07d3abe90b4b1b52') + version('2.3.4', sha256='763f2fdb203aa0b7b640e63385e38e5dd4e5aaa041bc8e42aa96f2ef156b06e8') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/pilon/package.py b/var/spack/repos/builtin/packages/pilon/package.py index 33290a75cea..e6e416e18bb 100644 --- a/var/spack/repos/builtin/packages/pilon/package.py +++ b/var/spack/repos/builtin/packages/pilon/package.py @@ -14,8 +14,8 @@ class Pilon(Package): homepage = "https://github.com/broadinstitute/pilon" url = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar" - version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False) - version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False) + version('1.22', sha256='ff738f3bbb964237f6b2cf69243ebf9a21cb7f4edf10bbdcc66fa4ebaad5d13d', expand=False) + version('1.13', sha256='c6195a054acbc76afc457e6a7615f75c91adc28faeb7b8738ee2b65309b0bbe3', expand=False) depends_on('java@1.7:', type='run') diff --git a/var/spack/repos/builtin/packages/pindel/package.py b/var/spack/repos/builtin/packages/pindel/package.py index b1dff4a1d4d..b99920b0ea7 100644 --- a/var/spack/repos/builtin/packages/pindel/package.py +++ b/var/spack/repos/builtin/packages/pindel/package.py @@ -12,13 +12,13 @@ class Pindel(MakefilePackage): homepage = "http://gmt.genome.wustl.edu/packages/pindel/" url = "https://github.com/genome/pindel/archive/v0.2.5.tar.gz" - version('0.2.5b8', 'e6de2ffb38ba1cb89351cdccabe78cde') - version('0.2.5b6', 'dc2febb18c203f0ef1ba02b7b882e94b') - version('0.2.5b5', '73e964bc19de9ab9e6e8a316353e3184') - version('0.2.5b4', 'b4aefd538d9f62578f46440c4bce497e') - version('0.2.5b1', 'a8e53e8919aa29093db13fad5ede93a5') - version('0.2.5a7', '5fb2bac6108547b5d60c38fc66abdfc4') - version('0.2.5', 'd4568cbb83ec25ef9f9f6f058b30053e') + version('0.2.5b8', sha256='7f21fda0b751d420831724d96e60873ce332139cfd24396e81c7f1ae2f707a19') + version('0.2.5b6', sha256='fe19aabdcf6334b9efe92d4509b80f0f266e621f1cc8db017b301d7e32e2eeac') + version('0.2.5b5', sha256='2ebe9d959d8c3862d9103d8a3768265dcc79eab547035857dca8ab8cfe2544e4') + version('0.2.5b4', sha256='0f6afd6b83f6cceb31be5dbb686c6ff518c54135274931097a8b83b3f5d0372a') + version('0.2.5b1', sha256='b626e23ddfb3590174cfe38458b537e96707eedc6c2b054504f72ca141ba306c') + version('0.2.5a7', sha256='0a270483dee9ef617d422eb61d3478334ee8f55e952d0a439529c2b21fcf8fb4') + version('0.2.5', sha256='9908940d090eff23d940c3b6f2f6b3fc2bb1fd3b7a2d553cc81eed240a23fd9f') depends_on('htslib@1.7:') # diff --git a/var/spack/repos/builtin/packages/piranha/package.py b/var/spack/repos/builtin/packages/piranha/package.py index a133aa56b17..c045e994de0 100644 --- a/var/spack/repos/builtin/packages/piranha/package.py +++ b/var/spack/repos/builtin/packages/piranha/package.py @@ -16,7 +16,7 @@ class Piranha(CMakePackage): git = "https://github.com/bluescarni/piranha.git" version('develop', branch='master') - version('0.5', '99546bae2be115737b6316751eb0b84d') + version('0.5', sha256='34a89bda8208ff48cfb116efa7d53c09e8a9b3838af4bb96ba2e19e4930b3a58') variant('python', default=True, description='Build the Python bindings') diff --git a/var/spack/repos/builtin/packages/pism/package.py b/var/spack/repos/builtin/packages/pism/package.py index 7e07bdcbad4..11dac2f4474 100644 --- a/var/spack/repos/builtin/packages/pism/package.py +++ b/var/spack/repos/builtin/packages/pism/package.py @@ -17,7 +17,7 @@ class Pism(CMakePackage): version('develop', branch='dev') version('1.1.4', sha256='8ccb867af3b37e8d103351dadc1d7e77512e64379519fe8a2592668deb27bc44') - version('0.7.3', '7cfb034100d99d5c313c4ac06b7f17b6') + version('0.7.3', md5='7cfb034100d99d5c313c4ac06b7f17b6') version('0.7.x', branch='stable0.7') version('icebin', branch='efischer/dev') diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py index 9fcfe977199..5a68b5ab4a0 100644 --- a/var/spack/repos/builtin/packages/pkg-config/package.py +++ b/var/spack/repos/builtin/packages/pkg-config/package.py @@ -13,9 +13,9 @@ class PkgConfig(AutotoolsPackage): homepage = "http://www.freedesktop.org/wiki/Software/pkg-config/" url = "http://pkgconfig.freedesktop.org/releases/pkg-config-0.29.2.tar.gz" - version('0.29.2', 'f6e931e319531b736fadc017f470e68a') - version('0.29.1', 'f739a28cae4e0ca291f82d1d41ef107d') - version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d') + version('0.29.2', sha256='6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591') + version('0.29.1', sha256='beb43c9e064555469bd4390dcfd8030b1536e0aa103f08d7abf7ae8cac0cb001') + version('0.28', sha256='6b6eb31c6ec4421174578652c7e141fdaae2dabad1021f420d8713206ac1f845') provides('pkgconfig') diff --git a/var/spack/repos/builtin/packages/pkgconf/package.py b/var/spack/repos/builtin/packages/pkgconf/package.py index ce4221d4d4e..36b78c0713e 100644 --- a/var/spack/repos/builtin/packages/pkgconf/package.py +++ b/var/spack/repos/builtin/packages/pkgconf/package.py @@ -16,14 +16,14 @@ class Pkgconf(AutotoolsPackage): # URL must remain http:// so Spack can bootstrap curl url = "http://distfiles.dereferenced.org/pkgconf/pkgconf-1.6.3.tar.xz" - version('1.6.3', sha256='61f0b31b0d5ea0e862b454a80c170f57bad47879c0c42bd8de89200ff62ea210') - version('1.6.1', sha256='22b9ee38438901f9d60f180e5182821180854fa738fd071f593ea26a81da208c') - version('1.6.0', sha256='6135a3abb576672ba54a899860442ba185063f0f90dae5892f64f7bae8e1ece5') - version('1.5.4', sha256='9c5864a4e08428ef52f05a41c948529555458dec6d283b50f8b7d32463c54664') - version('1.4.2', '678d242b4eef1754bba6a58642af10bb') - version('1.4.0', 'c509c0dad5a70aa4bc3210557b7eafce') - version('1.3.10', '9b63707bf6f8da6efb3868101d7525fe') - version('1.3.8', '484ba3360d983ce07416843d5bc916a8') + version('1.6.3', sha256='61f0b31b0d5ea0e862b454a80c170f57bad47879c0c42bd8de89200ff62ea210') + version('1.6.1', sha256='22b9ee38438901f9d60f180e5182821180854fa738fd071f593ea26a81da208c') + version('1.6.0', sha256='6135a3abb576672ba54a899860442ba185063f0f90dae5892f64f7bae8e1ece5') + version('1.5.4', sha256='9c5864a4e08428ef52f05a41c948529555458dec6d283b50f8b7d32463c54664') + version('1.4.2', sha256='bab39371d4ab972be1d539a8b10b6cc21f8eafc97f617102e667e82bd32eb234') + version('1.4.0', sha256='1d112ff35dad516ffbfbdb013df3a035140618fe7632ec44ffa894a9c713301b') + version('1.3.10', sha256='62577d265fa9415a57a77a59dede5526b7ece3ef59a750434b281b262f0c1da9') + version('1.3.8', sha256='fc06f058e6905435481f649865ca51000192c91808f307b1053ca5e859cb1488') provides('pkgconfig') diff --git a/var/spack/repos/builtin/packages/planck-likelihood/package.py b/var/spack/repos/builtin/packages/planck-likelihood/package.py index 94c7640d437..fc6e23cf782 100644 --- a/var/spack/repos/builtin/packages/planck-likelihood/package.py +++ b/var/spack/repos/builtin/packages/planck-likelihood/package.py @@ -13,7 +13,7 @@ class PlanckLikelihood(Package): homepage = "https://wiki.cosmos.esa.int/planckpla2015/index.php/CMB_spectrum_%26_Likelihood_Code" url = "http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Code-v2.0.R2.00.tar.bz2" - version('2.00', '7a081679ff249dc4f94fb7177e16e818', + version('2.00', sha256='c1efa208175b2751e75b2ad1c026dae744a7dd279eb74baa5db3098bc9c971bb', url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Code-v2.0.R2.00.tar.bz2") variant('lensing-ext', default=False, @@ -32,24 +32,24 @@ class PlanckLikelihood(Package): resource( name='baseline', url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-baseline_R2.00.tar.gz", - md5='7e784819cea65dbc290ea3619420295a', + sha256='7c62c5afc105bff28c2da3eddb870b8180536d30e31c4d419b307ad3996e17ab', destination='.') resource( name='lensing-ext', url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-lensing-ext.R2.00.tar.gz", - md5='091736f73b47a09162050bee27d68399', + sha256='0c017984bfd12315b94958f48f8e61e625361a84066838976f676fb5c2e76dbc', destination='.', when='+lensing-ext') resource( name='plik-DS', url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-plik-DS.R2.00.tar.gz", - md5='76ac04f989025eecab3825aba7e41f36', + sha256='f6b5ec6b284ea71008f071503faf8319dac48c3ea7fb13f5e5cbd23fff3efd84', destination='.', when='+plik-DS') resource( name='plik-HM-ext', url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-plik-HM-ext.R2.00.tar.gz", - md5='1c3bd8221f973b7bf7e76647451fd6e5', + sha256='b5b8ead297b31f9b2e4913b54b1d3bbe272075f85ce2ca9bf5d99dbbe1559f77', destination='.', when='+plik-HM-ext') resource( diff --git a/var/spack/repos/builtin/packages/platypus/package.py b/var/spack/repos/builtin/packages/platypus/package.py index 0a101542bcb..ba09c538692 100644 --- a/var/spack/repos/builtin/packages/platypus/package.py +++ b/var/spack/repos/builtin/packages/platypus/package.py @@ -12,7 +12,7 @@ class Platypus(Package): homepage = "http://www.well.ox.ac.uk/platypus" url = "http://www.well.ox.ac.uk/bioinformatics/Software/Platypus-latest.tgz" - version('0.8.1', 'edf3fb5bf080241ddb75a413c8529d57') + version('0.8.1', sha256='a0f39e800ebdc5590e9b568a791bc6746df0fde4d1c3622140db64dea175622b') depends_on('python@2.6:', type=('build', 'run')) depends_on('py-cython', type='build') diff --git a/var/spack/repos/builtin/packages/plink/package.py b/var/spack/repos/builtin/packages/plink/package.py index 7d91b1c955f..3a5096d93d5 100644 --- a/var/spack/repos/builtin/packages/plink/package.py +++ b/var/spack/repos/builtin/packages/plink/package.py @@ -13,11 +13,11 @@ class Plink(Package): homepage = "https://www.cog-genomics.org/plink/1.9/" - version('1.9-beta6.10', 'ef01956d0ca9344fe420cb3ea1d94698', + version('1.9-beta6.10', sha256='f8438656996c55a5edd95c223cce96277de6efaab1b9b1d457bfee0c272058d8', url='http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip') - version('1.9-beta5', '737545504ae19348a44a05fa69b75c28', + version('1.9-beta5', sha256='e00ef16ac5abeb6b4c4d77846bd655fafc62669fbebf8cd2e941f07b3111907e', url='https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz') - version('1.07', 'fd0bafeda42151b20534e4f97b0d97df', + version('1.07', sha256='70c52ee47eed854293832639dbabb41c7c036db3a4881c136e6a71ecff4ac7f4', url='http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip', preferred=True) diff --git a/var/spack/repos/builtin/packages/plplot/package.py b/var/spack/repos/builtin/packages/plplot/package.py index 6c6a5a4d784..bfbbf738957 100644 --- a/var/spack/repos/builtin/packages/plplot/package.py +++ b/var/spack/repos/builtin/packages/plplot/package.py @@ -12,9 +12,9 @@ class Plplot(CMakePackage): homepage = "http://plplot.sourceforge.net/" url = "https://sourceforge.net/projects/plplot/files/plplot/5.13.0%20Source/plplot-5.13.0.tar.gz/download" - version('5.13.0', 'bfefeae7fb9a23377c6dc37b44a7da8a') - version('5.12.0', '998a05be218e5de8f2faf988b8dbdc51') - version('5.11.0', '632c9e13b09f4e2b2517b3567bc3cece') + version('5.13.0', sha256='ec36bbee8b03d9d1c98f8fd88f7dc3415560e559b53eb1aa991c2dcf61b25d2b') + version('5.12.0', sha256='8dc5da5ef80e4e19993d4c3ef2a84a24cc0e44a5dade83201fca7160a6d352ce') + version('5.11.0', sha256='bfa8434e6e1e7139a5651203ec1256c8581e2fac3122f907f7d8d25ed3bd5f7e') variant('java', default=False, description='Enable Java binding') variant('lua', default=False, description='Enable Lua binding') diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index babcadc7ea8..8acc721cff3 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -23,15 +23,15 @@ class Plumed(AutotoolsPackage): homepage = 'http://www.plumed.org/' url = 'https://github.com/plumed/plumed2/archive/v2.5.0.tar.gz' - version('2.5.0', 'd1277d86a4aa766bfe97513d7969bfb7') - version('2.4.4', 'e8ef700fb4740b177cf660313c9805e6') - version('2.4.2', '0f66f24b4c763ae8b2f39574113e9935') - version('2.4.1', '6558e1fd02fc46e847ab6a3fb5ed5411') - version('2.3.5', '3cc5f025cb6f5d963f3c778f15c77d44') - version('2.3.3', '9f5729e406e79a06a16976fcb020e024') - version('2.3.0', 'a9b5728f115dca8f0519111f1f5a6fa5') - version('2.2.4', 'afb00da25a3fbd47acf377e53342059d') - version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8') + version('2.5.0', sha256='53e08187ec9f8af2326fa84407e34644a7c51d2af93034309fb70675eee5e4f7') + version('2.4.4', sha256='1e5c24109314481fad404da97d61c7339b219e27e120c9c80bacc79c9f6a51a8') + version('2.4.2', sha256='528ce57f1f5330480bcd403140166a4580efd2acaea39c85dfeca5e2cd649321') + version('2.4.1', sha256='f00410ebdd739c2ddf55fcd714ff4bd88a1029e02d2fc9cea0b5fca34e0fc4eb') + version('2.3.5', sha256='a6a66ca4582c1aecc6138c96be015e13cd06a718e8446b2f13e610fe34602e4f') + version('2.3.3', sha256='ac058ff529f207d5b4169fb5a87bdb3c77307dfef1ac543ad8b6c74c5de7fc91') + version('2.3.0', sha256='b1c8a54a313a0569e27e36420770074f35406453f73de70e55c424652abeddf1') + version('2.2.4', sha256='d7a1dba34a7fe03f23e8d39ab6e15b230c4851373fdceb3602e2de26ea53ce37') + version('2.2.3', sha256='2db19c5f6a2918833941d0bf47b5431d0865529d786df797ccc966d763ed7b0c') # Variants. PLUMED by default builds a number of optional modules. # The ones listed here are not built by default for various reasons, diff --git a/var/spack/repos/builtin/packages/pmgr-collective/package.py b/var/spack/repos/builtin/packages/pmgr-collective/package.py index dcdb0392100..3ce2f597cd6 100644 --- a/var/spack/repos/builtin/packages/pmgr-collective/package.py +++ b/var/spack/repos/builtin/packages/pmgr-collective/package.py @@ -12,7 +12,7 @@ class PmgrCollective(Package): homepage = "http://www.sourceforge.net/projects/pmgrcollective" url = "http://downloads.sourceforge.net/project/pmgrcollective/pmgrcollective/PMGR_COLLECTIVE-1.0/pmgr_collective-1.0.tgz" - version('1.0', '0384d008774274cc3fc7b4d810dfd07e') + version('1.0', sha256='c8022d1128ce5e8f637166af6e55c13700e665550e468b8cdb1531441c6bb7f5') def install(self, spec, prefix): make('PREFIX="' + prefix + '"') diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py index 6f5a398cd64..9bfe28a0813 100644 --- a/var/spack/repos/builtin/packages/pmix/package.py +++ b/var/spack/repos/builtin/packages/pmix/package.py @@ -43,8 +43,8 @@ class Pmix(AutotoolsPackage): version('2.1.4', sha256='eb72d292e76e200f02cf162a477eecea2559ef3ac2edf50ee95b3fe3983d033e') version('2.1.3', sha256='281283133498e7e5999ed5c6557542c22408bc9eb51ecbcf7696160616782a41') version('2.1.2', sha256='94bb9c801c51a6caa1b8cef2b85ecf67703a5dfa4d79262e6668c37c744bb643') - version('2.0.1', 'ba3193b485843516e6b4e8641e443b1e') - version('1.2.5', 'c3d20cd9d365a813dc367afdf0f41c37') + version('2.0.1', sha256='ba6e0f32936b1859741adb221e18b2c1ee7dc53a6b374b9f7831adf1692b15fd') + version('1.2.5', sha256='a2b02d489ee730c06ee40e7f9ffcebb6c35bcb4f95153fab7c4276a3add6ae31') depends_on('libevent@2.0.20:2.0.22,2.1.8') depends_on('hwloc@1.11.0:1.11.99,2.0.1:', when='@3.0.0:') diff --git a/var/spack/repos/builtin/packages/pnfft/package.py b/var/spack/repos/builtin/packages/pnfft/package.py index d1c724c9ed4..6518e49c3e2 100644 --- a/var/spack/repos/builtin/packages/pnfft/package.py +++ b/var/spack/repos/builtin/packages/pnfft/package.py @@ -13,7 +13,7 @@ class Pnfft(AutotoolsPackage): homepage = "https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en" url = "https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/pnfft-1.0.7-alpha.tar.gz" - version('1.0.7-alpha', '5caa7f214eed99de2281043ca2367e9e') + version('1.0.7-alpha', sha256='fda558ff57ee3119754363bb6e6739338680d2d6860fe7dc42009d85562bd67a') depends_on('pfft') depends_on('gsl') diff --git a/var/spack/repos/builtin/packages/pngwriter/package.py b/var/spack/repos/builtin/packages/pngwriter/package.py index 3207d5b640f..b14a672c967 100644 --- a/var/spack/repos/builtin/packages/pngwriter/package.py +++ b/var/spack/repos/builtin/packages/pngwriter/package.py @@ -24,9 +24,9 @@ class Pngwriter(CMakePackage): version('develop', branch='dev') version('master', branch='master') - version('0.7.0', 'a68aa0889f120f5bb07848afce278a95') - version('0.6.0', '0a19bc55c5f6379fea7343752fd3ffae') - version('0.5.6', 'c13bd1fdc0e331a246e6127b5f262136') + version('0.7.0', sha256='82d46eef109f434f95eba9cf5908710ae4e75f575fd3858178ad06e800152825') + version('0.6.0', sha256='5107c6be0bfadf76ba4d01a553f7e060b5a7763ca7d9374ef3e7e59746b3911e') + version('0.5.6', sha256='0c5f3c1fd6f2470e88951f4b8add64cf5f5a7e7038115dba69604139359b08f1') depends_on('libpng') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/pnmpi/package.py b/var/spack/repos/builtin/packages/pnmpi/package.py index 2f00bedce31..9e0c64faae2 100644 --- a/var/spack/repos/builtin/packages/pnmpi/package.py +++ b/var/spack/repos/builtin/packages/pnmpi/package.py @@ -13,7 +13,7 @@ class Pnmpi(CMakePackage): homepage = "https://github.com/LLNL/PnMPI" url = "https://github.com/LLNL/PnMPI/releases/download/v1.7/PnMPI-v1.7-full.tar.gz" - version('1.7', '8040c1558c0deaa3d964c35d1760f3a8') + version('1.7', sha256='523228bdc220ae417d6812c0766bba698a240d71c69981cb0cb2b09a75ef4a9e') variant('fortran', default=False, description='Configure PnMPI with Fortran support') diff --git a/var/spack/repos/builtin/packages/poamsa/package.py b/var/spack/repos/builtin/packages/poamsa/package.py index 81db83b2f9d..a6cf51dbde0 100644 --- a/var/spack/repos/builtin/packages/poamsa/package.py +++ b/var/spack/repos/builtin/packages/poamsa/package.py @@ -15,7 +15,7 @@ class Poamsa(MakefilePackage): homepage = "https://sourceforge.net/projects/poamsa" url = "https://downloads.sourceforge.net/project/poamsa/poamsa/2.0/poaV2.tar.gz" - version('2.0', '9e2eb270d4867114406f53dab1311b2b') + version('2.0', sha256='d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2') def url_for_version(self, version): url = "https://downloads.sourceforge.net/project/poamsa/poamsa/{0}/poaV{1}.tar.gz" diff --git a/var/spack/repos/builtin/packages/polymake/package.py b/var/spack/repos/builtin/packages/polymake/package.py index 12ff79b62c0..556d31a5873 100644 --- a/var/spack/repos/builtin/packages/polymake/package.py +++ b/var/spack/repos/builtin/packages/polymake/package.py @@ -12,8 +12,8 @@ class Polymake(Package): homepage = "https://polymake.org/doku.php" url = "https://polymake.org/lib/exe/fetch.php/download/polymake-3.0r1.tar.bz2" - version('3.0r2', '08584547589f052ea50e2148109202ab') - version('3.0r1', '63ecbecf9697c6826724d8a041d2cac0') + version('3.0r2', sha256='e7c0f8e3a45ea288d2fb4ae781a1dcea913ef9c275fed401632cdb11a672d6dc') + version('3.0r1', sha256='cdc223716b1cc3f4f3cc126089a438f9d12390caeed78291a87565717c7b504d') # Note: Could also be built with nauty instead of bliss diff --git a/var/spack/repos/builtin/packages/poppler-data/package.py b/var/spack/repos/builtin/packages/poppler-data/package.py index 5701ffd34f2..7bf3cd94b54 100644 --- a/var/spack/repos/builtin/packages/poppler-data/package.py +++ b/var/spack/repos/builtin/packages/poppler-data/package.py @@ -17,6 +17,6 @@ class PopplerData(CMakePackage): homepage = "https://poppler.freedesktop.org/" url = "https://poppler.freedesktop.org/poppler-data-0.4.9.tar.gz" - version('0.4.9', '35cc7beba00aa174631466f06732be40') + version('0.4.9', sha256='1f9c7e7de9ecd0db6ab287349e31bf815ca108a5a175cf906a90163bdbe32012') depends_on('cmake@2.6:', type='build') diff --git a/var/spack/repos/builtin/packages/poppler/package.py b/var/spack/repos/builtin/packages/poppler/package.py old mode 100755 new mode 100644 index b196fa6ef5b..23f2db80024 --- a/var/spack/repos/builtin/packages/poppler/package.py +++ b/var/spack/repos/builtin/packages/poppler/package.py @@ -18,8 +18,8 @@ class Poppler(CMakePackage): version('0.79.0', sha256='f985a4608fe592d2546d9d37d4182e502ff6b4c42f8db4be0a021a1c369528c8') version('0.77.0', sha256='7267eb4cbccd64a58244b8211603c1c1b6bf32c7f6a4ced2642865346102f36b') version('0.72.0', sha256='c1747eb8f26e9e753c4001ed951db2896edc1021b6d0f547a0bd2a27c30ada51') - version('0.65.0', 'b9a0af02e43deb26265f130343e90d78') - version('0.64.0', 'f7f687ebb60004f8ad61994575018044') + version('0.65.0', sha256='89c8cf73f83efda78c5a9bd37c28f4593ad0e8a51556dbe39ed81e1ae2dd8f07') + version('0.64.0', sha256='b21df92ca99f78067785cf2dc8e06deb04726b62389c0ee1f5d8b103c77f64b1') version('0.61.1', sha256='1266096343f5163c1a585124e9a6d44474e1345de5cdfe55dc7b47357bcfcda9') variant('cms', default=False, description='Use color management system') diff --git a/var/spack/repos/builtin/packages/portcullis/package.py b/var/spack/repos/builtin/packages/portcullis/package.py index 3e35ff6daa2..9b91a9fb39d 100644 --- a/var/spack/repos/builtin/packages/portcullis/package.py +++ b/var/spack/repos/builtin/packages/portcullis/package.py @@ -13,7 +13,7 @@ class Portcullis(AutotoolsPackage): homepage = "https://github.com/maplesond/portcullis" url = "https://github.com/maplesond/portcullis/archive/Release-1.1.2.tar.gz" - version('1.1.2', '5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749') + version('1.1.2', sha256='5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749') depends_on('autoconf@2.53:', type='build') depends_on('automake@1.11:', type='build') diff --git a/var/spack/repos/builtin/packages/postgresql/package.py b/var/spack/repos/builtin/packages/postgresql/package.py index ec0ea848c8b..63c76cbf35a 100644 --- a/var/spack/repos/builtin/packages/postgresql/package.py +++ b/var/spack/repos/builtin/packages/postgresql/package.py @@ -24,14 +24,14 @@ class Postgresql(AutotoolsPackage): version('10.6', sha256='68a8276f08bda8fbefe562faaf8831cb20664a7a1d3ffdbbcc5b83e08637624b') version('10.5', sha256='6c8e616c91a45142b85c0aeb1f29ebba4a361309e86469e0fb4617b6a73c4011') version('10.4', sha256='1b60812310bd5756c62d93a9f93de8c28ea63b0df254f428cd1cf1a4d9020048') - version('10.3', '506498796a314c549388cafb3d5c717a') - version('10.2', 'e97c3cc72bdf661441f29069299b260a') + version('10.3', sha256='6ea268780ee35e88c65cdb0af7955ad90b7d0ef34573867f223f14e43467931a') + version('10.2', sha256='fe32009b62ddb97f7f014307ce9d0edb6972f5a698e63cb531088e147d145bad') version('10.1', sha256='3ccb4e25fe7a7ea6308dea103cac202963e6b746697366d72ec2900449a5e713') version('10.0', sha256='712f5592e27b81c5b454df96b258c14d94b6b03836831e015c65d6deeae57fd1') version('9.6.12', sha256='2e8c8446ba94767bda8a26cf5a2152bf0ae68a86aaebf894132a763084579d84') version('9.6.11', sha256='38250adc69a1e8613fb926c894cda1d01031391a03648894b9a6e13ff354a530') - version('9.5.3', '3f0c388566c688c82b01a0edf1e6b7a0') - version('9.3.4', 'd0a41f54c377b2d2fab4a003b0dac762') + version('9.5.3', sha256='7385c01dc58acba8d7ac4e6ad42782bd7c0b59272862a3a3d5fe378d4503a0b4') + version('9.3.4', sha256='9ee819574dfc8798a448dc23a99510d2d8924c2f8b49f8228cd77e4efc8a6621') variant('client_only', default=False, description='Build and install client only.') diff --git a/var/spack/repos/builtin/packages/ppl/package.py b/var/spack/repos/builtin/packages/ppl/package.py index d58fe9e86ae..e511f001584 100644 --- a/var/spack/repos/builtin/packages/ppl/package.py +++ b/var/spack/repos/builtin/packages/ppl/package.py @@ -23,7 +23,7 @@ class Ppl(Package): homepage = "http://bugseng.com/products/ppl/" url = "http://bugseng.com/products/ppl/download/ftp/releases/1.1/ppl-1.1.tar.gz" - version('1.1', '4f2422c0ef3f409707af32108deb30a7') + version('1.1', sha256='46f073c0626234f0b1a479356c0022fe5dc3c9cf10df1a246c9cde81f7cf284d') depends_on("gmp") diff --git a/var/spack/repos/builtin/packages/pplacer/package.py b/var/spack/repos/builtin/packages/pplacer/package.py index be7588ffaf9..f971cdff733 100644 --- a/var/spack/repos/builtin/packages/pplacer/package.py +++ b/var/spack/repos/builtin/packages/pplacer/package.py @@ -17,7 +17,7 @@ class Pplacer(Package): homepage = "http://matsen.fhcrc.org/pplacer/" url = "https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip" - version('1.1.alpha19', 'e6b78604882d41d4bf13592c7edebfa2') + version('1.1.alpha19', sha256='9131b45c35ddb927f866385f149cf64af5dffe724234cd4548c22303a992347d') def install(self, spec, prefix): install_tree('scripts', prefix.bin) diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py index bc77a6f7b14..7666b705621 100644 --- a/var/spack/repos/builtin/packages/prank/package.py +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -12,8 +12,8 @@ class Prank(Package): homepage = "http://wasabiapp.org/software/prank/" url = "http://wasabiapp.org/download/prank/prank.source.150803.tgz" - version('170427', 'a5cda14dc4e5efe1f14b84eb7a7caabd') - version('150803', '71ac2659e91c385c96473712c0a23e8a') + version('170427', sha256='623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859') + version('150803', md5='71ac2659e91c385c96473712c0a23e8a') depends_on('mafft') depends_on('exonerate') diff --git a/var/spack/repos/builtin/packages/presentproto/package.py b/var/spack/repos/builtin/packages/presentproto/package.py index 35b8558818a..66a7ebbcd7a 100644 --- a/var/spack/repos/builtin/packages/presentproto/package.py +++ b/var/spack/repos/builtin/packages/presentproto/package.py @@ -12,7 +12,7 @@ class Presentproto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/presentproto/" url = "https://www.x.org/archive/individual/proto/presentproto-1.0.tar.gz" - version('1.0', '57eaf4bb58e86476ec89cfb42d675961') + version('1.0', sha256='02f8042cb351dd5c3699a0dbdb2ab25f86532efe3e1e3e97897e7f44b5c67040') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/preseq/package.py b/var/spack/repos/builtin/packages/preseq/package.py index aa7786249ed..1315a2fa0c9 100644 --- a/var/spack/repos/builtin/packages/preseq/package.py +++ b/var/spack/repos/builtin/packages/preseq/package.py @@ -16,7 +16,7 @@ class Preseq(MakefilePackage): homepage = "https://github.com/smithlabcode/preseq" url = "https://github.com/smithlabcode/preseq/releases/download/v2.0.2/preseq_v2.0.2.tar.bz2" - version('2.0.2', '9f2a7b597c9f08b821db6ee55e2ea39c') + version('2.0.2', sha256='1d7ea249bf4e5826e09697256643e6a2473bc302cd455f31d4eb34c23c10b97c') depends_on('samtools') depends_on('gsl') diff --git a/var/spack/repos/builtin/packages/price/package.py b/var/spack/repos/builtin/packages/price/package.py index 00179a2a8d0..3ab85f87249 100644 --- a/var/spack/repos/builtin/packages/price/package.py +++ b/var/spack/repos/builtin/packages/price/package.py @@ -13,7 +13,7 @@ class Price(MakefilePackage): homepage = "http://derisilab.ucsf.edu/software/price/" url = "http://derisilab.ucsf.edu/software/price/PriceSource140408.tar.gz" - version('140408', '2880274a514c34b812718b13a620813e') + version('140408', sha256='12276b2b15f4e020a772944a19fd2aaf089d3437cbc71e7486fa8db95014843f') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/primer3/package.py b/var/spack/repos/builtin/packages/primer3/package.py index 47de31b5c1b..b05adff2eab 100644 --- a/var/spack/repos/builtin/packages/primer3/package.py +++ b/var/spack/repos/builtin/packages/primer3/package.py @@ -15,7 +15,7 @@ class Primer3(MakefilePackage): homepage = "http://primer3.sourceforge.net/" url = "https://sourceforge.net/projects/primer3/files/primer3/2.3.7/primer3-2.3.7.tar.gz/download" - version('2.3.7', 'c6b89067bf465e62b6b1fd830b5b4418') + version('2.3.7', sha256='9e37a301d2ca9e5034c9a9d4afcb3e90041f6cc44c658b63598d0ccfcb176e5e') build_directory = 'src' diff --git a/var/spack/repos/builtin/packages/prinseq-lite/package.py b/var/spack/repos/builtin/packages/prinseq-lite/package.py index 03ecd1419d5..dd64857c83d 100644 --- a/var/spack/repos/builtin/packages/prinseq-lite/package.py +++ b/var/spack/repos/builtin/packages/prinseq-lite/package.py @@ -13,7 +13,7 @@ class PrinseqLite(Package): homepage = "http://prinseq.sourceforge.net" url = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz" - version('0.20.4', '3be1a572073ebbbecfeba42a42853ff5') + version('0.20.4', sha256='9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f') variant('nopca', default=True, description="Graphs version without PCA") diff --git a/var/spack/repos/builtin/packages/printproto/package.py b/var/spack/repos/builtin/packages/printproto/package.py index fb4e5a84026..22d2561ad47 100644 --- a/var/spack/repos/builtin/packages/printproto/package.py +++ b/var/spack/repos/builtin/packages/printproto/package.py @@ -13,7 +13,7 @@ class Printproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/printproto" url = "https://www.x.org/archive/individual/proto/printproto-1.0.5.tar.gz" - version('1.0.5', '5afeb3a7de8a14b417239a14ea724268') + version('1.0.5', sha256='e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/prng/package.py b/var/spack/repos/builtin/packages/prng/package.py index e57003bddaa..0a82a494afc 100644 --- a/var/spack/repos/builtin/packages/prng/package.py +++ b/var/spack/repos/builtin/packages/prng/package.py @@ -12,7 +12,7 @@ class Prng(AutotoolsPackage): homepage = "http://statmath.wu.ac.at/prng/" url = "http://statmath.wu.ac.at/prng/prng-3.0.2.tar.gz" - version('3.0.2', '80cb0870f2d18618bd2772f9e1dc1a70') + version('3.0.2', sha256='8299182b97c24b7891d74590a8a8438641a6c681ce34d6c3f7bc98a0649da48b') depends_on('automake', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/probconsrna/package.py b/var/spack/repos/builtin/packages/probconsrna/package.py index b819ec53c58..c2a649cb0b2 100644 --- a/var/spack/repos/builtin/packages/probconsrna/package.py +++ b/var/spack/repos/builtin/packages/probconsrna/package.py @@ -13,7 +13,7 @@ class Probconsrna(Package): homepage = "http://probcons.stanford.edu/" url = "http://probcons.stanford.edu/probconsRNA.tar.gz" - version('2005-6-7', '2aa13012124208ca5dd6b0a1d508208d') + version('2005-6-7', sha256='7fe4494bd423db1d5f33f5ece2c70f9f66a0d9112e28d3eaa7dfdfe7fa66eba8') def install(self, build, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/prodigal/package.py b/var/spack/repos/builtin/packages/prodigal/package.py index 457866e0758..2cf8fedafd6 100644 --- a/var/spack/repos/builtin/packages/prodigal/package.py +++ b/var/spack/repos/builtin/packages/prodigal/package.py @@ -13,7 +13,7 @@ class Prodigal(MakefilePackage): homepage = "https://github.com/hyattpd/Prodigal" url = "https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz" - version('2.6.3', '5181809fdb740e9a675cfdbb6c038466') + version('2.6.3', sha256='89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f') def install(self, spec, prefix): make('INSTALLDIR={0}'.format(self.prefix), 'install') diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py index d1228ad9373..795462742d2 100644 --- a/var/spack/repos/builtin/packages/proj/package.py +++ b/var/spack/repos/builtin/packages/proj/package.py @@ -22,21 +22,21 @@ class Proj(AutotoolsPackage): # See https://github.com/OSGeo/PROJ/wiki/proj.h-adoption-status version('6.1.0', sha256='676165c54319d2f03da4349cbd7344eb430b225fe867a90191d848dc64788008') version('6.0.0', sha256='4510a2c1c8f9056374708a867c51b1192e8d6f9a5198dd320bf6a168e44a3657') - version('5.2.0', 'ad285c7d03cbb138d9246e10e1f3191c') - version('5.1.0', '68c46f6da7e4cd5708f83fe47af80db6') - version('5.0.1', '15c8d7d6a8cb945c7878d0ff322a232c') - version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9') - version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c') - version('4.8.0', 'd815838c92a29179298c126effbb1537') - version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd') - version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493') + version('5.2.0', sha256='ef919499ffbc62a4aae2659a55e2b25ff09cccbbe230656ba71c6224056c7e60') + version('5.1.0', sha256='6b1379a53317d9b5b8c723c1dc7bf2e3a8eb22ceb46b8807a1ce48ef65685bb3') + version('5.0.1', sha256='a792f78897482ed2c4e2af4e8a1a02e294c64e32b591a635c5294cb9d49fdc8c') + version('4.9.2', sha256='60bf9ad1ed1c18158e652dfff97865ba6fb2b67f1511bc8dceae4b3c7e657796') + version('4.9.1', sha256='fca0388f3f8bc5a1a803d2f6ff30017532367992b30cf144f2d39be88f36c319') + version('4.8.0', sha256='2db2dbf0fece8d9880679154e0d6d1ce7c694dd8e08b4d091028093d87a9d1b5') + version('4.7.0', sha256='fc5440002a496532bfaf423c28bdfaf9e26cc96c84ccefcdefde911efbd98986') + version('4.6.1', sha256='76d174edd4fdb4c49c1c0ed8308a469216c01e7177a4510b1b303ef3c5f97b47') # https://github.com/OSGeo/proj.4#distribution-files-and-format # https://github.com/OSGeo/proj-datumgrid resource( name='proj-datumgrid', url='https://download.osgeo.org/proj/proj-datumgrid-1.8.tar.gz', - md5='be7e8f77c12714a4cd53732c1f3cf8d9', + sha256='3ff6618a0acc9f0b9b4f6a62e7ff0f7bf538fb4f74de47ad04da1317408fcc15', placement='nad' ) diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py index a76494c65d5..512fcb3d535 100644 --- a/var/spack/repos/builtin/packages/protobuf/package.py +++ b/var/spack/repos/builtin/packages/protobuf/package.py @@ -18,19 +18,19 @@ class Protobuf(CMakePackage): version('3.7.1', sha256='f1748989842b46fa208b2a6e4e2785133cfcc3e4d43c17fecb023733f0f5443f') version('3.7.0', sha256='a19dcfe9d156ae45d209b15e0faed5c7b5f109b6117bfc1974b6a7b98a850320') version('3.6.1', sha256='3d4e589d81b2006ca603c1ab712c9715a76227293032d05b26fca603f90b3f5b') - version('3.5.2', 'ff6742018c172c66ecc627029ad54280') - version('3.5.1.1', '5005003ae6b94773c4bbca87a644b131') - version('3.5.1', '710f1a75983092c9b45ecef207236104') - version('3.5.0.1', 'b3ed2401acf167207277b254fd7f9638') - version('3.5.0', 'd95db321e1a9901fffc51ed8994afd36') - version('3.4.1', '31b19dcfd6567095fdb66a8c07347222') - version('3.4.0', '1d077a7d4db3d75681f5c333f2de9b1a') - version('3.3.0', 'f0f712e98de3db0c65c0c417f5e7aca8') - version('3.2.0', 'efaa08ae635664fb5e7f31421a41a995') - version('3.1.0', '39d6a4fa549c0cce164aa3064b1492dc') - version('3.0.2', '7349a7f43433d72c6d805c6ca22b7eeb') + version('3.5.2', sha256='4ffd420f39f226e96aebc3554f9c66a912f6cad6261f39f194f16af8a1f6dab2') + version('3.5.1.1', sha256='56b5d9e1ab2bf4f5736c4cfba9f4981fbc6976246721e7ded5602fbaee6d6869') + version('3.5.1', sha256='826425182ee43990731217b917c5c3ea7190cfda141af4869e6d4ad9085a740f') + version('3.5.0.1', sha256='86be71e61c76575c60839452a4f265449a6ea51570d7983cb929f06ad294b5f5') + version('3.5.0', sha256='0cc6607e2daa675101e9b7398a436f09167dffb8ca0489b0307ff7260498c13c') + version('3.4.1', sha256='8e0236242106e680b4f9f576cc44b8cd711e948b20a9fc07769b0a20ceab9cc4') + version('3.4.0', sha256='f6600abeee3babfa18591961a0ff21e7db6a6d9ef82418a261ec4fee44ee6d44') + version('3.3.0', sha256='9a36bc1265fa83b8e818714c0d4f08b8cec97a1910de0754a321b11e66eb76de') + version('3.2.0', sha256='a839d3f1519ff9d68ab908de5a0f269650ef1fc501c10f6eefd4cae51d29b86f') + version('3.1.0', sha256='fb2a314f4be897491bb2446697be693d489af645cb0e165a85e7e64e07eb134d') + version('3.0.2', sha256='a0a265bcc9d4e98c87416e59c33afc37cede9fb277292523739417e449b18c1e') # does not build with CMake: - # version('2.5.0', '9c21577a03adc1879aba5b52d06e25cf') + # version('2.5.0', md5='9c21577a03adc1879aba5b52d06e25cf') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/proxymngr/package.py b/var/spack/repos/builtin/packages/proxymngr/package.py index 5088eba5017..6331b991f73 100644 --- a/var/spack/repos/builtin/packages/proxymngr/package.py +++ b/var/spack/repos/builtin/packages/proxymngr/package.py @@ -15,7 +15,7 @@ class Proxymngr(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/proxymngr" url = "https://www.x.org/archive/individual/app/proxymngr-1.0.4.tar.gz" - version('1.0.4', 'a165cf704f6a413f0bacf65ea470331f') + version('1.0.4', sha256='d40f2d15985ee8e8ef5320a85c0b1899a7bc95974a65137ae886e499bced86f4') depends_on('libice') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/pruners-ninja/package.py b/var/spack/repos/builtin/packages/pruners-ninja/package.py index 29ed7a95ef9..4213cd95c02 100644 --- a/var/spack/repos/builtin/packages/pruners-ninja/package.py +++ b/var/spack/repos/builtin/packages/pruners-ninja/package.py @@ -12,8 +12,8 @@ class PrunersNinja(AutotoolsPackage): homepage = "https://github.com/PRUNERS/NINJA" url = "https://github.com/PRUNERS/NINJA/releases/download/v1.0.0/NINJA-1.0.0.tar.gz" - version("1.0.1", "f0728cad61d8f1f970dffb7bb430addb") - version("1.0.0", "fee53c4712ac521ebec3cd8692e5185a") + version("1.0.1", sha256="53df5c019054b60c68e63d3e249127f1d5f267a70539c8809fb42a8ddbfcb29b") + version("1.0.0", sha256="f25c189783b57801f298dfff8770f42733a43f926668aceff4abd287b6e3a4d1") depends_on("mpi") depends_on("autoconf", type='build') diff --git a/var/spack/repos/builtin/packages/psm/package.py b/var/spack/repos/builtin/packages/psm/package.py index 1af2811365a..387299b8a59 100644 --- a/var/spack/repos/builtin/packages/psm/package.py +++ b/var/spack/repos/builtin/packages/psm/package.py @@ -13,7 +13,7 @@ class Psm(MakefilePackage): url = "https://github.com/intel/psm/archive/v3.3.tar.gz" git = "https://github.com/intel/psm.git" - version('3.3', '031eb27688c932867d55054e76d00875', preferred=True) + version('3.3', sha256='034b10e24d9f2967ef0f8d0f828572295e89cdfa1ba30c35e288b9b23c3dab8f', preferred=True) version('2017-04-28', commit='604758e') conflicts('%gcc@6:', when='@3.3') diff --git a/var/spack/repos/builtin/packages/pugixml/package.py b/var/spack/repos/builtin/packages/pugixml/package.py index da0e52aa716..52b4bfa3834 100644 --- a/var/spack/repos/builtin/packages/pugixml/package.py +++ b/var/spack/repos/builtin/packages/pugixml/package.py @@ -13,4 +13,4 @@ class Pugixml(CMakePackage): homepage = "http://pugixml.org/" url = "http://github.com/zeux/pugixml/tarball/v1.8.1" - version('1.8.1', 'bff935f82fa45bee4d31257d948bcba2') + version('1.8.1', sha256='929c4657c207260f8cc28e5b788b7499dffdba60d83d59f55ea33d873d729cd4') diff --git a/var/spack/repos/builtin/packages/pv/package.py b/var/spack/repos/builtin/packages/pv/package.py index e65def98efa..5e9d55a0e80 100644 --- a/var/spack/repos/builtin/packages/pv/package.py +++ b/var/spack/repos/builtin/packages/pv/package.py @@ -14,4 +14,4 @@ class Pv(AutotoolsPackage): homepage = "http://www.ivarch.com/programs/pv.shtml" url = "http://www.ivarch.com/programs/sources/pv-1.6.6.tar.bz2" - version('1.6.6', 'ff3564fddcc2b9bd4a9c1d143aba4b4c') + version('1.6.6', sha256='608ef935f7a377e1439c181c4fc188d247da10d51a19ef79bcdee5043b0973f1') diff --git a/var/spack/repos/builtin/packages/pvm/package.py b/var/spack/repos/builtin/packages/pvm/package.py index 9a614b2533d..0d19dd9f21d 100644 --- a/var/spack/repos/builtin/packages/pvm/package.py +++ b/var/spack/repos/builtin/packages/pvm/package.py @@ -15,7 +15,7 @@ class Pvm(MakefilePackage): homepage = "http://www.csm.ornl.gov/pvm/pvm_home.html" url = "http://www.netlib.org/pvm3/pvm3.4.6.tgz" - version('3.4.6', '7b5f0c80ea50b6b4b10b6128e197747b') + version('3.4.6', sha256='482665e9bc975d826bcdacf1df1d42e43deda9585a2c430fd3b7b7ed08eada44') parallel = False diff --git a/var/spack/repos/builtin/packages/pxz/package.py b/var/spack/repos/builtin/packages/pxz/package.py index 1d1346adedd..c0d695175a5 100644 --- a/var/spack/repos/builtin/packages/pxz/package.py +++ b/var/spack/repos/builtin/packages/pxz/package.py @@ -14,7 +14,7 @@ class Pxz(MakefilePackage): git = "https://github.com/jnovy/pxz.git" version('develop', branch='master') - version('4.999.9beta.20091201git', '4ae3926185978f5c95c9414dc4634451') + version('4.999.9beta.20091201git', sha256='df69f91103db6c20f0b523bb7f026d86ee662c49fe714647ed63f918cd39767a') depends_on('xz') diff --git a/var/spack/repos/builtin/packages/py-3to2/package.py b/var/spack/repos/builtin/packages/py-3to2/package.py index 720fb350bc2..23866e18c26 100644 --- a/var/spack/repos/builtin/packages/py-3to2/package.py +++ b/var/spack/repos/builtin/packages/py-3to2/package.py @@ -13,4 +13,4 @@ class Py3to2(PythonPackage): homepage = "https://pypi.python.org/pypi/3to2" url = "https://pypi.io/packages/source/3/3to2/3to2-1.1.1.zip" - version('1.1.1', 'cbeed28e350dbdaef86111ace3052824') + version('1.1.1', sha256='fef50b2b881ef743f269946e1090b77567b71bb9a9ce64b7f8e699b562ff685c') diff --git a/var/spack/repos/builtin/packages/py-4suite-xml/package.py b/var/spack/repos/builtin/packages/py-4suite-xml/package.py index efddb0631e9..b3114bbff01 100644 --- a/var/spack/repos/builtin/packages/py-4suite-xml/package.py +++ b/var/spack/repos/builtin/packages/py-4suite-xml/package.py @@ -13,6 +13,6 @@ class Py4suiteXml(PythonPackage): homepage = "http://4suite.org/" url = "https://pypi.io/packages/source/4/4Suite-XML/4Suite-XML-1.0.2.tar.gz" - version('1.0.2', '3ca3db95cb0263ad80beba034d1ff6ea') + version('1.0.2', sha256='f0c24132eb2567e64b33568abff29a780a2f0236154074d0b8f5262ce89d8c03') depends_on('python@2.2.1:') diff --git a/var/spack/repos/builtin/packages/py-abipy/package.py b/var/spack/repos/builtin/packages/py-abipy/package.py index 5cc4b3cec4c..aef20708b4a 100644 --- a/var/spack/repos/builtin/packages/py-abipy/package.py +++ b/var/spack/repos/builtin/packages/py-abipy/package.py @@ -13,7 +13,7 @@ class PyAbipy(PythonPackage): homepage = "https://github.com/abinit/abipy" url = "https://pypi.io/packages/source/a/abipy/abipy-0.2.0.tar.gz" - version('0.2.0', 'af9bc5cf7d5ca1a56ff73e2a65c5bcbd') + version('0.2.0', sha256='c72b796ba0f9ea4299eac3085bede092d2652e9e5e8074d3badd19ef7b600792') variant('gui', default=False, description='Build the GUI') variant('ipython', default=False, description='Build IPython support') diff --git a/var/spack/repos/builtin/packages/py-adios/package.py b/var/spack/repos/builtin/packages/py-adios/package.py index 2149c0e2236..0ce34ef3ca3 100644 --- a/var/spack/repos/builtin/packages/py-adios/package.py +++ b/var/spack/repos/builtin/packages/py-adios/package.py @@ -16,12 +16,12 @@ class PyAdios(PythonPackage): maintainers = ['ax3l'] version('develop', branch='master') - version('1.13.0', '68af36b821debbdf4748b20320a990ce') - version('1.12.0', '84a1c71b6698009224f6f748c5257fc9') - version('1.11.1', '5639bfc235e50bf17ba9dafb14ea4185') - version('1.11.0', '5eead5b2ccf962f5e6d5f254d29d5238') - version('1.10.0', 'eff450a4c0130479417cfd63186957f3') - version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678') + version('1.13.0', sha256='7b5ee8ff7a5f7215f157c484b20adb277ec0250f87510513edcc25d2c4739f50') + version('1.12.0', sha256='22bc22c157322abec2d1a0817a259efd9057f88c2113e67d918a9a5ebcb3d88d') + version('1.11.1', sha256='9f5c10b9471a721ba57d1cf6e5a55a7ad139a6c12da87b4dc128539e9eef370e') + version('1.11.0', sha256='e89d14ccbe7181777225e0ba6c272c0941539b8ccd440e72ed5a9457441dae83') + version('1.10.0', sha256='6713069259ee7bfd4d03f47640bf841874e9114bab24e7b0c58e310c42a0ec48') + version('1.9.0', sha256='23b2bb70540d51ab0855af0b205ca484fd1bd963c39580c29e3133f9e6fffd46') variant('mpi', default=True, description='Enable MPI support') diff --git a/var/spack/repos/builtin/packages/py-affine/package.py b/var/spack/repos/builtin/packages/py-affine/package.py index 0b83a13352d..a9e6946ec1c 100644 --- a/var/spack/repos/builtin/packages/py-affine/package.py +++ b/var/spack/repos/builtin/packages/py-affine/package.py @@ -14,4 +14,4 @@ class PyAffine(PythonPackage): depends_on('py-setuptools', type='build') - version('2.1.0', '99cf61c3ef484f93da9dc062dfbce4b5') + version('2.1.0', sha256='b67b7dee9a9865185a931758a3e347ad8583d0ac985895b90985a477ccfa4745') diff --git a/var/spack/repos/builtin/packages/py-alabaster/package.py b/var/spack/repos/builtin/packages/py-alabaster/package.py index b8c230efc05..d661750cffb 100644 --- a/var/spack/repos/builtin/packages/py-alabaster/package.py +++ b/var/spack/repos/builtin/packages/py-alabaster/package.py @@ -16,7 +16,7 @@ class PyAlabaster(PythonPackage): import_modules = ['alabaster'] version('0.7.12', sha256='a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02') - version('0.7.10', '7934dccf38801faa105f6e7b4784f493') - version('0.7.9', 'b29646a8bbe7aa52830375b7d17b5d7a') + version('0.7.10', sha256='37cdcb9e9954ed60912ebc1ca12a9d12178c26637abdf124e3cde2341c257fe0') + version('0.7.9', sha256='47afd43b08a4ecaa45e3496e139a193ce364571e7e10c6a87ca1a4c57eb7ea08') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py index 6d36d1c9ab7..690d62281c5 100644 --- a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py +++ b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py @@ -12,6 +12,6 @@ class PyApacheLibcloud(PythonPackage): homepage = "http://libcloud.apache.org" url = "https://pypi.io/packages/source/a/apache-libcloud/apache-libcloud-1.2.1.tar.gz" - version('1.2.1', '912e6fb1f2d13f7d3b58ee982b9f9d1f') + version('1.2.1', sha256='b26b542c6c9785dd4e34892d87421ffa4c043335c1cba301a97a8d9748c423f2') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-appdirs/package.py b/var/spack/repos/builtin/packages/py-appdirs/package.py index 1b4610318f4..1145924a7b5 100644 --- a/var/spack/repos/builtin/packages/py-appdirs/package.py +++ b/var/spack/repos/builtin/packages/py-appdirs/package.py @@ -15,8 +15,8 @@ class PyAppdirs(PythonPackage): import_modules = ['appdirs'] - version('1.4.3', '44c679904082a2133f5566c8a0d3ab42') - version('1.4.0', '1d17b4c9694ab84794e228f28dc3275b') + version('1.4.3', sha256='9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92') + version('1.4.0', sha256='8fc245efb4387a4e3e0ac8ebcc704582df7d72ff6a42a53f5600bbb18fdaadc5') patch('setuptools-import.patch', when='@:1.4.0') diff --git a/var/spack/repos/builtin/packages/py-appnope/package.py b/var/spack/repos/builtin/packages/py-appnope/package.py index e57db493f00..068f6e2426b 100644 --- a/var/spack/repos/builtin/packages/py-appnope/package.py +++ b/var/spack/repos/builtin/packages/py-appnope/package.py @@ -12,4 +12,4 @@ class PyAppnope(PythonPackage): homepage = "https://github.com/minrk/appnope" url = "https://pypi.io/packages/source/a/appnope/appnope-0.1.0.tar.gz" - version('0.1.0', '932fbaa73792c9b06754755a774dcac5') + version('0.1.0', sha256='8b995ffe925347a2138d7ac0fe77155e4311a0ea6d6da4f5128fe4b3cbe5ed71') diff --git a/var/spack/repos/builtin/packages/py-apscheduler/package.py b/var/spack/repos/builtin/packages/py-apscheduler/package.py index 5ef5375efb7..12aa3aa325c 100644 --- a/var/spack/repos/builtin/packages/py-apscheduler/package.py +++ b/var/spack/repos/builtin/packages/py-apscheduler/package.py @@ -12,8 +12,8 @@ class PyApscheduler(PythonPackage): homepage = "https://github.com/agronholm/apscheduler" url = "https://pypi.io/packages/source/A/APScheduler/APScheduler-3.3.1.tar.gz" - version('3.3.1', '6342b3b78b41920a8aa54fd3cd4a299d') - version('2.1.0', 'b837d23822fc46651862dd2186ec361a') + version('3.3.1', sha256='f68874dff1bdffcc6ce3adb7840c1e4d162c609a3e3f831351df30b75732767b') + version('2.1.0', sha256='3b4b44387616902ad6d13122961013630eb25519937e5aa7c450de85656c9753') depends_on('py-setuptools@0.7:', type='build') diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py index 94431b7d7a1..c5c8cc34fc3 100644 --- a/var/spack/repos/builtin/packages/py-argcomplete/package.py +++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py @@ -12,6 +12,6 @@ class PyArgcomplete(PythonPackage): homepage = "https://pypi.python.org/pypi/argcomplete" url = "https://pypi.io/packages/source/a/argcomplete/argcomplete-1.1.1.tar.gz" - version('1.1.1', '89a3839096c9f991ad33828e72d21abf') + version('1.1.1', sha256='cca45b5fe07000994f4f06a0b95bd71f7b51b04f81c3be0b4ea7b666e4f1f084') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-argparse/package.py b/var/spack/repos/builtin/packages/py-argparse/package.py index 6a0bee7d2de..a1257333828 100644 --- a/var/spack/repos/builtin/packages/py-argparse/package.py +++ b/var/spack/repos/builtin/packages/py-argparse/package.py @@ -12,7 +12,7 @@ class PyArgparse(PythonPackage): homepage = "https://github.com/ThomasWaldmann/argparse/" url = "https://pypi.io/packages/source/a/argparse/argparse-1.4.0.tar.gz" - version('1.4.0', '08062d2ceb6596fcbc5a7e725b53746f') + version('1.4.0', sha256='62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4') depends_on('python@2.3:') diff --git a/var/spack/repos/builtin/packages/py-ase/package.py b/var/spack/repos/builtin/packages/py-ase/package.py index b1f27979dda..39aaaea9ef0 100644 --- a/var/spack/repos/builtin/packages/py-ase/package.py +++ b/var/spack/repos/builtin/packages/py-ase/package.py @@ -16,8 +16,8 @@ class PyAse(PythonPackage): version('3.18.0', sha256='39d45f12def2669605bffc82926acfb13a0d0610e6d82740fa316aafa70f97f9') - version('3.15.0', '65a0143753517c2df157e53bd29a18e3') - version('3.13.0', 'e946a0addc5b61e5e2e75857e0f99b89') + version('3.15.0', sha256='5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8') + version('3.13.0', sha256='c4046c50debac28415b36616d79aa28e68ae2cd03c013c2aed6a1e3d465c0ee1') depends_on('python@2.6:', type=('build', 'run'), when='@:3.15.0') depends_on('python@3.5:', type=('build', 'run'), when='@3.18.0:') diff --git a/var/spack/repos/builtin/packages/py-asn1crypto/package.py b/var/spack/repos/builtin/packages/py-asn1crypto/package.py index 5deda4aefee..ad51bd828a3 100644 --- a/var/spack/repos/builtin/packages/py-asn1crypto/package.py +++ b/var/spack/repos/builtin/packages/py-asn1crypto/package.py @@ -13,6 +13,6 @@ class PyAsn1crypto(PythonPackage): homepage = "https://github.com/wbond/asn1crypto" url = "https://pypi.io/packages/source/a/asn1crypto/asn1crypto-0.22.0.tar.gz" - version('0.22.0', '74a8b9402625b38ef19cf3fa69ef8470') + version('0.22.0', sha256='cbbadd640d3165ab24b06ef25d1dca09a3441611ac15f6a6b452474fdf0aed1a') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py index 7b40cb49a5f..2dcc335375c 100644 --- a/var/spack/repos/builtin/packages/py-astroid/package.py +++ b/var/spack/repos/builtin/packages/py-astroid/package.py @@ -14,12 +14,12 @@ class PyAstroid(PythonPackage): url = "https://github.com/PyCQA/astroid/archive/astroid-1.4.5.tar.gz" version('2.2.0', sha256='7e289d0aa4a537b4aa798bd609fdf745de0f3c37e6b67642ed328e1482421a6d') - # version('1.5.3', '6f65e4ea8290ec032320460905afb828') # has broken unit tests - version('1.4.5', '7adfc55809908297ef430efe4ea20ac3') - version('1.4.4', '8ae6f63f6a2b260bb7f647dafccbc796') - version('1.4.3', '4647159de7d4d0c4b1de23ecbfb8e246') - version('1.4.2', '677f7965840f375af51b0e86403bee6a') - version('1.4.1', 'ed70bfed5e4b25be4292e7fe72da2c02') + # version('1.5.3', md5='6f65e4ea8290ec032320460905afb828') # has broken unit tests + version('1.4.5', sha256='28d8f5b898087ecf86fd66ca0934e5c0e51fc0beb5972cfc4e0c11080e0cb6ab') + version('1.4.4', sha256='a521dfdbb728ec36c4cc7a9287285e2c30233fb19faffcec8d080d1b2b2e7d1e') + version('1.4.3', sha256='381a8b1a7e3861b0e7f5f25fb8d70fccf5d6b19ed81fcf76f569a5c5affe1bcc') + version('1.4.2', sha256='f9007d651f4b3514ea5812127677a4bb681ff194164290cea358987920f24ee6') + version('1.4.1', sha256='f1ab3ee6f17f9d30981399a52b56a7a7d2747ba24f0aa504e411ee6205a01fc0') depends_on('py-lazy-object-proxy') depends_on('py-six') diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py index 90d8d712bc4..26e995985a5 100644 --- a/var/spack/repos/builtin/packages/py-astropy/package.py +++ b/var/spack/repos/builtin/packages/py-astropy/package.py @@ -16,8 +16,8 @@ class PyAstropy(PythonPackage): version('3.2.1', sha256='706c0457789c78285e5464a5a336f5f0b058d646d60f4e5f5ba1f7d5bf424b28') version('2.0.14', sha256='618807068609a4d8aeb403a07624e9984f566adc0dc0f5d6b477c3658f31aeb6') - version('1.1.2', 'cbe32023b5b1177d1e2498a0d00cda51') - version('1.1.post1', 'b52919f657a37d45cc45f5cb0f58c44d') + version('1.1.2', sha256='6f0d84cd7dfb304bb437dda666406a1d42208c16204043bc920308ff8ffdfad1') + version('1.1.post1', sha256='64427ec132620aeb038e4d8df94d6c30df4cc8b1c42a6d8c5b09907a31566a21') variant('extras', default=False, description='Enable extra functionality') diff --git a/var/spack/repos/builtin/packages/py-attrs/package.py b/var/spack/repos/builtin/packages/py-attrs/package.py index d79a3d826bd..66bb4df72de 100644 --- a/var/spack/repos/builtin/packages/py-attrs/package.py +++ b/var/spack/repos/builtin/packages/py-attrs/package.py @@ -14,8 +14,8 @@ class PyAttrs(PythonPackage): import_modules = ['attr'] - version('18.1.0', '3f3f3e0750dab74cfa1dc8b0fd7a5f86') - version('16.3.0', '4ec003c49360853cf935113d1ae56151') + version('18.1.0', sha256='e0d0eb91441a3b53dab4d9b743eafc1ac44476296a2053b6ca3af0b139faf87b') + version('16.3.0', sha256='80203177723e36f3bbe15aa8553da6e80d47bfe53647220ccaa9ad7a5e473ccc') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py index ae0d734f0fc..c701382661f 100644 --- a/var/spack/repos/builtin/packages/py-autopep8/package.py +++ b/var/spack/repos/builtin/packages/py-autopep8/package.py @@ -13,9 +13,9 @@ class PyAutopep8(PythonPackage): homepage = "https://github.com/hhatto/autopep8" url = "https://pypi.io/packages/source/a/autopep8/autopep8-1.2.4.tar.gz" - version('1.3.3', '8951f43748406015b663a54ab05d891a') - version('1.2.4', 'fcea19c0c5e505b425e2a78afb771f5c') - version('1.2.2', '3d97f9c89d14a0975bffd32a2c61c36c') + version('1.3.3', sha256='ff787bffb812818c3071784b5ce9a35f8c481a0de7ea0ce4f8b68b8788a12f30') + version('1.2.4', sha256='38e31e266e29808e8a65a307778ed8e402e1f0d87472009420d6d18146cdeaa2') + version('1.2.2', sha256='ecc51614755c7f697e83478f87eb6bbd009075a397c15080f0311aaecbbdfca8') extends('python', ignore='bin/pep8') depends_on('python@2.6:2.8,3.2:') diff --git a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py index e18d28ab647..029745dec16 100644 --- a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py +++ b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py @@ -12,7 +12,7 @@ class PyAvroJsonSerializer(PythonPackage): homepage = "https://github.com/linkedin/python-avro-json-serializer" url = "https://github.com/linkedin/python-avro-json-serializer/archive/0.4.tar.gz" - version('0.4', 'ee32f415e03820653cf8477bf5bfc779') + version('0.4', sha256='58df57e6c85b1b453668eb0bff2b049efcfd83d6e5dfa72cee1df220f330820d') depends_on('py-setuptools', type='build') depends_on('py-simplejson', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-avro/package.py b/var/spack/repos/builtin/packages/py-avro/package.py index e4c99530969..4a90296429b 100644 --- a/var/spack/repos/builtin/packages/py-avro/package.py +++ b/var/spack/repos/builtin/packages/py-avro/package.py @@ -12,6 +12,6 @@ class PyAvro(PythonPackage): homepage = "http://avro.apache.org/docs/current/" url = "https://pypi.io/packages/source/a/avro/avro-1.8.2.tar.gz" - version('1.8.2', '44ec007d432a2f3c35f87eee01f1e9ec') + version('1.8.2', sha256='8f9ee40830b70b5fb52a419711c9c4ad0336443a6fba7335060805f961b04b59') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-babel/package.py b/var/spack/repos/builtin/packages/py-babel/package.py index f648576d1d1..ed90f2efe64 100644 --- a/var/spack/repos/builtin/packages/py-babel/package.py +++ b/var/spack/repos/builtin/packages/py-babel/package.py @@ -16,9 +16,9 @@ class PyBabel(PythonPackage): import_modules = ['babel', 'babel.localtime', 'babel.messages'] - version('2.6.0', 'c384ac03026e8fe6f9b90f55201f1bff') - version('2.4.0', '90e7a0add19b2036a9b415630a0d9388') - version('2.3.4', 'afa20bc55b0e991833030129ad498f35') + version('2.6.0', sha256='8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23') + version('2.4.0', sha256='8c98f5e5f8f5f088571f2c6bd88d530e331cbbcb95a7311a0db69d3dca7ec563') + version('2.3.4', sha256='c535c4403802f6eb38173cd4863e419e2274921a01a8aad8a5b497c131c62875') depends_on('py-setuptools', type='build') depends_on('py-pytz', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-backcall/package.py b/var/spack/repos/builtin/packages/py-backcall/package.py index 4f2ed7d41ae..1dbef69ac3e 100644 --- a/var/spack/repos/builtin/packages/py-backcall/package.py +++ b/var/spack/repos/builtin/packages/py-backcall/package.py @@ -12,4 +12,4 @@ class PyBackcall(PythonPackage): homepage = "https://github.com/takluyver/backcall" url = "https://pypi.io/packages/source/b/backcall/backcall-0.1.0.tar.gz" - version('0.1.0', '87ce0c7839808e6a3427d57df6a792e7') + version('0.1.0', sha256='38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4') diff --git a/var/spack/repos/builtin/packages/py-backports-abc/package.py b/var/spack/repos/builtin/packages/py-backports-abc/package.py index ae55b4871db..b0851e1420b 100644 --- a/var/spack/repos/builtin/packages/py-backports-abc/package.py +++ b/var/spack/repos/builtin/packages/py-backports-abc/package.py @@ -12,6 +12,6 @@ class PyBackportsAbc(PythonPackage): homepage = "https://github.com/cython/backports_abc" url = "https://github.com/cython/backports_abc/archive/0.4.tar.gz" - version('0.4', 'e4246ae689221c9cbe84369fdb59e8c74d02b298') + version('0.4', sha256='2b5c4e91e37ba8bcd3fb8fecc8530f941578fc2c911497da3f09bf5fec6a6705') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py index 753afb96cfe..634638d5fa7 100644 --- a/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py +++ b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py @@ -14,9 +14,9 @@ class PyBackportsFunctoolsLruCache(PythonPackage): py_namespace = 'backports' - version('1.5', '20f53f54cd3f04b3346ce75a54959754') - version('1.4', 'b954e7d5e2ca0f0f66ad2ed12ba800e5') - version('1.0.1', 'c789ef439d189330b99872746a6d9e85', + version('1.5', sha256='9d98697f088eb1b0fa451391f91afb5e3ebde16bbdb272819fd091151fda4f1a') + version('1.4', sha256='31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f') + version('1.0.1', sha256='593275768571eb2bcfe0795a30108f8a0e85e14e98c3a5e498e789f891d82f3d', url="https://pypi.io/packages/source/b/backports.functools_lru_cache/backports.functools_lru_cache-1.0.1.zip") depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py index 807fba3ef22..d06efbd5bbc 100644 --- a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py +++ b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py @@ -15,7 +15,7 @@ class PyBackportsShutilGetTerminalSize(PythonPackage): py_namespace = 'backports' - version('1.0.0', '03267762480bd86b50580dc19dff3c66') + version('1.0.0', sha256='713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80') # newer setuptools version mess with "namespace" packages in an # incompatible way cf. https://github.com/pypa/setuptools/issues/900 diff --git a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py index 62f5c5782b8..25582a47b44 100644 --- a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py +++ b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py @@ -14,4 +14,4 @@ class PyBackportsSslMatchHostname(PythonPackage): py_namespace = 'backports' - version('3.5.0.1', 'c03fc5e2c7b3da46b81acf5cbacfe1e6') + version('3.5.0.1', sha256='502ad98707319f4a51fa2ca1c677bd659008d27ded9f6380c79e8932e38dcdf2') diff --git a/var/spack/repos/builtin/packages/py-basemap/package.py b/var/spack/repos/builtin/packages/py-basemap/package.py index 2eff7480dde..1403e24e9ab 100644 --- a/var/spack/repos/builtin/packages/py-basemap/package.py +++ b/var/spack/repos/builtin/packages/py-basemap/package.py @@ -13,8 +13,8 @@ class PyBasemap(PythonPackage): homepage = "http://matplotlib.org/basemap/" - version('1.2.0', 'f8e64bd150590223701a48d60408e939') - version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8') + version('1.2.0', sha256='bd5bf305918a2eb675939873b735238f9e3dfe6b5c290e37c41e5b082ff3639a') + version('1.0.7', sha256='e07ec2e0d63b24c9aed25a09fe8aff2598f82a85da8db74190bac81cbf104531') # Per Github issue #3813, setuptools is required at runtime in order # to make mpl_toolkits a namespace package that can span multiple diff --git a/var/spack/repos/builtin/packages/py-bcbio-gff/package.py b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py index 2a9acaa86de..f5ee74a636d 100644 --- a/var/spack/repos/builtin/packages/py-bcbio-gff/package.py +++ b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py @@ -13,7 +13,7 @@ class PyBcbioGff(PythonPackage): homepage = "https://pypi.python.org/pypi/bcbio-gff/0.6.2" url = "https://pypi.io/packages/source/b/bcbio-gff/bcbio-gff-0.6.2.tar.gz" - version('0.6.2', 'd5aae8b125cdad4291f15bec20cfb0ef') + version('0.6.2', sha256='c682dc46a90e9fdb124ab5723797a5f71b2e3534542ceff9f6572b64b9814e68') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py index 11f0de2e990..8a9febcdaee 100644 --- a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py +++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py @@ -15,9 +15,9 @@ class PyBeautifulsoup4(PythonPackage): url = "https://pypi.io/packages/source/b/beautifulsoup4/beautifulsoup4-4.8.0.tar.gz" version('4.8.0', sha256='25288c9e176f354bf277c0a10aa96c782a6a18a17122dba2e8cec4a97e03343b') - version('4.5.3', '937e0df0d699a1237646f38fd567f0c6') - version('4.5.1', '994abd90e691beaf7d42c00ffb2f3a67') - version('4.4.1', '8fbd9a7cac0704645fa20d1419036815') + version('4.5.3', sha256='b21ca09366fa596043578fd4188b052b46634d22059e68dd0077d9ee77e08a3e') + version('4.5.1', sha256='3c9474036afda9136aac6463def733f81017bf9ef3510d25634f335b0c87f5e1') + version('4.4.1', sha256='87d4013d0625d4789a4f56b8d79a04d5ce6db1152bb65f1d39744f7709a366b4') depends_on('py-setuptools', type='build') depends_on('py-soupsieve@1.2:', when='@4.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-binwalk/package.py b/var/spack/repos/builtin/packages/py-binwalk/package.py index b02b0208cc2..da9a3519362 100644 --- a/var/spack/repos/builtin/packages/py-binwalk/package.py +++ b/var/spack/repos/builtin/packages/py-binwalk/package.py @@ -14,7 +14,7 @@ class PyBinwalk(PythonPackage): homepage = "https://github.com/devttys0/binwalk" url = "https://pypi.io/packages/source/b/binwalk/binwalk-2.1.0.tar.gz" - version('2.1.0', '054867d9abe6a05f43200cf2591051e6') + version('2.1.0', sha256='218c8045c6cb3ed6e21814fb89cdb913808b02dfe5a6cc30f85f4a59e8129f6b') depends_on('python') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-biom-format/package.py b/var/spack/repos/builtin/packages/py-biom-format/package.py index 62c57fcf803..b316ff2ab0d 100644 --- a/var/spack/repos/builtin/packages/py-biom-format/package.py +++ b/var/spack/repos/builtin/packages/py-biom-format/package.py @@ -14,7 +14,7 @@ class PyBiomFormat(PythonPackage): homepage = "https://pypi.python.org/pypi/biom-format/2.1.6" url = "https://pypi.io/packages/source/b/biom-format/biom-format-2.1.6.tar.gz" - version('2.1.6', '1dd4925b74c56e8ee864d5e1973068de') + version('2.1.6', sha256='8eefc275a85cc937f6d6f408d91b7b45eae854cd5d1cbda411a3af51f5b49b0d') variant('h5py', default=True, description='For use with BIOM 2.0+ files') diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py index 9d1b30036ac..e9789eb1d32 100644 --- a/var/spack/repos/builtin/packages/py-biopython/package.py +++ b/var/spack/repos/builtin/packages/py-biopython/package.py @@ -16,8 +16,8 @@ class PyBiopython(PythonPackage): url = "http://biopython.org/DIST/biopython-1.65.tar.gz" version('1.73', sha256='70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0') - version('1.70', 'feff7a3e2777e43f9b13039b344e06ff') - version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67') + version('1.70', sha256='4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b') + version('1.65', sha256='463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e') depends_on('py-numpy', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-bitarray/package.py b/var/spack/repos/builtin/packages/py-bitarray/package.py index 5e2bb0a594c..87763f26e4e 100644 --- a/var/spack/repos/builtin/packages/py-bitarray/package.py +++ b/var/spack/repos/builtin/packages/py-bitarray/package.py @@ -12,7 +12,7 @@ class PyBitarray(PythonPackage): homepage = "https://pypi.python.org/pypi/bitarray" url = "https://pypi.io/packages/source/b/bitarray/bitarray-0.8.1.tar.gz" - version('0.8.1', '3825184f54f4d93508a28031b4c65d3b') + version('0.8.1', sha256='7da501356e48a83c61f479393681c1bc4b94e5a34ace7e08cb29e7dd9290ab18') depends_on('python') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-bitstring/package.py b/var/spack/repos/builtin/packages/py-bitstring/package.py index 589cab8834d..049584cfe6c 100644 --- a/var/spack/repos/builtin/packages/py-bitstring/package.py +++ b/var/spack/repos/builtin/packages/py-bitstring/package.py @@ -12,4 +12,4 @@ class PyBitstring(PythonPackage): homepage = "http://pythonhosted.org/bitstring" url = "https://pypi.io/packages/source/b/bitstring/bitstring-3.1.5.zip" - version('3.1.5', '70689a282f66625d0c7c3579a13e66db') + version('3.1.5', sha256='c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa') diff --git a/var/spack/repos/builtin/packages/py-bleach/package.py b/var/spack/repos/builtin/packages/py-bleach/package.py index 3f69ac9b45b..97cff7caac2 100644 --- a/var/spack/repos/builtin/packages/py-bleach/package.py +++ b/var/spack/repos/builtin/packages/py-bleach/package.py @@ -13,7 +13,7 @@ class PyBleach(PythonPackage): url = "https://pypi.io/packages/source/b/bleach/bleach-3.1.0.tar.gz" version('3.1.0', sha256='3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa') - version('1.5.0', 'b663300efdf421b3b727b19d7be9c7e7') + version('1.5.0', sha256='978e758599b54cd3caa2e160d74102879b230ea8dc93871d0783721eef58bc65') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py index 1503568183f..5d69833a8e2 100644 --- a/var/spack/repos/builtin/packages/py-blessings/package.py +++ b/var/spack/repos/builtin/packages/py-blessings/package.py @@ -11,6 +11,6 @@ class PyBlessings(PythonPackage): homepage = "https://github.com/erikrose/blessings" url = "https://pypi.io/packages/source/b/blessings/blessings-1.6.tar.gz" - version('1.6', '4f552a8ebcd4982693c92571beb99394') + version('1.6', sha256='edc5713061f10966048bf6b40d9a514b381e0ba849c64e034c4ef6c1847d3007') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-bokeh/package.py b/var/spack/repos/builtin/packages/py-bokeh/package.py index ee75f615c35..1f8ad215191 100644 --- a/var/spack/repos/builtin/packages/py-bokeh/package.py +++ b/var/spack/repos/builtin/packages/py-bokeh/package.py @@ -12,8 +12,8 @@ class PyBokeh(PythonPackage): homepage = "http://github.com/bokeh/bokeh" url = "https://pypi.io/packages/source/b/bokeh/bokeh-0.12.2.tar.gz" - version('1.3.4', 'e2d97bed5b199a10686486001fed5c854e4c04ebe28859923f27c52b93904754') - version('0.12.2', '2d1621bffe6e2ab9d42efbf733861c4f') + version('1.3.4', sha256='e2d97bed5b199a10686486001fed5c854e4c04ebe28859923f27c52b93904754') + version('0.12.2', sha256='0a840f6267b6d342e1bd720deee30b693989538c49644142521d247c0f2e6939') depends_on('python@2.6:', type=('build', 'run'), when='@0.12.2') depends_on('python@2.7:', type=('build', 'run'), when='@1.3.4:') diff --git a/var/spack/repos/builtin/packages/py-boltons/package.py b/var/spack/repos/builtin/packages/py-boltons/package.py index 32d6b6a1613..b8d33c6cf71 100644 --- a/var/spack/repos/builtin/packages/py-boltons/package.py +++ b/var/spack/repos/builtin/packages/py-boltons/package.py @@ -17,6 +17,6 @@ class PyBoltons(PythonPackage): homepage = "https://boltons.readthedocs.io/" url = "https://pypi.io/packages/source/b/boltons/boltons-16.5.1.tar.gz" - version('16.5.1', '014b10f240fa509fc333ebff4978111b') + version('16.5.1', sha256='fcded58596fa79bd1ada4488178e79fd11c7cb449f29ff9a6532411fb2db19b7') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index d687b45597b..3b426c4d71d 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -12,7 +12,7 @@ class PyBottleneck(PythonPackage): url = "https://pypi.io/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz" version('1.2.1', sha256='6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36') - version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') + version('1.0.0', sha256='8d9b7ad4fadf9648acc924a6ee522c7cb5b474e75faaad9d90dfd55e2805b495') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-breakseq2/package.py b/var/spack/repos/builtin/packages/py-breakseq2/package.py index 5ea4ddde8a3..4a4e72911f4 100644 --- a/var/spack/repos/builtin/packages/py-breakseq2/package.py +++ b/var/spack/repos/builtin/packages/py-breakseq2/package.py @@ -12,7 +12,7 @@ class PyBreakseq2(PythonPackage): homepage = "http://bioinform.github.io/breakseq2/" url = "https://github.com/bioinform/breakseq2/archive/2.2.tar.gz" - version('2.2', '6fd5a103c2781717b0b1d0efcbdc17e7') + version('2.2', sha256='d149e803191e6bb0b749abfba2c258716d94a38e942aaed40eb1630ae84f91ee') depends_on('py-setuptools', type='build') depends_on('py-biopython@1.65', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-brian/package.py b/var/spack/repos/builtin/packages/py-brian/package.py index a5b28336646..f00c3ea6e5a 100644 --- a/var/spack/repos/builtin/packages/py-brian/package.py +++ b/var/spack/repos/builtin/packages/py-brian/package.py @@ -12,7 +12,7 @@ class PyBrian(PythonPackage): homepage = "http://www.briansimulator.org" url = "https://pypi.io/packages/source/b/brian/brian-1.4.3.tar.gz" - version('1.4.3', '0570099bcce4d7afde73ff4126e6c30f') + version('1.4.3', sha256='c881dcfcd1a21990f9cb3cca76cdd868111cfd9e227ef5c1b13bb372d2efeaa4') depends_on('py-matplotlib@0.90.1:', type=('build', 'run')) depends_on('py-numpy@1.4.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-brian2/package.py b/var/spack/repos/builtin/packages/py-brian2/package.py index 26aa89eeba5..5ebb9f85bc9 100644 --- a/var/spack/repos/builtin/packages/py-brian2/package.py +++ b/var/spack/repos/builtin/packages/py-brian2/package.py @@ -12,8 +12,8 @@ class PyBrian2(PythonPackage): homepage = "http://www.briansimulator.org" url = "https://pypi.io/packages/source/B/Brian2/Brian2-2.0.1.tar.gz" - version('2.0.1', 'df5990e9a71f7344887bc02f54dfd0f0') - version('2.0rc3', '3100c5e4eb9eb83a06ff0413a7d43152') + version('2.0.1', sha256='195d8ced0d20e9069917776948f92aa70b7457bbc6b5222b8199654402ee1153') + version('2.0rc3', sha256='05f347f5fa6b25d1ce5ec152a2407bbce033599eb6664f32f5331946eb3c7d66') variant('doc', default=False, description='Build the documentation') diff --git a/var/spack/repos/builtin/packages/py-bsddb3/package.py b/var/spack/repos/builtin/packages/py-bsddb3/package.py index 6a3b9f19c3d..842ad1b9f11 100644 --- a/var/spack/repos/builtin/packages/py-bsddb3/package.py +++ b/var/spack/repos/builtin/packages/py-bsddb3/package.py @@ -15,7 +15,7 @@ class PyBsddb3(PythonPackage): homepage = "https://pypi.python.org/pypi/bsddb3/6.2.5" url = "https://pypi.io/packages/source/b/bsddb3/bsddb3-6.2.5.tar.gz" - version('6.2.5', '610267c189964c905a931990e1ba438c') + version('6.2.5', sha256='784bf40ad935258507594a89b32ea11f362cde120751c8b96de163955ced7db8') depends_on('python@2.6:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-bx-python/package.py b/var/spack/repos/builtin/packages/py-bx-python/package.py index 89157e4de4f..77fcace1eb5 100644 --- a/var/spack/repos/builtin/packages/py-bx-python/package.py +++ b/var/spack/repos/builtin/packages/py-bx-python/package.py @@ -13,7 +13,7 @@ class PyBxPython(PythonPackage): homepage = "https://github.com/bxlab/bx-python" url = "https://github.com/bxlab/bx-python/archive/v0.7.4.tar.gz" - version('0.7.4', 'a47b8cc55c104ac97440c6cc62be8697') + version('0.7.4', sha256='1066d1e56d062d0661f23c19942eb757bd7ab7cb8bc7d89a72fdc3931c995cb4') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cartopy/package.py b/var/spack/repos/builtin/packages/py-cartopy/package.py index 4cd54c6a9e6..b00c71645c4 100644 --- a/var/spack/repos/builtin/packages/py-cartopy/package.py +++ b/var/spack/repos/builtin/packages/py-cartopy/package.py @@ -12,7 +12,7 @@ class PyCartopy(PythonPackage): homepage = "http://scitools.org.uk/cartopy/" url = "https://github.com/SciTools/cartopy/archive/v0.16.0.tar.gz" - version('0.16.0', 'f9e2e528d7758da7c64f824548a53f32') + version('0.16.0', sha256='cadf62434492c965220b37f0548bc58180466ad6894a1db57dbc51cd43467e5c') depends_on('py-setuptools@0.7.2:', type='build') depends_on('py-cython@0.15.1:', type='build') diff --git a/var/spack/repos/builtin/packages/py-cclib/package.py b/var/spack/repos/builtin/packages/py-cclib/package.py index 3ee0fd8a600..98b7c315da8 100644 --- a/var/spack/repos/builtin/packages/py-cclib/package.py +++ b/var/spack/repos/builtin/packages/py-cclib/package.py @@ -12,7 +12,7 @@ class PyCclib(PythonPackage): homepage = "https://cclib.github.io/" - version('1.5.post1', '1a50be48e4597b1a6dabe943da82a43c', + version('1.5.post1', sha256='c2bf043432ab8df461d61b4289d0eb869fe134eee545ea5a78f8dea14b392f47', url="https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz") depends_on('py-numpy@1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cdat-lite/package.py b/var/spack/repos/builtin/packages/py-cdat-lite/package.py index b4022f32d8d..facb14a43f0 100644 --- a/var/spack/repos/builtin/packages/py-cdat-lite/package.py +++ b/var/spack/repos/builtin/packages/py-cdat-lite/package.py @@ -15,7 +15,7 @@ class PyCdatLite(PythonPackage): homepage = "http://proj.badc.rl.ac.uk/cedaservices/wiki/CdatLite" url = "https://pypi.io/packages/source/c/cdat-lite/cdat-lite-6.0.1.tar.gz" - version('6.0.1', '6d5a6e86f15ce15291d25feab8793248') + version('6.0.1', sha256='092ae4ff1fb03dee00096e8dd595b769b422759ce972d96525950adf8e1c9374') depends_on("netcdf") depends_on("python@2.5:2.8", type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cdo/package.py b/var/spack/repos/builtin/packages/py-cdo/package.py index bd3129f92d8..d61cb0ff0cd 100644 --- a/var/spack/repos/builtin/packages/py-cdo/package.py +++ b/var/spack/repos/builtin/packages/py-cdo/package.py @@ -13,7 +13,7 @@ class PyCdo(PythonPackage): homepage = "https://pypi.python.org/pypi/cdo" url = "https://pypi.io/packages/source/c/cdo/cdo-1.3.2.tar.gz" - version('1.3.2', '4b3686ec1b9b891f166c1c466c6db745') + version('1.3.2', sha256='9f78879d90d14134f2320565016d0d371b7dfe7ec71110fd313868ec1db34aee') depends_on('cdo') diff --git a/var/spack/repos/builtin/packages/py-certifi/package.py b/var/spack/repos/builtin/packages/py-certifi/package.py index 2cf00c83389..e4fe465ba7e 100644 --- a/var/spack/repos/builtin/packages/py-certifi/package.py +++ b/var/spack/repos/builtin/packages/py-certifi/package.py @@ -18,7 +18,7 @@ class PyCertifi(PythonPackage): version('2019.6.16', sha256='945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695') version('2017.4.17', sha256='f7527ebf7461582ce95f7a9e03dd141ce810d40590834f4ec20cddd54234c10a') - version('2017.1.23', 'b72521a8badff5e89a8eabea586d79ab') - version('2016.02.28', '5ccfc23bd5e931863f0b01ef3e9d2dbd3bef0e1b') + version('2017.1.23', sha256='81877fb7ac126e9215dfb15bfef7115fdc30e798e0013065158eed0707fd99ce') + version('2016.02.28', sha1='5ccfc23bd5e931863f0b01ef3e9d2dbd3bef0e1b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py index f3248f95eb1..2010aa1431c 100644 --- a/var/spack/repos/builtin/packages/py-cffi/package.py +++ b/var/spack/repos/builtin/packages/py-cffi/package.py @@ -14,10 +14,10 @@ class PyCffi(PythonPackage): import_modules = ['cffi'] - version('1.12.2', '4d7dcb6c7c738c15d2ece9bd4c5f86da') - version('1.11.5', 'ac8492f4ad952360737413e82d661908') - version('1.10.0', '2b5fa41182ed0edaf929a789e602a070') - version('1.1.2', 'ca6e6c45b45caa87aee9adc7c796eaea') + version('1.12.2', sha256='e113878a446c6228669144ae8a56e268c91b7f1fafae927adc4879d9849e0ea7') + version('1.11.5', sha256='e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4') + version('1.10.0', sha256='b3b02911eb1f6ada203b0763ba924234629b51586f72a21faacc638269f4ced5') + version('1.1.2', sha256='390970b602708c91ddc73953bb6929e56291c18a4d80f360afa00fad8b6f3339') depends_on('pkgconfig', type='build') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-chardet/package.py b/var/spack/repos/builtin/packages/py-chardet/package.py index d1997a4551c..eaa64eda36b 100644 --- a/var/spack/repos/builtin/packages/py-chardet/package.py +++ b/var/spack/repos/builtin/packages/py-chardet/package.py @@ -13,7 +13,7 @@ class PyChardet(PythonPackage): url = "https://pypi.io/packages/source/c/chardet/chardet-2.3.0.tar.gz" version('3.0.2', sha256='4f7832e7c583348a9eddd927ee8514b3bf717c061f57b21dbe7697211454d9bb') - version('2.3.0', '25274d664ccb5130adae08047416e1a8') + version('2.3.0', sha256='e53e38b3a4afe6d1132de62b7400a4ac363452dc5dfcf8d88e8e0cce663c68aa') depends_on('py-setuptools', type='build') depends_on('py-pytest-runner', type='build') diff --git a/var/spack/repos/builtin/packages/py-checkm-genome/package.py b/var/spack/repos/builtin/packages/py-checkm-genome/package.py index 25e37eeeb7a..2b99071d4a7 100644 --- a/var/spack/repos/builtin/packages/py-checkm-genome/package.py +++ b/var/spack/repos/builtin/packages/py-checkm-genome/package.py @@ -14,7 +14,7 @@ class PyCheckmGenome(PythonPackage): url = "https://pypi.io/packages/source/c/checkm-genome/checkm-genome-1.0.11.tar.gz" version('1.0.13', sha256='ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e') - version('1.0.11', '3058546ec324e2420cf72f0d2576114b') + version('1.0.11', sha256='e475d9817d12fa771dbccc80f47758b742fc67c25261dc8ca0c0dc898c2a5190') depends_on('hmmer@3.1b1:', type=('build', 'run')) depends_on('pplacer', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cheetah/package.py b/var/spack/repos/builtin/packages/py-cheetah/package.py index 539fdbd1084..aaf1a3a45d6 100644 --- a/var/spack/repos/builtin/packages/py-cheetah/package.py +++ b/var/spack/repos/builtin/packages/py-cheetah/package.py @@ -12,4 +12,4 @@ class PyCheetah(PythonPackage): homepage = "https://pypi.python.org/pypi/Cheetah/2.4.4" url = "https://pypi.io/packages/source/C/Cheetah/Cheetah-2.3.0.tar.gz" - version('2.3.0', 'e28ffef7f5c1660d66196639f162d9ce') + version('2.3.0', sha256='2a32d7f7f70be98c2d57aa581f979bc799d4bf17d09fc0e7d77280501edf3e53') diff --git a/var/spack/repos/builtin/packages/py-click-plugins/package.py b/var/spack/repos/builtin/packages/py-click-plugins/package.py index 234c406b050..bb94c4af5f3 100644 --- a/var/spack/repos/builtin/packages/py-click-plugins/package.py +++ b/var/spack/repos/builtin/packages/py-click-plugins/package.py @@ -13,7 +13,7 @@ class PyClickPlugins(PythonPackage): homepage = "https://pypi.org/project/click-plugins/" url = "https://pypi.io/packages/source/c/click-plugins/click-plugins-1.0.4.tar.gz" - version('1.0.4', '3db73ba58271e3d9644be9b9c03a9d8d') + version('1.0.4', sha256='dfed74b5063546a137de99baaaf742b4de4337ad2b3e1df5ec7c8a256adc0847') depends_on('py-setuptools', type='build') depends_on('py-click@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-click/package.py b/var/spack/repos/builtin/packages/py-click/package.py index b9917d778b5..6fc6c79f621 100644 --- a/var/spack/repos/builtin/packages/py-click/package.py +++ b/var/spack/repos/builtin/packages/py-click/package.py @@ -12,6 +12,6 @@ class PyClick(PythonPackage): homepage = "http://github.com/mitsuhiko/click" url = "https://pypi.io/packages/source/c/click/click-6.6.tar.gz" - version('6.6', 'd0b09582123605220ad6977175f3e51d') + version('6.6', sha256='cc6a19da8ebff6e7074f731447ef7e112bd23adf3de5c597cf9989f2fd8defe9') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cligj/package.py b/var/spack/repos/builtin/packages/py-cligj/package.py index 4d8d18bb772..72a8d507c04 100644 --- a/var/spack/repos/builtin/packages/py-cligj/package.py +++ b/var/spack/repos/builtin/packages/py-cligj/package.py @@ -14,7 +14,7 @@ class PyCligj(PythonPackage): url = "https://github.com/mapbox/cligj/archive/0.5.0.zip" version('0.5.0', sha256='ad158722a3f512f7eb33526479acf5cb53d9e59ca15cd494556440839783f106') - version('0.4.0', 'fe5376068b84c5ed01e2d3adf553e226') + version('0.4.0', sha256='5a5eb903ea66a8ccd41765dd276d9d08a6285f21dd99d41425ef80030d740351') depends_on('py-setuptools', type='build') depends_on('py-click', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cloudpickle/package.py b/var/spack/repos/builtin/packages/py-cloudpickle/package.py index 8d0c32dfd53..1be2b8d35f0 100644 --- a/var/spack/repos/builtin/packages/py-cloudpickle/package.py +++ b/var/spack/repos/builtin/packages/py-cloudpickle/package.py @@ -15,7 +15,7 @@ class PyCloudpickle(PythonPackage): import_modules = ['cloudpickle'] version('1.2.1', sha256='603244e0f552b72a267d47a7d9b347b27a3430f58a0536037a290e7e0e212ecf') - version('0.5.2', 'd0f6fc27882f865f2eb185fb0a32c84b') + version('0.5.2', sha256='b0e63dd89ed5285171a570186751bc9b84493675e99e12789e9a5dc5490ef554') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-colorama/package.py b/var/spack/repos/builtin/packages/py-colorama/package.py index 2f0b2082e55..073279d8387 100644 --- a/var/spack/repos/builtin/packages/py-colorama/package.py +++ b/var/spack/repos/builtin/packages/py-colorama/package.py @@ -12,6 +12,6 @@ class PyColorama(PythonPackage): homepage = "https://github.com/tartley/colorama" url = "https://pypi.io/packages/source/c/colorama/colorama-0.3.7.tar.gz" - version('0.3.7', '349d2b02618d3d39e5c6aede36fe3c1a') + version('0.3.7', sha256='e043c8d32527607223652021ff648fbb394d5e19cba9f1a698670b338c9d782b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-colormath/package.py b/var/spack/repos/builtin/packages/py-colormath/package.py index de8df395003..676360334dd 100644 --- a/var/spack/repos/builtin/packages/py-colormath/package.py +++ b/var/spack/repos/builtin/packages/py-colormath/package.py @@ -12,8 +12,8 @@ class PyColormath(PythonPackage): homepage = "https://pypi.python.org/pypi/colormath/2.1.1" url = "https://pypi.io/packages/source/c/colormath/colormath-2.1.1.tar.gz" - version('3.0.0', '3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217') - version('2.1.1', '10a0fb17e3c24363d0e1a3f2dccaa33b') + version('3.0.0', sha256='3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217') + version('2.1.1', sha256='003a2b2d9c1f43aa7d90addf1863fb2d822463c839b1166ae3092950792f9707') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-configparser/package.py b/var/spack/repos/builtin/packages/py-configparser/package.py index 1830fd74c65..a7804645ef4 100644 --- a/var/spack/repos/builtin/packages/py-configparser/package.py +++ b/var/spack/repos/builtin/packages/py-configparser/package.py @@ -14,7 +14,7 @@ class PyConfigparser(PythonPackage): url = "https://pypi.io/packages/source/c/configparser/configparser-3.5.0.tar.gz" version('3.5.1', sha256='f41e19cb29bebfccb1a78627b3f328ec198cc8f39510c7c55e7dfc0ab58c8c62') - version('3.5.0', 'cfdd915a5b7a6c09917a64a573140538') + version('3.5.0', sha256='5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a') depends_on('py-setuptools', type='build') depends_on('py-ordereddict', when='^python@:2.6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-counter/package.py b/var/spack/repos/builtin/packages/py-counter/package.py index 4febbd45349..566c6462197 100644 --- a/var/spack/repos/builtin/packages/py-counter/package.py +++ b/var/spack/repos/builtin/packages/py-counter/package.py @@ -15,6 +15,6 @@ class PyCounter(PythonPackage): homepage = "https://github.com/KelSolaar/Counter" url = "https://pypi.io/packages/source/C/Counter/Counter-1.0.0.tar.gz" - version('1.0.0', '1b49029693c28813ff276c2b16673f98') + version('1.0.0', sha256='9e008590e360936a66c98e1a01e7a9a0ecf6af19cc588107121f5fb4613bb60c') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py index df599b3be42..a8075f18f7d 100644 --- a/var/spack/repos/builtin/packages/py-coverage/package.py +++ b/var/spack/repos/builtin/packages/py-coverage/package.py @@ -12,7 +12,7 @@ class PyCoverage(PythonPackage): homepage = "http://nedbatchelder.com/code/coverage/" url = "https://pypi.io/packages/source/c/coverage/coverage-4.3.4.tar.gz" - version('4.3.4', '89759813309185efcf4af8b9f7762630') - version('4.0a6', '1bb4058062646148965bef0796b61efc') + version('4.3.4', sha256='eaaefe0f6aa33de5a65f48dd0040d7fe08cac9ac6c35a56d0a7db109c3e733df') + version('4.0a6', sha256='85c7f3efceb3724ab066a3fcccc05b9b89afcaefa5b669a7e2222d31eac4728d') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cpuinfo/package.py b/var/spack/repos/builtin/packages/py-cpuinfo/package.py index 4cc97c8b14a..e9f4db31426 100644 --- a/var/spack/repos/builtin/packages/py-cpuinfo/package.py +++ b/var/spack/repos/builtin/packages/py-cpuinfo/package.py @@ -12,6 +12,6 @@ class PyCpuinfo(PythonPackage): homepage = "https://github.com/workhorsy/py-cpuinfo" url = "https://pypi.io/packages/source/p/py-cpuinfo/py-cpuinfo-0.2.3.tar.gz" - version('0.2.3', '780ff46a0e122af09cb2c40b2706c6dc') + version('0.2.3', sha256='f6a016fdbc4e7fadf2d519090fcb4fa9d0831bad4e85245d938e5c2fe7623ca6') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-crispresso/package.py b/var/spack/repos/builtin/packages/py-crispresso/package.py index 3fe71aacccc..eaab99b35a8 100644 --- a/var/spack/repos/builtin/packages/py-crispresso/package.py +++ b/var/spack/repos/builtin/packages/py-crispresso/package.py @@ -13,7 +13,7 @@ class PyCrispresso(PythonPackage): homepage = "https://github.com/lucapinello/CRISPResso" url = "https://pypi.io/packages/source/C/CRISPResso/CRISPResso-1.0.8.tar.gz" - version('1.0.8', '2f9b52fe62cf49012a9525845f4aea45') + version('1.0.8', sha256='b04ac8781ff8ed56d018c357e741f146b72ad7e0d23c9e5bc1e1bcd1a873ebc3') depends_on('py-setuptools', type='build') depends_on('python@2.7.0:2.7.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cryptography/package.py b/var/spack/repos/builtin/packages/py-cryptography/package.py index 04572aec95b..2a3c99ffc63 100644 --- a/var/spack/repos/builtin/packages/py-cryptography/package.py +++ b/var/spack/repos/builtin/packages/py-cryptography/package.py @@ -14,8 +14,8 @@ class PyCryptography(PythonPackage): homepage = "https://pypi.python.org/pypi/cryptography" url = "https://pypi.io/packages/source/c/cryptography/cryptography-1.8.1.tar.gz" - version('2.3.1', '8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6') - version('1.8.1', '9f28a9c141995cd2300d0976b4fac3fb') + version('2.3.1', sha256='8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6') + version('1.8.1', sha256='323524312bb467565ebca7e50c8ae5e9674e544951d28a2904a50012a8828190') # dependencies taken from https://github.com/pyca/cryptography/blob/master/setup.py depends_on('py-setuptools@20.5:', type='build') diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py index c1941a8e4f1..f4e2ce67e7c 100644 --- a/var/spack/repos/builtin/packages/py-csvkit/package.py +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -13,7 +13,7 @@ class PyCsvkit(PythonPackage): homepage = 'http://csvkit.rtfd.org/' url = "https://pypi.io/packages/source/c/csvkit/csvkit-0.9.1.tar.gz" - version('0.9.1', '48d78920019d18846933ee969502fff6') + version('0.9.1', sha256='92f8b8647becb5cb1dccb3af92a13a4e85702d42ba465ce8447881fb38c9f93a') depends_on('py-setuptools', type='build') depends_on('py-python-dateutil@2.2', type=('build', 'run'), when='@0.9.1') diff --git a/var/spack/repos/builtin/packages/py-current/package.py b/var/spack/repos/builtin/packages/py-current/package.py index 5b837a83df8..7b3c28abe2a 100644 --- a/var/spack/repos/builtin/packages/py-current/package.py +++ b/var/spack/repos/builtin/packages/py-current/package.py @@ -12,6 +12,6 @@ class PyCurrent(PythonPackage): homepage = "http://github.com/xflr6/current" url = "https://pypi.io/packages/source/c/current/current-0.3.1.zip" - version('0.3.1', '6378769c64d76831e72a6930b47ced27') + version('0.3.1', sha256='207613dc19a6cc8e1a756f26e416733c8f82a70e4ae81103d22f483aae6492a8') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cutadapt/package.py b/var/spack/repos/builtin/packages/py-cutadapt/package.py index bcf0592910e..167a2b2175c 100644 --- a/var/spack/repos/builtin/packages/py-cutadapt/package.py +++ b/var/spack/repos/builtin/packages/py-cutadapt/package.py @@ -16,7 +16,7 @@ class PyCutadapt(PythonPackage): git = "https://github.com/marcelm/cutadapt.git" version('2.5', sha256='ced79e49b93e922e579d0bb9d21298dcb2d7b7b1ea721feed484277e08b1660b') - version('1.13', '2d2d14e0c20ad53d7d84b57bc3e63b4c') + version('1.13', sha256='aa9f2c1f33dc081fe94f42b1250e4382b8fb42cabbf6e70a76ff079f211d5fc0') depends_on('python@2.7:', type=('build', 'run'), when='@1.13') depends_on('python@3.4:', type=('build', 'run'), when='@2.5:') diff --git a/var/spack/repos/builtin/packages/py-cvxopt/package.py b/var/spack/repos/builtin/packages/py-cvxopt/package.py index eda664b855e..b12dcf4c875 100644 --- a/var/spack/repos/builtin/packages/py-cvxopt/package.py +++ b/var/spack/repos/builtin/packages/py-cvxopt/package.py @@ -15,7 +15,7 @@ class PyCvxopt(PythonPackage): import_modules = ['cvxopt'] - version('1.1.9', 'a56e7b23d76c2b5aaf3bea2a7c245ea7') + version('1.1.9', sha256='8f157e7397158812cabd340b68546f1baa55a486ed0aad8bc26877593dc2983d') variant('gsl', default=False, description='Use GSL random number generators for constructing random matrices') variant('fftw', default=False, description='Install the cvxopt.fftw interface to FFTW') diff --git a/var/spack/repos/builtin/packages/py-cycler/package.py b/var/spack/repos/builtin/packages/py-cycler/package.py index a9f5460abd4..9af98be2b47 100644 --- a/var/spack/repos/builtin/packages/py-cycler/package.py +++ b/var/spack/repos/builtin/packages/py-cycler/package.py @@ -12,7 +12,7 @@ class PyCycler(PythonPackage): homepage = "http://matplotlib.org/cycler/" url = "https://github.com/matplotlib/cycler/archive/v0.10.0.tar.gz" - version('0.10.0', '83dd0df7810e838b59e4dd9fa6e2d198') + version('0.10.0', sha256='b6d217635e03024196225367b1a438996dbbf0271bec488f00584f0e7dc15cfa') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index c75e151c1a4..35c1bb45499 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -23,14 +23,14 @@ class PyCython(PythonPackage): version('0.29.7', sha256='55d081162191b7c11c7bfcb7c68e913827dfd5de6ecdbab1b99dab190586c1e8') version('0.29.5', sha256='9d5290d749099a8e446422adfb0aa2142c711284800fb1eb70f595101e32cbf1') version('0.29', sha256='94916d1ede67682638d3cc0feb10648ff14dc51fb7a7f147f4fedce78eaaea97') - version('0.28.6', '3c3fb47806a4476f8e9429943439cc60') - version('0.28.3', '586f0eb70ba1fcc34334e9e10c5e68c0') - version('0.28.1', 'c549effadb52d90bdcb1affc1e5dbb97') - version('0.25.2', '642c81285e1bb833b14ab3f439964086') - version('0.23.5', '66b62989a67c55af016c916da36e7514') - version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e') - version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6') - version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') + version('0.28.6', sha256='68aa3c00ef1deccf4dd50f0201d47c268462978c12c42943bc33dc9dc816ac1b') + version('0.28.3', sha256='1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526') + version('0.28.1', sha256='152ee5f345012ca3bb7cc71da2d3736ee20f52cd8476e4d49e5e25c5a4102b12') + version('0.25.2', sha256='f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306') + version('0.23.5', sha256='0ae5a5451a190e03ee36922c4189ca2c88d1df40a89b4f224bc842d388a0d1b6') + version('0.23.4', sha256='fec42fecee35d6cc02887f1eef4e4952c97402ed2800bfe41bbd9ed1a0730d8e') + version('0.22', md5='1ae25add4ef7b63ee9b4af697300d6b6') + version('0.21.2', sha256='b01af23102143515e6138a4d5e185c2cfa588e0df61c0827de4257bac3393679') depends_on('python@:2', type=('build', 'run'), when='@:0.22') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py index 4208044c958..3e83bd08f38 100644 --- a/var/spack/repos/builtin/packages/py-dask/package.py +++ b/var/spack/repos/builtin/packages/py-dask/package.py @@ -14,8 +14,8 @@ class PyDask(PythonPackage): version('1.1.2', sha256='93b355b9a9c9a3ddbb39fab99d5759aad5cfd346f4520b87788970e80cf97256') version('1.1.0', sha256='e76088e8931b326c05a92d2658e07b94a6852b42c13a7560505a8b2354871454') - version('0.17.4', '4a7b9c5d7ddf52639b1c6b9e8a68d146') - version('0.8.1', '5dd8e3a3823b3bc62c9a6d192e2cb5b4') + version('0.17.4', sha256='c111475a3d1f8cba41c8094e1fb1831c65015390dcef0308042a11a9606a2f6d') + version('0.8.1', sha256='43deb1934cd033668e5e60b735f45c9c3ee2813f87bd51c243f975e55267fa43') variant('array', default=True, description='Install requirements for dask.array') variant('bag', default=True, description='Install requirements for dask.bag') diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py index 3c33d6a1326..f460fb4824a 100644 --- a/var/spack/repos/builtin/packages/py-dbf/package.py +++ b/var/spack/repos/builtin/packages/py-dbf/package.py @@ -13,5 +13,5 @@ class PyDbf(PythonPackage): homepage = 'https://pypi.python.org/pypi/dbf' url = "https://pypi.io/packages/source/d/dbf/dbf-0.96.005.tar.gz" - version('0.96.005', 'bce1a1ed8b454a30606e7e18dd2f8277') - version('0.94.003', '33a659ec90d7e8d8ffcd69d2189c0c6c') + version('0.96.005', sha256='d6e03f1dca40488c37cf38be9cb28b694c46cec747a064dcb0591987de58ed02') + version('0.94.003', sha256='c95b688d2f28944004368799cc6e2999d78af930a69bb2643ae098c721294444') diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py index d6c5450b670..2c85de8f028 100644 --- a/var/spack/repos/builtin/packages/py-decorator/package.py +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -14,6 +14,6 @@ class PyDecorator(PythonPackage): url = "https://pypi.io/packages/source/d/decorator/decorator-4.0.9.tar.gz" version('4.3.0', sha256='c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c') - version('4.0.9', 'f12c5651ccd707e12a0abaa4f76cd69a') + version('4.0.9', sha256='90022e83316363788a55352fe39cfbed357aa3a71d90e5f2803a35471de4bba8') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-dendropy/package.py b/var/spack/repos/builtin/packages/py-dendropy/package.py index 909d655a7b7..03ded6579e1 100644 --- a/var/spack/repos/builtin/packages/py-dendropy/package.py +++ b/var/spack/repos/builtin/packages/py-dendropy/package.py @@ -16,8 +16,8 @@ class PyDendropy(PythonPackage): homepage = "https://www.dendropy.org" url = "https://pypi.io/packages/source/d/dendropy/DendroPy-4.3.0.tar.gz" - version('4.3.0', '56c37eb7db69686c8ef3467562f4e7c5') - version('3.12.0', '6971ac9a8508b4198fd357fab0affc84') + version('4.3.0', sha256='bd5b35ce1a1c9253209b7b5f3939ac22beaa70e787f8129149b4f7ffe865d510') + version('3.12.0', sha256='38a0f36f2f7aae43ec5599408b0d0a4c80996b749589f025940d955a70fc82d4') depends_on('python@2.7:,3.4:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-descartes/package.py b/var/spack/repos/builtin/packages/py-descartes/package.py index ac5ed78fbca..f47b7846aee 100644 --- a/var/spack/repos/builtin/packages/py-descartes/package.py +++ b/var/spack/repos/builtin/packages/py-descartes/package.py @@ -13,7 +13,7 @@ class PyDescartes(PythonPackage): homepage = "https://pypi.org/project/descartes/" url = "https://pypi.io/packages/source/d/descartes/descartes-1.1.0.tar.gz" - version('1.1.0', 'ac608090f3c9f6e0ce856fdc29944096') + version('1.1.0', sha256='135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b') depends_on('py-setuptools', type='build') depends_on('py-matplotlib', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-dill/package.py b/var/spack/repos/builtin/packages/py-dill/package.py index 504ecbecb7a..49bac9470e6 100644 --- a/var/spack/repos/builtin/packages/py-dill/package.py +++ b/var/spack/repos/builtin/packages/py-dill/package.py @@ -12,13 +12,13 @@ class PyDill(PythonPackage): homepage = "https://github.com/uqfoundation/dill" url = "https://pypi.io/packages/source/d/dill/dill-0.2.6.zip" - version('0.2.6', 'f8b98b15223d23431024349f2102b4f9') - version('0.2.5', 'c9eecc32351f4934e2e67740a40397f6') - version('0.2.4', '5d10cd1cafea38a45bcd4542f2ca3adc') - version('0.2.3', '0b6c4f55da320893991cc32628a6e9be') - version('0.2.2', 'a282b81a6d289f91218bba8d07f49bd8') - version('0.2.1', 'b2354a5717da6228acae33cb13bc407b') - version('0.2', '759002d9b71605cde2a7a052dad96b5d') + version('0.2.6', sha256='6c1ccca68be483fa8c66e85a89ffc850206c26373aa77a97b83d8d0994e7f1fd') + version('0.2.5', sha256='e82b3db7b9d962911c9c2d5cf2bb4a04f43933f505a624fb7dc5f68b949f0a5c') + version('0.2.4', sha256='db68929eef0e886055d6bcd86f830141c1f653ddbf5d081c086e9d1c45efb334') + version('0.2.3', sha256='9abf049a5305cb982ebbdccf084273b108c8042b826a7606ba568fc5e063e582') + version('0.2.2', sha256='6ad223cc41614dcc8cf217e8d7a32857f13752cd0a5332580c80b9fa054ece69') + version('0.2.1', sha256='a54401bdfae419cfe1c9e0b48e9b290afccaa413d2319d9bb0fdb85c130a7923') + version('0.2', sha256='aba8d4c81c4136310e6ce333bd6f4f3ea2d53bd367e2f69c864428f260c0308c') depends_on('python@2.5:2.8,3.1:') diff --git a/var/spack/repos/builtin/packages/py-discover/package.py b/var/spack/repos/builtin/packages/py-discover/package.py index 7f7b751a1c6..d891f382153 100644 --- a/var/spack/repos/builtin/packages/py-discover/package.py +++ b/var/spack/repos/builtin/packages/py-discover/package.py @@ -12,4 +12,4 @@ class PyDiscover(PythonPackage): homepage = "https://pypi.python.org/pypi/discover" url = "https://pypi.io/packages/source/d/discover/discover-0.4.0.tar.gz" - version('0.4.0', '30bb643af4f5ea47fff572b5c346207d') + version('0.4.0', sha256='05c3fa9199e57d4b16fb653e02d65713adc1f89ef55324fb0c252b1cf9070d79') diff --git a/var/spack/repos/builtin/packages/py-dlcpar/package.py b/var/spack/repos/builtin/packages/py-dlcpar/package.py index d62bd4377d2..e3fe23f15ab 100644 --- a/var/spack/repos/builtin/packages/py-dlcpar/package.py +++ b/var/spack/repos/builtin/packages/py-dlcpar/package.py @@ -13,6 +13,6 @@ class PyDlcpar(PythonPackage): homepage = "https://www.cs.hmc.edu/~yjw/software/dlcpar/" url = "https://www.cs.hmc.edu/~yjw/software/dlcpar/pub/sw/dlcpar-1.0.tar.gz" - version('1.0', '0bf684436df3554e46d5e992349eeaec') + version('1.0', sha256='774319caba0f10d1230b8f85b8a147eda5871f9a316d7b3381b91c1bde97aa0a') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-docopt/package.py b/var/spack/repos/builtin/packages/py-docopt/package.py index 6998396852a..217b95cb8fa 100644 --- a/var/spack/repos/builtin/packages/py-docopt/package.py +++ b/var/spack/repos/builtin/packages/py-docopt/package.py @@ -14,6 +14,6 @@ class PyDocopt(PythonPackage): import_modules = ['docopt'] - version('0.6.2', '4bc74561b37fad5d3e7d037f82a4c3b1') + version('0.6.2', sha256='49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-docutils/package.py b/var/spack/repos/builtin/packages/py-docutils/package.py index f2863111f99..a61bf54c23e 100644 --- a/var/spack/repos/builtin/packages/py-docutils/package.py +++ b/var/spack/repos/builtin/packages/py-docutils/package.py @@ -28,5 +28,5 @@ class PyDocutils(PythonPackage): ] version('0.14', sha256='51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274') - version('0.13.1', 'ea4a893c633c788be9b8078b6b305d53') - version('0.12', '4622263b62c5c771c03502afa3157768') + version('0.13.1', sha256='718c0f5fb677be0f34b781e04241c4067cbd9327b66bdd8e763201130f5175be') + version('0.12', sha256='c7db717810ab6965f66c8cf0398a98c9d8df982da39b4cd7f162911eb89596fa') diff --git a/var/spack/repos/builtin/packages/py-doxypy/package.py b/var/spack/repos/builtin/packages/py-doxypy/package.py index 8bd651f09d4..2c4c7911758 100644 --- a/var/spack/repos/builtin/packages/py-doxypy/package.py +++ b/var/spack/repos/builtin/packages/py-doxypy/package.py @@ -12,6 +12,6 @@ class PyDoxypy(PythonPackage): homepage = "https://pypi.python.org/pypi/doxypy" url = "https://pypi.io/packages/source/d/doxypy/doxypy-0.3.tar.gz" - version('0.3', '3b52289e0962d31b92af8be0eef8cbb2') + version('0.3', sha256='55d621b0edebd9e2a58a266c0a1d086fc9892de8e07e04dfbb93880a7ae91f00') depends_on('python@:2.8') diff --git a/var/spack/repos/builtin/packages/py-doxypypy/package.py b/var/spack/repos/builtin/packages/py-doxypypy/package.py index ca8409b6ee5..cb2b719ca98 100644 --- a/var/spack/repos/builtin/packages/py-doxypypy/package.py +++ b/var/spack/repos/builtin/packages/py-doxypypy/package.py @@ -15,6 +15,6 @@ class PyDoxypypy(PythonPackage): homepage = "https://github.com/Feneric/doxypypy" url = "https://pypi.io/packages/source/d/doxypypy/doxypypy-0.8.8.6.tar.gz" - version('0.8.8.6', '6b3fe4eff5d459400071b626333fe15f') + version('0.8.8.6', sha256='627571455c537eb91d6998d95b32efc3c53562b2dbadafcb17e49593e0dae01b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-dryscrape/package.py b/var/spack/repos/builtin/packages/py-dryscrape/package.py index 93991007093..3f56b291cf6 100644 --- a/var/spack/repos/builtin/packages/py-dryscrape/package.py +++ b/var/spack/repos/builtin/packages/py-dryscrape/package.py @@ -15,7 +15,7 @@ class PyDryscrape(PythonPackage): git = "https://github.com/niklasb/dryscrape.git" version('develop', branch='master') - version('1.0', '267e380a8efaf9cd8fd94de1639d3198') + version('1.0', sha256='a99858786434947266cb81d5634cb1722de48aaf6b9cdffda15b7cd4a8e07340') depends_on('py-lxml', type=('build', 'run')) depends_on('py-webkit-server@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-dxchange/package.py b/var/spack/repos/builtin/packages/py-dxchange/package.py index f6fed8832c2..fb1cd4a5650 100644 --- a/var/spack/repos/builtin/packages/py-dxchange/package.py +++ b/var/spack/repos/builtin/packages/py-dxchange/package.py @@ -16,7 +16,7 @@ class PyDxchange(PythonPackage): import_modules = ['dxchange'] - version('0.1.2', '36633bb67a1e7d1fb60c2300adbcbab3') + version('0.1.2', sha256='d005b036b6323d0dffd5944c3da0b8a90496d96277654e72b53717058dd5fd87') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-dxfile/package.py b/var/spack/repos/builtin/packages/py-dxfile/package.py index 7adc25758e8..7dc3ad7ae39 100644 --- a/var/spack/repos/builtin/packages/py-dxfile/package.py +++ b/var/spack/repos/builtin/packages/py-dxfile/package.py @@ -15,7 +15,7 @@ class PyDxfile(PythonPackage): import_modules = ['dxfile'] - version('0.4', '0402cd38aefdfd5ce92feb43dda18947') + version('0.4', sha256='b7729eebdc7c99a66a8b339fc10019aa8565e02bd12708540fb3f47935f004c7') depends_on('py-setuptools', type='build') depends_on('py-h5py', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py index 8719f6924f3..29325ea39d2 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py @@ -16,7 +16,7 @@ class PyEasybuildEasyblocks(PythonPackage): maintainers = ['boegel'] version('4.0.0', sha256='a0fdef6c33c786e323bde1b28bab942fd8e535c26842877d705e692e85b31b07') - version('3.1.2', 'be08da30c07e67ed3e136e8d38905fbc') + version('3.1.2', sha256='5dcea0d612c5da92815f2c99a591dd2843fe9d76f4c0f4ff4a245d43c39001d8') depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py index cc610917ffa..6f7c61e583e 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py @@ -16,7 +16,7 @@ class PyEasybuildEasyconfigs(PythonPackage): maintainers = ['boegel'] version('4.0.0', sha256='90d4e8f8abb11e7ae2265745bbd1241cd69d02570e9b4530175c4b2e2aba754e') - version('3.1.2', '13a4a97fe8a5b9a94f885661cf497d13') + version('3.1.2', sha256='621d514bacd9a0a9a3d35b40dcc448533ffc545b2c79f50d303822778bcc4aa5') depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py index 47e78c51d1e..290f584cd11 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py @@ -16,7 +16,7 @@ class PyEasybuildFramework(PythonPackage): maintainers = ['boegel'] version('4.0.0', sha256='f5c40345cc8b9b5750f53263ade6c9c3a8cd3dfab488d58f76ac61a8ca7c5a77') - version('3.1.2', '283bc5f6bdcb90016b32986d52fd04a8') + version('3.1.2', sha256='a03598478574e2982587796afdb792d78b598f4c09ebf4bec1a690c06470c00d') depends_on('python@2.6:2.8', when='@:3', type=('build', 'run')) depends_on('python@2.6:2.8,3.5:', when='@4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-editdistance/package.py b/var/spack/repos/builtin/packages/py-editdistance/package.py index f5777baa1a4..559b948ce5c 100644 --- a/var/spack/repos/builtin/packages/py-editdistance/package.py +++ b/var/spack/repos/builtin/packages/py-editdistance/package.py @@ -12,6 +12,6 @@ class PyEditdistance(PythonPackage): homepage = "https://github.com/aflc/editdistance" url = "https://pypi.io/packages/source/e/editdistance/editdistance-0.4.tar.gz" - version('0.4', '27434720ca0930a9b6974b182b6237bc') + version('0.4', sha256='c765db6f8817d38922e4a50be4b9ab338b2c539377b6fcf0bca11dea72eeb8c1') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-elasticsearch/package.py b/var/spack/repos/builtin/packages/py-elasticsearch/package.py index 2ad1014043f..8603e47c567 100644 --- a/var/spack/repos/builtin/packages/py-elasticsearch/package.py +++ b/var/spack/repos/builtin/packages/py-elasticsearch/package.py @@ -12,8 +12,8 @@ class PyElasticsearch(PythonPackage): homepage = "https://github.com/elastic/elasticsearch-py" url = "https://pypi.io/packages/source/e/elasticsearch/elasticsearch-5.2.0.tar.gz" - version('5.2.0', '66692fd1b4189039206c2fde4a4d616a') - version('2.3.0', '2550f3b51629cf1ef9636608af92c340') + version('5.2.0', sha256='45d9f8fbe0878a1b7493afeb20f4f6677a43982776ed1a77d9373e9c5b9de966') + version('2.3.0', sha256='be3080a2bf32dff0a9f9fcc1c087515a25a357645673a976d25ef77166134d81') depends_on('py-setuptools', type='build') depends_on('py-urllib3@1.8:1.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-elephant/package.py b/var/spack/repos/builtin/packages/py-elephant/package.py index 6d4ec31fc0b..56098dc4b84 100644 --- a/var/spack/repos/builtin/packages/py-elephant/package.py +++ b/var/spack/repos/builtin/packages/py-elephant/package.py @@ -13,8 +13,8 @@ class PyElephant(PythonPackage): homepage = "http://neuralensemble.org/elephant" url = "https://pypi.io/packages/source/e/elephant/elephant-0.3.0.tar.gz" - version('0.4.1', '0e6214c96cae6ce777e4b3cf29bbdaa9') - version('0.3.0', '84e69e6628fd617af469780c30d2da6c') + version('0.4.1', sha256='86b21a44cbacdc09a6ba6f51738dcd5b42ecd553d73acb29f71a0be7c82eac81') + version('0.3.0', sha256='747251ccfb5820bdead6391411b5faf205b4ddf3ababaefe865f50b16540cfef') variant('doc', default=False, description='Build the documentation') variant('pandas', default=True, description='Build with pandas') diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py index 7aec8329ab7..1c263225989 100644 --- a/var/spack/repos/builtin/packages/py-emcee/package.py +++ b/var/spack/repos/builtin/packages/py-emcee/package.py @@ -14,7 +14,7 @@ class PyEmcee(PythonPackage): url = "https://pypi.io/packages/source/e/emcee/emcee-2.2.1.tar.gz" version('2.2.1', sha256='b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172') - version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7') + version('2.1.0', sha256='5ce1039a3d78fb9e7d53fcd768517585c5998193743bfcfaac407927d375ca63') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-entrypoints/package.py b/var/spack/repos/builtin/packages/py-entrypoints/package.py index e1937ba1062..0ea816d3f86 100644 --- a/var/spack/repos/builtin/packages/py-entrypoints/package.py +++ b/var/spack/repos/builtin/packages/py-entrypoints/package.py @@ -14,8 +14,8 @@ class PyEntrypoints(PythonPackage): import_modules = ['entrypoints'] - version('0.3', 'c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451') - version('0.2.3', '0d3ad1b0130d91e3596ef3a59f25a56c') + version('0.3', sha256='c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451') + version('0.2.3', sha256='d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f') depends_on('python@2.7:', type=('build', 'run')) depends_on('py-configparser', when='^python@:2.8', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-enum34/package.py b/var/spack/repos/builtin/packages/py-enum34/package.py index 50c9f861d5f..ee2d3e2ac6b 100644 --- a/var/spack/repos/builtin/packages/py-enum34/package.py +++ b/var/spack/repos/builtin/packages/py-enum34/package.py @@ -12,7 +12,7 @@ class PyEnum34(PythonPackage): homepage = "https://pypi.python.org/pypi/enum34" url = "https://pypi.io/packages/source/e/enum34/enum34-1.1.6.tar.gz" - version('1.1.6', '5f13a0841a61f7fc295c514490d120d0') + version('1.1.6', sha256='8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1') depends_on('python') conflicts('python@3.4:') diff --git a/var/spack/repos/builtin/packages/py-epydoc/package.py b/var/spack/repos/builtin/packages/py-epydoc/package.py index bae4dd235d8..1cd9f83a01d 100644 --- a/var/spack/repos/builtin/packages/py-epydoc/package.py +++ b/var/spack/repos/builtin/packages/py-epydoc/package.py @@ -12,4 +12,4 @@ class PyEpydoc(PythonPackage): homepage = "https://pypi.python.org/pypi/epydoc" url = "https://pypi.io/packages/source/e/epydoc/epydoc-3.0.1.tar.gz" - version('3.0.1', '36407974bd5da2af00bf90ca27feeb44') + version('3.0.1', sha256='c81469b853fab06ec42b39e35dd7cccbe9938dfddef324683d89c1e5176e48f2') diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py index 053119c3e42..6b528439b03 100644 --- a/var/spack/repos/builtin/packages/py-espressopp/package.py +++ b/var/spack/repos/builtin/packages/py-espressopp/package.py @@ -19,9 +19,9 @@ class PyEspressopp(CMakePackage): version('develop', branch='master') version('2.0.2', sha256='8cf4525bca06426379f5b9fbb8cc2603f559d28a2e74d1d7694df963b8f3dc6c') - version('1.9.5', '13a93c30b07132b5e5fa0d828aa17d79') - version('1.9.4.1', '0da74a6d4e1bfa6a2a24fca354245a4f') - version('1.9.4', 'f2a27993a83547ad014335006eea74ea') + version('1.9.5', sha256='8093f1a226f9fee8fb37c401767439a29ff3656dede3a44b4160169fc90d4d91') + version('1.9.4.1', md5='0da74a6d4e1bfa6a2a24fca354245a4f') + version('1.9.4', md5='f2a27993a83547ad014335006eea74ea') variant('ug', default=False, description='Build user guide') variant('pdf', default=False, description='Build user guide in pdf format') diff --git a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py index c43ef19407a..59594033eb4 100644 --- a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py +++ b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py @@ -12,6 +12,6 @@ class PyEtXmlfile(PythonPackage): homepage = "https://bitbucket.org/openpyxl/et_xmlfile" url = "https://pypi.io/packages/source/e/et_xmlfile/et_xmlfile-1.0.1.tar.gz" - version('1.0.1', 'f47940fd9d556375420b2e276476cfaf') + version('1.0.1', sha256='614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-eventlet/package.py b/var/spack/repos/builtin/packages/py-eventlet/package.py index 0a8460fe6b0..a0e20e15e6d 100644 --- a/var/spack/repos/builtin/packages/py-eventlet/package.py +++ b/var/spack/repos/builtin/packages/py-eventlet/package.py @@ -12,7 +12,7 @@ class PyEventlet(PythonPackage): homepage = "https://github.com/eventlet/eventlet" url = "https://github.com/eventlet/eventlet/releases/download/v0.22.0/eventlet-0.22.0.tar.gz" - version('0.22.0', 'a1199cecd44d7ce2ea624ac6c21db877') + version('0.22.0', sha256='6d22464f448fdf144a9d566c157299d686bbe324554dd7729df9ccd05ca66439') depends_on('py-setuptools', type='build') depends_on('py-greenlet@0.3:') diff --git a/var/spack/repos/builtin/packages/py-execnet/package.py b/var/spack/repos/builtin/packages/py-execnet/package.py index 2fb64454c75..7c44ca40f79 100644 --- a/var/spack/repos/builtin/packages/py-execnet/package.py +++ b/var/spack/repos/builtin/packages/py-execnet/package.py @@ -14,7 +14,7 @@ class PyExecnet(PythonPackage): homepage = "http://codespeak.net/execnet" url = "https://pypi.io/packages/source/e/execnet/execnet-1.4.1.tar.gz" - version('1.4.1', '0ff84b6c79d0dafb7e2971629c4d127a') + version('1.4.1', sha256='f66dd4a7519725a1b7e14ad9ae7d3df8e09b2da88062386e08e941cafc0ef3e6') depends_on('py-setuptools', type='build') depends_on('py-setuptools-scm', type='build') diff --git a/var/spack/repos/builtin/packages/py-fastaindex/package.py b/var/spack/repos/builtin/packages/py-fastaindex/package.py index 3a3d465075c..47e896d2a4d 100644 --- a/var/spack/repos/builtin/packages/py-fastaindex/package.py +++ b/var/spack/repos/builtin/packages/py-fastaindex/package.py @@ -13,6 +13,6 @@ class PyFastaindex(PythonPackage): homepage = "https://github.com/lpryszcz/FastaIndex" url = "https://pypi.io/packages/source/F/FastaIndex/FastaIndex-0.11rc7.tar.gz" - version('0.11rc7', '882c973d968d9db596edfd0fbb07e3a8') + version('0.11rc7', sha256='c130a2146bb178ea4f9d228e0d360787046ab4cb0ab53b5b43711dd57e31aff7') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-fasteners/package.py b/var/spack/repos/builtin/packages/py-fasteners/package.py index b22631e195c..0a5299ea7fa 100644 --- a/var/spack/repos/builtin/packages/py-fasteners/package.py +++ b/var/spack/repos/builtin/packages/py-fasteners/package.py @@ -12,7 +12,7 @@ class PyFasteners(PythonPackage): homepage = "https://github.com/harlowja/fasteners" url = "https://pypi.io/packages/source/f/fasteners/fasteners-0.14.1.tar.gz" - version('0.14.1', 'fcb13261c9b0039d9b1c4feb9bc75e04') + version('0.14.1', sha256='427c76773fe036ddfa41e57d89086ea03111bbac57c55fc55f3006d027107e18') depends_on('py-setuptools', type='build') depends_on('py-monotonic@0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-faststructure/package.py b/var/spack/repos/builtin/packages/py-faststructure/package.py index bf6a57de317..100f8adc05a 100644 --- a/var/spack/repos/builtin/packages/py-faststructure/package.py +++ b/var/spack/repos/builtin/packages/py-faststructure/package.py @@ -13,7 +13,7 @@ class PyFaststructure(PythonPackage): homepage = "https://github.com/rajanil/fastStructure" url = "https://github.com/rajanil/fastStructure/archive/v1.0.tar.gz" - version('1.0', '5cbb76e7d49e27a57046ab641b666f97') + version('1.0', sha256='f1bfb24bb5ecd108bc3a90145fad232012165c1e60608003f1c87d200f867b81') depends_on('py-cython', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-filelock/package.py b/var/spack/repos/builtin/packages/py-filelock/package.py index 827716a722d..b82459a2568 100644 --- a/var/spack/repos/builtin/packages/py-filelock/package.py +++ b/var/spack/repos/builtin/packages/py-filelock/package.py @@ -14,13 +14,13 @@ class PyFilelock(PythonPackage): homepage = "https://github.com/benediktschmitt/py-filelock" url = "https://github.com/benediktschmitt/py-filelock/archive/v3.0.4.tar.gz" - version('3.0.4', '3cafce82375c3b635f2c872acaf3a00b') - version('3.0.3', 'e4bd69f15ebcc6d5a3d684cea3694840') - version('3.0.1', 'cbf41ad3d89c89e2b752bc85b501dff6') - version('3.0.0', '29d199e8998ac324d0d7cab7aa814943') - version('2.0.13', 'cdd0c4f3e905fbab76d1202ce8e8b454') - version('2.0.12', 'fffda24b6cfd459ea5d2d5c335e949e2') - version('2.0.11', '9e8cbbe18494d12647050bb32a7e624d') - version('2.0.10', '1791e72bb19e503fdd0f365fb8ce2a4d') - version('2.0.9', 'b0269e7f77a090cc0d5fc9cf5fbe6ac2') - version('2.0.8', '939ec6d4e2ecdc353a1f27fc452d8e8c') + version('3.0.4', sha256='8521523f3eafb7bbbdd0a5a7a15ddb8076ea6f106385bbfc4c9d055db2585214') + version('3.0.3', sha256='8e1b1ad91de70e091de381ab8705b37e41d240c211d8d888dcf1d0e31d6274bb') + version('3.0.1', sha256='533107ab60de691030b7e90105ab38c8b0d60d52de382fe5302819cba95561f8') + version('3.0.0', sha256='f41bed24b280b2fd11b2f12fecdfd2a21e5f9babc4e89929b316946288fa195c') + version('2.0.13', sha256='85e2a001693c2995854e42783a8c11994d143f8ba9c92d31f573476a22a5b3b3') + version('2.0.12', sha256='3b67cddd8c405c27b9118a1383d5257b5b6e066d3a9a30ab03d42b4dc6828cbb') + version('2.0.11', sha256='97c36de6e0c2eaed6638a9575a96d176e4ec2820b888f3da3194bbb852f86c5e') + version('2.0.10', sha256='f15d99cfa3e89072d7709bf3b5d354cf1c9096cffdb1127c4dbff1ca4a89cb84') + version('2.0.9', sha256='86d8e95afe77bc92a94c2e0db2b452c067b453b017fd78edfbb679b199dadbd5') + version('2.0.8', sha256='4f69474338ebf6ead2e0c2e91c5f94a25af8125d307f539db10886a19e2e2628') diff --git a/var/spack/repos/builtin/packages/py-fiscalyear/package.py b/var/spack/repos/builtin/packages/py-fiscalyear/package.py index 067f3278738..c4ffdbdbe64 100644 --- a/var/spack/repos/builtin/packages/py-fiscalyear/package.py +++ b/var/spack/repos/builtin/packages/py-fiscalyear/package.py @@ -20,7 +20,7 @@ class PyFiscalyear(PythonPackage): import_modules = ['fiscalyear'] version('master', branch='master') - version('0.1.0', '30e36b259f3e72e4929abbf259335742') + version('0.1.0', sha256='3fde4a12eeb72da446beb487e078adf1223a92d130520e589b82d7d1509701a2') depends_on('python@2.5:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py index 8a31d4ca3d9..3c3292d09b2 100644 --- a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py +++ b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py @@ -14,7 +14,7 @@ class PyFlake8Polyfill(PythonPackage): homepage = "https://pypi.org/project/flake8-polyfill/" url = "https://files.pythonhosted.org/packages/e6/67/1c26634a770db5c442e361311bee73cb3a177adb2eb3f7af8953cfd9f553/flake8-polyfill-1.0.2.tar.gz" - version('1.0.2', 'e44b087597f6da52ec6393a709e7108b2905317d0c0b744cdca6208e670d8eda') + version('1.0.2', sha256='e44b087597f6da52ec6393a709e7108b2905317d0c0b744cdca6208e670d8eda') extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)') depends_on('py-flake8', type='run') diff --git a/var/spack/repos/builtin/packages/py-flake8/package.py b/var/spack/repos/builtin/packages/py-flake8/package.py index 269fd841b41..e447b91b86c 100644 --- a/var/spack/repos/builtin/packages/py-flake8/package.py +++ b/var/spack/repos/builtin/packages/py-flake8/package.py @@ -15,9 +15,9 @@ class PyFlake8(PythonPackage): version('3.7.8', sha256='201720797dc9691dd349819994e4a0bc281b70ee2ff77b0c928bb1d3c5aa9810') version('3.7.7', sha256='b3f76b02351008dc772276e74b09dd3d4b5c567ff8c6ab573352cb8fd7007444') - version('3.5.0', '4e312803bbd8e4a1e566ffac887ae647') - version('3.0.4', 'cf2a7d8c92070f7b62253404ffb54df7') - version('2.5.4', '366dd1de6c300254c830b81e66979f06') + version('3.5.0', sha256='60ffe2fdacce4ebe7cadc30f310cf1edfd8ff654ef79525d90cf0756e69de44e') + version('3.0.4', sha256='87a2b642900a569fc2f27ab3b79573e0d02d2fee7445c6abab84eb33dcb60365') + version('2.5.4', sha256='ce03cc1acbe1726775ca57b40fab1d177550debb2f2f6b7a3c860541f3971cf5') extends('python', ignore='bin/(pyflakes|pycodestyle)') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-flask-compress/package.py b/var/spack/repos/builtin/packages/py-flask-compress/package.py index 67f6f597790..27914ccd820 100644 --- a/var/spack/repos/builtin/packages/py-flask-compress/package.py +++ b/var/spack/repos/builtin/packages/py-flask-compress/package.py @@ -13,7 +13,7 @@ class PyFlaskCompress(PythonPackage): homepage = "https://github.com/libwilliam/flask-compress" url = "https://pypi.io/packages/source/F/Flask-Compress/Flask-Compress-1.4.0.tar.gz" - version('1.4.0', 'd997f73e4ed5793ec526c135aa765e15') + version('1.4.0', sha256='468693f4ddd11ac6a41bca4eb5f94b071b763256d54136f77957cfee635badb3') depends_on('py-setuptools', type='build') depends_on('py-flask@0.9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-flask-socketio/package.py b/var/spack/repos/builtin/packages/py-flask-socketio/package.py index 9d3569b9354..b2a99926bfc 100644 --- a/var/spack/repos/builtin/packages/py-flask-socketio/package.py +++ b/var/spack/repos/builtin/packages/py-flask-socketio/package.py @@ -17,7 +17,7 @@ class PyFlaskSocketio(PythonPackage): homepage = "https://flask-socketio.readthedocs.io" url = "https://pypi.io/packages/source/F/Flask-SocketIO/Flask-SocketIO-2.9.6.tar.gz" - version('2.9.6', 'bca83faf38355bd91911f2f140f9b50f') + version('2.9.6', sha256='f49edfd3a44458fbb9f7a04a57069ffc0c37f000495194f943a25d370436bb69') depends_on('py-setuptools', type='build') depends_on('py-flask@0.9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-flask/package.py b/var/spack/repos/builtin/packages/py-flask/package.py index 24c08b86714..bb7f5781837 100644 --- a/var/spack/repos/builtin/packages/py-flask/package.py +++ b/var/spack/repos/builtin/packages/py-flask/package.py @@ -12,9 +12,9 @@ class PyFlask(PythonPackage): homepage = "http://github.com/pallets/flask" url = "https://pypi.io/packages/source/F/Flask/Flask-0.11.1.tar.gz" - version('0.12.2', '97278dfdafda98ba7902e890b0289177') - version('0.12.1', '76e9fee5c3afcf4634b9baf96c578207') - version('0.11.1', 'd2af95d8fe79cf7da099f062dd122a08') + version('0.12.2', sha256='49f44461237b69ecd901cc7ce66feea0319b9158743dd27a2899962ab214dac1') + version('0.12.1', sha256='9dce4b6bfbb5b062181d3f7da8f727ff70c1156cbb4024351eafd426deb5fb88') + version('0.11.1', sha256='b4713f2bfb9ebc2966b8a49903ae0d3984781d5c878591cf2f7b484d28756b0e') depends_on('py-setuptools', type='build') depends_on('py-werkzeug@0.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-flexx/package.py b/var/spack/repos/builtin/packages/py-flexx/package.py index 76313fd9b29..965986549c1 100644 --- a/var/spack/repos/builtin/packages/py-flexx/package.py +++ b/var/spack/repos/builtin/packages/py-flexx/package.py @@ -12,7 +12,7 @@ class PyFlexx(PythonPackage): homepage = "http://flexx.readthedocs.io" url = "https://pypi.io/packages/source/f/flexx/flexx-0.4.1.zip" - version('0.4.1', '7138a378aa68d781212c4b2cfb6ddfcb') + version('0.4.1', sha256='54be868f01d943018d0907821f2562f6eb31c568b3932abfd8518f75c29b8be1') depends_on('py-setuptools', type='build') depends_on('py-tornado', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-fn/package.py b/var/spack/repos/builtin/packages/py-fn/package.py index 1bf7938a6b6..95cf3d4adfb 100644 --- a/var/spack/repos/builtin/packages/py-fn/package.py +++ b/var/spack/repos/builtin/packages/py-fn/package.py @@ -13,6 +13,6 @@ class PyFn(PythonPackage): homepage = "https://github.com/fnpy/fn.py" url = "https://github.com/fnpy/fn.py/archive/v0.5.2.tar.gz" - version('0.5.2', '48c168fe335e31fc6152ea0944741be2') + version('0.5.2', sha256='fda2253d792867a79514496932630622df9340f214a2f4b2d597b60a8cc3d96b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-fparser/package.py b/var/spack/repos/builtin/packages/py-fparser/package.py index 0025dc76e50..b88ed738457 100644 --- a/var/spack/repos/builtin/packages/py-fparser/package.py +++ b/var/spack/repos/builtin/packages/py-fparser/package.py @@ -15,8 +15,8 @@ class PyFparser(PythonPackage): git = "https://github.com/stfc/fparser.git" version('develop', branch='master') - version('0.0.6', '15553fde76b4685fa8edb0a5472b1b53d308c3b8') - version('0.0.5', '14630afdb8c8bd025e5504c5ab19d133aa8cf8c7') + version('0.0.6', sha256='6ced61573257d11037d25c02d5f0ea92ca9bf1783018bf5f0de30d245ae631ac') + version('0.0.5', sha256='7668b331b9423d15353d502ab26d1d561acd5247882dab672f1e45565dabaf08') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-fsspec/package.py b/var/spack/repos/builtin/packages/py-fsspec/package.py index 3a781a7bd79..7d7372f66a6 100644 --- a/var/spack/repos/builtin/packages/py-fsspec/package.py +++ b/var/spack/repos/builtin/packages/py-fsspec/package.py @@ -12,7 +12,7 @@ class PyFsspec(PythonPackage): homepage = "https://github.com/intake/filesystem_spec" url = "https://github.com/intake/filesystem_spec/archive/0.4.4.tar.gz" - version('0.4.4', '27dfc3dab37d5c037683c7a3eaf7acd8b24ee56e4ce3edb14af54bdb43973d43') + version('0.4.4', sha256='27dfc3dab37d5c037683c7a3eaf7acd8b24ee56e4ce3edb14af54bdb43973d43') depends_on('python@3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py index f97c51b0945..935b31bbc25 100644 --- a/var/spack/repos/builtin/packages/py-funcsigs/package.py +++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py @@ -14,8 +14,8 @@ class PyFuncsigs(PythonPackage): import_modules = ['funcsigs'] - version('1.0.2', '7e583285b1fb8a76305d6d68f4ccc14e') - version('0.4', 'fb1d031f284233e09701f6db1281c2a5') + version('1.0.2', sha256='a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50') + version('0.4', sha256='d83ce6df0b0ea6618700fe1db353526391a8a3ada1b7aba52fed7a61da772033') depends_on('py-setuptools@17.1:', type='build') depends_on('py-unittest2', type='test') diff --git a/var/spack/repos/builtin/packages/py-functools32/package.py b/var/spack/repos/builtin/packages/py-functools32/package.py index 5776dba230a..9662cbea441 100644 --- a/var/spack/repos/builtin/packages/py-functools32/package.py +++ b/var/spack/repos/builtin/packages/py-functools32/package.py @@ -13,4 +13,4 @@ class PyFunctools32(PythonPackage): homepage = "https://github.com/MiCHiLU/python-functools32" url = "https://pypi.io/packages/source/f/functools32/functools32-3.2.3-2.tar.gz" - version('3.2.3-2', '09f24ffd9af9f6cd0f63cb9f4e23d4b2') + version('3.2.3-2', sha256='f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d') diff --git a/var/spack/repos/builtin/packages/py-future/package.py b/var/spack/repos/builtin/packages/py-future/package.py index 64a93a1d519..0394a0bd01c 100644 --- a/var/spack/repos/builtin/packages/py-future/package.py +++ b/var/spack/repos/builtin/packages/py-future/package.py @@ -14,8 +14,8 @@ class PyFuture(PythonPackage): version('0.17.1', sha256='67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8') version('0.17.0', sha256='eb6d4df04f1fb538c99f69c9a28b255d1ee4e825d479b9c62fc38c0cf38065a4') - version('0.16.0', '3e8e88a2bda48d54b1da7634d04760d7') - version('0.15.2', 'a68eb3c90b3b76714c5ceb8c09ea3a06') + version('0.16.0', sha256='e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb') + version('0.15.2', sha256='3d3b193f20ca62ba7d8782589922878820d0a023b885882deec830adbf639b97') depends_on('py-setuptools', type='build') depends_on('py-importlib', type=('build', 'run'), when='^python@:2.6') diff --git a/var/spack/repos/builtin/packages/py-futures/package.py b/var/spack/repos/builtin/packages/py-futures/package.py index c3fadaae638..4ed3f594165 100644 --- a/var/spack/repos/builtin/packages/py-futures/package.py +++ b/var/spack/repos/builtin/packages/py-futures/package.py @@ -12,6 +12,6 @@ class PyFutures(PythonPackage): homepage = "https://pypi.python.org/pypi/futures" url = "https://pypi.io/packages/source/f/futures/futures-3.0.5.tar.gz" - version('3.0.5', 'ced2c365e518242512d7a398b515ff95') + version('3.0.5', sha256='0542525145d5afc984c88f914a0c85c77527f65946617edb5274f72406f981df') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-gdbgui/package.py b/var/spack/repos/builtin/packages/py-gdbgui/package.py index d2a65c3b735..1142c14fb34 100644 --- a/var/spack/repos/builtin/packages/py-gdbgui/package.py +++ b/var/spack/repos/builtin/packages/py-gdbgui/package.py @@ -12,7 +12,7 @@ class PyGdbgui(PythonPackage): homepage = "https://gdbgui.com" url = "https://pypi.io/packages/source/g/gdbgui/gdbgui-0.11.2.1.tar.gz" - version('0.11.2.1', 'c15dd3f60fe372b2e93f705c7ee75f51') + version('0.11.2.1', sha256='280945a37414c31a798f68f70c1bffbedd12dfb0ce77418357e7d42b667491c7') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-flask@0.12.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-genders/package.py b/var/spack/repos/builtin/packages/py-genders/package.py index 35804247b36..13df2acdc30 100644 --- a/var/spack/repos/builtin/packages/py-genders/package.py +++ b/var/spack/repos/builtin/packages/py-genders/package.py @@ -13,7 +13,7 @@ class PyGenders(Package): homepage = "https://github.com/chaos/genders" url = "https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz" - version('1.22', '9ea59a024dcbddb85b0ed25ddca9bc8e', + version('1.22', sha256='0ff292825a29201106239c4d47d9ce4c6bda3f51c78c0463eb2634ecc337b774', url='https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz') extends('python') diff --git a/var/spack/repos/builtin/packages/py-genshi/package.py b/var/spack/repos/builtin/packages/py-genshi/package.py index 6c15b634b82..082ca12d1af 100644 --- a/var/spack/repos/builtin/packages/py-genshi/package.py +++ b/var/spack/repos/builtin/packages/py-genshi/package.py @@ -11,8 +11,8 @@ class PyGenshi(PythonPackage): homepage = "https://genshi.edgewall.org/" url = "http://ftp.edgewall.com/pub/genshi/Genshi-0.7.tar.gz" - version('0.7', '54e64dd69da3ec961f86e686e0848a82') - version('0.6.1', '372c368c8931110b0a521fa6091742d7') - version('0.6', '604e8b23b4697655d36a69c2d8ef7187') + version('0.7', sha256='1d154402e68bc444a55bcac101f96cb4e59373100cc7a2da07fbf3e5cc5d7352') + version('0.6.1', sha256='fed947f11dbcb6792bb7161701ec3b9804055ad68c8af0ab4f0f9b25e9a18dbd') + version('0.6', sha256='32aaf76a03f88efa04143bf80700399e6d84eead818fdd19d763fd76af972a4b') depends_on("py-setuptools", type='build') diff --git a/var/spack/repos/builtin/packages/py-gevent/package.py b/var/spack/repos/builtin/packages/py-gevent/package.py index 81a83286036..66587fbee4b 100644 --- a/var/spack/repos/builtin/packages/py-gevent/package.py +++ b/var/spack/repos/builtin/packages/py-gevent/package.py @@ -12,7 +12,7 @@ class PyGevent(PythonPackage): homepage = "http://www.gevent.org" url = "https://pypi.io/packages/source/g/gevent/gevent-1.3a2.tar.gz" - version('1.3a2', '8d73a7b0ceb0ca791b22e6f7b7061e9e') + version('1.3a2', sha256='f7ab82697111ea233c7beeadf5240f669dfad9c4bbc89a3ec80a49e2c48a65bd') depends_on('py-setuptools@24.2:', type='build') depends_on('py-cython@0.27:', type='build') diff --git a/var/spack/repos/builtin/packages/py-git-review/package.py b/var/spack/repos/builtin/packages/py-git-review/package.py index bfbb448c810..d42a20e6511 100644 --- a/var/spack/repos/builtin/packages/py-git-review/package.py +++ b/var/spack/repos/builtin/packages/py-git-review/package.py @@ -12,12 +12,12 @@ class PyGitReview(PythonPackage): homepage = "http://docs.openstack.org/infra/git-review" url = "https://pypi.io/packages/source/g/git-review/git-review-1.25.0.tar.gz" - version('1.26.0', 'dec20e8a259c03fe19c9dd2362c4ec3f') - version('1.25.0', '0a061d0e23ee9b93c6212a3fe68fb7ab') - version('1.24', '145116fe58a3487c3ad1bf55538fd741') - version('1.23', 'b0023ad8c037ab710da81412194c6a3a') - version('1.22', 'e889df5838c059362e5e0d411bde9c48') - version('1.21', 'eee88bdef1aa37a55cc8becd48c6aba9') + version('1.26.0', sha256='487c3c1d7cc81d02b303a1245e432579f683695c827ad454685b3953f70f0b94') + version('1.25.0', sha256='087e0a7dc2415796a9f21c484a6f652c5410e6ba4562c36291c5399f9395a11d') + version('1.24', md5='145116fe58a3487c3ad1bf55538fd741') + version('1.23', md5='b0023ad8c037ab710da81412194c6a3a') + version('1.22', md5='e889df5838c059362e5e0d411bde9c48') + version('1.21', md5='eee88bdef1aa37a55cc8becd48c6aba9') extends('python') diff --git a/var/spack/repos/builtin/packages/py-git2/package.py b/var/spack/repos/builtin/packages/py-git2/package.py index be416060004..a4c6404ef13 100644 --- a/var/spack/repos/builtin/packages/py-git2/package.py +++ b/var/spack/repos/builtin/packages/py-git2/package.py @@ -14,7 +14,7 @@ class PyGit2(PythonPackage): homepage = "http://www.pygit2.org/" url = "https://pypi.io/packages/source/p/pygit2/pygit2-0.24.1.tar.gz" - version('0.24.1', 'dd98b6a9fded731e36ca5a40484c8545') + version('0.24.1', sha256='4d1d0196b38d6012faf0a7c45e235c208315672b6035da504566c605ba494064') extends('python') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py index 1143fdcfcf1..719d2fd01ca 100644 --- a/var/spack/repos/builtin/packages/py-gnuplot/package.py +++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py @@ -12,6 +12,6 @@ class PyGnuplot(PythonPackage): homepage = "http://gnuplot-py.sourceforge.net/" url = "http://downloads.sourceforge.net/project/gnuplot-py/Gnuplot-py/1.8/gnuplot-py-1.8.tar.gz" - version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1') + version('1.8', sha256='ab339be7847d30a8acfd616f27b5021bfde0999b7bf2d68400fbe62c53106e21') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-goatools/package.py b/var/spack/repos/builtin/packages/py-goatools/package.py index f31182fd9cd..10a3ed7a4a1 100644 --- a/var/spack/repos/builtin/packages/py-goatools/package.py +++ b/var/spack/repos/builtin/packages/py-goatools/package.py @@ -12,7 +12,7 @@ class PyGoatools(PythonPackage): homepage = "https://github.com/tanghaibao/goatools" url = "https://pypi.io/packages/source/g/goatools/goatools-0.7.11.tar.gz" - version('0.7.11', 'f2ab989ec9c4acdd80504b263c3b3188') + version('0.7.11', sha256='753c6fb8c901367aa5d64ce5ad487d82903e424cf8ec7bac50ee069b307f6364') depends_on('py-nose', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-gpaw/package.py b/var/spack/repos/builtin/packages/py-gpaw/package.py index bc26e1bf104..f17f740f3da 100644 --- a/var/spack/repos/builtin/packages/py-gpaw/package.py +++ b/var/spack/repos/builtin/packages/py-gpaw/package.py @@ -15,7 +15,7 @@ class PyGpaw(PythonPackage): url = "https://pypi.io/packages/source/g/gpaw/gpaw-1.3.0.tar.gz" version('19.8.1', sha256='79dee367d695d68409c4d69edcbad5c8679137d6715da403f6c2500cb2178c2a') - version('1.3.0', '82e8c80e637696248db00b5713cdffd1') + version('1.3.0', sha256='cf601c69ac496421e36111682bcc1d23da2dba2aabc96be51accf73dea30655c') variant('mpi', default=True, description='Build with MPI support') variant('scalapack', default=True, diff --git a/var/spack/repos/builtin/packages/py-greenlet/package.py b/var/spack/repos/builtin/packages/py-greenlet/package.py index 2be7f701464..d37e061254b 100644 --- a/var/spack/repos/builtin/packages/py-greenlet/package.py +++ b/var/spack/repos/builtin/packages/py-greenlet/package.py @@ -12,4 +12,4 @@ class PyGreenlet(PythonPackage): homepage = "https://github.com/python-greenlet/greenlet" url = "https://pypi.io/packages/source/g/greenlet/greenlet-0.4.13.tar.gz" - version('0.4.13', '6e0b9dd5385f81d478451ec8ed1d62b3') + version('0.4.13', sha256='0fef83d43bf87a5196c91e73cb9772f945a4caaff91242766c5916d1dd1381e4') diff --git a/var/spack/repos/builtin/packages/py-griddataformats/package.py b/var/spack/repos/builtin/packages/py-griddataformats/package.py index 0df602014cc..e91aec673c6 100644 --- a/var/spack/repos/builtin/packages/py-griddataformats/package.py +++ b/var/spack/repos/builtin/packages/py-griddataformats/package.py @@ -15,7 +15,7 @@ class PyGriddataformats(PythonPackage): homepage = "http://www.mdanalysis.org/GridDataFormats" url = "https://pypi.io/packages/source/G/GridDataFormats/GridDataFormats-0.3.3.tar.gz" - version('0.3.3', '5c83d3bdd421eebcee10111942c5a21f') + version('0.3.3', sha256='938f0efcb3bc2f58ec85048b933942da8a52c134170acc97cb095f09d3698fbd') depends_on('python@2.7:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-guidata/package.py b/var/spack/repos/builtin/packages/py-guidata/package.py index 80108cd400d..c3b2f96cca6 100644 --- a/var/spack/repos/builtin/packages/py-guidata/package.py +++ b/var/spack/repos/builtin/packages/py-guidata/package.py @@ -13,7 +13,7 @@ class PyGuidata(PythonPackage): homepage = "https://github.com/PierreRaybaut/guidata" url = "https://pypi.io/packages/source/g/guidata/guidata-1.7.5.zip" - version('1.7.5', '915188c02ad3c89951ee260db65d84a7') + version('1.7.5', sha256='531d5e9ea784120c2e14212cfbd9c63f78fc7a77bcb9c5497be984584ee455c0') depends_on('py-setuptools', type='build') depends_on('py-pyqt4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-guiqwt/package.py b/var/spack/repos/builtin/packages/py-guiqwt/package.py index 32cfe2e07d7..b7ca220b127 100644 --- a/var/spack/repos/builtin/packages/py-guiqwt/package.py +++ b/var/spack/repos/builtin/packages/py-guiqwt/package.py @@ -13,7 +13,7 @@ class PyGuiqwt(PythonPackage): homepage = "https://github.com/PierreRaybaut/guiqwt" url = "https://pypi.io/packages/source/g/guiqwt/guiqwt-3.0.2.zip" - version('3.0.2', 'b49cd9706f56eb5d519390ba709d8c8c') + version('3.0.2', sha256='387c0b9430624ecc87931e33ff963785194968c9f848337eb050eca48c6cd858') depends_on('py-setuptools', type='build') depends_on('py-numpy@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index c207f3cec1d..d3c67a813e3 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -16,12 +16,12 @@ class PyH5py(PythonPackage): import_modules = ['h5py', 'h5py._hl'] version('2.9.0', sha256='9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002') - version('2.8.0', 'ece4f358e69fc8a416f95953b91bc373') - version('2.7.1', 'da630aebe3ab9fa218ac405a218e95e0') - version('2.7.0', 'f62937f40f68d3b128b3941be239dd93') - version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4') - version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74') - version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758') + version('2.8.0', sha256='e626c65a8587921ebc7fb8d31a49addfdd0b9a9aa96315ea484c09803337b955') + version('2.7.1', sha256='180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc') + version('2.7.0', sha256='79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310') + version('2.6.0', sha256='b2afc35430d5e4c3435c996e4f4ea2aba1ea5610e2d2f46c9cae9f785e33c435') + version('2.5.0', sha256='9833df8a679e108b561670b245bcf9f3a827b10ccb3a5fa1341523852cfac2f6') + version('2.4.0', sha256='faaeadf4b8ca14c054b7568842e0d12690de7d5d68af4ecce5d7b8fc104d8e60') variant('mpi', default=True, description='Build with MPI support') diff --git a/var/spack/repos/builtin/packages/py-hepdata-validator/package.py b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py index 34add50b353..6df139ea420 100644 --- a/var/spack/repos/builtin/packages/py-hepdata-validator/package.py +++ b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py @@ -12,10 +12,10 @@ class PyHepdataValidator(PythonPackage): homepage = "https://github.com/hepdata/hepdata-validator" url = "https://pypi.io/packages/source/h/hepdata_validator/hepdata_validator-0.1.16.tar.gz" - version('0.1.16', '62e80db7425a4a48050af29e05295e0d') - version('0.1.15', 'e29aa75780b9963997e79f572ca0209f') - version('0.1.14', '386a2440f23fda7d877764d120bf61fb') - version('0.1.8', '5bf388a507a857afbe0deba0857125c7') + version('0.1.16', sha256='3d7f725328ecdbb66826bff2e48a40a1d9234249859c8092ca0e92be7fb78111') + version('0.1.15', sha256='1030654b1a1cfc387c2759f8613f033da467c8182dc027e181227aeb52854bb2') + version('0.1.14', sha256='d1596741fb26be234c2adb6972306908f09b049dc670d8312cf2636f1a615a52') + version('0.1.8', sha256='08686563e0130c5dd6d9fb8d5c7bf5a2617a637b105a42f7106b96a31eaffa61') depends_on('py-setuptools', type='build') depends_on('py-jsonschema', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-html2text/package.py b/var/spack/repos/builtin/packages/py-html2text/package.py index 4458ba90917..5d01275747c 100644 --- a/var/spack/repos/builtin/packages/py-html2text/package.py +++ b/var/spack/repos/builtin/packages/py-html2text/package.py @@ -12,6 +12,6 @@ class PyHtml2text(PythonPackage): homepage = "https://github.com/Alir3z4/html2text/" url = "https://pypi.io/packages/source/h/html2text/html2text-2016.9.19.tar.gz" - version('2016.9.19', 'd6b07e32ed21f186496f012691e02dd5') + version('2016.9.19', sha256='554ef5fd6c6cf6e3e4f725a62a3e9ec86a0e4d33cd0928136d1c79dbeb7b2d55') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-html5lib/package.py b/var/spack/repos/builtin/packages/py-html5lib/package.py index 8a7e7867839..2e9181ef4f0 100644 --- a/var/spack/repos/builtin/packages/py-html5lib/package.py +++ b/var/spack/repos/builtin/packages/py-html5lib/package.py @@ -12,8 +12,8 @@ class PyHtml5lib(PythonPackage): homepage = "https://github.com/html5lib/html5lib-python" url = "https://pypi.io/packages/source/h/html5lib/html5lib-0.9999999.tar.gz" - version('1.0.1', '66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736') - version('0.9999999', 'ef43cb05e9e799f25d65d1135838a96f') + version('1.0.1', sha256='66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736') + version('0.9999999', sha256='2612a191a8d5842bfa057e41ba50bbb9dcb722419d2408c78cff4758d0754868') depends_on('python@2.6:2.8,3.2:', when='@0.9999999', type=('build', 'run')) depends_on('python@2.6:2.8,3.3:', when='@1.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-htseq/package.py b/var/spack/repos/builtin/packages/py-htseq/package.py index 533a76a30e4..f5a33d41299 100644 --- a/var/spack/repos/builtin/packages/py-htseq/package.py +++ b/var/spack/repos/builtin/packages/py-htseq/package.py @@ -14,7 +14,7 @@ class PyHtseq(PythonPackage): url = "https://github.com/simon-anders/htseq/archive/release_0.9.1.tar.gz" version('0.11.2', sha256='dfc707effa699d5ba9034e1bb9f13c0fb4e9bc60d31ede2444aa49c7e2fc71aa') - version('0.9.1', '269e7de5d39fc31f609cccd4a4740e61') + version('0.9.1', sha256='28b41d68aa233fce0d57699e649b69bb11957f8f1b9b7b82dfe3415849719534') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-httpbin/package.py b/var/spack/repos/builtin/packages/py-httpbin/package.py index de31425c912..3933c8c4601 100644 --- a/var/spack/repos/builtin/packages/py-httpbin/package.py +++ b/var/spack/repos/builtin/packages/py-httpbin/package.py @@ -12,7 +12,7 @@ class PyHttpbin(PythonPackage): homepage = "https://github.com/Runscope/httpbin" url = "https://pypi.io/packages/source/h/httpbin/httpbin-0.5.0.tar.gz" - version('0.5.0', '923793df99156caa484975ade96ee115') + version('0.5.0', sha256='79fbc5d27e4194ea908b0fa18e09a59d95d287c91667aa69bcd010342d1589b5') depends_on('py-setuptools', type='build') depends_on('py-decorator@3.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-hypothesis/package.py b/var/spack/repos/builtin/packages/py-hypothesis/package.py index 19ea3e5551f..cc50b5b85b3 100644 --- a/var/spack/repos/builtin/packages/py-hypothesis/package.py +++ b/var/spack/repos/builtin/packages/py-hypothesis/package.py @@ -21,7 +21,7 @@ class PyHypothesis(PythonPackage): # TODO: Add missing dependency required to import hypothesis.extra.django version('4.7.2', sha256='87944c6379f77634474b88abbf1e5ed5fe966637cc926131eda5e2af5b54a608') - version('3.7.0', '4afb25fa6785fceac034b63eaa2dfe28') + version('3.7.0', sha256='0fea49d08f2d5884f014151a5af6fb48d862f6ad567ffc4a2e84abf2f186c423') depends_on('py-setuptools', type='build') depends_on('py-enum34', type=('build', 'run'), when='^python@:2') diff --git a/var/spack/repos/builtin/packages/py-idna/package.py b/var/spack/repos/builtin/packages/py-idna/package.py index fddbef2964a..6d4aa05f2ce 100644 --- a/var/spack/repos/builtin/packages/py-idna/package.py +++ b/var/spack/repos/builtin/packages/py-idna/package.py @@ -13,7 +13,7 @@ class PyIdna(PythonPackage): homepage = "https://github.com/kjd/idna" url = "https://pypi.io/packages/source/i/idna/idna-2.5.tar.gz" - version('2.5', 'fc1d992bef73e8824db411bb5d21f012') + version('2.5', sha256='3cb5ce08046c4e3a560fc02f138d0ac63e00f8ce5901a56b32ec8b7994082aab') depends_on('py-setuptools', type=('build', 'link')) depends_on('python@2.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-igraph/package.py index b1494bdc228..e6f6ccdf209 100644 --- a/var/spack/repos/builtin/packages/py-igraph/package.py +++ b/var/spack/repos/builtin/packages/py-igraph/package.py @@ -13,7 +13,7 @@ class PyIgraph(PythonPackage): homepage = "http://igraph.org/" url = "http://igraph.org/nightly/get/python/python-igraph-0.7.0.tar.gz" - version('0.7.0', '32a3238cb9041b1686d7d0ba152235bf') + version('0.7.0', sha256='64ac270e80a92066d489407be1900a329df8e26844430f941ecc88771188c471') depends_on('py-setuptools', type='build') depends_on('igraph') diff --git a/var/spack/repos/builtin/packages/py-illumina-utils/package.py b/var/spack/repos/builtin/packages/py-illumina-utils/package.py index 8e7dbe79e09..711ab6af884 100644 --- a/var/spack/repos/builtin/packages/py-illumina-utils/package.py +++ b/var/spack/repos/builtin/packages/py-illumina-utils/package.py @@ -13,8 +13,8 @@ class PyIlluminaUtils(PythonPackage): homepage = "https://github.com/meren/illumina-utils" url = "https://pypi.io/packages/source/i/illumina-utils/illumina-utils-2.2.tar.gz" - version('2.3', 'c0af71723e52ab2b14660d2138620e39') - version('2.2', '9e19cf112ccc38a903fc41f431804d21') + version('2.3', sha256='0e8407b91d530d9a53d8ec3c83e60f25e7f8f80d06ce17b8e4f57a02d3262441') + version('2.2', sha256='6039c72d077c101710fe4fdbfeaa30caa1c3c2c84ffa6295456927d82def8e6d') depends_on('python@3:', type=('build', 'run')) depends_on('py-pip', type='build') diff --git a/var/spack/repos/builtin/packages/py-imageio/package.py b/var/spack/repos/builtin/packages/py-imageio/package.py index 6fec54c19c4..e39965b5747 100644 --- a/var/spack/repos/builtin/packages/py-imageio/package.py +++ b/var/spack/repos/builtin/packages/py-imageio/package.py @@ -17,7 +17,7 @@ class PyImageio(PythonPackage): version('2.5.0', sha256='42e65aadfc3d57a1043615c92bdf6319b67589e49a0aae2b985b82144aceacad') version('2.4.1', sha256='16b8077bc8a5fa7a58b3e744f7ecbb156d8c088132df31e0f4f546c98de3514a') - version('2.3.0', '4722c4e1c366748abcb18729881cffb8') + version('2.3.0', sha256='c4fd5183c342d47fdc2e98552d14e3f24386021bbc3efedd1e3b579d7d249c07') # TODO: Add variants for plugins, and optional dependencies diff --git a/var/spack/repos/builtin/packages/py-imagesize/package.py b/var/spack/repos/builtin/packages/py-imagesize/package.py index 689b2c24f1f..994535b0aad 100644 --- a/var/spack/repos/builtin/packages/py-imagesize/package.py +++ b/var/spack/repos/builtin/packages/py-imagesize/package.py @@ -16,6 +16,6 @@ class PyImagesize(PythonPackage): import_modules = ['imagesize'] version('1.1.0', sha256='f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5') - version('0.7.1', '976148283286a6ba5f69b0f81aef8052') + version('0.7.1', sha256='0ab2c62b87987e3252f89d30b7cedbec12a01af9274af9ffa48108f2c13c6062') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py index 40036e1c855..48109815b18 100644 --- a/var/spack/repos/builtin/packages/py-iminuit/package.py +++ b/var/spack/repos/builtin/packages/py-iminuit/package.py @@ -12,7 +12,7 @@ class PyIminuit(PythonPackage): homepage = "https://pypi.python.org/pypi/iminuit" url = "https://pypi.io/packages/source/i/iminuit/iminuit-1.2.tar.gz" - version('1.2', '4701ec472cae42015e26251703e6e984') + version('1.2', sha256='7651105fc3f186cfb5742f075ffebcc5088bf7797d8ed124c00977eebe0d1c64') # Required dependencies depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-importlib/package.py b/var/spack/repos/builtin/packages/py-importlib/package.py index 3173455d911..f7994065070 100644 --- a/var/spack/repos/builtin/packages/py-importlib/package.py +++ b/var/spack/repos/builtin/packages/py-importlib/package.py @@ -12,4 +12,4 @@ class PyImportlib(PythonPackage): homepage = "https://github.com/brettcannon/importlib" url = "https://pypi.io/packages/source/i/importlib/importlib-1.0.4.zip" - version('1.0.4', '5f9a0803bca7ba95f670d1464984296f') + version('1.0.4', sha256='b6ee7066fea66e35f8d0acee24d98006de1a0a8a94a8ce6efe73a9a23c8d9826') diff --git a/var/spack/repos/builtin/packages/py-invoke/package.py b/var/spack/repos/builtin/packages/py-invoke/package.py index 44028af8dfc..3bc3bbae160 100644 --- a/var/spack/repos/builtin/packages/py-invoke/package.py +++ b/var/spack/repos/builtin/packages/py-invoke/package.py @@ -12,7 +12,7 @@ class PyInvoke(PythonPackage): homepage = "http://www.pyinvoke.org/" url = "https://pypi.io/packages/source/i/invoke/invoke-1.2.0.tar.gz" - version('1.2.0', 'dc492f8f17a0746e92081aec3f86ae0b4750bf41607ea2ad87e5a7b5705121b7') + version('1.2.0', sha256='dc492f8f17a0746e92081aec3f86ae0b4750bf41607ea2ad87e5a7b5705121b7') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-ipaddress/package.py b/var/spack/repos/builtin/packages/py-ipaddress/package.py index d65da944602..e2aff6fd1dc 100644 --- a/var/spack/repos/builtin/packages/py-ipaddress/package.py +++ b/var/spack/repos/builtin/packages/py-ipaddress/package.py @@ -13,6 +13,6 @@ class PyIpaddress(PythonPackage): homepage = "https://github.com/phihag/ipaddress" url = "https://pypi.io/packages/source/i/ipaddress/ipaddress-1.0.18.tar.gz" - version('1.0.18', '310c2dfd64eb6f0df44aa8c59f2334a7') + version('1.0.18', sha256='5d8534c8e185f2d8a1fda1ef73f2c8f4b23264e8e30063feeb9511d492a413e1') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-ipdb/package.py b/var/spack/repos/builtin/packages/py-ipdb/package.py index d40b7c02315..bb99a117f60 100644 --- a/var/spack/repos/builtin/packages/py-ipdb/package.py +++ b/var/spack/repos/builtin/packages/py-ipdb/package.py @@ -13,7 +13,7 @@ class PyIpdb(PythonPackage): homepage = "https://pypi.python.org/pypi/ipdb" url = "https://pypi.io/packages/source/i/ipdb/ipdb-0.10.1.tar.gz" - version('0.10.1', '4aeab65f633ddc98ebdb5eebf08dc713') + version('0.10.1', sha256='bb2948e726dbfb2687f4a582088b3f170b2556ba8e54ae1231c783c97e99ec87') # :TODO: # There might be potential to add variants here, but at the time of writing diff --git a/var/spack/repos/builtin/packages/py-ipykernel/package.py b/var/spack/repos/builtin/packages/py-ipykernel/package.py index ad4046018ff..d38f9ea52ed 100644 --- a/var/spack/repos/builtin/packages/py-ipykernel/package.py +++ b/var/spack/repos/builtin/packages/py-ipykernel/package.py @@ -13,16 +13,16 @@ class PyIpykernel(PythonPackage): url = "https://github.com/ipython/ipykernel/archive/4.5.0.tar.gz" version('5.1.0', sha256='30f01a2a1470d3fabbad03f5c43606c1bc2142850fc4ccedcf44281664ae9122') - version('4.5.0', 'ea6aaf431b100452905aaca208edac72') - version('4.4.1', 'c0033e524aa9e05ed18879641ffe6e0f') - version('4.4.0', '8e626a1708ceff83412180d2ff2f3e57') - version('4.3.1', '971eee85d630eb4bafcd52531c79673f') - version('4.3.0', '5961164fe908faf798232a265ed48c73') - version('4.2.2', '4ac8ae11f1eef4920bf4a5383e13ab50') - version('4.2.1', 'de583ee9c84db6296269ce7de0afb63f') - version('4.2.0', 'fc535e4e020a41cd2b55508302b155bb') - version('4.1.1', '51376850c46fb006e1f8d1cd353507c5') - version('4.1.0', '638a43e4f8a15872f749090c3f0827b6') + version('4.5.0', sha256='c5ec5130f5f7eda71345b9ef638c9213c4c2f41610a9ad338a0f1d0819421adf') + version('4.4.1', sha256='62fe16252e40fb3d443fcf31fc52e5596965cf17620571c10ea64502a6d51db7') + version('4.4.0', sha256='a042bf202c5675da58dba66b9bd1e7aecc62d4f82058508b620a09e2f7baa0f2') + version('4.3.1', sha256='f38b366053567c36464ae6d04d72ed72d74f77e63d49a6fa38826278ed7848fd') + version('4.3.0', sha256='cf21ee03b258ee5d1fcef8189c5cecba017e22f3517ff8d49730102ff74d61af') + version('4.2.2', sha256='9cfa31b893a430ce0800a0780b6326a15658543651d2116849e0283ec39e67fc') + version('4.2.1', sha256='12c30f3d267068db4d31897d12653908cf543358faed5bad37d60eede6a909c4') + version('4.2.0', sha256='43f6847f816e4683842878e33c6c11d5311c2be9f1fe1f44c391f5abefd35e72') + version('4.1.1', sha256='59e7e1ca516b9ee109e9a51b942bda03ac8e214891956e787da997b252f5e736') + version('4.1.0', sha256='b72c3354ac12a219b9be928ff3b5125e5c861e9592fb4eb342f1d47592cb3740') depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('python@3.4:', when='@5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py index 553517d0a08..a5a31973e07 100644 --- a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py +++ b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py @@ -12,7 +12,7 @@ class PyIpythonGenutils(PythonPackage): homepage = "https://pypi.python.org/pypi/ipython_genutils" url = "https://pypi.io/packages/source/i/ipython_genutils/ipython_genutils-0.1.0.tar.gz" - version('0.2.0', '5a4f9781f78466da0ea1a648f3e1f79f') - version('0.1.0', '9a8afbe0978adbcbfcb3b35b2d015a56') + version('0.2.0', sha256='eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8') + version('0.1.0', sha256='3a0624a251a26463c9dfa0ffa635ec51c4265380980d9a50d65611c3c2bd82a6') depends_on('python@2.7:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py index 3efd37b0eca..0b13d59860d 100644 --- a/var/spack/repos/builtin/packages/py-ipython/package.py +++ b/var/spack/repos/builtin/packages/py-ipython/package.py @@ -12,10 +12,10 @@ class PyIpython(PythonPackage): homepage = "https://pypi.python.org/pypi/ipython" url = "https://pypi.io/packages/source/i/ipython/ipython-2.3.1.tar.gz" - version('7.3.0', '2aec01154a78c6075c5b7f1bfea4abd3') - version('5.1.0', '47c8122420f65b58784cb4b9b4af35e3') - version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f') - version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf') + version('7.3.0', sha256='06de667a9e406924f97781bda22d5d76bfb39762b678762d86a466e63f65dc39') + version('5.1.0', sha256='7ef4694e1345913182126b219aaa4a0047e191af414256da6772cf249571b961') + version('3.1.0', sha256='532092d3f06f82b1d8d1e5c37097eae19fcf025f8f6a4b670dd49c3c338d5624') + version('2.3.1', sha256='3e98466aa2fe54540bcba9aa6e01a39f40110d67668c297340c4b9514b7cc49c') depends_on('python@2.7:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-ipywidgets/package.py b/var/spack/repos/builtin/packages/py-ipywidgets/package.py index 103b928e129..d5c066b14b1 100644 --- a/var/spack/repos/builtin/packages/py-ipywidgets/package.py +++ b/var/spack/repos/builtin/packages/py-ipywidgets/package.py @@ -12,7 +12,7 @@ class PyIpywidgets(PythonPackage): homepage = "https://github.com/ipython/ipywidgets" url = "https://github.com/ipython/ipywidgets/archive/5.2.2.tar.gz" - version('5.2.2', '112f3daa4aa0f42f8dda831cea3649c8') + version('5.2.2', sha256='d61ab8bb12b90981a3a6010429816d70eaa041e622043207bcb74239b664d4f3') depends_on('python@2.7:2.8,3.3:') depends_on('py-ipython@4.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-isort/package.py b/var/spack/repos/builtin/packages/py-isort/package.py index 8f4d115e9c8..1ba594611e6 100644 --- a/var/spack/repos/builtin/packages/py-isort/package.py +++ b/var/spack/repos/builtin/packages/py-isort/package.py @@ -12,6 +12,6 @@ class PyIsort(PythonPackage): homepage = "https://github.com/timothycrosley/isort" url = "https://pypi.io/packages/source/i/isort/isort-4.2.15.tar.gz" - version('4.2.15', '34915a2ce60e6fe3dbcbf5982deef9b4') + version('4.2.15', sha256='79f46172d3a4e2e53e7016e663cc7a8b538bec525c36675fcfd2767df30b3983') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-itsdangerous/package.py b/var/spack/repos/builtin/packages/py-itsdangerous/package.py index 46df99046d6..e7098c2d85c 100644 --- a/var/spack/repos/builtin/packages/py-itsdangerous/package.py +++ b/var/spack/repos/builtin/packages/py-itsdangerous/package.py @@ -12,6 +12,6 @@ class PyItsdangerous(PythonPackage): homepage = "http://github.com/mitsuhiko/itsdangerous" url = "https://pypi.io/packages/source/i/itsdangerous/itsdangerous-0.24.tar.gz" - version('0.24', 'a3d55aa79369aef5345c036a8a26307f') + version('0.24', sha256='cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py index d4a8c2ac399..1d3d1eff067 100644 --- a/var/spack/repos/builtin/packages/py-jdcal/package.py +++ b/var/spack/repos/builtin/packages/py-jdcal/package.py @@ -12,7 +12,7 @@ class PyJdcal(PythonPackage): homepage = "http://github.com/phn/jdcal" url = "https://pypi.io/packages/source/j/jdcal/jdcal-1.3.tar.gz" - version('1.3', '885ba61d28992f26acffec131bd2a17e') - version('1.2', 'ab8d5ba300fd1eb01514f363d19b1eb9') + version('1.3', sha256='b760160f8dc8cc51d17875c6b663fafe64be699e10ce34b6a95184b5aa0fdc9e') + version('1.2', sha256='5ebedb58b95ebabd30f56abef65139c6f69ec1687cf1d2f3a7c503f9a2cdfa4d') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-jedi/package.py b/var/spack/repos/builtin/packages/py-jedi/package.py index be7ba7ccd8a..7c9c2208954 100644 --- a/var/spack/repos/builtin/packages/py-jedi/package.py +++ b/var/spack/repos/builtin/packages/py-jedi/package.py @@ -13,8 +13,8 @@ class PyJedi(PythonPackage): url = "https://pypi.io/packages/source/j/jedi/jedi-0.9.0.tar.gz" # unfortunately pypi.io only offers a .whl - version('0.10.0', '89ed853d4a283bfa0fdbcf688b4d35fe', + version('0.10.0', sha256='d6a7344df9c80562c3f62199278004ccc7c5889be9f1a6aa5abde117ec085123', url='https://github.com/davidhalter/jedi/archive/v0.10.0.tar.gz') - version('0.9.0', '2fee93d273622527ef8c97ac736e92bd') + version('0.9.0', sha256='3b4c19fba31bdead9ab7350fb9fa7c914c59b0a807dcdd5c00a05feb85491d31') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py index b4a5f82fd60..530a2503788 100644 --- a/var/spack/repos/builtin/packages/py-jinja2/package.py +++ b/var/spack/repos/builtin/packages/py-jinja2/package.py @@ -16,13 +16,13 @@ class PyJinja2(PythonPackage): import_modules = ['jinja2'] - version('2.10', '61ef1117f945486472850819b8d1eb3d') - version('2.9.6', '6411537324b4dba0956aaa8109f3c77b') - version('2.8', 'edb51693fe22c53cee5403775c71a99e') - version('2.7.3', 'b9dffd2f3b43d673802fe857c8445b1a') - version('2.7.2', 'df1581455564e97010e38bc792012aa5') - version('2.7.1', '282aed153e69f970d6e76f78ed9d027a') - version('2.7', 'c2fb12cbbb523c57d3d15bfe4dc0e8fe') + version('2.10', sha256='f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4') + version('2.9.6', sha256='ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff') + version('2.8', sha256='bc1ff2ff88dbfacefde4ddde471d1417d3b304e8df103a7a9437d47269201bf4') + version('2.7.3', sha256='2e24ac5d004db5714976a04ac0e80c6df6e47e98c354cb2c0d82f8879d4f8fdb') + version('2.7.2', sha256='310a35fbccac3af13ebf927297f871ac656b9da1d248b1fe6765affa71b53235') + version('2.7.1', sha256='5cc0a087a81dca1c08368482fb7a92fe2bdd8cfbb22bc0fccfe6c85affb04c8b') + version('2.7', sha256='474f1518d189ae7e318b139fecc1d30b943f124448cfa0f09582ca23e069fa4d') depends_on('py-setuptools', type='build') depends_on('py-markupsafe', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-joblib/package.py b/var/spack/repos/builtin/packages/py-joblib/package.py index 66dfb07c32a..56e9e1b548e 100644 --- a/var/spack/repos/builtin/packages/py-joblib/package.py +++ b/var/spack/repos/builtin/packages/py-joblib/package.py @@ -18,6 +18,6 @@ class PyJoblib(PythonPackage): ] version('0.13.2', sha256='315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524') - version('0.10.3', '455401ccfaf399538d8e5333086df2d3') - version('0.10.2', 'ebb42af4342c2445b175f86bd478d869') - version('0.10.0', '61e40322c4fed5c22905f67d7d1aa557') + version('0.10.3', sha256='29b2965a9efbc90a5fe66a389ae35ac5b5b0c1feabfc7cab7fd5d19f429a071d') + version('0.10.2', sha256='3123553bdad83b143428033537c9e1939caf4a4d8813dade6a2246948c94494b') + version('0.10.0', sha256='49b3a0ba956eaa2f077e1ebd230b3c8d7b98afc67520207ada20a4d8b8efd071') diff --git a/var/spack/repos/builtin/packages/py-jpype/package.py b/var/spack/repos/builtin/packages/py-jpype/package.py index c7ecac9a7ee..f8292f41320 100644 --- a/var/spack/repos/builtin/packages/py-jpype/package.py +++ b/var/spack/repos/builtin/packages/py-jpype/package.py @@ -13,9 +13,9 @@ class PyJpype(PythonPackage): homepage = "https://github.com/originell/jpype" url = "https://pypi.io/packages/source/J/JPype1/JPype1-0.6.2.tar.gz" - version('0.6.2', '16e5ee92b29563dcc63bbc75556810c1') - version('0.6.1', '468ca2d4b2cff7802138789e951d5d58') - version('0.6.0', 'f0cbbe1d0c4b563f7e435d2bffc31736') + version('0.6.2', sha256='99206412d80b9d5a81a7cc205267ca63554403eb57f13420302e2f39bfad7f25') + version('0.6.1', sha256='0d366228b7b37b0266184161cc7ea1ce58f60199f6ec9451985149ea873774be') + version('0.6.0', sha256='f5d783520cb4c30595c3bc509065e30fc292ec7cfb57045141eae77c518bcdb0') depends_on('python@2.6:') diff --git a/var/spack/repos/builtin/packages/py-jsonschema/package.py b/var/spack/repos/builtin/packages/py-jsonschema/package.py index 90a0079e4ea..51d0e17ffcc 100644 --- a/var/spack/repos/builtin/packages/py-jsonschema/package.py +++ b/var/spack/repos/builtin/packages/py-jsonschema/package.py @@ -13,7 +13,7 @@ class PyJsonschema(PythonPackage): url = "https://pypi.io/packages/source/j/jsonschema/jsonschema-2.6.0.tar.gz" version('2.6.0', sha256='6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02') - version('2.5.1', '374e848fdb69a3ce8b7e778b47c30640') + version('2.5.1', sha256='36673ac378feed3daa5956276a829699056523d7961027911f064b52255ead41') depends_on('py-setuptools', type='build') depends_on('py-vcversioner', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-junit-xml/package.py b/var/spack/repos/builtin/packages/py-junit-xml/package.py index f9e4a8d0fa9..bbdaf9a41bd 100644 --- a/var/spack/repos/builtin/packages/py-junit-xml/package.py +++ b/var/spack/repos/builtin/packages/py-junit-xml/package.py @@ -13,7 +13,7 @@ class PyJunitXml(PythonPackage): homepage = "https://github.com/kyrus/python-junit-xml" url = "https://pypi.io/packages/source/j/junit-xml/junit-xml-1.7.tar.gz" - version('1.7', '5e6a96edb8a1592f2832241cfd99983e') + version('1.7', sha256='5bc851b53e3e2153dcc62278ce2aa796a8ae9208f1dec36d1507b5af445ce355') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jupyter-client/package.py b/var/spack/repos/builtin/packages/py-jupyter-client/package.py index 5559efd3eab..1b69aa1e4ee 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-client/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-client/package.py @@ -12,14 +12,14 @@ class PyJupyterClient(PythonPackage): homepage = "https://github.com/jupyter/jupyter_client" url = "https://github.com/jupyter/jupyter_client/archive/4.4.0.tar.gz" - version('4.4.0', 'a0bd6fe6ba7c504fbc962a88a2a56a90') - version('4.3.0', '257d9f5429dac4d9511db84d201d3a9e') - version('4.2.2', '988ea87554215a83c6ad52e554d8d8c4') - version('4.2.1', '16994e5cace322c777456bc5a26502d7') - version('4.2.0', '61c43c9f243e42f1945fae5d56d0d23c') - version('4.1.1', '8436e4a3266a442f576cdfef39dc0e19') - version('4.1.0', 'cf42048b889c8434fbb5813a9eec1d34') - version('4.0.0', '00fa63c67cb3adf359d09dc4d803aff5') + version('4.4.0', sha256='2fda7fe1af35f0b4a77c4a2fd4ee38ac3666ed7f4d92a5b6ff8aaf764c38e199') + version('4.3.0', sha256='90b6ea3ced910ed94c5d558373490a81b33c672d877c1ffdc76b281e3216f1f6') + version('4.2.2', sha256='bf3e8ea4c44f07dbe2991e41031f6dab242734be424f4d40b72cc58a12c7d2ca') + version('4.2.1', sha256='547d443fb38ea667b468a6625ac374d476f8ac90fe17c3e35d75cab3cb8d40ba') + version('4.2.0', sha256='00eab54615fb10f1e508d8e7a952fbeeb2a82cd67b17582bd61be51a08a61d89') + version('4.1.1', sha256='ca6f3f66d5dc1e9bca81696ae607a93d652210c3ee9385a7c31c067d5ba88e6e') + version('4.1.0', sha256='ecf76a159381ec9880fd2c31388c6983b1d855f92f0292cf0667a90dd63f51c0') + version('4.0.0', sha256='33b15abb1307d8d3716b0d3b5d07aa22fdfbbf65a9f1aedf478a274a6adc11c0') depends_on('python@2.7:2.8,3.3:') depends_on('py-traitlets', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jupyter-console/package.py b/var/spack/repos/builtin/packages/py-jupyter-console/package.py index fe66dc55e8b..89aecd40cc4 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-console/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-console/package.py @@ -12,12 +12,12 @@ class PyJupyterConsole(PythonPackage): homepage = "https://github.com/jupyter/jupyter_console" url = "https://github.com/jupyter/jupyter_console/archive/5.0.0.tar.gz" - version('5.2.0', 'a783ec26193b2835caa94e255e05e080') - version('5.0.0', '08a9fde32a45c9e2e0b4cec6eca249c2') - version('4.1.1', 'a8b077ae0a5c57e9518ac039ad5febb8') - version('4.1.0', '9c655076262760bdbeeada9d7f586237') - version('4.0.3', '0e928ea261e7f8154698cf69ed4f2459') - version('4.0.2', 'f2e174938c91136549b908bd39fa5d59') + version('5.2.0', sha256='371d03aeefcf48967f2f00af4c1709f52d2a688deee33f395c6330e4e8aa171c') + version('5.0.0', sha256='e966b2b5bf9a1e8c5bd11a6335bb11f68ec585ea39b801721b2ed9dd964468fa') + version('4.1.1', sha256='0bb06a1f878d0c44c2f6f66406a80f949bcd86f3508035500af7dceffb9cc7dc') + version('4.1.0', sha256='9c72097721676ba13d036e68d82ef9ef76772254c8a995a474339a8bd48aaf91') + version('4.0.3', sha256='b1867a89b693f247e9089a8f367fa4f27af6eac27930cad2966054adfa7b9aa1') + version('4.0.2', sha256='116a56763899bbb12c762f865372eb52c08619ef070c237c7f1387e192bfd3df') depends_on('python@2.7:2.8,3.3:') depends_on('py-jupyter-client', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jupyter-core/package.py b/var/spack/repos/builtin/packages/py-jupyter-core/package.py index 9c0ff4847bf..109eddef3d7 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-core/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-core/package.py @@ -12,17 +12,17 @@ class PyJupyterCore(PythonPackage): homepage = "http://jupyter-core.readthedocs.io/" url = "https://github.com/jupyter/jupyter_core/archive/4.2.0.tar.gz" - version('4.4.0', 'f2bdb8be2959d3043b77508dd6498687') - version('4.2.0', '25c1fc68b1b73c0a2e616c76f02bf061') - version('4.1.1', '2fce5ff60291bc01b39b1f00b3cbb784') - version('4.1.0', 'b7e928f965f68aef13fea1bf9d6384aa') - version('4.0.6', '50a73c3a4a8ed047a3674d2b5274cc3b') - version('4.0.5', 'c09bd3be58f141b49b90cdb2ba22f77f') - version('4.0.4', '5b6ca0e73bf559f4fe6106a6e412f913') - version('4.0.3', 'f2608f6e92f992ec8e37646b52c922a6') - version('4.0.2', 'ae0d0197c4febf43c050a97ac6277263') - version('4.0.1', 'f849136b2badaaba2a8a3b397bf04639') - version('4.0', 'b6b37cb4f40bd0fcd20433cb2cc7a4c1') + version('4.4.0', sha256='a3c693cb4cd1251f887f034eba4b74e5ad1beab5baef43cc3ae9387450e72367') + version('4.2.0', sha256='ca2db4bc44b870ad9039bfdcad81bb0466e6bf0e6e2e03626815977ee73dc7a7') + version('4.1.1', sha256='1908dd9eceb8994c1f0b1bb81c20a52dbb01692e4f1fdf5d12e04846b94eb05c') + version('4.1.0', sha256='80b78d215399760f4678cc1512118257543e17b48316254d1e1dbddfafa2dffc') + version('4.0.6', sha256='76d9f95eec679d1ce8a07fba4e373bda3b17ca89e3b03ee6186a7dbdc117d7e8') + version('4.0.5', sha256='783c2be522010db9dd0ff54c28fcdf31afe73a5f7d956eb89ddce2c48f381548') + version('4.0.4', sha256='ee81c1e2c67afe0b9c1097043f76063b452670fc63377ab4656ce1b2826cd166') + version('4.0.3', sha256='5ecc177e8c711a410f857adc65f8413b06ea1f2fa2330559a723d6c1981852f8') + version('4.0.2', sha256='ad2f537aacaa9978b37ac5d39d9bd582d2a9dfc104b3d289b88687c1c5a0ece0') + version('4.0.1', sha256='faa3878b286f63d1853aec3e4b80e2a7299f580a9acebd4a1cafa36b264ec0a3') + version('4.0', sha256='2b491a5da687ffab4e5702e37d3cb8b6b184cd46520cae9c459bdb1fd144f026') depends_on('python@2.7:2.8,3.3:') depends_on('py-traitlets', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-kiwisolver/package.py b/var/spack/repos/builtin/packages/py-kiwisolver/package.py index 00396dfa841..0afcec72c65 100644 --- a/var/spack/repos/builtin/packages/py-kiwisolver/package.py +++ b/var/spack/repos/builtin/packages/py-kiwisolver/package.py @@ -12,6 +12,6 @@ class PyKiwisolver(PythonPackage): homepage = "https://github.com/nucleic/kiwi" url = "https://pypi.io/packages/source/k/kiwisolver/kiwisolver-1.0.1.tar.gz" - version('1.0.1', 'e2a1718b837e2cd001f7c06934616fcd') + version('1.0.1', sha256='ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-lark-parser/package.py b/var/spack/repos/builtin/packages/py-lark-parser/package.py index 21e4cdaff05..3772f52f7be 100644 --- a/var/spack/repos/builtin/packages/py-lark-parser/package.py +++ b/var/spack/repos/builtin/packages/py-lark-parser/package.py @@ -13,6 +13,6 @@ class PyLarkParser(PythonPackage): url = "https://pypi.io/packages/source/l/lark-parser/lark-parser-0.6.2.tar.gz" version('0.7.1', sha256='8455e05d062fa7f9d59a2735583cf02291545f944955c4056bf1144c4e625344') - version('0.6.2', '675058937a7f41e661bcf2b3bfdb7ceb') + version('0.6.2', sha256='7e2934371e0e3a5daf9afc2e3ddda76117cabcd3c3f2edf7987c1e4e9b9e503c') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-latexcodec/package.py b/var/spack/repos/builtin/packages/py-latexcodec/package.py index c7ed753eb91..b61bc629bef 100644 --- a/var/spack/repos/builtin/packages/py-latexcodec/package.py +++ b/var/spack/repos/builtin/packages/py-latexcodec/package.py @@ -14,7 +14,7 @@ class PyLatexcodec(PythonPackage): import_modules = ['latexcodec'] - version('1.0.4', '72010ec2a55227a5802239cff6fd32d6') + version('1.0.4', sha256='62bf8a3ee298f169a4d014dad5522bc1325b54dc98789a453fd338620387cb6c') depends_on('py-setuptools', type='build') depends_on('py-six@1.4.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py index 500d7aed2eb..f4d4c288bb5 100644 --- a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py +++ b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py @@ -12,7 +12,7 @@ class PyLazyObjectProxy(PythonPackage): homepage = "https://github.com/ionelmc/python-lazy-object-proxy" url = "https://pypi.io/packages/source/l/lazy-object-proxy/lazy-object-proxy-1.3.1.tar.gz" - version('1.3.1', 'e128152b76eb5b9ba759504936139fd0') + version('1.3.1', sha256='eb91be369f945f10d3a49f5f9be8b3d0b93a4c2be8f8a5b83b0571b8123e0a7a') conflicts('^python@3.0:3.2.99') diff --git a/var/spack/repos/builtin/packages/py-lazy-property/package.py b/var/spack/repos/builtin/packages/py-lazy-property/package.py index 8e8ecdb98fb..8c36f09269c 100644 --- a/var/spack/repos/builtin/packages/py-lazy-property/package.py +++ b/var/spack/repos/builtin/packages/py-lazy-property/package.py @@ -12,7 +12,7 @@ class PyLazyProperty(PythonPackage): homepage = "https://github.com/jackmaney/lazy-property" url = "https://github.com/jackmaney/lazy-property/archive/0.0.1.tar.gz" - version('0.0.1', '7e046c2441abe1bd272d5360827237b3') - version('0.0.0', 'fda622b7f1c46ee72ad25f5e88c928f5') + version('0.0.1', sha256='2cde89dc6f06366b3ab2423da65c469e1fe8b19f52bbd264698d1cdfdb1ef102') + version('0.0.0', sha256='f43bea2619656eda1f80e5c781f771fee191ac3dba225f0583852be8f6d03c3f') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-lazy/package.py b/var/spack/repos/builtin/packages/py-lazy/package.py index 661d5bd59cf..9d5bdb5a3da 100644 --- a/var/spack/repos/builtin/packages/py-lazy/package.py +++ b/var/spack/repos/builtin/packages/py-lazy/package.py @@ -12,6 +12,6 @@ class PyLazy(PythonPackage): homepage = "https://pypi.python.org/pypi/lazy" url = "https://pypi.io/packages/source/l/lazy/lazy-1.2.zip" - version('1.2', '02713784e0a92ff9b6af1df8863dd79d') + version('1.2', sha256='127ea610418057b953f0d102bed83f2c367be13b59f8d0ddf3b8a86c7d31b970') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-lazyarray/package.py b/var/spack/repos/builtin/packages/py-lazyarray/package.py index 465f0389f14..254a59361c6 100644 --- a/var/spack/repos/builtin/packages/py-lazyarray/package.py +++ b/var/spack/repos/builtin/packages/py-lazyarray/package.py @@ -13,8 +13,8 @@ class PyLazyarray(PythonPackage): homepage = "http://bitbucket.org/apdavison/lazyarray/" url = "https://pypi.io/packages/source/l/lazyarray/lazyarray-0.2.8.tar.gz" - version('0.2.10', '336033357459e66cbca5543bf003a2ba') - version('0.2.8', '8e0072f0892b9fc0516e7048f96e9d74') + version('0.2.10', sha256='7a53f81b5f3a098c04003d2ad179fc197451fd96bc921510f8534c6af8cc8e19') + version('0.2.8', sha256='aaee4e18117cc512de7a4e64522f37bc6f4bf125ecffdbdbf4e4e390fbdd9ba2') depends_on('py-numpy@1.3:', type=('build', 'run')) depends_on('py-numpy@1.5:', type=('build', 'run'), when='^python@3:') diff --git a/var/spack/repos/builtin/packages/py-libconf/package.py b/var/spack/repos/builtin/packages/py-libconf/package.py index aee6e2b00ce..c57a6544281 100644 --- a/var/spack/repos/builtin/packages/py-libconf/package.py +++ b/var/spack/repos/builtin/packages/py-libconf/package.py @@ -12,6 +12,6 @@ class PyLibconf(PythonPackage): homepage = "https://pypi.python.org/pypi/libconf" url = "https://pypi.io/packages/source/l/libconf/libconf-1.0.1.tar.gz" - version('1.0.1', 'd37d355b3248f99802c46669ba38e406') + version('1.0.1', sha256='6dd62847bb69ab5a09155cb8be2328cce01e7ef88a35e7c37bea2b1a70f8bd58') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-libensemble/package.py b/var/spack/repos/builtin/packages/py-libensemble/package.py index 4cfdf304a70..ed752518d3a 100644 --- a/var/spack/repos/builtin/packages/py-libensemble/package.py +++ b/var/spack/repos/builtin/packages/py-libensemble/package.py @@ -21,8 +21,8 @@ class PyLibensemble(PythonPackage): version('0.4.1', sha256='282c32ffb79d84cc80b5cc7043c202d5f0b8ebff10f63924752f092e3938db5e') version('0.4.0', sha256='9384aa3a58cbc20bbd1c6fddfadb5e6a943d593a3a81c8665f030dbc6d76e76e') version('0.3.0', sha256='c8efdf45d0da0ef6299ee778cea1c285c95972af70d3a729ee6dc855e66f9294') - version('0.2.0', 'ee96047594a3f5a1533f24d3b1f365f9') - version('0.1.0', '0c3d45dd139429de1a5273e5bd8e46ec') + version('0.2.0', sha256='ecac7275d4d0f4a5e497e5c9ef2cd998da82b2c020a0fb87546eeea262f495ff') + version('0.1.0', sha256='0b27c59ae80f7af8b1bee92fcf2eb6c9a8fd3494bf2eb6b3ea17a7c03d3726bb') variant('mpi', default=False, description='Install with MPI') variant('scipy', default=False, description='Install with scipy') diff --git a/var/spack/repos/builtin/packages/py-line-profiler/package.py b/var/spack/repos/builtin/packages/py-line-profiler/package.py index 2399602e775..c06a8968ea1 100644 --- a/var/spack/repos/builtin/packages/py-line-profiler/package.py +++ b/var/spack/repos/builtin/packages/py-line-profiler/package.py @@ -15,7 +15,7 @@ class PyLineProfiler(PythonPackage): url = "https://pypi.io/packages/source/l/line_profiler/line_profiler-2.0.tar.gz" version('2.1.2', sha256='efa66e9e3045aa7cb1dd4bf0106e07dec9f80bc781a993fbaf8162a36c20af5c') - version('2.0', 'fc93c6bcfac3b7cb1912cb28836d7ee6') + version('2.0', sha256='739f8ad0e4bcd0cb82e99afc09e00a0351234f6b3f0b1f7f0090a8a2fbbf8381') depends_on('python@2.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-linecache2/package.py b/var/spack/repos/builtin/packages/py-linecache2/package.py index a5aa44c2fb4..e05e540e942 100644 --- a/var/spack/repos/builtin/packages/py-linecache2/package.py +++ b/var/spack/repos/builtin/packages/py-linecache2/package.py @@ -12,7 +12,7 @@ class PyLinecache2(PythonPackage): homepage = "https://github.com/testing-cabal/linecache2" url = "https://pypi.io/packages/source/l/linecache2/linecache2-1.0.0.tar.gz" - version('1.0.0', '7b25d0289ec36bff1f9e63c4329ce65c') + version('1.0.0', sha256='4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c') depends_on('py-setuptools', type='build') depends_on('py-pbr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-lit/package.py b/var/spack/repos/builtin/packages/py-lit/package.py index be6b5a7e3b0..cfade2e9a38 100644 --- a/var/spack/repos/builtin/packages/py-lit/package.py +++ b/var/spack/repos/builtin/packages/py-lit/package.py @@ -16,6 +16,6 @@ class PyLit(PythonPackage): url = "https://pypi.io/packages/source/l/lit/lit-0.5.0.tar.gz" version('0.7.1', sha256='ecef2833aef7f411cb923dac109c7c9dcc7dbe7cafce0650c1e8d19c243d955f') - version('0.5.0', '8144660cc692be8fb903395a5f06564d') + version('0.5.0', sha256='3ea4251e78ebeb2e07be2feb33243d1f8931d956efc96ccc2b0846ced212b58c') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-llvmlite/package.py b/var/spack/repos/builtin/packages/py-llvmlite/package.py index 49f007e9413..e9d075ab2e9 100644 --- a/var/spack/repos/builtin/packages/py-llvmlite/package.py +++ b/var/spack/repos/builtin/packages/py-llvmlite/package.py @@ -15,8 +15,8 @@ class PyLlvmlite(PythonPackage): version('0.27.1', sha256='48a1c3ae69fd8920cba153bfed8a46ac46474bc706a2100226df4abffe0000ab') version('0.26.0', sha256='13e84fe6ebb0667233074b429fd44955f309dead3161ec89d9169145dbad2ebf') version('0.25.0', sha256='fd64def9a51dd7dc61913a7a08eeba5b9785522740bec5a7c5995b2a90525025') - version('0.23.0', '6fc856576a11dbeef71de862f7c419de') - version('0.20.0', 'f2aa60d0981842b7930ba001b03679ab') + version('0.23.0', sha256='bc8b1b46274d05b578fe9e980a6d98fa71c8727f6f9ed31d4d8468dce7aa5762') + version('0.20.0', sha256='b2f174848df16bb9195a07fec102110a06d018da736bd9b3570a54d44c797c29') depends_on('py-setuptools', type='build') depends_on('python@2.6:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-lmfit/package.py b/var/spack/repos/builtin/packages/py-lmfit/package.py index 6a7f8719ae8..3da5e6c0c03 100644 --- a/var/spack/repos/builtin/packages/py-lmfit/package.py +++ b/var/spack/repos/builtin/packages/py-lmfit/package.py @@ -12,7 +12,7 @@ class PyLmfit(PythonPackage): homepage = "http://lmfit.github.io/lmfit-py/" url = "https://pypi.io/packages/source/l/lmfit/lmfit-0.9.5.tar.gz" - version('0.9.5', '3a38aa3e4510a564d9e2f606d2537522') + version('0.9.5', sha256='eebc3c34ed9f3e51bdd927559a5482548c423ad5a0690c6fdcc414bfb5be6667') depends_on('py-numpy@1.5:', type=('build', 'run')) depends_on('py-scipy@0.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-localcider/package.py b/var/spack/repos/builtin/packages/py-localcider/package.py index 9de67203989..e72dd898f6e 100644 --- a/var/spack/repos/builtin/packages/py-localcider/package.py +++ b/var/spack/repos/builtin/packages/py-localcider/package.py @@ -12,7 +12,7 @@ class PyLocalcider(PythonPackage): homepage = "http://pappulab.github.io/localCIDER" url = "https://pypi.io/packages/source/l/localcider/localcider-0.1.14.tar.gz" - version('0.1.14', 'cd3c992595c5cb280374de3750663cfa') + version('0.1.14', sha256='54ff29e8a011947cca5df79e96f3c69a76c49c4db41dcf1608663992be3e3f5f') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-locket/package.py b/var/spack/repos/builtin/packages/py-locket/package.py index 7da7895da26..de7ea763253 100644 --- a/var/spack/repos/builtin/packages/py-locket/package.py +++ b/var/spack/repos/builtin/packages/py-locket/package.py @@ -14,4 +14,4 @@ class PyLocket(PythonPackage): import_modules = ['locket'] - version('0.2.0', 'fe870949c513d8f7079ba352463833ca') + version('0.2.0', sha256='1fee63c1153db602b50154684f5725564e63a0f6d09366a1cb13dffcec179fb4') diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py index 5d8c3a6d69e..674bba7cdb5 100644 --- a/var/spack/repos/builtin/packages/py-lockfile/package.py +++ b/var/spack/repos/builtin/packages/py-lockfile/package.py @@ -20,6 +20,6 @@ class PyLockfile(PythonPackage): homepage = "https://pypi.python.org/pypi/lockfile" url = "https://pypi.io/packages/source/l/lockfile/lockfile-0.10.2.tar.gz" - version('0.10.2', '1aa6175a6d57f082cd12e7ac6102ab15') + version('0.10.2', sha256='9e42252f17d1dd89ee31745e0c4fbe58862c25147eb0ef5295c9cd9bcb4ea2c1') depends_on("py-setuptools", type='build') diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py index 65fddac3ee4..548050f1664 100644 --- a/var/spack/repos/builtin/packages/py-logilab-common/package.py +++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py @@ -11,7 +11,7 @@ class PyLogilabCommon(PythonPackage): homepage = "https://www.logilab.org/project/logilab-common" url = "https://pypi.io/packages/source/l/logilab-common/logilab-common-1.2.0.tar.gz" - version('1.2.0', 'f7b51351b7bfe052746fa04c03253c0b') + version('1.2.0', sha256='d4e5cec3be3a89f06ff05e359a221e69bd1da33cb7096cad648ddcccea8465b7') extends('python', ignore=r'bin/pytest') depends_on("py-setuptools", type='build') diff --git a/var/spack/repos/builtin/packages/py-lrudict/package.py b/var/spack/repos/builtin/packages/py-lrudict/package.py index aa96b583d38..79c35502192 100644 --- a/var/spack/repos/builtin/packages/py-lrudict/package.py +++ b/var/spack/repos/builtin/packages/py-lrudict/package.py @@ -13,7 +13,7 @@ class PyLrudict(PythonPackage): homepage = "https://github.com/amitdev/lru-dict" url = "https://pypi.io/packages/source/l/lru-dict/lru-dict-1.1.6.tar.gz" - version('1.1.6', 'b33f54f1257ab541f4df4bacc7509f5a') + version('1.1.6', sha256='365457660e3d05b76f1aba3e0f7fedbfcd6528e97c5115a351ddd0db488354cc') depends_on('python@2.7:') depends_on('py-setuptools', type=('build')) diff --git a/var/spack/repos/builtin/packages/py-lxml/package.py b/var/spack/repos/builtin/packages/py-lxml/package.py index 6c86cf72be0..e045f9597d9 100644 --- a/var/spack/repos/builtin/packages/py-lxml/package.py +++ b/var/spack/repos/builtin/packages/py-lxml/package.py @@ -13,9 +13,9 @@ class PyLxml(PythonPackage): homepage = "http://lxml.de/" url = "https://pypi.io/packages/source/l/lxml/lxml-2.3.tar.gz" - version('4.2.5', 'ce042575c4459c4994f68b9a862a72a4') - version('3.7.3', '075692ce442e69bbd604d44e21c02753') - version('2.3', 'a245a015fd59b63e220005f263e1682a') + version('4.2.5', sha256='36720698c29e7a9626a0dc802ef8885f8f0239bfd1689628ecd459a061f2807f') + version('3.7.3', sha256='aa502d78a51ee7d127b4824ff96500f0181d3c7826e6ee7b800d068be79361c7') + version('2.3', sha256='eea1b8d29532739c1383cb4794c5eacd6176f0972b59e8d29348335b87ff2e66') depends_on('py-setuptools@0.6c5:', type='build') depends_on('py-cython@0.20:', type='build') diff --git a/var/spack/repos/builtin/packages/py-lzstring/package.py b/var/spack/repos/builtin/packages/py-lzstring/package.py index 140b5746e9a..7a1fe90847b 100644 --- a/var/spack/repos/builtin/packages/py-lzstring/package.py +++ b/var/spack/repos/builtin/packages/py-lzstring/package.py @@ -12,7 +12,7 @@ class PyLzstring(PythonPackage): homepage = "https://github.com/gkovacs/lz-string-python" url = "https://pypi.io/packages/source/l/lzstring/lzstring-1.0.3.tar.gz" - version('1.0.3', '1c636543484629020a26432740f81443') + version('1.0.3', sha256='d54dd5a5f86837ccfc1343cc9f1cb0674d2d6ebd4b49f6408c35104f0a996cb4') depends_on('py-setuptools', type='build') depends_on('py-future', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-machotools/package.py b/var/spack/repos/builtin/packages/py-machotools/package.py index 6c0d7ecd42f..4d69883206d 100644 --- a/var/spack/repos/builtin/packages/py-machotools/package.py +++ b/var/spack/repos/builtin/packages/py-machotools/package.py @@ -12,7 +12,7 @@ class PyMachotools(PythonPackage): homepage = "https://pypi.python.org/pypi/machotools" url = "https://pypi.io/packages/source/m/machotools/machotools-0.2.0.tar.gz" - version('0.2.0', 'bcc68332c4a80b4f84ec9c8083465416') + version('0.2.0', sha256='e3950fa263169087d44a3d0521a3267d5128efd1b85252670c7171955939ab58') depends_on('py-setuptools', type='build') depends_on('py-macholib', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-macs2/package.py b/var/spack/repos/builtin/packages/py-macs2/package.py index c273202c0d7..3db1a170673 100644 --- a/var/spack/repos/builtin/packages/py-macs2/package.py +++ b/var/spack/repos/builtin/packages/py-macs2/package.py @@ -13,7 +13,7 @@ class PyMacs2(PythonPackage): homepage = "https://github.com/taoliu/MACS" url = "https://pypi.io/packages/source/M/MACS2/MACS2-2.1.1.20160309.tar.gz" - version('2.1.1.20160309', '2008ba838f83f34f8e0fddefe2a3a0159f4a740707c68058f815b31ddad53d26') + version('2.1.1.20160309', sha256='2008ba838f83f34f8e0fddefe2a3a0159f4a740707c68058f815b31ddad53d26') depends_on('python@2.7:2.8') diff --git a/var/spack/repos/builtin/packages/py-maestrowf/package.py b/var/spack/repos/builtin/packages/py-maestrowf/package.py index 0dcfd381d29..e090b847016 100644 --- a/var/spack/repos/builtin/packages/py-maestrowf/package.py +++ b/var/spack/repos/builtin/packages/py-maestrowf/package.py @@ -15,12 +15,12 @@ class PyMaestrowf(PythonPackage): maintainers = ['FrankD412'] - version('1.1.4', 'e2da101fb1cad9a164d375eccb1f07ce') - version('1.1.3', '0299e4ae3ec8b8c0296df0efaa8b517f') - version('1.1.2', 'a9e05d82910cd2dd077321fb9b0c8dcd') - version('1.1.1', 'd38bbf634de4f29fd01d1864ba2f70e0') - version('1.1.0', '3c20bf36fbb85d14c3bfdb865944a409') - version('1.0.1', '6838fc8bdc7ca0c1adbb6a0333f005b4') + version('1.1.4', sha256='2cb0fa6f6281d8618ac79217ea5f4fd8cb24955c4315e873657f96b815f171d5') + version('1.1.3', md5='0299e4ae3ec8b8c0296df0efaa8b517f') + version('1.1.2', sha256='ebb45bff54625435bc9f2462e1bdc3b5bdc4d943378c53e7810c11836794c5e0') + version('1.1.1', sha256='a476ad4b40846d7b7f9540d6413df1b42eb655735e8d3c6c07e0baa68e20a8bb') + version('1.1.0', sha256='14e701d6a10ab758215aab6b6809817d9a39416a4f477cd2f2551883fc68477b') + version('1.0.1', sha256='cdd503f0b11db9114405132274b28766044402d1183b5836406ed91d558fd06c') depends_on('py-setuptools', type='build') depends_on('py-pyyaml@4.2b1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py index 14c69556f40..3221f8711f3 100644 --- a/var/spack/repos/builtin/packages/py-mako/package.py +++ b/var/spack/repos/builtin/packages/py-mako/package.py @@ -13,8 +13,8 @@ class PyMako(PythonPackage): homepage = "https://pypi.python.org/pypi/mako" url = "https://pypi.io/packages/source/M/Mako/Mako-1.0.1.tar.gz" - version('1.0.4', 'c5fc31a323dd4990683d2f2da02d4e20') - version('1.0.1', '9f0aafd177b039ef67b90ea350497a54') + version('1.0.4', sha256='fed99dbe4d0ddb27a33ee4910d8708aca9ef1fe854e668387a9ab9a90cbf9059') + version('1.0.1', sha256='45f0869febea59dab7efd256fb451c377cbb7947bef386ff0bb44627c31a8d1c') depends_on('py-setuptools', type='build') depends_on('py-mock', type='test') diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py index 4aba0af89a6..dcae1c3ae9f 100644 --- a/var/spack/repos/builtin/packages/py-markupsafe/package.py +++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py @@ -17,11 +17,11 @@ class PyMarkupsafe(PythonPackage): import_modules = ['markupsafe'] - version('1.0', '2fcedc9284d50e577b5192e8e3578355') - version('0.23', 'f5ab3deee4c37cd6a922fb81e730da6e') - version('0.22', 'cb3ec29fd5361add24cfd0c6e2953b3e') - version('0.21', 'fde838d9337fa51744283f46a1db2e74') - version('0.20', '7da066d9cb191a70aa85d0a3d43565d1') - version('0.19', 'ccb3f746c807c5500850987006854a6d') + version('1.0', sha256='a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665') + version('0.23', sha256='a4ec1aff59b95a14b45eb2e23761a0179e98319da5a7eb76b56ea8cdc7b871c3') + version('0.22', sha256='7642852b6d1e55c9e12e00a552c0b8943880f2172e55141ccb41eb5f8675dfa5') + version('0.21', sha256='c6465cd6ed2b96509ef0100e7fff8718ed52c2affab1860ed5a9b67f604dd59a') + version('0.20', sha256='f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8') + version('0.19', sha256='62fcc5d641df8b5ad271ebbd6b77a19cd92eceba1e1a990de4e96c867789f037') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 36d1f5254be..a53c2c892b1 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -29,16 +29,16 @@ class PyMatplotlib(PythonPackage): ] version('3.1.1', sha256='1febd22afe1489b13c6749ea059d392c03261b2950d1d45c17e3aed812080c93') - version('3.0.2', 'd6af3dfae557ea4046fef96cf617fa24') - version('3.0.0', '39c7f44c8fa0f24cbf684137371ce4ae') - version('2.2.3', '403b0bddd751d71187416f20d4cff100') - version('2.2.2', 'dd1e49e041309a7fd4e32be8bf17c3b6') - version('2.0.2', '061111784278bde89b5d4987014be4ca') - version('2.0.0', '7aa54b06327f0e1c4f3877fc2f7d6b17') - version('1.5.3', 'ba993b06113040fee6628d74b80af0fd') - version('1.5.1', 'f51847d8692cb63df64cd0bd0304fd20') - version('1.4.3', '86af2e3e3c61849ac7576a6f5ca44267') - version('1.4.2', '7d22efb6cce475025733c50487bd8898') + version('3.0.2', sha256='c94b792af431f6adb6859eb218137acd9a35f4f7442cea57e4a59c54751c36af') + version('3.0.0', sha256='b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9') + version('2.2.3', sha256='7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5') + version('2.2.2', sha256='4dc7ef528aad21f22be85e95725234c5178c0f938e2228ca76640e5e84d8cde8') + version('2.0.2', sha256='0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1') + version('2.0.0', sha256='36cf0985829c1ab2b8b1dae5e2272e53ae681bf33ab8bedceed4f0565af5f813') + version('1.5.3', sha256='a0a5dc39f785014f2088fed2c6d2d129f0444f71afbb9c44f7bdf1b14d86ebbc') + version('1.5.1', sha256='3ab8d968eac602145642d0db63dd8d67c85e9a5444ce0e2ecb2a8fedc7224d40') + version('1.4.3', sha256='61f201c6a82e89e4d9e324266203fad44f95fd8f36d8eec0d8690273e1182f75') + version('1.4.2', sha256='17a3c7154f152d8dfed1f37517c0a8c5db6ade4f6334f684989c36dab84ddb54') # https://matplotlib.org/tutorials/introductory/usage.html#backends # From `matplotlib.rcsetup`: diff --git a/var/spack/repos/builtin/packages/py-mccabe/package.py b/var/spack/repos/builtin/packages/py-mccabe/package.py index 1227f5fd72b..82ff0dc819d 100644 --- a/var/spack/repos/builtin/packages/py-mccabe/package.py +++ b/var/spack/repos/builtin/packages/py-mccabe/package.py @@ -12,18 +12,18 @@ class PyMccabe(PythonPackage): homepage = "https://github.com/PyCQA/mccabe" url = "https://github.com/PyCQA/mccabe/archive/0.5.2.tar.gz" - version('0.6.1', '0360af86f0bce7a839bd3cba517edf9c') - version('0.6.0', '38f46ff70b5d2c02155f8fd4d96fb791') - version('0.5.3', 'a75f57079ce10556fd3c63a5f6b4d706') - version('0.5.2', '3cdf2d7faa1464b18905fe9a7063a632') - version('0.5.1', '864b364829156701bec797712be8ece0') - version('0.5.0', '71c0ce5e5c4676753525154f6c5d3af8') - version('0.4.0', '9cf5712e5f1785aaa27273a4328babe4') - version('0.3.1', '45c48c0978e6fc1f31fedcb918178abb') - version('0.3', 'c583f58ea28be12842c001473d77504d') - version('0.2.1', 'fcba311ebd999f48359a8ab28da94b30') - version('0.2', '36d4808c37e187dbb1fe2373a0ac6645') - version('0.1', '3c9e8e72612a9c01d865630cc569150a') + version('0.6.1', sha256='2748af6516175b94be318cd8226fa50b5339b9dc886bce378ac2afb37a157524') + version('0.6.0', sha256='f42593f451106965053fa852dfd395b85a2fcb6df960e268cb7a1d60d4aec291') + version('0.5.3', sha256='4a1582dfe070e630387710169e4731a1b0a4eab736431fa25e91f1fcaf3cbe94') + version('0.5.2', sha256='a456c9e2529bf4e7e9e690b20557c5ae5d9cbe25df2a0bbc73dcc39b1b959f4b') + version('0.5.1', sha256='31377e7d65ac6458b1f788bf50c34f788f173334383cbfeadd701f772a0f3fe1') + version('0.5.0', sha256='b10a4de7987f0e4d6be2a073d1bc91ceed5f0a3715c6088520253e2452ea5dfe') + version('0.4.0', sha256='1c0b443fb11dbf90e7caff4366299c0fd69d6bb0c6fedb46fa74283628d8d3ff') + version('0.3.1', sha256='244134b78607b74d885ba45f29e495e55c75a261b02de62976233d47e64949ea') + version('0.3', sha256='8ef89519a7ce6036597a6bd4d0f28a921cb949cba1bbe42570e5255c6f31456b') + version('0.2.1', sha256='88506c11597a4258719b1c7e72317b2145cb43da63314b05d11cd5433dd5a813') + version('0.2', sha256='3cc0ff234082035ef4f73640d96ca3f52d6e2e9865a38181093e836370b5f7c3') + version('0.1', sha256='10023fc9a64ea25b6cde1f6d0b824990a9882c9086a54b2bcfb8aa70d5ca179f') depends_on('python@2.7:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py index ee83b8b72cd..6d0ad83f18a 100644 --- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py +++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py @@ -24,7 +24,7 @@ class PyMdanalysis(PythonPackage): version('0.16.2', sha256='407d9a9ff1ab8a5e47973714d06fabff220f8d08a28792dee93e88e70e995b0a') version('0.16.1', sha256='3dc8f5d639ab3a0d152cbd7259ae9372ec8a9bac0f8cb7d3b80ce5adc1e3ee57') version('0.16.0', sha256='c4824fa1fddd336daa39371436187ebb023366885fb250c2827ed7fce2546bd4') - version('0.15.0', '19e5a8e6c2bfe85f6209d1d7a36e4f20') + version('0.15.0', sha256='9088786048b47339cba1f8a586977bbb3bb04ae1bcd0462b59e45bda37e25533') variant('analysis', default=True, description='Enable analysis packages: matplotlib, scipy, seaborn') diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-meep/package.py index b7dea8b7980..81a219145f4 100644 --- a/var/spack/repos/builtin/packages/py-meep/package.py +++ b/var/spack/repos/builtin/packages/py-meep/package.py @@ -13,7 +13,7 @@ class PyMeep(PythonPackage): homepage = "https://launchpad.net/python-meep" url = "https://launchpad.net/python-meep/1.4/1.4/+download/python-meep-1.4.2.tar" - version('1.4.2', 'f8913542d18b0dda92ebc64f0a10ce56') + version('1.4.2', sha256='d91428aa4727c308383cea31ca9cdacee409320c686e9a8368769933e56c8762') variant('mpi', default=True, description='Enable MPI support') diff --git a/var/spack/repos/builtin/packages/py-memory-profiler/package.py b/var/spack/repos/builtin/packages/py-memory-profiler/package.py index b87e2934145..97aea2dd13b 100644 --- a/var/spack/repos/builtin/packages/py-memory-profiler/package.py +++ b/var/spack/repos/builtin/packages/py-memory-profiler/package.py @@ -12,7 +12,7 @@ class PyMemoryProfiler(PythonPackage): homepage = "https://github.com/fabianp/memory_profiler" url = "https://pypi.io/packages/source/m/memory_profiler/memory_profiler-0.47.tar.gz" - version('0.47', 'ed340aaaa0c7118f2a4c5b4edec6da1e') + version('0.47', sha256='e992f2a341a5332dad1ad4a008eeac7cfe78c7ea4abdf7535a3e7e79093328cb') depends_on('py-setuptools', type='build') depends_on('py-psutil', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-methylcode/package.py b/var/spack/repos/builtin/packages/py-methylcode/package.py index e1d920349f1..512d1f2d014 100644 --- a/var/spack/repos/builtin/packages/py-methylcode/package.py +++ b/var/spack/repos/builtin/packages/py-methylcode/package.py @@ -13,7 +13,7 @@ class PyMethylcode(PythonPackage): homepage = "https://github.com/brentp/methylcode" url = "https://github.com/brentp/methylcode/archive/master.zip" - version('1.0.0', 'd0ba07c1ab2c74adddd1b23f8e5823e7') + version('1.0.0', sha256='30f707a690a887e3161c8debba3c322bd313865df40212275b02203c52a416ae') depends_on('python@2.7.0:2.7.999') depends_on('py-six') diff --git a/var/spack/repos/builtin/packages/py-misopy/package.py b/var/spack/repos/builtin/packages/py-misopy/package.py index 413cedbbf66..93a2df80860 100644 --- a/var/spack/repos/builtin/packages/py-misopy/package.py +++ b/var/spack/repos/builtin/packages/py-misopy/package.py @@ -15,7 +15,7 @@ class PyMisopy(PythonPackage): homepage = "http://miso.readthedocs.io/en/fastmiso/" url = "https://pypi.io/packages/source/m/misopy/misopy-0.5.4.tar.gz" - version('0.5.4', 'fe0c9c2613304defbdead12ea99e4194') + version('0.5.4', sha256='377a28b0c254b1920ffdc2d89cf96c3a21cadf1cf148ee6d6ef7a88ada067dfc') depends_on('py-setuptools', type='build') depends_on('python@2.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-mistune/package.py b/var/spack/repos/builtin/packages/py-mistune/package.py index d390418ede5..5abb62288ea 100644 --- a/var/spack/repos/builtin/packages/py-mistune/package.py +++ b/var/spack/repos/builtin/packages/py-mistune/package.py @@ -13,10 +13,10 @@ class PyMistune(PythonPackage): homepage = "http://mistune.readthedocs.org/en/latest/" url = "https://github.com/lepture/mistune/archive/v0.7.1.tar.gz" - version('0.7.1', '0d9c29700c670790c5b2471070d32ec2') - version('0.7', '77750ae8b8d0d584894224a7e0c0523a') - version('0.6', 'd4f3d4f28a69e715f82b591d5dacf9a6') - version('0.5.1', '1c6cfce28a4aa90cf125217cd6c6fe6c') - version('0.5', '997736554f1f95eea78c66ae339b5722') + version('0.7.1', sha256='d6684534174caa30e0169e106a7152aee14507796a610b76be9fe9b335b18410') + version('0.7', sha256='9b2cac8053d21dde5f2b3edb01948dac8ee5c3a85eeeeb6913c3ddf2f773c7b6') + version('0.6', sha256='c2d976c06c099edb525b8ac3745f3d3b5c49af6189edb6de390ddf9c248913cf') + version('0.5.1', sha256='c4ecfbb99acbb034c4f4580496502bde6b33f3dfc47873c59ee7e509c05dc822') + version('0.5', sha256='3320b7fd80e44a1ac27658e19e67215f464c080b02c8af9fce57050d411560d2') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py index 274d8efcdfa..516f1aff2df 100644 --- a/var/spack/repos/builtin/packages/py-mock/package.py +++ b/var/spack/repos/builtin/packages/py-mock/package.py @@ -14,8 +14,8 @@ class PyMock(PythonPackage): homepage = "https://github.com/testing-cabal/mock" url = "https://pypi.io/packages/source/m/mock/mock-1.3.0.tar.gz" - version('2.0.0', '0febfafd14330c9dcaa40de2d82d40ad') - version('1.3.0', '73ee8a4afb3ff4da1b4afa287f39fdeb') + version('2.0.0', sha256='b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba') + version('1.3.0', sha256='1e247dbecc6ce057299eb7ee019ad68314bb93152e81d9a6110d35f4d5eca0f6') depends_on('py-pbr@0.11:', type=('build', 'run')) depends_on('py-six@1.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-moltemplate/package.py b/var/spack/repos/builtin/packages/py-moltemplate/package.py index b8925e2cc3a..7d05b4cc69a 100644 --- a/var/spack/repos/builtin/packages/py-moltemplate/package.py +++ b/var/spack/repos/builtin/packages/py-moltemplate/package.py @@ -13,7 +13,7 @@ class PyMoltemplate(PythonPackage): homepage = "http://moltemplate.org" url = "https://github.com/jewettaij/moltemplate/archive/v2.5.8.tar.gz" - version('2.5.8', '9e127a254a206222e8a31684780f8dba') + version('2.5.8', sha256='f1e2d52249e996d85f5b1b7b50f50037da9e4b9c252cdfc622b21e79aa21162f') depends_on('python@2.7:', type=('build', 'run')) depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-mongo/package.py b/var/spack/repos/builtin/packages/py-mongo/package.py index f40334d66a4..117c59cf704 100644 --- a/var/spack/repos/builtin/packages/py-mongo/package.py +++ b/var/spack/repos/builtin/packages/py-mongo/package.py @@ -12,8 +12,8 @@ class PyMongo(PythonPackage): homepage = "http://github.com/mongodb/mongo-python-driver" url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.6.0.tar.gz" - version('3.6.0', '2f64fa7691c77535b72050704cc12afb') - version('3.3.0', '42cd12a5014fb7d3e1987ca04f5c651f') + version('3.6.0', sha256='c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8') + version('3.3.0', sha256='3d45302fc2622fabf34356ba274c69df41285bac71bbd229f1587283b851b91e') depends_on('python@2.6:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-monotonic/package.py b/var/spack/repos/builtin/packages/py-monotonic/package.py index ed2a46ae58c..08afbabbe15 100644 --- a/var/spack/repos/builtin/packages/py-monotonic/package.py +++ b/var/spack/repos/builtin/packages/py-monotonic/package.py @@ -12,6 +12,6 @@ class PyMonotonic(PythonPackage): homepage = "https://pypi.python.org/pypi/monotonic" url = "https://pypi.io/packages/source/m/monotonic/monotonic-1.2.tar.gz" - version('1.2', 'd14c93aabc3d6af25ef086b032b123cf') + version('1.2', sha256='c0e1ceca563ca6bb30b0fb047ee1002503ae6ad3585fc9c6af37a8f77ec274ba') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-monty/package.py b/var/spack/repos/builtin/packages/py-monty/package.py index fc88563afe0..7b6ceedff7f 100644 --- a/var/spack/repos/builtin/packages/py-monty/package.py +++ b/var/spack/repos/builtin/packages/py-monty/package.py @@ -12,7 +12,7 @@ class PyMonty(PythonPackage): homepage = "https://github.com/materialsvirtuallab/monty" url = "https://pypi.io/packages/source/m/monty/monty-0.9.6.tar.gz" - version('0.9.6', '406ea69fdd112feacfdf208624d56903') + version('0.9.6', sha256='bbf05646c4e86731c2398a57b1044add7487fc4ad03122578599ddd9a8892780') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-more-itertools/package.py b/var/spack/repos/builtin/packages/py-more-itertools/package.py index acea1eac7e2..4a7e569dc25 100644 --- a/var/spack/repos/builtin/packages/py-more-itertools/package.py +++ b/var/spack/repos/builtin/packages/py-more-itertools/package.py @@ -14,9 +14,9 @@ class PyMoreItertools(PythonPackage): import_modules = ['more_itertools', 'more_itertools.tests'] - version('4.3.0', '42157ef9b677bdf6d3609ed6eadcbd4a') - version('4.1.0', '246f46686d95879fbad37855c115dc52') - version('2.2', 'b8d328a33f966bf40bb829bcf8da35ce') + version('4.3.0', sha256='c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e') + version('4.1.0', sha256='c9ce7eccdcb901a2c75d326ea134e0886abfbea5f93e91cc95de9507c0816c44') + version('2.2', sha256='93e62e05c7ad3da1a233def6731e8285156701e3419a5fe279017c429ec67ce0') depends_on('py-setuptools', type='build') depends_on('py-six@1.0.0:1.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py index 25b4d96a461..86b176081c9 100644 --- a/var/spack/repos/builtin/packages/py-mpi4py/package.py +++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py @@ -17,10 +17,10 @@ class PyMpi4py(PythonPackage): git = "https://github.com/mpi4py/mpi4py.git" version('develop', branch='master') - version('3.0.1', '969bcde3188fb98e0be61b5d78a8745f') - version('3.0.0', 'bfe19f20cef5e92f6e49e50fb627ee70') - version('2.0.0', '4f7d8126d7367c239fd67615680990e3') - version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c') + version('3.0.1', sha256='6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851') + version('3.0.0', sha256='b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7') + version('2.0.0', sha256='6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81') + version('1.3.1', sha256='e7bd2044aaac5a6ea87a87b2ecc73b310bb6efe5026031e33067ea3c2efc3507') depends_on('python@2.7:2.8,3.3:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-mpmath/package.py b/var/spack/repos/builtin/packages/py-mpmath/package.py index 2de76568124..218c53f7e48 100644 --- a/var/spack/repos/builtin/packages/py-mpmath/package.py +++ b/var/spack/repos/builtin/packages/py-mpmath/package.py @@ -12,5 +12,5 @@ class PyMpmath(PythonPackage): url = "https://pypi.io/packages/source/m/mpmath/mpmath-1.0.0.tar.gz" version('1.1.0', sha256='fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6') - version('1.0.0', '998f10cb231af62743212ca80693f1b5') - version('0.19', 'af5cc956b2673b33a25c3e57299bae7b') + version('1.0.0', sha256='04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c') + version('0.19', sha256='68ddf6426dcda445323467d89892d2cffbbd1ae0b31ac1241b1b671749d63222') diff --git a/var/spack/repos/builtin/packages/py-multiprocess/package.py b/var/spack/repos/builtin/packages/py-multiprocess/package.py index 3c393fdb78d..086b0023916 100644 --- a/var/spack/repos/builtin/packages/py-multiprocess/package.py +++ b/var/spack/repos/builtin/packages/py-multiprocess/package.py @@ -12,8 +12,8 @@ class PyMultiprocess(PythonPackage): homepage = "https://github.com/uqfoundation/multiprocess" url = "https://pypi.io/packages/source/m/multiprocess/multiprocess-0.70.5.zip" - version('0.70.5', 'bfe394368b1d98192f1f62cc0060be20') - version('0.70.4', '443336d84c574106da6c67d4574b7614') + version('0.70.5', sha256='c4c196f3c4561dc1d78139c3e73709906a222d2fc166ef3eef895d8623df7267') + version('0.70.4', sha256='a692c6dc8392c25b29391abb58a9fbdc1ac38bca73c6f27d787774201e68e12c') depends_on('python@2.6:2.8,3.1:') diff --git a/var/spack/repos/builtin/packages/py-multiqc/package.py b/var/spack/repos/builtin/packages/py-multiqc/package.py index 93a63688ba7..52d2a2bcbc3 100644 --- a/var/spack/repos/builtin/packages/py-multiqc/package.py +++ b/var/spack/repos/builtin/packages/py-multiqc/package.py @@ -14,10 +14,10 @@ class PyMultiqc(PythonPackage): homepage = "https://multiqc.info" url = "https://pypi.io/packages/source/m/multiqc/multiqc-1.0.tar.gz" - version('1.7', '02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68') - version('1.5', 'fe0ffd2b0d1067365ba4e54ae8991f2f779c7c684b037549b617020ea883310a') - version('1.3', 'cde17845680131e16521ace04235bb9496c78c44cdc7b5a0fb6fd93f4ad7a13b') - version('1.0', '1a49331a3d3f2e591a6e9902bc99b16e9205731f0cd2d6eaeee0da3d0f0664c9') + version('1.7', sha256='02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68') + version('1.5', sha256='fe0ffd2b0d1067365ba4e54ae8991f2f779c7c684b037549b617020ea883310a') + version('1.3', sha256='cde17845680131e16521ace04235bb9496c78c44cdc7b5a0fb6fd93f4ad7a13b') + version('1.0', sha256='1a49331a3d3f2e591a6e9902bc99b16e9205731f0cd2d6eaeee0da3d0f0664c9') depends_on('python@2.7:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-munch/package.py b/var/spack/repos/builtin/packages/py-munch/package.py index c4336c93997..560fdfb801c 100644 --- a/var/spack/repos/builtin/packages/py-munch/package.py +++ b/var/spack/repos/builtin/packages/py-munch/package.py @@ -13,7 +13,7 @@ class PyMunch(PythonPackage): homepage = "https://github.com/Infinidat/munch" url = "https://github.com/Infinidat/munch/archive/2.2.0.tar.gz" - version('2.2.0', 'a50f0e4d770b5106f0c440a6cff3617f') + version('2.2.0', sha256='f354ea638e5e582c52d3e47eb54199d3eade94ee3552d64453ddfcbe953973f0') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-mx/package.py b/var/spack/repos/builtin/packages/py-mx/package.py index a8f7534e2bc..0428d384109 100644 --- a/var/spack/repos/builtin/packages/py-mx/package.py +++ b/var/spack/repos/builtin/packages/py-mx/package.py @@ -16,4 +16,4 @@ class PyMx(PythonPackage): homepage = "http://www.egenix.com/products/python/mxBase/" url = "https://downloads.egenix.com/python/egenix-mx-base-3.2.8.tar.gz" - version('3.2.8', '9d9d3a25f9dc051a15e97f452413423b') + version('3.2.8', sha256='0da55233e45bc3f88870e62e60a79c2c86bad4098b8128343fd7be877f44a3c0') diff --git a/var/spack/repos/builtin/packages/py-myhdl/package.py b/var/spack/repos/builtin/packages/py-myhdl/package.py index d501d3d1037..ca6cb5a1e00 100644 --- a/var/spack/repos/builtin/packages/py-myhdl/package.py +++ b/var/spack/repos/builtin/packages/py-myhdl/package.py @@ -13,7 +13,7 @@ class PyMyhdl(PythonPackage): homepage = "http://www.myhdl.org" url = "https://pypi.io/packages/source/m/myhdl/myhdl-0.9.0.tar.gz" - version('0.9.0', 'c3b4e7b857b6f51d43720413546df15c') + version('0.9.0', sha256='52d12a5fe2cda22558806272af3c2b519b6f7095292b8e6c8ad255fb604507a5') depends_on('python@2.6:2.8,3.4:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py index 79e195d8d4b..28966f890ac 100644 --- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py +++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py @@ -11,7 +11,7 @@ class PyMysqldb1(PythonPackage): homepage = "https://github.com/farcepest/MySQLdb1" url = "https://github.com/farcepest/MySQLdb1/archive/MySQLdb-1.2.5.tar.gz" - version('1.2.5', '332c8f4955b6bc0c79ea15170bf7321b', + version('1.2.5', sha256='905dd8be887ff596641ace5411fed17cfd08dd33699ea627d3fb44f8a922c2f0', url="https://github.com/farcepest/MySQLdb1/archive/MySQLdb-1.2.5.tar.gz") depends_on('mysql@:6') diff --git a/var/spack/repos/builtin/packages/py-natsort/package.py b/var/spack/repos/builtin/packages/py-natsort/package.py index a410c9ddb29..c171847962c 100644 --- a/var/spack/repos/builtin/packages/py-natsort/package.py +++ b/var/spack/repos/builtin/packages/py-natsort/package.py @@ -12,15 +12,15 @@ class PyNatsort(PythonPackage): homepage = "https://pypi.org/project/natsort/" url = "https://github.com/SethMMorton/natsort/archive/5.2.0.zip" - version('5.2.0', '2ed2826550eef1f9ea3dd04f08b5da8b') - version('5.1.1', '0525d4897fc98f40df5cc5a4a05f3c82') - version('5.1.0', '518688548936d548775fb00afba999fb') - version('5.0.3', '11147d75693995a946656927df7617d0') - version('5.0.2', '1eb11a69086a5fb21d03f8189f1afed3') - version('5.0.1', 'ca21c728bb3dd5dcfb010fa50b9c5e3c') - version('5.0.0', 'fc7800fea50dcccbf8b116e1dff2ebf8') - version('4.0.4', '7478ba31ec7fe554fcbfda41bb01f5ef') - version('4.0.3', '2dc4fb1eb6ebfe4c9d95a12c2406df33') - version('4.0.1', '659cf6ce95951003de0c85fc80b9f135') + version('5.2.0', sha256='0ae15082842e8a3598750b4bbaa4f7c138caf004e59c7040429d56bf9e9631bd') + version('5.1.1', sha256='6467eeca268d9accb2e3149acace49649f865b0051a672006a64b20597f04561') + version('5.1.0', sha256='79279792cc97a0005b2075ed2bc9b8a3e25e5edffe43ee2fb26b116283f5dab4') + version('5.0.3', sha256='408f6fa87f6bbe3e09b255286d4db7b678bf22d6a5cd1651d05bfc1f99792a2e') + version('5.0.2', sha256='6315d94b6651edd9bf1e29cfd513a0349ec46a38ed38d33121a11d5162dbe556') + version('5.0.1', sha256='fe915cd4ddc90182947758b77873dda42935d5493819df8439f2daef01ffaacb') + version('5.0.0', sha256='b46b3569ac69e8f4a88f1a479d108872857538c7564226c32df1fd75e809c240') + version('4.0.4', sha256='14e5ddaf689de2f5ac33aa7963554fa2944b019f526ece1036d74fe60528531b') + version('4.0.3', sha256='8824792d7ebc37a57010e1ba301244653f8655ea20ddab6b0d546cf1d9ffedda') + version('4.0.1', sha256='1c1d29150938ca71f0943363a06765dbb2cea01f9c4d760ba880cc65f39baba0') depends_on('py-setuptools', type=('build')) diff --git a/var/spack/repos/builtin/packages/py-nbconvert/package.py b/var/spack/repos/builtin/packages/py-nbconvert/package.py index 4ea61deaeb7..0634c6b5d0b 100644 --- a/var/spack/repos/builtin/packages/py-nbconvert/package.py +++ b/var/spack/repos/builtin/packages/py-nbconvert/package.py @@ -13,9 +13,9 @@ class PyNbconvert(PythonPackage): homepage = "https://github.com/jupyter/nbconvert" url = "https://github.com/jupyter/nbconvert/archive/4.2.0.tar.gz" - version('4.2.0', '8bd88771cc00f575d5edcd0b5197f964') - version('4.1.0', '06655576713ba1ff7cece2b92760c187') - version('4.0.0', '9661620b1e10a7b46f314588d2d0932f') + version('4.2.0', sha256='32394be5a20f39f99fabfb9b2f2625df17f1c2a6699182ca41598e98e7cc9610') + version('4.1.0', sha256='459f23381411fd1ff9ec5ed71fcd56b8c080d97b3a1e47dae1c5c391f9a47266') + version('4.0.0', sha256='00e25eeca90523ba6b774b289073631ef5ac65bb2de9774e9b7f29604516265c') depends_on('py-pycurl', type='build') depends_on('python@2.7:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-nbformat/package.py b/var/spack/repos/builtin/packages/py-nbformat/package.py index f73d992a11b..aa58e035583 100644 --- a/var/spack/repos/builtin/packages/py-nbformat/package.py +++ b/var/spack/repos/builtin/packages/py-nbformat/package.py @@ -12,9 +12,9 @@ class PyNbformat(PythonPackage): homepage = "https://github.com/jupyter/nbformat" url = "https://github.com/jupyter/nbformat/archive/4.1.0.tar.gz" - version('4.1.0', '826b4fc4ec42553b20144f53b57b4e7b') - version('4.0.1', 'ab7172e517c9d561c0c01eef5631b4c8') - version('4.0.0', '7cf61359fa4e9cf3ef5e969e2fcb909e') + version('4.1.0', sha256='751e77b58b66319be3977f86cc23a459763bded466a0113bbe39f137ec747872') + version('4.0.1', sha256='5c46c21349f29379fa55bf19e4359afcd605fd4b5693a56807355874a2e87f78') + version('4.0.0', sha256='f0dc6c6b47b9b0dcda1dfb02dd99c0818eb709571690a688d4e38a3129d2e95b') depends_on('py-ipython-genutils', type=('build', 'run')) depends_on('py-traitlets', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-neo/package.py b/var/spack/repos/builtin/packages/py-neo/package.py index cd19d72cc99..8375b69839d 100644 --- a/var/spack/repos/builtin/packages/py-neo/package.py +++ b/var/spack/repos/builtin/packages/py-neo/package.py @@ -14,8 +14,8 @@ class PyNeo(PythonPackage): homepage = "http://neuralensemble.org/neo" url = "https://pypi.io/packages/source/n/neo/neo-0.4.1.tar.gz" - version('0.5.2', 'e2b55b112ae245f24cc8ad63cfef986c') - version('0.4.1', 'f706df3a1bce835cb490b812ac198a6e') + version('0.5.2', sha256='1de436b7d5e72a5b4f1baa68bae5b790624a9ac44b2673811cb0b6ef554d3f8b') + version('0.4.1', sha256='a5a4f3aa31654d52789f679717c9fb622ad4f59b56d227dca490357b9de0a1ce') depends_on('py-setuptools', type='build') depends_on('py-numpy@1.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py index 207b972386d..8b2fb69a7e0 100644 --- a/var/spack/repos/builtin/packages/py-nestle/package.py +++ b/var/spack/repos/builtin/packages/py-nestle/package.py @@ -12,7 +12,7 @@ class PyNestle(PythonPackage): homepage = "http://kbarbary.github.io/nestle/" url = "https://pypi.io/packages/source/n/nestle/nestle-0.1.1.tar.gz" - version('0.1.1', '4875c0f9a0a8e263c1d7f5fa6ce604c5') + version('0.1.1', sha256='d236a04f25494af5cda572eecf62729592b3231fbd874b1f72aff54718a3bb08') # Required dependencies depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py index 84f3346d84e..ef9bbafad14 100644 --- a/var/spack/repos/builtin/packages/py-netcdf4/package.py +++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py @@ -13,8 +13,8 @@ class PyNetcdf4(PythonPackage): url = "https://pypi.io/packages/source/n/netCDF4/netCDF4-1.2.7.tar.gz" version('1.4.2', sha256='b934af350459cf9041bcdf5472e2aa56ed7321c018d918e9f325ec9a1f9d1a30') - version('1.2.7', '77b357d78f9658dd973dee901f6d86f8') - version('1.2.3.1', '24fc0101c7c441709c230e76af611d53') + version('1.2.7', sha256='0c449b60183ee06238a8f9a75de7b0eed3acaa7a374952ff9f1ff06beb8f94ba') + version('1.2.3.1', sha256='55edd74ef9aabb1f7d1ea3ffbab9c555da2a95632a97f91c0242281dc5eb919f') depends_on('py-setuptools', type='build') depends_on('py-cython@0.19:', type='build') diff --git a/var/spack/repos/builtin/packages/py-netifaces/package.py b/var/spack/repos/builtin/packages/py-netifaces/package.py index 510a591e093..56736539c10 100644 --- a/var/spack/repos/builtin/packages/py-netifaces/package.py +++ b/var/spack/repos/builtin/packages/py-netifaces/package.py @@ -12,6 +12,6 @@ class PyNetifaces(PythonPackage): homepage = "https://bitbucket.org/al45tair/netifaces" url = "https://pypi.io/packages/source/n/netifaces/netifaces-0.10.5.tar.gz" - version('0.10.5', '5b4d1f1310ed279e6df27ef3a9b71519') + version('0.10.5', sha256='59d8ad52dd3116fcb6635e175751b250dc783fb011adba539558bd764e5d628b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index ecbb609f87f..678e7644ee4 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -16,8 +16,8 @@ class PyNetworkx(PythonPackage): url='https://pypi.io/packages/source/n/networkx/networkx-2.2.zip') version('2.1', sha256='64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1', url='https://pypi.io/packages/source/n/networkx/networkx-2.1.zip') - version('1.11', md5='6ef584a879e9163013e9a762e1cf7cd1') - version('1.10', md5='eb7a065e37250a4cc009919dacfe7a9d') + version('1.11', sha256='0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8') + version('1.10', sha256='ced4095ab83b7451cec1172183eff419ed32e21397ea4e1971d92a5808ed6fb8') depends_on('py-decorator', type=('build', 'run')) depends_on('py-decorator@4.1.0:', type=('build', 'run'), when='@2.1:') diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index 3fc4ad87b59..a87ef5305aa 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -17,8 +17,8 @@ class PyNose(PythonPackage): 'nose', 'nose.ext', 'nose.plugins', 'nose.sphinx', 'nose.tools' ] - version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') - version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') - version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') + version('1.3.7', sha256='f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98') + version('1.3.6', sha256='f61e0909a743eed37b1207e38a8e7b4a2fe0a82185e36f2be252ef1b3f901758') + version('1.3.4', sha256='76bc63a4e2d5e5a0df77ca7d18f0f56e2c46cfb62b71103ba92a92c79fab1e03') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-nosexcover/package.py b/var/spack/repos/builtin/packages/py-nosexcover/package.py index b9e7961b0c8..47071043989 100644 --- a/var/spack/repos/builtin/packages/py-nosexcover/package.py +++ b/var/spack/repos/builtin/packages/py-nosexcover/package.py @@ -13,7 +13,7 @@ class PyNosexcover(PythonPackage): homepage = "https://github.com/cmheisel/nose-xcover" url = "https://pypi.io/packages/source/n/nosexcover/nosexcover-1.0.11.tar.gz" - version('1.0.11', 'f32ef4824b4484343e9766b2c376365d') + version('1.0.11', sha256='298c3c655da587f6cab8a666e9f4b150320032431062dea91353988d45c8b883') depends_on('py-setuptools', type='build') depends_on('py-nose', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-numba/package.py b/var/spack/repos/builtin/packages/py-numba/package.py index e5e7bf1e632..efad3b2a17d 100644 --- a/var/spack/repos/builtin/packages/py-numba/package.py +++ b/var/spack/repos/builtin/packages/py-numba/package.py @@ -13,7 +13,7 @@ class PyNumba(PythonPackage): url = "https://pypi.io/packages/source/n/numba/numba-0.35.0.tar.gz" version('0.40.1', sha256='52d046c13bcf0de79dbfb936874b7228f141b9b8e3447cc35855e9ad3e12aa33') - version('0.35.0', '4f447383406f54aaf18ffaba3a0e79e8') + version('0.35.0', sha256='11564937757605bee590c5758c73cfe9fd6d569726b56d970316a6228971ecc3') depends_on('python@3.3:3.7.9999', type=('build', 'run'), when='@0.40.1:') depends_on('python@3.3:3.6.9999', type=('build', 'run'), when='@:0.35.0') diff --git a/var/spack/repos/builtin/packages/py-numexpr3/package.py b/var/spack/repos/builtin/packages/py-numexpr3/package.py index 727777c1f6d..50a023c4afd 100644 --- a/var/spack/repos/builtin/packages/py-numexpr3/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr3/package.py @@ -20,7 +20,7 @@ class PyNumexpr3(PythonPackage): homepage = "https://github.com/pydata/numexpr/tree/numexpr-3.0" url = "https://pypi.io/packages/source/n/numexpr3/numexpr3-3.0.1a1.tar.gz" - version('3.0.1.a1', '9fa8dc59b149aa1956fc755f982a78ad') + version('3.0.1.a1', sha256sum='de06f1b4206704b5bc19ea09b5c94350b97c211c26bc866f275252a8461b87e6') # TODO: Add CMake build system for better control of passing flags related # to CPU ISA. diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 186ecb4227b..e1b19ee4d71 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -40,28 +40,28 @@ class PyNumpy(PythonPackage): version('1.15.3', sha256='1c0c80e74759fa4942298044274f2c11b08c86230b25b8b819e55e644f5ff2b6') version('1.15.2', sha256='27a0d018f608a3fe34ac5e2b876f4c23c47e38295c47dd0775cc294cd2614bc1') version('1.15.2', sha256='27a0d018f608a3fe34ac5e2b876f4c23c47e38295c47dd0775cc294cd2614bc1') - version('1.15.1', '898004d5be091fde59ae353e3008fe9b') + version('1.15.1', sha256='7b9e37f194f8bcdca8e9e6af92e2cbad79e360542effc2dd6b98d63955d8d8a3') version('1.15.0', sha256='f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9') version('1.14.6', sha256='1250edf6f6c43e1d7823f0967416bc18258bb271dc536298eb0ea00a9e45b80a') version('1.14.5', sha256='a4a433b3a264dbc9aa9c7c241e87c0358a503ea6394f8737df1683c7c9a102ac') version('1.14.4', sha256='2185a0f31ecaa0792264fa968c8e0ba6d96acf144b26e2e1d1cd5b77fc11a691') - version('1.14.3', '97416212c0a172db4bc6b905e9c4634b') - version('1.14.2', '080f01a19707cf467393e426382c7619') - version('1.14.1', 'b8324ef90ac9064cd0eac46b8b388674') - version('1.14.0', 'c12d4bf380ac925fcdc8a59ada6c3298') - version('1.13.3', '300a6f0528122128ac07c6deb5c95917') - version('1.13.1', '2c3c0f4edf720c3a7b525dacc825b9ae') - version('1.13.0', 'fd044f0b8079abeaf5e6d2e93b2c1d03') - version('1.12.1', 'c75b072a984028ac746a6a332c209a91') - version('1.12.0', '33e5a84579f31829bbbba084fe0a4300') + version('1.14.3', sha256='9016692c7d390f9d378fc88b7a799dc9caa7eb938163dda5276d3f3d6f75debf') + version('1.14.2', sha256='facc6f925c3099ac01a1f03758100772560a0b020fb9d70f210404be08006bcb') + version('1.14.1', sha256='fa0944650d5d3fb95869eaacd8eedbd2d83610c85e271bd9d3495ffa9bc4dc9c') + version('1.14.0', sha256='3de643935b212307b420248018323a44ec51987a336d1d747c1322afc3c099fb') + version('1.13.3', sha256='36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750') + version('1.13.1', sha256='c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb') + version('1.13.0', sha256='dcff367b725586830ff0e20b805c7654c876c2d4585c0834a6049502b9d6cf7e') + version('1.12.1', sha256='a65266a4ad6ec8936a1bc85ce51f8600634a31a258b722c9274a80ff189d9542') + version('1.12.0', sha256='ff320ecfe41c6581c8981dce892fe6d7e69806459a899e294e4bf8229737b154') version('1.11.3', sha256='2e0fc5248246a64628656fe14fcab0a959741a2820e003bd15538226501b82f7') - version('1.11.2', '8308cc97be154d2f64a2387ea863c2ac') - version('1.11.1', '5caa3428b24aaa07e72c79d115140e46') - version('1.11.0', '19ce5c4eb16d663a0713daf0018a3021') - version('1.10.4', '510ffc322c635511e7be95d225b6bcbb') + version('1.11.2', sha256='c1ed4d1d2a795409c7df1eb4bfee65c0e3326cfc7c57875fa39e5c7414116d9a') + version('1.11.1', sha256='4e9c289b9d764d10353a224a5286dda3e0425b13b112719bdc3e9864ae648d79') + version('1.11.0', sha256='9109f260850627e4b83a3c4bcef4f2f99357eb4a5eaae75dec51c32f3c197aa3') + version('1.10.4', sha256='8ce443dc79656a9fc97a7837f1444d324aef2c9b53f31f83441f57ad1f1f3659') version('1.9.3', sha256='baa074bb1c7f9c822122fb81459b7caa5fc49267ca94cca69465c8dcfd63ac79') - version('1.9.2', 'e80c19d2fb25af576460bb7dac31c59a') - version('1.9.1', '223532d8e1bdaff5d30936439701d6e1') + version('1.9.2', sha256='e37805754f4ebb575c434d134f6bebb8b857d9843c393f6943c7be71ef57311c') + version('1.9.1', sha256='2a545c0d096d86035b12160fcba5e4c0a08dcabbf902b4f867eb64deb31a2b7a') variant('blas', default=True, description='Build with BLAS support') variant('lapack', default=True, description='Build with LAPACK support') diff --git a/var/spack/repos/builtin/packages/py-numpydoc/package.py b/var/spack/repos/builtin/packages/py-numpydoc/package.py index e7096081e5c..bd9607c7c40 100644 --- a/var/spack/repos/builtin/packages/py-numpydoc/package.py +++ b/var/spack/repos/builtin/packages/py-numpydoc/package.py @@ -12,7 +12,7 @@ class PyNumpydoc(PythonPackage): homepage = "https://github.com/numpy/numpydoc" url = "https://pypi.io/packages/source/n/numpydoc/numpydoc-0.6.0.tar.gz" - version('0.6.0', '5f1763c44e613850d56ba1b1cf1cb146') + version('0.6.0', sha256='1ec573e91f6d868a9940d90a6599f3e834a2d6c064030fbe078d922ee21dcfa1') depends_on('python@2.6:2.8,3.3:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-olefile/package.py b/var/spack/repos/builtin/packages/py-olefile/package.py index 97668d645b1..44f256319fc 100644 --- a/var/spack/repos/builtin/packages/py-olefile/package.py +++ b/var/spack/repos/builtin/packages/py-olefile/package.py @@ -14,6 +14,6 @@ class PyOlefile(PythonPackage): import_modules = ['olefile'] - version('0.44', 'fc625554e4e7f0c2ddcd00baa3c74ff5') + version('0.44', sha256='61f2ca0cd0aa77279eb943c07f607438edf374096b66332fae1ee64a6f0f73ad') depends_on('python@2.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py index cec2f634d96..fbbd3e22a39 100644 --- a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py +++ b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py @@ -17,7 +17,7 @@ class PyOntFast5Api(PythonPackage): homepage = "https://github.com/nanoporetech/ont_fast5_api" url = "https://pypi.io/packages/source/o/ont-fast5-api/ont-fast5-api-0.3.2.tar.gz" - version('0.3.2', '2ccfdbcd55239ffae712bb6e70ebfe8c') + version('0.3.2', sha256='ae44b1bcd812e8acf8beff3db92456647c343cf19340f97cff4847de5cc905d8') depends_on('py-setuptools', type='build') depends_on('py-h5py', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-openpmd-validator/package.py b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py index 07cdf90ee86..4018c8419f1 100644 --- a/var/spack/repos/builtin/packages/py-openpmd-validator/package.py +++ b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py @@ -15,7 +15,7 @@ class PyOpenpmdValidator(PythonPackage): url = "https://github.com/openPMD/openPMD-validator/archive/1.0.0.2.tar.gz" maintainers = ['ax3l'] - version('1.0.0.2', '2b71b786288c1e7a2134bd6818ad1999') + version('1.0.0.2', sha256='1b97452991feb0f0ac1ffb3c92b7f9743a86b0b5390dbbfb21160e04f0a35a95') depends_on('py-setuptools', type='build') depends_on('py-numpy@1.6.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py index 4502183054a..3b75d17a6d4 100644 --- a/var/spack/repos/builtin/packages/py-openpyxl/package.py +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -12,8 +12,8 @@ class PyOpenpyxl(PythonPackage): homepage = "http://openpyxl.readthedocs.org/" url = "https://pypi.io/packages/source/o/openpyxl/openpyxl-2.4.5.tar.gz" - version('2.4.5', '3de13dc9b731e1a9dd61b873d9b35a8a') - version('2.2.0-b1', 'eeefabe384f6e53166c8c2e6abe5d11b') + version('2.4.5', sha256='78c331e819fb0a63a1339d452ba0b575d1a31f09fdcce793a31bec7e9ef4ef21') + version('2.2.0-b1', md5='eeefabe384f6e53166c8c2e6abe5d11b') depends_on('python@2.6:2.8,3.0:3.1,3.3:') diff --git a/var/spack/repos/builtin/packages/py-openslide-python/package.py b/var/spack/repos/builtin/packages/py-openslide-python/package.py index 085e6a36bf1..ff1632a150b 100644 --- a/var/spack/repos/builtin/packages/py-openslide-python/package.py +++ b/var/spack/repos/builtin/packages/py-openslide-python/package.py @@ -12,7 +12,7 @@ class PyOpenslidePython(PythonPackage): homepage = "https://github.com/openslide/openslide-python" url = "https://github.com/openslide/openslide-python/archive/v1.1.1.tar.gz" - version('1.1.1', '8c207e48069887b63ea1c7bc9eb7dfc0') + version('1.1.1', sha256='33c390fe43e3d7d443fafdd66969392d3e9efd2ecd5d4af73c3dbac374485ed5') import_modules = ['openslide'] diff --git a/var/spack/repos/builtin/packages/py-ordereddict/package.py b/var/spack/repos/builtin/packages/py-ordereddict/package.py index fc15571ce6c..4e40791d62a 100644 --- a/var/spack/repos/builtin/packages/py-ordereddict/package.py +++ b/var/spack/repos/builtin/packages/py-ordereddict/package.py @@ -15,4 +15,4 @@ class PyOrdereddict(PythonPackage): import_modules = ['ordereddict'] - version('1.1', 'a0ed854ee442051b249bfad0f638bbec') + version('1.1', sha256='1c35b4ac206cef2d24816c89f89cf289dd3d38cf7c449bb3fab7bf6d43f01b1f') diff --git a/var/spack/repos/builtin/packages/py-oset/package.py b/var/spack/repos/builtin/packages/py-oset/package.py index 60b5a1f7762..225d7a62caa 100644 --- a/var/spack/repos/builtin/packages/py-oset/package.py +++ b/var/spack/repos/builtin/packages/py-oset/package.py @@ -14,7 +14,7 @@ class PyOset(PythonPackage): import_modules = ['oset'] - version('0.1.3', 'f23e5a545d2c77df3916398d2d39a3ab') + version('0.1.3', sha256='4c1fd7dec96eeff9d3260995a8e37f9f415d0bdb79975f57824e68716ac8f904') depends_on('py-setuptools', type='build') depends_on('python@2.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-owslib/package.py b/var/spack/repos/builtin/packages/py-owslib/package.py index 09a3993719c..3d0a8adc99f 100644 --- a/var/spack/repos/builtin/packages/py-owslib/package.py +++ b/var/spack/repos/builtin/packages/py-owslib/package.py @@ -14,7 +14,7 @@ class PyOwslib(PythonPackage): homepage = "http://http://geopython.github.io/OWSLib/#installation" url = "https://pypi.io/packages/source/O/OWSLib/OWSLib-0.16.0.tar.gz" - version('0.16.0', '7ff9c9edde95eadeb27ea8d8fbd1a2cf') + version('0.16.0', sha256='ec95a5e93c145a5d84b0074b9ea27570943486552a669151140debf08a100554') depends_on('py-setuptools', type='build') depends_on('py-python-dateutil@1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-packaging/package.py b/var/spack/repos/builtin/packages/py-packaging/package.py index 3417c52dd8b..f6c51442a30 100644 --- a/var/spack/repos/builtin/packages/py-packaging/package.py +++ b/var/spack/repos/builtin/packages/py-packaging/package.py @@ -15,8 +15,8 @@ class PyPackaging(PythonPackage): import_modules = ['packaging'] version('19.1', sha256='c491ca87294da7cc01902edbe30a5bc6c4c28172b5138ab4e4aa1b9d7bfaeafe') - version('17.1', '8baf8241d1b6b0a5fae9b00f359976a8') - version('16.8', '53895cdca04ecff80b54128e475b5d3b') + version('17.1', sha256='f019b770dd64e585a99714f1fd5e01c7a8f11b45635aa953fd41c689a657375b') + version('16.8', sha256='5d50835fdf0a7edf0b55e311b7c887786504efea1177abd7e69329a8e5ea619e') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-attrs', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-palettable/package.py b/var/spack/repos/builtin/packages/py-palettable/package.py index 135dd7664c9..1646f6dfb73 100644 --- a/var/spack/repos/builtin/packages/py-palettable/package.py +++ b/var/spack/repos/builtin/packages/py-palettable/package.py @@ -12,6 +12,6 @@ class PyPalettable(PythonPackage): homepage = "https://jiffyclub.github.io/palettable/" url = "https://pypi.io/packages/source/p/palettable/palettable-3.0.0.tar.gz" - version('3.0.0', '6e430319fe01386c81dbbc62534e3cc4') + version('3.0.0', sha256='eed9eb0399386ff42f90ca61d4fa38a1819a93d5adfc2d546e3e2869d9972c31') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 4da6ba3cc93..80075772d66 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -38,13 +38,13 @@ class PyPandas(PythonPackage): version('0.24.2', sha256='4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2') version('0.24.1', sha256='435821cb2501eabbcee7e83614bd710940dc0cf28b5afbc4bdb816c31cec71af') version('0.23.4', sha256='5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4') - version('0.21.1', '42ae7f81b81a86c3f91f663b66c525f7') + version('0.21.1', sha256='c5f5cba88bf0659554c41c909e1f78139f6fce8fa9315a29a23692b38ff9788a') version('0.20.0', sha256='54f7a2bb2a7832c0446ad51d779806f07ec4ea2bb7c9aea4b83669fa97e778c4') - version('0.19.2', '26df3ef7cd5686fa284321f4f48b38cd') - version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3') - version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') - version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') - version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73') + version('0.19.2', sha256='6f0f4f598c2b16746803c8bafef7c721c57e4844da752d36240c0acf97658014') + version('0.19.0', sha256='4697606cdf023c6b7fcb74e48aaf25cf282a1a00e339d2d274cf1b663748805b') + version('0.18.0', sha256='c975710ce8154b50f39a46aa3ea88d95b680191d1d9d4b5dd91eae7215e01814') + version('0.16.1', sha256='570d243f8cb068bf780461b9225d2e7bef7c90aa10d43cf908fe541fc92df8b6') + version('0.16.0', sha256='4013de6f8796ca9d2871218861823bd9878a8dfacd26e08ccf9afdd01bbad9f1') # https://dev.pandas.io/install.html#dependencies # Required dependencies diff --git a/var/spack/repos/builtin/packages/py-paramiko/package.py b/var/spack/repos/builtin/packages/py-paramiko/package.py index 554f3ad29a1..a5f68cf46bb 100644 --- a/var/spack/repos/builtin/packages/py-paramiko/package.py +++ b/var/spack/repos/builtin/packages/py-paramiko/package.py @@ -13,7 +13,7 @@ class PyParamiko(PythonPackage): homepage = "http://www.paramiko.org/" url = "https://pypi.io/packages/source/p/paramiko/paramiko-2.1.2.tar.gz" - version('2.1.2', '41a8ea0e8abb03a6bf59870670d4f46c') + version('2.1.2', sha256='5fae49bed35e2e3d45c4f7b0db2d38b9ca626312d91119b3991d0ecf8125e310') depends_on('py-setuptools', type='build') depends_on('py-pyasn1@0.1.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-partd/package.py b/var/spack/repos/builtin/packages/py-partd/package.py index 6bc45cfbceb..e40968871f2 100644 --- a/var/spack/repos/builtin/packages/py-partd/package.py +++ b/var/spack/repos/builtin/packages/py-partd/package.py @@ -14,7 +14,7 @@ class PyPartd(PythonPackage): import_modules = ['partd'] - version('0.3.8', '554d0e6511c0df4c907f034858be847f') + version('0.3.8', sha256='67291f1c4827cde3e0148b3be5d69af64b6d6169feb9ba88f0a6cfe77089400f') depends_on('py-setuptools', type='build') depends_on('py-locket', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pathlib2/package.py b/var/spack/repos/builtin/packages/py-pathlib2/package.py index b251f485663..25a852d1f4d 100644 --- a/var/spack/repos/builtin/packages/py-pathlib2/package.py +++ b/var/spack/repos/builtin/packages/py-pathlib2/package.py @@ -14,8 +14,8 @@ class PyPathlib2(PythonPackage): import_modules = ['pathlib2'] - version('2.3.2', 'fd76fb5d0baa798bfe12fb7965da97f8') - version('2.1.0', '38e4f58b4d69dfcb9edb49a54a8b28d2') + version('2.3.2', sha256='8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83') + version('2.1.0', sha256='deb3a960c1d55868dfbcac98432358b92ba89d95029cddd4040db1f27405055c') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pathos/package.py b/var/spack/repos/builtin/packages/py-pathos/package.py index 679e682eaef..73930a0303d 100644 --- a/var/spack/repos/builtin/packages/py-pathos/package.py +++ b/var/spack/repos/builtin/packages/py-pathos/package.py @@ -12,7 +12,7 @@ class PyPathos(PythonPackage): homepage = "https://github.com/uqfoundation/pathos" url = "https://pypi.io/packages/source/p/pathos/pathos-0.2.0.zip" - version('0.2.0', '7a840ce6c3a67d71e6ad7339034ec53e') + version('0.2.0', sha256='2f4e67e7914c95fb0cce766bab173eb2c5860ee420108fa183099557ac2e50e9') depends_on('python@2.6:2.8,3.1:') diff --git a/var/spack/repos/builtin/packages/py-pathspec/package.py b/var/spack/repos/builtin/packages/py-pathspec/package.py index 3bafca8c7d0..75de04f4a5b 100644 --- a/var/spack/repos/builtin/packages/py-pathspec/package.py +++ b/var/spack/repos/builtin/packages/py-pathspec/package.py @@ -13,6 +13,6 @@ class PyPathspec(PythonPackage): homepage = "https://pypi.python.org/pypi/pathspec" url = "https://pypi.io/packages/source/p/pathspec/pathspec-0.3.4.tar.gz" - version('0.3.4', '2a4af9bf2dee98845d583ec61a00d05d') + version('0.3.4', sha256='7605ca5c26f554766afe1d177164a2275a85bb803b76eba3428f422972f66728') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-patsy/package.py b/var/spack/repos/builtin/packages/py-patsy/package.py index 6ffd4e19b91..d5e744d1d0f 100644 --- a/var/spack/repos/builtin/packages/py-patsy/package.py +++ b/var/spack/repos/builtin/packages/py-patsy/package.py @@ -11,7 +11,7 @@ class PyPatsy(PythonPackage): homepage = "https://github.com/pydata/patsy" url = "https://pypi.io/packages/source/p/patsy/patsy-0.4.1.zip" - version('0.4.1', '9445f29e3426d1ed30d683a1e1453f84') + version('0.4.1', sha256='dc1cc280045b0e6e50c04706fd1e26d2a00ea400aa112f88e8142f88b0b7d3d4') variant('splines', default=False, description="Offers spline related functions") diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py index 7b0e26864e6..4d737ffbcde 100644 --- a/var/spack/repos/builtin/packages/py-pbr/package.py +++ b/var/spack/repos/builtin/packages/py-pbr/package.py @@ -12,10 +12,10 @@ class PyPbr(PythonPackage): homepage = "https://pypi.python.org/pypi/pbr" url = "https://pypi.io/packages/source/p/pbr/pbr-1.10.0.tar.gz" - version('3.1.1', '4e82c2e07af544c56a5b71c801525b00') - version('2.0.0', 'dfc1c3788eff06acfaade6f1655fa490') - version('1.10.0', '8e4968c587268f030e38329feb9c8f17') - version('1.8.1', 'c8f9285e1a4ca6f9654c529b158baa3a') + version('3.1.1', sha256='05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1') + version('2.0.0', sha256='0ccd2db529afd070df815b1521f01401d43de03941170f8a800e7531faba265d') + version('1.10.0', sha256='186428c270309e6fdfe2d5ab0949ab21ae5f7dea831eab96701b86bd666af39c') + version('1.8.1', sha256='e2127626a91e6c885db89668976db31020f0af2da728924b56480fc7ccf09649') depends_on('py-setuptools', type='build') # Only needed for py<3.4, however when='^python@:3.4.2' syntax might be diff --git a/var/spack/repos/builtin/packages/py-pep8-naming/package.py b/var/spack/repos/builtin/packages/py-pep8-naming/package.py index 7dfbbee6a4b..3783fa2afa7 100644 --- a/var/spack/repos/builtin/packages/py-pep8-naming/package.py +++ b/var/spack/repos/builtin/packages/py-pep8-naming/package.py @@ -13,6 +13,6 @@ class PyPep8Naming(PythonPackage): url = "https://files.pythonhosted.org/packages/3e/4a/125425d6b1e017f48dfc9c961f4bb9510168db7a090618906c750184ed03/pep8-naming-0.7.0.tar.gz" extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)') - version('0.7.0', '624258e0dd06ef32a9daf3c36cc925ff7314da7233209c5b01f7e5cdd3c34826') + version('0.7.0', sha256='624258e0dd06ef32a9daf3c36cc925ff7314da7233209c5b01f7e5cdd3c34826') depends_on('py-flake8-polyfill', type='run') diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py index 0ed974cf34b..0e260347570 100644 --- a/var/spack/repos/builtin/packages/py-periodictable/package.py +++ b/var/spack/repos/builtin/packages/py-periodictable/package.py @@ -14,7 +14,7 @@ class PyPeriodictable(PythonPackage): url = "https://pypi.io/packages/source/p/periodictable/periodictable-1.4.1.tar.gz" version('1.5.0', sha256='b020c04c6765d21903e4604a76ca33cda98677003fe6eb48ed3690cfb03253b2') - version('1.4.1', '7246b63cc0b6b1be6e86b6616f9e866e') + version('1.4.1', sha256='f42e66f6efca33caec4f27dad8d6a6d4e59da147ecf5adfce152cb84e7bd160b') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pexpect/package.py b/var/spack/repos/builtin/packages/py-pexpect/package.py index 02f1995fe92..0c9e08dc2a8 100644 --- a/var/spack/repos/builtin/packages/py-pexpect/package.py +++ b/var/spack/repos/builtin/packages/py-pexpect/package.py @@ -11,8 +11,8 @@ class PyPexpect(PythonPackage): homepage = "https://pypi.python.org/pypi/pexpect" url = "https://pypi.io/packages/source/p/pexpect/pexpect-4.2.1.tar.gz" - version('4.6.0', 'd4f3372965a996238d57d19b95d2e03a') - version('4.2.1', '3694410001a99dff83f0b500a1ca1c95') - version('3.3', '0de72541d3f1374b795472fed841dce8') + version('4.6.0', sha256='2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba') + version('4.2.1', sha256='3d132465a75b57aa818341c6521392a06cc660feb3988d7f1074f39bd23c9a92') + version('3.3', sha256='dfea618d43e83cfff21504f18f98019ba520f330e4142e5185ef7c73527de5ba') depends_on('py-ptyprocess', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py index 48f0c5e0aeb..6b3202df4ab 100644 --- a/var/spack/repos/builtin/packages/py-phonopy/package.py +++ b/var/spack/repos/builtin/packages/py-phonopy/package.py @@ -12,7 +12,7 @@ class PyPhonopy(PythonPackage): homepage = "http://atztogo.github.io/phonopy/index.html" url = "http://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz" - version('1.10.0', '973ed1bcea46e21b9bf747aab9061ff6') + version('1.10.0', sha256='6b7c540bbbb033203c45b8472696db02a3a55913a0e5eb23de4dc9a3bee473f7') depends_on('py-numpy', type=('build', 'run')) depends_on('py-scipy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pickleshare/package.py b/var/spack/repos/builtin/packages/py-pickleshare/package.py index 54bb9e5b4c3..c8a9a61e44a 100644 --- a/var/spack/repos/builtin/packages/py-pickleshare/package.py +++ b/var/spack/repos/builtin/packages/py-pickleshare/package.py @@ -12,6 +12,6 @@ class PyPickleshare(PythonPackage): homepage = "https://pypi.python.org/pypi/pickleshare" url = "https://pypi.io/packages/source/p/pickleshare/pickleshare-0.7.4.tar.gz" - version('0.7.4', '6a9e5dd8dfc023031f6b7b3f824cab12') + version('0.7.4', sha256='84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pil/package.py b/var/spack/repos/builtin/packages/py-pil/package.py index 88d737bf88b..a5bd284d886 100644 --- a/var/spack/repos/builtin/packages/py-pil/package.py +++ b/var/spack/repos/builtin/packages/py-pil/package.py @@ -14,7 +14,7 @@ class PyPil(PythonPackage): homepage = "http://www.pythonware.com/products/pil/" url = "http://effbot.org/media/downloads/Imaging-1.1.7.tar.gz" - version('1.1.7', 'fc14a54e1ce02a0225be8854bfba478e') + version('1.1.7', sha256='895bc7c2498c8e1f9b99938f1a40dc86b3f149741f105cf7c7bd2e0725405211') provides('pil') diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index ddb3bca652b..861dca8b41f 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -16,10 +16,10 @@ class PyPillow(PythonPackage): homepage = "https://python-pillow.org/" url = "https://pypi.io/packages/source/P/Pillow/Pillow-5.1.0.tar.gz" - version('5.4.1', 'f7d0ce066fc7ea7a685739227887aeaf') - version('5.1.0', '308f9c13b376abce96ab6ebd6c889cc4') - version('3.2.0', '7cfd093c11205d9e2ebe3c51dfcad510') - version('3.0.0', 'fc8ac44e93da09678eac7e30c9b7377d') + version('5.4.1', sha256='5233664eadfa342c639b9b9977190d64ad7aca4edc51a966394d7e08e7f38a9f') + version('5.1.0', sha256='cee9bc75bff455d317b6947081df0824a8f118de2786dc3d74a3503fd631f4ef') + version('3.2.0', sha256='64b0a057210c480aea99406c9391180cd866fc0fd8f0b53367e3af21b195784a') + version('3.0.0', sha256='ad50bef540fe5518a4653c3820452a881b6a042cb0f8bb7657c491c6bd3654bb') provides('pil') diff --git a/var/spack/repos/builtin/packages/py-pint/package.py b/var/spack/repos/builtin/packages/py-pint/package.py index f78549a7dd1..4466111348a 100644 --- a/var/spack/repos/builtin/packages/py-pint/package.py +++ b/var/spack/repos/builtin/packages/py-pint/package.py @@ -15,6 +15,6 @@ class PyPint(PythonPackage): homepage = "https://pypi.python.org/pypi/pint" url = "https://pypi.io/packages/source/p/pint/Pint-0.8.1.tar.gz" - version('0.8.1', 'afcf31443a478c32bbac4b00337ee9026a13d0e2ac83d30c79151462513bb0d4') + version('0.8.1', sha256='afcf31443a478c32bbac4b00337ee9026a13d0e2ac83d30c79151462513bb0d4') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pip/package.py b/var/spack/repos/builtin/packages/py-pip/package.py index bc000d0aad8..28a58dea5f0 100644 --- a/var/spack/repos/builtin/packages/py-pip/package.py +++ b/var/spack/repos/builtin/packages/py-pip/package.py @@ -14,8 +14,8 @@ class PyPip(PythonPackage): version('19.0.3', sha256='6e6f197a1abfb45118dbb878b5c859a0edbdd33fd250100bc015b67fded4b9f2') version('18.1', sha256='c0a292bd977ef590379a3f05d7b7f65135487b67470f6281289a94e015650ea1') - version('10.0.1', '83a177756e2c801d0b3a6f7b0d4f3f7e') - version('9.0.1', '35f01da33009719497f01a4ba69d63c9') + version('10.0.1', sha256='f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68') + version('9.0.1', sha256='09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d') depends_on('python@2.6:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-pipits/package.py b/var/spack/repos/builtin/packages/py-pipits/package.py index b97ef7b61b4..666e738cfc0 100644 --- a/var/spack/repos/builtin/packages/py-pipits/package.py +++ b/var/spack/repos/builtin/packages/py-pipits/package.py @@ -13,7 +13,7 @@ class PyPipits(PythonPackage): url = "https://github.com/hsgweon/pipits/archive/2.4.tar.gz" version('2.4', sha256='b08a9d70ac6e5dd1c64d56b77384afd69e21e7d641b2fc4416feff862a2cd054') - version('1.5.0', '3f9b52bd7ffbcdb96d7bec150275070a') + version('1.5.0', sha256='6c76fff42a9db62ff4bb1d4d520ebee6cb20d5a726f12c3d5a3d42314947a659') # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pipits/meta.yaml depends_on('python@3:', type=('build', 'run'), when='@2:') diff --git a/var/spack/repos/builtin/packages/py-pkgconfig/package.py b/var/spack/repos/builtin/packages/py-pkgconfig/package.py index b5c647846f1..d1d0ab004ac 100644 --- a/var/spack/repos/builtin/packages/py-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/py-pkgconfig/package.py @@ -13,7 +13,7 @@ class PyPkgconfig(PythonPackage): url = "https://pypi.io/packages/source/p/pkgconfig/pkgconfig-1.2.2.tar.gz" version('1.4.0', sha256='048c3b457da7b6f686b647ab10bf09e2250e4c50acfe6f215398a8b5e6fcdb52') - version('1.2.2', '81a8f6ef3371831d081e03db39e09683') + version('1.2.2', sha256='3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa') depends_on('python@2.6:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-plotly/package.py b/var/spack/repos/builtin/packages/py-plotly/package.py index d3d9aa15cc2..cd315180ed3 100644 --- a/var/spack/repos/builtin/packages/py-plotly/package.py +++ b/var/spack/repos/builtin/packages/py-plotly/package.py @@ -12,7 +12,7 @@ class PyPlotly(PythonPackage): homepage = "https://plot.ly/python/" url = "https://github.com/plotly/plotly.py/archive/v2.2.0.tar.gz" - version('2.2.0', '835802cdc6743439ff993447dfe47a0e') + version('2.2.0', sha256='dad2a49fe355dddb6ae159e96c10ac22413a33cbac513b4dbf3791e63ec33c1f') depends_on('py-setuptools', type='build') depends_on('py-requests@2.3.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pluggy/package.py b/var/spack/repos/builtin/packages/py-pluggy/package.py index 3486c7158f6..d1462389e08 100644 --- a/var/spack/repos/builtin/packages/py-pluggy/package.py +++ b/var/spack/repos/builtin/packages/py-pluggy/package.py @@ -15,8 +15,8 @@ class PyPluggy(PythonPackage): import_modules = ['pluggy'] version('0.12.0', sha256='0825a152ac059776623854c1543d65a4ad408eb3d33ee114dff91e57ec6ae6fc') - version('0.7.1', 'cd5cc1003143f86dd6e2a865a20f8837') - version('0.6.0', 'ffdde7c3a5ba9a440404570366ffb6d5') + version('0.7.1', sha256='95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1') + version('0.6.0', sha256='7f8ae7f5bdf75671a718d2daf0a64b7885f74510bcd98b1a0bb420eb9a9d0cff') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ply/package.py b/var/spack/repos/builtin/packages/py-ply/package.py index 999e2b69890..8c2b20c67ba 100644 --- a/var/spack/repos/builtin/packages/py-ply/package.py +++ b/var/spack/repos/builtin/packages/py-ply/package.py @@ -11,5 +11,5 @@ class PyPly(PythonPackage): homepage = "http://www.dabeaz.com/ply" url = "http://www.dabeaz.com/ply/ply-3.11.tar.gz" - version('3.11', '6465f602e656455affcd7c5734c638f8') - version('3.8', '94726411496c52c87c2b9429b12d5c50') + version('3.11', sha256='00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3') + version('3.8', sha256='e7d1bdff026beb159c9942f7a17e102c375638d9478a7ecd4cc0c76afd8de0b8') diff --git a/var/spack/repos/builtin/packages/py-pmw/package.py b/var/spack/repos/builtin/packages/py-pmw/package.py index 028e12a5add..33b1d2e6800 100644 --- a/var/spack/repos/builtin/packages/py-pmw/package.py +++ b/var/spack/repos/builtin/packages/py-pmw/package.py @@ -12,5 +12,5 @@ class PyPmw(PythonPackage): homepage = "https://pypi.python.org/pypi/Pmw" url = "https://pypi.io/packages/source/P/Pmw/Pmw-2.0.0.tar.gz" - version('2.0.1', '8080b0fabc731ff236f97e88e13b3938') - version('2.0.0', 'c7c3f26c4f5abaa99807edefee578fc0') + version('2.0.1', sha256='0b9d28f52755a7a081b44591c3dd912054f896e56c9a627db4dd228306ad1120') + version('2.0.0', sha256='2babb2855feaabeea1003c6908b61c9d39cff606d418685f0559952714c680bb') diff --git a/var/spack/repos/builtin/packages/py-poster/package.py b/var/spack/repos/builtin/packages/py-poster/package.py index 1a32dc731e9..d7952fe6cb6 100644 --- a/var/spack/repos/builtin/packages/py-poster/package.py +++ b/var/spack/repos/builtin/packages/py-poster/package.py @@ -12,7 +12,7 @@ class PyPoster(PythonPackage): homepage = "https://pypi.org/project/poster/" url = "https://atlee.ca/software/poster/dist/0.8.1/poster-0.8.1.tar.gz" - version('0.8.1', '2db12704538781fbaa7e63f1505d6fc8') + version('0.8.1', sha256='af5bf45da4a916db2b638cffd9e9d6668b33020e2b8ca9f864db79b49331c6ff') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pox/package.py b/var/spack/repos/builtin/packages/py-pox/package.py index 4c3c00766fb..d0c3f99810f 100644 --- a/var/spack/repos/builtin/packages/py-pox/package.py +++ b/var/spack/repos/builtin/packages/py-pox/package.py @@ -12,9 +12,9 @@ class PyPox(PythonPackage): homepage = "https://github.com/uqfoundation/pox" url = "https://pypi.io/packages/source/p/pox/pox-0.2.3.zip" - version('0.2.3', 'fcdfd9a9ab0f72367258b675554f6a83') - version('0.2.2', 'e1e2ce99a63d7226ea3c1a2ce389610d') - version('0.2.1', '517dc13c2bc2429d36a0c636f3ce42db') + version('0.2.3', sha256='d3e8167a1ebe08ae56262a0b9359118d90bc4648cd284b5d10ae240343100a75') + version('0.2.2', sha256='c0b88e59ef0e4f2fa4839e11bf90d2c32d6ceb5abaf01f0c8138f7558e6f87c1') + version('0.2.1', sha256='580bf731fee233c58eac0974011b5bf0698efb7337b0a1696d289043b4fcd7f4') depends_on('python@2.5:2.8,3.1:') diff --git a/var/spack/repos/builtin/packages/py-ppft/package.py b/var/spack/repos/builtin/packages/py-ppft/package.py index b377ad006bc..49fa256cdc5 100644 --- a/var/spack/repos/builtin/packages/py-ppft/package.py +++ b/var/spack/repos/builtin/packages/py-ppft/package.py @@ -12,9 +12,9 @@ class PyPpft(PythonPackage): homepage = "https://github.com/uqfoundation/ppft" url = "https://pypi.io/packages/source/p/ppft/ppft-1.6.4.7.1.zip" - version('1.6.4.7.1', '2b196a03bfbc102773f849c6b21e617b') - version('1.6.4.6', 'e533432bfba4b5a523a07d58011df209') - version('1.6.4.5', 'd2b1f9f07eae22b31bfe90f544dd3044') + version('1.6.4.7.1', sha256='f94b26491b4a36adc975fc51dba7568089a24756007a3a4ef3414a98d7337651') + version('1.6.4.6', sha256='92d09061f5425634c43dbf99c5558f2cf2a2e1e351929f8da7e85f4649c11095') + version('1.6.4.5', sha256='d47da9d2e553848b75727ce7c510f9e149965d5c68f9fc56c774a7c6a3d18214') depends_on('python@2.5:2.8,3.1:') diff --git a/var/spack/repos/builtin/packages/py-prettytable/package.py b/var/spack/repos/builtin/packages/py-prettytable/package.py index 572b47f4437..f4aecdd8a15 100644 --- a/var/spack/repos/builtin/packages/py-prettytable/package.py +++ b/var/spack/repos/builtin/packages/py-prettytable/package.py @@ -15,6 +15,6 @@ class PyPrettytable(PythonPackage): homepage = "https://code.google.com/archive/p/prettytable/" url = "https://pypi.io/packages/source/p/prettytable/prettytable-0.7.2.tar.gz" - version('0.7.2', 'a6b80afeef286ce66733d54a0296b13b') + version('0.7.2', sha256='2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9') depends_on("py-setuptools", type='build') diff --git a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py index 1e8a04f5cd8..212fa469f5b 100644 --- a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py +++ b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py @@ -13,7 +13,7 @@ class PyPromptToolkit(PythonPackage): url = "https://pypi.io/packages/source/p/prompt_toolkit/prompt_toolkit-1.0.9.tar.gz" version('2.0.9', sha256='2519ad1d8038fd5fc8e770362237ad0364d16a7650fb5724af6997ed5515e3c1') - version('1.0.9', 'a39f91a54308fb7446b1a421c11f227c') + version('1.0.9', sha256='cd6523b36adc174cc10d54b1193eb626b4268609ff6ea92c15bcf1996609599c') depends_on('py-setuptools', type='build') depends_on('py-six@1.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py index c23029faa11..edab6e1524f 100644 --- a/var/spack/repos/builtin/packages/py-protobuf/package.py +++ b/var/spack/repos/builtin/packages/py-protobuf/package.py @@ -22,14 +22,14 @@ class PyProtobuf(PythonPackage): version('3.7.1', sha256='21e395d7959551e759d604940a115c51c6347d90a475c9baf471a1a86b5604a9') version('3.6.1', sha256='1489b376b0f364bcc6f89519718c057eb191d7ad6f1b395ffd93d1aa45587811') - version('3.5.2.post1', '3b60685732bd0cbdc802dfcb6071efbcf5d927ce3127c13c33ea1a8efae3aa76') - version('3.5.2', '09879a295fd7234e523b62066223b128c5a8a88f682e3aff62fb115e4a0d8be0') - version('3.5.1', '95b78959572de7d7fafa3acb718ed71f482932ddddddbd29ba8319c10639d863') - version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83') - version('2.6.1', '6bf843912193f70073db7f22e2ea55e2') - version('2.5.0', '338813f3629d59e9579fed9035ecd457') - version('2.4.1', '72f5141d20ab1bcae6b1e00acfb1068a') - version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd') + version('3.5.2.post1', sha256='3b60685732bd0cbdc802dfcb6071efbcf5d927ce3127c13c33ea1a8efae3aa76') + version('3.5.2', sha256='09879a295fd7234e523b62066223b128c5a8a88f682e3aff62fb115e4a0d8be0') + version('3.5.1', sha256='95b78959572de7d7fafa3acb718ed71f482932ddddddbd29ba8319c10639d863') + version('3.0.0b2', sha256='d5b560bbc4b7d97cc2455c05cad9299d9db02d7bd11193b05684e3a86303c229') + version('2.6.1', sha256='8faca1fb462ee1be58d00f5efb4ca4f64bde92187fe61fde32615bbee7b3e745') + version('2.5.0', sha256='58292c459598c9297258bf57acc055f701c727f0154a86af8c0947dde37d8172') + version('2.4.1', sha256='df30b98acb6ef892da8b4776175510cff2131908fd0526b6bad960c55a830a1b') + version('2.3.0', sha256='374bb047874a506507912c3717d0ce62affbaa9a22bcb494d63d60326a0867b5') depends_on('py-setuptools', type='build') depends_on('protobuf', when='+cpp') diff --git a/var/spack/repos/builtin/packages/py-psutil/package.py b/var/spack/repos/builtin/packages/py-psutil/package.py index 9e90d23dbe9..2e4abedf6cf 100644 --- a/var/spack/repos/builtin/packages/py-psutil/package.py +++ b/var/spack/repos/builtin/packages/py-psutil/package.py @@ -14,9 +14,9 @@ class PyPsutil(PythonPackage): homepage = "https://pypi.python.org/pypi/psutil" url = "https://pypi.io/packages/source/p/psutil/psutil-5.4.5.tar.gz" - version('5.5.1', '81d6969ba8392cd3b6f5cba6c4e77caa') - version('5.4.5', '7d3d7954782bba4a400e106e66f10656') - version('5.0.1', '153dc8be94badc4072016ceeac7808dc') + version('5.5.1', sha256='72cebfaa422b7978a1d3632b65ff734a34c6b34f4578b68a5c204d633756b810') + version('5.4.5', sha256='ebe293be36bb24b95cdefc5131635496e88b17fabbcf1e4bc9b5c01f5e489cfe') + version('5.0.1', sha256='9d8b7f8353a2b2eb6eb7271d42ec99d0d264a9338a37be46424d56b4e473b39e') depends_on('python@2.6:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-psycopg2/package.py b/var/spack/repos/builtin/packages/py-psycopg2/package.py index f478ee0a06a..0483c794afb 100644 --- a/var/spack/repos/builtin/packages/py-psycopg2/package.py +++ b/var/spack/repos/builtin/packages/py-psycopg2/package.py @@ -12,7 +12,7 @@ class PyPsycopg2(PythonPackage): homepage = "http://initd.org/psycopg/" url = "http://initd.org/psycopg/tarballs/PSYCOPG-2-7/psycopg2-2.7.5.tar.gz" - version('2.7.5', '9e7d6f695fc7f8d1c42a7905449246c9') + version('2.7.5', sha256='eccf962d41ca46e6326b97c8fe0a6687b58dfc1a5f6540ed071ff1474cea749e') depends_on('py-setuptools', type='build') depends_on('postgresql', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ptyprocess/package.py b/var/spack/repos/builtin/packages/py-ptyprocess/package.py index 21097dba633..c0734d41cbe 100644 --- a/var/spack/repos/builtin/packages/py-ptyprocess/package.py +++ b/var/spack/repos/builtin/packages/py-ptyprocess/package.py @@ -12,4 +12,4 @@ class PyPtyprocess(PythonPackage): homepage = "https://pypi.python.org/pypi/ptyprocess" url = "https://pypi.io/packages/source/p/ptyprocess/ptyprocess-0.5.1.tar.gz" - version('0.5.1', '94e537122914cc9ec9c1eadcd36e73a1') + version('0.5.1', sha256='0530ce63a9295bfae7bd06edc02b6aa935619f486f0f1dc0972f516265ee81a6') diff --git a/var/spack/repos/builtin/packages/py-pudb/package.py b/var/spack/repos/builtin/packages/py-pudb/package.py index b0c357bb5f3..4826be0031d 100644 --- a/var/spack/repos/builtin/packages/py-pudb/package.py +++ b/var/spack/repos/builtin/packages/py-pudb/package.py @@ -13,8 +13,8 @@ class PyPudb(PythonPackage): homepage = "http://mathema.tician.de/software/pudb" url = "https://pypi.io/packages/source/p/pudb/pudb-2017.1.1.tar.gz" - version('2017.1.1', '4ec3302ef90f22b13c60db16b3557c56') - version('2016.2', '4573b70163329c1cb59836a357bfdf7c') + version('2017.1.1', sha256='87117640902c5f602c8517d0167eb5c953a5bdede97975ba29ff17e3d570442c') + version('2016.2', sha256='e958d7f7b1771cf297714e95054075df3b2a47455d7a740be4abbbd41289505a') # Most Python packages only require setuptools as a build dependency. # However, pudb requires setuptools during runtime as well. diff --git a/var/spack/repos/builtin/packages/py-py/package.py b/var/spack/repos/builtin/packages/py-py/package.py index 54c4fdf3302..4ac93458a99 100644 --- a/var/spack/repos/builtin/packages/py-py/package.py +++ b/var/spack/repos/builtin/packages/py-py/package.py @@ -17,10 +17,10 @@ class PyPy(PythonPackage): 'py._log', 'py._code', 'py._io' ] - version('1.5.4', '7502d66fa68ea4ae5b61c511cd177d6a') - version('1.5.3', '667d37a148ad9fb81266492903f2d880') - version('1.4.33', '15d7107cbb8b86593bf9afa16e56da65') - version('1.4.31', '5d2c63c56dc3f2115ec35c066ecd582b') + version('1.5.4', sha256='3fd59af7435864e1a243790d322d763925431213b6b8529c6ca71081ace3bbf7') + version('1.5.3', sha256='29c9fab495d7528e80ba1e343b958684f4ace687327e6f789a94bf3d1915f881') + version('1.4.33', sha256='1f9a981438f2acc20470b301a07a496375641f902320f70e31916fe3377385a9') + version('1.4.31', sha256='a6501963c725fc2554dabfece8ae9a8fb5e149c0ac0a42fd2b02c5c1c57fc114') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-py2bit/package.py b/var/spack/repos/builtin/packages/py-py2bit/package.py index ae27dbea36a..ca0c7fd0cab 100644 --- a/var/spack/repos/builtin/packages/py-py2bit/package.py +++ b/var/spack/repos/builtin/packages/py-py2bit/package.py @@ -12,6 +12,6 @@ class PyPy2bit(PythonPackage): homepage = "https://pypi.python.org/pypi/py2bit" url = "https://pypi.io/packages/source/p/py2bit/py2bit-0.2.1.tar.gz" - version('0.2.1', 'eaf5b1c80a0bbf0b35af1f002f83a556') + version('0.2.1', sha256='34f7ac22be0eb4b5493063826bcc2016a78eb216bb7130890b50f3572926aeb1') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-py2cairo/package.py b/var/spack/repos/builtin/packages/py-py2cairo/package.py index 565aa57518f..10d22b74b82 100644 --- a/var/spack/repos/builtin/packages/py-py2cairo/package.py +++ b/var/spack/repos/builtin/packages/py-py2cairo/package.py @@ -12,7 +12,7 @@ class PyPy2cairo(WafPackage): homepage = "https://www.cairographics.org/pycairo/" url = "https://cairographics.org/releases/py2cairo-1.10.0.tar.bz2" - version('1.10.0', '20337132c4ab06c1146ad384d55372c5') + version('1.10.0', sha256='d30439f06c2ec1a39e27464c6c828b6eface3b22ee17b2de05dc409e429a7431') extends('python') diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py index 21214d7f8ab..573b84be1b5 100644 --- a/var/spack/repos/builtin/packages/py-py2neo/package.py +++ b/var/spack/repos/builtin/packages/py-py2neo/package.py @@ -13,10 +13,10 @@ class PyPy2neo(PythonPackage): homepage = "http://py2neo.org/" url = "https://github.com/nigelsmall/py2neo/archive/py2neo-2.0.8.tar.gz" - version('2.0.8', 'e3ec5172a9e006515ef4155688a05a55') - version('2.0.7', '4cfbc5b7dfd7757f3d2e324805faa639') - version('2.0.6', '53e4cdb1a95fbae501c66e541d5f4929') - version('2.0.5', '143b1f9c0aa22faf170c1b9f84c7343b') - version('2.0.4', 'b3f7efd3344dc3f66db4eda11e5899f7') + version('2.0.8', sha256='57b4a1c4aa800e03904b2adfd7c8ec467b072bae2d24baf150fd580916255f2e') + version('2.0.7', sha256='aa7c86fec70823111d2f932cb20a978889f1c47c2f58461309f644ecb9a22204') + version('2.0.6', sha256='bcf00ebc82a80c7e2da00288e8f90f81682abfc991e19d92d21726c2deac823f') + version('2.0.5', sha256='024b42261b06e5e2c92a1f24e62398847f090862005add0b5c69a79a7e1e87b5') + version('2.0.4', sha256='19074b7b892f2e989f39eae21fc59b26a05e1a820adad8aa58bc470b70d9056d') depends_on("py-setuptools", type='build') diff --git a/var/spack/repos/builtin/packages/py-pyani/package.py b/var/spack/repos/builtin/packages/py-pyani/package.py index f8700b34309..a5a0f12faa0 100644 --- a/var/spack/repos/builtin/packages/py-pyani/package.py +++ b/var/spack/repos/builtin/packages/py-pyani/package.py @@ -16,8 +16,8 @@ class PyPyani(PythonPackage): homepage = "http://widdowquinn.github.io/pyani" url = "https://pypi.io/packages/source/p/pyani/pyani-0.2.7.tar.gz" - version('0.2.7', '239ba630d375a81c35b7c60fb9bec6fa') - version('0.2.6', 'd5524b9a3c62c36063ed474ea95785c9') + version('0.2.7', sha256='dbc6c71c46fbbfeced3f8237b84474221268b51170caf044bec8559987a7deb9') + version('0.2.6', sha256='e9d899bccfefaabe7bfa17d48eef9c713d321d2d15465f7328c8984807c3dd8d') depends_on('python@3.5:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyasn1/package.py b/var/spack/repos/builtin/packages/py-pyasn1/package.py index fa25d7a6326..acfab10948e 100644 --- a/var/spack/repos/builtin/packages/py-pyasn1/package.py +++ b/var/spack/repos/builtin/packages/py-pyasn1/package.py @@ -15,7 +15,7 @@ class PyPyasn1(PythonPackage): url = "https://pypi.io/packages/source/p/pyasn1/pyasn1-0.4.6.tar.gz" version('0.4.6', sha256='b773d5c9196ffbc3a1e13bdf909d446cad80a039aa3340bcad72f395b76ebc86') - version('0.2.3', '79f98135071c8dd5c37b6c923c51be45') + version('0.2.3', sha256='738c4ebd88a718e700ee35c8d129acce2286542daa80a82823a7073644f706ad') depends_on('python@2.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pybind11/package.py b/var/spack/repos/builtin/packages/py-pybind11/package.py index 98265904454..ac4b684450c 100644 --- a/var/spack/repos/builtin/packages/py-pybind11/package.py +++ b/var/spack/repos/builtin/packages/py-pybind11/package.py @@ -22,13 +22,13 @@ class PyPybind11(CMakePackage): version('develop', branch='master') version('2.3.0', sha256='0f34838f2c8024a6765168227ba587b3687729ebf03dc912f88ff75c7aa9cfe8') - version('2.2.4', 'b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e') - version('2.2.3', '55b637945bbf47d99d2c906bf0c13f49') - version('2.2.2', 'fc174e1bbfe7ec069af7eea86ec37b5c') - version('2.2.1', 'bab1d46bbc465af5af3a4129b12bfa3b') - version('2.2.0', '978b26aea1c6bfc4f88518ef33771af2') - version('2.1.1', '5518988698df937ccee53fb6ba91d12a') - version('2.1.0', '3cf07043d677d200720c928569635e12') + version('2.2.4', sha256='b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e') + version('2.2.3', sha256='3a3b7b651afab1c5ba557f4c37d785a522b8030dfc765da26adc2ecd1de940ea') + version('2.2.2', sha256='b639a2b2cbf1c467849660801c4665ffc1a4d0a9e153ae1996ed6f21c492064e') + version('2.2.1', sha256='f8bd1509578b2a1e7407d52e6ee8afe64268909a1bbda620ca407318598927e7') + version('2.2.0', sha256='1b0fda17c650c493f5862902e90f426df6751da8c0b58c05983ab009951ed769') + version('2.1.1', sha256='f2c6874f1ea5b4ad4ffffe352413f7d2cd1a49f9050940805c2a082348621540') + version('2.1.0', sha256='2860f2b8d0c9f65f0698289a161385f59d099b7ead1bf64e8993c486f2b93ee0') depends_on('py-pytest', type='test') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py index bf3b73f3c6b..0cffded42f5 100644 --- a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py +++ b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py @@ -14,7 +14,7 @@ class PyPybtexDocutils(PythonPackage): import_modules = ['pybtex_docutils'] - version('0.2.1', '7ae4b00562bd8881f582edf95009cc62') + version('0.2.1', sha256='e4b075641c1d68a3e98a6d73ad3d029293fcf9e0773512315ef9c8482f251337') depends_on('py-setuptools', type='build') depends_on('py-docutils@0.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pybtex/package.py b/var/spack/repos/builtin/packages/py-pybtex/package.py index 36a722dc56a..5b39a3a7662 100644 --- a/var/spack/repos/builtin/packages/py-pybtex/package.py +++ b/var/spack/repos/builtin/packages/py-pybtex/package.py @@ -26,7 +26,7 @@ class PyPybtex(PythonPackage): 'pybtex.database.convert' ] - version('0.21', 'e7b320b2bcb34c664c4385533a2ea831') + version('0.21', sha256='af8a6c7c74954ad305553b118d2757f68bc77c5dd5d5de2cc1fd16db90046000') depends_on('py-setuptools', type='build') depends_on('py-latexcodec@1.0.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pycairo/package.py b/var/spack/repos/builtin/packages/py-pycairo/package.py index 7a9cf4778eb..106a5babd5d 100644 --- a/var/spack/repos/builtin/packages/py-pycairo/package.py +++ b/var/spack/repos/builtin/packages/py-pycairo/package.py @@ -14,7 +14,7 @@ class PyPycairo(PythonPackage): url = "https://github.com/pygobject/pycairo/releases/download/v1.17.1/pycairo-1.17.1.tar.gz" url = "https://files.pythonhosted.org/packages/68/76/340ff847897296b2c8174dfa5a5ec3406e3ed783a2abac918cf326abad86/pycairo-1.17.1.tar.gz" - version('1.17.1', '34c1ee106655b450c4bd57e29371a4a7') + version('1.17.1', sha256='0f0a35ec923d87bc495f6753b1e540fd046d95db56a35250c44089fbce03b698') depends_on('cairo@1.2.0:') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/py-pycares/package.py b/var/spack/repos/builtin/packages/py-pycares/package.py index 27ef3c48692..13322bd1449 100644 --- a/var/spack/repos/builtin/packages/py-pycares/package.py +++ b/var/spack/repos/builtin/packages/py-pycares/package.py @@ -14,7 +14,7 @@ class PyPycares(PythonPackage): homepage = "https://github.com/saghul/pycares" url = "https://github.com/saghul/pycares/archive/pycares-3.0.0.tar.gz" - version('3.0.0', '5f938c037c5905ebc5617a157c654088') + version('3.0.0', sha256='28dc2bd59cf20399a6af4383cc8f57970cfca8b808ca05d6493812862ef0ca9c') depends_on('python@2.6:') depends_on('py-cffi') diff --git a/var/spack/repos/builtin/packages/py-pychecker/package.py b/var/spack/repos/builtin/packages/py-pychecker/package.py index 31e5ee6cf38..a8c535293c1 100644 --- a/var/spack/repos/builtin/packages/py-pychecker/package.py +++ b/var/spack/repos/builtin/packages/py-pychecker/package.py @@ -11,4 +11,4 @@ class PyPychecker(PythonPackage): homepage = "http://pychecker.sourceforge.net/" url = "http://sourceforge.net/projects/pychecker/files/pychecker/0.8.19/pychecker-0.8.19.tar.gz" - version('0.8.19', 'c37182863dfb09209d6ba4f38fce9d2b') + version('0.8.19', sha256='44fb26668f74aca3738f02d072813762a37ce1242f50dbff573720fa2e953279') diff --git a/var/spack/repos/builtin/packages/py-pycodestyle/package.py b/var/spack/repos/builtin/packages/py-pycodestyle/package.py index ffc00ec8abd..bba9848748d 100644 --- a/var/spack/repos/builtin/packages/py-pycodestyle/package.py +++ b/var/spack/repos/builtin/packages/py-pycodestyle/package.py @@ -13,20 +13,20 @@ class PyPycodestyle(PythonPackage): homepage = "https://github.com/PyCQA/pycodestyle" url = "https://github.com/PyCQA/pycodestyle/archive/2.0.0.tar.gz" - version('2.5.0', 'a603453c07e8d8e15a43cf062aa7174741b74b4a27b110f9ad03d74d519173b5') - version('2.3.1', '4185319f6137833eec9057dbf3293629') - version('2.3.0', '1b2019b3c39c20becadbb7fdec6dcb5a') - version('2.2.0', '6e21aab2e038c3dd38dca585011a6f38') - version('2.1.0', '1e606c687a6cf01d51305417d0e97824') - version('2.0.0', '5c3e90001f538bf3b7896d60e92eb6f6') - version('1.7.0', '31070a3a6391928893cbf5fa523eb8d9') - version('1.6.2', '8df18246d82ddd3d19ffe7518f983955') - version('1.6.1', '9d59bdc7c60f46f7cee86c732e28aa1a') - version('1.6', '340fa7e39bb44fb08db6eddf7cdc880a') - version('1.5.7', '6d0f5fc7d95755999bc9275cad5cbf3e') - version('1.5.6', 'c5c30e3d267b48bf3dfe7568e803a813') - version('1.5.5', 'cfa12df9b86b3a1dfb13aced1927e12f') - version('1.5.4', '3977a760829652543544074c684610ee') + version('2.5.0', sha256='a603453c07e8d8e15a43cf062aa7174741b74b4a27b110f9ad03d74d519173b5') + version('2.3.1', sha256='e9fc1ca3fd85648f45c0d2e33591b608a17d8b9b78e22c5f898e831351bacb03') + version('2.3.0', sha256='ac2a849987316521a56814b5618668d36cd5f3b04843803832a15b93b8383a50') + version('2.2.0', sha256='aa663451c9de97d00eff396eeffe1095fd1597491341ca3c0be54983b25b1a7d') + version('2.1.0', sha256='2190466d2b421da0d915b506eb690a6784feaef3ba33043665bf86581b02ccd9') + version('2.0.0', sha256='7e65a888def0abc467fa2cf614b3f84a74a8991045a2adcf11e1c225d8798796') + version('1.7.0', sha256='3f62d19b5cbcbdcb7810f967dcc2fbdd090256e090c32b457e2580a841d118ef') + version('1.6.2', sha256='508bfd7d457046891bf4b8fbfc95ccac7995c37cdfdb3daf97bfeb7a13fa4c9c') + version('1.6.1', sha256='3a910a0d0d998d4c3c2b8152a4816b98938b27cc73a4433c61202449706a73c8') + version('1.6', sha256='5e7bb5156af311079345b5e81f8154c3e1420d723150a6cba5a70245eb0d515a') + version('1.5.7', sha256='9bf020638986f2e254823aee62cfd97e55ba08ad51503cd5ae26172c47f48401') + version('1.5.6', sha256='9f164c1211854678b2cb269954bc8aac2dcfa142d40c99f7bab08f9344cf3241') + version('1.5.5', sha256='e55204c5477a29eb094835ad6e83be292aa3e06be12e51f5b4cc67f38d0d61ba') + version('1.5.4', sha256='bc234f7935a350c79c953421b01163db01010f39caeddfa8602ff54f76a6fd9e') # Most Python packages only require py-setuptools as a build dependency. # However, py-pycodestyle requires py-setuptools during runtime as well. diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py index 707abcf47ac..e93ff6879f9 100644 --- a/var/spack/repos/builtin/packages/py-pycparser/package.py +++ b/var/spack/repos/builtin/packages/py-pycparser/package.py @@ -13,8 +13,8 @@ class PyPycparser(PythonPackage): import_modules = ['pycparser', 'pycparser.ply'] - version('2.18', '72370da54358202a60130e223d488136') - version('2.17', 'ca98dcb50bc1276f230118f6af5a40c7') - version('2.13', 'e4fe1a2d341b22e25da0d22f034ef32f') + version('2.18', sha256='99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226') + version('2.17', sha256='0aac31e917c24cb3357f5a4d5566f2cc91a19ca41862f6c3c22dc60a629673b6') + version('2.13', sha256='b399599a8a0e386bfcbc5e01a38d79dd6e926781f9e358cd5512f41ab7d20eb7') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pycrypto/package.py b/var/spack/repos/builtin/packages/py-pycrypto/package.py index c53902080f5..d79fb549c99 100644 --- a/var/spack/repos/builtin/packages/py-pycrypto/package.py +++ b/var/spack/repos/builtin/packages/py-pycrypto/package.py @@ -13,7 +13,7 @@ class PyPycrypto(PythonPackage): homepage = "https://www.dlitz.net/software/pycrypto/" url = "https://pypi.io/packages/source/p/pycrypto/pycrypto-2.6.1.tar.gz" - version('2.6.1', '55a61a054aa66812daf5161a0d5d7eda') + version('2.6.1', sha256='f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c') # depends_on('py-setuptools', type='build') depends_on('gmp') diff --git a/var/spack/repos/builtin/packages/py-pycurl/package.py b/var/spack/repos/builtin/packages/py-pycurl/package.py index c1789a42183..fa8c22fd794 100644 --- a/var/spack/repos/builtin/packages/py-pycurl/package.py +++ b/var/spack/repos/builtin/packages/py-pycurl/package.py @@ -13,7 +13,7 @@ class PyPycurl(PythonPackage): homepage = "http://pycurl.io/" url = "https://pypi.io/packages/source/p/pycurl/pycurl-7.43.0.tar.gz" - version('7.43.0', 'c94bdba01da6004fa38325e9bd6b9760') + version('7.43.0', sha256='aa975c19b79b6aa6c0518c0cc2ae33528900478f0b500531dbcdbf05beec584c') depends_on('python@2.6:') depends_on('curl@7.19.0:') diff --git a/var/spack/repos/builtin/packages/py-pydatalog/package.py b/var/spack/repos/builtin/packages/py-pydatalog/package.py index 9bc50918f96..398baf31137 100644 --- a/var/spack/repos/builtin/packages/py-pydatalog/package.py +++ b/var/spack/repos/builtin/packages/py-pydatalog/package.py @@ -11,4 +11,4 @@ class PyPydatalog(PythonPackage): homepage = 'https://pypi.python.org/pypi/pyDatalog/' url = 'https://pypi.io/packages/source/p/pyDatalog/pyDatalog-0.17.1.zip' - version('0.17.1', '6b2682301200068d208d6f2d01723939') + version('0.17.1', sha256='b3d9cff0b9431e0fd0b2d5eefe4414c3d3c20bd18fdd7d1b42b2f01f25bac808') diff --git a/var/spack/repos/builtin/packages/py-pydispatcher/package.py b/var/spack/repos/builtin/packages/py-pydispatcher/package.py index e5ca12b5baa..77eaf09aca3 100644 --- a/var/spack/repos/builtin/packages/py-pydispatcher/package.py +++ b/var/spack/repos/builtin/packages/py-pydispatcher/package.py @@ -12,6 +12,6 @@ class PyPydispatcher(PythonPackage): homepage = "http://pydispatcher.sourceforge.net/" url = "https://pypi.io/packages/source/P/PyDispatcher/PyDispatcher-2.0.5.tar.gz" - version('2.0.5', '1b9c2ca33580c2770577add7130b0b28') + version('2.0.5', sha256='5570069e1b1769af1fe481de6dd1d3a388492acddd2cdad7a3bde145615d5caf') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pydot/package.py b/var/spack/repos/builtin/packages/py-pydot/package.py index 16e12fa18e9..8f42147fe1d 100644 --- a/var/spack/repos/builtin/packages/py-pydot/package.py +++ b/var/spack/repos/builtin/packages/py-pydot/package.py @@ -12,9 +12,9 @@ class PyPydot(PythonPackage): homepage = "https://github.com/erocarrera/pydot/" url = "https://pypi.io/packages/source/p/pydot/pydot-1.2.3.tar.gz" - version('1.4.1', '0ee9da6823c2fcad4ea380f65730dec5') - version('1.2.3', '5b50fd8cf022811d8718562ebc8aefb2') - version('1.2.2', 'fad67d9798dbb33bb3dca3e6d4c47665') + version('1.4.1', sha256='d49c9d4dd1913beec2a997f831543c8cbd53e535b1a739e921642fe416235f01') + version('1.2.3', sha256='edb5d3f249f97fbd9c4bb16959e61bc32ecf40eee1a9f6d27abe8d01c0a73502') + version('1.2.2', sha256='04a97a885ed418dcc193135cc525fa356cad8b16719293295a149b30718ce400') depends_on('py-setuptools', type='build') depends_on('py-pyparsing@2.1.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pydv/package.py b/var/spack/repos/builtin/packages/py-pydv/package.py index 53042bec029..2da0b177f5a 100644 --- a/var/spack/repos/builtin/packages/py-pydv/package.py +++ b/var/spack/repos/builtin/packages/py-pydv/package.py @@ -13,7 +13,7 @@ class PyPydv(PythonPackage): homepage = "https://github.com/griffin28/PyDV" url = "https://github.com/griffin28/PyDV/archive/pydv-2.4.2.tar.gz" - version('2.4.2', 'fff9560177387a258f765c2d900bb241') + version('2.4.2', sha256='46bda76e27e85beaad446455d0cc279388d455f05912a8ff8e4fb66de983992c') depends_on('py-backports-functools-lru-cache', type=('build', 'run')) depends_on('py-cycler', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pyelftools/package.py b/var/spack/repos/builtin/packages/py-pyelftools/package.py index d3b2e50e88b..e9a02af8e4d 100644 --- a/var/spack/repos/builtin/packages/py-pyelftools/package.py +++ b/var/spack/repos/builtin/packages/py-pyelftools/package.py @@ -12,4 +12,4 @@ class PyPyelftools(PythonPackage): homepage = "https://pypi.python.org/pypi/pyelftools" url = "https://pypi.io/packages/source/p/pyelftools/pyelftools-0.23.tar.gz" - version('0.23', 'aa7cefa8bd2f63d7b017440c9084f310') + version('0.23', sha256='fc57aadd096e8f9b9b03f1a9578f673ee645e1513a5ff0192ef439e77eab21de') diff --git a/var/spack/repos/builtin/packages/py-pyepsg/package.py b/var/spack/repos/builtin/packages/py-pyepsg/package.py index 8eaf0b36e8b..bdcc59d1711 100644 --- a/var/spack/repos/builtin/packages/py-pyepsg/package.py +++ b/var/spack/repos/builtin/packages/py-pyepsg/package.py @@ -12,7 +12,7 @@ class PyPyepsg(PythonPackage): homepage = "https://pyepsg.readthedocs.io/en/latest/" url = "https://pypi.io/packages/source/p/pyepsg/pyepsg-0.3.2.tar.gz" - version('0.3.2', 'b0644187068a9b58378a5c58ad55b991') + version('0.3.2', sha256='597ef8c0e8c1be3db8f68c5985bcfbbc32e22f087e93e81ceb03ff094898e059') depends_on('py-setuptools', type='build') depends_on('py-requests', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pyfasta/package.py b/var/spack/repos/builtin/packages/py-pyfasta/package.py index 72a6df18964..eafd6777fdb 100644 --- a/var/spack/repos/builtin/packages/py-pyfasta/package.py +++ b/var/spack/repos/builtin/packages/py-pyfasta/package.py @@ -13,7 +13,7 @@ class PyPyfasta(PythonPackage): homepage = "https://pypi.python.org/pypi/pyfasta/" url = "https://pypi.io/packages/source/p/pyfasta/pyfasta-0.5.2.tar.gz" - version('0.5.2', 'bf61ab997dca329675c3eb2ee7cdfcf2') + version('0.5.2', sha256='ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258') depends_on('python@2.6:') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-pyfftw/package.py b/var/spack/repos/builtin/packages/py-pyfftw/package.py index 12202e667b2..98e0cbc30c7 100644 --- a/var/spack/repos/builtin/packages/py-pyfftw/package.py +++ b/var/spack/repos/builtin/packages/py-pyfftw/package.py @@ -14,7 +14,7 @@ class PyPyfftw(PythonPackage): url = "https://pypi.io/packages/source/p/pyFFTW/pyFFTW-0.10.4.tar.gz" version('0.11.1', sha256='05ea28dede4c3aaaf5c66f56eb0f71849d0d50f5bc0f53ca0ffa69534af14926') - version('0.10.4', '7fb59450308881bb48d9f178947d950e') + version('0.10.4', sha256='739b436b7c0aeddf99a48749380260364d2dc027cf1d5f63dafb5f50068ede1a') depends_on('fftw') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyflakes/package.py b/var/spack/repos/builtin/packages/py-pyflakes/package.py index 2f8aa1dfcb8..898c8dc9f87 100644 --- a/var/spack/repos/builtin/packages/py-pyflakes/package.py +++ b/var/spack/repos/builtin/packages/py-pyflakes/package.py @@ -12,20 +12,20 @@ class PyPyflakes(PythonPackage): homepage = "https://github.com/PyCQA/pyflakes" url = "https://github.com/PyCQA/pyflakes/archive/1.3.0.tar.gz" - version('2.1.0', '5a02e0c28b8c30d7740fe1be02475fbe') - version('1.6.0', '68eff61e54964e6389f8fb1d2122fc5b') - version('1.5.0', '1dee2ca8a0520061aac5a82f3b539fa0') - version('1.4.0', 'ed832ef1cbd59463e5f0f6340254f603') - version('1.3.0', 'a76173deb7a84fe860c0b60e2fbcdfe2') - version('1.2.3', '2ac2e148a5c46b6bb06c4785be76f7cc') - version('1.2.2', 'fe759b9381a6500e67a2ddbbeb5161a4') - version('1.2.1', '444a06b256e0a70e41c11698b7190e84') - version('1.2.0', '5d1c87bf09696c4c35dc3103f2a1185c') - version('1.1.0', '4e18bf78c0455ebcd41e5d6104392c88') - version('1.0.0', 'e2ea22a825c5100f12e54b71771cde71') - version('0.9.2', 'd02d5f68e944085fd6ec163a34737a96') - version('0.9.1', '8108d2248e93ca6a315fa2dd31ee9bb1') - version('0.9.0', '43c2bcee88606bde55dbf25a253ef886') + version('2.1.0', sha256='6cd8775b6430daad386c0de00dfbc27ce2c24468cdcc4d3da41e4aa39d8ce167') + version('1.6.0', sha256='f9c72359e05bf8dc27eaaee8cdcae464497f2ccadae87ac6517605ba6040ec99') + version('1.5.0', sha256='943ba426420a66b5adebdbe8007e676bba11bf4006e7964d9d9ae98478c57792') + version('1.4.0', sha256='7b0c1fe9be9c2b8ebc13bcc7e73f6d1862426c880d467126822a3ad1f8f3be79') + version('1.3.0', sha256='7370356f3e20b537e61dfbcaf1ce7bf60aa7147e9e3e639e6401b445acfa3228') + version('1.2.3', sha256='4c1c30a63e5ede3cb61ebbe238d4414a039b767b99f85f0574099e314e7102a2') + version('1.2.2', sha256='c014aa6a936ccb29eaa89ef1ed4770eec650ea6e3f2c736b667428939fda5532') + version('1.2.1', sha256='7de610c7a1dfba2cd34910732db399050ed969b459acc773797f6ff1f742725f') + version('1.2.0', sha256='8860de31de5ea68586c3f92f0a81ea78282145bd536d80fe5f717462c9d11c6c') + version('1.1.0', sha256='eb660821bed20c269dbacb5630fd8e9200012b8fbec2bdf63b0a5237773ea165') + version('1.0.0', sha256='06fe9162e0ef561ca00b32766daa2196587d2faefaea8fa28f72af202b046587') + version('0.9.2', sha256='ef67b057b4fc4ce463a7303688d45c50a7e420e8b4b3dabcd443cb265d4081b5') + version('0.9.1', sha256='e22d2e24cc97a03db24aa8d96cb0fc66ca110adabc321215f5feca2f1068d29a') + version('0.9.0', sha256='b1d395d1af3922edbfdbd05ac7082d855a2613aff2cd949ff0f29e25fb51f7f3') # Most Python packages only require py-setuptools as a build dependency. # However, py-pyflakes requires py-setuptools during runtime as well. diff --git a/var/spack/repos/builtin/packages/py-pygdbmi/package.py b/var/spack/repos/builtin/packages/py-pygdbmi/package.py index 2a1db37248f..cb7d59bfd0f 100644 --- a/var/spack/repos/builtin/packages/py-pygdbmi/package.py +++ b/var/spack/repos/builtin/packages/py-pygdbmi/package.py @@ -12,6 +12,6 @@ class PyPygdbmi(PythonPackage): homepage = "https://github.com/cs01/pygdbmi" url = "https://pypi.io/packages/source/p/pygdbmi/pygdbmi-0.8.2.0.tar.gz" - version('0.8.2.0', 'e74d3d02fa5eef1223b5dedb13f9bbad') + version('0.8.2.0', sha256='47cece65808ca42edf6966ac48e2aedca7ae1c675c4d2f0d001c7f3a7fa245fe') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py index 7c191d672b9..d3e3445e985 100644 --- a/var/spack/repos/builtin/packages/py-pygments/package.py +++ b/var/spack/repos/builtin/packages/py-pygments/package.py @@ -17,10 +17,10 @@ class PyPygments(PythonPackage): 'pygments.lexers', 'pygments.styles' ] - version('2.3.1', 'b7d04e2cd87c405938f1e494e2969814') - version('2.2.0', '13037baca42f16917cbd5ad2fab50844') - version('2.1.3', 'ed3fba2467c8afcda4d317e4ef2c6150') - version('2.0.1', 'e0daf4c14a4fe5b630da765904de4d6c') - version('2.0.2', '238587a1370d62405edabd0794b3ec4a') + version('2.3.1', sha256='5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a') + version('2.2.0', sha256='dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc') + version('2.1.3', sha256='88e4c8a91b2af5962bfa5ea2447ec6dd357018e86e94c7d14bd8cacbc5b55d81') + version('2.0.1', sha256='5e039e1d40d232981ed58914b6d1ac2e453a7e83ddea22ef9f3eeadd01de45cb') + version('2.0.2', sha256='7320919084e6dac8f4540638a46447a3bd730fca172afc17d2c03eed22cf4f51') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pygobject/package.py b/var/spack/repos/builtin/packages/py-pygobject/package.py index ee7d8d0aa8d..2bcfbc22b34 100644 --- a/var/spack/repos/builtin/packages/py-pygobject/package.py +++ b/var/spack/repos/builtin/packages/py-pygobject/package.py @@ -12,9 +12,9 @@ class PyPygobject(PythonPackage): homepage = "https://pypi.python.org/pypi/pygobject" - version('3.28.3', '3bac63c86bb963aa401f97859464aa90') - version('2.28.6', '9415cb7f2b3a847f2310ccea258b101e') - version('2.28.3', 'aa64900b274c4661a5c32e52922977f9', + version('3.28.3', sha256='3dd3e21015d06e00482ea665fc1733b77e754a6ab656a5db5d7f7bfaf31ad0b0') + version('2.28.6', sha256='fb8a1d4f665130a125011659bd347c7339c944232163dbb9a34fd0686577adb8') + version('2.28.3', sha256='7da88c169a56efccc516cebd9237da3fe518a343095a664607b368fe21df95b6', url='http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.28/pygobject-2.28.3.tar.bz2') extends('python') diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py index 8f68422094f..dfa0fe4790f 100644 --- a/var/spack/repos/builtin/packages/py-pygpu/package.py +++ b/var/spack/repos/builtin/packages/py-pygpu/package.py @@ -12,16 +12,16 @@ class PyPygpu(PythonPackage): homepage = "http://deeplearning.net/software/libgpuarray/" url = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz" - version('0.7.5', '2534011464555c3e99d14231db965c20') - version('0.7.4', '19f57cd381175162048c8154f5251546') - version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d') - version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e') - version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb') - version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e') - version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0') - version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4') - version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2') - version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b') + version('0.7.5', sha256='39c4d2e743848be43c8819c736e089ae51b11aa446cc6ee05af945c2dfd63420') + version('0.7.4', md5='19f57cd381175162048c8154f5251546') + version('0.7.3', md5='cb44aeb8482330974abdb36b0a477e5d') + version('0.7.2', sha256='ef11ee6f8d62d53831277fd3dcab662aa770a5b5de2d30fe3018c4af959204da') + version('0.7.1', sha256='4d0f9dd63b0595a8c04d8cee91b2619847c033b011c71d776caa784322382ed6') + version('0.7.0', sha256='afe7907435dcbf78b3ea9b9f6c97e5a0d4a219a7170f5025ca0db1c289bb88df') + version('0.6.9', sha256='689716feecb4e495f4d383ec1518cf3ba70a2a642a903cc445b6b6ffc119bc25') + version('0.6.2', sha256='04756c6270c0ce3b91a9bf01be38c4fc743f5356acc18d9f807198021677bcc8') + version('0.6.1', sha256='b2466311e0e3bacdf7a586bba0263f6d232bf9f8d785e91ddb447653741e6ea5') + version('0.6.0', sha256='a58a0624e894475a4955aaea25e82261c69b4d22c8f15ec07041a4ba176d35af') depends_on('libgpuarray') # not just build-time, requires pkg_resources diff --git a/var/spack/repos/builtin/packages/py-pygresql/package.py b/var/spack/repos/builtin/packages/py-pygresql/package.py index acdb70bd060..9a532cb47cb 100644 --- a/var/spack/repos/builtin/packages/py-pygresql/package.py +++ b/var/spack/repos/builtin/packages/py-pygresql/package.py @@ -13,7 +13,7 @@ class PyPygresql(PythonPackage): homepage = "http://www.pygresql.org" url = "http://www.pygresql.org/files/PyGreSQL-5.0.5.tar.gz" - version('5.0.5', 'c7d1558e85568d3369a98609174ca6a0') + version('5.0.5', sha256='ff5e76b840600d4912b79daf347b44274a1c0368663e7b57529c406f8426479c') depends_on('py-setuptools', type='build') depends_on('postgresql', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pygtk/package.py b/var/spack/repos/builtin/packages/py-pygtk/package.py index 17c3d545c6e..a94d19f1e18 100644 --- a/var/spack/repos/builtin/packages/py-pygtk/package.py +++ b/var/spack/repos/builtin/packages/py-pygtk/package.py @@ -12,7 +12,7 @@ class PyPygtk(AutotoolsPackage): homepage = "http://www.pygtk.org/" url = "http://ftp.gnome.org/pub/GNOME/sources/pygtk/2.24/pygtk-2.24.0.tar.gz" - version('2.24.0', 'd27c7f245a9e027f6b6cd9acb7468e36') + version('2.24.0', sha256='6e3e54fa6e65a69ac60bd58cb2e60a57f3346ac52efe995f3d10b6c38c972fd8') extends('python') diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py index 09877f9f37f..5ee8763e8c5 100644 --- a/var/spack/repos/builtin/packages/py-pylint/package.py +++ b/var/spack/repos/builtin/packages/py-pylint/package.py @@ -13,10 +13,10 @@ class PyPylint(PythonPackage): url = "https://pypi.io/packages/source/p/pylint/pylint-1.6.5.tar.gz" version('2.3.0', sha256='ee80c7af4f127b2a480d83010c9f0e97beb8eaa652b78c2837d3ed30b12e1182') - # version('1.7.2', '27ee752cdcfacb05bf4940947e6b35c6') # see dependencies - version('1.6.5', '31da2185bf59142479e4fa16d8a9e347') - version('1.4.3', '5924c1c7ca5ca23647812f5971d0ea44') - version('1.4.1', 'df7c679bdcce5019389038847e4de622') + # version('1.7.2', md5='27ee752cdcfacb05bf4940947e6b35c6') # see dependencies + version('1.6.5', sha256='a673984a8dd78e4a8b8cfdee5359a1309d833cf38405008f4a249994a8456719') + version('1.4.3', sha256='1dce8c143a5aa15e0638887c2b395e2e823223c63ebaf8d5f432a99e44b29f60') + version('1.4.1', sha256='3e383060edd432cbbd0e8bd686f5facfe918047ffe1bb401ab5897cb6ee0f030') extends('python', ignore=r'bin/pytest') depends_on('py-astroid', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pymatgen/package.py b/var/spack/repos/builtin/packages/py-pymatgen/package.py index be3a85238f5..78c62422f02 100644 --- a/var/spack/repos/builtin/packages/py-pymatgen/package.py +++ b/var/spack/repos/builtin/packages/py-pymatgen/package.py @@ -15,8 +15,8 @@ class PyPymatgen(PythonPackage): homepage = "http://www.pymatgen.org/" url = "https://pypi.io/packages/source/p/pymatgen/pymatgen-4.7.2.tar.gz" - version('4.7.2', '9c3a6e8608671c216e4ef89778646fd6') - version('4.6.2', '508f77fdc3e783587348e93e4dfed1b8') + version('4.7.2', sha256='e439b78cc3833a03963c3c3efe349d8a0e52a1550c8a05c56a89aa1b86657436') + version('4.6.2', sha256='f34349090c6f604f7d402cb09cd486830b38523639d7160d7fd282d504036a0e') extends('python', ignore='bin/tabulate') diff --git a/var/spack/repos/builtin/packages/py-pyminifier/package.py b/var/spack/repos/builtin/packages/py-pyminifier/package.py index 6565a6877f1..dd83e744210 100644 --- a/var/spack/repos/builtin/packages/py-pyminifier/package.py +++ b/var/spack/repos/builtin/packages/py-pyminifier/package.py @@ -12,6 +12,6 @@ class PyPyminifier(PythonPackage): homepage = "http://liftoff.github.io/pyminifier/" url = "https://pypi.io/packages/source/p/pyminifier/pyminifier-2.1.tar.gz" - version('2.1', 'c1a6b92e69f664005f7adf188c514de7') + version('2.1', sha256='e192618fe901830e9298825b32828bc9555ae8649e05af37bfab2db328546777') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pymol/package.py b/var/spack/repos/builtin/packages/py-pymol/package.py index 6499a605166..c85f380d24f 100644 --- a/var/spack/repos/builtin/packages/py-pymol/package.py +++ b/var/spack/repos/builtin/packages/py-pymol/package.py @@ -15,7 +15,7 @@ class PyPymol(PythonPackage): homepage = "https://pymol.org" url = "https://sourceforge.net/projects/pymol/files/pymol/2/pymol-v2.1.0.tar.bz2" - version('2.1.0', 'ef2ab2ce11d65785ca3258b4e6982dfb') + version('2.1.0', sha256='7ae8ebb899533d691a67c1ec731b00518dea456ab3e258aa052a65c24b63eae2') depends_on('python+tkinter', type=('build', 'run')) depends_on('tcl') diff --git a/var/spack/repos/builtin/packages/py-pympler/package.py b/var/spack/repos/builtin/packages/py-pympler/package.py index 398cd91f16e..c525133a8fa 100644 --- a/var/spack/repos/builtin/packages/py-pympler/package.py +++ b/var/spack/repos/builtin/packages/py-pympler/package.py @@ -14,10 +14,10 @@ class PyPympler(PythonPackage): homepage = "https://github.com/pympler/pympler" url = "https://pypi.io/packages/source/P/Pympler/Pympler-0.4.3.tar.gz" - version('0.4.3', 'bbb4239126e9c99e2effc83b02bf8755') - version('0.4.2', '6bdfd913ad4c94036e8a2b358e49abd7') - version('0.4.1', '2d54032a6da91ff438f48d5f36b719a6') - version('0.4', '68e4a8aa4a268996fa6a321b664918af') - version('0.3.1', '906ce437f46fb30991007671a59d4319') + version('0.4.3', sha256='430528fff6cde1bae0a305e8df647b158c3cc4930cff122bf228293829ee1e56') + version('0.4.2', sha256='3c3f9d8eb3dddf4f29c433433ea77c9c3f2f0dcc06575c0c2a9d81b2602893b2') + version('0.4.1', sha256='6a8bfd2972c4ec34ac8750358515950be4a4ca13dfa6a05a9a22419786745f90') + version('0.4', sha256='b280480502df658b18cb6310d2c744fabf05d4c518f873377884b4d4b5d2992d') + version('0.3.1', sha256='8cb170fddfe592342856590e2239e8c20ac61eacf18bc4f65a95ccaf74475e3e') depends_on('python@2.5:') diff --git a/var/spack/repos/builtin/packages/py-pynn/package.py b/var/spack/repos/builtin/packages/py-pynn/package.py index 1de7ffbd561..4e09d56dbdd 100644 --- a/var/spack/repos/builtin/packages/py-pynn/package.py +++ b/var/spack/repos/builtin/packages/py-pynn/package.py @@ -15,11 +15,11 @@ class PyPynn(PythonPackage): url = "https://pypi.io/packages/source/P/PyNN/PyNN-0.8.3.tar.gz" git = "https://github.com/NeuralEnsemble/PyNN.git" - version('0.9.1', '3b8a6c63dc59d7ac751029f84dcaf7e6') - version('0.8.3', '28c63f898093806a57198e9271ed7b82') + version('0.9.1', sha256='bbc60fea3235427191feb2daa0e2fa07eb1c3946104c068ac8a2a0501263b0b1') + version('0.8.3', sha256='9d59e6cffa4714f0c892ec6b32d1f5f8f75ba3a20d8635bac50c047aa6f2537e') version('0.8beta', commit='ffb0cb1661f2b0f2778db8f71865978fe7a7a6a4') - version('0.8.1', '7fb165ed5af35a115cb9c60991645ae6') - version('0.7.5', 'd8280544e4c9b34b40fd372b16342841') + version('0.8.1', sha256='ce94246284588414d1570c1d5d697805f781384e771816727c830b01ee30fe39') + version('0.7.5', sha256='15f75f422f3b71c6129ecef23f29d8baeb3ed6502e7a321b8a2596c78ef7e03c') depends_on('python@2.6:2.8,3.3:') depends_on('py-jinja2@2.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pypar/package.py b/var/spack/repos/builtin/packages/py-pypar/package.py index 74bcbde092c..6cd04aca09d 100644 --- a/var/spack/repos/builtin/packages/py-pypar/package.py +++ b/var/spack/repos/builtin/packages/py-pypar/package.py @@ -13,7 +13,7 @@ class PyPypar(PythonPackage): homepage = "http://code.google.com/p/pypar/" url = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pypar/pypar-2.1.5_108.tgz" - version('2.1.5_108', '7a1f28327d2a3b679f9455c843d850b8') + version('2.1.5_108', sha256='6076c47d32d48424a07c7b7b29ac16e12cc4b2d28b681b895f94fa76cd82fa12') depends_on('mpi') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pyparsing/package.py b/var/spack/repos/builtin/packages/py-pyparsing/package.py index cda8e67f9b3..a4aa1e7a9dd 100644 --- a/var/spack/repos/builtin/packages/py-pyparsing/package.py +++ b/var/spack/repos/builtin/packages/py-pyparsing/package.py @@ -13,10 +13,10 @@ class PyPyparsing(PythonPackage): import_modules = ['pyparsing'] - version('2.3.1', '630e86b719619a251de0ba4a97239cec') - version('2.2.0', '0214e42d63af850256962b6744c948d9') - version('2.1.10', '065908b92904e0d3634eb156f44cc80e') - version('2.0.3', '0fe479be09fc2cf005f753d3acc35939') + version('2.3.1', sha256='66c9268862641abcac4a96ba74506e594c884e3f57690a696d21ad8210ed667a') + version('2.2.0', sha256='0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04') + version('2.1.10', sha256='811c3e7b0031021137fc83e051795025fcb98674d07eb8fe922ba4de53d39188') + version('2.0.3', sha256='06e729e1cbf5274703b1f47b6135ed8335999d547f9d8cf048b210fb8ebf844f') patch('setuptools-import.patch', when='@:2.1.10') diff --git a/var/spack/repos/builtin/packages/py-pyprof2html/package.py b/var/spack/repos/builtin/packages/py-pyprof2html/package.py index 41d8a294217..4d33e96d31c 100644 --- a/var/spack/repos/builtin/packages/py-pyprof2html/package.py +++ b/var/spack/repos/builtin/packages/py-pyprof2html/package.py @@ -12,7 +12,7 @@ class PyPyprof2html(PythonPackage): homepage = "https://pypi.python.org/pypi/pyprof2html/" url = "https://pypi.io/packages/source/p/pyprof2html/pyprof2html-0.3.1.tar.gz" - version('0.3.1', 'aa65a1635aac95e0487d7749a6351c43') + version('0.3.1', sha256='db2d37e21d8c76f2fd25fb1ba9273c9b3ff4a98a327e37d943fed1ea225a6720') patch('version_0.3.1.patch', when="@0.3.1") diff --git a/var/spack/repos/builtin/packages/py-pyqi/package.py b/var/spack/repos/builtin/packages/py-pyqi/package.py index 9b5348c86f8..2b4b7ce36c6 100644 --- a/var/spack/repos/builtin/packages/py-pyqi/package.py +++ b/var/spack/repos/builtin/packages/py-pyqi/package.py @@ -14,6 +14,6 @@ class PyPyqi(PythonPackage): homepage = "https://pyqi.readthedocs.io" url = "https://pypi.io/packages/source/p/pyqi/pyqi-0.3.2.tar.gz" - version('0.3.2', '9507c06eeb22a816d963c860ad8e92ae') + version('0.3.2', sha256='8f1711835779704e085e62194833fed9ac2985e398b4ceac6faf6c7f40f5d15f') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyqt4/package.py b/var/spack/repos/builtin/packages/py-pyqt4/package.py index 6554cf78a6a..b13eaba22b3 100644 --- a/var/spack/repos/builtin/packages/py-pyqt4/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt4/package.py @@ -25,7 +25,7 @@ class PyPyqt4(SIPPackage): ] version('4.12.3', sha256='a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472') - version('4.11.3', '997c3e443165a89a559e0d96b061bf70', + version('4.11.3', sha256='853780dcdbe2e6ba785d703d059b096e1fc49369d3e8d41a060be874b8745686', url='http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3/PyQt-x11-gpl-4.11.3.tar.gz') # Supposedly can also be built with Qt 5 compatibility layer diff --git a/var/spack/repos/builtin/packages/py-pyrad/package.py b/var/spack/repos/builtin/packages/py-pyrad/package.py index 3d96cea2f39..6ecbd7c4d7e 100644 --- a/var/spack/repos/builtin/packages/py-pyrad/package.py +++ b/var/spack/repos/builtin/packages/py-pyrad/package.py @@ -12,7 +12,7 @@ class PyPyrad(PythonPackage): homepage = "http://dereneaton.com/software/pyrad/" url = "https://github.com/dereneaton/pyrad/archive/3.0.66.tar.gz" - version('3.0.66', '19b8bcd73a574f8a25582d6e8978f0aa') + version('3.0.66', sha256='7dbd67e532058f7b7de76d14cf631fd3e3c841cd80fac4e55fbce8bb52ac6537') depends_on('python@:2.999', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py index 05842cc1fba..f95031cd3b9 100644 --- a/var/spack/repos/builtin/packages/py-pysam/package.py +++ b/var/spack/repos/builtin/packages/py-pysam/package.py @@ -15,10 +15,10 @@ class PyPysam(PythonPackage): version('0.15.2', sha256='8cb3dd70f0d825086ac059ec2445ebd2ec5f14af73e7f1f4bd358966aaee5ed3') version('0.15.1', sha256='12221285af17e32b8f3fed033f90c6177a798afe41420eb5c3352d4e18ee12ed') - version('0.14.1', 'ad88fa5bbcc0fdf4a936734691d9c9d1') - version('0.13', 'a9b502dd1a7e6403e35e6972211688a2') - version('0.11.2.2', '56230cd5f55b503845915b76c22d620a') - version('0.7.7', 'eaf9f37cbccc5e2708754d045909c1a0') + version('0.14.1', sha256='d2bb40cd083c1357768e4683377f03471d160cfe8421136630bfa47f5adb3219') + version('0.13', md5='a9b502dd1a7e6403e35e6972211688a2') + version('0.11.2.2', md5='56230cd5f55b503845915b76c22d620a') + version('0.7.7', md5='eaf9f37cbccc5e2708754d045909c1a0') depends_on('py-setuptools', type='build') depends_on('py-cython@0.21:', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyscaf/package.py b/var/spack/repos/builtin/packages/py-pyscaf/package.py index a4063137059..a64f870e94a 100644 --- a/var/spack/repos/builtin/packages/py-pyscaf/package.py +++ b/var/spack/repos/builtin/packages/py-pyscaf/package.py @@ -13,7 +13,7 @@ class PyPyscaf(PythonPackage): homepage = "https://pypi.python.org/pypi/pyScaf" url = "https://pypi.io/packages/source/p/pyScaf/pyScaf-0.12a4.tar.gz" - version('0.12a4', 'c67526747eb04d1e28279ac310916d40') + version('0.12a4', sha256='3ce3f6fe80bd058831b6a38a56d464ef10f3ebbdd6bc3dcb0d7f127c0b2c1b36') depends_on('py-setuptools', type='build') depends_on('py-fastaindex', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pyserial/package.py b/var/spack/repos/builtin/packages/py-pyserial/package.py index 55ac1b30417..e5074b0e19d 100644 --- a/var/spack/repos/builtin/packages/py-pyserial/package.py +++ b/var/spack/repos/builtin/packages/py-pyserial/package.py @@ -12,6 +12,6 @@ class PyPyserial(PythonPackage): homepage = "https://github.com/pyserial/pyserial" url = "https://pypi.io/packages/source/p/pyserial/pyserial-3.1.1.tar.gz" - version('3.1.1', '2f72100de3e410b36d575e12e82e9d27') + version('3.1.1', sha256='d657051249ce3cbd0446bcfb2be07a435e1029da4d63f53ed9b4cdde7373364c') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyshp/package.py b/var/spack/repos/builtin/packages/py-pyshp/package.py index 5a07f3110b4..20bc7e25452 100644 --- a/var/spack/repos/builtin/packages/py-pyshp/package.py +++ b/var/spack/repos/builtin/packages/py-pyshp/package.py @@ -13,6 +13,6 @@ class PyPyshp(PythonPackage): homepage = "https://github.com/GeospatialPython/pyshp" url = "https://pypi.io/packages/source/p/pyshp/pyshp-1.2.12.tar.gz" - version('1.2.12', '63d33d151ac308f1db71ea0f22c30d8b') + version('1.2.12', sha256='8dcd65e0aa2aa2951527ddb7339ea6e69023543d8a20a73fc51e2829b9ed6179') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py index a4ba28d6384..17f3277fa4a 100644 --- a/var/spack/repos/builtin/packages/py-pyside/package.py +++ b/var/spack/repos/builtin/packages/py-pyside/package.py @@ -21,13 +21,13 @@ class PyPyside(PythonPackage): # https://github.com/PySide/pyside-setup/issues/58 # Meanwhile, developers have moved onto pyside2 (for Qt5), # and show little interest in certifying PySide 1.2.4 for Python. - version('1.2.4', '3cb7174c13bd45e3e8f77638926cb8c0') # rpath problems + version('1.2.4', sha256='1421bc1bf612c396070de9e1ffe227c07c1f3129278bc7d30c754b5146be2433') # rpath problems # This is not available from pypi - # version('1.2.3', 'fa5d5438b045ede36104bba25a6ccc10') + # version('1.2.3', md5='fa5d5438b045ede36104bba25a6ccc10') # v1.2.2 does not work with Python3 - version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d', preferred=True) + version('1.2.2', sha256='53129fd85e133ef630144c0598d25c451eab72019cdcb1012f2aec773a3f25be', preferred=True) depends_on('cmake', type='build') diff --git a/var/spack/repos/builtin/packages/py-pysocks/package.py b/var/spack/repos/builtin/packages/py-pysocks/package.py index a15a4cfb440..da0c2f620a0 100644 --- a/var/spack/repos/builtin/packages/py-pysocks/package.py +++ b/var/spack/repos/builtin/packages/py-pysocks/package.py @@ -12,5 +12,5 @@ class PyPysocks(PythonPackage): homepage = "https://github.com/Anorov/PySocks" url = "https://pypi.io/packages/source/P/PySocks/PySocks-1.6.6.tar.gz" - version('1.6.6', '571f4c23982fa86bf0e7a441f1b6c881') - version('1.5.7', '68f4ad7a8d4fa725656ae3e9dd142d29') + version('1.6.6', sha256='02419a225ff5dcfc3c9695ef8fc9b4d8cc99658e650c6d4718d4c8f451e63f41') + version('1.5.7', sha256='e51c7694b10288e6fd9a28e15c0bcce9aca0327e7b32ebcd9af05fcd56f38b88') diff --git a/var/spack/repos/builtin/packages/py-pysqlite/package.py b/var/spack/repos/builtin/packages/py-pysqlite/package.py index b72851c89a7..48f41cedb9d 100644 --- a/var/spack/repos/builtin/packages/py-pysqlite/package.py +++ b/var/spack/repos/builtin/packages/py-pysqlite/package.py @@ -12,7 +12,7 @@ class PyPysqlite(PythonPackage): homepage = "https://github.com/ghaering/pysqlite" url = "https://pypi.io/packages/source/p/pysqlite/pysqlite-2.8.3.tar.gz" - version('2.8.3', '033f17b8644577715aee55e8832ac9fc') + version('2.8.3', sha256='17d3335863e8cf8392eea71add33dab3f96d060666fe68ab7382469d307f4490') # pysqlite is built into Python3 depends_on('python@2.7.0:2.7.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pytest-cov/package.py b/var/spack/repos/builtin/packages/py-pytest-cov/package.py index 37ffdefc773..c70dad68b8a 100644 --- a/var/spack/repos/builtin/packages/py-pytest-cov/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-cov/package.py @@ -12,7 +12,7 @@ class PyPytestCov(PythonPackage): homepage = "https://github.com/pytest-dev/pytest-cov" url = "https://pypi.io/packages/source/p/pytest-cov/pytest-cov-2.3.1.tar.gz" - version('2.3.1', '8e7475454313a035d08f387ee6d725cb') + version('2.3.1', sha256='fa0a212283cdf52e2eecc24dd6459bb7687cc29adb60cb84258fab73be8dda0f') extends('python', ignore=r'bin/*') diff --git a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py index 043ab81b695..bdd6b9af89d 100644 --- a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py @@ -12,7 +12,7 @@ class PyPytestFlake8(PythonPackage): homepage = "https://github.com/tholo/pytest-flake8" url = "https://pypi.io/packages/source/p/pytest-flake8/pytest-flake8-0.8.1.tar.gz" - version('0.8.1', '39b64ebceb2849805975a2ff4ea7e947') + version('0.8.1', sha256='aa10a6db147485d71dad391d4149388904c3072194d51755f64784ff128845fd') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py index 0927728e739..02fdaeddd30 100644 --- a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py @@ -12,7 +12,7 @@ class PyPytestHttpbin(PythonPackage): homepage = "https://github.com/kevin1024/pytest-httpbin" url = "https://pypi.io/packages/source/p/pytest-httpbin/pytest-httpbin-0.2.3.tar.gz" - version('0.2.3', 'b8ebb8e2fbac1a445fb5d044f7fec556') + version('0.2.3', sha256='c5b698dfa474ffc9caebcb35e34346b753eb226aea5c2e1b69fefedbcf161bf8') extends('python', ignore=r'bin/flask') diff --git a/var/spack/repos/builtin/packages/py-pytest-mock/package.py b/var/spack/repos/builtin/packages/py-pytest-mock/package.py index a159a04f805..45a3ffb163b 100644 --- a/var/spack/repos/builtin/packages/py-pytest-mock/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-mock/package.py @@ -12,7 +12,7 @@ class PyPytestMock(PythonPackage): homepage = "https://github.com/pytest-dev/pytest-mock" url = "https://pypi.io/packages/source/p/pytest-mock/pytest-mock-1.2.zip" - version('1.2', 'a7fa820f7bc71698660945836ff93c73') + version('1.2', sha256='f78971ed376fcb265255d1e4bb313731b3a1be92d7f3ecb19ea7fedc4a56fd0f') extends('python', ignore=r'bin/*') diff --git a/var/spack/repos/builtin/packages/py-pytest-runner/package.py b/var/spack/repos/builtin/packages/py-pytest-runner/package.py index 161413de799..a2826ae4f8f 100644 --- a/var/spack/repos/builtin/packages/py-pytest-runner/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-runner/package.py @@ -14,7 +14,7 @@ class PyPytestRunner(PythonPackage): import_modules = ['ptr'] - version('2.11.1', 'bdb73eb18eca2727944a2dcf963c5a81') + version('2.11.1', sha256='983a31eab45e375240e250161a556163bc8d250edaba97960909338c273a89b3') depends_on('py-setuptools', type='build') depends_on('py-setuptools-scm@1.15:', type='build') diff --git a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py index 093a6370b58..688e19878c0 100644 --- a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py @@ -12,7 +12,7 @@ class PyPytestXdist(PythonPackage): homepage = "https://github.com/pytest-dev/pytest-xdist" url = "https://pypi.io/packages/source/p/pytest-xdist/pytest-xdist-1.16.0.tar.gz" - version('1.16.0', '68dabf856981ad93b14960b098b05bff') + version('1.16.0', sha256='42e5a1e5da9d7cff3e74b07f8692598382f95624f234ff7e00a3b1237e0feba2') depends_on('py-setuptools', type='build') depends_on('py-execnet@1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pytest/package.py b/var/spack/repos/builtin/packages/py-pytest/package.py index 4d32290d780..88855880c03 100644 --- a/var/spack/repos/builtin/packages/py-pytest/package.py +++ b/var/spack/repos/builtin/packages/py-pytest/package.py @@ -16,12 +16,12 @@ class PyPytest(PythonPackage): version('5.1.1', sha256='c3d5020755f70c82eceda3feaf556af9a341334414a8eca521a18f463bcead88') version('4.6.5', sha256='8fc39199bdda3d9d025d3b1f4eb99a192c20828030ea7c9a0d2840721de7d347') - version('4.3.0', 'e1913b607c5c4e7d886ba6f13a43617e') - version('3.7.2', 'd12d0d556a21fd8633e105f1a8d5a0f9') - version('3.7.1', '2704e16bb2c11af494167f80a7cd37c4') - version('3.5.1', 'ffd870ee3ca561695d2f916f0f0f3c0b') - version('3.0.7', '89c60546507dc7eb6e9e40a6e9f720bd') - version('3.0.2', '61dc36e65a6f6c11c53b1388e043a9f5') + version('4.3.0', sha256='067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c') + version('3.7.2', sha256='3459a123ad5532852d36f6f4501dfe1acf4af1dd9541834a164666aa40395b02') + version('3.7.1', sha256='86a8dbf407e437351cef4dba46736e9c5a6e3c3ac71b2e942209748e76ff2086') + version('3.5.1', sha256='54713b26c97538db6ff0703a12b19aeaeb60b5e599de542e7fca0ec83b9038e8') + version('3.0.7', sha256='b70696ebd1a5e6b627e7e3ac1365a4bc60aaf3495e843c1e70448966c5224cab') + version('3.0.2', sha256='64d8937626dd2a4bc15ef0edd307d26636a72a3f3f9664c424d78e40efb1e339') depends_on('python@3.5:', when='@5:', type=('build', 'run')) depends_on('python@2.7:2.8,3.4:', when='@3.3:4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py index d7dfb2e0a33..95f31f01096 100644 --- a/var/spack/repos/builtin/packages/py-python-daemon/package.py +++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py @@ -21,7 +21,7 @@ class PyPythonDaemon(PythonPackage): homepage = "https://pypi.python.org/pypi/python-daemon/" url = "https://pypi.io/packages/source/p/python-daemon/python-daemon-2.0.5.tar.gz" - version('2.0.5', '73e7f49f525c51fa4a995aea4d80de41') + version('2.0.5', sha256='afde4fa433d94d007206ee31a0941d55b5eb232a5422b670aad628547b46bf68') depends_on("py-setuptools", type='build') depends_on("py-lockfile", type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-python-dateutil/package.py b/var/spack/repos/builtin/packages/py-python-dateutil/package.py index 114a787a7ac..397c4ae0852 100644 --- a/var/spack/repos/builtin/packages/py-python-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-python-dateutil/package.py @@ -18,10 +18,10 @@ class PyPythonDateutil(PythonPackage): version('2.8.0', sha256='c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e') version('2.7.5', sha256='88f9287c0174266bb0d8cedd395cfba9c58e87e5ad86b2ce58859bc11be3cf02') - version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6') - version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2') - version('2.4.0', '75714163bb96bedd07685cdb2071b8bc') - version('2.2', 'c1f654d0ff7e33999380a8ba9783fd5c') + version('2.5.2', sha256='063907ef47f6e187b8fe0728952e4effb587a34f2dc356888646f9b71fbb2e4b') + version('2.4.2', sha256='3e95445c1db500a344079a47b171c45ef18f57d188dffdb0e4165c71bea8eb3d') + version('2.4.0', sha256='439df33ce47ef1478a4f4765f3390eab0ed3ec4ae10be32f2930000c8d19f417') + version('2.2', sha256='eec865307ebe7f329a6a9945c15453265a449cdaaf3710340828a1934d53e468') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools@24.3:', type='build') diff --git a/var/spack/repos/builtin/packages/py-python-engineio/package.py b/var/spack/repos/builtin/packages/py-python-engineio/package.py index db0e97ea83c..1878e073817 100644 --- a/var/spack/repos/builtin/packages/py-python-engineio/package.py +++ b/var/spack/repos/builtin/packages/py-python-engineio/package.py @@ -14,7 +14,7 @@ class PyPythonEngineio(PythonPackage): homepage = "http://python-engineio.readthedocs.io/en/latest/" url = "https://github.com/miguelgrinberg/python-engineio/archive/v2.0.2.tar.gz" - version('2.0.2', 'b91c6fa900905f9a96b86c3e141e2754') + version('2.0.2', sha256='9fbe531108a95bc61518b61c4718e2661fc81d32b54fd6af34799bf10a367a6b') depends_on('py-setuptools', type='build') depends_on('py-six@1.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-python-gitlab/package.py b/var/spack/repos/builtin/packages/py-python-gitlab/package.py index 2d258bfe1df..50a6783b8d0 100644 --- a/var/spack/repos/builtin/packages/py-python-gitlab/package.py +++ b/var/spack/repos/builtin/packages/py-python-gitlab/package.py @@ -12,10 +12,10 @@ class PyPythonGitlab(PythonPackage): homepage = "https://github.com/gpocentek/python-gitlab" url = "https://pypi.io/packages/source/p/python-gitlab/python-gitlab-0.19.tar.gz" - version('0.19', '6564d7204c2b7e65c54b3fa89ec91df6') - version('0.18', 'c31dae1d0bab3966cb830f2308a96308') - version('0.17', '8a69c602e07dd4731856531d79bb58eb') - version('0.16', 'e0421d930718021e7d796d74d2ad7194') + version('0.19', sha256='88b65591db7a10a0d9979797e4e654a113e2b93b3a559309f6092b27ab93934a') + version('0.18', sha256='d60d67c82fedd8c3e4f0bb8b5241bf2df32307c98fdf2f02a94850e21db2d804') + version('0.17', sha256='f79337cd8b2343195b7ac0909e0483624d4235cca78fc76196a0ee4e109c9a70') + version('0.16', sha256='2c50dc0bd3ed7c6b1edb6e556b0f0109493ae9dfa46e3bffcf3e5e67228d7d53') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-python-levenshtein/package.py b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py index 6e932fc2669..ec536420a0f 100644 --- a/var/spack/repos/builtin/packages/py-python-levenshtein/package.py +++ b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py @@ -13,6 +13,6 @@ class PyPythonLevenshtein(PythonPackage): homepage = "https://github.com/ztane/python-Levenshtein" url = "https://pypi.io/packages/source/p/python-Levenshtein/python-Levenshtein-0.12.0.tar.gz" - version('0.12.0', 'e8cde197d6d304bbdc3adae66fec99fb') + version('0.12.0', sha256='033a11de5e3d19ea25c9302d11224e1a1898fe5abd23c61c7c360c25195e3eb1') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-python-socketio/package.py b/var/spack/repos/builtin/packages/py-python-socketio/package.py index 34d1422e9da..1065a1473ad 100644 --- a/var/spack/repos/builtin/packages/py-python-socketio/package.py +++ b/var/spack/repos/builtin/packages/py-python-socketio/package.py @@ -12,7 +12,7 @@ class PyPythonSocketio(PythonPackage): homepage = "https://github.com/miguelgrinberg/python-socketio" url = "https://pypi.io/packages/source/p/python-socketio/python-socketio-1.8.4.tar.gz" - version('1.8.4', '9de73990f6c32c701278c01b0fa1a0c3') + version('1.8.4', sha256='13807ce17e85371d15b31295a43b1fac1c0dba1eb5fc233353a3efd53aa122cc') variant('eventlet', default=True, description="Pulls in optional eventlet dependency, required" diff --git a/var/spack/repos/builtin/packages/py-pythonqwt/package.py b/var/spack/repos/builtin/packages/py-pythonqwt/package.py index 2bc32b69c4d..582b3b45703 100644 --- a/var/spack/repos/builtin/packages/py-pythonqwt/package.py +++ b/var/spack/repos/builtin/packages/py-pythonqwt/package.py @@ -12,7 +12,7 @@ class PyPythonqwt(PythonPackage): homepage = "https://github.com/PierreRaybaut/PythonQwt" url = "https://pypi.io/packages/source/P/PythonQwt/PythonQwt-0.5.5.zip" - version('0.5.5', 'a60c7da9fbca667337d14aca094b6fda') + version('0.5.5', sha256='1f13cc8b555a57f8fe0f806d6c2f6d847050e4d837649503932b81316d12788a') variant('doc', default=False, description="Build documentation.") diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index fe021c2066e..e46202e584f 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -15,12 +15,12 @@ class PyPytz(PythonPackage): import_modules = ['pytz'] version('2018.4', sha256='c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749') - version('2017.2', 'f89bde8a811c8a1a5bac17eaaa94383c') - version('2016.10', 'cc9f16ba436efabdcef3c4d32ae4919c') - version('2016.6.1', 'b6c28a3b968bc1d8badfb61b93874e03') - version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7') - version('2014.9', 'd42bda2f4c1e873e02fbd1e4acfd1b8c') - version('2015.4', '417a47b1c432d90333e42084a605d3d8') - version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29') + version('2017.2', md5='f89bde8a811c8a1a5bac17eaaa94383c') + version('2016.10', sha256='9a43e20aa537cfad8fe7a1715165c91cb4a6935d40947f2d070e4c80f2dcd22b') + version('2016.6.1', sha256='6f57732f0f8849817e9853eb9d50d85d1ebb1404f702dbc44ee627c642a486ca') + version('2014.10', sha256='a94138b638907491f473c875e8c95203a6a02efef52b6562be302e435016f4f3') + version('2014.9', sha256='c5bcbd11cf9847096ae1eb4e83dde75d10ac62efe6e73c4600f3f980968cdbd2') + version('2015.4', sha256='c4ee70cb407f9284517ac368f121cf0796a7134b961e53d9daf1aaae8f44fb90') + version('2016.3', sha256='3449da19051655d4c0bb5c37191331748bcad15804d81676a88451ef299370a8') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyutilib/package.py b/var/spack/repos/builtin/packages/py-pyutilib/package.py index 12319c0aded..ed620b16268 100644 --- a/var/spack/repos/builtin/packages/py-pyutilib/package.py +++ b/var/spack/repos/builtin/packages/py-pyutilib/package.py @@ -17,16 +17,16 @@ class PyPyutilib(PythonPackage): homepage = "https://github.com/PyUtilib/pyutilib" url = "https://github.com/PyUtilib/pyutilib/archive/5.5.1.tar.gz" - version('5.6.2', '60c6ea5083e512211984347ffeca19d2') - version('5.6.1', 'ddc7e896304b6fabe4d21eb5fdec386e') - version('5.6', '5bfcdbf118264f1a1b8c6cac9dea8bca') - version('5.5.1', 'c4990cbced152d879812d109aaa857ff') - version('5.5', '7940563bf951332cf836f418d67b2134') - version('5.4.1', 'b34b5798757e4ab73868b7655c5c8f8a') - version('5.4', '9410e5a76885412310b03074d2f97e55') - version('5.3.5', '85e41e65f24f6711261229bcde6eb825') - version('5.3.4', '4fe1a8387c027f64b62ca99424275368') - version('5.3.3', '27a713ca8d49714244646e1ce38778b9') + version('5.6.2', sha256='3f9f500cf1f15a92e7eb0b3c3ca2af537a2a9e61fe70ad6be4d2d08d9e47764f') + version('5.6.1', sha256='0d0d57921877dc292dd9de39596fabc83b5d072adf10a90c979f678662ddb752') + version('5.6', sha256='ea1e263652d8199322759e169e4a40fc23964c49e82ae1470ab83a613a6e6b25') + version('5.5.1', sha256='0e9070551abc82a90b977f9bf875a91ceebfdfa5d7327028ece60324ef66f3ab') + version('5.5', sha256='442f5abbd2a61c6f51698e0450cddbb4fc10047f350a939218f0c4b92a90f8ef') + version('5.4.1', sha256='7d6bf66d3ebaf8769e9395748f618a13a7e02cc88a62f8be8889f40816502b14') + version('5.4', sha256='c778e89a22d882ebf0096eca3abc4cc312f6e1fa1b7869b416710a2f467cb4d6') + version('5.3.5', sha256='8b9c2be34f80da0ae18ecc2e46ac7467d35b2e9f33411e7331c6edddea108906') + version('5.3.4', sha256='475c97bf1213add6b7fefaa3f05affef3613e6aecc9fcb3cc0693304671b73c3') + version('5.3.3', sha256='318f4d60c9552493fe81a4b2e0418d2cf43aaab68e6d23e2c9a68ef010c9cf21') depends_on('py-nose', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pywavelets/package.py b/var/spack/repos/builtin/packages/py-pywavelets/package.py index 1039d220b24..d5c459a4e09 100644 --- a/var/spack/repos/builtin/packages/py-pywavelets/package.py +++ b/var/spack/repos/builtin/packages/py-pywavelets/package.py @@ -14,7 +14,7 @@ class PyPywavelets(PythonPackage): homepage = "https://github.com/PyWavelets" url = "https://pypi.io/packages/source/P/PyWavelets/PyWavelets-0.5.2.tar.gz" - version('0.5.2', 'aedda732f064cf9395f03d37f1003d1a') + version('0.5.2', sha256='ce36e2f0648ea1781490b09515363f1f64446b0eac524603e5db5e180113bed9') import_modules = ['pywt', 'pywt.data'] diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py index 042c197bf3e..3761663c1de 100644 --- a/var/spack/repos/builtin/packages/py-pyyaml/package.py +++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py @@ -12,5 +12,5 @@ class PyPyyaml(PythonPackage): url = "http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz" version('3.13', sha256='3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf') - version('3.12', '4c129761b661d181ebf7ff4eb2d79950') - version('3.11', 'f50e08ef0fe55178479d3a618efe21db') + version('3.12', sha256='592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab') + version('3.11', sha256='c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8') diff --git a/var/spack/repos/builtin/packages/py-qtawesome/package.py b/var/spack/repos/builtin/packages/py-qtawesome/package.py index 166e49a9ad3..28babe1528b 100644 --- a/var/spack/repos/builtin/packages/py-qtawesome/package.py +++ b/var/spack/repos/builtin/packages/py-qtawesome/package.py @@ -12,8 +12,8 @@ class PyQtawesome(PythonPackage): homepage = "https://github.com/spyder-ide/qtawesome" url = "https://pypi.io/packages/source/Q/QtAwesome/QtAwesome-0.4.1.tar.gz" - version('0.4.1', 'd55472b231eba07059794769bdfe07b2') - version('0.3.3', '830677aa6ca4e7014e228147475183d3') + version('0.4.1', sha256='9ea91efeb83e8b73f814aeca898c29cade0c087acec58e91b4f384595aeb4cfd') + version('0.3.3', sha256='c3c98ee4df0133ae42d202fea20253f8746266b4541c5df4269ca4131792ce0f') depends_on('py-setuptools', type='build') depends_on('py-qtpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-qtconsole/package.py b/var/spack/repos/builtin/packages/py-qtconsole/package.py index 0c9b83ebfdc..fb81aaa70a6 100644 --- a/var/spack/repos/builtin/packages/py-qtconsole/package.py +++ b/var/spack/repos/builtin/packages/py-qtconsole/package.py @@ -12,7 +12,7 @@ class PyQtconsole(PythonPackage): homepage = "http://ipython.org" url = "https://pypi.io/packages/source/q/qtconsole/qtconsole-4.2.1.tar.gz" - version('4.2.1', 'c08ebebc7a60629ebadf685361ca0798') + version('4.2.1', sha256='25ec7d345528b3e8f3c91be349dd3c699755f206dc4b6ec668e2e5dd60ea18ef') variant('doc', default=False, description='Build documentation') diff --git a/var/spack/repos/builtin/packages/py-qtpy/package.py b/var/spack/repos/builtin/packages/py-qtpy/package.py index 7e46682111f..9ee1d42f719 100644 --- a/var/spack/repos/builtin/packages/py-qtpy/package.py +++ b/var/spack/repos/builtin/packages/py-qtpy/package.py @@ -12,7 +12,7 @@ class PyQtpy(PythonPackage): homepage = "https://github.com/spyder-ide/qtpy" url = "https://pypi.io/packages/source/Q/QtPy/QtPy-1.2.1.tar.gz" - version('1.2.1', 'e2f783fb7f8e502815237bd8d30c6d11') + version('1.2.1', sha256='5803ce31f50b24295e8e600b76cc91d7f2a3140a5a0d526d40226f9ec5e9097d') depends_on('py-setuptools', type='build') depends_on('py-pyqt4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-quantities/package.py b/var/spack/repos/builtin/packages/py-quantities/package.py index e8fce2537e0..2f6e4c24e40 100644 --- a/var/spack/repos/builtin/packages/py-quantities/package.py +++ b/var/spack/repos/builtin/packages/py-quantities/package.py @@ -12,8 +12,8 @@ class PyQuantities(PythonPackage): homepage = "http://python-quantities.readthedocs.org" url = "https://pypi.io/packages/source/q/quantities/quantities-0.12.1.tar.gz" - version('0.12.1', '9c9ecda15e905cccfc420e5341199512') - version('0.11.1', 'f4c6287bfd2e93322b25a7c1311a0243', + version('0.12.1', sha256='0a03e8511db603c57ca80dee851c43f08d0457f4d592bcac2e154570756cb934') + version('0.11.1', sha256='4382098a501b55bf0fdb3dba2061a161041253697d78811ecfd7c55449836660', url="https://pypi.io/packages/source/q/quantities/quantities-0.11.1.zip") conflicts('py-numpy@1.13:', when='@:0.11.99') diff --git a/var/spack/repos/builtin/packages/py-quast/package.py b/var/spack/repos/builtin/packages/py-quast/package.py index 940ad4e800c..fd232743ace 100644 --- a/var/spack/repos/builtin/packages/py-quast/package.py +++ b/var/spack/repos/builtin/packages/py-quast/package.py @@ -12,9 +12,9 @@ class PyQuast(PythonPackage): homepage = "http://cab.spbu.ru/software/quast" url = "https://github.com/ablab/quast/archive/quast_4.6.1.tar.gz" - version('4.6.3', '16d77acb2e0f6436b58d9df7b732fb76') - version('4.6.1', '37ccd34e0040c17aa6f990353a92475c') - version('4.6.0', 'c04d62c50ec4d9caa9d7388950b8d144') + version('4.6.3', sha256='d7f5e670563d17d683f6df057086f7b816b6a088266c6270f7114a1406aaab63') + version('4.6.1', sha256='a8071188545710e5c0806eac612daaabde9f730819df2c44be3ffa9317b76a58') + version('4.6.0', sha256='6bee86654b457a981718a19acacffca6a3e74f30997ad06162a70fd2a181ca2e') depends_on('boost@1.56.0') depends_on('perl@5.6.0:') diff --git a/var/spack/repos/builtin/packages/py-radical-utils/package.py b/var/spack/repos/builtin/packages/py-radical-utils/package.py index 8f39f46851e..0961beaed73 100644 --- a/var/spack/repos/builtin/packages/py-radical-utils/package.py +++ b/var/spack/repos/builtin/packages/py-radical-utils/package.py @@ -12,8 +12,8 @@ class PyRadicalUtils(PythonPackage): homepage = "http://radical.rutgers.edu" url = "https://pypi.io/packages/source/r/radical.utils/radical.utils-0.45.tar.gz" - version('0.45', 'c0bec2a0951b0dc990366d82e78e65fe') - version('0.41.1', '923446539545dc157768026c957cecb2') + version('0.45', sha256='1333cff1a69532e51d4484fbac3fad6b172d415d2055a3141117c7cf8bdee6c5') + version('0.41.1', sha256='582900e0434f49b69885a89bc65dc787362756e1014d52a4afac0bb61bcaa3ce') depends_on('py-setuptools', type='build') depends_on('py-colorama', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ranger/package.py b/var/spack/repos/builtin/packages/py-ranger/package.py index 1b74137366c..2676d513542 100644 --- a/var/spack/repos/builtin/packages/py-ranger/package.py +++ b/var/spack/repos/builtin/packages/py-ranger/package.py @@ -13,6 +13,6 @@ class PyRanger(PythonPackage): homepage = "http://ranger.nongnu.org/" url = "https://github.com/ranger/ranger/archive/v1.7.2.tar.gz" - version('1.7.2', '27805c3ab7ec4b129e1b93249506d925') + version('1.7.2', sha256='80917c93396e46272b6de63816d925eb708291a9f7a559d49b24c571ea0eeeb3') depends_on('python@2.6:') diff --git a/var/spack/repos/builtin/packages/py-readme-renderer/package.py b/var/spack/repos/builtin/packages/py-readme-renderer/package.py index bbea9facf72..b604ff787ba 100644 --- a/var/spack/repos/builtin/packages/py-readme-renderer/package.py +++ b/var/spack/repos/builtin/packages/py-readme-renderer/package.py @@ -13,7 +13,7 @@ class PyReadmeRenderer(PythonPackage): homepage = "https://github.com/pypa/readme_renderer" url = "https://pypi.io/packages/source/r/readme_renderer/readme_renderer-16.0.tar.gz" - version('16.0', '70321cea986956bcf2deef9981569f39') + version('16.0', sha256='c46b3418ddef3c3c3f819a4a9cfd56ede15c03d12197962a7e7a89edf1823dd5') depends_on('python@2.6:2.8,3.2:3.3') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-regex/package.py b/var/spack/repos/builtin/packages/py-regex/package.py index 65d9382a122..c7a11de7316 100644 --- a/var/spack/repos/builtin/packages/py-regex/package.py +++ b/var/spack/repos/builtin/packages/py-regex/package.py @@ -12,6 +12,6 @@ class PyRegex(PythonPackage): homepage = "https://pypi.python.org/pypi/regex/" url = "https://pypi.io/packages/source/r/regex/regex-2017.07.11.tar.gz" - version('2017.07.11', '95f81ebb5273c7ad9a0c4d1ac5a94eb4') + version('2017.07.11', sha256='dbda8bdc31a1c85445f1a1b29d04abda46e5c690f8f933a9cc3a85a358969616') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-reportlab/package.py b/var/spack/repos/builtin/packages/py-reportlab/package.py index 867c4c084ab..46c3d8d897a 100644 --- a/var/spack/repos/builtin/packages/py-reportlab/package.py +++ b/var/spack/repos/builtin/packages/py-reportlab/package.py @@ -13,7 +13,7 @@ class PyReportlab(PythonPackage): homepage = "https://pypi.python.org/pypi/reportlab" url = "https://pypi.io/packages/source/r/reportlab/reportlab-3.4.0.tar.gz" - version('3.4.0', '3f2522cf3b69cd84426c216619bbff53') + version('3.4.0', sha256='5beaf35e59dfd5ebd814fdefd76908292e818c982bd7332b5d347dfd2f01c343') # py-reportlab provides binaries that duplicate those of other packages, # thus interfering with activation. diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py index 9ef51af3203..5645ab4e00f 100644 --- a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py +++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py @@ -13,7 +13,7 @@ class PyRequestsToolbelt(PythonPackage): homepage = "https://toolbelt.readthedocs.org/" url = "https://github.com/requests/toolbelt/archive/0.8.0.tar.gz" - version('0.8.0', 'de9bf7fbcc6ae341a5c4fd9f8912bcac') + version('0.8.0', sha256='f151c07e88148dc05b6f31cc75dfb7a6770968e4a5c8e6690325eed4e79160a1') depends_on('py-setuptools', type='build') depends_on('py-requests@2.0.1:3.0.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-requests/package.py b/var/spack/repos/builtin/packages/py-requests/package.py index 872512276f6..8a76d9622f7 100644 --- a/var/spack/repos/builtin/packages/py-requests/package.py +++ b/var/spack/repos/builtin/packages/py-requests/package.py @@ -24,10 +24,10 @@ class PyRequests(PythonPackage): ] version('2.21.0', sha256='502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e') - version('2.14.2', '4c3c169ed67466088a2a6947784fe444') - version('2.13.0', '921ec6b48f2ddafc8bb6160957baf444') - version('2.11.1', 'ad5f9c47b5c5dfdb28363ad7546b0763') - version('2.3.0', '7449ffdc8ec9ac37bbcd286003c80f00') + version('2.14.2', sha256='a274abba399a23e8713ffd2b5706535ae280ebe2b8069ee6a941cb089440d153') + version('2.13.0', sha256='5722cd09762faa01276230270ff16af7acf7c5c45d623868d9ba116f15791ce8') + version('2.11.1', sha256='5acf980358283faba0b897c73959cecf8b841205bb4b2ad3ef545f46eae1a133') + version('2.3.0', sha256='1c1473875d846fe563d70868acf05b1953a4472f4695b7b3566d1d978957b8fc') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-restview/package.py b/var/spack/repos/builtin/packages/py-restview/package.py index 0e05c727106..1ea038cfe23 100644 --- a/var/spack/repos/builtin/packages/py-restview/package.py +++ b/var/spack/repos/builtin/packages/py-restview/package.py @@ -12,7 +12,7 @@ class PyRestview(PythonPackage): homepage = "https://mg.pov.lt/restview/" url = "https://pypi.io/packages/source/r/restview/restview-2.6.1.tar.gz" - version('2.6.1', 'ac8b70e15b8f1732d1733d674813666b') + version('2.6.1', sha256='14d261ee0edf30e0ebc1eb320428ef4898e97422b00337863556966b851fb5af') depends_on('python@2.7:2.8,3.3:3.5') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py index 192bf4884c8..6d5eca51953 100644 --- a/var/spack/repos/builtin/packages/py-rpy2/package.py +++ b/var/spack/repos/builtin/packages/py-rpy2/package.py @@ -16,11 +16,11 @@ class PyRpy2(PythonPackage): homepage = "https://pypi.python.org/pypi/rpy2" url = "https://pypi.io/packages/source/r/rpy2/rpy2-2.5.4.tar.gz" - version('3.0.0', '4ea39c4ff42f5bc611e338ff66d18c9f') - version('2.9.4', '7df2562cdf43a0ccdd1e44ee1c16614f') - version('2.8.6', '85046aa58ba586622f67271fbca05933') - version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f') - version('2.5.4', '115a20ac30883f096da2bdfcab55196d') + version('3.0.0', sha256='34efc2935d9015527837d6b1de29641863d184b19d39ad415d5384be8a015bce') + version('2.9.4', sha256='be57f741d0c284b5d8785ab03dff0e829303e5ac30e548d5ceb46e05b168812e') + version('2.8.6', sha256='004d13734a7b9a85cbc1e7a93ec87df741e28db1273ab5b0d9efaac04a9c5f98') + version('2.5.6', sha256='d0d584c435b5ed376925a95a4525dbe87de7fa9260117e9f208029e0c919ad06') + version('2.5.4', sha256='d521ecdd05cd0c31ab017cb63e9f63c29b524e46ec9063a920f640b5875f8a90') # FIXME: Missing dependencies: # ld: cannot find -licuuc diff --git a/var/spack/repos/builtin/packages/py-rsa/package.py b/var/spack/repos/builtin/packages/py-rsa/package.py index baf7830f2a2..c991be58e76 100644 --- a/var/spack/repos/builtin/packages/py-rsa/package.py +++ b/var/spack/repos/builtin/packages/py-rsa/package.py @@ -14,7 +14,7 @@ class PyRsa(PythonPackage): import_modules = ['rsa'] - version('3.4.2', 'b315f47882c24030ee6b5aad628cccdb') + version('3.4.2', sha256='25df4e10c263fb88b5ace923dd84bf9aa7f5019687b5e55382ffcdb8bede9db5') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-pyasn1@0.1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-rseqc/package.py b/var/spack/repos/builtin/packages/py-rseqc/package.py index 411fb1c59e2..d7e078b29b0 100644 --- a/var/spack/repos/builtin/packages/py-rseqc/package.py +++ b/var/spack/repos/builtin/packages/py-rseqc/package.py @@ -14,7 +14,7 @@ class PyRseqc(PythonPackage): homepage = "http://rseqc.sourceforge.net" url = "https://pypi.io/packages/source/R/RSeQC/RSeQC-2.6.4.tar.gz" - version('2.6.4', '935779c452ffc84f3b8b9fb3d485c782') + version('2.6.4', sha256='e11df661bda1c24fc950f0bce06f586a68ab5f4a2c356f43e4a0dfdc1e184315') depends_on('py-setuptools', type='build') depends_on('py-bx-python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-rtree/package.py b/var/spack/repos/builtin/packages/py-rtree/package.py index 7f4db74b72f..4d0db48ecb4 100644 --- a/var/spack/repos/builtin/packages/py-rtree/package.py +++ b/var/spack/repos/builtin/packages/py-rtree/package.py @@ -11,7 +11,7 @@ class PyRtree(PythonPackage): homepage = "http://toblerity.org/rtree/" url = "https://pypi.io/packages/source/R/Rtree/Rtree-0.8.3.tar.gz" - version('0.8.3', 'a27cb05a85eed0a3605c45ebccc432f8') + version('0.8.3', sha256='6cb9cf3000963ea6a3db777a597baee2bc55c4fc891e4f1967f262cc96148649') depends_on('py-setuptools', type='build') depends_on('libspatialindex') diff --git a/var/spack/repos/builtin/packages/py-saga-python/package.py b/var/spack/repos/builtin/packages/py-saga-python/package.py index 2feedd0e02e..746095fba9d 100644 --- a/var/spack/repos/builtin/packages/py-saga-python/package.py +++ b/var/spack/repos/builtin/packages/py-saga-python/package.py @@ -12,7 +12,7 @@ class PySagaPython(PythonPackage): homepage = "http://radical.rutgers.edu" url = "https://pypi.io/packages/source/s/saga-python/saga-python-0.41.3.tar.gz" - version('0.41.3', '3f92e16a53635ffe529fca4bae3b705d') + version('0.41.3', sha256='b30961e634f32f6008e292aa1fe40560f257d5294b0cda95baac1cf5391feb5d') depends_on('py-setuptools', type='build') depends_on('py-apache-libcloud', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-scandir/package.py b/var/spack/repos/builtin/packages/py-scandir/package.py index ab41c476b2b..4d4bfb5868b 100644 --- a/var/spack/repos/builtin/packages/py-scandir/package.py +++ b/var/spack/repos/builtin/packages/py-scandir/package.py @@ -14,7 +14,7 @@ class PyScandir(PythonPackage): import_modules = ['scandir'] - version('1.9.0', '506c4cc5f38c00b301642a9cb0433910') - version('1.6', '0180ddb97c96cbb2d4f25d2ae11c64ac') + version('1.9.0', sha256='44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064') + version('1.6', sha256='e0278a2d4bc6c0569aedbe66bf26c8ab5b2b08378b3289de49257f23ac624338') depends_on('py-setuptools', type=('build')) diff --git a/var/spack/repos/builtin/packages/py-scientificpython/package.py b/var/spack/repos/builtin/packages/py-scientificpython/package.py index a58515a40e7..aabec4e81c5 100644 --- a/var/spack/repos/builtin/packages/py-scientificpython/package.py +++ b/var/spack/repos/builtin/packages/py-scientificpython/package.py @@ -14,6 +14,6 @@ class PyScientificpython(PythonPackage): homepage = "https://sourcesup.renater.fr/projects/scientific-py/" url = "https://sourcesup.renater.fr/frs/download.php/file/4411/ScientificPython-2.8.1.tar.gz" - version('2.8.1', '73ee0df19c7b58cdf2954261f0763c77') + version('2.8.1', sha256='d9ef354736410bbb2e8be33cb7433cf62114307a44e3a96baaa793b58b4b518b') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index d8c5e9c7b48..c60a13477a9 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -14,7 +14,7 @@ class PyScikitImage(PythonPackage): url = "https://pypi.io/packages/source/s/scikit-image/scikit-image-0.12.3.tar.gz" version('0.14.2', sha256='1afd0b84eefd77afd1071c5c1c402553d67be2d7db8950b32d6f773f25850c1f') - version('0.12.3', '04ea833383e0b6ad5f65da21292c25e1') + version('0.12.3', sha256='82da192f0e524701e89c5379c79200bc6dc21373f48bf7778a864c583897d7c7') extends('python', ignore=r'bin/.*\.py$') diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py index 3b63e6e0203..13137c0da01 100644 --- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py @@ -37,12 +37,12 @@ class PyScikitLearn(PythonPackage): version('0.21.1', sha256='228d0611e69e5250946f8cd7bbefec75347950f0ca426d0c518db8f06583f660') version('0.20.2', sha256='bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6') version('0.20.0', sha256='97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18') - version('0.19.1', 'b67143988c108862735a96cf2b1e827a') - version('0.18.1', '6b0ff1eaa5010043895dd63d1e3c60c9') - version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d') - version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e') - version('0.17.1', 'a2f8b877e6d99b1ed737144f5a478dfc') - version('0.13.1', 'acba398e1d46274b8470f40d0926e6a4') + version('0.19.1', sha256='5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0') + version('0.18.1', sha256='1eddfc27bb37597a5d514de1299981758e660e0af56981c0bfdf462c9568a60c') + version('0.15.2', sha256='1a8a881f6f13edc0ac58931ce21f899eb7920af50aa08802413d1239e2aa5fa6') + version('0.16.1', sha256='c0721e295056c95c7002e05726f2bd271a7923e88bdeab34a2b60aac2b0ee6e4') + version('0.17.1', sha256='9f4cf58e57d81783289fc503caaed1f210bab49b7a6f680bf3c04b1e0a96e5f0') + version('0.13.1', sha256='a6e4759a779ba792435d096c882a0d66ee29d369755c09209f1a4e50877bdc94') variant('openmp', default=True, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index 7d549e10815..b173be57eac 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -34,15 +34,15 @@ class PyScipy(PythonPackage): version('1.3.0', sha256='c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a') version('1.2.2', sha256='a4331e0b8dab1ff75d2c67b5158a8bb9a83c799d7140094dda936d876c7cfbb1') version('1.2.1', sha256='e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c') - version('1.1.0', 'aa6bcc85276b6f25e17bcfc4dede8718') - version('1.0.0', '53fa34bd3733a9a4216842b6000f7316') - version('0.19.1', '6b4d91b62f1926282b127194a06b72b3') - version('0.19.0', '91b8396231eec780222a57703d3ec550', + version('1.1.0', sha256='878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1') + version('1.0.0', sha256='87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10') + version('0.19.1', sha256='a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6') + version('0.19.0', sha256='4190d34bf9a09626cd42100bbb12e3d96b2daf1a8a3244e991263eb693732122', url="https://pypi.io/packages/source/s/scipy/scipy-0.19.0.zip") - version('0.18.1', '5fb5fb7ccb113ab3a039702b6c2f3327') - version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224') - version('0.15.1', 'be56cd8e60591d6332aac792a5880110') - version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') + version('0.18.1', sha256='8ab6e9c808bf2fb3e8576cd8cf07226d9cdc18b012c06d9708429a821ac6634e') + version('0.17.0', sha256='f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089') + version('0.15.1', sha256='a212cbc3b79e9a563aa45fc5c517b3499198bd7eb7e7be1e047568a5f48c259a') + version('0.15.0', sha256='0c74e31e08acc8bf9b6ceb9bced73df2ae0cc76003e0366350bc7b26292bf8b1') depends_on('python@2.6:2.8,3.2:') depends_on('python@2.7:2.8,3.4:', when='@0.18:') diff --git a/var/spack/repos/builtin/packages/py-seaborn/package.py b/var/spack/repos/builtin/packages/py-seaborn/package.py index e096444d8cd..a4dc90e7666 100644 --- a/var/spack/repos/builtin/packages/py-seaborn/package.py +++ b/var/spack/repos/builtin/packages/py-seaborn/package.py @@ -17,8 +17,8 @@ class PySeaborn(PythonPackage): homepage = "http://seaborn.pydata.org/" url = "https://pypi.io/packages/source/s/seaborn/seaborn-0.7.1.tar.gz" - version('0.9.0', '76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f') - version('0.7.1', 'ef07e29e0f8a1f2726abe506c1a36e93') + version('0.9.0', sha256='76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f') + version('0.7.1', sha256='fa274344b1ee72f723bab751c40a5c671801d47a29ee9b5e69fcf63a18ce5c5d') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-setuptools-git/package.py b/var/spack/repos/builtin/packages/py-setuptools-git/package.py index 56a9380ca9c..e89d358ca47 100644 --- a/var/spack/repos/builtin/packages/py-setuptools-git/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools-git/package.py @@ -12,7 +12,7 @@ class PySetuptoolsGit(PythonPackage): homepage = "https://pypi.python.org/pypi/setuptools-git" url = "https://pypi.io/packages/source/s/setuptools-git/setuptools-git-1.2.tar.gz" - version('1.2', '40b2ef7687a384ea144503c2e5bc67e2') + version('1.2', sha256='ff64136da01aabba76ae88b050e7197918d8b2139ccbf6144e14d472b9c40445') depends_on('py-setuptools', type='build') depends_on('git') diff --git a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py index 35a72f28e87..69f69a23859 100644 --- a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py @@ -14,8 +14,8 @@ class PySetuptoolsScm(PythonPackage): import_modules = ['setuptools_scm'] - version('3.1.0', '52a8dee23c9e5f7d7d18094563db516c') - version('1.15.6', 'f17493d53f0d842bb0152f214775640b') + version('3.1.0', sha256='1191f2a136b5e86f7ca8ab00a97ef7aef997131f1f6d4971be69a1ef387d8b40') + version('1.15.6', sha256='49ab4685589986a42da85706b3311a2f74f1af567d39fee6cb1e088d7a75fb5f') depends_on('py-setuptools', type='build') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 78e32d21cd5..0c7afe3c67d 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -24,20 +24,20 @@ class PySetuptools(PythonPackage): version('41.0.1', sha256='a222d126f5471598053c9a77f4b5d4f26eaa1f150ad6e01dcf1a42e185d05613') version('40.8.0', sha256='6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d') version('40.4.3', sha256='acbc5740dd63f243f46c2b4b8e2c7fd92259c2ddb55a4115b16418a2ed371b15') - version('40.2.0', '592efabea3a65d8e97a025ed52f69b12') - version('39.2.0', 'dd4e3fa83a21bf7bf9c51026dc8a4e59') - version('39.0.1', '75310b72ca0ab4e673bf7679f69d7a62') - version('35.0.2', 'c368b4970d3ad3eab5afe4ef4dbe2437') - version('34.4.1', '5f9b07aeaafd29eac2548fc0b89a4934') - version('34.2.0', '41b630da4ea6cfa5894d9eb3142922be') - version('25.2.0', 'a0dbb65889c46214c691f6c516cf959c') - version('20.7.0', '5d12b39bf3e75e80fdce54e44b255615') - version('20.6.7', '45d6110f3ec14924e44c33411db64fe6') - version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') - version('19.2', '78353b1f80375ca5e088f4b4627ffe03') - version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') - version('16.0', '0ace0b96233516fc5f7c857d086aa3ad') - version('11.3.1', '01f69212e019a2420c1693fb43593930') + version('40.2.0', sha256='47881d54ede4da9c15273bac65f9340f8929d4f0213193fa7894be384f2dcfa6') + version('39.2.0', sha256='f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2') + version('39.0.1', sha256='bec7badf0f60e7fc8153fac47836edc41b74e5d541d7692e614e635720d6a7c7') + version('35.0.2', sha256='1e55496ca8058db68ae12ac29a985d1ee2c2483a5901f7692fb68fa2f9a250fd') + version('34.4.1', sha256='704cc0c9fe6c97edd3c6370d165c5a754dfde318b671058523ed3226d944ea1b') + version('34.2.0', sha256='7b551f5070f9414d48c08dda58bcb879c8d9276199283a99dc8e1362e2f378a2') + version('25.2.0', sha256='b2757ddac2c41173140b111e246d200768f6dd314110e1e40661d0ecf9b4d6a6') + version('20.7.0', sha256='505cdf282c5f6e3a056e79f0244b8945f3632257bba8469386c6b9b396400233') + version('20.6.7', sha256='d20152ee6337323d3b6d95cd733fb719d6b4f3fbc40f61f7a48e5a1bb96478b2') + version('20.5', md5='fadc1e1123ddbe31006e5e43e927362b') + version('19.2', sha256='f90ed8eb70b14b0594ba74e9de4ffca040c0ec8ee505cbf3570499467859f71a') + version('18.1', sha256='ad52a9d5b3a6f39c2a1c2deb96cc4f6aff29d6511bdea2994322c40b60c9c36a') + version('16.0', sha256='aa86255dee2c4a0056509750008007667c29306b7a6c13801468515b2c672845') + version('11.3.1', sha256='bd25f17de4ecf00116a9f7368b614a54ca1612d7945d2eafe5d97bc08c138bc5') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sfepy/package.py b/var/spack/repos/builtin/packages/py-sfepy/package.py index 11dca452e69..9d78ff14210 100644 --- a/var/spack/repos/builtin/packages/py-sfepy/package.py +++ b/var/spack/repos/builtin/packages/py-sfepy/package.py @@ -16,7 +16,7 @@ class PySfepy(PythonPackage): homepage = "http://sfepy.org" url = "https://github.com/sfepy/sfepy/archive/release_2017.3.tar.gz" - version('2017.3', '65ab606a9fe80fccf17a7eb5ab8fd025') + version('2017.3', sha256='d13642b7abed63b83b7eaef4dfce6e84a5afc5798bc7ffa1c413e3e44b5e5996') variant('petsc', default=False, description='Enable PETSc support') diff --git a/var/spack/repos/builtin/packages/py-sh/package.py b/var/spack/repos/builtin/packages/py-sh/package.py index 6297d149203..6438d991287 100644 --- a/var/spack/repos/builtin/packages/py-sh/package.py +++ b/var/spack/repos/builtin/packages/py-sh/package.py @@ -12,7 +12,7 @@ class PySh(PythonPackage): homepage = "https://github.com/amoffat/sh" url = "https://pypi.io/packages/source/s/sh/sh-1.12.9.tar.gz" - version('1.12.9', 'ddc128a8d943d25afa6e01af11e0063b') - version('1.11', '7af8df6c92d29ff927b6db0146bddec3') + version('1.12.9', sha256='579aa19bae7fe86b607df1afaf4e8537c453d2ce3d84e1d3957e099359a51677') + version('1.11', sha256='590fb9b84abf8b1f560df92d73d87965f1e85c6b8330f8a5f6b336b36f0559a4') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-shapely/package.py b/var/spack/repos/builtin/packages/py-shapely/package.py index 18467641bd1..c1809767cfe 100644 --- a/var/spack/repos/builtin/packages/py-shapely/package.py +++ b/var/spack/repos/builtin/packages/py-shapely/package.py @@ -20,7 +20,7 @@ class PyShapely(PythonPackage): ] version('1.6.4.post2', sha256='c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f') - version('1.6.4', '7581ef2d0fb346f9ed157f3efc75f6a4') + version('1.6.4', sha256='b10bc4199cfefcf1c0e5d932eac89369550320ca4bdf40559328d85f1ca4f655') depends_on('python@2.6:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py index b42c1195a79..d5ddcbe667e 100644 --- a/var/spack/repos/builtin/packages/py-shiboken/package.py +++ b/var/spack/repos/builtin/packages/py-shiboken/package.py @@ -12,7 +12,7 @@ class PyShiboken(PythonPackage): homepage = "https://shiboken.readthedocs.org/" url = "https://pypi.io/packages/source/S/Shiboken/Shiboken-1.2.2.tar.gz" - version('1.2.2', '345cfebda221f525842e079a6141e555') + version('1.2.2', sha256='0baee03c6244ab56e42e4200d0cb5e234682b11cc296ed0a192fe457d054972f') depends_on('cmake', type='build') diff --git a/var/spack/repos/builtin/packages/py-simplegeneric/package.py b/var/spack/repos/builtin/packages/py-simplegeneric/package.py index b9d05d2e933..faec17ca840 100644 --- a/var/spack/repos/builtin/packages/py-simplegeneric/package.py +++ b/var/spack/repos/builtin/packages/py-simplegeneric/package.py @@ -13,7 +13,7 @@ class PySimplegeneric(PythonPackage): homepage = "https://pypi.python.org/pypi/simplegeneric" url = "https://pypi.io/packages/source/s/simplegeneric/simplegeneric-0.8.zip" - version('0.8.1', 'f9c1fab00fd981be588fc32759f474e3') - version('0.8', 'eaa358a5f9517a8b475d03fbee3ec90f') + version('0.8.1', sha256='dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173') + version('0.8', sha256='8c0c4963da2695ba7c0f953f2cdac31d2c41d619fe9419e9d75432f8a231f966') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-simplejson/package.py b/var/spack/repos/builtin/packages/py-simplejson/package.py index c7321c09126..8cae5d59e2e 100644 --- a/var/spack/repos/builtin/packages/py-simplejson/package.py +++ b/var/spack/repos/builtin/packages/py-simplejson/package.py @@ -13,10 +13,10 @@ class PySimplejson(PythonPackage): homepage = "https://github.com/simplejson/simplejson" url = "https://pypi.io/packages/source/s/simplejson/simplejson-3.10.0.tar.gz" - version('3.10.0', '426a9631d22851a7a970b1a677368b15') - version('3.9.0', '01db2db1b96bd8e59bcab45bca12639b') - version('3.8.2', '53b1371bbf883b129a12d594a97e9a18') - version('3.8.1', 'b8441f1053edd9dc335ded8c7f98a974') - version('3.8.0', '72f3b93a6f9808df81535f79e79565a2') + version('3.10.0', sha256='953be622e88323c6f43fad61ffd05bebe73b9fd9863a46d68b052d2aa7d71ce2') + version('3.9.0', sha256='e9abeee37424f4bfcd27d001d943582fb8c729ffc0b74b72bd0e9b626ed0d1b6') + version('3.8.2', sha256='d58439c548433adcda98e695be53e526ba940a4b9c44fb9a05d92cd495cdd47f') + version('3.8.1', sha256='428ac8f3219c78fb04ce05895d5dff9bd813c05a9a7922c53dc879cd32a12493') + version('3.8.0', sha256='217e4797da3a9a4a9fbe6722e0db98070b8443a88212d7acdbd241a7668141d9') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-singledispatch/package.py b/var/spack/repos/builtin/packages/py-singledispatch/package.py index eee929ec02f..2a4d1fdedcc 100644 --- a/var/spack/repos/builtin/packages/py-singledispatch/package.py +++ b/var/spack/repos/builtin/packages/py-singledispatch/package.py @@ -12,7 +12,7 @@ class PySingledispatch(PythonPackage): homepage = "https://pypi.python.org/pypi/singledispatch" url = "https://pypi.io/packages/source/s/singledispatch/singledispatch-3.4.0.3.tar.gz" - version('3.4.0.3', 'af2fc6a3d6cc5a02d0bf54d909785fcb') + version('3.4.0.3', sha256='5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py index 7bb1c24a9c4..dc09ad6902d 100644 --- a/var/spack/repos/builtin/packages/py-sip/package.py +++ b/var/spack/repos/builtin/packages/py-sip/package.py @@ -18,8 +18,8 @@ class PySip(Package): version('develop', hg=hg) # wasn't actually able to clone this version('4.19.18', sha256='c0bd863800ed9b15dcad477c4017cdb73fa805c25908b0240564add74d697e1e') version('4.19.13', sha256='e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e') - version('4.16.7', '32abc003980599d33ffd789734de4c36') - version('4.16.5', '6d01ea966a53e4c7ae5c5e48c40e49e5') + version('4.16.7', md5='32abc003980599d33ffd789734de4c36') + version('4.16.5', md5='6d01ea966a53e4c7ae5c5e48c40e49e5') variant('module', default='sip', description='Name of private SIP module', values=str, multi=False) diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index 408ea4fdcc8..ce2acc70139 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -14,11 +14,11 @@ class PySix(PythonPackage): import_modules = ['six'] - version('1.12.0', '9ae5d1feed8c0215f4ae4adcd9207fcb') - version('1.11.0', 'd12789f9baf7e9fb2524c0c64f1773f8') - version('1.10.0', '34eed507548117b2ab523ab14b2f8b55') - version('1.9.0', '476881ef4012262dfc8adc645ee786c4') - version('1.8.0', '1626eb24cc889110c38f7e786ec69885') + version('1.12.0', sha256='d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73') + version('1.11.0', sha256='70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9') + version('1.10.0', sha256='105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a') + version('1.9.0', sha256='e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5') + version('1.8.0', sha256='047bbbba41bac37c444c75ddfdf0573dd6e2f1fbd824e6247bb26fa7d8fa3830') extends('python', ignore=r'bin/pytest') diff --git a/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py index 11f1842ba63..1233492b115 100644 --- a/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py +++ b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py @@ -12,8 +12,8 @@ class PySlurmPipeline(PythonPackage): homepage = "https://github.com/acorg/slurm-pipeline" url = "https://pypi.io/packages/source/s/slurm-pipeline/slurm-pipeline-1.1.13.tar.gz" - version('2.0.9', '7f97d2410db441081b79ac5c3395b8d0') - version('1.1.13', 'd1f8c78a64718ec5e2e40ba1b6816017') + version('2.0.9', sha256='2360e43965ecfa3701f287b7d597c99b4accd4dc8faf9d55cfdcc2228c4054cc') + version('1.1.13', sha256='6d6ca2e96a16780fd9520957166afd06272c57abd962e76bfe74c4d394b38da1') depends_on('py-setuptools', type='build') # using open range although requirements*.txt give explicit versions diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py index 5b60e996aeb..5709d140ffd 100644 --- a/var/spack/repos/builtin/packages/py-sncosmo/package.py +++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py @@ -13,7 +13,7 @@ class PySncosmo(PythonPackage): homepage = "http://sncosmo.readthedocs.io/" url = "https://pypi.io/packages/source/s/sncosmo/sncosmo-1.2.0.tar.gz" - version('1.2.0', '028e6d1dc84ab1c17d2f3b6378b2cb1e') + version('1.2.0', sha256='f3969eec5b25f60c70418dbd64765a2b4735bb53c210c61d0aab68916daea588') # Required dependencies # py-sncosmo binaries are duplicates of those from py-astropy diff --git a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py index d894130d580..19a26ca5cf5 100644 --- a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py +++ b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py @@ -15,4 +15,4 @@ class PySnowballstemmer(PythonPackage): import_modules = ['snowballstemmer'] - version('1.2.1', '643b019667a708a922172e33a99bf2fa') + version('1.2.1', sha256='919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128') diff --git a/var/spack/repos/builtin/packages/py-snuggs/package.py b/var/spack/repos/builtin/packages/py-snuggs/package.py index 894120d52d8..510152b0738 100644 --- a/var/spack/repos/builtin/packages/py-snuggs/package.py +++ b/var/spack/repos/builtin/packages/py-snuggs/package.py @@ -12,7 +12,7 @@ class PySnuggs(PythonPackage): homepage = "https://github.com/mapbox/snuggs""" url = "https://github.com/mapbox/snuggs/archive/1.4.1.zip" - version('1.4.1', 'bfc4058c32faa4ef76ab7946755557cc') + version('1.4.1', sha256='b37ed4e11c5f372695dc6fe66fce6cede124c90a920fe4726c970c9293b71233') depends_on('py-numpy', type=('build', 'run')) depends_on('py-click', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-spectra/package.py b/var/spack/repos/builtin/packages/py-spectra/package.py index 6430476aebb..f15d97d9c6d 100644 --- a/var/spack/repos/builtin/packages/py-spectra/package.py +++ b/var/spack/repos/builtin/packages/py-spectra/package.py @@ -13,7 +13,7 @@ class PySpectra(PythonPackage): url = "https://pypi.io/packages/source/s/spectra/spectra-0.0.8.tar.gz" version('0.0.11', sha256='8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8') - version('0.0.8', '83020b29e584389f24c7720f38f0136c') + version('0.0.8', sha256='851b88c9c0bba84e0be1fce5b9c02a7b4ef139a2b3e590b0d082d679e19f0759') depends_on('py-setuptools', type='build') depends_on('py-colormath', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-spglib/package.py b/var/spack/repos/builtin/packages/py-spglib/package.py index 0a7a8ef82fe..a2584342346 100644 --- a/var/spack/repos/builtin/packages/py-spglib/package.py +++ b/var/spack/repos/builtin/packages/py-spglib/package.py @@ -13,7 +13,7 @@ class PySpglib(PythonPackage): homepage = "http://atztogo.github.io/spglib/" url = "https://pypi.io/packages/source/s/spglib/spglib-1.9.9.18.tar.gz" - version('1.9.9.18', 'b8b46268d3aeada7b9b201b11882548f') + version('1.9.9.18', sha256='cbbb8383320b500dc6100b83d5e914a26a97ef8fc97c82d8921b10220e4126cd') # Most Python packages only require setuptools as a build dependency. # However, spglib requires setuptools during runtime as well. diff --git a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py index 92bc0ebc936..227d8a7f040 100644 --- a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py @@ -12,6 +12,6 @@ class PySphinxBootstrapTheme(PythonPackage): homepage = "https://pypi.python.org/pypi/sphinx-bootstrap-theme/" url = "https://pypi.io/packages/source/s/sphinx-bootstrap-theme/sphinx-bootstrap-theme-0.4.13.tar.gz" - version('0.4.13', '32e513a9c8ffbb8c1e4b036e8f74fb51') + version('0.4.13', sha256='47f7719e56304026f285455bbb115525d227a6e23341d4b7f6f0b48b2eface82') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py index 17616c3a349..901faec4b8b 100644 --- a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py @@ -15,7 +15,7 @@ class PySphinxRtdTheme(PythonPackage): import_modules = ['sphinx_rtd_theme'] version('0.4.3', sha256='728607e34d60456d736cc7991fd236afb828b21b82f956c5ea75f94c8414040a') - version('0.2.5b1', '0923473a43bd2527f32151f195f2a521') - version('0.1.10a0', '83bd95cae55aa8b773a8cc3a41094282') + version('0.2.5b1', sha256='d99513e7f2f8b9da8fdc189ad83df926b83d7fb15ad7ed07f24665d1f29d38da') + version('0.1.10a0', sha256='1225df3fc8337b14d53779435381b7f7705b9f4819610f6b74e555684cee2ac4') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py index 73f941303f4..aaf21e6eec6 100644 --- a/var/spack/repos/builtin/packages/py-sphinx/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx/package.py @@ -23,12 +23,12 @@ class PySphinx(PythonPackage): version('1.8.4', sha256='c1c00fc4f6e8b101a0d037065043460dffc2d507257f2f11acaed71fd2b0c83c') version('1.8.2', sha256='120732cbddb1b2364471c3d9f8bfd4b0c5b550862f99a65736c77f970b142aea') - version('1.7.4', '95f3b83f521314600e5b09e99cf32c46') - version('1.6.3', 'c5ad61f4e0974375ca2c2b58ef8d5411') - version('1.6.1', '26cb1cdca7aa4afc8c925d926b6268e7') - version('1.5.5', 'f9581b3556df9722143c47290273bcf8') - version('1.4.5', '5c2cd2dac45dfa6123d067e32a89e89a') - version('1.3.1', '8786a194acf9673464c5455b11fd4332') + version('1.7.4', sha256='e9b1a75a3eae05dded19c80eb17325be675e0698975baae976df603b6ed1eb10') + version('1.6.3', sha256='af8bdb8c714552b77d01d4536e3d6d2879d6cb9d25423d29163d5788e27046e6') + version('1.6.1', sha256='7581d82c3f206f0ac380edeeba890a2e2d2be011e5abe94684ceb0df4b6acc3f') + version('1.5.5', sha256='4064ea6c56feeb268838cb8fbbee507d0c3d5d92fa63a7df935a916b52c9e2f5') + version('1.4.5', sha256='c5df65d97a58365cbf4ea10212186a9a45d89c61ed2c071de6090cdf9ddb4028') + version('1.3.1', sha256='1a6e5130c2b42d2de301693c299f78cc4bd3501e78b610c08e45efc70e2b5114') extends('python', ignore='bin/(pybabel|pygmentize)') diff --git a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py index fda235612f6..0781ea59f3b 100644 --- a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py @@ -12,7 +12,7 @@ class PySphinxautomodapi(PythonPackage): homepage = "https://sphinx-automodapi.readthedocs.io/en/latest/" url = "https://github.com/astropy/sphinx-automodapi/archive/v0.9.tar.gz" - version('0.9', '017817812e9266319fdcfcc89ddfbe570935ca87a3bda62d61c8507cf1337aa8') + version('0.9', sha256='017817812e9266319fdcfcc89ddfbe570935ca87a3bda62d61c8507cf1337aa8') depends_on('py-setuptools', type='build') depends_on('py-sphinx@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py index 251d9a43e1c..48eb4a239cc 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py @@ -14,7 +14,7 @@ class PySphinxcontribBibtex(PythonPackage): import_modules = ['sphinxcontrib', 'sphinxcontrib.bibtex'] - version('0.3.5', 'd3c86836e2f6227b55a5ca9108590b1c') + version('0.3.5', sha256='c93e2b4a0d14f0ab726f95f0a33c1675965e9df3ed04839635577b8f978206cd') depends_on('py-setuptools', type='build') depends_on('py-latexcodec@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py index 275d8f58ec0..cc50f20af18 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py @@ -16,7 +16,7 @@ class PySphinxcontribProgramoutput(PythonPackage): # FIXME: These import tests don't work for some reason # import_modules = ['sphinxcontrib', 'sphinxcontrib.programoutput'] - version('0.10', '8e511e476c67696c7ae2c08b15644eb4') + version('0.10', sha256='fdee94fcebb0d8fddfccac5c4fa560f6177d5340c4349ee447c890bea8857094') depends_on('py-setuptools', type='build') depends_on('py-sphinx@1.3.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py index 9d8549702e4..0d3ba39c5d8 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py @@ -20,7 +20,7 @@ class PySphinxcontribWebsupport(PythonPackage): # ] version('1.1.0', sha256='9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9') - version('1.0.1', '84df26463b1ba65b07f926dbe2055665') + version('1.0.1', sha256='7a85961326aa3a400cd4ad3c816d70ed6f7c740acd7ce5d78cd0a67825072eb9') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-spyder/package.py b/var/spack/repos/builtin/packages/py-spyder/package.py index ced5e85266b..5566a4a44e5 100644 --- a/var/spack/repos/builtin/packages/py-spyder/package.py +++ b/var/spack/repos/builtin/packages/py-spyder/package.py @@ -12,8 +12,8 @@ class PySpyder(PythonPackage): homepage = "https://github.com/spyder-ide/spyder" url = "https://pypi.io/packages/source/s/spyder/spyder-3.1.3.tar.gz" - version('3.1.3', '4b9b7c8c3e6dc00001e6e98473473c36') - version('2.3.9', 'dd01e07a77123c128ff79ba57b97c1d7') + version('3.1.3', sha256='4978872cc5a006803bc8742d0a8fb43c49aef9524f0a9fcb8bd6dfcfdc2d2d6a') + version('2.3.9', md5='dd01e07a77123c128ff79ba57b97c1d7') depends_on('python@2.7.0:2.8.0,3.3.0:', type=('build', 'run')) depends_on('py-rope@0.9.4:', type=('build', 'run'), when='^python@:3') diff --git a/var/spack/repos/builtin/packages/py-spykeutils/package.py b/var/spack/repos/builtin/packages/py-spykeutils/package.py index 89fc19bcdc4..19ee496146c 100644 --- a/var/spack/repos/builtin/packages/py-spykeutils/package.py +++ b/var/spack/repos/builtin/packages/py-spykeutils/package.py @@ -12,7 +12,7 @@ class PySpykeutils(PythonPackage): homepage = "https://github.com/rproepp/spykeutils" url = "https://pypi.io/packages/source/s/spykeutils/spykeutils-0.4.3.tar.gz" - version('0.4.3', 'cefe4c48ebfdb9bac7a6cbfaf49dd485') + version('0.4.3', sha256='ff6206d9116d665024109c997377bfed37d953a4cac2859b79a610f395b6b37b') depends_on('py-setuptools', type='build') depends_on('py-scipy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py index 8eea38eeee4..7f6512a60ad 100644 --- a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py +++ b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py @@ -15,7 +15,7 @@ class PySqlalchemy(PythonPackage): version('1.3.9', sha256='272a835758908412e75e87f75dd0179a51422715c125ce42109632910526b1fd') version('1.2.19', sha256='5bb2c4fc2bcc3447ad45716c66581eab982c007dcf925482498d8733f86f17c7') version('1.1.18', sha256='8b0ec71af9291191ba83a91c03d157b19ab3e7119e27da97932a4773a3f664a9') - version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4') + version('1.0.12', sha256='6679e20eae780b67ba136a4a76f83bb264debaac2542beefe02069d0206518d1') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-statsmodels/package.py b/var/spack/repos/builtin/packages/py-statsmodels/package.py index 2829b5cd5e4..79f3ae49be7 100644 --- a/var/spack/repos/builtin/packages/py-statsmodels/package.py +++ b/var/spack/repos/builtin/packages/py-statsmodels/package.py @@ -12,7 +12,7 @@ class PyStatsmodels(PythonPackage): homepage = "http://www.statsmodels.org" url = "https://pypi.io/packages/source/s/statsmodels/statsmodels-0.8.0.tar.gz" - version('0.8.0', 'b3e5911cc9b00b71228d5d39a880bba0') + version('0.8.0', sha256='26431ab706fbae896db7870a0892743bfbb9f5c83231644692166a31d2d86048') variant('plotting', default=False, description='With matplotlib') diff --git a/var/spack/repos/builtin/packages/py-stevedore/package.py b/var/spack/repos/builtin/packages/py-stevedore/package.py index 9eb0dc816e7..33bad888f90 100644 --- a/var/spack/repos/builtin/packages/py-stevedore/package.py +++ b/var/spack/repos/builtin/packages/py-stevedore/package.py @@ -12,7 +12,7 @@ class PyStevedore(PythonPackage): homepage = "https://docs.openstack.org/stevedore/latest/" url = "https://pypi.io/packages/source/s/stevedore/stevedore-1.28.0.tar.gz" - version('1.28.0', 'b736a71431a2ff5831bbff4a6ccec0c1') + version('1.28.0', sha256='f1c7518e7b160336040fee272174f1f7b29a46febb3632502a8f2055f973d60b') depends_on('python@2.6:') diff --git a/var/spack/repos/builtin/packages/py-storm/package.py b/var/spack/repos/builtin/packages/py-storm/package.py index 3f3b7c875db..0e31547293c 100644 --- a/var/spack/repos/builtin/packages/py-storm/package.py +++ b/var/spack/repos/builtin/packages/py-storm/package.py @@ -11,6 +11,6 @@ class PyStorm(PythonPackage): homepage = "https://storm.canonical.com/" url = "https://launchpad.net/storm/trunk/0.20/+download/storm-0.20.tar.gz" - version('0.20', '8628503141f0f06c0749d607ac09b9c7') + version('0.20', sha256='0fa70043bb1a1c178c2f760db35f5956244cecf50dab7fb22d78be7507726603') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-subprocess32/package.py b/var/spack/repos/builtin/packages/py-subprocess32/package.py index 9c61b128cc2..728be86016d 100644 --- a/var/spack/repos/builtin/packages/py-subprocess32/package.py +++ b/var/spack/repos/builtin/packages/py-subprocess32/package.py @@ -12,4 +12,4 @@ class PySubprocess32(PythonPackage): homepage = "https://pypi.python.org/pypi/subprocess32" url = "https://pypi.io/packages/source/s/subprocess32/subprocess32-3.2.7.tar.gz" - version('3.2.7', '824c801e479d3e916879aae3e9c15e16') + version('3.2.7', sha256='1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590') diff --git a/var/spack/repos/builtin/packages/py-symengine/package.py b/var/spack/repos/builtin/packages/py-symengine/package.py index c0d66a5eca3..3e3664f0758 100644 --- a/var/spack/repos/builtin/packages/py-symengine/package.py +++ b/var/spack/repos/builtin/packages/py-symengine/package.py @@ -14,7 +14,7 @@ class PySymengine(PythonPackage): git = "https://github.com/symengine/symengine.py.git" version('develop', branch='master') - version('0.2.0', 'e1d114fa12be4c8c7e9f24007e07718c') + version('0.2.0', sha256='8f6468137baa7f799e047dd0b9149c4017d8d32e755f1e0329209680879c1f8f') # Build dependencies depends_on('python@2.7:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-symfit/package.py b/var/spack/repos/builtin/packages/py-symfit/package.py index 757b434f8c0..6fac0315f38 100644 --- a/var/spack/repos/builtin/packages/py-symfit/package.py +++ b/var/spack/repos/builtin/packages/py-symfit/package.py @@ -12,7 +12,7 @@ class PySymfit(PythonPackage): homepage = "http://symfit.readthedocs.org" url = "https://pypi.io/packages/source/s/symfit/symfit-0.3.5.tar.gz" - version('0.3.5', '7f62552ffeba4b4d203c01ff52fe15d5') + version('0.3.5', sha256='24c66305895c590249da7e61f62f128ee1c0c43c0a8c8e33b8abd3e0931f0881') depends_on('py-setuptools@17.1:', type='build') depends_on('py-pbr@1.9:', type='build') diff --git a/var/spack/repos/builtin/packages/py-sympy/package.py b/var/spack/repos/builtin/packages/py-sympy/package.py index 0858e8aa69b..ec7b668c5c4 100644 --- a/var/spack/repos/builtin/packages/py-sympy/package.py +++ b/var/spack/repos/builtin/packages/py-sympy/package.py @@ -12,8 +12,8 @@ class PySympy(PythonPackage): url = "https://pypi.io/packages/source/s/sympy/sympy-0.7.6.tar.gz" version('1.3', sha256='e1319b556207a3758a0efebae14e5e52c648fc1db8975953b05fff12b6871b54') - version('1.1.1', 'c410a9c2346878716d16ec873d72e72a') - version('1.0', '43e797de799f00f9e8fd2307dba9fab1') - version('0.7.6', '3d04753974306d8a13830008e17babca') + version('1.1.1', sha256='ac5b57691bc43919dcc21167660a57cc51797c28a4301a6144eff07b751216a4') + version('1.0', sha256='3eacd210d839e4db911d216a9258a3ac6f936992f66db211e22767983297ffae') + version('0.7.6', sha256='dfa3927e9befdfa7da7a18783ccbc2fe489ce4c46aa335a879e49e48fc03d7a7') depends_on('py-mpmath', when='@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-tables/package.py b/var/spack/repos/builtin/packages/py-tables/package.py index 70d2dda73bc..e837cc9d7df 100644 --- a/var/spack/repos/builtin/packages/py-tables/package.py +++ b/var/spack/repos/builtin/packages/py-tables/package.py @@ -18,9 +18,9 @@ class PyTables(PythonPackage): ] version('3.5.2', sha256='e4fc6f1194f02a8b10ff923e77364fb70710592f620d7de35f4d4e064dc70e91') - version('3.4.4', '2cd52095ebb097f5bf58fa65dc6574bb') - version('3.3.0', '056c161ae0fd2d6e585b766adacf3b0b') - version('3.2.2', '7cbb0972e4d6580f629996a5bed92441', + version('3.4.4', sha256='c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114') + version('3.3.0', sha256='dceb15fef556a2775121bcc695561df4ff0e09248e0ce3a2d58f5244a9f61421') + version('3.2.2', sha256='2626e874caa6b3fcf2bfc28b9dd6a40a3f859c72e19ce0764a60a6d77e350008', url='https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz') variant('zlib', default=True, description='Support for zlib compression') diff --git a/var/spack/repos/builtin/packages/py-tabulate/package.py b/var/spack/repos/builtin/packages/py-tabulate/package.py index b8cb55f5b08..17fc9e34f52 100644 --- a/var/spack/repos/builtin/packages/py-tabulate/package.py +++ b/var/spack/repos/builtin/packages/py-tabulate/package.py @@ -12,6 +12,6 @@ class PyTabulate(PythonPackage): homepage = "https://bitbucket.org/astanin/python-tabulate" url = "https://pypi.io/packages/source/t/tabulate/tabulate-0.7.7.tar.gz" - version('0.7.7', '39a21aaa9c10be0749c545be34552559') + version('0.7.7', sha256='83a0b8e17c09f012090a50e1e97ae897300a72b35e0c86c0b53d3bd2ae86d8c6') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tappy/package.py index 54966347a91..1c97e7a763a 100644 --- a/var/spack/repos/builtin/packages/py-tappy/package.py +++ b/var/spack/repos/builtin/packages/py-tappy/package.py @@ -12,7 +12,7 @@ class PyTappy(PythonPackage): # base https://pypi.python.org/pypi/cffi url = "https://pypi.io/packages/source/t/tap.py/tap.py-1.6.tar.gz" - version('1.6', 'c8bdb93ad66e05f939905172a301bedf') + version('1.6', sha256='3ee315567cd1cf444501c405b7f7146ffdb2e630bac58d0840d378a3b9a0dbe4') extends('python', ignore='bin/nosetests|bin/pygmentize') diff --git a/var/spack/repos/builtin/packages/py-terminado/package.py b/var/spack/repos/builtin/packages/py-terminado/package.py index 3b499ff686b..6df259b230b 100644 --- a/var/spack/repos/builtin/packages/py-terminado/package.py +++ b/var/spack/repos/builtin/packages/py-terminado/package.py @@ -12,8 +12,8 @@ class PyTerminado(PythonPackage): homepage = "https://pypi.python.org/pypi/terminado" url = "https://pypi.io/packages/source/t/terminado/terminado-0.6.tar.gz" - version('0.8.1', '616515f562939e979b67c72b667afba9') - version('0.6', '5b6c65da27fe1ed07a9f80f0588cdaba') + version('0.8.1', sha256='55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a') + version('0.6', sha256='2c0ba1f624067dccaaead7d2247cfe029806355cef124dc2ccb53c83229f0126') depends_on('py-tornado@4:', type=('build', 'run')) depends_on('py-ptyprocess', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-testinfra/package.py b/var/spack/repos/builtin/packages/py-testinfra/package.py index 7b1619c8070..de913179088 100644 --- a/var/spack/repos/builtin/packages/py-testinfra/package.py +++ b/var/spack/repos/builtin/packages/py-testinfra/package.py @@ -15,9 +15,9 @@ class PyTestinfra(PythonPackage): url = "https://pypi.python.org/packages/source/t/testinfra/testinfra-1.11.1.tar.gz" version('1.18.0', sha256='4a0a70355b007729d78446c86bffd80bcea4ffe9adc9571f9c9779476c49153d') - version('1.13.0', '1e0a135c784207f8609e7730901f1291') - version('1.12.0', '9784c01d7af3d624c6ec3cd25cce2011') - version('1.11.1', 'c64ce6b16661d647c62c9508de419f5f') + version('1.13.0', sha256='b5afa23d71ee49ad81aed104e4a0f1c02819ef791291cd308fe27aa7f3d3b01f') + version('1.12.0', sha256='ecf6f21b71bf5f4fe531c84149bfd5175465de910a6a0bb9a42c14828be7bdc1') + version('1.11.1', sha256='a54224c39d71fe120c1f4c88330397ddcb6f6362dc38e1ce9fd53290bccbf153') depends_on('py-setuptools', type='build') depends_on('py-importlib', when='^python@2.6.0:2.6.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-tetoolkit/package.py b/var/spack/repos/builtin/packages/py-tetoolkit/package.py index 86b696839a0..c53b4a0494e 100644 --- a/var/spack/repos/builtin/packages/py-tetoolkit/package.py +++ b/var/spack/repos/builtin/packages/py-tetoolkit/package.py @@ -16,7 +16,7 @@ class PyTetoolkit(PythonPackage): url = "https://pypi.io/packages/source/T/TEToolkit/TEToolkit-1.5.1.tar.gz" version('2.0.3', sha256='1d0f5928b30c6cd9dbef8e092ae0c11e9e707faf92a19af8eed3e360da7d4e46') - version('1.5.1', '05745b2d5109911e95593e423446a831') + version('1.5.1', sha256='22c13ca45bccc89e9d9bf48d59ae6db1fa4c634def64fc56ba9bffd23aa689ac') depends_on('py-setuptools') depends_on('python@2.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-theano/package.py b/var/spack/repos/builtin/packages/py-theano/package.py index 0c22e55051e..78e77fec03c 100644 --- a/var/spack/repos/builtin/packages/py-theano/package.py +++ b/var/spack/repos/builtin/packages/py-theano/package.py @@ -16,9 +16,9 @@ class PyTheano(PythonPackage): version('master', branch='master') version('1.0.4', sha256='35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913') - version('1.0.2', 'fcae24dfa76babe15f5f3c556d67c9f2') - version('1.0.1', 'a38b36c0fdc3126c574163db0a253e69') - version('0.8.2', 'f2d0dfe7df141115201077cd933b2c52') + version('1.0.2', sha256='6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde') + version('1.0.1', sha256='88d8aba1fe2b6b75eacf455d01bc7e31e838c5a0fb8c13dde2d9472495ff4662') + version('0.8.2', sha256='7463c8f7ed1a787bf881f36d38a38607150186697e7ce7e78bfb94b7c6af8930') variant('gpu', default=False, description='Builds with support for GPUs via CUDA and cuDNN') diff --git a/var/spack/repos/builtin/packages/py-tifffile/package.py b/var/spack/repos/builtin/packages/py-tifffile/package.py index 846ecebd22c..f90e68530ca 100644 --- a/var/spack/repos/builtin/packages/py-tifffile/package.py +++ b/var/spack/repos/builtin/packages/py-tifffile/package.py @@ -14,7 +14,7 @@ class PyTifffile(PythonPackage): import_modules = ['tifffile'] - version('0.12.1', '8a8afa74dd0df7915ac376a6cd7eeffc') + version('0.12.1', sha256='802367effe86b0d1e64cb5c2ed886771f677fa63260b945e51a27acccdc08fa1') depends_on('py-setuptools', type='build') depends_on('py-numpy@1.8.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-toolz/package.py b/var/spack/repos/builtin/packages/py-toolz/package.py index e6d44b9c512..e4e591d0a8c 100644 --- a/var/spack/repos/builtin/packages/py-toolz/package.py +++ b/var/spack/repos/builtin/packages/py-toolz/package.py @@ -14,6 +14,6 @@ class PyToolz(PythonPackage): import_modules = ['toolz', 'tlz', 'toolz.curried', 'toolz.sandbox'] - version('0.9.0', '6fd07249389dd0b3bfe71d4282314328') + version('0.9.0', sha256='929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-tornado/package.py b/var/spack/repos/builtin/packages/py-tornado/package.py index 666d2a0a02c..0a1fa8df0d6 100644 --- a/var/spack/repos/builtin/packages/py-tornado/package.py +++ b/var/spack/repos/builtin/packages/py-tornado/package.py @@ -13,7 +13,7 @@ class PyTornado(PythonPackage): url = "https://github.com/tornadoweb/tornado/archive/v6.0.3.tar.gz" version('6.0.3', sha256='a97ac3b8c95867e534b48cb6fbbf156f5ca5b20c423bb06894c17b240d7a18fc') - version('4.4.0', 'c28675e944f364ee96dda3a8d2527a87ed28cfa3') + version('4.4.0', sha256='ae556a0848e5d428d00597a18b38b9ca9d20f4600535e1dd33b3a576ab234194') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-tqdm/package.py b/var/spack/repos/builtin/packages/py-tqdm/package.py index b8cf68ebe55..a10b078ea7d 100644 --- a/var/spack/repos/builtin/packages/py-tqdm/package.py +++ b/var/spack/repos/builtin/packages/py-tqdm/package.py @@ -12,6 +12,6 @@ class PyTqdm(PythonPackage): homepage = "https://github.com/tqdm/tqdm" url = "https://pypi.io/packages/source/t/tqdm/tqdm-4.8.4.tar.gz" - version('4.8.4', 'b30a0aa20641d239296eab1c48a06b4e') + version('4.8.4', sha256='bab05f8bb6efd2702ab6c532e5e6a758a66c0d2f443e09784b73e4066e6b3a37') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-traceback2/package.py b/var/spack/repos/builtin/packages/py-traceback2/package.py index 18bb3091503..1f76eefac0f 100644 --- a/var/spack/repos/builtin/packages/py-traceback2/package.py +++ b/var/spack/repos/builtin/packages/py-traceback2/package.py @@ -12,7 +12,7 @@ class PyTraceback2(PythonPackage): homepage = "https://github.com/testing-cabal/traceback2" url = "https://pypi.io/packages/source/t/traceback2/traceback2-1.4.0.tar.gz" - version('1.4.0', '9e9723f4d70bfc6308fa992dd193c400') + version('1.4.0', sha256='05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030') depends_on('py-setuptools', type='build') depends_on('py-linecache2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-traitlets/package.py b/var/spack/repos/builtin/packages/py-traitlets/package.py index 5c125acd311..6c886e21220 100644 --- a/var/spack/repos/builtin/packages/py-traitlets/package.py +++ b/var/spack/repos/builtin/packages/py-traitlets/package.py @@ -14,14 +14,14 @@ class PyTraitlets(PythonPackage): version('4.3.3', sha256='b686c1aadf6ee5a9ee4c22df23bc5cd5bb7b5cfa18afe092e0a139cc2f05fe2e') version('4.3.2', sha256='370f938ad730d52272ef74f96f831cb21138f6168e46fe582fe256c35cc656ce') - version('4.3.1', '146a4885ea64079f62a33b2049841543') - version('4.3.0', '17af8d1306a401c42dbc92a080722422') - version('4.2.2', 'ffc03056dc5c8d1fc5dbd6eac76e1e46') - version('4.2.1', 'fc7f46a76b99ebc5068f99033d268dcf') - version('4.2.0', '53553a10d124e264fd2e234d0571b7d0') - version('4.1.0', 'd5bc75c7bd529afb40afce86c2facc3a') - version('4.0.0', 'b5b95ea5941fd9619b4704dfd8201568') - version('4.0', '14544e25ccf8e920ed1cbf833852481f') + version('4.3.1', sha256='3d50b2968f2e1477bd0de4b9656df40fd5624fc85cd1fc15f6c885cd68a4f6a1') + version('4.3.0', sha256='2f6cbc367fb56cbde91b2585202ef0a5bd41ae205a70aeecca1aeb4cb5b64e66') + version('4.2.2', sha256='bc749e08dd89c6007eb70e98c958f16d41e9a1fa42fdc9e9ba24e67469efa0ef') + version('4.2.1', sha256='a9ea45313f7130c555d8c1832529bf3f522ffc584093436783bc4b9611e8c4a9') + version('4.2.0', sha256='923cbe84bef30c27d2083f014f23a5da0ebe7da2e67a683d97acb07002e2ce0d') + version('4.1.0', sha256='93ead8dbf7e9617c88b79620072bfc499e7f25613f3df2234e5fdf08348c0a83') + version('4.0.0', sha256='03f380cb2e47689ae55dbe9a5dccbdde5cad8c4637312d720f4c3a991fb15cd2') + version('4.0', md5='14544e25ccf8e920ed1cbf833852481f') depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py index d21c71e49ef..222d0da5664 100644 --- a/var/spack/repos/builtin/packages/py-tuiview/package.py +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -14,7 +14,7 @@ class PyTuiview(PythonPackage): homepage = "https://bitbucket.org/chchrsc/tuiview" url = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz" - version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30') + version('1.1.7', sha256='fbf0bf29cc775357dad4f8a2f0c2ffa98bbf69d603a96353e75b321adef67573') depends_on("py-pyqt4", type=('build', 'run')) depends_on("py-numpy", type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py index cdd85968ad6..fcfb04fc057 100644 --- a/var/spack/repos/builtin/packages/py-twisted/package.py +++ b/var/spack/repos/builtin/packages/py-twisted/package.py @@ -11,7 +11,7 @@ class PyTwisted(PythonPackage): homepage = "https://twistedmatrix.com/" url = "https://pypi.io/packages/source/T/Twisted/Twisted-15.3.0.tar.bz2" - version('15.4.0', '5337ffb6aeeff3790981a2cd56db9655') - version('15.3.0', 'b58e83da2f00b3352afad74d0c5c4599') + version('15.4.0', sha256='78862662fa9ae29654bc2b9d349c3f1d887e6b2ed978512c4442d53ea861f05c') + version('15.3.0', sha256='025729751cf898842262375a40f70ae1d246daea88369eab9f6bb96e528bf285') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-typing/package.py b/var/spack/repos/builtin/packages/py-typing/package.py index 0df0ffb6217..6dd46be526f 100644 --- a/var/spack/repos/builtin/packages/py-typing/package.py +++ b/var/spack/repos/builtin/packages/py-typing/package.py @@ -15,8 +15,8 @@ class PyTyping(PythonPackage): import_modules = ['typing'] - version('3.6.4', '5b2ade08d83be488f17b5fe587c27c74') - version('3.6.1', '3fec97415bae6f742fb3c3013dedeb89') + version('3.6.4', sha256='d400a9344254803a2368533e4533a4200d21eb7b6b729c173bc38201a74db3f2') + version('3.6.1', sha256='c36dec260238e7464213dcd50d4b5ef63a507972f5780652e835d0228d0edace') # You need Python 2.7 or 3.3+ to install the typing package depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-tzlocal/package.py b/var/spack/repos/builtin/packages/py-tzlocal/package.py index 7fcce12b569..18b14719989 100644 --- a/var/spack/repos/builtin/packages/py-tzlocal/package.py +++ b/var/spack/repos/builtin/packages/py-tzlocal/package.py @@ -12,7 +12,7 @@ class PyTzlocal(PythonPackage): homepage = "https://github.com/regebro/tzlocal" url = "https://pypi.io/packages/source/t/tzlocal/tzlocal-1.3.tar.gz" - version('1.3', '3cb544b3975b59f91a793850a072d4a8') + version('1.3', sha256='d160c2ce4f8b1831dabfe766bd844cf9012f766539cf84139c2faac5201882ce') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-umi-tools/package.py b/var/spack/repos/builtin/packages/py-umi-tools/package.py index 52bf213e829..a4740c07974 100644 --- a/var/spack/repos/builtin/packages/py-umi-tools/package.py +++ b/var/spack/repos/builtin/packages/py-umi-tools/package.py @@ -15,7 +15,7 @@ class PyUmiTools(PythonPackage): version('1.0.0', sha256='7f73ef29120134123351c19089e9b7b7c03a8f241a19f8cb0e43d17f0e2f9fc7') version('0.5.5', sha256='9834a4388dd1ea0b971071009db7ccdbd447c6019796a3c061b0bb383c9ad992') version('0.5.4', sha256='a03e6babf188d0618a63f083b4da18120b9e8b4d473af71b585dba7de347e962') - version('0.5.3', '08bdebe30f84867d352ff5e1a2fe4d94') + version('0.5.3', sha256='d599f15c48c96a96ba667db1f364ebfed4ba733dd30469f9656c1717282d2ecb') depends_on('python@2.7:') depends_on('py-setuptools@1.1:', type='build') diff --git a/var/spack/repos/builtin/packages/py-unicycler/package.py b/var/spack/repos/builtin/packages/py-unicycler/package.py index 4018baa4ba4..6950d87a716 100644 --- a/var/spack/repos/builtin/packages/py-unicycler/package.py +++ b/var/spack/repos/builtin/packages/py-unicycler/package.py @@ -17,9 +17,9 @@ class PyUnicycler(PythonPackage): homepage = "https://github.com/rrwick/Unicycler" url = "https://github.com/rrwick/Unicycler/archive/v0.4.5.tar.gz" - version('0.4.7', '10ee4fef4bd9a46702de83537a902164') - version('0.4.6', '78633a5f557af23e62d6b37d1caedf53') - version('0.4.5', 'f7b4f6b712fee6a4fa86a046a6781768') + version('0.4.7', sha256='a8cf65e46dc2694b0fbd4e9190c73a1f300921457aadfab27a1792b785620d63') + version('0.4.6', sha256='56f6f358a5d1f8dd0fcd1df04504079fc42cec8453a36ee59ff89295535d03f5') + version('0.4.5', sha256='67043656b31a4809f8fa8f73368580ba7658c8440b9f6d042c7f70b5eb6b19ae') depends_on('python@3.4:', type=('build', 'link', 'run')) depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py index 2ef22619b68..828b12f117e 100644 --- a/var/spack/repos/builtin/packages/py-unittest2/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2/package.py @@ -13,7 +13,7 @@ class PyUnittest2(PythonPackage): homepage = "https://pypi.python.org/pypi/unittest2" url = "https://pypi.io/packages/source/u/unittest2/unittest2-1.1.0.tar.gz" - version('1.1.0', 'f72dae5d44f091df36b6b513305ea000') + version('1.1.0', sha256='22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579') depends_on('py-setuptools', type='build') depends_on('py-enum34', when='^python@:3.3', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py index 0422afcd6c0..53dbfa38ec0 100644 --- a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py @@ -14,7 +14,7 @@ class PyUnittest2py3k(PythonPackage): homepage = "https://pypi.python.org/pypi/unittest2py3k" url = "https://pypi.io/packages/source/u/unittest2py3k/unittest2py3k-0.5.1.tar.gz" - version('0.5.1', '8824ff92044310d9365f90d892bf0f09') + version('0.5.1', sha256='78249c5f1ac508a34d9d131d43a89d77bf154186f3ea5f7a6b993d3f3535d403') depends_on('python@3:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-urllib3/package.py b/var/spack/repos/builtin/packages/py-urllib3/package.py index b249209be1c..542df740761 100644 --- a/var/spack/repos/builtin/packages/py-urllib3/package.py +++ b/var/spack/repos/builtin/packages/py-urllib3/package.py @@ -14,7 +14,7 @@ class PyUrllib3(PythonPackage): url = "https://pypi.io/packages/source/u/urllib3/urllib3-1.20.tar.gz" version('1.21.1', sha256='b14486978518ca0901a76ba973d7821047409d7f726f22156b24e83fd71382a5') - version('1.20', '34691d4e7e20a8e9cdb452ea24fc38e7') - version('1.14', '5e1407428ac33b521c71a7ac273b3847') + version('1.20', sha256='97ef2b6e2878d84c0126b9f4e608e37a951ca7848e4855a7f7f4437d5c34a72f') + version('1.14', sha256='dd4fb13a4ce50b18338c7e4d665b21fd38632c5d4b1d9f1a1379276bd3c08d37') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py index f8423f9c68e..2e91029a10d 100644 --- a/var/spack/repos/builtin/packages/py-urwid/package.py +++ b/var/spack/repos/builtin/packages/py-urwid/package.py @@ -11,6 +11,6 @@ class PyUrwid(PythonPackage): homepage = "http://urwid.org/" url = "https://pypi.io/packages/source/u/urwid/urwid-1.3.0.tar.gz" - version('1.3.0', 'a989acd54f4ff1a554add464803a9175') + version('1.3.0', sha256='29f04fad3bf0a79c5491f7ebec2d50fa086e9d16359896c9204c6a92bc07aba2') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-vcversioner/package.py b/var/spack/repos/builtin/packages/py-vcversioner/package.py index 4d83aa79d36..4f68c42bd15 100644 --- a/var/spack/repos/builtin/packages/py-vcversioner/package.py +++ b/var/spack/repos/builtin/packages/py-vcversioner/package.py @@ -12,6 +12,6 @@ class PyVcversioner(PythonPackage): homepage = "https://github.com/habnabit/vcversioner" url = "https://pypi.io/packages/source/v/vcversioner/vcversioner-2.16.0.0.tar.gz" - version('2.16.0.0', 'aab6ef5e0cf8614a1b1140ed5b7f107d') + version('2.16.0.0', sha256='dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py index 897241e880a..9e9648dc134 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py @@ -12,7 +12,7 @@ class PyVirtualenvClone(PythonPackage): homepage = "https://github.com/edwardgeorge/virtualenv-clone" url = "https://pypi.io/packages/source/v/virtualenv-clone/virtualenv-clone-0.2.6.tar.gz" - version('0.2.6', 'fb03cd8c7a2be75937a13756d14068fc') + version('0.2.6', sha256='6b3be5cab59e455f08c9eda573d23006b7d6fb41fae974ddaa2b275c93cc4405') depends_on('python@2.6:') # not just build-time, requires pkg_resources diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index 610c8d1c529..db0baa73466 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -13,11 +13,11 @@ class PyVirtualenv(PythonPackage): url = "https://pypi.io/packages/source/v/virtualenv/virtualenv-15.1.0.tar.gz" version('16.4.1', sha256='5a3ecdfbde67a4a3b3111301c4d64a5b71cf862c8c42958d30cf3253df1f29dd') - version('16.0.0', '4feb74ee26255dd7e62e36ce96bcc4c6') - version('15.1.0', '44e19f4134906fe2d75124427dc9b716') - version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc') - version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db') - version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49') + version('16.0.0', sha256='ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752') + version('15.1.0', sha256='02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a') + version('15.0.1', sha256='1a74278b8adb383ce4c7619e33c753b1eb7b58dc1e449601c096ca4b76125f84') + version('13.0.1', sha256='36c2cfae0f9c6462264bb19c478fc6bab3478cf0575f1027452e975a1ed84dbd') + version('1.11.6', sha256='3e7a4c151e2ee97f51db0215bfd2a073b04a91e9786df6cb67c916f16abe04f7') depends_on('python@2.6:') diff --git a/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py index 14686049cc5..f41eee94d87 100644 --- a/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py @@ -16,7 +16,7 @@ class PyVirtualenvwrapper(PythonPackage): homepage = "https://bitbucket.org/virtualenvwrapper/virtualenvwrapper.git" url = "https://pypi.io/packages/source/v/virtualenvwrapper/virtualenvwrapper-4.8.2.tar.gz" - version('4.8.2', '8e3af0e0d42733f15c5e36df484a952e') + version('4.8.2', sha256='18d8e4c500c4c4ee794f704e050cf2bbb492537532a4521d1047e7dd1ee4e374') depends_on('python@2.6:') depends_on('py-virtualenv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-vsc-base/package.py b/var/spack/repos/builtin/packages/py-vsc-base/package.py index df12e28e945..77537a2cb37 100644 --- a/var/spack/repos/builtin/packages/py-vsc-base/package.py +++ b/var/spack/repos/builtin/packages/py-vsc-base/package.py @@ -12,6 +12,6 @@ class PyVscBase(PythonPackage): homepage = 'https://github.com/hpcugent/vsc-base/' url = 'https://pypi.io/packages/source/v/vsc-base/vsc-base-2.5.8.tar.gz' - version('2.5.8', '57f3f49eab7aa15a96be76e6c89a72d8') + version('2.5.8', sha256='7fcd300f842edf4baade7d0b7a3b462ca7dfb2a411a7532694a90127c6646ee2') depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-vsc-install/package.py b/var/spack/repos/builtin/packages/py-vsc-install/package.py index 2ddbb19d9c8..fb0a4c2a83c 100644 --- a/var/spack/repos/builtin/packages/py-vsc-install/package.py +++ b/var/spack/repos/builtin/packages/py-vsc-install/package.py @@ -14,6 +14,6 @@ class PyVscInstall(PythonPackage): homepage = 'https://github.com/hpcugent/vsc-install/' url = 'https://pypi.io/packages/source/v/vsc-install/vsc-install-0.10.25.tar.gz' - version('0.10.25', 'd1b9453a75cb56dba0deb7a878047b51') + version('0.10.25', sha256='744fa52b45577251d94e9298ecb115afd295f2530eba64c524f469b5e283f19c') depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py index 337eae910c7..b654e18e4e8 100644 --- a/var/spack/repos/builtin/packages/py-wcsaxes/package.py +++ b/var/spack/repos/builtin/packages/py-wcsaxes/package.py @@ -13,7 +13,7 @@ class PyWcsaxes(PythonPackage): homepage = "http://wcsaxes.readthedocs.io/en/latest/index.html" url = "https://github.com/astrofrog/wcsaxes/archive/v0.8.tar.gz" - version('0.8', 'de1c60fdae4c330bf5ddb9f1ab5ab920') + version('0.8', sha256='9c6addc1ec04cc99617850354b2c03dbd4099d2e43b45a81f8bc3069de9c8e83') extends('python', ignore=r'bin/') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-wcwidth/package.py b/var/spack/repos/builtin/packages/py-wcwidth/package.py index ac5948d241d..2b9c5151e72 100644 --- a/var/spack/repos/builtin/packages/py-wcwidth/package.py +++ b/var/spack/repos/builtin/packages/py-wcwidth/package.py @@ -12,6 +12,6 @@ class PyWcwidth(PythonPackage): homepage = "https://pypi.python.org/pypi/wcwidth" url = "https://pypi.io/packages/source/w/wcwidth/wcwidth-0.1.7.tar.gz" - version('0.1.7', 'b3b6a0a08f0c8a34d1de8cf44150a4ad') + version('0.1.7', sha256='3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-webencodings/package.py b/var/spack/repos/builtin/packages/py-webencodings/package.py index 9f565d64434..199d8e3fca9 100644 --- a/var/spack/repos/builtin/packages/py-webencodings/package.py +++ b/var/spack/repos/builtin/packages/py-webencodings/package.py @@ -12,7 +12,7 @@ class PyWebencodings(PythonPackage): homepage = "https://github.com/gsnedders/python-webencodings" url = "https://pypi.io/packages/source/w/webencodings/webencodings-0.5.1.tar.gz" - version('0.5.1', '32f6e261d52e57bf7e1c4d41546d15b8') + version('0.5.1', sha256='b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923') depends_on('py-setuptools', type='build') depends_on('python@2.6:2.8,3.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-webkit-server/package.py b/var/spack/repos/builtin/packages/py-webkit-server/package.py index bbe16e59e38..11703d596dd 100644 --- a/var/spack/repos/builtin/packages/py-webkit-server/package.py +++ b/var/spack/repos/builtin/packages/py-webkit-server/package.py @@ -14,4 +14,4 @@ class PyWebkitServer(PythonPackage): git = "https://github.com/niklasb/webkit-server.git" version('develop', branch='master') - version('1.0', '8463245c2b4f0264d934c0ae20bd4654') + version('1.0', sha256='836dac18c823bf7737461a2d938c66c7b3601c858897e6c92c7ba0e33574a2bc') diff --git a/var/spack/repos/builtin/packages/py-weblogo/package.py b/var/spack/repos/builtin/packages/py-weblogo/package.py index a6ff93fae83..59de581a4b8 100644 --- a/var/spack/repos/builtin/packages/py-weblogo/package.py +++ b/var/spack/repos/builtin/packages/py-weblogo/package.py @@ -13,7 +13,7 @@ class PyWeblogo(PythonPackage): homepage = "http://weblogo.threeplusone.com" url = "https://pypi.io/packages/source/w/weblogo/weblogo-3.6.0.tar.gz" - version('3.6.0', 'd0764f218057543fa664d2ae17d37b6d') + version('3.6.0', sha256='af5a9f065581f18d71bd7c22b160c1e443932f22cab992d439d3dc8757c80a85') depends_on('py-setuptools', type='build') depends_on('ghostscript', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-werkzeug/package.py b/var/spack/repos/builtin/packages/py-werkzeug/package.py index 02547b7b59a..43f200fb02c 100644 --- a/var/spack/repos/builtin/packages/py-werkzeug/package.py +++ b/var/spack/repos/builtin/packages/py-werkzeug/package.py @@ -12,7 +12,7 @@ class PyWerkzeug(PythonPackage): homepage = "http://werkzeug.pocoo.org" url = "https://pypi.io/packages/source/W/Werkzeug/Werkzeug-0.11.11.tar.gz" - version('0.11.15', 'cb4010478dd33905f95920e4880204a2') - version('0.11.11', '1d34afa1f19abcef4c0da51ebc2c4ea7') + version('0.11.15', sha256='455d7798ac263266dbd38d4841f7534dd35ca9c3da4a8df303f8488f38f3bcc0') + version('0.11.11', sha256='e72c46bc14405cba7a26bd2ce28df734471bc9016bc8b4cb69466c2c14c2f7e5') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py index ee37b9f60db..0554e214cbf 100644 --- a/var/spack/repos/builtin/packages/py-wheel/package.py +++ b/var/spack/repos/builtin/packages/py-wheel/package.py @@ -13,7 +13,7 @@ class PyWheel(PythonPackage): url = "https://pypi.io/packages/source/w/wheel/wheel-0.29.0.tar.gz" version('0.33.1', sha256='66a8fd76f28977bb664b098372daef2b27f60dc4d1688cfab7b37a09448f0e9d') - version('0.29.0', '555a67e4507cedee23a0deb9651e452f') - version('0.26.0', '4cfc6e7e3dc7377d0164914623922a10') + version('0.29.0', sha256='1ebb8ad7e26b448e9caa4773d2357849bf80ff9e313964bcaf79cbf0201a1648') + version('0.26.0', sha256='eaad353805c180a47545a256e6508835b65a8e830ba1093ed8162f19a50a530c') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py index 1a305ffdb17..589e733c77b 100644 --- a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py +++ b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py @@ -12,7 +12,7 @@ class PyWidgetsnbextension(PythonPackage): homepage = "https://pypi.python.org/pypi/widgetsnbextension" url = "https://pypi.io/packages/source/w/widgetsnbextension/widgetsnbextension-1.2.6.tar.gz" - version('1.2.6', '0aa4e152c9ba2d704389dc2453f448c7') + version('1.2.6', sha256='c618cfb32978c9517caf0b4ef3aec312f8dd138577745e7b0d4abfcc7315ce51') depends_on('py-setuptools', type='build') depends_on('python@2.7:2.8,3.3:') diff --git a/var/spack/repos/builtin/packages/py-wrapt/package.py b/var/spack/repos/builtin/packages/py-wrapt/package.py index 933bb9b87f8..7e3bb32f98f 100644 --- a/var/spack/repos/builtin/packages/py-wrapt/package.py +++ b/var/spack/repos/builtin/packages/py-wrapt/package.py @@ -12,4 +12,4 @@ class PyWrapt(PythonPackage): homepage = "https://github.com/GrahamDumpleton/wrapt" url = "https://pypi.io/packages/source/w/wrapt/wrapt-1.10.10.tar.gz" - version('1.10.10', '97365e906afa8b431f266866ec4e2e18') + version('1.10.10', sha256='42160c91b77f1bc64a955890038e02f2f72986c01d462d53cb6cb039b995cdd9') diff --git a/var/spack/repos/builtin/packages/py-xarray/package.py b/var/spack/repos/builtin/packages/py-xarray/package.py index ca1507200e9..006b2826435 100644 --- a/var/spack/repos/builtin/packages/py-xarray/package.py +++ b/var/spack/repos/builtin/packages/py-xarray/package.py @@ -12,7 +12,7 @@ class PyXarray(PythonPackage): homepage = "https://github.com/pydata/xarray" url = "https://pypi.io/packages/source/x/xarray/xarray-0.9.1.tar.gz" - version('0.9.1', '24cc99f19da95427604846c9d1e20e70') + version('0.9.1', sha256='89772ed0e23f0e71c3fb8323746374999ecbe79c113e3fadc7ae6374e6dc0525') depends_on('py-setuptools', type='build') depends_on('py-pandas@0.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-xdot/package.py b/var/spack/repos/builtin/packages/py-xdot/package.py index 873dddeb531..ecdc47e4941 100644 --- a/var/spack/repos/builtin/packages/py-xdot/package.py +++ b/var/spack/repos/builtin/packages/py-xdot/package.py @@ -15,8 +15,8 @@ class PyXdot(PythonPackage): git = "https://github.com/jrfonseca/xdot.py.git" version('master', branch="master") - version('1.0', '4e60c42d009a8802db6c1b4dab519863') - version('0.9', '19c78311d73b0f9ea059a6febf42eeea') + version('1.0', sha256='a8594f94f43f938e01e42ff6015c7e00e3ee1a00c7f06d6287d8c939ffa94f76') + version('0.9', sha256='df7790db573d7a5512e6fa618d9051508c43cf64ca432d97c2207c87b6f20dbd') # setuptools is required at runtime to avoid: # No module named 'pkg_resources' diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py index 4a7b85011a9..1c23bf825bf 100644 --- a/var/spack/repos/builtin/packages/py-xlrd/package.py +++ b/var/spack/repos/builtin/packages/py-xlrd/package.py @@ -13,4 +13,4 @@ class PyXlrd(PythonPackage): homepage = 'http://www.python-excel.org/' url = "https://pypi.io/packages/source/x/xlrd/xlrd-0.9.4.tar.gz" - version('0.9.4', '911839f534d29fe04525ef8cd88fe865') + version('0.9.4', sha256='8e8d3359f39541a6ff937f4030db54864836a06e42988c452db5b6b86d29ea72') diff --git a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py index 1a859fa885d..520a50e0a7c 100644 --- a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py +++ b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py @@ -13,4 +13,4 @@ class PyXlsxwriter(PythonPackage): homepage = "https://pypi.python.org/pypi/XlsxWriter" url = "https://pypi.io/packages/source/X/XlsxWriter/XlsxWriter-1.0.2.tar.gz" - version('1.0.2', '586f97beeb458c5707794882125330d2') + version('1.0.2', sha256='a26bbbafff88abffce592ffd5dfaa4c9f08dc44ef4afbf45c70d3e270325f856') diff --git a/var/spack/repos/builtin/packages/py-xmlrunner/package.py b/var/spack/repos/builtin/packages/py-xmlrunner/package.py index d2acdedb4eb..266a30a95cc 100644 --- a/var/spack/repos/builtin/packages/py-xmlrunner/package.py +++ b/var/spack/repos/builtin/packages/py-xmlrunner/package.py @@ -12,7 +12,7 @@ class PyXmlrunner(PythonPackage): homepage = "https://github.com/pycontribs/xmlrunner" url = "https://pypi.io/packages/source/x/xmlrunner/xmlrunner-1.7.7.tar.gz" - version('1.7.7', '7b0b152ed2d278516aedbc0cac22dfb3') + version('1.7.7', sha256='5a6113d049eca7646111ee657266966e5bbfb0b5ceb2e83ee0772e16d7110f39') depends_on('py-setuptools', type='build') depends_on('py-unittest2', type=('build', 'run'), when='^python@:2.8') diff --git a/var/spack/repos/builtin/packages/py-xopen/package.py b/var/spack/repos/builtin/packages/py-xopen/package.py index 3e6cc906207..8a22562784f 100644 --- a/var/spack/repos/builtin/packages/py-xopen/package.py +++ b/var/spack/repos/builtin/packages/py-xopen/package.py @@ -17,7 +17,7 @@ class PyXopen(PythonPackage): version('0.8.2', sha256='003749e09af74103a29e9c64c468c03e084aa6dfe6feff4fe22366679a6534f7') version('0.5.0', sha256='b097cd25e8afec42b6e1780c1f6315016171b5b6936100cdf307d121e2cbab9f') - version('0.1.1', '4e0e955546ee6bee4ea736b54623a671') + version('0.1.1', sha256='d1320ca46ed464a59db4c27c7a44caf5e268301e68319f0295d06bf6a9afa6f3') depends_on('py-setuptools', type='build') depends_on('py-bz2file', type=('build', 'run'), when='@0.5: ^python@:2.8') diff --git a/var/spack/repos/builtin/packages/py-xpyb/package.py b/var/spack/repos/builtin/packages/py-xpyb/package.py index 4ea95494279..f5cf29a28ed 100644 --- a/var/spack/repos/builtin/packages/py-xpyb/package.py +++ b/var/spack/repos/builtin/packages/py-xpyb/package.py @@ -13,7 +13,7 @@ class PyXpyb(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xpyb-1.3.1.tar.gz" - version('1.3.1', '75d567e25517fb883a56f10b77fd2757') + version('1.3.1', sha256='4056d11f94f17ed4342563955682193c7d004e80e5fa689816f87f3795549c17') extends('python') diff --git a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py index ccb83d7bb72..26890b992c0 100644 --- a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py +++ b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py @@ -12,7 +12,7 @@ class PyXvfbwrapper(PythonPackage): homepage = "https://pypi.python.org/pypi/xvfbwrapper/0.2.9" url = "https://pypi.io/packages/source/x/xvfbwrapper/xvfbwrapper-0.2.9.tar.gz" - version('0.2.9', '3f3cbed698606f4b14e76ccc7b5dd366') + version('0.2.9', sha256='bcf4ae571941b40254faf7a73432dfc119ad21ce688f1fdec533067037ecfc24') depends_on('py-setuptools', type='build') # Eventually add xvfb! diff --git a/var/spack/repos/builtin/packages/py-yamlreader/package.py b/var/spack/repos/builtin/packages/py-yamlreader/package.py index 0cabee94b7e..88a7656968c 100644 --- a/var/spack/repos/builtin/packages/py-yamlreader/package.py +++ b/var/spack/repos/builtin/packages/py-yamlreader/package.py @@ -13,7 +13,7 @@ class PyYamlreader(PythonPackage): homepage = "http://pyyaml.org/wiki/PyYAML" url = "https://pypi.io/packages/source/y/yamlreader/yamlreader-3.0.4.tar.gz" - version('3.0.4', '542179b5b5bedae941245b8b673119db') + version('3.0.4', sha256='765688036d57104ac26e4500ab088d42f4f2d06687ce3daa26543d7ae38c2470') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-pyyaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py index f9e378887d1..233404d0ea6 100644 --- a/var/spack/repos/builtin/packages/py-yapf/package.py +++ b/var/spack/repos/builtin/packages/py-yapf/package.py @@ -12,6 +12,6 @@ class PyYapf(PythonPackage): # base https://pypi.python.org/pypi/cffi url = "https://github.com/google/yapf/archive/v0.2.1.tar.gz" - version('0.2.1', '348ccf86cf2057872e4451b204fb914c') + version('0.2.1', sha256='13158055acd8e3c2f3a577528051a1c5057237f699150211a86fb405c4ea3936') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-zmq/package.py b/var/spack/repos/builtin/packages/py-zmq/package.py index f66ee1e3c3e..7d2d783a7ac 100644 --- a/var/spack/repos/builtin/packages/py-zmq/package.py +++ b/var/spack/repos/builtin/packages/py-zmq/package.py @@ -11,9 +11,9 @@ class PyZmq(PythonPackage): homepage = "https://github.com/zeromq/pyzmq" url = "https://github.com/zeromq/pyzmq/archive/v14.7.0.tar.gz" - version('17.1.2', 'b368115d2c5989dc45ec63a9da801df6') - version('16.0.2', '4cf14a2995742253b2b009541f4436f4') - version('14.7.0', 'bf304fb73d72aee314ff82d3554328c179938ecf') + version('17.1.2', sha256='77a32350440e321466b1748e6063b34a8a73768b62cb674e7d799fbc654b7c45') + version('16.0.2', sha256='717dd902c3cf432b1c68e7b299ad028b0de0d0a823858e440b81d5f1baa2b1c1') + version('14.7.0', sha256='809a5fcc720d286c840f7f64696e60322b5b2544795a73db626f09b344d16a15') depends_on('py-cython@0.16:', type=('build', 'run')) depends_on('py-py', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-zope-event/package.py b/var/spack/repos/builtin/packages/py-zope-event/package.py index d72661223f1..af746d12185 100644 --- a/var/spack/repos/builtin/packages/py-zope-event/package.py +++ b/var/spack/repos/builtin/packages/py-zope-event/package.py @@ -16,6 +16,6 @@ class PyZopeEvent(PythonPackage): # Maybe some kind of namespace issue? # import_modules = ['zope.event'] - version('4.3.0', '8ca737960741c6fd112972f3313303bd') + version('4.3.0', sha256='e0ecea24247a837c71c106b0341a7a997e3653da820d21ef6c08b32548f733e7') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-zope-interface/package.py b/var/spack/repos/builtin/packages/py-zope-interface/package.py index 7b9d0c9ff38..743cb7594de 100644 --- a/var/spack/repos/builtin/packages/py-zope-interface/package.py +++ b/var/spack/repos/builtin/packages/py-zope-interface/package.py @@ -19,7 +19,7 @@ class PyZopeInterface(PythonPackage): # Maybe some kind of namespace issue? # import_modules = ['zope.interface', 'zope.interface.common'] - version('4.5.0', '7b669cd692d817772c61d2e3ad0f1e71') + version('4.5.0', sha256='57c38470d9f57e37afb460c399eb254e7193ac7fb8042bd09bdc001981a9c74c') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 5c49b1af1e7..35a99bc31f1 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -35,34 +35,34 @@ class Python(AutotoolsPackage): version('3.7.3', sha256='d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff') version('3.7.2', sha256='f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d') version('3.7.1', sha256='36c1b81ac29d0f8341f727ef40864d99d8206897be96be73dc34d4739c9c9f06') - version('3.7.0', '41b6595deb4147a1ed517a7d9a580271') + version('3.7.0', sha256='85bb9feb6863e04fb1700b018d9d42d1caac178559ffa453d7e6a436e259fd0d') version('3.6.8', sha256='7f5b1f08b3b0a595387ef6c64c85b1b13b38abef0dd871835ee923262e4f32f0') version('3.6.7', sha256='b7c36f7ed8f7143b2c46153b7332db2227669f583ea0cce753facf549d1a4239') version('3.6.6', sha256='7d56dadf6c7d92a238702389e80cfe66fbfae73e584189ed6f89c75bbf3eda58') - version('3.6.5', 'ab25d24b1f8cc4990ade979f6dc37883') - version('3.6.4', '9de6494314ea199e3633211696735f65') - version('3.6.3', 'e9180c69ed9a878a4a8a3ab221e32fa9') - version('3.6.2', 'e1a36bfffdd1d3a780b1825daf16e56c') - version('3.6.1', '2d0fc9f3a5940707590e07f03ecb08b9') - version('3.6.0', '3f7062ccf8be76491884d0e47ac8b251') + version('3.6.5', sha256='53a3e17d77cd15c5230192b6a8c1e031c07cd9f34a2f089a731c6f6bd343d5c6') + version('3.6.4', sha256='7dc453e1a93c083388eb1a23a256862407f8234a96dc4fae0fc7682020227486') + version('3.6.3', sha256='ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91') + version('3.6.2', sha256='7919489310a5f17f7acbab64d731e46dca0702874840dadce8bd4b2b3b8e7a82') + version('3.6.1', sha256='aa50b0143df7c89ce91be020fe41382613a817354b33acdc6641b44f8ced3828') + version('3.6.0', sha256='aa472515800d25a3739833f76ca3735d9f4b2fe77c3cb21f69275e0cce30cb2b') version('3.5.7', sha256='542d94920a2a06a471a73b51614805ad65366af98145b0369bc374cf248b521b') - version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72') - version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') - version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') + version('3.5.2', sha256='1524b840e42cf3b909e8f8df67c1724012c7dc7f9d076d4feef2d3eff031e8a0') + version('3.5.1', sha256='687e067d9f391da645423c7eda8205bae9d35edc0c76ef5218dcbe4cc770d0d7') + version('3.5.0', sha256='584e3d5a02692ca52fce505e68ecd77248a6f2c99adf9db144a39087336b0fe0') version('3.4.10', sha256='217757699249ab432571b381386d441e12b433100ab5f908051fcb7cced2539d') - version('3.4.3', '4281ff86778db65892c05151d5de738d') - version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9') - version('3.2.6', '23815d82ae706e9b781ca65865353d39') - version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab') - version('2.7.16', 'f1a2ace631068444831d01485466ece0', preferred=True) - version('2.7.15', '045fb3440219a1f6923fefdabde63342') - version('2.7.14', 'cee2e4b33ad3750da77b2e85f2f8b724') - version('2.7.13', '17add4bf0ad0ec2f08e0cae6d205c700') - version('2.7.12', '88d61f82e3616a4be952828b3694109d') - version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b') - version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521') - version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') - version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') + version('3.4.3', sha256='8b743f56e9e50bf0923b9e9c45dd927c071d7aa56cd46569d8818add8cf01147') + version('3.3.6', sha256='0a58ad1f1def4ecc90b18b0c410a3a0e1a48cf7692c75d1f83d0af080e5d2034') + version('3.2.6', sha256='fc1e41296e29d476f696303acae293ae7a2310f0f9d0d637905e722a3f16163e') + version('3.1.5', sha256='d12dae6d06f52ef6bf1271db4d5b4d14b5dd39813e324314e72b648ef1bc0103') + version('2.7.16', sha256='01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5', preferred=True) + version('2.7.15', sha256='18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db') + version('2.7.14', sha256='304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8') + version('2.7.13', sha256='a4f05a0720ce0fd92626f0278b6b433eee9a6173ddf2bced7957dfb599a5ece1') + version('2.7.12', sha256='3cb522d17463dfa69a155ab18cffa399b358c966c0363d6c8b5b3bf1384da4b6') + version('2.7.11', sha256='82929b96fd6afc8da838b149107078c02fa1744b7e60999a8babbc0d3fa86fc6') + version('2.7.10', sha256='eda8ce6eec03e74991abb5384170e7c65fcd7522e409b8e83d7e6372add0f12a') + version('2.7.9', sha256='c8bba33e66ac3201dabdc556f0ea7cfe6ac11946ec32d357c4c6f9b018c12c5b') + version('2.7.8', sha256='74d70b914da4487aa1d97222b29e9554d042f825f26cb2b93abd20fdda56b557') extendable = True diff --git a/var/spack/repos/builtin/packages/qbox/package.py b/var/spack/repos/builtin/packages/qbox/package.py index 0c831cf2b83..52def22bbde 100644 --- a/var/spack/repos/builtin/packages/qbox/package.py +++ b/var/spack/repos/builtin/packages/qbox/package.py @@ -14,29 +14,29 @@ class Qbox(MakefilePackage): homepage = "http://qboxcode.org/" url = "http://qboxcode.org/download/qbox-1.63.7.tgz" - version('1.63.7', '6b0cf5656f816a1a59e22b268387af33') - version('1.63.5', 'da3161ab6a455793f2133dd03c04077c') - version('1.63.4', '8596f32c8fb7e7baa96571c655aaee07') - version('1.63.2', '55e8f13f37c8e1f43ca831791e3af1da') - version('1.63.0', '1436c884c553ab026b7f787307e5e6ed') - version('1.62.3', 'f07e038ab92b85956794e91a40346dbf') - version('1.60.9', '53b0df612e56bb65e8220d9d9dc8d395') - version('1.60.4', '060846c9fa03b1f3d7d5ce24a9491de2') - version('1.60.0', '3856cdc38a27dc17705844c4b9241a21') - version('1.58.0', 'ec0e6b79fa0ed06742212b1142e36b6a') - version('1.56.2', 'df7a4217d059a5d351d92e480ed14112') - version('1.54.4', '8f1a23af7d871317de93810b664ad3aa') - version('1.54.2', 'aeefee061255dbb36ca7e49378f63ad5') - version('1.52.3', '1862f2b2056cdf49ec4f746d45a7f1a6') - version('1.52.2', 'e406deb4c46176f1c15c226868bf61e2') - version('1.50.4', 'b06ff877257884e4fac321fb5a486266') - version('1.50.2', '171660b1bb5e57637f019fef055fb764') - version('1.50.1', '1da528b39da134f86f134432e8fada79') - version('1.47.0', '86f402651d440e05adc94168d6105da7') - version('1.45.3', '73b99a73dcbb1b5be9f66f3284750205') - version('1.45.1', '59e0c2583769b7586981c0d6ffa1b267') - version('1.45.0', '2c5bfbadfffd330c8c2fe294a10a08e4') - version('1.44.0', 'c46a2f0f68fe9229aa77779da188cea9') + version('1.63.7', sha256='40acf4535c4dcab16066c218b1c2a083c238a1f54c43a1d2d4afcefb578086ed') + version('1.63.5', sha256='fa6d0e41622690f14b7cd0c2735d3d8d703152eb2c51042cdd77a055926cd90a') + version('1.63.4', sha256='829ae57e43ecb79f7dca8fb02aa70c85b0bbb68684a087d3cd1048b50fbc8e96') + version('1.63.2', sha256='17873414fed5298b6a4b66ae659ea8348119238b36b532df8a7c8fca0ed4eada') + version('1.63.0', sha256='8ad0727e4ebe709b2647a281756675e4840b3f29799f7169f79a9100c6538d31') + version('1.62.3', sha256='e82df8307d038af75471f22d9449a5f5e2ad00bb34a89b1b2c25cc65da83c9b5') + version('1.60.9', sha256='d82434031ab8214879274eb6f8674c6004b65ad5f9a07635101b82300af6d43c') + version('1.60.4', sha256='7707a3bbecb05864e651d4f8885685299edd8f95fcd300dc401ff6652e85a351') + version('1.60.0', sha256='802b531c7fe67d8fad27618911b2e158f7c69099677c0e08202dca24f81e10fd') + version('1.58.0', sha256='662f55adedfe1154f8affd060b4f846cd37751f020fe854ef560aeb435fd0312') + version('1.56.2', sha256='63df818e071cfc826645ee266a239a0cc00cea874d266f572fc20b1e2db7b351') + version('1.54.4', sha256='8f556fde5307b96ed03612b339f793fc2933841f91555b6e7000cbb003709b7a') + version('1.54.2', sha256='45ef811c05c9224baee87626d5a5bae91008a8b117df7e964c5976f27e54e9e9') + version('1.52.3', sha256='9424eaf56dbf33394674f0be76aecf76637702d060e45c5edc95d872a165cd42') + version('1.52.2', sha256='39d892f1bacd355d6ab4dbdd0ee4303ac6916fa9decf0e828f16003e61d59798') + version('1.50.4', sha256='2babf332132005dc93f280b274c68e8e44ecd8e2d1cf21cc91e212f17f8644a8') + version('1.50.2', sha256='0defe312319ac460b5b667eca982e4cd6a23750e5bdaa214d1c127ce2aba0a21') + version('1.50.1', sha256='114363654d7059662b0f3269615d0af1514298f4f488889d8e7ef8f1c4b8898d') + version('1.47.0', sha256='5c45aa8f6b2f774c04423c50b4e340dc35ca1deb2826ead8f1a508cd027974a9') + version('1.45.3', sha256='986e82a69f90a96cccd1a192921024ffdcefb3b86df361946d88b12669156a80') + version('1.45.1', sha256='3cea45743c0cd24cd02865c39a360c55030dab0f4b9b7b46e615af9b3b65c1da') + version('1.45.0', sha256='cc722641bf3c3a172bdb396216a945f2830cc64de60d716b7054145ba52ab431') + version('1.44.0', sha256='f29cf2a727235d4fa6bded7725a1a667888ab103278e995c46dd754654f112f1') depends_on('mpi') depends_on('blas') diff --git a/var/spack/repos/builtin/packages/qca/package.py b/var/spack/repos/builtin/packages/qca/package.py index cb85a92765d..7b2b02cac69 100644 --- a/var/spack/repos/builtin/packages/qca/package.py +++ b/var/spack/repos/builtin/packages/qca/package.py @@ -21,7 +21,7 @@ class Qca(CMakePackage): url = "https://github.com/KDE/qca/archive/v2.1.3.tar.gz" version('2.2.1', sha256='c67fc0fa8ae6cb3d0ba0fbd8fca8ee8e4c5061b99f1fd685fd7d9800cef17f6b') - version('2.1.3', 'bd646d08fdc1d9be63331a836ecd528f') + version('2.1.3', sha256='a5135ffb0250a40e9c361eb10cd3fe28293f0cf4e5c69d3761481eafd7968067') depends_on('qt@4.2:') diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py index 2a2725ae536..9e156aaf447 100644 --- a/var/spack/repos/builtin/packages/qhull/package.py +++ b/var/spack/repos/builtin/packages/qhull/package.py @@ -18,10 +18,10 @@ class Qhull(CMakePackage): homepage = "http://www.qhull.org" - version('2015.2', 'e6270733a826a6a7c32b796e005ec3dc', + version('2015.2', sha256='78b010925c3b577adc3d58278787d7df08f7c8fb02c3490e375eab91bb58a436', url="http://www.qhull.org/download/qhull-2015-src-7.2.0.tgz") - version('2012.1', 'd0f978c0d8dfb2e919caefa56ea2953c', + version('2012.1', sha256='a35ecaa610550b7f05c3ce373d89c30cf74b059a69880f03080c556daebcff88', url="http://www.qhull.org/download/qhull-2012.1-src.tgz") patch('qhull-unused-intel-17.02.patch', when='@2015.2') diff --git a/var/spack/repos/builtin/packages/qjson/package.py b/var/spack/repos/builtin/packages/qjson/package.py index a129b4b898d..28aa3acd7e7 100644 --- a/var/spack/repos/builtin/packages/qjson/package.py +++ b/var/spack/repos/builtin/packages/qjson/package.py @@ -13,7 +13,7 @@ class Qjson(CMakePackage): homepage = "http://qjson.sourceforge.net/" url = "https://github.com/flavio/qjson/archive/0.9.0.tar.gz" - version('0.9.0', '2846278bb5fc9aeacab80ac14b8ed48d') + version('0.9.0', sha256='e812617477f3c2bb990561767a4cd8b1d3803a52018d4878da302529552610d4') depends_on('qt') diff --git a/var/spack/repos/builtin/packages/qmd-progress/package.py b/var/spack/repos/builtin/packages/qmd-progress/package.py index 1ba9224db4f..47319800295 100644 --- a/var/spack/repos/builtin/packages/qmd-progress/package.py +++ b/var/spack/repos/builtin/packages/qmd-progress/package.py @@ -17,8 +17,8 @@ class QmdProgress(CMakePackage): git = "https://github.com/lanl/qmd-progress.git" version('develop', branch='master') - version('1.1.0', 'dda155134f0925629bf116e562c0a4bd') - version('1.0.0', 'c950bead2719a47a78864e3376ba143e') + version('1.1.0', sha256='2c5eac252067bfb55d715c9ce5de2e4306b20b4273979dda15b4a2f71f69bb0b') + version('1.0.0', sha256='28c99eb80d9a6b09e1d01d61538b3b924850d89c6a8bfb5d3e8b6490be822296') variant('graphlib', default=False, description='Build with Metis Suppport') variant('mpi', default=True, description='Build with MPI Support') diff --git a/var/spack/repos/builtin/packages/qorts/package.py b/var/spack/repos/builtin/packages/qorts/package.py index bdf22605262..c40aa26a2b3 100644 --- a/var/spack/repos/builtin/packages/qorts/package.py +++ b/var/spack/repos/builtin/packages/qorts/package.py @@ -18,14 +18,14 @@ class Qorts(RPackage): homepage = "https://github.com/hartleys/QoRTs" url = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz" - version('1.2.42', '7d46162327b0da70bfe483fe2f2b7829') + version('1.2.42', sha256='c9f73ce8d5aac1036d13c50475458a61a24cbe5c0baf7ac65b87a7118c51ec08') depends_on('java', type='run') resource( name='QoRTs.jar', url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar', - md5='918df4291538218c12caa3ab98c535e9', + sha256='e808d2e05c67ee41eee605b7821aafa7ae894288ebb01d8b1bfb136970c801ce', placement='jarfile', expand=False ) diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py index 648a0ff055a..f26de74c69c 100644 --- a/var/spack/repos/builtin/packages/qrupdate/package.py +++ b/var/spack/repos/builtin/packages/qrupdate/package.py @@ -15,7 +15,7 @@ class Qrupdate(MakefilePackage): homepage = "http://sourceforge.net/projects/qrupdate/" url = "https://downloads.sourceforge.net/qrupdate/qrupdate-1.1.2.tar.gz" - version('1.1.2', '6d073887c6e858c24aeda5b54c57a8c4') + version('1.1.2', sha256='e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08') depends_on("blas") depends_on("lapack") diff --git a/var/spack/repos/builtin/packages/qt-creator/package.py b/var/spack/repos/builtin/packages/qt-creator/package.py index 1a15f7ec072..4d8bd4808a0 100644 --- a/var/spack/repos/builtin/packages/qt-creator/package.py +++ b/var/spack/repos/builtin/packages/qt-creator/package.py @@ -14,10 +14,10 @@ class QtCreator(QMakePackage): list_url = 'http://download.qt.io/official_releases/qtcreator/' list_depth = 2 - version('4.8.0', '9e75b07f068d8577ca7160a827bcecae') - version('4.4.0', 'bae2e08bb5087aba65d41eb3f9328d9a') - version('4.3.1', '6769ea47f287e2d9e30ff92acb899eef') - version('4.1.0', '657727e4209befa4bf5889dff62d9e0a') + version('4.8.0', sha256='4c4813454637141a45aa8f18be5733e4ba993335d95940aadf12fda66cf6f849') + version('4.4.0', md5='bae2e08bb5087aba65d41eb3f9328d9a') + version('4.3.1', md5='6769ea47f287e2d9e30ff92acb899eef') + version('4.1.0', md5='657727e4209befa4bf5889dff62d9e0a') depends_on('qt@5.6.0:+opengl') # Qt Creator comes bundled with its own copy of sqlite. Qt has a build diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index bf76caa0084..7a4232ee228 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -21,26 +21,26 @@ class Qt(Package): phases = ['configure', 'build', 'install'] - version('5.13.1', 'adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e') - version('5.12.5', 'a2299e21db7767caf98242767bffb18a2a88a42fee2d6a393bedd234f8c91298') - version('5.12.2', '59b8cb4e728450b21224dcaaa40eb25bafc5196b6988f2225c394c6b7f881ff5') - version('5.11.3', '859417642713cee2493ee3646a7fee782c9f1db39e41d7bb1322bba0c5f0ff4d') - version('5.11.2', 'c6104b840b6caee596fa9a35bc5f57f67ed5a99d6a36497b6fe66f990a53ca81') - version('5.10.0', 'c5e275ab0ed7ee61d0f4b82cd471770d') - version('5.9.1', '77b4af61c49a09833d4df824c806acaf') - version('5.9.0', '9c8bc8b828c2b56721980368266df9d9') - version('5.8.0', 'a9f2494f75f966e2f22358ec367d8f41') - version('5.7.1', '031fb3fd0c3cc0f1082644492683f18d') - version('5.7.0', '9a46cce61fc64c20c3ac0a0e0fa41b42') - version('5.5.1', '59f0216819152b77536cf660b015d784') - version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5') - version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6') - version('5.3.2', 'febb001129927a70174467ecb508a682') - version('5.2.1', 'a78408c887c04c34ce615da690e0b4c8') - version('4.8.7', 'd990ee66bf7ab0c785589776f35ba6ad') - version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb') - version('4.8.5', '1864987bdbb2f58f8ae8b350dfdbe133') - version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009') + version('5.13.1', sha256='adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e') + version('5.12.5', sha256='a2299e21db7767caf98242767bffb18a2a88a42fee2d6a393bedd234f8c91298') + version('5.12.2', sha256='59b8cb4e728450b21224dcaaa40eb25bafc5196b6988f2225c394c6b7f881ff5') + version('5.11.3', sha256='859417642713cee2493ee3646a7fee782c9f1db39e41d7bb1322bba0c5f0ff4d') + version('5.11.2', sha256='c6104b840b6caee596fa9a35bc5f57f67ed5a99d6a36497b6fe66f990a53ca81') + version('5.10.0', sha256='936d4cf5d577298f4f9fdb220e85b008ae321554a5fcd38072dc327a7296230e') + version('5.9.1', sha256='7b41a37d4fe5e120cdb7114862c0153f86c07abbec8db71500443d2ce0c89795') + version('5.9.0', sha256='f70b5c66161191489fc13c7b7eb69bf9df3881596b183e7f6d94305a39837517') + version('5.8.0', sha256='9dc5932307ae452855863f6405be1f7273d91173dcbe4257561676a599bd58d3') + version('5.7.1', sha256='c86684203be61ae7b33a6cf33c23ec377f246d697bd9fb737d16f0ad798f89b7') + version('5.7.0', sha256='4661905915d6265243e17fe59852930a229cf5b054ce5af5f48b34da9112ab5f') + version('5.5.1', sha256='c7fad41a009af1996b62ec494e438aedcb072b3234b2ad3eeea6e6b1f64be3b3') + version('5.4.2', sha256='cfc768c55f0a0cd232bed914a9022528f8f2e50cb010bf0e4f3f62db3dfa17bd') + version('5.4.0', sha256='1739633424bde3d89164ae6ff1c5c913be38b9997e451558ef873aac4bbc408a') + version('5.3.2', sha256='c8d3fd2ead30705c6673c5e4af6c6f3973346b4fb2bd6079c7be0943a5b0282d') + version('5.2.1', sha256='84e924181d4ad6db00239d87250cc89868484a14841f77fb85ab1f1dbdcd7da1') + version('4.8.7', sha256='e2882295097e47fe089f8ac741a95fef47e0a73a3f3cdf21b56990638f626ea0') + version('4.8.6', sha256='8b14dd91b52862e09b8e6a963507b74bc2580787d171feda197badfa7034032c') + version('4.8.5', sha256='eb728f8268831dc4373be6403b7dd5d5dde03c169ad6882f9a8cb560df6aa138') + version('3.3.8b', sha256='1b7a1ff62ec5a9cb7a388e2ba28fda6f960b27f27999482ebeceeadb72ac9f6e') # Add patch for compile issues with qt3 found with use in the # OpenSpeedShop project diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py index 1b29f587f50..923d9a329f8 100644 --- a/var/spack/repos/builtin/packages/qthreads/package.py +++ b/var/spack/repos/builtin/packages/qthreads/package.py @@ -20,10 +20,10 @@ class Qthreads(AutotoolsPackage): homepage = "http://www.cs.sandia.gov/qthreads/" url = "https://github.com/Qthreads/qthreads/releases/download/1.10/qthread-1.10.tar.bz2" - version("1.14", "3e6eb58baf78dc961b19a37b2dc4f9a5") - version("1.12", "c857d175f8135eaa669f3f8fa0fb0c09") - version("1.11", "68b5f9a41cfd1a2ac112cc4db0612326") - version("1.10", "d1cf3cf3f30586921359f7840171e551") + version("1.14", sha256="16f15e5b2e35b6329a857d24c283a1e43cd49921ee49a1446d4f31bf9c6f5cf9") + version("1.12", sha256="2c13a5f6f45bc2f22038d272be2e748e027649d3343a9f824da9e86a88b594c9") + version("1.11", sha256="dbde6c7cb7de7e89921e47363d09cecaebf775c9d090496c2be8350355055571") + version("1.10", sha256="29fbc2e54bcbc814c1be13049790ee98c505f22f22ccee34b7c29a4295475656") patch("restrict.patch", when="@:1.10") patch("trap.patch", when="@:1.10") diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py index 16cf5627e8a..2c68a6fbf50 100644 --- a/var/spack/repos/builtin/packages/quantum-espresso/package.py +++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py @@ -23,13 +23,13 @@ class QuantumEspresso(Package): version('develop', branch='develop') version('6.4.1', sha256='b0d7e9f617b848753ad923d8c6ca5490d5d82495f82b032b71a0ff2f2e9cfa08') version('6.4', sha256='781366d03da75516fdcf9100a1caadb26ccdd1dedd942a6f8595ff0edca74bfe') - version('6.3', '1b67687d90d1d16781d566d44d14634c') - version('6.2.1', '769cc973382156bffd35254c3dbaf453') - version('6.2.0', '972176a58d16ae8cf0c9a308479e2b97') - version('6.1.0', '3fe861dcb5f6ec3d15f802319d5d801b') - version('6.0.0', 'd915f2faf69d0e499f8e1681c42cbfc9') - version('5.4', '085f7e4de0952e266957bbc79563c54e') - version('5.3', 'be3f8778e302cffb89258a5f936a7592') + version('6.3', sha256='4067c8fffa957aabbd5cf2439e2fcb6cf3752325393c67a17d99fd09edf8689c') + version('6.2.1', sha256='11fe24b4a9d85834f8b6d429baebed8b360a685ecfae222887ed451e118a9156') + version('6.2.0', sha256='e204df367c8ea1a50c7534b44481841d835a542a23ae71c3e33ad712fc636c8b') + version('6.1.0', sha256='fd2c2eb346b3ca8f08138df5ef3f69b466c256d2119db40eea1b578b0a42c66e') + version('6.0.0', sha256='bc77d9553bf5a9253ae74058dffb1d6e5fb61093188e78d3b8d8564755136f19') + version('5.4', sha256='e3993fccae9cea04a5c6492e8b961a053a63727051cb5c4eb6008f62cda8f335') + version('5.3', sha256='3b26038efb9e3f8ac7a2b950c31d8c29169a3556c0b68c299eb88a4be8dc9048') variant('mpi', default=True, description='Builds with mpi support') variant('openmp', default=False, description='Enables openMP support') @@ -137,14 +137,14 @@ class QuantumEspresso(Package): # QE upstream patches # QE 6.3 requires multiple patches to fix MKL detection # There may still be problems on Mac with MKL detection - patch_url = 'https://gitlab.com/QEF/q-e/commit/0796e1b7c55c9361ecb6515a0979280e78865e36.diff' - patch_checksum = 'bc8c5b8523156cee002d97dab42a5976dffae20605da485a427b902a236d7e6b' - patch(patch_url, sha256=patch_checksum, when='@6.3:6.3.0') + patch('https://gitlab.com/QEF/q-e/commit/0796e1b7c55c9361ecb6515a0979280e78865e36.diff', + sha256='bc8c5b8523156cee002d97dab42a5976dffae20605da485a427b902a236d7e6b', + when='@6.3:6.3.0') # QE 6.3 `make install` broken and a patch must be applied - patch_url = 'https://gitlab.com/QEF/q-e/commit/88e6558646dbbcfcafa5f3fa758217f6062ab91c.diff' - patch_checksum = 'b776890d008e16cca28c31299c62f47de0ba606b900b17cbc27c041f45e564ca' - patch(patch_url, sha256=patch_checksum, when='@6.3:6.3.0') + patch('https://gitlab.com/QEF/q-e/commit/88e6558646dbbcfcafa5f3fa758217f6062ab91c.diff', + sha256='b776890d008e16cca28c31299c62f47de0ba606b900b17cbc27c041f45e564ca', + when='@6.3:6.3.0') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/qwt/package.py b/var/spack/repos/builtin/packages/qwt/package.py index 3f333b96268..43de3816fb3 100644 --- a/var/spack/repos/builtin/packages/qwt/package.py +++ b/var/spack/repos/builtin/packages/qwt/package.py @@ -16,8 +16,8 @@ class Qwt(QMakePackage): homepage = "http://qwt.sourceforge.net/" url = "https://sourceforge.net/projects/qwt/files/qwt/6.1.3/qwt-6.1.3.tar.bz2" - version('6.1.3', '19d1f5fa5e22054d22ee3accc37c54ba') - version('5.2.2', '70d77e4008a6cc86763737f0f24726ca') + version('6.1.3', sha256='f3ecd34e72a9a2b08422fb6c8e909ca76f4ce5fa77acad7a2883b701f4309733') + version('5.2.2', sha256='36bf2ee51ca9c74fde1322510ffd39baac0db60d5d410bb157968a78d9c1464b') variant('designer', default=False, description="Build extensions to QT designer") diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index 0174733ccf1..e7ebcfa0001 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -17,6 +17,6 @@ class RAbind(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/abind" version('1.4-5', sha256='3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c') - version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') + version('1.4-3', sha256='b6c255878c1ab81701ae701f34546e88be115629b984ac4272e311fa3c0ea6ce') depends_on('r@1.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acepack/package.py b/var/spack/repos/builtin/packages/r-acepack/package.py index f10d79caba8..f0690b027a5 100644 --- a/var/spack/repos/builtin/packages/r-acepack/package.py +++ b/var/spack/repos/builtin/packages/r-acepack/package.py @@ -13,4 +13,4 @@ class RAcepack(RPackage): url = "https://cloud.r-project.org/src/contrib/acepack_1.4.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/acepack" - version('1.4.1', 'a35354655e5260afa0e1860fcc68d871') + version('1.4.1', sha256='82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9') diff --git a/var/spack/repos/builtin/packages/r-ada/package.py b/var/spack/repos/builtin/packages/r-ada/package.py index ef015df04e6..03e2a0305ee 100644 --- a/var/spack/repos/builtin/packages/r-ada/package.py +++ b/var/spack/repos/builtin/packages/r-ada/package.py @@ -14,7 +14,7 @@ class RAda(RPackage): url = "https://cloud.r-project.org/src/contrib/ada_2.0-5.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/ada" - version('2.0-5', '25ac0dc2650fba9e19f3d15c7c6721c1') + version('2.0-5', sha256='d900172059eebeef30c27944fc29737a231fc4f92e3c2661868383fbd9016ac0') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rpart', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py index ce7a675430b..640e339e152 100644 --- a/var/spack/repos/builtin/packages/r-adabag/package.py +++ b/var/spack/repos/builtin/packages/r-adabag/package.py @@ -14,7 +14,7 @@ class RAdabag(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/adabag" version('4.2', sha256='47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81') - version('4.1', '2e019f053d49f62ebb3b1697bbb50afa') + version('4.1', sha256='ff938c36122cdf58a71a59a6bf79a3c7816966ee7cc4907c4a0a3c0732e3d028') depends_on('r-rpart', type=('build', 'run')) depends_on('r-mlbench', when='@:4.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py index ef6ff1a84ca..9097af588fa 100644 --- a/var/spack/repos/builtin/packages/r-ade4/package.py +++ b/var/spack/repos/builtin/packages/r-ade4/package.py @@ -16,7 +16,7 @@ class RAde4(RPackage): version('1.7-13', sha256='f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b') version('1.7-11', sha256='4ccd799ae99bd625840b866a697c4a48adb751660470bf0d6cf9207b1927a572') - version('1.7-6', '63401ca369677538c96c3d7b75b3f4a1') + version('1.7-6', sha256='80848e1650dcc0ec921c130efa6f7e9b307f0d107c63e49faa52296eda19cc52') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py index 563ed378a6d..00ea41d638c 100644 --- a/var/spack/repos/builtin/packages/r-adegenet/package.py +++ b/var/spack/repos/builtin/packages/r-adegenet/package.py @@ -23,7 +23,7 @@ class RAdegenet(RPackage): version('2.1.1', sha256='3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a') version('2.1.0', sha256='7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a') - version('2.0.1', 'ecb1220ce7c9affaba2987bc7f38adda') + version('2.0.1', sha256='7eddf46e64f680d54d034b68c50900d9bd5bc2e08309d062e230121b7460bb10') depends_on('r@2.14:', type=('build', 'run')) depends_on('r-ade4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aer/package.py b/var/spack/repos/builtin/packages/r-aer/package.py index c31dc05fcc1..59e03886d48 100644 --- a/var/spack/repos/builtin/packages/r-aer/package.py +++ b/var/spack/repos/builtin/packages/r-aer/package.py @@ -18,7 +18,7 @@ class RAer(RPackage): version('1.2-7', sha256='3aee5c606313710c2dca6c1e9b2c20a145aa33f2a3ecc5cfcec66c8e91838a93') version('1.2-6', sha256='653c3a2d253819e0ce8c2cf12cff2ab222bf3d19dbf382b7c4b4c3d762469474') - version('1.2-5', '419df9dc8ee6e5edd79678fee06719ae') + version('1.2-5', sha256='ef0cf14ff9d3de2b97e5855243426cc918808eb1011f0e2253b3b00043927a62') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-car@2.0-19:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-als/package.py b/var/spack/repos/builtin/packages/r-als/package.py index 685fbf5f628..f686341854a 100644 --- a/var/spack/repos/builtin/packages/r-als/package.py +++ b/var/spack/repos/builtin/packages/r-als/package.py @@ -19,7 +19,7 @@ class RAls(RPackage): url = "https://cloud.r-project.org/src/contrib/ALS_0.0.6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/ALS" - version('0.0.6', 'b72d97911e8ab7e4f8aed1a710b3d62d') + version('0.0.6', sha256='ca90d27115ae9e476967f521bf6935723e410a3bf92477e7570e14bfd3b099eb') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-iso', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py index 2e88e9525ed..f1b7b88ccfb 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -17,5 +17,5 @@ class RAssertthat(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/assertthat" version('0.2.1', sha256='85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f') - version('0.2.0', '8134f0072c6a84fd738d3bfc5e7f68ef') - version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') + version('0.2.0', sha256='d73ef79b1e75293ed889a99571b237a95829c099f7da094d4763f83ea6fde5f2') + version('0.1', sha256='1363645a9a128f615aa0641dc5f5c5abd960b1c38320492366dad1e7a5c29a37') diff --git a/var/spack/repos/builtin/packages/r-backports/package.py b/var/spack/repos/builtin/packages/r-backports/package.py index 6aef4037501..c15cb48fee6 100644 --- a/var/spack/repos/builtin/packages/r-backports/package.py +++ b/var/spack/repos/builtin/packages/r-backports/package.py @@ -21,7 +21,7 @@ class RBackports(RPackage): version('1.1.4', sha256='ee4b5efef22fa7ef27d7983ffcd31db52f81e1fbb7189c6e89ee09b69349ff03') version('1.1.3', sha256='e41bd146824ec921994f1b176d0e4cca0b36dd3db32ca7a954d872a5ba214cc1') - version('1.1.1', '969543a0af32dc23bba9bb37ec82008c') - version('1.1.0', 'b97a71b026fd7ede0e449be93d160c17') + version('1.1.1', sha256='494e81a4829339c8f1cc3e015daa807e9138b8e21b929965fc7c00b1abbe8897') + version('1.1.0', sha256='c5536966ed6ca93f20c9a21d4f569cc1c6865d3352445ea66448f82590349fcd') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-base64/package.py b/var/spack/repos/builtin/packages/r-base64/package.py index 9aa2ae08647..67c69434bbb 100644 --- a/var/spack/repos/builtin/packages/r-base64/package.py +++ b/var/spack/repos/builtin/packages/r-base64/package.py @@ -15,6 +15,6 @@ class RBase64(RPackage): url = "https://cloud.r-project.org/src/contrib/base64_2.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/base64" - version('2.0', 'f5a653842f75ad717ef6a00969868ae5') + version('2.0', sha256='8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1') depends_on('r-openssl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py index 5c1fcc99799..6d7e0b0a8cb 100644 --- a/var/spack/repos/builtin/packages/r-base64enc/package.py +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -14,6 +14,6 @@ class RBase64enc(RPackage): url = "https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/base64enc" - version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') + version('0.1-3', sha256='6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d') depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bayesm/package.py b/var/spack/repos/builtin/packages/r-bayesm/package.py index 10dc0cc7f1c..6481b69fb1a 100644 --- a/var/spack/repos/builtin/packages/r-bayesm/package.py +++ b/var/spack/repos/builtin/packages/r-bayesm/package.py @@ -16,7 +16,7 @@ class RBayesm(RPackage): version('3.1-3', sha256='51e4827eca8cd4cf3626f3c2282543df7c392b3ffb843f4bfb386fe104642a10') version('3.1-2', sha256='a332f16e998ab10b17a2b1b9838d61660c36e914fe4d2e388a59f031d52ad736') version('3.1-1', sha256='4854517dec30ab7c994de862aae1998c2d0c5e71265fd9eb7ed36891d4676078') - version('3.1-0.1', '34998382cafd3e7972d8a03245eac768') + version('3.1-0.1', sha256='5879823b7fb6e6df0c0fe98faabc1044a4149bb65989062df4ade64e19d26411') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-rcpp@0.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bbmisc/package.py b/var/spack/repos/builtin/packages/r-bbmisc/package.py index 400b7c8972e..aa29c826b79 100644 --- a/var/spack/repos/builtin/packages/r-bbmisc/package.py +++ b/var/spack/repos/builtin/packages/r-bbmisc/package.py @@ -14,6 +14,6 @@ class RBbmisc(RPackage): url = "https://cloud.r-project.org/src/contrib/BBmisc_1.11.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/BBmisc" - version('1.11', '681642628037406beb6088d5f773473d') + version('1.11', sha256='1ea48c281825349d8642a661bb447e23bfd651db3599bf72593bfebe17b101d2') depends_on('r-checkmate@1.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-beanplot/package.py b/var/spack/repos/builtin/packages/r-beanplot/package.py index db560b5772a..a2b93950ffb 100644 --- a/var/spack/repos/builtin/packages/r-beanplot/package.py +++ b/var/spack/repos/builtin/packages/r-beanplot/package.py @@ -14,4 +14,4 @@ class RBeanplot(RPackage): url = "https://cloud.r-project.org/src/contrib/beanplot_1.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/beanplot" - version('1.2', 'b24943208a4e61ee9ee0dc152634d5da') + version('1.2', sha256='49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372') diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py index 23d2909ddd1..603bad10f83 100644 --- a/var/spack/repos/builtin/packages/r-bh/package.py +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -27,5 +27,5 @@ class RBh(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/BH" version('1.69.0-1', sha256='a0fd4364b7e368f09c56dec030823f52c16da0787580af7e4615eddeb99baca2') - version('1.65.0-1', '7d0402188e4af59f4103f36616d6ee55') - version('1.60.0-2', 'b50fdc85285da05add4e9da664a2d551') + version('1.65.0-1', sha256='82baa78afe8f1edc3c7e84e1c9924321047e14c1e990df9b848407baf3f7cb58') + version('1.60.0-2', sha256='e441aede925d760dc0142be77079ebd7a46f2392772b875cde6ca567dd49c48c') diff --git a/var/spack/repos/builtin/packages/r-bindr/package.py b/var/spack/repos/builtin/packages/r-bindr/package.py index a3556e3b88c..92b38f8bc87 100644 --- a/var/spack/repos/builtin/packages/r-bindr/package.py +++ b/var/spack/repos/builtin/packages/r-bindr/package.py @@ -14,5 +14,5 @@ class RBindr(RPackage): url = "https://cloud.r-project.org/src/contrib/bindr_0.1.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/bindr" - version('0.1.1', 'cfa02c563196a79bf8bb4db2e66585fd') - version('0.1', 'f3897a70cbad2d2981272772fa30bb59') + version('0.1.1', sha256='7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0') + version('0.1', sha256='cca166612eeafd6e1c961b34aaf177f9b47f8b4bc37520e277b9920eaa8b2535') diff --git a/var/spack/repos/builtin/packages/r-bindrcpp/package.py b/var/spack/repos/builtin/packages/r-bindrcpp/package.py index f20e62f7293..32261fc3c66 100644 --- a/var/spack/repos/builtin/packages/r-bindrcpp/package.py +++ b/var/spack/repos/builtin/packages/r-bindrcpp/package.py @@ -14,8 +14,8 @@ class RBindrcpp(RPackage): url = "https://cloud.r-project.org/src/contrib/bindrcpp_0.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/bindrcpp" - version('0.2.2', '48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467') - version('0.2', '2ed7f19fd9a12587f882d90060e7a343') + version('0.2.2', sha256='48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467') + version('0.2', sha256='d0efa1313cb8148880f7902a4267de1dcedae916f28d9a0ef5911f44bf103450') depends_on('r-rcpp@0.12.16:', type=('build', 'run')) depends_on('r-bindr@0.1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bit/package.py b/var/spack/repos/builtin/packages/r-bit/package.py index ceb1975d7da..49d2c0bd1dd 100644 --- a/var/spack/repos/builtin/packages/r-bit/package.py +++ b/var/spack/repos/builtin/packages/r-bit/package.py @@ -14,6 +14,6 @@ class RBit(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/bit" version('1.1-14', sha256='5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254') - version('1.1-12', 'c4473017beb93f151a8e672e4d5747af') + version('1.1-12', sha256='ce281c87fb7602bf1a599e72f3e25f9ff7a13e390c124a4506087f69ad79d128') depends_on('r@2.9.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bit64/package.py b/var/spack/repos/builtin/packages/r-bit64/package.py index 5155c6a196d..64b5dbc8a5c 100644 --- a/var/spack/repos/builtin/packages/r-bit64/package.py +++ b/var/spack/repos/builtin/packages/r-bit64/package.py @@ -24,7 +24,7 @@ class RBit64(RPackage): url = "https://cloud.r-project.org/src/contrib/bit64_0.9-7.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/bit64" - version('0.9-7', 'ac4bc39827338c552d329d3d4d2339c2') + version('0.9-7', sha256='7b9aaa7f971198728c3629f9ba1a1b24d53db5c7e459498b0fdf86bbd3dff61f') depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-bit@1.1-12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py index 1d1cde59fdf..58bfcd76eab 100644 --- a/var/spack/repos/builtin/packages/r-bitops/package.py +++ b/var/spack/repos/builtin/packages/r-bitops/package.py @@ -14,4 +14,4 @@ class RBitops(RPackage): url = "https://cloud.r-project.org/src/contrib/bitops_1.0-6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/bitops" - version('1.0-6', 'fba16485a51b1ccd354abde5816b6bdd') + version('1.0-6', sha256='9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c') diff --git a/var/spack/repos/builtin/packages/r-blob/package.py b/var/spack/repos/builtin/packages/r-blob/package.py index 3a979ba3842..f2d1fdfed6c 100644 --- a/var/spack/repos/builtin/packages/r-blob/package.py +++ b/var/spack/repos/builtin/packages/r-blob/package.py @@ -17,7 +17,7 @@ class RBlob(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/blob" version('1.2.0', sha256='1af1cfa28607bc0e2f1f01598a00a7d5d1385ef160a9e79e568f30f56538e023') - version('1.1.0', '1c729aca36fd5193d81b1cd5ed9d8a00') + version('1.1.0', sha256='16d6603df3ddba177f0ac4d9469c938f89131c4bf8834345db838defd9ffea16') depends_on('r-tibble', when='@:1.1.0', type=('build', 'run')) depends_on('r-prettyunits', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bookdown/package.py b/var/spack/repos/builtin/packages/r-bookdown/package.py index 1cbe28a1206..e56af27d9e8 100644 --- a/var/spack/repos/builtin/packages/r-bookdown/package.py +++ b/var/spack/repos/builtin/packages/r-bookdown/package.py @@ -15,7 +15,7 @@ class RBookdown(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/bookdown" version('0.12', sha256='38eb4c5b877ccd85b16cfe74a48c3bc53de2f276da98e5515f37e7a06e065bb0') - version('0.5', '7bad360948e2b22d28397870b9319f17') + version('0.5', sha256='b7331fd56f64bd2bddc34e2a188fc491f9ff5308f44f7e3151721247f21ca67e') depends_on('r-yaml@2.1.14:', when='@:0.10', type=('build', 'run')) depends_on('r-rmarkdown@1.12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py index 3f7632f13d4..9e79231c0e5 100644 --- a/var/spack/repos/builtin/packages/r-boot/package.py +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -17,7 +17,7 @@ class RBoot(RPackage): version('1.3-23', sha256='30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f') version('1.3-22', sha256='cf1f0cb1e0a7a36dcb6ae038f5d0211a0e7a009c149bc9d21acb9c58c38b4dfc') - version('1.3-20', 'bb879fb4204a4f94ab82c98dd1ad5eca') - version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f') + version('1.3-20', sha256='adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a') + version('1.3-18', sha256='12fd237f810a69cc8d0a51a67c57eaf9506bf0341c764f8ab7c1feb73722235e') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py index c6e882e825a..5dacd7ed822 100644 --- a/var/spack/repos/builtin/packages/r-brew/package.py +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -15,4 +15,4 @@ class RBrew(RPackage): url = "https://cloud.r-project.org/src/contrib/brew_1.0-6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/brew" - version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806') + version('1.0-6', sha256='d70d1a9a01cf4a923b4f11e4374ffd887ad3ff964f35c6f9dc0f29c8d657f0ed') diff --git a/var/spack/repos/builtin/packages/r-broom/package.py b/var/spack/repos/builtin/packages/r-broom/package.py index 51305071093..3f863da0718 100644 --- a/var/spack/repos/builtin/packages/r-broom/package.py +++ b/var/spack/repos/builtin/packages/r-broom/package.py @@ -22,7 +22,7 @@ class RBroom(RPackage): version('0.5.2', sha256='16af7b446b24bc14461efbda9bea1521cf738c778c5e48fcc7bad45660a4ac62') version('0.5.1', sha256='da9e6bf7cb8f960b83309cf107743976cc32b54524675f6471982abe3d1aae2e') - version('0.4.2', '6eabab1f2eaec10f93cf9aa56d6a61de') + version('0.4.2', sha256='9f409413623cf25e7110452e6215353af5114f7044d73af182bd6c10971c5a44') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-plyr', when='@:0.4.2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py index 0ca78a69be3..68705e3a212 100644 --- a/var/spack/repos/builtin/packages/r-c50/package.py +++ b/var/spack/repos/builtin/packages/r-c50/package.py @@ -16,7 +16,7 @@ class RC50(RPackage): version('0.1.2', sha256='8f459856e0309274bee24462b7145db4eba1d71031c236db39000a5375bdfaba') version('0.1.1', sha256='03bc1fc2f64bcd5c680568a24902deafab1965074a66f8802bc4cd0335bd01df') - version('0.1.0-24', '42631e65c5c579532cc6edf5ea175949') + version('0.1.0-24', sha256='617ee8ae617a075213414c07739ce92d9e6927783d01588fd0e2315157065e9d') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-partykit', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cairo/package.py b/var/spack/repos/builtin/packages/r-cairo/package.py index e0004484e44..58f892369af 100644 --- a/var/spack/repos/builtin/packages/r-cairo/package.py +++ b/var/spack/repos/builtin/packages/r-cairo/package.py @@ -16,7 +16,7 @@ class RCairo(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/Cairo" version('1.5-10', sha256='7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5') - version('1.5-9', '2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4') + version('1.5-9', sha256='2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4') depends_on('r@2.4.0:', type=('build', 'run')) depends_on('cairo@1.2:') diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py index 1cce1052596..5ed4f0a698a 100644 --- a/var/spack/repos/builtin/packages/r-callr/package.py +++ b/var/spack/repos/builtin/packages/r-callr/package.py @@ -18,7 +18,7 @@ class RCallr(RPackage): version('3.3.1', sha256='bf60da47357d3336aa395b0c9643235a621763c80d28bc9bb2257767d0a37967') version('3.2.0', sha256='4bb47b1018e8eb5c683a86c05d0d9b8b25848db1f1b30e92cfebedc0ce14b0e8') version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7') - version('1.0.0', 'd9af99bb95696310fa1e5d1cb7166c91') + version('1.0.0', sha256='2c56808c723aba2ea8a8b6bbdc9b8332c96f59b119079861dd52f5988c27f715') depends_on('r-processx@3.4.0:', type=('build', 'run'), when='@3.0.0:') depends_on('r-r6', type=('build', 'run'), when='@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index fbd5266bfee..6f98b07ff1a 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -16,8 +16,8 @@ class RCar(RPackage): version('3.0-3', sha256='fa807cb12f6e7fb38ec534cac4eef54747945c2119a7d51155a2492ad778c36f') version('3.0-2', sha256='df59a9ba8fed67eef5ddb8f92f2b41745df715d5695c71d562d7031513f37c50') - version('2.1-4', 'a66c307e8ccf0c336ed197c0f1799565') - version('2.1-2', '0f78ad74ef7130126d319acec23951a0') + version('2.1-4', sha256='fd39cf1750cb560a66623fea3fa9e6a94fc24e3dc36367aff24df7d0743edb28') + version('2.1-2', sha256='8cc3e57f172c8782a08960b508906d3201596a21f4b6c1dab8d4e59353093652') depends_on('r@3.2.0:', when='@:3.0-2', type=('build', 'run')) depends_on('r@3.5.0:', when='@3.0-3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py index fcbf54004bb..e203e3d2edc 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -16,8 +16,8 @@ class RCaret(RPackage): version('6.0-84', sha256='a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d') version('6.0-83', sha256='9bde5e4da1f0b690bfe06c2439c0136504e851a8d360bf56b644f171fe20dcef') - version('6.0-73', 'ca869e3357b5358f028fb926eb62eb70') - version('6.0-70', '202d7abb6a679af716ea69fb2573f108') + version('6.0-73', sha256='90a0a4a10f1a3b37502cb0ed7d8830063d059a548faabb9cc5d8d34736c7eacb') + version('6.0-70', sha256='21c5bdf7cf07bece38729465366564d8ca104c2466ee9fd800ca1fd88eb82f38') depends_on('r@2.10:', when='@:6.0-81', type=('build', 'run')) depends_on('r@3.2.0:', when='@6.0-82:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py index 9898ab68b35..087847f99b3 100644 --- a/var/spack/repos/builtin/packages/r-catools/package.py +++ b/var/spack/repos/builtin/packages/r-catools/package.py @@ -19,7 +19,7 @@ class RCatools(RPackage): version('1.17.1.2', sha256='69cc542fab5677462b1a768709d0c4a0a0790f5db53e1fe9ae7123787c18726b') version('1.17.1.1', sha256='d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06') - version('1.17.1', '5c872bbc78b177b306f36709deb44498') + version('1.17.1', sha256='d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4') depends_on('r@2.2.0:', type=('build', 'run')) depends_on('r-bitops', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cdcfluview/package.py b/var/spack/repos/builtin/packages/r-cdcfluview/package.py index fa99d27ca99..e4421546e9c 100644 --- a/var/spack/repos/builtin/packages/r-cdcfluview/package.py +++ b/var/spack/repos/builtin/packages/r-cdcfluview/package.py @@ -19,7 +19,7 @@ class RCdcfluview(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/cdcfluview" version('0.9.0', sha256='1b2064886858cbb1790ef808d88fbab75d3a9cf55e720638221a3377ff8dd244') - version('0.7.0', 'd592606fab3da3536f39a15c0fdbcd17') + version('0.7.0', sha256='8c8978d081f8472a6ed5ec54c4e6dd906f97ee28d0f88eef1514088f041ecc03') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cellranger/package.py b/var/spack/repos/builtin/packages/r-cellranger/package.py index 4f8205d51fe..7da69c13956 100644 --- a/var/spack/repos/builtin/packages/r-cellranger/package.py +++ b/var/spack/repos/builtin/packages/r-cellranger/package.py @@ -14,7 +14,7 @@ class RCellranger(RPackage): url = "https://cloud.r-project.org/src/contrib/cellranger_1.1.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/cellranger" - version('1.1.0', '1abcfea6af5ab2e277cb99e86880456f') + version('1.1.0', sha256='5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rematch', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-checkmate/package.py b/var/spack/repos/builtin/packages/r-checkmate/package.py index df1abd2b6ba..2ec531fcf41 100644 --- a/var/spack/repos/builtin/packages/r-checkmate/package.py +++ b/var/spack/repos/builtin/packages/r-checkmate/package.py @@ -16,7 +16,7 @@ class RCheckmate(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/checkmate" version('1.9.4', sha256='faa25754b757fe483b876f5d07b73f76f69a1baa971420892fadec4af4bbad21') - version('1.8.4', '00bd2c464386614da208f82c4b21910b') + version('1.8.4', sha256='6f948883e5a885a1c409d997f0c782e754a549227ec3c8eb18318deceb38f8f6') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-backports@1.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index 258a7ee7677..6079866f31b 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -18,7 +18,7 @@ class RCheckpoint(RPackage): version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') version('0.4.3', sha256='c3e862f89f8838183d6028f7ed13683aec562e6dab77ad4b6a5e24ec653cfb64') - version('0.3.18', '021d7faeb72c36167951e103b2b065ea') - version('0.3.15', 'a4aa8320338f1434a330d984e97981ea') + version('0.3.18', md5='021d7faeb72c36167951e103b2b065ea') + version('0.3.15', sha256='09f1feeb2b5b8b409a2e16a9185827b8da5e555f1aa84442a287f15e452beed7') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py index d2854903d13..6ce8e29ecf2 100644 --- a/var/spack/repos/builtin/packages/r-chemometrics/package.py +++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py @@ -14,11 +14,11 @@ class RChemometrics(RPackage): url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/chemometrics" - version('1.4.2', '8137b0ca4004add9cc2ea81d2c54427f') - version('1.4.1', '1e5a89442bb4a61db0da884eedd74fc2') - version('1.3.9', '2b619791896db1513ca3d714acb68af3') - version('1.3.8', '7fad828bd094b5485fbf20bdf7d3d0d1') - version('1.3.7', 'a9e2f32efb1545421dd96185fd849184') + version('1.4.2', sha256='b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a') + version('1.4.1', sha256='7646da0077657d672356204aa2094be68e10ec13617f92ae97ff53a389053905') + version('1.3.9', sha256='553eda53789b6a4d0f77842c175f98be5b9a04bccc9d2ba0ecde1bb5c8a53f21') + version('1.3.8', sha256='5a977bf1a9475d4dd4764ec9e99cbce237c5b624ef9aa96fcaf08406b1b8a56d') + version('1.3.7', sha256='653a4f728c996983a4b5e5144229d0cf8b6754fb7e85e9014eeaf34fa19da42f') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rpart', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py index 3defd1653b4..43bd8f20e28 100644 --- a/var/spack/repos/builtin/packages/r-chron/package.py +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -15,6 +15,6 @@ class RChron(RPackage): version('2.3-53', sha256='521814b46ba958eae28e29d8766aebd285da5e6fa16c5806603df3ae39f77309') version('2.3-52', sha256='c47fcf4abb635babe6337604c876d4853d8a24639a98b71523746c56ce75b4a0') - version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f') + version('2.3-47', sha256='9a8c771021165de517e54c3369c622aaac1bf3e220a2fbf595aba285e60445f6') depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-circlize/package.py b/var/spack/repos/builtin/packages/r-circlize/package.py index 31dd662d76f..d8d8ac2e7f4 100644 --- a/var/spack/repos/builtin/packages/r-circlize/package.py +++ b/var/spack/repos/builtin/packages/r-circlize/package.py @@ -23,8 +23,8 @@ class RCirclize(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/circlize" version('0.4.6', sha256='cec88cfc5e512a111cc37177552c25698ccc0e9bbecb0d6e60657e7b115a56fa') - version('0.4.1', '6818830654f485abbdc8c74ec9087377') - version('0.4.0', '0dbf1b481930a759d6f413d17f8ae1c4') + version('0.4.1', sha256='204a170ae3b982f09b652c4583189907cfa42a29bc7efaba02a1e0d79f1cf1f0') + version('0.4.0', sha256='abdc1bbe264be42c1d7b65869979da7cd131032fd6fd3f11f9744dae54e83f5c') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-globaloptions@0.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index 472c8dbd4aa..ff585126c8c 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -15,7 +15,7 @@ class RClass(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/class" version('7.3-15', sha256='f6bf33d610c726d58622b6cea78a808c7d6a317d02409d27c17741dfd1c730f4') - version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') + version('7.3-14', sha256='18b876dbc18bebe6a00890eab7d04ef72b903ba0049d5ce50731406a82426b9c') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-classint/package.py b/var/spack/repos/builtin/packages/r-classint/package.py index fb859c3e7cf..a3d5050b8ac 100644 --- a/var/spack/repos/builtin/packages/r-classint/package.py +++ b/var/spack/repos/builtin/packages/r-classint/package.py @@ -17,7 +17,7 @@ class RClassint(RPackage): version('0.4-1', sha256='39c63f8e37b379033d73d57929b5b8ea41b0023626cc1cec648d66bade5d0103') version('0.3-3', sha256='a93e685ef9c40d5977bb91d7116505a25303b229897a20544722a94ea1365f30') version('0.3-1', sha256='e2e6f857b544dfecb482b99346aa3ecfdc27b4d401c3537ee8fbaf91caca92b9') - version('0.1-24', '45f1bde3ec7601ce17c99189be5c0fd5') + version('0.1-24', sha256='f3dc9084450ea3da07e1ea5eeb097fd2fedc7e29e5d7794b418bcb438c4fcfa2') depends_on('r@2.2:', type=('build', 'run')) depends_on('r-e1071', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py index e841226979d..268f062b973 100644 --- a/var/spack/repos/builtin/packages/r-cli/package.py +++ b/var/spack/repos/builtin/packages/r-cli/package.py @@ -16,8 +16,8 @@ class RCli(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/cli" version('1.1.0', sha256='4fc00fcdf4fdbdf9b5792faee8c7cf1ed5c4f45b1221d961332cda82dbe60d0a') - version('1.0.1', 'ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4') - version('1.0.0', 'e6c4169541d394d6d435c4b430b1dd77') + version('1.0.1', sha256='ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4') + version('1.0.0', sha256='8fa3dbfc954ca61b8510f767ede9e8a365dac2ef95fe87c715a0f37d721b5a1d') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-clipr/package.py b/var/spack/repos/builtin/packages/r-clipr/package.py index bd6a07923cc..10198a42e22 100644 --- a/var/spack/repos/builtin/packages/r-clipr/package.py +++ b/var/spack/repos/builtin/packages/r-clipr/package.py @@ -16,6 +16,6 @@ class RClipr(RPackage): version('0.7.0', sha256='03a4e4b72ec63bd08b53fe62673ffc19a004cc846957a335be2b30d046b8c2e2') version('0.5.0', sha256='fd303f8b7f29badcdf490bb2d579acdfc4f4e1aa9c90ac77ab9d05ce3d053dbf') - version('0.4.0', '4012a31eb3b7a36bd3bac00f916e56a7') + version('0.4.0', sha256='44a2f1ab4fde53e4fe81cf5800aa6ad45b72b5da93d6fe4d3661d7397220e8af') depends_on('xclip') diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index 44a36e5b00f..8b657d5c44e 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -16,9 +16,9 @@ class RCluster(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/cluster" version('2.1.0', sha256='eaf955bef8f616ea563351ec7f597c445aec43e65991ca975e382ef1fd70aa14') - version('2.0.7-1', 'a37add21b91d3e4f3883d005331e0d45') - version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a') - version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') + version('2.0.7-1', sha256='b10141090cf3c2b62260611a0ea822eb2f7bab9f4fd656c48bdc12b65c5c3dbf') + version('2.0.5', sha256='4b309133bc2ad7b8fe4fa538dd69635bc8a4cd724a3c95f01084098876c57bae') + version('2.0.4', sha256='d4d925c4fc1fc4f2e2e3c9208e518507aad6c28bb143b4358a05a8a8944ac6e4') depends_on('r@3.0.1:', when='@:2.0.6', type=('build', 'run')) depends_on('r@3.2.0:', when='@2.0.7:2.0.7-1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py index b69c0f5a80f..fd884ea86c9 100644 --- a/var/spack/repos/builtin/packages/r-coda/package.py +++ b/var/spack/repos/builtin/packages/r-coda/package.py @@ -18,7 +18,7 @@ class RCoda(RPackage): version('0.19-3', sha256='d3df1fc848bcf1af8fae13d61eeab60e99a3d4b4db384bec4326f909f502c5d6') version('0.19-2', sha256='678a7e6a87a2723089daeb780ea37ac3d4319b37eabe26928ea3fa9c9b1eda0d') - version('0.19-1', '0d2aca6a5a3bdae9542708817c1ec001') + version('0.19-1', sha256='d41ff5731da6805170769dba75dd011ab33f916d15b2336001f279e21a524491') depends_on('r@2.14:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index 5ccaa4914cf..60ea74198ac 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -14,7 +14,7 @@ class RCodetools(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/codetools" version('0.2-16', sha256='f67a66175cb5d8882457d1e9b91ea2f16813d554fa74f80c1fd6e17cf1877501') - version('0.2-15', '37419cbc3de81984cf6d9b207d4f62d4') - version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') + version('0.2-15', sha256='4e0798ed79281a614f8cdd199e25f2c1bd8f35ecec902b03016544bd7795fa40') + version('0.2-14', sha256='270d603b89076081af8d2db0256927e55ffeed4c27309d50deea75b444253979') depends_on('r@2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py index b52fff5e772..5b83e7d6a18 100644 --- a/var/spack/repos/builtin/packages/r-coin/package.py +++ b/var/spack/repos/builtin/packages/r-coin/package.py @@ -17,7 +17,7 @@ class RCoin(RPackage): version('1.3-0', sha256='adcebb37e0a7dfddbf8ec1e09c12a809bd76d90b5b8ff2b1048a75252ba11ef8') version('1.2-2', sha256='d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb') - version('1.1-3', '97d3d21f1e4a5762e36dd718dd2d0661') + version('1.1-3', sha256='8b88ecc25903c83539dfc73cdc31a160e2aa4a7bea1773b22c79133d2f006035') depends_on('r@2.14.0:', when='@:1.2-2', type=('build', 'run')) depends_on('r@3.4.0:', when='@1.3-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index 9aaec8933ec..8e68f4a366e 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -18,7 +18,7 @@ class RColorspace(RPackage): version('1.4-1', sha256='693d713a050f8bfecdb7322739f04b40d99b55aed168803686e43401d5f0d673') version('1.4-0', sha256='ce003c5958dd704697959e9dc8a108c8cb568f8d78ece113235732afc5dff556') - version('1.3-2', '63000bab81d995ff167df76fb97b2984') - version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1') + version('1.3-2', sha256='dd9fd2342b650456901d014e7ff6d2e201f8bec0b555be63b1a878d2e1513e34') + version('1.2-6', sha256='ba3165c5b906edadcd1c37cad0ef58f780b0af651f3fdeb49fbb2dc825251679') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-compositions/package.py b/var/spack/repos/builtin/packages/r-compositions/package.py index 112af5a1e53..5077a7e651c 100644 --- a/var/spack/repos/builtin/packages/r-compositions/package.py +++ b/var/spack/repos/builtin/packages/r-compositions/package.py @@ -13,7 +13,7 @@ class RCompositions(RPackage): url = "https://cloud.r-project.org/src/contrib/compositions_1.40-2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/compositions" - version('1.40-2', 'ad87efe2fb303d95472e73c8ca8d9a01') + version('1.40-2', sha256='110d71ae000561987cb73fc76cd953bd69d37562cb401ed3c36dca137d01b78a') depends_on('r@2.2.0:', type=('build', 'run')) depends_on('r-tensora', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py index 36902848095..ad4f8fc61c4 100644 --- a/var/spack/repos/builtin/packages/r-corpcor/package.py +++ b/var/spack/repos/builtin/packages/r-corpcor/package.py @@ -13,6 +13,6 @@ class RCorpcor(RPackage): url = "https://cloud.r-project.org/src/contrib/corpcor_1.6.9.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/corpcor" - version('1.6.9', '7f447d9f389e5d7dedb5fe5baedca925') + version('1.6.9', sha256='2e4fabd1d3936fecea67fa365233590147ca50bb45cf80efb53a10345a8a23c2') depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-corrplot/package.py b/var/spack/repos/builtin/packages/r-corrplot/package.py index 71ded1da625..490d0966b8a 100644 --- a/var/spack/repos/builtin/packages/r-corrplot/package.py +++ b/var/spack/repos/builtin/packages/r-corrplot/package.py @@ -15,4 +15,4 @@ class RCorrplot(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/corrplot" version('0.84', sha256='0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc') - version('0.77', '2a5d54fd5c65618b9afba1a32f6b4542') + version('0.77', sha256='54b66ff995eaf2eee3f3002509c6f27bb5bd970b0abde41893ed9387e93828d3') diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py index 1f62a54c170..22becf9e7e2 100644 --- a/var/spack/repos/builtin/packages/r-covr/package.py +++ b/var/spack/repos/builtin/packages/r-covr/package.py @@ -23,7 +23,7 @@ class RCovr(RPackage): version('3.3.0', sha256='c0aa0bd7b2dc05effdc2367c59d45294f46858930d1b14efb393b205021fc65a') version('3.2.1', sha256='ea90daa48011e4ac4431ae47ee02fad98f54b529fc3900281cbeef7a2edef0a0') version('3.2.0', sha256='b26135306b1d6b14dd4deb481359dd919a7ca1e802ca5479fed394dcf35f0ef9') - version('3.0.1', 'f88383f751fe5aa830a2b2e5c14aa66a') + version('3.0.1', sha256='66b799fd03cb83a9ab382d9cf4ff40603d1e3f3a89905a3174546b0c63e8d184') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-digest', when='@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py index 4a5cd951453..123da7c0d36 100644 --- a/var/spack/repos/builtin/packages/r-crayon/package.py +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -17,5 +17,5 @@ class RCrayon(RPackage): url = "https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/crayon" - version('1.3.4', '77c7c2906c59a3141306d86c89ffc7d3') - version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9') + version('1.3.4', sha256='fc6e9bf990e9532c4fcf1a3d2ce22d8cf12d25a95e4779adfa17713ed836fa68') + version('1.3.2', sha256='9a6b75d63c05fe64baf222f1921330ceb727924bcc5fc2753ff0528d42555e68') diff --git a/var/spack/repos/builtin/packages/r-crosstalk/package.py b/var/spack/repos/builtin/packages/r-crosstalk/package.py index ad17c33aa6f..b505bd68e20 100644 --- a/var/spack/repos/builtin/packages/r-crosstalk/package.py +++ b/var/spack/repos/builtin/packages/r-crosstalk/package.py @@ -14,7 +14,7 @@ class RCrosstalk(RPackage): url = "https://cloud.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/crosstalk" - version('1.0.0', 'c13c21b81af2154be3f08870fd3a7077') + version('1.0.0', sha256='b31eada24cac26f24c9763d9a8cbe0adfd87b264cf57f8725027fe0c7742ca51') depends_on('r-htmltools@0.3.5:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py index 7ed968d5bc5..8651d1fb42b 100644 --- a/var/spack/repos/builtin/packages/r-cubature/package.py +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -15,6 +15,6 @@ class RCubature(RPackage): version('2.0.3', sha256='79bf03ebdb64b0de1ef19d24051b9d922df9310254bee459bb47764522407a73') version('2.0.2', sha256='641165c665ff490c523bccc05c42bb6851e42676b6b366b55fc442a51a8fbe8c') - version('1.1-2', '5617e1d82baa803a3814d92461da45c9') + version('1.1-2', sha256='0a05469bdc85d6bd8165a42a3fc5c35a06700d279e4e8b3cf4669df19edffeed') depends_on('r-rcpp', when='@2.0.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py index a41928e6639..36c0eeb35e9 100644 --- a/var/spack/repos/builtin/packages/r-cubist/package.py +++ b/var/spack/repos/builtin/packages/r-cubist/package.py @@ -15,7 +15,7 @@ class RCubist(RPackage): version('0.2.2', sha256='cd3e152cc72ab33f720a8fb6b8b6787171e1c037cfda48f1735ab692ed6d85d4') version('0.2.1', sha256='b310c3f166f15fa3e16f8d110d39931b0bb1b0aa8d0c9ac2af5a9a45081588a3') - version('0.0.19', 'bf9364f655536ec03717fd2ad6223a47') + version('0.0.19', sha256='101379979acb12a58bcf32a912fef32d497b00263ebea918f2b85a2c32934aae') depends_on('r-lattice', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index 2a720b2a99a..01a385f2f3e 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -23,10 +23,10 @@ class RCurl(RPackage): version('4.0', sha256='09a99c9c86666449188fbb211cb1e9fbdb5108ab56f0d09322cd0ae50e926171') version('3.3', sha256='0cb0b9a9280edc42ebed94708541ec86b4f48779e722171e45227eab8a88a5bd') - version('3.0', '741202626eacd1f9c022b0a4d7be6d6a') - version('2.3', '7250ee8caed98ba76906ab4d32da60f8') - version('1.0', '93d34926d6071e1fba7e728b482f0dd9') - version('0.9.7', 'a101f7de948cb828fef571c730f39217') + version('3.0', sha256='7bf8e3ae7cc77802ae300277e85d925d4c0611a9b7dad5c5601e0d2cbe14a506') + version('2.3', sha256='f901dad6bb70a6875a85da75bcbb42afffdcdf4ef221909733826bcb012d7c3d') + version('1.0', sha256='f8927228754fdfb21dbf08b9e67c5f97e06764c4adf327a4126eed84b1508f3d') + version('0.9.7', sha256='46e150998723fd1937da598f47f49fe47e40c1f57ec594436c6ef1e0145b44dc') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('curl') diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py index bd8e4289e3e..b927abd2a32 100644 --- a/var/spack/repos/builtin/packages/r-dbi/package.py +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -16,7 +16,7 @@ class RDbi(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/DBI" version('1.0.0', sha256='ff16f118eb3f759183441835e932b87358dd80ab9800ce576a8f3df1b6f01cf5') - version('0.4-1', 'c7ee8f1c5037c2284e99c62698d0f087') - version('0.7', '66065dd687d758b72d638adb6a8cab2e') + version('0.4-1', sha256='eff14a9af4975f23f8e1f4347d82c33c32c0b4f4f3e11370c582a89aeb8ac68e') + version('0.7', sha256='2557d5d59a45620ec9de340c2c25eec4cc478d3fc3f8b87979cf337c5bcfde11') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py index f206bc6a6bf..b2fdd549ad3 100644 --- a/var/spack/repos/builtin/packages/r-deldir/package.py +++ b/var/spack/repos/builtin/packages/r-deldir/package.py @@ -19,6 +19,6 @@ class RDeldir(RPackage): version('0.1-23', sha256='e0112bce9fc94daf73596a0fff9b3958b80872e3bbb487be73e157b13a6f201d') version('0.1-21', sha256='b9dabcc1813c7a0f8edaf720a94bdd611a83baf3d3e52e861d352369e815690c') - version('0.1-14', '6a22b13d962615cd9d51b6eae403409f') + version('0.1-14', sha256='89d365a980ef8589971e5d311c6bd59fe32c48dbac8000a880b9655032c99289') depends_on('r@0.99:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py index b1e578164c1..746867f19de 100644 --- a/var/spack/repos/builtin/packages/r-dendextend/package.py +++ b/var/spack/repos/builtin/packages/r-dendextend/package.py @@ -15,7 +15,7 @@ class RDendextend(RPackage): version('1.12.0', sha256='b487fed8c1878a23b9e28394ee11f16a1831b76c90793eb486e6963c7162fa55') version('1.10.0', sha256='88f0fb3362d69144daf4f35d0ea09f32c2df1adf614e040327a42552a8fd3224') - version('1.5.2', '1134869d94005727c63cf3037e2f1bbf') + version('1.5.2', sha256='8228cf9cfd31ec30038aaa61a35959179bad748582d796999cd9ad78152a5f12') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-magrittr@1.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py index a17bd18179f..3105f98e614 100644 --- a/var/spack/repos/builtin/packages/r-deoptim/package.py +++ b/var/spack/repos/builtin/packages/r-deoptim/package.py @@ -16,4 +16,4 @@ class RDeoptim(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptim" version('2.2-4', sha256='0a547784090d1e9b93efc53768110621f35bed3692864f6ce5c0dda2ebd6d482') - version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326') + version('2.2-3', sha256='af2120feea3a736ee7a5a93c6767d464abc0d45ce75568074b233405e73c9a5d') diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py index a48e98af481..9102c744b9a 100644 --- a/var/spack/repos/builtin/packages/r-deoptimr/package.py +++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py @@ -15,4 +15,4 @@ class RDeoptimr(RPackage): url = "https://cloud.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptimR" - version('1.0-8', 'c85836a504fbe4166e3c8eba0efe705d') + version('1.0-8', sha256='846911c1b2561a9fae73a8c60a21a5680963ebb0050af3c1f1147ae9a121e5ef') diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py index 466c8107ed4..a0e705394d0 100644 --- a/var/spack/repos/builtin/packages/r-desolve/package.py +++ b/var/spack/repos/builtin/packages/r-desolve/package.py @@ -18,6 +18,6 @@ class RDesolve(RPackage): version('1.24', sha256='3aa52c822abb0348a904d5bbe738fcea2b2ba858caab9f2831125d07f0d57b42') version('1.21', sha256='45c372d458fe4c7c11943d4c409517849b1be6782dc05bd9a74b066e67250c63') - version('1.20', '85c6a2d8568944ae8eef27ac7c35fb25') + version('1.20', sha256='56e945835b0c66d36ebc4ec8b55197b616e387d990788a2e52e924ce551ddda2') depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index b5a11517027..b132f9dcbf6 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -15,8 +15,8 @@ class RDevtools(RPackage): version('2.1.0', sha256='c1f75346a90adf0669b5508fe68cc78bd3b114c1303fa7d22bf90991edd9230d') version('2.0.2', sha256='99a2fa957068254b8ecdb3fc2d50e2950230910ea31c314fc0e7d934e4bd1709') - version('1.12.0', '73b46c446273566e5b21c9f5f72aeca3') - version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') + version('1.12.0', sha256='8a3e2ca3988dffe29341e45a160bb588995eae43485d6a811a9ae4836d37afd4') + version('1.11.1', sha256='51c876f9ddbfdf611f6ea0b06c0b46da8cefcb8cc98d60e06d576b61f0a06346') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-httr@0.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py index 23ad11daf88..dc86a07bd17 100644 --- a/var/spack/repos/builtin/packages/r-diagrammer/package.py +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -15,7 +15,7 @@ class RDiagrammer(RPackage): version('1.0.1', sha256='ccee8acf608fc909e73c6de4374cef5a570cb62e5f454ac55dda736f22f3f013') version('1.0.0', sha256='2b186dae1b19018681b979e9444bf16559c42740d8382676fbaf3b0f8a44337e') - version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a') + version('0.8.4', sha256='0503935fa120c7c7cdcfd4dce85558b23fd0bcb7e6b32fa6989087d3c88ec404') depends_on('r@3.2.0:', when='@0.9.2:', type=('build', 'run')) depends_on('r-htmlwidgets@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dicekriging/package.py b/var/spack/repos/builtin/packages/r-dicekriging/package.py index 0f00d6ea5ad..7ce3fedd96e 100644 --- a/var/spack/repos/builtin/packages/r-dicekriging/package.py +++ b/var/spack/repos/builtin/packages/r-dicekriging/package.py @@ -15,4 +15,4 @@ class RDicekriging(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/DiceKriging" version('1.5.6', sha256='25466d2db9f17083d1c7b9545e5ec88f630be934f9373c2f7b36c38de4e64e92') - version('1.5.5', 'ee3e2d7a91d4a712467ef4f0b69c2844') + version('1.5.5', sha256='55fe161f867a0c3772023c3047041b877aa54d29cb474ec87293ec31cc5cb30c') diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py index cda69069013..90434ae5155 100644 --- a/var/spack/repos/builtin/packages/r-dichromat/package.py +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -14,6 +14,6 @@ class RDichromat(RPackage): url = "https://cloud.r-project.org/src/contrib/dichromat_2.0-0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/dichromat" - version('2.0-0', '84e194ac95a69763d740947a7ee346a6') + version('2.0-0', sha256='31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diffusionmap/package.py b/var/spack/repos/builtin/packages/r-diffusionmap/package.py index 84fb7c20841..b6508e937ab 100644 --- a/var/spack/repos/builtin/packages/r-diffusionmap/package.py +++ b/var/spack/repos/builtin/packages/r-diffusionmap/package.py @@ -16,10 +16,10 @@ class RDiffusionmap(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/diffusionMap" version('1.1-0.1', sha256='b24cf841af2566ac36f4ede2885f2ff355a7905398444d6d89747315d99a8486') - version('1.1-0', 'cc7d728087ba08d9299ae3a64a8d8919') - version('1.0-0', 'bca462e6efe45c5eaa48d38621f0bd6f') - version('0.0-2', 'b599f47ebf30127e34ce2219dc3e43ae') - version('0.0-1', '20c2cc2fffb5237d5c0216207016c2a1') + version('1.1-0', sha256='637b810140145fa0cbafb1c13da347c2f456c425334ae554d11a3107052e28d1') + version('1.0-0', sha256='1e3c54f72cbb2bce1b06b85fda33242b9041d30d4ac8c12df4dc9a3a95a44044') + version('0.0-2', sha256='b08b9d8a7b2b49d8f809ed14ab40cec92a635a284e43af068eb34e74172c0bcf') + version('0.0-1', sha256='38c4af2d2a4fa4116c2e01a5e67ba313e7a8e76f724a3312a3c12b26e299f844') depends_on('r@2.4.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py index feb608e7f42..875d2e4b766 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -30,9 +30,9 @@ class RDigest(RPackage): version('0.6.20', sha256='05674b0b5d888461ff770176c67b10a11be062b0fee5dbd9298f25a9a49830c7') version('0.6.19', sha256='28d159bd589ecbd01b8da0826eaed417f5c1bf5a11b79e76bf67ce8d935cccf4') - version('0.6.12', '738efd4d9a37c5a4001ae66e954ce07e') - version('0.6.11', '52a864f55846b48b3cab0b5d0304a82a') - version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') + version('0.6.12', sha256='a479463f120037ad8e88bb1387170842e635a1f07ce7e3575316efd6e14d9eab') + version('0.6.11', sha256='edab2ca2a38bd7ee19482c9d2531cd169d5123cde4aa2a3dd65c0bcf3d1d5209') + version('0.6.9', sha256='95fdc36011869fcfe21b40c3b822b931bc01f8a531e2c9260582ba79560dbe47') depends_on('r@2.4.1:', when='@:0.6.15', type=('build', 'run')) depends_on('r@3.1.0:', when='@0.6.16:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py index 0e5edc21eff..e2cedec894e 100644 --- a/var/spack/repos/builtin/packages/r-diptest/package.py +++ b/var/spack/repos/builtin/packages/r-diptest/package.py @@ -13,4 +13,4 @@ class RDiptest(RPackage): url = "https://cloud.r-project.org/src/contrib/diptest_0.75-7.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/diptest" - version('0.75-7', '1a4a958fda763f7c99cb485dbe5954ab') + version('0.75-7', sha256='462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b') diff --git a/var/spack/repos/builtin/packages/r-do-db/package.py b/var/spack/repos/builtin/packages/r-do-db/package.py index 4df7aa52917..3be01b4dc50 100644 --- a/var/spack/repos/builtin/packages/r-do-db/package.py +++ b/var/spack/repos/builtin/packages/r-do-db/package.py @@ -13,6 +13,6 @@ class RDoDb(RPackage): homepage = "https://bioconductor.org/packages/DO.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/DO.db_2.9.tar.gz" - version('2.9', '63dda6d46d2fe40c52a2e79260a7fb9d') + version('2.9', sha256='762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py index 9488d31952a..3a50cb689e2 100644 --- a/var/spack/repos/builtin/packages/r-domc/package.py +++ b/var/spack/repos/builtin/packages/r-domc/package.py @@ -15,7 +15,7 @@ class RDomc(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/doMC" version('1.3.6', sha256='2977fc9e2dc54d85d45b4a36cd286dff72834fbc73f38b6ee45a6eb8557fc9b2') - version('1.3.4', 'f965b09add9056e84f99a831dc3af7d1') + version('1.3.4', sha256='76a1092fca59b441e6f89eb7e2fb3a12de807f736a217949c80339f20c958778') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-foreach@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py index 250e396dfbb..c6e9013fbc6 100644 --- a/var/spack/repos/builtin/packages/r-doparallel/package.py +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -15,8 +15,8 @@ class RDoparallel(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/doParallel" version('1.0.15', sha256='71ad7ea69616468996aefdd8d02a4a234759a21ddde9ed1657e3c537145cd86e') - version('1.0.11', 'd7822f0efd7bdf7582d8b43c986be86c') - version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43') + version('1.0.11', sha256='4ccbd2eb46d3e4f5251b0c3de4d93d9168b02bb0be493656d6aea236667ff76a') + version('1.0.10', sha256='70024b6950025cc027022ee409f382e5ad3680c0a25bcd404bfc16418be8add5') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-foreach@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dorng/package.py b/var/spack/repos/builtin/packages/r-dorng/package.py index a493805a36f..41c5ecac3d6 100644 --- a/var/spack/repos/builtin/packages/r-dorng/package.py +++ b/var/spack/repos/builtin/packages/r-dorng/package.py @@ -20,7 +20,7 @@ class RDorng(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/doRNG" version('1.7.1', sha256='27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9') - version('1.6.6', 'ffb26024c58c8c99229470293fbf35cf') + version('1.6.6', sha256='939c2282c72c0b89fc7510f4bff901a4e99007dc006f46762c8f594c0ecbd876') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-downloader/package.py b/var/spack/repos/builtin/packages/r-downloader/package.py index 7b59089be6c..0faeb142278 100644 --- a/var/spack/repos/builtin/packages/r-downloader/package.py +++ b/var/spack/repos/builtin/packages/r-downloader/package.py @@ -18,6 +18,6 @@ class RDownloader(RPackage): url = "https://cloud.r-project.org/src/contrib/downloader_0.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/downloader" - version('0.4', 'f26daf8fbeb29a1882bf102f62008594') + version('0.4', sha256='1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab') depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dtw/package.py b/var/spack/repos/builtin/packages/r-dtw/package.py index f963965161f..8847298c3c3 100644 --- a/var/spack/repos/builtin/packages/r-dtw/package.py +++ b/var/spack/repos/builtin/packages/r-dtw/package.py @@ -16,11 +16,11 @@ class RDtw(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/dtw" version('1.20-1', sha256='43ca1a47a7c81a2b5d5054da1be8b8af79a85d6f9ce7b4512e9ed91f790f60f0') - version('1.18-1', '5e9995a198a62f28045c29461265d536') - version('1.17-1', 'e8be988fe528acd6b44afdf5aa06b745') - version('1.16', '260bd22d9db429394eb39739db4a4686') - version('1.15', 'd3b6fdb0b866ff2e5b178c37bcfc7c55') - version('1.14-3', 'a7b878e8dda7a61df22356d0a81540c5') + version('1.18-1', sha256='d9dab25bdf61705f9f28dc5ca1c96a7465b269233e878516c52c01b5a0da21ad') + version('1.17-1', sha256='0fc3afcebc58135c78abd7545a3549466ac051a058f913db16214c12141a6e4d') + version('1.16', sha256='7d7e34c41ff6021991bcf8a913b2b6b82680018f65fdd90af2150a07457e9cdb') + version('1.15', sha256='28ba2110d4c305f332fad93337cdae24b9de4163b8ddf33d476f9dddc63160f1') + version('1.14-3', sha256='6989358d8d97428418c2b34ae38647efcee2e0ce095800a657d5d83d7083c9e3') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-proxy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py index f286e5363f3..0f2448edd25 100644 --- a/var/spack/repos/builtin/packages/r-dygraphs/package.py +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -19,7 +19,7 @@ class RDygraphs(RPackage): version('1.1.1.6', sha256='c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208') version('1.1.1.5', sha256='274035988fdd6833121fd5831692355d383acc828d540788dbcecaf88eb2d72d') - version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833') + version('0.9', sha256='2aa4754a7d824d8994c2a97ee02bab163319f065b4d10d289337dc8398c0646c') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py index 41ada9809e1..f38f6621b38 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -17,6 +17,6 @@ class RE1071(RPackage): version('1.7-2', sha256='721c299ce83047312acfa3e0c4b3d4c223d84a4c53400c73465cca2c92913752') version('1.7-1', sha256='5c5f04a51c1cd2c7dbdf69987adef9bc07116804c63992cd36d804a1daf89dfe') - version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') + version('1.6-7', sha256='7048fbc0ac17d7e3420fe68081d0e0a2176b1154ee3191d53558ea9724c7c980') depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py index abd9783b0f1..43ec1ffd144 100644 --- a/var/spack/repos/builtin/packages/r-ellipse/package.py +++ b/var/spack/repos/builtin/packages/r-ellipse/package.py @@ -15,6 +15,6 @@ class REllipse(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/ellipse" version('0.4.1', sha256='1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d') - version('0.3-8', '385f5ec5e49bcda4317ca9dffd33f771') + version('0.3-8', sha256='508d474c142f0770c25763d6c8f8f8c9dcf8205afd42ffa22e6be1e0360e7f45') depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-energy/package.py b/var/spack/repos/builtin/packages/r-energy/package.py index ab2ef621dee..161e7efae91 100644 --- a/var/spack/repos/builtin/packages/r-energy/package.py +++ b/var/spack/repos/builtin/packages/r-energy/package.py @@ -14,7 +14,7 @@ class REnergy(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/energy" version('1.7-6', sha256='900edbb28e1f1bccd78580828470628cf75eb6333b63e1a58e4da7fc5c5fa89a') - version('1.7-5', 'd13c76c26b5221ba29aade6a824f32d6') + version('1.7-5', sha256='24c2cf080939f8f56cd9cda06d2dfc30d0389cd3ec7250af4f9a09a4c06b6996') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rcpp@0.12.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py index 9fedc0c078c..0a252cfe0f7 100644 --- a/var/spack/repos/builtin/packages/r-ergm/package.py +++ b/var/spack/repos/builtin/packages/r-ergm/package.py @@ -17,7 +17,7 @@ class RErgm(RPackage): version('3.10.4', sha256='885f0b1a23c5a2c1947962350cfab66683dfdfd1db173c115e90396d00831f22') version('3.10.1', sha256='a2ac249ff07ba55b3359242f20389a892543b4fff5956d74143d2d41fa6d4beb') - version('3.7.1', '431ae430c76b2408988f469831d80126') + version('3.7.1', sha256='91dd011953b93ecb2b84bb3ababe7bddae25d9d86e69337156effd1da84b54c3') depends_on('r-robustbase@0.93-5:', type=('build', 'run')) depends_on('r-coda@0.19-2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index c56425716d5..e0f52918a0f 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -15,9 +15,9 @@ class REvaluate(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/evaluate" version('0.14', sha256='a8c88bdbe4e60046d95ddf7e181ee15a6f41cdf92127c9678f6f3d328a3c5e28') - version('0.10.1', '1dde5a35e2b9d57f1b1bb16791b35ff5') - version('0.10', 'c49326babf984a8b36e7e276da370ad2') - version('0.9', '877d89ce8a9ef7f403b1089ca1021775') + version('0.10.1', sha256='c9a763895d3f460dbf87c43a6469e4b41a251a74477df8c5d7e7d2b66cdd1b1c') + version('0.10', sha256='6163baeb382c2c1e87d4e36a2e986ef74673d8a92ea8508c39ac662ff3519657') + version('0.9', sha256='e8118c9d6ec479c0e712913848404431b6b6c0282f3c131acaf9a677ab5fc6ae') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-stringr@0.6.2:', when='@:0.11', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-expm/package.py b/var/spack/repos/builtin/packages/r-expm/package.py index f7e5588e4ed..6c51216793a 100644 --- a/var/spack/repos/builtin/packages/r-expm/package.py +++ b/var/spack/repos/builtin/packages/r-expm/package.py @@ -16,6 +16,6 @@ class RExpm(RPackage): version('0.999-4', sha256='58d06427a08c9442462b00a5531e2575800be13ed450c5a1546261251e536096') version('0.999-3', sha256='511bac5860cc5b3888bca626cdf23241b6118eabcc82d100935386039e516412') - version('0.999-2', 'e05fa3f995754af92bd03227625da984') + version('0.999-2', sha256='38f1e5bfa90f794486789695d0d9e49158c7eb9445dc171dd83dec3d8fa130d6') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py index 562dc81c951..a252d0ebde6 100644 --- a/var/spack/repos/builtin/packages/r-factoextra/package.py +++ b/var/spack/repos/builtin/packages/r-factoextra/package.py @@ -15,7 +15,7 @@ class RFactoextra(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/factoextra" version('1.0.5', sha256='8177a3f5107883ae248b2cd0afa388a1794741f5155a9455b3883788cf44d5d0') - version('1.0.4', 'aa4c81ca610f17fdee0c9f3379e35429') + version('1.0.4', sha256='e4a000a04ef5b9aa0790dc6e5277451c482a19ba10dda9474f6c6982424aeed3') depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fastmatch/package.py b/var/spack/repos/builtin/packages/r-fastmatch/package.py index 88ef290d707..c1fa6b2857c 100644 --- a/var/spack/repos/builtin/packages/r-fastmatch/package.py +++ b/var/spack/repos/builtin/packages/r-fastmatch/package.py @@ -16,4 +16,4 @@ class RFastmatch(RPackage): url = "https://cloud.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/fastmatch" - version('1.1-0', '900c2363c15059ac9d63c4c71ea2d6b2') + version('1.1-0', sha256='20b51aa4838dbe829e11e951444a9c77257dcaf85130807508f6d7e76797007d') diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py index 6b352a20085..87e0e48ec43 100644 --- a/var/spack/repos/builtin/packages/r-ff/package.py +++ b/var/spack/repos/builtin/packages/r-ff/package.py @@ -15,7 +15,7 @@ class RFf(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/ff" version('2.2-14', sha256='1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0') - version('2.2-13', '4adf8840d24cb6e2927a3ef885c86fcd') + version('2.2-13', sha256='8bfb08afe0651ef3c23aaad49208146d5f929af5af12a25262fe7743fa346ddb') depends_on('r@2.10.1:', type=('build', 'run')) depends_on('r-bit@1.1-13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fftwtools/package.py b/var/spack/repos/builtin/packages/r-fftwtools/package.py index 418347cd8e9..c2708d2b72c 100644 --- a/var/spack/repos/builtin/packages/r-fftwtools/package.py +++ b/var/spack/repos/builtin/packages/r-fftwtools/package.py @@ -19,7 +19,7 @@ class RFftwtools(RPackage): url = "https://cloud.r-project.org/src/contrib/fftwtools_0.9-8.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/fftwtools" - version('0.9-8', '2d1258fbaf0940b57ed61c8d6cd6694d') + version('0.9-8', sha256='4641c8cd70938c2a8bde0b6da6cf7f83e96175ef52f1ca42ec3920a1dabf1bdb') depends_on('r@2.15.2:', type=('build', 'run')) depends_on('fftw@3.1.2:') diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index 8a44c29f703..f2684c872e8 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -23,6 +23,6 @@ class RFilehash(RPackage): version('2.4-2', sha256='b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93') version('2.4-1', sha256='d0e087d338d89372c251c18fc93b53fb24b1750ea154833216ff16aff3b1eaf4') - version('2.3', '01fffafe09b148ccadc9814c103bdc2f') + version('2.3', sha256='63b098df9a2cf4aac862cd7bf86ae516e00852a8ad0f3090f9721b6b173e6edb') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fit-models/package.py b/var/spack/repos/builtin/packages/r-fit-models/package.py index 3f1619d2e2b..0cda9e2efcb 100644 --- a/var/spack/repos/builtin/packages/r-fit-models/package.py +++ b/var/spack/repos/builtin/packages/r-fit-models/package.py @@ -13,7 +13,7 @@ class RFitModels(RPackage): url = "https://cloud.r-project.org/src/contrib/fit.models_0.5-14.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/fit.models" - version('0.5-14', '159b5c57953db4c917bc186ddacdff51') - version('0.5-13', 'c9ff87e98189bcc3be597e3833408497') + version('0.5-14', sha256='93b9d119e97b36c648a19c891fc5e69f5306eb5b9bac16bf377555057afd4b6e') + version('0.5-13', sha256='7df545fce135159e9abf0a19076628d3ec2999e89f018e142a7a970428823d48') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py index 6564e50a2bc..bf4ef4ffb06 100644 --- a/var/spack/repos/builtin/packages/r-flashclust/package.py +++ b/var/spack/repos/builtin/packages/r-flashclust/package.py @@ -13,6 +13,6 @@ class RFlashclust(RPackage): url = "https://cloud.r-project.org/src/contrib/flashClust_1.01-2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/flashClust" - version('1.01-2', '23409aeeef98bf35d0b3d5dd755fdeff') + version('1.01-2', sha256='48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450') depends_on('r@2.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flexclust/package.py b/var/spack/repos/builtin/packages/r-flexclust/package.py index 324839aa7d3..6253dc27011 100644 --- a/var/spack/repos/builtin/packages/r-flexclust/package.py +++ b/var/spack/repos/builtin/packages/r-flexclust/package.py @@ -20,7 +20,7 @@ class RFlexclust(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/flexclust" version('1.4-0', sha256='82fe445075a795c724644864c7ee803c5dd332a89ea9e6ccf7cd1ae2d1ecfc74') - version('1.3-5', '90226a0e3a4f256f392a278e9543f8f4') + version('1.3-5', sha256='dbf49969c93a7b314d9dc3299a0764ed9a804ba7dcbdc08a1235f244f4b85059') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py index a8d3e03d9a6..989ee3ccd11 100644 --- a/var/spack/repos/builtin/packages/r-flexmix/package.py +++ b/var/spack/repos/builtin/packages/r-flexmix/package.py @@ -14,7 +14,7 @@ class RFlexmix(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/flexmix" version('2.3-15', sha256='ba444c0bfe33ab87d440ab590c06b03605710acd75811c1622253171bb123f43') - version('2.3-14', '5be4f7764e6a697f4586e60c2bf6e960') + version('2.3-14', sha256='837c7f175a211b3c484b2c7b81ec9729889a614c5c6e7d70c95a2c1d60ff846a') depends_on('r@2.15.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py index 02afb622d2e..8da9b999d34 100644 --- a/var/spack/repos/builtin/packages/r-fnn/package.py +++ b/var/spack/repos/builtin/packages/r-fnn/package.py @@ -17,10 +17,10 @@ class RFnn(RPackage): version('1.1.3', sha256='de763a25c9cfbd19d144586b9ed158135ec49cf7b812938954be54eb2dc59432') version('1.1.2.2', sha256='b51a60fbbeff58c48cc90c2023c48972d5082d68efd02284c17ccd9820986326') - version('1.1', '8ba8f5b8be271785593e13eae7b8c393') - version('1.0', 'e9a47dc69d1ba55165be0877b8443fe0') - version('0.6-4', '1c105df9763ceb7b13989cdbcb542fcc') - version('0.6-3', 'f0f0184e50f9f30a36ed5cff24d6cff2') - version('0.6-2', '20648ba934ea32b1b00dafb75e1a830c') + version('1.1', sha256='b2a2e97af14aa50ef4dce15a170e1d7329aebb7643bab4a6cf35609555acccce') + version('1.0', sha256='5606cc656c5488b56ee9227088bec662539589fd626ea5aae0e4d57d70a6fe03') + version('0.6-4', sha256='2d0eb7b2aab9ff2e4deaf0b5e39b817f3f3701c0dcefa8a380bdc7111e68d853') + version('0.6-3', sha256='9ac1817852427a056b5c6ad6ac5212bc43abd29ce15f98441a6261b25cf5f810') + version('0.6-2', sha256='f1fc410c341175bdb11a75b063c8c987e15b632378b56148d3566b91fca53a31') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-forcats/package.py b/var/spack/repos/builtin/packages/r-forcats/package.py index e6cf5b73e2d..176288c679e 100644 --- a/var/spack/repos/builtin/packages/r-forcats/package.py +++ b/var/spack/repos/builtin/packages/r-forcats/package.py @@ -18,7 +18,7 @@ class RForcats(RPackage): version('0.4.0', sha256='7c83cb576aa6fe1379d7506dcc332f7560068b2025f9e3ab5cd0a5f28780d2b2') version('0.3.0', sha256='95814610ec18b8a8830eba63751954387f9d21400d6ab40394ed0ff22c0cb657') - version('0.2.0', 'e4ba2c0a59dcdfcc02274c519bf3dbfc') + version('0.2.0', sha256='b5bce370422d4c0ec9509249ae645373949bfbe9217cdf50dce2bfbdad9f7cd7') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py index 37baf00b4b2..f9322f2ea7a 100644 --- a/var/spack/repos/builtin/packages/r-foreach/package.py +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -20,7 +20,7 @@ class RForeach(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/foreach" version('1.4.7', sha256='95632c0b1182fc01490718d82fa3b2bce864f2a011ae53282431c7c2a3f5f160') - version('1.4.3', 'ef45768126661b259f9b8994462c49a0') + version('1.4.3', sha256='1ef03f770f726a62e3753f2402eb26b226245958fa99d570d003fc9e47d35881') depends_on('r@2.5.0:', type=('build', 'run')) depends_on('r-codetools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-forecast/package.py b/var/spack/repos/builtin/packages/r-forecast/package.py index 6b33bdd1eb9..9fac86177ae 100644 --- a/var/spack/repos/builtin/packages/r-forecast/package.py +++ b/var/spack/repos/builtin/packages/r-forecast/package.py @@ -17,7 +17,7 @@ class RForecast(RPackage): version('8.8', sha256='d077074d77d3ea00e9215c828b3689a8c841a16af1e6859bb2dfdede081c2c1d') version('8.6', sha256='4279e4f700e26310bae39419ab4a9b5918a850148667a5e577a4807d53eb4d02') - version('8.2', '3ef095258984364c100b771b3c90d15e') + version('8.2', sha256='eb3fab64ed139d068e7d026cd3880f1b623f4153a832fb71845488fa75e8b812') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py index 9bba9e81a02..3ee2e55fbcf 100644 --- a/var/spack/repos/builtin/packages/r-foreign/package.py +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -17,6 +17,6 @@ class RForeign(RPackage): version('0.8-72', sha256='439c17c9cd387e180b1bb640efff3ed1696b1016d0f7b3b3b884e89884488c88') version('0.8-70.2', sha256='ae82fad68159860b8ca75b49538406ef3d2522818e649d7ccc209c18085ef179') - version('0.8-66', 'ff12190f4631dca31e30ca786c2c8f62') + version('0.8-66', sha256='d7401e5fcab9ce6e697d3520dbb8475e229c30341c0004c4fa489c82aa4447a4') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 15914e209f8..024d5d1ad4c 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -20,7 +20,7 @@ class RFormatr(RPackage): version('1.7', sha256='a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb') version('1.6', sha256='f5c98f0c3506ca51599671a2cdbc17738d0f326e8e3bb18b7a38e9f172122229') - version('1.5', 'ac735515b8e4c32097154f1b68c5ecc7') - version('1.4', '98b9b64b2785b35f9df403e1aab6c73c') + version('1.5', sha256='874c197ae3720ec11b44984a055655b99a698e1912104eb9034c11fdf6104da7') + version('1.4', sha256='6ec47a7b1f18efb5fd7559b81427363b66415d81cded9d5e7e2907e900b67ebb') depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py index 38b50015d9f..7e963e82e23 100644 --- a/var/spack/repos/builtin/packages/r-formula/package.py +++ b/var/spack/repos/builtin/packages/r-formula/package.py @@ -16,7 +16,7 @@ class RFormula(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/Formula" version('1.2-3', sha256='1411349b20bd09611a9fd0ee6d15f780c758ad2b0e490e908facb49433823872') - version('1.2-2', 'c69bb0522811cf8eb9f1cc6c3d182b6e') - version('1.2-1', '2afb31e637cecd0c1106317aca1e4849') + version('1.2-2', sha256='8def4600fb7457d38db8083733477501b54528974aa216e4adf8871bff4aa429') + version('1.2-1', sha256='5db1ef55119b299c9d291e1c5c08e2d51b696303daf4e7295c38ff5fc428360a') depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py index fd20c495dcc..9729437db95 100644 --- a/var/spack/repos/builtin/packages/r-fpc/package.py +++ b/var/spack/repos/builtin/packages/r-fpc/package.py @@ -15,7 +15,7 @@ class RFpc(RPackage): version('2.2-3', sha256='8100a74e6ff96b1cd65fd22494f2d200e54ea5ea533cfca321fa494914bdc3b7') version('2.2-2', sha256='b6907019eb161d5c8c814cf02a4663cc8aae6322699932881ce5b02f45ecf8d3') - version('2.1-10', '75e5340e416cd13d7751e06f1c07866b') + version('2.1-10', sha256='5d17c5f475c3f24a4809678cbc6186a357276240cf7fcb00d5670b9e68baa096') depends_on('r@2.0.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fracdiff/package.py b/var/spack/repos/builtin/packages/r-fracdiff/package.py index 8f902428ec9..0eec16d4e38 100644 --- a/var/spack/repos/builtin/packages/r-fracdiff/package.py +++ b/var/spack/repos/builtin/packages/r-fracdiff/package.py @@ -15,4 +15,4 @@ class RFracdiff(RPackage): url = "https://cloud.r-project.org/src/contrib/fracdiff_1.4-2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/fracdiff" - version('1.4-2', '6a6977d175ad963d9675736a8f8d41f7') + version('1.4-2', sha256='983781cedc2b4e3ba9fa020213957d5133ae9cd6710bc61d6225728e2f6e850e') diff --git a/var/spack/repos/builtin/packages/r-futile-logger/package.py b/var/spack/repos/builtin/packages/r-futile-logger/package.py index d45418aa72b..39030a14b1e 100644 --- a/var/spack/repos/builtin/packages/r-futile-logger/package.py +++ b/var/spack/repos/builtin/packages/r-futile-logger/package.py @@ -15,7 +15,7 @@ class RFutileLogger(RPackage): url = "https://cloud.r-project.org/src/contrib/futile.logger_1.4.3.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/futile.logger" - version('1.4.3', 'ba0e8d2dfb5a970b51c21907bbf8bfc2') + version('1.4.3', sha256='5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-lambda-r@1.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-futile-options/package.py b/var/spack/repos/builtin/packages/r-futile-options/package.py index c493ac0ea6e..1c9554f5a4e 100644 --- a/var/spack/repos/builtin/packages/r-futile-options/package.py +++ b/var/spack/repos/builtin/packages/r-futile-options/package.py @@ -14,6 +14,6 @@ class RFutileOptions(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/futile.options" version('1.0.1', sha256='7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570') - version('1.0.0', '8fd845774bbce56f41f7c43c3b4c13ba') + version('1.0.0', sha256='ee84ece359397fbb63f145d11af678f5c8618570971e78cc64ac60dc0d14e8c2') depends_on('r@2.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gbm/package.py b/var/spack/repos/builtin/packages/r-gbm/package.py index 1846290c448..61887664dc0 100644 --- a/var/spack/repos/builtin/packages/r-gbm/package.py +++ b/var/spack/repos/builtin/packages/r-gbm/package.py @@ -14,7 +14,7 @@ class RGbm(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/gbm" version('2.1.5', sha256='06fbde10639dfa886554379b40a7402d1f1236a9152eca517e97738895a4466f') - version('2.1.3', '9b2f32c892c6e31b01c1162e3b16b3f4') + version('2.1.3', sha256='eaf24be931d762f1ccca4f90e15997719d01005f152160a3d20d858a0bbed92b') depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-gridextra', when='@2.1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py index 40f27d4e009..bc4d2441f17 100644 --- a/var/spack/repos/builtin/packages/r-gdata/package.py +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -29,8 +29,8 @@ class RGdata(RPackage): url = "https://cloud.r-project.org/src/contrib/gdata_2.18.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/gdata" - version('2.18.0', 'f831019aa743fe11dcf0a051e4280921') - version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f') + version('2.18.0', sha256='4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f') + version('2.17.0', sha256='8097ec0e4868f6bf746f821cff7842f696e874bb3a84f1b2aa977ecd961c3e4e') depends_on('r@2.3.0:', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py index bc2abfdabdb..92ef12322bb 100644 --- a/var/spack/repos/builtin/packages/r-geiger/package.py +++ b/var/spack/repos/builtin/packages/r-geiger/package.py @@ -15,7 +15,7 @@ class RGeiger(RPackage): version('2.0.6.2', sha256='9153047b608d652821251206d1450bb3f517c8884379f498a695315574ae001d') version('2.0.6.1', sha256='2a95e20a3a90c096343b014344dd97e699e954da99c151c17fc6c245c77dba0b') - version('2.0.6', 'e5e1a407ea56805227d0f91bf6d95afc') + version('2.0.6', sha256='e13b2c526378eaf9356b00bbe21b3c2c956327f8062fed638ccc1f49591c3eff') depends_on('r@2.15.0:', type=('build', 'run')) depends_on('r-ape@3.0-6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py index dfb977d9bcc..ea436ffaefb 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py @@ -13,8 +13,8 @@ class RGenomeinfodbdata(RPackage): homepage = "https://bioconductor.org/packages/GenomeInfoDbData/" url = "https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz" - version('1.1.0', '6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c', + version('1.1.0', sha256='6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c', url='https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz') - version('0.99.0', '85977b51061dd02a90153db887040d05') + version('0.99.0', sha256='457049804bbd70f218c1c84067a23e83bdecb7304a3e4d8b697fee0b16dc1888') depends_on('r@3.4.0:3.4.9', when='@0.99.0', type=('build', 'run')) depends_on('r@3.5.0:3.5.9', when='@1.1.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geomorph/package.py b/var/spack/repos/builtin/packages/r-geomorph/package.py index 32049e61e34..8d03f2d1685 100644 --- a/var/spack/repos/builtin/packages/r-geomorph/package.py +++ b/var/spack/repos/builtin/packages/r-geomorph/package.py @@ -19,7 +19,7 @@ class RGeomorph(RPackage): version('3.1.2', sha256='29cf1c484f756cb44808cfdbc20137a6fbc4bd0c5c6f98c6c3f397c5aebda8f1') version('3.1.1', sha256='8eb222011433100860b308beef6f02ade7c421785f575ab4461ee25e38dfa1bd') version('3.0.7', sha256='68f8942e1a5bc3f0298c9f5b8f69c4702c8e12ecb2275d740fda4d04d66d38e1') - version('3.0.5', '240e69fe260ca3ef4d84b4281d61396c') + version('3.0.5', sha256='7a3a587b253770a5e7e70536234dee13e6a073f1fdf1d644ae4f11d2eb95b104') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-rgl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geor/package.py b/var/spack/repos/builtin/packages/r-geor/package.py index 2c499a19b83..91c6773e1d3 100644 --- a/var/spack/repos/builtin/packages/r-geor/package.py +++ b/var/spack/repos/builtin/packages/r-geor/package.py @@ -14,7 +14,7 @@ class RGeor(RPackage): url = "https://cloud.r-project.org/src/contrib/geoR_1.7-5.2.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/geoR" - version('1.7-5.2.1', 'a50f477bea1bec9070a4de01f69b831c') + version('1.7-5.2.1', sha256='3895e49c005a5745738d190ccaad43bb0aa49c74465d4d0b4dd88c5850ed63b9') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py index 689e2f3c1d3..ceb3c891f02 100644 --- a/var/spack/repos/builtin/packages/r-geosphere/package.py +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -17,7 +17,7 @@ class RGeosphere(RPackage): version('1.5-10', sha256='56cd4f787101e2e18f19ddb83794154b58697e63cad81168f0936f60ab7eb497') version('1.5-7', sha256='9d9b555e2d59a5ae174ae654652121f169fbc3e9cf66c2491bfbe0684b6dd8a0') - version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e') + version('1.5-5', sha256='8b6fe012744fc45b88e0ef6f20e60e103ef013e761e99dcff3f9dceeedbdce6d') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-getopt/package.py b/var/spack/repos/builtin/packages/r-getopt/package.py index 08c8b97611c..65e1c577ef3 100644 --- a/var/spack/repos/builtin/packages/r-getopt/package.py +++ b/var/spack/repos/builtin/packages/r-getopt/package.py @@ -19,4 +19,4 @@ class RGetopt(RPackage): version('1.20.3', sha256='531f5fdfdcd6b96a73df2b39928418de342160ac1b0043861e9ea844f9fbf57f') version('1.20.2', sha256='3d6c12d32d6cd4b2909be626e570e158b3ed960e4739510e3a251e7f172de38e') - version('1.20.1', '323cf2846e306f49236b8174bc3d4e47') + version('1.20.1', sha256='1522c35b13e8546979725a68b75e3bc9d156fb06569067472405f6b8591d8654') diff --git a/var/spack/repos/builtin/packages/r-getoptlong/package.py b/var/spack/repos/builtin/packages/r-getoptlong/package.py index e6064611e5f..f16e100229d 100644 --- a/var/spack/repos/builtin/packages/r-getoptlong/package.py +++ b/var/spack/repos/builtin/packages/r-getoptlong/package.py @@ -17,7 +17,7 @@ class RGetoptlong(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/GetoptLong" version('0.1.7', sha256='b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba') - version('0.1.6', 'e4b964d0817cb6c6a707297b21405749') + version('0.1.6', sha256='f526f006e3ed8507f1f236430ac9e97341c1ee9c207fbb68f936dd4d377b28b5') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rjson', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggally/package.py b/var/spack/repos/builtin/packages/r-ggally/package.py index 7ccb73a1285..8ebe105b757 100644 --- a/var/spack/repos/builtin/packages/r-ggally/package.py +++ b/var/spack/repos/builtin/packages/r-ggally/package.py @@ -19,7 +19,7 @@ class RGgally(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/GGally" version('1.4.0', sha256='9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe') - version('1.3.2', 'efe58133ba8431198af7afb6bcb76264') + version('1.3.2', sha256='f4143f45254fed794be991180aeffe459f6756bfa08acad963707d8e843cfd0a') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggdendro/package.py b/var/spack/repos/builtin/packages/r-ggdendro/package.py index 87052809cc7..545fedcf2f7 100644 --- a/var/spack/repos/builtin/packages/r-ggdendro/package.py +++ b/var/spack/repos/builtin/packages/r-ggdendro/package.py @@ -20,7 +20,7 @@ class RGgdendro(RPackage): url = "https://cloud.r-project.org/src/contrib/ggdendro_0.1-20.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/ggdendro" - version('0.1-20', '787552e346432c758633d8f4b2675eb6') + version('0.1-20', sha256='125cae904fa5d426cccaf32ebe9c6297e9ef0c6fd3f19f61513834d03a0cf8ff') depends_on('r-ggplot2@0.9.2:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggjoy/package.py b/var/spack/repos/builtin/packages/r-ggjoy/package.py index 3262750b38c..6cab9a9cb67 100644 --- a/var/spack/repos/builtin/packages/r-ggjoy/package.py +++ b/var/spack/repos/builtin/packages/r-ggjoy/package.py @@ -15,9 +15,9 @@ class RGgjoy(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/ggjoy" version('0.4.1', sha256='d2f778bc40203d7fbb7c81b40beed8614c36ea10448e911663cc6109aa685504') - version('0.4.0', 'c63782e2395a9cfc435d08e078e6596b') - version('0.3.0', '59bd34a846270d43f2eeb1e90b03a127') - version('0.2.0', '8584cd154e228f8505b324e91d2e50d7') + version('0.4.0', sha256='cb9ef790921ffcd3cfb6a55b409d17ccae9e8f5fdd2a28e55ea2ccfa8efd44e8') + version('0.3.0', sha256='bb6d5172deda6cc54d2647644c1056944bc886d48fe1f11a23afd518eaf5cc97') + version('0.2.0', sha256='27c28e9b3aa333ee6f518ee5c1cf6533fdaefa4e205396cd4636bcf0d193e6a2') depends_on('r@3.2:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py index a468f4b18cc..284d716fe22 100644 --- a/var/spack/repos/builtin/packages/r-ggmap/package.py +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -18,7 +18,7 @@ class RGgmap(RPackage): version('3.0.0', sha256='96c24ffdc0710d0633ac4721d599d2c06f43a29c59d1e85c94ff0af30dfdb58d') version('2.6.2', sha256='4e9cf53ab108fc70805d971dadb69b26fe67ea289c23c38adf6e30b198379d90') - version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a') + version('2.6.1', sha256='fc450ef422005fc7d2018a34f6b410fbdf80824f9ed60351d91205c413585a57') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index 59e9b46b350..7b2367abb65 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -21,8 +21,8 @@ class RGgplot2(RPackage): version('3.2.0', sha256='31b6897fb65acb37913ff6e2bdc1b57f652360098ae3aa660abdcf54f84d73b3') version('3.1.1', sha256='bfde297f3b4732e7f560078f4ce131812a70877e6b5b1d41a772c394939e0c79') - version('2.2.1', '14c5a3507bc123c6e7e9ad3bef7cee5c') - version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') + version('2.2.1', sha256='5fbc89fec3160ad14ba90bd545b151c7a2e7baad021c0ab4b950ecd6043a8314') + version('2.1.0', sha256='f2c323ae855d6c089e3a52138aa7bc25b9fe1429b8df9eae89d28ce3c0dd3969') depends_on('r@3.1:', when='@:3.1.1', type=('build', 'run')) depends_on('r@3.2:', when='@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py index fcd2fc9e93b..16c4be4ffe3 100644 --- a/var/spack/repos/builtin/packages/r-ggpubr/package.py +++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py @@ -16,7 +16,7 @@ class RGgpubr(RPackage): version('0.2.2', sha256='1c93dc6d1f08680dd00a10b6842445700d1fccb11f18599fbdf51e70c6b6b364') version('0.2.1', sha256='611e650da9bd15d7157fdcdc4e926fee3b88df3aba87410fdb1c8a7294d98d28') version('0.2', sha256='06c3075d8c452840662f5d041c3d966494b87254a52a858c849b9e1e96647766') - version('0.1.2', '42a5749ae44121597ef511a7424429d1') + version('0.1.2', sha256='9b4749fe1a6e0e4c5201a587c57c1b4bed34253f95ab4fb365f7e892b86003fe') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py index aca5c2fee38..e694e6bb5d5 100644 --- a/var/spack/repos/builtin/packages/r-ggrepel/package.py +++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py @@ -15,7 +15,7 @@ class RGgrepel(RPackage): version('0.8.1', sha256='d5d03a77ab6d8c831934bc46e840cc4e3df487272ab591fa72767ad42bcb7283') version('0.8.0', sha256='6386606e716d326354a29fcb6cd09f9b3d3b5e7c5ba0d5f7ff35416b1a4177d4') - version('0.6.5', '7e2732cd4840efe2dc9e4bc689cf1ee5') + version('0.6.5', sha256='360ae9d199755f9e260fefbd3baba3448fad3f024f20bcd9942a862b8c41a752') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggridges/package.py b/var/spack/repos/builtin/packages/r-ggridges/package.py index c63fc86b41a..2451b2348e5 100644 --- a/var/spack/repos/builtin/packages/r-ggridges/package.py +++ b/var/spack/repos/builtin/packages/r-ggridges/package.py @@ -16,8 +16,8 @@ class RGgridges(RPackage): version('0.5.1', sha256='01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36') version('0.5.0', sha256='124bc84044e56728fa965682f8232fc868f2af7d3eb7276f6b0df53be8d2dbfe') - version('0.4.1', '21d53b3f7263beb17f629f0ebfb7b67a') - version('0.4.0', 'da94ed1ee856a7fa5fb87712c84ec4c9') + version('0.4.1', sha256='03d2013df6adf07c9741d4476df96865b878a88359763ac36b98aa86591cca4d') + version('0.4.0', sha256='c62153fb47f55468c873e6cf882b46754b6eedec423dacf3992ab23c474d521c') depends_on('r@3.2:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py index fa4fe4130f6..3ce84eae8b8 100644 --- a/var/spack/repos/builtin/packages/r-ggsci/package.py +++ b/var/spack/repos/builtin/packages/r-ggsci/package.py @@ -16,7 +16,7 @@ class RGgsci(RPackage): version('2.9', sha256='4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c') version('2.8', sha256='b4ce7adce7ef23edf777866086f98e29b2b45b58fed085bbd1ffe6ab52d74ae8') - version('2.4', '8e5dc2fcf84352cacbb91363e26c7175') + version('2.4', sha256='9682c18176fee8e808c68062ec918aaef630d4d833e7a0bd6ae6c63553b56f00') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index bf4b902e1d4..54bdea87b34 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -16,8 +16,8 @@ class RGgvis(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/ggvis" version('0.4.4', sha256='1332ea122b768688c8a407a483be80febc4576de0ec8929077738421b27cafaf') - version('0.4.3', '30297d464278a7974fb125bcc7d84e77') - version('0.4.2', '039f45e5c7f1e0652779163d7d99f922') + version('0.4.3', sha256='34d517783016aaa1c4bef8972f4c06df5cd9ca0568035b647e60a8369043ecdc') + version('0.4.2', sha256='2fcc2b6ca4fbdc69fe75a2c58c12cb43096ab418160c98367e5ac0fd19fc591d') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py index ca1d6127ca2..ce698fa368f 100644 --- a/var/spack/repos/builtin/packages/r-gistr/package.py +++ b/var/spack/repos/builtin/packages/r-gistr/package.py @@ -21,7 +21,7 @@ class RGistr(RPackage): version('0.4.2', sha256='43c00c7f565732125f45f6c067724771ba1b337d6dd3a6e301639fe16e11032e') version('0.4.0', sha256='51771a257379a17552d0c88ada72ca6263954bbe896997f8a66cde3bf0b83ce0') - version('0.3.6', '49d548cb3eca0e66711aece37757a2c0') + version('0.3.6', sha256='ab22523b79510ec03be336e1d4600ec8a3a65afe57c5843621a4cf8f966b52e5') depends_on('r-jsonlite@1.4:', type=('build', 'run')) depends_on('r-httr@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py index 0e6ce008710..073cc54d3eb 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -17,8 +17,8 @@ class RGit2r(RPackage): version('0.26.1', sha256='13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435') version('0.26.0', sha256='56671389c3a50591e1dae3be8c3b0112d06d291f897d7fe14db17aea175616cf') - version('0.18.0', 'fb5741eb490c3d6e23a751a72336f24d') - version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') + version('0.18.0', sha256='91b32e49afb859c0c4f6f77988343645e9499e5046ef08d945d4d8149b6eff2d') + version('0.15.0', sha256='682ab9e7f71b2ed13a9ef95840df3c6b429eeea070edeb4d21d725cf0b72ede6') depends_on('r@3.1:', type=('build', 'run')) depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py index 0e98d4ff0d2..a198ca9bee1 100644 --- a/var/spack/repos/builtin/packages/r-glmnet/package.py +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -19,8 +19,8 @@ class RGlmnet(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/glmnet" version('2.0-18', sha256='e8dce9d7b8105f9cc18ba981d420de64a53b09abee219660d3612915d554256b') - version('2.0-13', '1dd5636388df5c3a29207d0bf1253343') - version('2.0-5', '049b18caa29529614cd684db3beaec2a') + version('2.0-13', sha256='f3288dcaddb2f7014d42b755bede6563f73c17bc87f8292c2ef7776cb9b9b8fd') + version('2.0-5', sha256='2ca95352c8fbd93aa7800f3d972ee6c1a5fcfeabc6be8c10deee0cb457fd77b1') depends_on('r-matrix@1.0-6:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-globaloptions/package.py b/var/spack/repos/builtin/packages/r-globaloptions/package.py index 6831b436bf5..e1ef6172731 100644 --- a/var/spack/repos/builtin/packages/r-globaloptions/package.py +++ b/var/spack/repos/builtin/packages/r-globaloptions/package.py @@ -15,7 +15,7 @@ class RGlobaloptions(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/GlobalOptions" version('0.1.0', sha256='567a0a51f6b7b14127302f00e6e4944befd4964c069f96a9e61256e8c3c79ef2') - version('0.0.12', '6c268b3b27874918ba62eb0f6aa0a3e5') + version('0.0.12', sha256='c09da3f9b1646d0f815056cdbeb5fff7dda29f7dd8742d245f5f6dc7066077a9') depends_on('r@2.10:', when='@:0.0.12', type=('build', 'run')) depends_on('r@3.3.0:', when='@0.0.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py index c4886be7a44..3e547feeb2e 100644 --- a/var/spack/repos/builtin/packages/r-glue/package.py +++ b/var/spack/repos/builtin/packages/r-glue/package.py @@ -19,6 +19,6 @@ class RGlue(RPackage): version('1.3.1', sha256='4fc1f2899d71a634e1f0adb7942772feb5ac73223891abe30ea9bd91d3633ea8') version('1.3.0', sha256='789e5a44c3635c3d3db26666e635e88adcf61cd02b75465125d95d7a12291cee') - version('1.2.0', '77d06b6d86abc882fa1c0599e457c5e2') + version('1.2.0', sha256='19275b34ee6a1bcad05360b7eb996cebaa1402f189a5dfb084e695d423f2296e') depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py index 6eee5281566..2655261ef26 100644 --- a/var/spack/repos/builtin/packages/r-gmodels/package.py +++ b/var/spack/repos/builtin/packages/r-gmodels/package.py @@ -14,7 +14,7 @@ class RGmodels(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/gmodels" version('2.18.1', sha256='626140a34eb8c53dd0a06511a76c71bc61c48777fa76fcc5e6934c9c276a1369') - version('2.16.2', 'f13e5feb2a8b9f0cd47fdf25ddc74228') + version('2.16.2', sha256='ab018894bdb376c5bd6bc4fbc4fe6e86590f4106795a586ef196fbb6699ec47d') depends_on('r@1.9.0:', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py index 0070a61fdf3..9df781f8b51 100644 --- a/var/spack/repos/builtin/packages/r-gmp/package.py +++ b/var/spack/repos/builtin/packages/r-gmp/package.py @@ -17,7 +17,7 @@ class RGmp(RPackage): version('0.5-13.5', sha256='f681ab2ff3d1e379ba8ac44a8abddd08d08170723e885abc0b469b6fa8fe5510') version('0.5-13.4', sha256='f05605b40fc39fc589e3a4d2f526a591a649faa45eef7f95c096e1bff8775196') - version('0.5-13.1', '4a45d45e53bf7140720bd44f10b075ed') + version('0.5-13.1', sha256='2f805374a26742cd43f6b2054130d8670eda1940070aabb9971e9e48226d0976') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('gmp@4.2.3:') diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py index 32d1a92ccc6..4f0fc1057e2 100644 --- a/var/spack/repos/builtin/packages/r-go-db/package.py +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -13,5 +13,5 @@ class RGoDb(RPackage): homepage = "https://www.bioconductor.org/packages/GO.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" - version('3.4.1', 'e16ee8921d8adc1ed3cbac2a3e35e386') + version('3.4.1', sha256='2fc2048e9d26edb98e35e4adc4d18c6df54f44836b5cc4a482d36ed99e058cc1') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py index 5ac11e6a7aa..5f961635672 100644 --- a/var/spack/repos/builtin/packages/r-googlevis/package.py +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -19,7 +19,7 @@ class RGooglevis(RPackage): version('0.6.4', sha256='7dcaf0e9d5e5598c17e8bd474141708de37eeb2578b09788431b9d871edb7eb8') version('0.6.3', sha256='17d104c5d4e6ab7b984df229cd51be19681e4726077afec7c61a33f6e4c0b6ef') - version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468') + version('0.6.0', sha256='862708097fbb5d4e83193777f40979d7848f9841d94d48ee8a74106266acc440') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gplots/package.py b/var/spack/repos/builtin/packages/r-gplots/package.py index 3ba000a5ddd..02b9b74b927 100644 --- a/var/spack/repos/builtin/packages/r-gplots/package.py +++ b/var/spack/repos/builtin/packages/r-gplots/package.py @@ -16,7 +16,7 @@ class RGplots(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/gplots" version('3.0.1.1', sha256='7db103f903a25d174cddcdfc7b946039b61e236c95084b90ad17f1a41da3770c') - version('3.0.1', '6116822401d55add044beb120ca93d14') + version('3.0.1', sha256='343df84327ac3d03494992e79ee3afc78ba3bdc08af9a305ee3fb0a38745cb0a') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py index 38d7b684a22..972b2e782a0 100644 --- a/var/spack/repos/builtin/packages/r-gridbase/package.py +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -13,6 +13,6 @@ class RGridbase(RPackage): url = "https://cloud.r-project.org/src/contrib/gridBase_0.4-7.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/gridBase" - version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f') + version('0.4-7', sha256='be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26') depends_on('r@2.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index 3f26f2ef564..c37978e0b18 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -14,7 +14,7 @@ class RGridextra(RPackage): url = "https://cloud.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/gridExtras" - version('2.3', '01e0ea88610756a0fd3b260e83c9bd43') - version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2') + version('2.3', sha256='81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b') + version('2.2.1', sha256='44fe455a5bcdf48a4ece7a542f83e7749cf251dc1df6ae7634470240398c6818') depends_on('r-gtable', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gss/package.py b/var/spack/repos/builtin/packages/r-gss/package.py index 0c652099fc8..02db31e5996 100644 --- a/var/spack/repos/builtin/packages/r-gss/package.py +++ b/var/spack/repos/builtin/packages/r-gss/package.py @@ -15,6 +15,6 @@ class RGss(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/gss" version('2.1-10', sha256='26c47ecae6a9b7854a1b531c09f869cf8b813462bd8093e3618e1091ace61ee2') - version('2.1-7', '4a6bd96339d22b40c932895b64504fb2') + version('2.1-7', sha256='0405bb5e4c4d60b466335e5da07be4f9570045a24aed09e7bc0640e1a00f3adb') depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gsubfn/package.py b/var/spack/repos/builtin/packages/r-gsubfn/package.py index b5c9d95eff8..a12f2bc48d6 100644 --- a/var/spack/repos/builtin/packages/r-gsubfn/package.py +++ b/var/spack/repos/builtin/packages/r-gsubfn/package.py @@ -26,6 +26,6 @@ class RGsubfn(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/gsubfn" version('0.7', sha256='89351df9e65722d2862f26a0a3985666de3c86e8400808ced8a6eb6e165a4602') - version('0.6-6', '94195ff3502706c736d9c593c07252bc') + version('0.6-6', sha256='bbc5d29bb48e836407f81880aeb368544a54a5513dacb3411c9838180723dda4') depends_on('r-proto', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py index 6df80edc585..faff7a9e07b 100644 --- a/var/spack/repos/builtin/packages/r-gtable/package.py +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -14,6 +14,6 @@ class RGtable(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/gtable" version('0.3.0', sha256='fd386cc4610b1cc7627dac34dba8367f7efe114b968503027fb2e1265c67d6d3') - version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab') + version('0.2.0', sha256='801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f') depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py index 752dd44437f..3f795ad1a20 100644 --- a/var/spack/repos/builtin/packages/r-gtools/package.py +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -45,4 +45,4 @@ class RGtools(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/gtools" version('3.8.1', sha256='051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38') - version('3.5.0', '45f8800c0336d35046641fbacc56bdbb') + version('3.5.0', sha256='86b6a51a92ddb3c78095e0c5dc20414c67f6e28f915bf0ee11406adad3e476f6') diff --git a/var/spack/repos/builtin/packages/r-haven/package.py b/var/spack/repos/builtin/packages/r-haven/package.py index 1ddb4e0bff1..64b626cbafb 100644 --- a/var/spack/repos/builtin/packages/r-haven/package.py +++ b/var/spack/repos/builtin/packages/r-haven/package.py @@ -16,7 +16,7 @@ class RHaven(RPackage): version('2.1.1', sha256='90bcb4e7f24960e7aa3e15c06b95cd897f08de149cec43fd8ba110b14526068a') version('2.1.0', sha256='c0a1cf1b039549fb3ad833f9644ed3f142790236ad755d2ee7bd3d8109e3ae74') - version('1.1.0', '8edd4b7683f8c36b5bb68582ac1b8733') + version('1.1.0', sha256='089fb4d0955f320abc48d0a3031799f96f3a20b82492474743903fdf12001d19') depends_on('r@3.1:', when='@:2.1.0', type=('build', 'run')) depends_on('r@3.2:', when='@2.1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index adfec4c76bc..a887c0c6e74 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -17,7 +17,7 @@ class RHexbin(RPackage): version('1.27.3', sha256='7ea422a76542c2fc2840df601af1b7803aa96df4fee6d51dec456ac36940c191') version('1.27.2', sha256='46d47b1efef75d6f126af686a4dd614228b60418b9a5bde9e9e5d11200a0ee52') - version('1.27.1', '7590ed158f8a57a71901bf6ca26f81be') + version('1.27.1', sha256='075935a3ae2d90e44aca6ebbd368dc6f7e59d322e36e0e0932dedbf01330ad08') depends_on('r@2.0.1:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py index fb600dc5677..d4445d48ceb 100644 --- a/var/spack/repos/builtin/packages/r-highr/package.py +++ b/var/spack/repos/builtin/packages/r-highr/package.py @@ -18,7 +18,7 @@ class RHighr(RPackage): version('0.8', sha256='4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657') version('0.7', sha256='cabba5b6f2ea82024a49c5ced5f1aa476f864bc52bc129038e319e4e26b6f3b7') - version('0.6', 'bf47388c5f57dc61962362fb7e1d8b16') + version('0.6', sha256='43e152b2dea596df6e14c44398c74fcd438ece15eaae5bdb84aef8d61b213b59') depends_on('r@3.0.2:', when='@:0.7', type=('build', 'run')) depends_on('r@3.2.3:', when='@0.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py index 1ef0b1aa917..8d041a28c01 100644 --- a/var/spack/repos/builtin/packages/r-hmisc/package.py +++ b/var/spack/repos/builtin/packages/r-hmisc/package.py @@ -19,8 +19,8 @@ class RHmisc(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/Hmisc" version('4.2-0', sha256='9e9614673288dd00295f250fa0bf96fc9e9fed692c69bf97691081c1a01411d9') - version('4.1-1', 'd255611f2b108d3cc0212b8a98fef6e3') - version('4.0-3', '7091924db1e473419d8116c3335f82da') + version('4.1-1', sha256='991db21cdf73ffbf5b0239a4876b2e76fd243ea33528afd88dc968792f281498') + version('4.0-3', md5='7091924db1e473419d8116c3335f82da') depends_on('r-lattice', type=('build', 'run')) depends_on('r-survival@2.40-1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hms/package.py b/var/spack/repos/builtin/packages/r-hms/package.py index b39d7f4ee5d..bceece54ba7 100644 --- a/var/spack/repos/builtin/packages/r-hms/package.py +++ b/var/spack/repos/builtin/packages/r-hms/package.py @@ -15,7 +15,7 @@ class RHms(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/hms" version('0.5.0', sha256='a87872665c3bf3901f597d78c152e7805f7129e4dbe27397051de4cf1a76561b') - version('0.3', '92c4a0cf0c402a35145b5bb57212873e') + version('0.3', sha256='9368259cbc1094ce0e4cf61544875ec30088ef690d6667e6b0b564218ab3ff88') depends_on('r-pkgconfig', when='@0.5.0:', type=('build', 'run')) depends_on('r-rlang', when='@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-htmltable/package.py b/var/spack/repos/builtin/packages/r-htmltable/package.py index 8693a8d8cc2..64a0b138ce9 100644 --- a/var/spack/repos/builtin/packages/r-htmltable/package.py +++ b/var/spack/repos/builtin/packages/r-htmltable/package.py @@ -20,8 +20,8 @@ class RHtmltable(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/htmlTable" version('1.13.1', sha256='689f32b65da6a57ad500e8d9ef3309d346401dca277c6b264a46c8d7c75884d0') - version('1.11.2', '473e6d486e7714f8dd7f16a31480c896') - version('1.9', '08c62c19e1ffe570e7d8fa57db5094b9') + version('1.11.2', sha256='64a273b1cdf07a7c57b9031315ca665f95d78e70b4320d020f64a139278877d1') + version('1.9', sha256='5b487a7f33af77db7d987bf61f3ef2ba18bb629fe7b9802409f8b3485c603132') depends_on('r-stringr', type=('build', 'run')) depends_on('r-knitr@1.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 866f20fe56d..914e7a5bb65 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -13,8 +13,8 @@ class RHtmltools(RPackage): url = "https://cloud.r-project.org/src/contrib/htmltools_0.3.6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/htmltools" - version('0.3.6', '336419c2143f958862e01ef1bbc9c253') - version('0.3.5', '5f001aff4a39e329f7342dcec5139724') + version('0.3.6', sha256='44affb82f9c2fd76c9e2b58f9229adb003217932b68c3fdbf1327c8d74c868a2') + version('0.3.5', sha256='29fb7e075744bbffdff8ba4fce3860076de66f39a59a100ee4cfb4fc00722b49') depends_on('r@2.14.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py index aed9faa579b..f5cbf91b93e 100644 --- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -16,9 +16,9 @@ class RHtmlwidgets(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/htmlwidgets" version('1.3', sha256='f1e4ffabc29e6cfe857f627da095be3cfcbe0e1f02ae75e572f10b4a026c5a12') - version('0.9', 'b42730691eca8fc9a28903c272d11605') - version('0.8', '06b0404a00e25736946607a36ee5351d') - version('0.6', '7fa522d2eda97593978021bda9670c0e') + version('0.9', sha256='1154b541ccd868e41d3cf0d7f188f7275ec99f61fe2c7de21c8a05edb19b985e') + version('0.8', sha256='9232b78727c1ecd006cd8e607ef76417d795f011b0e4a7535e6d673228bfc3b5') + version('0.6', sha256='9c227f93ada71526d6e195e39a8efef41255af5567e39db3a6417ea9fed192ea') depends_on('r-htmltools@0.3:', type=('build', 'run')) depends_on('r-jsonlite@0.9.16:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index 9bc6326d95e..fa6721c3193 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -20,8 +20,8 @@ class RHttpuv(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/httpuv" version('1.5.1', sha256='b5bb6b3b2f1a6d792568a70f3f357d6b3a35a5e26dd0c668c61a31f2ae8f5710') - version('1.3.5', '48d894ff0067148f41a651634fbb2012') - version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') + version('1.3.5', sha256='4336b993afccca2a194aca577b1975b89a35ac863423b18a11cdbb3f8470e4e9') + version('1.3.3', sha256='bb37452ddc4d9381bee84cdf524582859af6a988e291debb71c8a2e120d02b2a') depends_on('r@2.15.1:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index 7f79836f9aa..fb50987c9d1 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -17,9 +17,9 @@ class RHttr(RPackage): version('1.4.1', sha256='675c7e07bbe82c48284ee1ab929bb14a6e653abae2860d854dc41a3c028de156') version('1.4.0', sha256='d633f1425da514f65f3b8c034ae0a8b6911995009840c6bb9657ceedb99ddb48') - version('1.3.1', '5acfb6b2a6f2f26cd6dfad0458fe3351') - version('1.2.1', 'c469948dedac9ab3926f23cf484b33d9') - version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') + version('1.3.1', sha256='22134d7426b2eba37f0cc34b99285499b8bac9fe75a7bc3222fbad179bf8f258') + version('1.2.1', sha256='e7b90b90ee52c826e152efcfadf98e078fa75b65a6baaeb8fd25eeed2195730e') + version('1.1.0', sha256='d7c0cdc11b2ded3132544580f52ebe5dad2a426cde1a5029f2cc693b2f195823') depends_on('r@3.0.0:', when='@:1.3.1', type=('build', 'run')) depends_on('r@3.1:', when='@1.4.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hwriter/package.py b/var/spack/repos/builtin/packages/r-hwriter/package.py index de980bb2d58..6c6cdf71c8e 100644 --- a/var/spack/repos/builtin/packages/r-hwriter/package.py +++ b/var/spack/repos/builtin/packages/r-hwriter/package.py @@ -14,6 +14,6 @@ class RHwriter(RPackage): url = "https://cloud.r-project.org/src/contrib/hwriter_1.3.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/hwriter" - version('1.3.2', '9eef49df2eb68bbf3a16b5860d933517') + version('1.3.2', sha256='6b3531d2e7a239be9d6e3a1aa3256b2745eb68aa0bdffd2076d36552d0d7322b') depends_on('r@2.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ica/package.py b/var/spack/repos/builtin/packages/r-ica/package.py index aea4b44ead5..d5bd431c772 100644 --- a/var/spack/repos/builtin/packages/r-ica/package.py +++ b/var/spack/repos/builtin/packages/r-ica/package.py @@ -16,5 +16,5 @@ class RIca(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/ica" version('1.0-2', sha256='e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179') - version('1.0-1', '15c8d5afeec2804beec55dd14abc585d') - version('1.0-0', '3ade2b3b00eb39c348d802f24d2afd1d') + version('1.0-1', sha256='98559a8bb12dd134a40ce8fd133803e2a38456b45d0e2a507d66022a8e2274ae') + version('1.0-0', sha256='9ff4ec7f4525bdce9d7859b22a1a170a1f6f9f7fb9f3d0b537dcaec77cd83d01') diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py index 2dbc16b1738..8fbb28fad63 100644 --- a/var/spack/repos/builtin/packages/r-igraph/package.py +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -17,8 +17,8 @@ class RIgraph(RPackage): version('1.2.4.1', sha256='891acc763b5a4a4a245358a95dee69280f4013c342f14dd6a438e7bb2bf2e480') version('1.2.4', sha256='1048eb26ab6b592815bc269c1d91e974c86c9ab827ccb80ae0a40042019592cb') - version('1.1.2', 'ca1617aea272852d2856c4661ad1c7d8') - version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065') + version('1.1.2', sha256='89b16b41bc77949ea208419e52a18b78b5d418c7fedc52cd47d06a51a6e746ec') + version('1.0.1', sha256='dc64ed09b8b5f8d66ed4936cde3491974d6bc5178dd259b6eab7ef3936aa5602') depends_on('r-matrix', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py index 51447618501..9bbcd98ae9b 100644 --- a/var/spack/repos/builtin/packages/r-influencer/package.py +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -20,7 +20,7 @@ class RInfluencer(RPackage): url = "https://cloud.r-project.org/src/contrib/influenceR_0.1.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/influenceR" - version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5') + version('0.1.0', sha256='4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-igraph@1.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py index 6083319dbd7..4902ad2f4ae 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -16,6 +16,6 @@ class RInline(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/inline" version('0.3.15', sha256='ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68') - version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca') + version('0.3.14', sha256='fd34d6bf965148d26d983a022a0ff7bc1a5831f6ca066deee3f6139894dfc931') depends_on('r@2.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ipred/package.py b/var/spack/repos/builtin/packages/r-ipred/package.py index 43d91530921..690b6b089d3 100644 --- a/var/spack/repos/builtin/packages/r-ipred/package.py +++ b/var/spack/repos/builtin/packages/r-ipred/package.py @@ -17,7 +17,7 @@ class RIpred(RPackage): version('0.9-9', sha256='0da87a70730d5a60b97e46b2421088765e7d6a7cc2695757eba0f9d31d86416f') version('0.9-8', sha256='9c1d11c3cb0d72be7870e70a216e589e403bbfee38c796fe75cd0611d878ac07') - version('0.9-5', 'ce8768547a7aa9554ad3650b18ea3cbd') + version('0.9-5', sha256='3a466417808e17c4c6cd0f2b577407355d9da79a341558b42a8b76e24b6f6ba4') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rpart@3.1-8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py index c246abbae03..a78590697a1 100644 --- a/var/spack/repos/builtin/packages/r-irdisplay/package.py +++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py @@ -17,7 +17,7 @@ class RIrdisplay(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/IRdisplay" version('0.7.0', sha256='91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089') - version('0.4.4', '5be672fb82185b90f23bd99ac1e1cdb6') + version('0.4.4', sha256='e83a0bc52800618bf9a3ac5ef3d432512e00f392b7216fd515fca319377584a6') depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-repr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py index 46a5d712dc5..963c5720732 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -17,7 +17,7 @@ class RIrlba(RPackage): version('2.3.3', sha256='6ee233697bcd579813bd0af5e1f4e6dd1eea971e8919c748408130d970fef5c0') version('2.3.2', sha256='3fdf2d8fefa6ab14cd0992740de7958f9f501c71aca93229f5eb03c54558fc38') - version('2.1.2', '290940abf6662ed10c0c5a8db1bc6e88') - version('2.0.0', '557674cf8b68fea5b9f231058c324d26') + version('2.1.2', sha256='5183e8dd7943df11c0f44460566adf06c03d5320f142699298f516d423b06ce1') + version('2.0.0', sha256='15f8d6c1107d6bb872411efd61e6077d9d7ac826f4da2d378999889a7b1ebabe') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-iso/package.py b/var/spack/repos/builtin/packages/r-iso/package.py index 9640af6cbf2..0ace73b5bd7 100644 --- a/var/spack/repos/builtin/packages/r-iso/package.py +++ b/var/spack/repos/builtin/packages/r-iso/package.py @@ -15,6 +15,6 @@ class RIso(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/Iso" version('0.0-18', sha256='2d7e8c4452653364ee086d95cea620c50378e30acfcff129b7261e1756a99504') - version('0.0-17', 'bf99821efb6a44fa75fdbf5e5c4c91e4') + version('0.0-17', sha256='c007d6eaf6335a15c1912b0804276ff39abce27b7a61539a91b8fda653629252') depends_on('r@1.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py index da880c792fc..ba993dbb78c 100644 --- a/var/spack/repos/builtin/packages/r-iterators/package.py +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -16,6 +16,6 @@ class RIterators(RPackage): version('1.0.12', sha256='96bf31d60ebd23aefae105d9b7790715e63327eec0deb2ddfb3d543994ea9f4b') version('1.0.9', sha256='de001e063805fdd124953b571ccb0ed2838c55e40cca2e9d283d8a90b0645e9b') - version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee') + version('1.0.8', sha256='ae4ea23385776eb0c06c992a3da6b0256a6c84558c1061034c5a1fbdd43d05b8') depends_on('r@2.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-janitor/package.py b/var/spack/repos/builtin/packages/r-janitor/package.py index a754eb61ee5..88e94b86ebc 100644 --- a/var/spack/repos/builtin/packages/r-janitor/package.py +++ b/var/spack/repos/builtin/packages/r-janitor/package.py @@ -25,7 +25,7 @@ class RJanitor(RPackage): version('1.2.0', sha256='5e15a2292c65c5ddd6160289dec2604b05a813651a2be0d7854ace4548a32b8c') version('1.1.1', sha256='404b41f56e571fab4c95ef62e79cb4f3bb34d5bb6e4ea737e748ff269536176b') - version('0.3.0', '76036c54693b91aef19d468107ae066a') + version('0.3.0', sha256='5e4d8ef895ed9c7b8fa91aeb93e25c009366b4c5faaf3d02265f64b33d4a45f4') depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-dplyr@0.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py index 8fcbd881b25..181d68285b4 100644 --- a/var/spack/repos/builtin/packages/r-jomo/package.py +++ b/var/spack/repos/builtin/packages/r-jomo/package.py @@ -21,7 +21,7 @@ class RJomo(RPackage): version('2.6-9', sha256='b90f47071e62b8863b00b1ae710a56ae6efbfe2baeb9963f8a91a10d6183cc9b') version('2.6-7', sha256='6e83dab51103511038a3e9a3c762e00cc45ae7080c0a0f64e37bcea8c488db53') - version('2.6-2', 'eff4a6c1a971708959d65b3224c98a25') + version('2.6-2', sha256='67496d6d69ddbe9a796789fd8b3ac32cada09a81cf5a8e7b925a21e085e2d87f') depends_on('r-lme4', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py index 53b986d6d64..4191b0dc1ee 100644 --- a/var/spack/repos/builtin/packages/r-jpeg/package.py +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -15,7 +15,7 @@ class RJpeg(RPackage): url = "https://cloud.r-project.org/src/contrib/jpeg_0.1-8.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/jpeg" - version('0.1-8', '696007451d14395b1ed1d0e9af667a57') + version('0.1-8', sha256='d032befeb3a414cefdbf70ba29a6c01541c54387cc0a1a98a4022d86cbe60a16') depends_on('r@2.9.0:', type=('build', 'run')) depends_on('jpeg') diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 6cbdf132a8b..4b3de1ddf80 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -23,7 +23,7 @@ class RJsonlite(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/jsonlite" version('1.6', sha256='88c5b425229966b7409145a6cabc72db9ed04f8c37ee95901af0146bb285db53') - version('1.5', '2a81c261a702fccbbd5d2b32df108f76') - version('1.2', '80cd2678ae77254be470f5931db71c51') - version('1.0', 'c8524e086de22ab39b8ac8000220cc87') - version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') + version('1.5', sha256='6490371082a387cb1834048ad8cdecacb8b6b6643751b50298c741490c798e02') + version('1.2', sha256='cb6b4660468d2db84ed09c7b8fefd169fcfc13e1e6b4e7ce64dce2713f34264d') + version('1.0', sha256='d756dd6367e3fc515c855bb0b34a3a81955f8aeb494db029a893f3cdfcff962d') + version('0.9.21', sha256='079349342ea6eb92bd5fa8f6a7c08d9e3652c3d41010b64afbc3297671eb3791') diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py index a219051f1d6..474300e0d60 100644 --- a/var/spack/repos/builtin/packages/r-kegg-db/package.py +++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py @@ -12,5 +12,5 @@ class RKeggDb(RPackage): homepage = "https://www.bioconductor.org/packages/KEGG.db/" url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" - version('3.2.3', '023ac22f57063627c2e62d1ae5e011b0') + version('3.2.3', sha256='02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py index 3eedaac2795..e1181faf39e 100644 --- a/var/spack/repos/builtin/packages/r-kernlab/package.py +++ b/var/spack/repos/builtin/packages/r-kernlab/package.py @@ -18,6 +18,6 @@ class RKernlab(RPackage): version('0.9-27', sha256='f6add50ed4097f04d09411491625f8d46eafc4f003b1c1cff78a6fff8cc31dd4') version('0.9-26', sha256='954940478c6fcf60433e50e43cf10d70bcb0a809848ca8b9d683bf371cd56077') - version('0.9-25', '1182a2a336a79fd2cf70b4bc5a35353f') + version('0.9-25', sha256='b9de072754bb03c02c4d6a5ca20f2290fd090de328b55ab334ac0b397ac2ca62') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py index d39ea1e4ff7..393d71f81af 100644 --- a/var/spack/repos/builtin/packages/r-kernsmooth/package.py +++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py @@ -13,6 +13,6 @@ class RKernsmooth(RPackage): url = "https://cloud.r-project.org/src/contrib/KernSmooth_2.23-15.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/KernSmooth" - version('2.23-15', '746cdf26dec72004cf19978e87dcc982') + version('2.23-15', sha256='8b72d23ed121a54af188b2cda4441e3ce2646359309885f6455b82c0275210f6') depends_on('r@2.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py index c63bbf2d6ad..1d12e18406e 100644 --- a/var/spack/repos/builtin/packages/r-kknn/package.py +++ b/var/spack/repos/builtin/packages/r-kknn/package.py @@ -14,7 +14,7 @@ class RKknn(RPackage): url = "https://cloud.r-project.org/src/contrib/kknn_1.3.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/kknn" - version('1.3.1', '372cd84f618cd5005f8c4c5721755117') + version('1.3.1', sha256='22840e70ec2afa40371e274b583634c8f6d27149a87253ee411747d5db78f3db') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-igraph@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index 90f3cbb334b..812478b0ccf 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -17,9 +17,9 @@ class RKnitr(RPackage): version('1.24', sha256='e80c2043b445a7e576b62ae8510cce89322660fe388881d799a706d35cd27b89') version('1.23', sha256='063bfb3300fc9f3e7d223c346e19b93beced0e6784470b9bef2524868a206a99') - version('1.17', '4407ccf8f2a51629800d6d5243cf3e70') - version('1.14', 'ef0fbeaa9372f99ffbc57212a7781511') - version('0.6', 'c67d6db84cd55594a9e870c90651a3db') + version('1.17', sha256='9484a2b2c7b0c2aae24ab7f4eec6db48affbceb0e42bd3d69e34d953fe92f401') + version('1.14', sha256='ba6d301482d020a911390d5eff181e1771f0e02ac3f3d9853a9724b1ec041aec') + version('0.6', md5='c67d6db84cd55594a9e870c90651a3db') depends_on('r@2.14.1:', when='@:1.9', type=('build', 'run')) depends_on('r@3.0.2:', when='@1.10:1.14', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py index 49b481f61c7..27b50786da7 100644 --- a/var/spack/repos/builtin/packages/r-labeling/package.py +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -13,4 +13,4 @@ class RLabeling(RPackage): url = "https://cloud.r-project.org/src/contrib/labeling_0.3.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/labeling" - version('0.3', 'ccd7082ec0b211aba8a89d85176bb534') + version('0.3', sha256='0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f') diff --git a/var/spack/repos/builtin/packages/r-lambda-r/package.py b/var/spack/repos/builtin/packages/r-lambda-r/package.py index 459ac5a3416..f2ff206836f 100644 --- a/var/spack/repos/builtin/packages/r-lambda-r/package.py +++ b/var/spack/repos/builtin/packages/r-lambda-r/package.py @@ -16,7 +16,7 @@ class RLambdaR(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/lambda.r" version('1.2.3', sha256='0cd8e37ba1a0960888016a85d492da51a57df54bd65ff920b08c79a3bfbe8631') - version('1.2', 'bda49898b85ad5902880a31f43b432e2') + version('1.2', sha256='7dc4188ce1d4a6b026a1b128719ff60234ae1e3ffa583941bbcd8473ad18146f') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-formatr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py index 60bfe0ba76a..7128678cc65 100644 --- a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py +++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py @@ -17,6 +17,6 @@ class RLaplacesdemon(RPackage): version('16.1.1', sha256='779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77') version('16.1.0', sha256='41d99261e8fc33c977b43ecf66ebed8ef1c84d9bd46b271609e9aadddc2ca8bb') - version('16.0.1', '1e4dab2dd0e27251734d68b0bfdbe911') + version('16.0.1', sha256='be21eff3c821b4fe0b4724f03c9221c2456257f93d91f864de11e95dc35e8679') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py index e2595d3c3ac..5fd720451b3 100644 --- a/var/spack/repos/builtin/packages/r-lars/package.py +++ b/var/spack/repos/builtin/packages/r-lars/package.py @@ -14,8 +14,8 @@ class RLars(RPackage): url = "https://cloud.r-project.org/src/contrib/lars_1.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/lars" - version('1.2', '2571bae325f6cba1ad0202ea61695b8c') - version('1.1', 'e94f6902aade09b13ec25ba2381384e5') - version('0.9-8', 'e6f9fffab2d83898f6d3d811f04d177f') + version('1.2', sha256='64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e') + version('1.1', sha256='a8e4a0efb9ca6760dec1cadf395d9a805508455a2c3ced18cc53d9b8fa70cdc0') + version('0.9-8', sha256='8c64cb31073ea0785346bb716485da8db2fae14153a52e5a8d151bc9cb4906e5') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index c47360d7017..c8f3ecae76a 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -17,7 +17,7 @@ class RLattice(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/lattice" version('0.20-38', sha256='fdeb5e3e50dbbd9d3c5e2fa3eef865132b3eef30fbe53a10c24c7b7dfe5c0a2d') - version('0.20-35', '07f1814623b3da6278ca61554ff7bfe6') - version('0.20-34', 'c2a648b22d4206ae7526fb70b8e90fed') + version('0.20-35', sha256='0829ab0f4dec55aac6a73bc3411af68441ddb1b5b078d680a7c2643abeaa965d') + version('0.20-34', sha256='4a1a1cafa9c6660fb9a433b3a51898b8ec8e83abf143c80f99e3e4cf92812518') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-latticeextra/package.py b/var/spack/repos/builtin/packages/r-latticeextra/package.py index 7cf8b7da490..7c64d00fc6a 100644 --- a/var/spack/repos/builtin/packages/r-latticeextra/package.py +++ b/var/spack/repos/builtin/packages/r-latticeextra/package.py @@ -16,7 +16,7 @@ class RLatticeextra(RPackage): url = "https://cloud.r-project.org/src/contrib/latticeExtra_0.6-28.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/latticeExtra" - version('0.6-28', '771938f25d0983763369b48a1153b26c') + version('0.6-28', sha256='780695323dfadac108fb27000011c734e2927b1e0f069f247d65d27994c67ec2') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py index b9daaf2e3a5..61dbf84081a 100644 --- a/var/spack/repos/builtin/packages/r-lava/package.py +++ b/var/spack/repos/builtin/packages/r-lava/package.py @@ -15,7 +15,7 @@ class RLava(RPackage): version('1.6.6', sha256='7abc84dd99cce450a45ac4f232812cde3a322e432da3472f43b057fb5c59ca59') version('1.6.4', sha256='41c6eeb96eaef9e1bfb04b31f7203e250a5ea7e7860be4d95f7f96f2a8644718') - version('1.4.7', '28039248a7039ba9281d172e4dbf9543') + version('1.4.7', sha256='d5cbd4835a94855478efb93051eece965db116ead203f4dd4e09d9a12d52f4bf') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-numderiv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py index 5650181c562..3ce18f8cd1c 100644 --- a/var/spack/repos/builtin/packages/r-lazyeval/package.py +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -17,6 +17,6 @@ class RLazyeval(RPackage): version('0.2.2', sha256='d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4') version('0.2.1', sha256='83b3a43e94c40fe7977e43eb607be0a3cd64c02800eae4f2774e7866d1e93f61') - version('0.2.0', 'df1daac908dcf02ae7e12f4335b1b13b') + version('0.2.0', sha256='13738f55b2044184fe91f53d17516a445dfb508227527921218cda6f01f98dcb') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py index 3a436e009ab..e6b8e3f212d 100644 --- a/var/spack/repos/builtin/packages/r-leaflet/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -17,7 +17,7 @@ class RLeaflet(RPackage): version('2.0.2', sha256='fa448d20940e01e953e0706fc5064b0fa347e69fa967792599eb03c52b2e3114') version('2.0.1', sha256='9876d5adf3235ea5683db79ec2435d3997c626774e8c4ec4ef14022e24dfcf06') - version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df') + version('1.0.1', sha256='f25a8e10c9616ccb5504bb874c533bc44fb7e438e073d4fe4484dee0951a9bc3') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py index b02ab2cfe4c..e4708ed2346 100644 --- a/var/spack/repos/builtin/packages/r-leaps/package.py +++ b/var/spack/repos/builtin/packages/r-leaps/package.py @@ -13,4 +13,4 @@ class RLeaps(RPackage): url = "https://cloud.r-project.org/src/contrib/leaps_3.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/leaps" - version('3.0', '30823138890680e0493d1491c8f43edc') + version('3.0', sha256='55a879cdad5a4c9bc3b5697dd4d364b3a094a49d8facb6692f5ce6af82adf285') diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py index 71644b853b3..21f6554a18a 100644 --- a/var/spack/repos/builtin/packages/r-learnbayes/package.py +++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py @@ -20,4 +20,4 @@ class RLearnbayes(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/LearnBayes" version('2.15.1', sha256='9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532') - version('2.15', '213713664707bc79fd6d3a109555ef76') + version('2.15', sha256='45c91114b4aaa0314feeb4311dbe78f5b75a3b76bb2d1ca0f8adb2e0f1cbe233') diff --git a/var/spack/repos/builtin/packages/r-lhs/package.py b/var/spack/repos/builtin/packages/r-lhs/package.py index da10bff6586..a4f295f5971 100644 --- a/var/spack/repos/builtin/packages/r-lhs/package.py +++ b/var/spack/repos/builtin/packages/r-lhs/package.py @@ -16,7 +16,7 @@ class RLhs(RPackage): version('1.0.1', sha256='a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53') version('1.0', sha256='38c53482b360bdea89ddcfadf6d45476c80b99aee8902f97c5e97975903e2745') - version('0.16', '088e593e5283414951e7e541a50ec2d1') + version('0.16', sha256='9cd199c3b5b2be1736d585ef0fd39a00e31fc015a053333a7a319668d0809425') depends_on('r@3.3.0:', when='@:0.16', type=('build', 'run')) depends_on('r@3.4.0:', when='@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index 64a021616cf..ac77229c84c 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -18,7 +18,7 @@ class RLme4(RPackage): version('1.1-21', sha256='7f5554b69ff8ce9bac21e8842131ea940fb7a7dfa2de03684f236d3e3114b20c') version('1.1-20', sha256='44f45f5cd20ec6a50bf96a939b1db44b1a180dbc871a5e3042baf7a107016b2c') - version('1.1-12', 'da8aaebb67477ecb5631851c46207804') + version('1.1-12', sha256='2976b567a4a2144814ff9db987b0aa55c16122c78ecb51b9e09b87fe66a1c048') depends_on('r@3.0.2:', when='@:1.1-15', type=('build', 'run')) depends_on('r@3.2.0:', when='@1.1-16:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py index ad59ed29c7e..98bad18240f 100644 --- a/var/spack/repos/builtin/packages/r-lmtest/package.py +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -17,7 +17,7 @@ class RLmtest(RPackage): version('0.9-37', sha256='ddc929f94bf055974832fa4a20fdd0c1eb3a84ee11f716c287936f2141d5ca0a') version('0.9-36', sha256='be9f168d6554e9cd2be0f9d8fc3244f055dce90d1fca00f05bcbd01daa4ed56b') - version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe') + version('0.9-34', sha256='86eead67ed6d6c6be3fbee97d5ce45e6ca06a981f974ce01a7754a9e33770d2e') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-locfit/package.py b/var/spack/repos/builtin/packages/r-locfit/package.py index ce7536500f3..2ed5f6e7365 100644 --- a/var/spack/repos/builtin/packages/r-locfit/package.py +++ b/var/spack/repos/builtin/packages/r-locfit/package.py @@ -13,7 +13,7 @@ class RLocfit(RPackage): url = "https://cloud.r-project.org/src/contrib/locfit_1.5-9.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/locfit" - version('1.5-9.1', '38af7791c9cda78e2804020e65ac7fb4') + version('1.5-9.1', sha256='f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51') depends_on('r@2.0.1:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-log4r/package.py b/var/spack/repos/builtin/packages/r-log4r/package.py index 82d73f3bf8a..d32c4a68367 100644 --- a/var/spack/repos/builtin/packages/r-log4r/package.py +++ b/var/spack/repos/builtin/packages/r-log4r/package.py @@ -15,4 +15,4 @@ class RLog4r(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/log4r" version('0.3.0', sha256='8e5d0221298410e48bee9d9a983a23e1834ce88592f9d931471bfdb05f37a691') - version('0.2', 'f3fcb7b1f48526c6543b2e00e278ff65') + version('0.2', sha256='321bee6babb92376b538624027a36e7d2a6c8edb360aa38ab0a6762dfea9081f') diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py index c118b4ebfc0..dc855bc1c17 100644 --- a/var/spack/repos/builtin/packages/r-lpsolve/package.py +++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py @@ -20,4 +20,4 @@ class RLpsolve(RPackage): version('5.6.13.2', sha256='75f0c0af5cbdc219ac29c792342ecd625903632ad86e581c408879958aa88539') version('5.6.13.1', sha256='6ad8dc430f72a4698fc4a615bb5ecb73690b3c4520e84d9094af51a528f720b8') - version('5.6.13', '8471654d9ae76e0f85ff3449433d4bc1') + version('5.6.13', sha256='d5d41c53212dead4fd8e6425a9d3c5767cdc5feb19d768a4704116d791cf498d') diff --git a/var/spack/repos/builtin/packages/r-lsei/package.py b/var/spack/repos/builtin/packages/r-lsei/package.py index e23f0e2033f..1c4545eeb5e 100644 --- a/var/spack/repos/builtin/packages/r-lsei/package.py +++ b/var/spack/repos/builtin/packages/r-lsei/package.py @@ -19,4 +19,4 @@ class RLsei(RPackage): url = "https://cloud.r-project.org/src/contrib/lsei_1.2-0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/lsei" - version('1.2-0', '18a9322d7a79ecb86b8788645c4b7e3c') + version('1.2-0', sha256='4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6') diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 675cdaf0987..72bc815f7e0 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -20,8 +20,8 @@ class RLubridate(RPackage): version('1.7.4', sha256='510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891') version('1.7.3', sha256='2cffbf54afce1d068e65241fb876a77b10ee907d5a19d2ffa84d5ba8a2c3f3df') - version('1.7.1', '17dcb4c6a95189941bbdcffecf61b83b') - version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') + version('1.7.1', sha256='898c3f482ab8f5e5b415eecd13d1238769c88faed19b63fcb074ffe5ff57fb5f') + version('1.5.6', sha256='9b1627ba3212e132ce2b9a29d7513e250cc682ab9b4069f6788a22e84bf8d2c4') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rcpp@0.12.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index c4a04edc8d8..475c1dcdd90 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -18,7 +18,7 @@ class RMagic(RPackage): version('1.5-9', sha256='fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a') version('1.5-8', sha256='7f8bc26e05003168e9d2dadf64eb9a34b51bc41beba482208874803dee7d6c20') - version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') + version('1.5-6', sha256='1b6c3f5bef0ddc28c4b68894051df5d9c0d4985d9e6ad81892369d0f7fe0298d') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-abind', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py index 5f9cda54b49..2356cef2fab 100644 --- a/var/spack/repos/builtin/packages/r-magrittr/package.py +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -17,4 +17,4 @@ class RMagrittr(RPackage): url = "https://cloud.r-project.org/src/contrib/magrittr_1.5.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/magrittr" - version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a') + version('1.5', sha256='05c45943ada9443134caa0ab24db4a962b629f00b755ccf039a2a2a7b2c92ae8') diff --git a/var/spack/repos/builtin/packages/r-maldiquant/package.py b/var/spack/repos/builtin/packages/r-maldiquant/package.py index 6e596d92b13..74fb09d720b 100644 --- a/var/spack/repos/builtin/packages/r-maldiquant/package.py +++ b/var/spack/repos/builtin/packages/r-maldiquant/package.py @@ -23,6 +23,6 @@ class RMaldiquant(RPackage): version('1.19.3', sha256='a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c') version('1.19.2', sha256='8c6efc4ae4f1af4770b079db29743049f2fd597bcdefeaeb16f623be43ddeb87') - version('1.16.4', '83200e7496d05c5a99292e45d2b11c67') + version('1.16.4', sha256='9b910dbd5dd1a739a17a7ee3f83d7e1ebad2fee89fd01a5b274415d2b6d3b0de') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py index a30907c0558..e9afb537b1e 100644 --- a/var/spack/repos/builtin/packages/r-mapproj/package.py +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -15,7 +15,7 @@ class RMapproj(RPackage): version('1.2.6', sha256='62a5aa97837ae95ef9f973d95fe45fe43dbbf482dfa922e9df60f3c510e7efe5') version('1.2-5', sha256='f3026a3a69a550c923b44c18b1ccc60d98e52670a438250d13f3c74cf2195f66') - version('1.2-4', '10e22bde1c790e1540672f15ddcaee71') + version('1.2-4', sha256='cf8a1535f57e7cca0a71b3a551e77ad3e7a78f61a94bb19effd3de19dbe7dceb') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-maps@2.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py index 4e98fbbff46..623d0e0ead7 100644 --- a/var/spack/repos/builtin/packages/r-maps/package.py +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -16,6 +16,6 @@ class RMaps(RPackage): version('3.3.0', sha256='199afe19a4edcef966ae79ef802f5dcc15a022f9c357fcb8cae8925fe8bd2216') version('3.2.0', sha256='437abeb4fa4ad4a36af6165d319634b89bfc6bf2b1827ca86c478d56d670e714') - version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764') + version('3.1.1', sha256='972260e5ce9519ecc09b18e5d7a28e01bed313fadbccd7b06c571af349cb4d2a') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py index 131a57bf887..c5d512ad6c3 100644 --- a/var/spack/repos/builtin/packages/r-maptools/package.py +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -19,7 +19,7 @@ class RMaptools(RPackage): version('0.9-5', sha256='5d9511f09fb49d57a51f28495b02239800596a4fcfad7b03ee1074d793657bdd') version('0.9-4', sha256='930875f598a516f0f9049fa2fae7391bc9bdf7e3e5db696059ab4ec2fc9ba39c') - version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836') + version('0.8-39', sha256='4b81e313e45dbb75e0fbb180b02985d1c34aaa5669e483283b632788e6a67dd2') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-sp@1.0-11:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py index b90967ce5ab..7dab7408fda 100644 --- a/var/spack/repos/builtin/packages/r-markdown/package.py +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -20,8 +20,8 @@ class RMarkdown(RPackage): version('1.1', sha256='8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b') version('1.0', sha256='172d8072d1829644ee6cdf54282a55718e2cfe9c9915d3589ca5f9a016f8d9a6') version('0.9', sha256='3068c6a41ca7a76cbedeb93b7371798f4d8437eea69a23c0ed5204c716d1bf23') - version('0.8', '5dde829a865ad65bab37a2b9d243b071') - version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff') + version('0.8', sha256='538fd912b2220f2df344c6cca58304ce11e0960de7bd7bd573b3385105d48fed') + version('0.7.7', sha256='0b86c3a4e42bbc425be229f70a4a0efdca0522f48c6ea1bf0285c6b122854102') depends_on('r@2.11.1:', type=('build', 'run')) depends_on('r-mime@0.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index 35356a63752..33516c27cd9 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -16,7 +16,7 @@ class RMass(RPackage): version('7.3-51.4', sha256='9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74') version('7.3-51.3', sha256='5b0e0e7704d43a94b08dcc4b3fe600b9723d1b3e446dd393e82d39ddf66608b6') - version('7.3-47', '2ef69aa9e25c0a445661a9877e117594') - version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b') + version('7.3-47', sha256='ed44cdabe84fff3553122267ade61d5cc68071c435f7645d36c8f2e4e9f9c6bf') + version('7.3-45', md5='aba3d12fab30f1793bee168a1efea88b') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py index 47e2f782a62..b77b3540f7b 100644 --- a/var/spack/repos/builtin/packages/r-matr/package.py +++ b/var/spack/repos/builtin/packages/r-matr/package.py @@ -19,7 +19,7 @@ class RMatr(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/matR" version('0.9.1', sha256='554aeff37b27d0f17ddeb62b2e1004aa1f29190300e4946b1bec1d7c2bde82e3') - version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a') + version('0.9', sha256='5750e6a876cf85fe66038292adefbfcb18e2584fa2e841f39dbe67f3c51b3052') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mgraster', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index c624e1c89e2..558d02308b5 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -15,11 +15,11 @@ class RMatrix(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/Matrix" version('1.2-17', sha256='db43e6f0196fd5dfd05a7e88cac193877352c60d771d4ec8772763e645723fcc') - version('1.2-14', 'b2babcf1515625196b75592c9b345bba') - version('1.2-12', '0ade6e374716f08650cc8b8da99a313c') - version('1.2-11', 'b7d2a639aa52228dfde7c3c3ee68b38e') - version('1.2-8', '4a6406666bf97d3ec6b698eea5d9c0f5') - version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') + version('1.2-14', sha256='49a6403547b66675cb44c1afb04bb87130c054510cb2b94971435a826ab41396') + version('1.2-12', md5='0ade6e374716f08650cc8b8da99a313c') + version('1.2-11', sha256='ba8cd6565612552fe397e909721817b6cc0604a91299d56d118208006888dc0b') + version('1.2-8', sha256='3cd2a187c45fc18a0766dc148b7f83dbf6f2163c256e887c41cbaa7c9a20dbb7') + version('1.2-6', sha256='4b49b639b7bf612fa3d1c1b1c68125ec7859c8cdadae0c13f499f24099fd5f20') depends_on('r@3.0.1:', when='@:1.2-12', type=('build', 'run')) depends_on('r@3.2.0:', when='@1.2.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py index ced334ea4f3..141dc232810 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -14,7 +14,7 @@ class RMatrixmodels(RPackage): url = "https://cloud.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/MatrixModels" - version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') + version('0.4-1', sha256='fe878e401e697992a480cd146421c3a10fa331f6b37a51bac83b5c1119dcce33') depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-matrix@1.1-5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py index 5918f8b8a5e..2b3a5da2461 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -19,6 +19,6 @@ class RMatrixstats(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/matrixStats" version('0.54.0', sha256='8f0db4e181300a208b9aedbebfdf522a2626e6675d2662656efb8ba71b05a06f') - version('0.52.2', '41b987d3ae96ee6895875c413adcba3c') + version('0.52.2', sha256='39da6aa6b109f89a141dab8913d981abc4fbd3f8be9e206f92e382cc5270d2a5') depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py index aca88d788f0..276c51b0b49 100644 --- a/var/spack/repos/builtin/packages/r-mclust/package.py +++ b/var/spack/repos/builtin/packages/r-mclust/package.py @@ -16,6 +16,6 @@ class RMclust(RPackage): version('5.4.5', sha256='75f2963082669485953e4306ffa93db98335ee6afdc1318b95d605d56cb30a72') version('5.4.4', sha256='ccc31b0ad445e121a447b04988e73232a085c506fcc7ebdf11a3e0754aae3e0d') - version('5.3', '74aac9fccdfc78373ce733c1a09176ef') + version('5.3', sha256='2b1b6d8266ae16b0e96f118df81559f208a568744a7c105af9f9abf1eef6ba40') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py index 4c952a3271c..d2d2e719d86 100644 --- a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py +++ b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py @@ -15,7 +15,7 @@ class RMcmcglmm(RPackage): version('2.29', sha256='13ba7837ea2049e892c04e7ec5c83d5b599a7e4820b9d875f55ec40fc2cc67b4') version('2.28', sha256='7d92e6d35638e5e060a590b92c3b1bfc02a11386276a8ab99bceec5d797bfc2a') - version('2.25', '260527ef6fecdd87f762fd07406d674a') + version('2.25', sha256='3072316bf5c66f6db5447cb488395ff019f6c47122813467384474f340643133') depends_on('r-matrix', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mco/package.py b/var/spack/repos/builtin/packages/r-mco/package.py index a6cee70aa36..39078a5b376 100644 --- a/var/spack/repos/builtin/packages/r-mco/package.py +++ b/var/spack/repos/builtin/packages/r-mco/package.py @@ -14,7 +14,7 @@ class RMco(RPackage): url = "https://cloud.r-project.org/src/contrib/mco_1.0-15.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/mco" - version('1.0-15.1', '1768dea61d0561d71be2bbc6ac3dccfa') - version('1.0-15', '0b444e085c59d919611224e86b5637f8') + version('1.0-15.1', sha256='3c13ebc8c1f1bfa18f3f95b3998c57fde5259876e92456b6c6d4c59bef07c193') + version('1.0-15', sha256='a25e3effbb6dcae735fdbd6c0bfc775e9fbbcc00dc00076b69c53fe250627055') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mda/package.py b/var/spack/repos/builtin/packages/r-mda/package.py index 2568f2fc5bf..7eaeec26bf0 100644 --- a/var/spack/repos/builtin/packages/r-mda/package.py +++ b/var/spack/repos/builtin/packages/r-mda/package.py @@ -15,7 +15,7 @@ class RMda(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/mda" version('0.4-10', sha256='7036bc622a8fea5b2de94fc19e6b64f5f0c27e5d743ae7646e116af08c9de6a5') - version('0.4-9', '2ce1446c4a013e0ebcc1099a00269ad9') + version('0.4-9', sha256='b72456d2fa5b49895644489735d21cf4836d3d597f5e693e6103cce1887ffd85') depends_on('r@1.9.0:', type=('build', 'run')) depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index 627b4e16095..083cd1a0f89 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -13,7 +13,7 @@ class RMemoise(RPackage): homepage = "https://github.com/hadley/memoise" url = "https://cloud.r-project.org/src/contrib/memoise_1.1.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/memoise" - version('1.1.0', '493209ee04673f0fcab473c3dd80fb8c') - version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac') + version('1.1.0', sha256='b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c') + version('1.0.0', sha256='fd1b6cf12929890db7819f74a44a1dbe3d6f25c8a608a956d827f8be2f6c026b') depends_on('r-digest@0.6.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index c4e2d98b7a6..a15b1f0865a 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -18,14 +18,14 @@ class RMgcv(RPackage): version('1.8-28', sha256='b55ea8227cd5c263c266c3885fa3299aa6bd23b54186517f9299bf38a7bdd3ea') version('1.8-27', sha256='c88b99fb518decd7e9cd17a4c267e74f98a78172f056784194b5b127ca0f7d1b') - version('1.8-22', 'b42079b33b46de784f293a74c824b877') - version('1.8-21', 'aae8262a07c8698ca8d6213065c4983f') - version('1.8-20', '58eb94404aad7ff8a0cf11a2f098f8bf') - version('1.8-19', 'f9a4e29464f4d10b7b2cb9d0bec3fa9e') - version('1.8-18', 'c134fc2db253530233b95f2e36b56a2f') - version('1.8-17', '398582d0f999ac34749f4f5f1d103f75') - version('1.8-16', '4c1d85e0f80b017bccb4b63395842911') - version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') + version('1.8-22', sha256='d4af7767e097ebde91c61d5ab4c62975dcb6b4ed6f545c09f5276a44ebc585cf') + version('1.8-21', sha256='b1826e40af816226d230f5b7dad6e7646cfefe840036e50c6433e90a23f9f2ed') + version('1.8-20', sha256='6540358c6f11341c997f8712a6edb590c8af0b1546e14e92724021a8d49f1375') + version('1.8-19', sha256='b9a43281fc25fb96de94cf2a7ca48aafa1ca895b279d980398bc3a4f3074996c') + version('1.8-18', sha256='29ae8ebc76f40cc5cfa775ffece99aea437d9f2f48482c48bd4b31727175df6a') + version('1.8-17', sha256='8ff3eb28c83ba7c9003005e7fe08028627fb673b9b07c0462b410e45e81042fe') + version('1.8-16', sha256='9266a0cbd783717fc6130db4e0034e69465d177397687f35daf6a8ccdb0b435e') + version('1.8-13', sha256='74bc819708ef59da94b777a446ef00d7f14b428eec843533e824017c29cc524b') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-nlme@3.1-64:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mgraster/package.py b/var/spack/repos/builtin/packages/r-mgraster/package.py index 9aa0023095c..688993d6ccf 100644 --- a/var/spack/repos/builtin/packages/r-mgraster/package.py +++ b/var/spack/repos/builtin/packages/r-mgraster/package.py @@ -15,6 +15,6 @@ class RMgraster(RPackage): url = "https://cloud.r-project.org/src/contrib/MGRASTer_0.9.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/MGRASTer" - version('0.9', '902c7ad4180b858d6b6428ea26d7652a') + version('0.9', sha256='f727b5270ed4bd6dcacaecb49e1ace7eb40827754be9801230db940c4012ae4a') depends_on('r@3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mice/package.py b/var/spack/repos/builtin/packages/r-mice/package.py index daaefe5a9c5..cdf57abd6c0 100644 --- a/var/spack/repos/builtin/packages/r-mice/package.py +++ b/var/spack/repos/builtin/packages/r-mice/package.py @@ -26,7 +26,7 @@ class RMice(RPackage): version('3.6.0', sha256='7bc72bdb631bc9f67d8f76ffb48a7bb275228d861075e20c24c09c736bebec5d') version('3.5.0', sha256='4fccecdf9e8d8f9f63558597bfbbf054a873b2d0b0820ceefa7b6911066b9e45') - version('3.0.0', 'fb54a29679536c474c756cca4538d7e3') + version('3.0.0', sha256='98b6bb1c5f8fb099bd0024779da8c865146edb25219cc0c9542a8254152c0add') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-broom', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index 8c99d8d720f..bc64eabd3e2 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -16,5 +16,5 @@ class RMime(RPackage): version('0.7', sha256='11083ee44c92569aadbb9baf60a2e079ab7a721c849b74d102694975cc8d778b') version('0.6', sha256='4775b605ab0117406bee7953c8af59eea8b35e67d1bd63f4007686a7097fc401') - version('0.5', '87e00b6d57b581465c19ae869a723c4d') - version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') + version('0.5', sha256='fcc72115afb0eb43237da872754464f37ae9ae097f332ec7984149b5e3a82145') + version('0.4', sha256='d790c7e38371d03774a7d53f75aed3151835b1aebbb663b0fe828b221e6bac90') diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py index f579dbdf574..0f585121c8e 100644 --- a/var/spack/repos/builtin/packages/r-minqa/package.py +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -14,7 +14,7 @@ class RMinqa(RPackage): url = "https://cloud.r-project.org/src/contrib/minqa_1.2.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/minqa" - version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105') + version('1.2.4', sha256='cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c') depends_on('r-rcpp@0.9.10:', type=('build', 'run')) depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-misc3d/package.py b/var/spack/repos/builtin/packages/r-misc3d/package.py index a4043961aee..0bf82caa20b 100644 --- a/var/spack/repos/builtin/packages/r-misc3d/package.py +++ b/var/spack/repos/builtin/packages/r-misc3d/package.py @@ -13,4 +13,4 @@ class RMisc3d(RPackage): url = "https://cloud.r-project.org/src/contrib/misc3d_0.8-4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/misc3d" - version('0.8-4', 'aefa27e67a243c21a1046868540343fe') + version('0.8-4', sha256='75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62') diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py index 4980a9e157b..8bb251f1b8b 100644 --- a/var/spack/repos/builtin/packages/r-mitml/package.py +++ b/var/spack/repos/builtin/packages/r-mitml/package.py @@ -18,7 +18,7 @@ class RMitml(RPackage): version('0.3-7', sha256='c6f796d0059f1b093b599a89d955982fa257de9c45763ecc2cbbce10fdec1e7b') version('0.3-6', sha256='bc59bdc802eb882340393752535446560c716f12c6fca2b95f03c6af30d978de') - version('0.3-5', '6f8659c33696915bf510241287b2a34d') + version('0.3-5', sha256='8bcfeb18f3fb8a58a516348c37369eb8356af4bd3e0688c84a2366e1534608e9') depends_on('r-pan', type=('build', 'run')) depends_on('r-jomo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mixtools/package.py b/var/spack/repos/builtin/packages/r-mixtools/package.py index f8180067545..2472b945a3f 100644 --- a/var/spack/repos/builtin/packages/r-mixtools/package.py +++ b/var/spack/repos/builtin/packages/r-mixtools/package.py @@ -16,8 +16,8 @@ class RMixtools(RPackage): url = "https://cloud.r-project.org/src/contrib/mixtools_1.1.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/mixtools" - version('1.1.0', 'c7d59110dd42964d40593a05b98acd5f') - version('1.0.4', 'c0e6ec44d16ec8914797fb74a651d3e5') + version('1.1.0', sha256='543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f') + version('1.0.4', sha256='62f4b0a17ce520c4f8ed50ab44f120e459143b461a9e420cd39056ee4fc8798c') depends_on('r@3.2:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlbench/package.py b/var/spack/repos/builtin/packages/r-mlbench/package.py index f861d6a5476..45eef323311 100644 --- a/var/spack/repos/builtin/packages/r-mlbench/package.py +++ b/var/spack/repos/builtin/packages/r-mlbench/package.py @@ -14,6 +14,6 @@ class RMlbench(RPackage): url = "https://cloud.r-project.org/src/contrib/mlbench_2.1-1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/mlbench" - version('2.1-1', '9f06848b8e137b8a37417c92d8e57f3b') + version('2.1-1', sha256='748141d56531a39dc4d37cf0a5165a40b653a04c507e916854053ed77119e0e6') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlr/package.py b/var/spack/repos/builtin/packages/r-mlr/package.py index 34a8f8f1fdb..cbbf4d1c889 100644 --- a/var/spack/repos/builtin/packages/r-mlr/package.py +++ b/var/spack/repos/builtin/packages/r-mlr/package.py @@ -25,8 +25,8 @@ class RMlr(RPackage): version('2.15.0', sha256='a3c2c2bd65a87d90b5e5e877b1ef8e7712e76b4eb1660d3f69672a1860ca5324') version('2.14.0', sha256='1f72184400678386c7c44297c4c92a448b50148de700df5ba0438d4e486e944a') version('2.13', sha256='e8729be7acddc1ea124c44f9493a8b903c5f54b97e09c714366553aed733011d') - version('2.12.1', 'abddfc9dfe95f290a233ecd97969a4ec') - version('2.12', '94ee7495aeafb432c8af5a8bdd26c25f') + version('2.12.1', sha256='9cbb98b82eb493b783fe8808a18d76f32881d941364466ef8829b852fabbc82c') + version('2.12', sha256='cfe00089ae4cd88c6d03826eda43d4fe29e467e3a7c95d103fafca8308f5c161') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-paramhelpers@1.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlrmbo/package.py b/var/spack/repos/builtin/packages/r-mlrmbo/package.py index 3caeec50dcb..d0bc16c7521 100644 --- a/var/spack/repos/builtin/packages/r-mlrmbo/package.py +++ b/var/spack/repos/builtin/packages/r-mlrmbo/package.py @@ -26,8 +26,8 @@ class RMlrmbo(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/mlrMBO" version('1.1.2', sha256='8e84caaa5d5d443d7019128f88ebb212fb095870b3a128697c9b64fe988f3efe') - version('1.1.1', '9a35b41ceb8754111af294dee0ae76e0') - version('1.1.0', '9e27ff8498225d24863b8da758d2918e') + version('1.1.1', sha256='e87d9912a9b4a968364584205b8ef6f7fea0b5aa043c8d31331a7b7be02dd7e4') + version('1.1.0', sha256='6ae82731a566333f06085ea2ce23ff2a1007029db46eea57d06194850350a8a0') depends_on('r-mlr@2.10:', type=('build', 'run')) depends_on('r-paramhelpers@1.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mmwrweek/package.py b/var/spack/repos/builtin/packages/r-mmwrweek/package.py index cb36d6e6fb6..c4be88a8044 100644 --- a/var/spack/repos/builtin/packages/r-mmwrweek/package.py +++ b/var/spack/repos/builtin/packages/r-mmwrweek/package.py @@ -18,4 +18,4 @@ class RMmwrweek(RPackage): url = "https://cloud.r-project.org/src/contrib/MMWRweek_0.1.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/MMWRweek" - version('0.1.1', 'a1245025126f8a96c72be8f7b06b0499') + version('0.1.1', sha256='969fd18535f3b78dd360d62d29d5f15409fc059f4af5d345abfde711e4adbc99') diff --git a/var/spack/repos/builtin/packages/r-mnormt/package.py b/var/spack/repos/builtin/packages/r-mnormt/package.py index e322a43d12a..7bbea166195 100644 --- a/var/spack/repos/builtin/packages/r-mnormt/package.py +++ b/var/spack/repos/builtin/packages/r-mnormt/package.py @@ -18,6 +18,6 @@ class RMnormt(RPackage): url = "https://cloud.r-project.org/src/contrib/mnormt_1.5-5.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/mnormt" - version('1.5-5', '19b5be2e9ed33b92d7a716bfcca6b2c7') + version('1.5-5', sha256='ff78d5f935278935f1814a69e5a913d93d6dd2ac1b5681ba86b30c6773ef64ac') depends_on('r@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modelmetrics/package.py b/var/spack/repos/builtin/packages/r-modelmetrics/package.py index 47e925e4da2..f26f4bc4db5 100644 --- a/var/spack/repos/builtin/packages/r-modelmetrics/package.py +++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py @@ -16,7 +16,7 @@ class RModelmetrics(RPackage): version('1.2.2', sha256='66d6fc75658287fdbae4d437b51d26781e138b8baa558345fb9e5a2df86a0d95') version('1.2.0', sha256='3021ae88733695a35d66e279e8e61861431f14c9916a341f0a562f675cf6ede9') - version('1.1.0', 'd43175001f0531b8810d2802d76b7b44') + version('1.1.0', sha256='487d53fda57da4b29f83a927dda8b1ae6655ab044ee3eec33c38aeb27eed3d85') depends_on('r@3.2.2:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modelr/package.py b/var/spack/repos/builtin/packages/r-modelr/package.py index b65d8ec3232..609266d475c 100644 --- a/var/spack/repos/builtin/packages/r-modelr/package.py +++ b/var/spack/repos/builtin/packages/r-modelr/package.py @@ -17,7 +17,7 @@ class RModelr(RPackage): version('0.1.5', sha256='45bbee387c6ba154f9f8642e9f03ea333cce0863c324ff15d23096f33f85ce5a') version('0.1.4', sha256='b4da77c1244bbda512ce323751c8338741eeaa195283f172a0feec2917bcfdd9') version('0.1.3', sha256='e536b247c17d6cacf10565dd8a1b744efc90a8815c70edd54371e413e6d1b423') - version('0.1.1', 'ce5fd088fb7850228ab1e34d241a975d') + version('0.1.1', sha256='25b95198d6aa23e28a0bd97dcdc78264ef168ae403928bff01e1ee81ca021ce7') depends_on('r@3.1:', when='@:0.1.4', type=('build', 'run')) depends_on('r@3.2:', when='@0.1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modeltools/package.py b/var/spack/repos/builtin/packages/r-modeltools/package.py index 16f2c631162..61087e9b680 100644 --- a/var/spack/repos/builtin/packages/r-modeltools/package.py +++ b/var/spack/repos/builtin/packages/r-modeltools/package.py @@ -14,4 +14,4 @@ class RModeltools(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/modeltools" version('0.2-22', sha256='256a088fc80b0d9182f984f9bd3d6207fb7c1e743f72e2ecb480e6c1d4ac34e9') - version('0.2-21', '3bf56b2e7bf78981444385d87eeccdd7') + version('0.2-21', sha256='07b331475625674ab00e6ddfc479cbdbf0b22d5d237e8c25d83ddf3e0ad1cd7a') diff --git a/var/spack/repos/builtin/packages/r-mpm/package.py b/var/spack/repos/builtin/packages/r-mpm/package.py index ef159313d9e..f5b5b40235b 100644 --- a/var/spack/repos/builtin/packages/r-mpm/package.py +++ b/var/spack/repos/builtin/packages/r-mpm/package.py @@ -15,7 +15,7 @@ class RMpm(RPackage): url = "https://cloud.r-project.org/src/contrib/mpm_1.0-22.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/mpm" - version('1.0-22', '91885c421cafd89ce8893ccf827165a2') + version('1.0-22', sha256='d3ba4053cd57a189cb65c5fa20e6a4152374aead8c985254cb6e550e36e23272') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index db2bf153129..e66d05cd255 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -19,7 +19,7 @@ class RMultcomp(RPackage): version('1.4-10', sha256='29bcc635c0262e304551b139cd9ee655ab25a908d9693e1cacabfc2a936df5cf') version('1.4-8', sha256='a20876619312310e9523d67e9090af501383ce49dc6113c6b4ca30f9c943a73a') - version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') + version('1.4-6', sha256='fe9efbe671416a49819cbdb9137cc218faebcd76e0f170fd1c8d3c84c42eeda2') depends_on('r-mvtnorm@1.0-10:', type=('build', 'run')) depends_on('r-survival@2.39-4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index 8a0678d5d43..efff472a170 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -18,6 +18,6 @@ class RMunsell(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/munsell" version('0.5.0', sha256='d0f3a9fb30e2b5d411fa61db56d4be5733a2621c0edf017d090bdfa5e377e199') - version('0.4.3', 'ebd205323dc37c948f499ee08be9c476') + version('0.4.3', sha256='397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49') depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index bd7b6eab461..bf277619143 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -16,8 +16,8 @@ class RMvtnorm(RPackage): version('1.0-11', sha256='0321612de99aa9bc75a45c7e029d3372736014223cbdefb80d8cae600cbc7252') version('1.0-10', sha256='31df19cd8b4cab9d9a70dba00442b7684e625d4ca143a2c023c2c5872b07ad12') - version('1.0-6', 'cb69426868fd3e330412b8491901d9d4') - version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') + version('1.0-6', sha256='4a015b57b645b520151b213eb04b7331598c06442a3f652c7dc149425bd2e444') + version('1.0-5', sha256='d00f9f758f0d0d4b999f259223485dc55d23cbec09004014816f180045ac81dd') depends_on('r@1.9.0:', when='@:1.0-8', type=('build', 'run')) depends_on('r@3.5.0:', when='@1.0-9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nanotime/package.py b/var/spack/repos/builtin/packages/r-nanotime/package.py index 8d0b6c7cc0c..61cd98ba9fc 100644 --- a/var/spack/repos/builtin/packages/r-nanotime/package.py +++ b/var/spack/repos/builtin/packages/r-nanotime/package.py @@ -17,7 +17,7 @@ class RNanotime(RPackage): version('0.2.4', sha256='2dfb7e7435fec59634b87563a215467e7793e2711e302749c0533901c74eb184') version('0.2.3', sha256='7d6df69a4223ae154f610b650e24ece38ce4aa706edfa38bec27d15473229f5d') - version('0.2.0', '796b1f7d0bb43e2f3d98e3cc6f4b0657') + version('0.2.0', sha256='9ce420707dc4f0cb4241763579b849d842904a3aa0d88de8ffef334d08fa188d') depends_on('r-bit64', type=('build', 'run')) depends_on('r-rcppcctz@0.2.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py index f01a2035dd4..b84ff8c9614 100644 --- a/var/spack/repos/builtin/packages/r-ncbit/package.py +++ b/var/spack/repos/builtin/packages/r-ncbit/package.py @@ -14,6 +14,6 @@ class RNcbit(RPackage): url = "https://cloud.r-project.org/src/contrib/ncbit_2013.03.29.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/ncbit" - version('2013.03.29', '29582d7e5c8bbf9683c57c4f6ac3e891') + version('2013.03.29', sha256='4480271f14953615c8ddc2e0666866bb1d0964398ba0fab6cc29046436820738') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index a040454530b..14e12733811 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -28,6 +28,6 @@ class RNcdf4(RPackage): version('1.16.1', sha256='0dde2d6d1e8474f4abd15a61af8a2f7de564f13da00f1a01d7a479ab88587a20') version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253') - version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a') + version('1.15', sha256='d58298f4317c6c80a041a70216126492fd09ba8ecde9da09d5145ae26f324d4d') depends_on('netcdf@4.1:') diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py index 03f728256fe..dad4a541a2f 100644 --- a/var/spack/repos/builtin/packages/r-network/package.py +++ b/var/spack/repos/builtin/packages/r-network/package.py @@ -17,7 +17,7 @@ class RNetwork(RPackage): version('1.15', sha256='5cbe5c0369e5f8363e33a86f14fd33ce8727166106381627ecd13b7452e14cb3') version('1.14-377', sha256='013c02f8d97f1f87f2c421760534df9353d2a8c2277f20b46b59fb79822d3e46') - version('1.13.0', 'd0b967d6f1aad43b6479d72f29b705de') + version('1.13.0', sha256='7a04ea89261cdf32ccb52222810699d5fca59a849053e306b5ec9dd5c1184f87') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-tibble', when='@1.14-377:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py index 976f313fcdc..633b2580fc8 100644 --- a/var/spack/repos/builtin/packages/r-networkd3/package.py +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -16,7 +16,7 @@ class RNetworkd3(RPackage): version('0.4', sha256='33b82585f1eec6233303ec14033a703d0b17def441c7a0a67bf7e6764c9c9d0b') version('0.3', sha256='6f9d6b35bb1562883df734bef8fbec166dd365e34c6e656da7be5f8a8d42343c') - version('0.2.12', '356fe4be59698e6fb052644bd9659d84') + version('0.2.12', sha256='b81b59c3c992609e25e1621e51d1240e3d086c2b9c3e9da49a6cb0c9ef7f4ea5') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-htmlwidgets@0.3.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index bd13d96c202..d03e9a3e8ea 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -15,9 +15,9 @@ class RNlme(RPackage): version('3.1-141', sha256='910046260a03d8f776ac7b0766b5adee91556829d0d8a70165b2c695ce038056') version('3.1-139', sha256='0460fc69d85122177e7ef01bad665d56bcaf63d31bdbfdbdfdcba2c082085739') - version('3.1-131', '0f1215ec4d4e3bca939282d122f4d1fa') - version('3.1-130', '1935d6e308a8018ed8e45d25c8731288') - version('3.1-128', '3d75ae7380bf123761b95a073eb55008') + version('3.1-131', sha256='79daa167eb9bc7d8dba506da4b24b5250665b051d4e0a51dfccbb0087fdb564c') + version('3.1-130', sha256='ec576bd906ef2e1c79b6a4382743d425846f63be2a43de1cce6aa397b40e290e') + version('3.1-128', md5='3d75ae7380bf123761b95a073eb55008') depends_on('r@3.0.2:', when='@:3.1-131', type=('build', 'run')) depends_on('r@3.3.0:', when='@3.1-131.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py index f6f7502524e..9607bd1faab 100644 --- a/var/spack/repos/builtin/packages/r-nloptr/package.py +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -21,7 +21,7 @@ class RNloptr(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/nloptr" version('1.2.1', sha256='1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97') - version('1.0.4', 'f2775dfb4f7f5552d46937a04c062b0d') + version('1.0.4', sha256='84225b993cb1ef7854edda9629858662cc8592b0d1344baadea4177486ece1eb') depends_on('nlopt') diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index 91c356d794f..a96023e11be 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -19,7 +19,7 @@ class RNmf(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') - version('0.20.6', '81df07b3bf710a611db5af24730ff3d0') + version('0.20.6', md5='81df07b3bf710a611db5af24730ff3d0') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-pkgmaker@0.20:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py index dada76423e1..aea3a898a35 100644 --- a/var/spack/repos/builtin/packages/r-nnet/package.py +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -14,6 +14,6 @@ class RNnet(RPackage): url = "https://cloud.r-project.org/src/contrib/nnet_7.3-12.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/nnet" - version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e') + version('7.3-12', sha256='2723523e8581cc0e2215435ac773033577a16087a3f41d111757dd96b8c5559d') depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nnls/package.py b/var/spack/repos/builtin/packages/r-nnls/package.py index 815f35b925f..6966bbde466 100644 --- a/var/spack/repos/builtin/packages/r-nnls/package.py +++ b/var/spack/repos/builtin/packages/r-nnls/package.py @@ -15,4 +15,4 @@ class RNnls(RPackage): url = "https://cloud.r-project.org/src/contrib/nnls_1.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/nnls" - version('1.4', 'cdb3640120f73e0ccb6079108e0ef361') + version('1.4', sha256='0e5d77abae12bc50639d34354f96a8e079408c9d7138a360743b73bd7bce6c1f') diff --git a/var/spack/repos/builtin/packages/r-nor1mix/package.py b/var/spack/repos/builtin/packages/r-nor1mix/package.py index 050252b7e39..1bb824bada5 100644 --- a/var/spack/repos/builtin/packages/r-nor1mix/package.py +++ b/var/spack/repos/builtin/packages/r-nor1mix/package.py @@ -18,4 +18,4 @@ class RNor1mix(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/nor1mix" version('1.3-0', sha256='9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0') - version('1.2-3', '60eb5cc1ea6b366f53042087a080b105') + version('1.2-3', sha256='435e6519e832ef5229c51ccb2619640e6b50dfc7470f70f0c938d18a114273af') diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py index 0a7e9835355..e20a04d6819 100644 --- a/var/spack/repos/builtin/packages/r-np/package.py +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -21,7 +21,7 @@ class RNp(RPackage): version('0.60-9', sha256='fe31a8985f0b1a576a7775022b7131093b1c9a8337734136d5fcad85fa6592fc') version('0.60-8', sha256='924c342feb2a862fa3871a45db5f8434dbbfb900cfc40c001a0872108a3a069e') - version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389') + version('0.60-2', sha256='25d667fc1056899516584b9d5d933377e6f4694d8e5e868dd047db572b69417f') depends_on('r-boot', type=('build', 'run')) depends_on('r-cubature', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-numderiv/package.py b/var/spack/repos/builtin/packages/r-numderiv/package.py index d234dca5386..cdad79a7002 100644 --- a/var/spack/repos/builtin/packages/r-numderiv/package.py +++ b/var/spack/repos/builtin/packages/r-numderiv/package.py @@ -15,6 +15,6 @@ class RNumderiv(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/numDeriv" version('2016.8-1.1', sha256='d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345') - version('2016.8-1', '30e486298d5126d86560095be8e8aac1') + version('2016.8-1', sha256='1b681d273697dc780a3ac5bedabb4a257785732d9ca4ef68e4e4aac8b328d11e') depends_on('r@2.11.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index 72ef2426672..de7782cf421 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -24,9 +24,9 @@ class ROpenssl(RPackage): version('1.4.1', sha256='f7fbecc75254fc43297a95a4338c674ab9ba2ec056b59e027d16d23122161fc6') version('1.3', sha256='1c83f4d529adc1f5ec40e477c690a8d5b0a42422f3e542f1fc39062dcfaca4bf') - version('0.9.7', '86773824dce7d3d79abfef574ce2531a') - version('0.9.6', '7ef137929d9dd07db690d35db242ba4b') - version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') + version('0.9.7', sha256='697d9e86f99270163744538dc3dc4d19d00af89a8570a1d304b110e1d2650e9d') + version('0.9.6', sha256='6dd6d1cade4004962d516ad761fff0812beec0232318b385d286761423a5dc39') + version('0.9.4', sha256='cb7349defa5428acc0907629a4f53f82d2519af219e5d6a41f852cf55b1feb66') depends_on('r-askpass', when='@1.2:', type=('build', 'run')) depends_on('openssl@1.0.1:') diff --git a/var/spack/repos/builtin/packages/r-optparse/package.py b/var/spack/repos/builtin/packages/r-optparse/package.py index be8c989605d..1dec5d57bbc 100644 --- a/var/spack/repos/builtin/packages/r-optparse/package.py +++ b/var/spack/repos/builtin/packages/r-optparse/package.py @@ -17,7 +17,7 @@ class ROptparse(RPackage): version('1.6.2', sha256='b5a5a49ae05005f20359868329b73daac83d50f5e088981dcf5c41399534377f') version('1.6.1', sha256='819be3eff54cb7f3f18703eed9714fc655290ab8e169f87605433d069b597e13') - version('1.6.0', '8d0bd89b2e25cc1580437cdeeb1faac2') + version('1.6.0', sha256='10e816bb8f5b08d52cfd3a0028903a8c62ef9cf7bfd85f9dae8af442e82bfbb4') depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-getopt@1.20.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py index 9ba2e9dce9a..0677d405f1e 100644 --- a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py +++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py @@ -13,7 +13,7 @@ class ROrgHsEgDb(RPackage): homepage = "https://bioconductor.org/packages/org.Hs.eg.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz" - version('3.4.1', '0a987ef7d6167df70e91e6f48145e41c') + version('3.4.1', sha256='0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00') depends_on('r@3.4.0:3.4.9', when='@3.4.1') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py index 427843d0806..9ddd728b043 100644 --- a/var/spack/repos/builtin/packages/r-packrat/package.py +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -16,7 +16,7 @@ class RPackrat(RPackage): version('0.5.0', sha256='d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7') version('0.4.9-3', sha256='87299938a751defc54eb00a029aecd3522d6349d900aaa8b3e1aa6bf31e98234') - version('0.4.8-1', '14e82feba55fcda923396282fc490038') - version('0.4.7-1', '80c2413269b292ade163a70ba5053e84') + version('0.4.8-1', sha256='a283caf4fda419e6571ae9ca6210a59002a030721feb8a50c0d0787fd6f672f3') + version('0.4.7-1', sha256='6e5067edd41a4086bb828617d3378210a3dbc995e223b02af811549519f3223a') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py index fef678b671a..ae4627cf272 100644 --- a/var/spack/repos/builtin/packages/r-pacman/package.py +++ b/var/spack/repos/builtin/packages/r-pacman/package.py @@ -18,7 +18,7 @@ class RPacman(RPackage): version('0.5.1', sha256='9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c') version('0.5.0', sha256='61294757212ab0aa0153219d7d031f58be6f30ead88d84859001d58caa76603d') - version('0.4.1', 'bf18fe6d1407d31e00b337d9b07fb648') + version('0.4.1', sha256='fffa72307912cbd5aa5bee0a9b65931500483036ccffb1791dd808eb5eb70362') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r@3.5.0:', when='@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pamr/package.py b/var/spack/repos/builtin/packages/r-pamr/package.py index f4697f4c179..d61717c0fd7 100644 --- a/var/spack/repos/builtin/packages/r-pamr/package.py +++ b/var/spack/repos/builtin/packages/r-pamr/package.py @@ -14,7 +14,7 @@ class RPamr(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/pamr" version('1.56.1', sha256='d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779') - version('1.55', '108932d006a4de3a178b6f57f5d1a006') + version('1.55', sha256='ed910194937a6097ec79234d84777856fd520b111a7c79f7c86dc607169cc3c3') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py index 176104e3dff..ef42bcf6b7a 100644 --- a/var/spack/repos/builtin/packages/r-pan/package.py +++ b/var/spack/repos/builtin/packages/r-pan/package.py @@ -14,4 +14,4 @@ class RPan(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/pan" version('1.6', sha256='adc0df816ae38bc188bce0aef3aeb71d19c0fc26e063107eeee71a81a49463b6') - version('1.4', 'cdead963110561fc42dc544a60ac44ed') + version('1.4', sha256='e6a83f0799cc9714f5052f159be6e82ececd013d1626f40c828cda0ceb8b76dc') diff --git a/var/spack/repos/builtin/packages/r-parallelmap/package.py b/var/spack/repos/builtin/packages/r-parallelmap/package.py index cc437937287..e6c46c51499 100644 --- a/var/spack/repos/builtin/packages/r-parallelmap/package.py +++ b/var/spack/repos/builtin/packages/r-parallelmap/package.py @@ -19,7 +19,7 @@ class RParallelmap(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/parallelMap" version('1.4', sha256='fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b') - version('1.3', 'dd62866b395847b0bd5b13bed98c0081') + version('1.3', sha256='a52d93572c1b85281e41d8e3c2db97dda5fce96c222e04171b4489ec5000cd08') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-bbmisc@1.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-paramhelpers/package.py b/var/spack/repos/builtin/packages/r-paramhelpers/package.py index 2aa307b30de..2a422c6fdc9 100644 --- a/var/spack/repos/builtin/packages/r-paramhelpers/package.py +++ b/var/spack/repos/builtin/packages/r-paramhelpers/package.py @@ -19,7 +19,7 @@ class RParamhelpers(RPackage): version('1.12', sha256='b54db9e6608ba530345c380c757a60cb2b78ab08992a890b1a41914ce7abcc14') version('1.11', sha256='1614f4c0842cf822befc01228ab7263417f3423dd6a1dc24347b14f8491637a0') - version('1.10', '36e9060488ebd484d62cd991a4693332') + version('1.10', sha256='80629ba62e93b0b706bf2e451578b94fbb9c5b95ff109ecfb5b011bfe0a0fa5b') depends_on('r-bbmisc@1.10:', type=('build', 'run')) depends_on('r-checkmate@1.8.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-party/package.py b/var/spack/repos/builtin/packages/r-party/package.py index db876b5faf0..4ca371f37e7 100644 --- a/var/spack/repos/builtin/packages/r-party/package.py +++ b/var/spack/repos/builtin/packages/r-party/package.py @@ -15,7 +15,7 @@ class RParty(RPackage): version('1.3-3', sha256='9f72eea02d43a4cee105790ae7185b0478deb6011ab049cc9d31a0df3abf7ce9') version('1.3-2', sha256='9f350fa21114151c49bccc3d5f8536dbc5a608cfd88f60461c9805a4c630510b') - version('1.1-2', '40a00336cf8418042d2ab616675c8ddf') + version('1.1-2', sha256='c3632b4b02dc12ec949e2ee5b24004e4a4768b0bc9737432e9a85acbc2ed0e74') depends_on('r@2.14.0:', when='@:1.2-2', type=('build', 'run')) depends_on('r@3.0.0:', when='@1.2-3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py index 1e914397a0a..039949f867d 100644 --- a/var/spack/repos/builtin/packages/r-partykit/package.py +++ b/var/spack/repos/builtin/packages/r-partykit/package.py @@ -23,7 +23,7 @@ class RPartykit(RPackage): version('1.2-5', sha256='f48e30790f93fa5d03e68e8ce71ce33d009d107d46d45d85da2016b38b27629c') version('1.2-3', sha256='56749b246e283f94ac2ad2cdcfc0a477e05cd44b5e8f6e462c26f4dff818da35') - version('1.1-1', '8fcb31d73ec1b8cd3bcd9789639a9277') + version('1.1-1', sha256='d9f4762690cd85ee4e3dc44f5a14069d10a1900afdfbcdc284d2a94b4a8e8332') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbapply/package.py b/var/spack/repos/builtin/packages/r-pbapply/package.py index cc481c277a4..f8457b74524 100644 --- a/var/spack/repos/builtin/packages/r-pbapply/package.py +++ b/var/spack/repos/builtin/packages/r-pbapply/package.py @@ -16,10 +16,10 @@ class RPbapply(RPackage): version('1.4-1', sha256='b3633349181db944e1dfc4422b4728a6562e454117a232cbb51633906cd27cad') version('1.3-4', sha256='cdfdaf9b8aecbe48daac858aecaf65a766b74a363d1eb7cd6ebf27c0549f6552') - version('1.3-3', '570db6795179a1439c174be881c77d18') - version('1.3-2', 'd72a777bfe4a28ba4e1585e31680f82e') - version('1.3-1', '13d64dead441426aa96a3bf3fde29daf') - version('1.3-0', 'a3f93cd05054657a01893a3817fa1f08') - version('1.2-2', '23e2bfe531c704b79308b0b5fbe1ace8') + version('1.3-3', sha256='7379b21d1176db5769f5cac858dd12c975736e80a600870180cec9625cf51047') + version('1.3-2', sha256='196367da93fcd31431d8e78c177d4afccf9c634513edf24a7229adce2d95b5e9') + version('1.3-1', sha256='fc4f1ea9d3290bab20a0ec74a3195c8887592b022ab6abb8d7754006a4487114') + version('1.3-0', sha256='a6d4bf88ade12a3b25662e271329fe54d170596335cba2a2dd210bbb7e8a5936') + version('1.2-2', sha256='81e5a8a5e0c7ce24b25679d0f69e8773908c9ce569f1e5984e52d4cef33ac34e') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index 48625786c1b..4ec6ee90557 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -22,7 +22,7 @@ class RPbdzmq(RPackage): version('0.3-3', sha256='ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca') version('0.3-2', sha256='ece2a2881c662f77126e4801ba4e01c991331842b0d636ce5a2b591b9de3fc37') - version('0.2-4', 'e5afb70199aa54d737ee7a0e26bde060') + version('0.2-4', sha256='bfacac88b0d4156c70cf63fc4cb9969a950693996901a4fa3dcd59949ec065f6') depends_on('r@3.0.0:', when='@:0.2-5', type=('build', 'run')) depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index a696abf87af..fd0ba857df3 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -18,8 +18,8 @@ class RPbkrtest(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/pbkrtest" version('0.4-7', sha256='5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea') - version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') - version('0.4-4', '5e54b1b1b35413dd1d24ef15735ec645') + version('0.4-6', sha256='9d28b8916fea3ffec8d5958bb8c531279b1e273f21fdbeb2fcad6d7e300a9c01') + version('0.4-4', sha256='a685392ef3fca0ddc2254f6cc9bba6bc22b298fa823359fc4515e64e753abd31') depends_on('r@3.0.2:', when='@:0.4-5', type=('build', 'run')) depends_on('r@3.2.3:', when='@0.4-6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py index bcc1b7a4722..fe62e5a7144 100644 --- a/var/spack/repos/builtin/packages/r-pcapp/package.py +++ b/var/spack/repos/builtin/packages/r-pcapp/package.py @@ -15,10 +15,10 @@ class RPcapp(RPackage): version('1.9-73', sha256='ca4566b0babfbe83ef9418283b08a12b3420dc362f93c6562f265df7926b53fc') version('1.9-72.1', sha256='a9e39ee15a650930c07672092f9f0c431807869b68b5471037eb7290a4d65bd5') - version('1.9-72', '87c08f8ecab69311bba395c026bbc91c') - version('1.9-70', '3fcc809ec1cdc910f10e9ebf372888e8') - version('1.9-61', '1bd5bc3aff968b168493e8c523d726ea') - version('1.9-60', '23dd468abb9fedc11e40166446df1017') - version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3') + version('1.9-72', sha256='58bd0bfb5931aecd734801654bac95f28dab6d30fd043c66c5b719b497104844') + version('1.9-70', sha256='359e2b376b8b7e2de68b0f33f772d99ecbe9a94f8f460574ac2e3c07513c96d5') + version('1.9-61', sha256='7dc395e159ff1a56135baaf0b1bea40f871c30f6dadd38992f4ccdfc4e88dc29') + version('1.9-60', sha256='9a4b471957ac39ed7c860e3165bf8e099b5b55cf814654adb58f9d19df2718e7') + version('1.9-50', sha256='137637314fba6e11883c63b0475d8e50aa7f363e064baa1e70245f7692565b56') depends_on('r-mvtnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py index a386df053b4..9a3b0aa97f2 100644 --- a/var/spack/repos/builtin/packages/r-permute/package.py +++ b/var/spack/repos/builtin/packages/r-permute/package.py @@ -20,6 +20,6 @@ class RPermute(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/permute" version('0.9-5', sha256='d2885384a07497e8df273689d6713fc7c57a7c161f6935f3572015e16ab94865') - version('0.9-4', '569fc2442d72a1e3b7e2d456019674c9') + version('0.9-4', sha256='a541a5f5636ddd67fd856d3e11224f15bc068e96e23aabe3e607a7e7c2fc1cf1') depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py index f7ff0f07928..67d06960aeb 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -13,7 +13,7 @@ class RPfamDb(RPackage): homepage = "https://www.bioconductor.org/packages/PFAM.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" - version('3.4.1', '65ed35887ecc44f5ac9f9c8563e03f44') + version('3.4.1', sha256='fc45a0d53139daf85873f67bd3f1b68f2d883617f4447caddbd2d7dcc58a393f') depends_on('r@3.4.0:3.4.9', when='@3.4.1') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phangorn/package.py b/var/spack/repos/builtin/packages/r-phangorn/package.py index 3b0c34fb7e3..a2853158853 100644 --- a/var/spack/repos/builtin/packages/r-phangorn/package.py +++ b/var/spack/repos/builtin/packages/r-phangorn/package.py @@ -18,7 +18,7 @@ class RPhangorn(RPackage): version('2.5.5', sha256='c58dc1ace26cb4358619a15da3ea4765dbdde1557acccc5103c85589a7571346') version('2.5.3', sha256='a306585a0aabe7360a2adaf9116ae2993fb5ceff641b198f2e01e4329d3768af') - version('2.3.1', '85e7309900d061432508ab6f7e3e627e') + version('2.3.1', sha256='518c31f5b2c5f0a655d02a3c71b00c30caea2794dfc31f9d63f3d505bd7863eb') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-ape@5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py index af1a409bc58..e1825092c11 100644 --- a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py +++ b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py @@ -15,7 +15,7 @@ class RPhantompeakqualtools(RPackage): homepage = "https://github.com/kundajelab/phantompeakqualtools" url = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz" - version('1.14', '4de207d570999170c1bf45bcba8c6d2d') + version('1.14', sha256='d03be6163e82aed72298e54a92c181570f9975a395f57a69b21ac02b1001520b') depends_on('boost@1.41.0:') depends_on('r-catools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-picante/package.py b/var/spack/repos/builtin/packages/r-picante/package.py index 6cfa91cfc2d..10ed4c03293 100644 --- a/var/spack/repos/builtin/packages/r-picante/package.py +++ b/var/spack/repos/builtin/packages/r-picante/package.py @@ -15,8 +15,8 @@ class RPicante(RPackage): version('1.8', sha256='81a6308dbb53c9cdab30c1f9ac727abee76314351823b3a2142c21ed8e1498ad') version('1.7', sha256='75e4d73080db67e776562a1d58685438461cbde39af46900c7838da56aef0a62') - version('1.6-2', 'e3eba6ef254068d2cfa9e96760bcd7a3') - version('1.6-1', '73d86b90eceda582654e995d47236d6e') + version('1.6-2', sha256='4db3a5a0fe5e4e9197c96245195843294fbb8d0a324edcde70c6ab01276ab7ff') + version('1.6-1', sha256='2708315b26737857a6729fd67bde06bc939930035c5b09a8bba472a593f24000') depends_on('r-ape', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgconfig/package.py b/var/spack/repos/builtin/packages/r-pkgconfig/package.py index 947d6f4ee53..bda85a518d3 100644 --- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py @@ -16,4 +16,4 @@ class RPkgconfig(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgconfig" version('2.0.2', sha256='25997754d1adbe7a251e3bf9879bb52dced27dd8b84767d558f0f644ca8d69ca') - version('2.0.1', 'a20fd9588e37995995fa62dc4828002e') + version('2.0.1', sha256='ab02b2a4b639ba94dcba882a059fe9cddae5498a4309841f764b62ec46ba5a40') diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index b89ec59b809..c6a312f2c09 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -20,7 +20,7 @@ class RPkgmaker(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') - version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4') + version('0.22', md5='73a0c6d3e84c6dadf3de7582ef7e88a4') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-registry', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plogr/package.py b/var/spack/repos/builtin/packages/r-plogr/package.py index c35e0900e4c..fbcdbee52a9 100644 --- a/var/spack/repos/builtin/packages/r-plogr/package.py +++ b/var/spack/repos/builtin/packages/r-plogr/package.py @@ -16,4 +16,4 @@ class RPlogr(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/plogr" version('0.2.0', sha256='0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29') - version('0.1-1', '5ee46ed21b5c571d02900219098517c0') + version('0.1-1', sha256='22755c93c76c26252841f43195df31681ea865e91aa89726010bd1b9288ef48f') diff --git a/var/spack/repos/builtin/packages/r-plot3d/package.py b/var/spack/repos/builtin/packages/r-plot3d/package.py index 8e338d123bc..6a8ed0ac0ab 100644 --- a/var/spack/repos/builtin/packages/r-plot3d/package.py +++ b/var/spack/repos/builtin/packages/r-plot3d/package.py @@ -15,7 +15,7 @@ class RPlot3d(RPackage): url = "https://cloud.r-project.org/src/contrib/plot3D_1.1.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/plot3D" - version('1.1.1', '5135aa1f3cf6106f2ded3f393a24e75d') + version('1.1.1', sha256='f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632') depends_on('r@2.15:', type=('build', 'run')) depends_on('r-misc3d', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plotly/package.py b/var/spack/repos/builtin/packages/r-plotly/package.py index 29d1ea37a59..f6be7e55bde 100644 --- a/var/spack/repos/builtin/packages/r-plotly/package.py +++ b/var/spack/repos/builtin/packages/r-plotly/package.py @@ -16,11 +16,11 @@ class RPlotly(RPackage): version('4.9.0', sha256='f761148338231f210fd7fe2f8325ffe9cfdaaaeddd7b933b65c44ebb4f85e2cf') version('4.8.0', sha256='78f90282c831bbbb675ed4811fb506a98dd05e37251fabd42ebc263c80bae8a6') - version('4.7.1', '4799c8b429291d4c52fb904380806548') - version('4.7.0', '5bd52d515c01af7ff291c30a6cf23bec') - version('4.6.0', '27ff3de288bacfaad6e6694752ea2929') - version('4.5.6', 'e6e00177fa64dc6b1a199facfd73f585') - version('4.5.2', '7eb11b24a9faa9a572657fd89ed72fa5') + version('4.7.1', sha256='7cd4b040f9bfd9356a8a2aba59ccf318cae6b5d94ded7463e2e823c10fa74972') + version('4.7.0', sha256='daf2af53b4dc9413805bb62d668d1a3defbb7f755e3440e657195cdf18d318fc') + version('4.6.0', sha256='c0de45b2aff4122dc8aa9dbfe1cd88fa0a50e9415f397b5fe85cbacc0156d613') + version('4.5.6', sha256='1d3a4a4ff613d394a9670664fbaf51ddf7fc534278443b4fd99dd1eecf49dc27') + version('4.5.2', sha256='81ff375d4da69aeabe96e8edf2479c21f0ca97fb99b421af035a260f31d05023') depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index a03e77b93af..edb9c9f0d22 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -15,7 +15,7 @@ class RPlotrix(RPackage): version('3.7-6', sha256='83d5f7574592953288b4fe39c4c0dd7670d097598ad7f6bddbb0687a32954e46') version('3.7-5', sha256='b22f3f9d93961d23ad46e41597d1e45d2665ced04dcad8c40f6806a67cded14c') - version('3.6-4', 'efe9b9b093d8903228a9b56c46d943fa') - version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') + version('3.6-4', sha256='883b7d0a00c1b2b418f9167c72ed9e86eca3c9865d34158a7a6ad0b9bf95bff3') + version('3.6-3', sha256='217164bdd04405c3280a0c8b2691f289287f9851fa8248648a5ae38f54962741') depends_on('r@3.5.0:', when='@3.7-6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py index d310c5d5fb8..28977bfa951 100644 --- a/var/spack/repos/builtin/packages/r-pls/package.py +++ b/var/spack/repos/builtin/packages/r-pls/package.py @@ -17,6 +17,6 @@ class RPls(RPackage): version('2.7-1', sha256='f8fd817fc2aa046970c49a9a481489a3a2aef8b6f09293fb1f0218f00bfd834b') version('2.7-0', sha256='5ddc1249a14d69a7a39cc4ae81595ac8c0fbb1e46c911af67907baddeac35875') - version('2.6-0', '04e02e8e46d983c5ed53c1f952b329df') + version('2.6-0', sha256='3d8708fb7f45863d3861fd231e06955e6750bcbe717e1ccfcc6d66d0cb4d4596') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index c5fc1bf68d5..c51d3581249 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -19,7 +19,7 @@ class RPlyr(RPackage): url = "https://cloud.r-project.org/src/contrib/plyr_1.8.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/plyr" - version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b') + version('1.8.4', sha256='60b522d75961007658c9806f8394db27989f1154727cb0bb970062c96ec9eac5') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pmcmr/package.py b/var/spack/repos/builtin/packages/r-pmcmr/package.py index 3097e0861f8..505927ce057 100644 --- a/var/spack/repos/builtin/packages/r-pmcmr/package.py +++ b/var/spack/repos/builtin/packages/r-pmcmr/package.py @@ -26,6 +26,6 @@ class RPmcmr(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/PMCMR" version('4.3', sha256='328a2880dd614dc412e8dca21d29ed9d5eea29ccbe0eff98c8068100856c7b25') - version('4.1', 'b9c0c4e4cb4f73ae36f45a47abae986a') + version('4.1', sha256='6c164e2976c59ddd27297433a34fa61b1e70b9e26265abdf9c8af1b639d2d555') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py index a9bdc3318ba..d43ccb73141 100644 --- a/var/spack/repos/builtin/packages/r-png/package.py +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -15,7 +15,7 @@ class RPng(RPackage): url = "https://cloud.r-project.org/src/contrib/png_0.1-7.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/png" - version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f') + version('0.1-7', sha256='e269ff968f04384fc9421d17cfc7c10cf7756b11c2d6d126e9776f5aca65553c') depends_on('r@2.9.0:', type=('build', 'run')) depends_on('libpng') diff --git a/var/spack/repos/builtin/packages/r-powerlaw/package.py b/var/spack/repos/builtin/packages/r-powerlaw/package.py index 0ee38127a04..1f2382d6f7d 100644 --- a/var/spack/repos/builtin/packages/r-powerlaw/package.py +++ b/var/spack/repos/builtin/packages/r-powerlaw/package.py @@ -17,7 +17,7 @@ class RPowerlaw(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/poweRlaw" version('0.70.2', sha256='240f1454389b1a00ad483fb63e5b53243cc9367f21a3e7253ab2c293673459ab') - version('0.70.1', '4117cb95c37f72441f320ea12f553065') + version('0.70.1', sha256='15b1b8dadeb550c01b9f1308cfa64720be6fbf56afb80f6a096987d6a0055913') depends_on('r@3.1.0:', when='@:0.70.1', type=('build', 'run')) depends_on('r@3.4.0:', when='@0.70.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py index fd12aaddee5..7ed08e4f1ed 100644 --- a/var/spack/repos/builtin/packages/r-prabclus/package.py +++ b/var/spack/repos/builtin/packages/r-prabclus/package.py @@ -16,7 +16,7 @@ class RPrabclus(RPackage): version('2.3-1', sha256='ef3294767d43bc3f72478fdaf0d1f13c8de18881bf9040c9f1add68af808b3c0') version('2.2-7.1', sha256='2c5bf3bbb0d225e04c53bb0e11e9c2a6809f0e46d95b8f6dc14b9dd6a2452975') - version('2.2-6', '7f835dcc113243e1db74aad28ce93d11') + version('2.2-6', sha256='41792980e40ba18204fab92d85120dcd468860e2204e52fb42636c6f7aee5a62') depends_on('r@2.1.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py index 830b9cfc00c..706c23ee6a6 100644 --- a/var/spack/repos/builtin/packages/r-praise/package.py +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -14,4 +14,4 @@ class RPraise(RPackage): url = "https://cloud.r-project.org/src/contrib/praise_1.0.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/praise" - version('1.0.0', '9318724cec0454884b5f762bee2da6a1') + version('1.0.0', sha256='5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd') diff --git a/var/spack/repos/builtin/packages/r-prettyunits/package.py b/var/spack/repos/builtin/packages/r-prettyunits/package.py index 00d903db5c9..4d57055ef15 100644 --- a/var/spack/repos/builtin/packages/r-prettyunits/package.py +++ b/var/spack/repos/builtin/packages/r-prettyunits/package.py @@ -15,7 +15,7 @@ class RPrettyunits(RPackage): url = "https://cloud.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/prettyunits" - version('1.0.2', '0a091a297e8b37df54e7fcf28697ee50') + version('1.0.2', sha256='35a4980586c20650538ae1e4fed4d80fdde3f212b98546fc3c7d9469a1207f5c') depends_on('r-magrittr', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py index e945333a1cf..022f3a6f612 100644 --- a/var/spack/repos/builtin/packages/r-prodlim/package.py +++ b/var/spack/repos/builtin/packages/r-prodlim/package.py @@ -17,7 +17,7 @@ class RProdlim(RPackage): version('2018.04.18', sha256='4b22b54fdf712439309be0ff74f63cde9080464667b00e19823372ac0fc254ab') version('1.6.1', sha256='3f2665257118a3db8682731a500b1ae4d669af344672dc2037f987bee3cca154') - version('1.5.9', 'e0843053c9270e41b657a733d6675dc9') + version('1.5.9', sha256='853644886c57102e7f6dd26b6e03e54bf3f9e126f54c76f8d63a3324811f7b42') depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-progress/package.py b/var/spack/repos/builtin/packages/r-progress/package.py index 1d74872e341..13f2217c49f 100644 --- a/var/spack/repos/builtin/packages/r-progress/package.py +++ b/var/spack/repos/builtin/packages/r-progress/package.py @@ -19,7 +19,7 @@ class RProgress(RPackage): version('1.2.2', sha256='b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35') version('1.2.1', sha256='7401e86ff76bef4d26508b74ee8bd169a0377b2738d9ec79ebff0b7fd5c55326') - version('1.1.2', 'b3698672896125137e0077bc97132428') + version('1.1.2', sha256='a9f4abfd9579b80967cd681041643fe9dfcc4eb3beeba45391bb64e9209baabb') depends_on('r-r6', type=('build', 'run')) depends_on('r-prettyunits', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py index d2f5012ccb2..346cf3cf928 100644 --- a/var/spack/repos/builtin/packages/r-proto/package.py +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -15,4 +15,4 @@ class RProto(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/proto" version('1.0.0', sha256='9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1') - version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212') + version('0.3-10', sha256='d0d941bfbf247879b3510c8ef3e35853b1fbe83ff3ce952e93d3f8244afcbb0e') diff --git a/var/spack/repos/builtin/packages/r-proxy/package.py b/var/spack/repos/builtin/packages/r-proxy/package.py index 94c954f821a..93063a3fc82 100644 --- a/var/spack/repos/builtin/packages/r-proxy/package.py +++ b/var/spack/repos/builtin/packages/r-proxy/package.py @@ -16,7 +16,7 @@ class RProxy(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/proxy" version('0.4-23', sha256='9dd4eb0978f40e4fcb55c8a8a26266d32eff9c63ac9dfe70cf1f664ca9c3669d') - version('0.4-19', '279a01a1cc12ed50208c98196d78a5d7') + version('0.4-19', sha256='6b27e275018366e6024382704da9a9757c8878535dbcd7d450824b70e2e34d51') depends_on('r@3.3.2:', when='@:0.4-20', type=('build', 'run')) depends_on('r@3.4.0:', when='@0.4-21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py index a3ba60d71e3..81a59b02c85 100644 --- a/var/spack/repos/builtin/packages/r-pryr/package.py +++ b/var/spack/repos/builtin/packages/r-pryr/package.py @@ -17,7 +17,7 @@ class RPryr(RPackage): version('0.1.4', sha256='d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b') version('0.1.3', sha256='6acd88341dde4fe247a5cafd3949b281dc6742b7d60f68b57c1feb84b96739ac') - version('0.1.2', '66b597a762aa15a3b7037779522983b6') + version('0.1.2', sha256='65c2b7c9f96e2aa683ac9cdab3c215fd3039ecd66a2ba7002a8e77881428c3c6') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-psych/package.py b/var/spack/repos/builtin/packages/r-psych/package.py index e98d427f3d7..fcabd1e0c91 100644 --- a/var/spack/repos/builtin/packages/r-psych/package.py +++ b/var/spack/repos/builtin/packages/r-psych/package.py @@ -30,7 +30,7 @@ class RPsych(RPackage): version('1.8.12', sha256='6e175e049bc1ee5b79a9e51ccafb22b962b4e6c839ce5c9cfa1ad83967037743') version('1.8.10', sha256='e8901ddab14729bfccbd82a8824fbb6523c10c2cd8fb7199b1ca56a7ffcb6e58') - version('1.7.8', 'db37f2f85ff5470ee40bbc0a58ebe22b') + version('1.7.8', sha256='f328ea602e22b0e7e5f310a8d19f305d8e0a3a86040cdfb64863b68b56d55135') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mnormt', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ptw/package.py b/var/spack/repos/builtin/packages/r-ptw/package.py index a571c31e308..19c11a51d76 100644 --- a/var/spack/repos/builtin/packages/r-ptw/package.py +++ b/var/spack/repos/builtin/packages/r-ptw/package.py @@ -23,6 +23,6 @@ class RPtw(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/ptw" version('1.9-13', sha256='7855e74a167db3d3eba9df9d9c3daa25d7cf487cbcfe8b095f16d96eba862f46') - version('1.9-12', 'ddff887752d789ea72db3ee235ae7c67') + version('1.9-12', sha256='cdb1752e04e661e379f11867b0a17e2177e9ee647c54bbcc37d39d6b8c062b84') depends_on('r-nloptr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py index 5e80aec44e3..b948f733fa1 100644 --- a/var/spack/repos/builtin/packages/r-purrr/package.py +++ b/var/spack/repos/builtin/packages/r-purrr/package.py @@ -15,7 +15,7 @@ class RPurrr(RPackage): version('0.3.2', sha256='27c74dd9e4f6f14bf442473df22bcafc068822f7f138f0870326532f143a9a31') version('0.3.1', sha256='c2a3c9901192efd8a04976676f84885a005db88deb1432e4750900c7b3b7883b') - version('0.2.4', 'd9a11e6c14771beb3ebe8f4771a552f3') + version('0.2.4', sha256='ed8d0f69d29b95c2289ae52be08a0e65f8171abb6d2587de7b57328bf3b2eb71') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-magrittr@1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quadprog/package.py b/var/spack/repos/builtin/packages/r-quadprog/package.py index d9ff67e8040..7296854f129 100644 --- a/var/spack/repos/builtin/packages/r-quadprog/package.py +++ b/var/spack/repos/builtin/packages/r-quadprog/package.py @@ -16,6 +16,6 @@ class RQuadprog(RPackage): version('1.5-7', sha256='1af41e57df6f2d08ee8b72a1a5ada137beadb36c7ec9ab9bdb7c05226e8ae76d') version('1.5-6', sha256='1443e5ffdf884b13dd454e4f6aa260fce6ec47e6845d85b62238c206ce57dcba') - version('1.5-5', '8442f37afd8d0b19b12e77d63e6515ad') + version('1.5-5', sha256='d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py index 9fb04ff133f..717dccfd2d6 100644 --- a/var/spack/repos/builtin/packages/r-quantmod/package.py +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -16,8 +16,8 @@ class RQuantmod(RPackage): version('0.4-15', sha256='7ef2e798d4d8e4d2af0a5b2b9fecebec30568087afbd24bfd923cdeb8b53df53') version('0.4-14', sha256='d95b1acf73328d675bbad18a93fa3c40faf58959e0401458ad21cf6b9f9254b3') - version('0.4-10', 'e4119c673567801eee16dcbbd0265de8') - version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631') + version('0.4-10', sha256='030040aa567adaba1ea4a1f05eb45712dbdaabbabca72733e7fb2984051f688b') + version('0.4-5', sha256='c7889eb55a21296e7bda1242c46e734a0a8bd6dcbf5726aafae5313354eec893') depends_on('r@3.2.0:', when='@0.4-11:', type=('build', 'run')) depends_on('r-xts@0.9-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py index 65b538146e1..f96d0bf704e 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -21,8 +21,8 @@ class RQuantreg(RPackage): version('5.51', sha256='df1330d245f66ee6d924b209bd4c15d44ff8cce52667959ec0d299975428bdb1') version('5.42.1', sha256='4cc2b0883c52694e58fcfde83e30e4a54be9f4d9cbcf6138f6498cc8e0b3ccab') version('5.40', sha256='86e310a235009ab85635dfb8803c175f80a35892e237db2525c4ef37a98936eb') - version('5.29', '643ca728200d13f8c2e62365204e9907') - version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') + version('5.29', sha256='bb4638e8f295579afa5c40c4de7266a6ea9221436ba4ca802f94cdb43bf20f25') + version('5.26', sha256='9d7403f7c5ee219ec155838648401a1c4915a46a74f5774a0f6876c537ef2c87') depends_on('r@2.6:', type=('build', 'run')) depends_on('r-sparsem', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r-methodss3/package.py b/var/spack/repos/builtin/packages/r-r-methodss3/package.py index e2887c572d8..585e4cdd6b5 100644 --- a/var/spack/repos/builtin/packages/r-r-methodss3/package.py +++ b/var/spack/repos/builtin/packages/r-r-methodss3/package.py @@ -21,6 +21,6 @@ class RRMethodss3(RPackage): url = "https://cloud.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/R.methodsS3" - version('1.7.1', 'c88e815837f268affd4f2a39c737d969') + version('1.7.1', sha256='44b840399266cd27f8f9157777b4d9d85ab7bd31bfdc143b3fc45079a2d8e687') depends_on('r@2.13.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r-oo/package.py b/var/spack/repos/builtin/packages/r-r-oo/package.py index 8dc62a1b166..cc2d2b1f02a 100644 --- a/var/spack/repos/builtin/packages/r-r-oo/package.py +++ b/var/spack/repos/builtin/packages/r-r-oo/package.py @@ -20,7 +20,7 @@ class RROo(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/R.oo" version('1.22.0', sha256='c0862e4608fb2b8f91ec4494d46c2f3ba7bc44999f9aa3d7b9625d3792e7dd4c') - version('1.21.0', 'f0062095c763faaeba30558303f68bc3') + version('1.21.0', sha256='645ceec2f815ed39650ca72db87fb4ece7357857875a4ec73e18bfaf647f431c') depends_on('r@2.13.0:', type=('build', 'run')) depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r-utils/package.py b/var/spack/repos/builtin/packages/r-r-utils/package.py index 9318bdc1d9c..eb8a18b5db8 100644 --- a/var/spack/repos/builtin/packages/r-r-utils/package.py +++ b/var/spack/repos/builtin/packages/r-r-utils/package.py @@ -15,7 +15,7 @@ class RRUtils(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/R.utils" version('2.9.0', sha256='b2aacc5a55d3ea86c41ac576d2583e446af145f4cb1103ad7b6f95b09ab09ff0') - version('2.5.0', 'a728ef3ceb35cafc4c39ea577cecc38b') + version('2.5.0', sha256='1ae1a0f0c6a4972bb2369a2dbccd29ade87d747255ff9cb5a0bd784a5be1039f') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-r-oo@1.22.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py index 983cabee2de..3b2c3867a08 100644 --- a/var/spack/repos/builtin/packages/r-r6/package.py +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -19,8 +19,8 @@ class RR6(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/R6" version('2.4.0', sha256='70be110174fbf5f5304049b186a6f9c05b77bfaec6d8caf980fcef5da6e0abce') - version('2.2.2', '635b58c65bff624a1fab69c6b1989801') - version('2.2.0', '659d83b2d3f7a308a48332b4cfbdab49') - version('2.1.2', 'b6afb9430e48707be87638675390e457') + version('2.2.2', sha256='087756f471884c3b3ead80215a7cc5636a78b8a956e91675acfe2896426eae8f') + version('2.2.0', sha256='7d7bddc4303fafa99954182ccad938166d681499d4e9ae7001d21b0fd60d25c7') + version('2.1.2', sha256='1bfbb14d9da85b5f8eb865aa6355b2c71c9f86b71f616bfe5a28939b62484d79') depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomfields/package.py b/var/spack/repos/builtin/packages/r-randomfields/package.py index 815eba35570..42be2728a19 100644 --- a/var/spack/repos/builtin/packages/r-randomfields/package.py +++ b/var/spack/repos/builtin/packages/r-randomfields/package.py @@ -17,7 +17,7 @@ class RRandomfields(RPackage): version('3.3.6', sha256='51b7bfb4e5bd7fd0ce1207c77f428508a6cd3dfc9de01545a8724dfd9c050213') version('3.3.4', sha256='a340d4f3ba7950d62acdfa19b9724c82e439d7b1a9f73340124038b7c90c73d4') - version('3.1.50', 'fd91aea76365427c0ba3b25fb3af43a6') + version('3.1.50', sha256='2d6a07c3a716ce20f9c685deb59e8fcc64fd52c8a50b0f04baf451b6b928e848') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index fa51ba6c9ab..587b0e356fc 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -18,6 +18,6 @@ class RRandomfieldsutils(RPackage): version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') version('0.5.1', sha256='a95aab4e2025c4247503ff513570a65aa3c8e63cb7ce2979c9317a2798dfaca2') - version('0.3.25', '026c15a23296c9726012135891f016d5') + version('0.3.25', md5='026c15a23296c9726012135891f016d5') depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py index b24defd121c..d20c4d32c47 100644 --- a/var/spack/repos/builtin/packages/r-randomforest/package.py +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -15,7 +15,7 @@ class RRandomforest(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/randomForest" version('4.6-14', sha256='f4b88920419eb0a89d0bc5744af0416d92d112988702dc726882394128a8754d') - version('4.6-12', '071c03af974198e861f1475c5bab9e7a') + version('4.6-12', sha256='6e512f8f88a51c01a918360acba61f1f39432f6e690bc231b7864218558b83c4') depends_on('r@2.5.0:', when='@:4.6-12', type=('build', 'run')) depends_on('r@3.2.2:', when='@4.6-14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ranger/package.py b/var/spack/repos/builtin/packages/r-ranger/package.py index a8cf0f0d0af..b16c2e2eada 100644 --- a/var/spack/repos/builtin/packages/r-ranger/package.py +++ b/var/spack/repos/builtin/packages/r-ranger/package.py @@ -16,11 +16,11 @@ class RRanger(RPackage): version('0.11.2', sha256='13ac8a9433fdd92f62f66de44abc52477dcbb436b2045c1947951a266bffbeeb') version('0.11.1', sha256='999fb114602e27601ff0fe8ab461c39d667c6f5e8434e7feb3d21c7caf0dcffb') - version('0.8.0', '1501380f418e784a6159bc1fb06fd32c') - version('0.7.0', 'c7fbcbab7c195bc8e65b1ceb3baeb87f') - version('0.6.0', '047ad26289c9b528b7476aa4811b4111') - version('0.5.0', 'd45001c8ff58d3078de7353971219927') - version('0.4.0', 'd404d8a9142372e3c77482b6b7dc469b') + version('0.8.0', sha256='7f0fdee2f2d553a0aec56c2a4a4ff9dd972e1c7284118d9ea570749e0eaaabb9') + version('0.7.0', sha256='83f4b06c6e63da979a20b757aaf0042928db453c12d89281afd40046e6b5393c') + version('0.6.0', sha256='2759c2a3271098a4cfb63cd3ea68acaf645c92cb24c86fba098ada06e2e298bb') + version('0.5.0', sha256='bc55811e723c9076c35aac4d82f29770ef84b40846198235d8b0ea9a4e91f144') + version('0.4.0', sha256='d9f5761c3b07357aa586270cf7cbc97fc3db56ba731b6d0f3baf296f635f2be5') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rappdirs/package.py b/var/spack/repos/builtin/packages/r-rappdirs/package.py index 5366f074940..25644aa1f2e 100644 --- a/var/spack/repos/builtin/packages/r-rappdirs/package.py +++ b/var/spack/repos/builtin/packages/r-rappdirs/package.py @@ -15,6 +15,6 @@ class RRappdirs(RPackage): url = "https://cloud.r-project.org/src/contrib/rappdirs_0.3.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rappdirs" - version('0.3.1', 'fbbdceda2aa49374e61c7d387bf9ea21') + version('0.3.1', sha256='2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a') depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py index 912f9c17e05..80e83d79c27 100644 --- a/var/spack/repos/builtin/packages/r-raster/package.py +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -17,7 +17,7 @@ class RRaster(RPackage): version('2.9-23', sha256='90aaec9e3b1e3e6015d9993ea7491e008f2f71990f8abb8610f979c4e28b38af') version('2.9-22', sha256='8107d95f1aa85cea801c8101c6aa391becfef4b5b915d9bc7a323531fee26128') - version('2.5-8', '2a7db931c74d50516e82d04687c0a577') + version('2.5-8', sha256='47992abd783450513fbce3770298cc257030bf0eb77e42aa3a4b3924b16264cc') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-sp@1.2-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py index b0e8e510f76..619e67050cf 100644 --- a/var/spack/repos/builtin/packages/r-rbokeh/package.py +++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py @@ -15,7 +15,7 @@ class RRbokeh(RPackage): url = "https://cloud.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rbokeh" - version('0.5.0', '4e14778c3fbd9286460ca28c68f57d10') + version('0.5.0', sha256='499c3224a7dcaeb4bb60fd645b3ef528a20e59437747a073713941b80cbcebd2') depends_on('r-htmlwidgets@0.5:', type=('build', 'run')) depends_on('r-maps', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py index b2cb38aa1f2..d3770d93b53 100644 --- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -14,6 +14,6 @@ class RRcolorbrewer(RPackage): url = "https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/RColorBrewer" - version('1.1-2', '66054d83eade4dff8a43ad4732691182') + version('1.1-2', sha256='f3e9781e84e114b7a88eb099825936cc5ae7276bbba5af94d35adb1b3ea2ccdd') depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index e2abba3b833..5053b32ce14 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -26,14 +26,14 @@ class RRcpp(RPackage): version('0.12.19', sha256='63aeb6d4b58cd2899ded26f38a77d461397d5b0dc5936f187d3ca6cd958ab582') version('0.12.18', sha256='fcecd01e53cfcbcf58dec19842b7235a917b8d98988e4003cc090478c5bbd300') version('0.12.17', sha256='4227c45c92416b5378ed5761495f9b3932d481bae9a190fb584d17c10744af23') - version('0.12.16', 'ab5107766c63d66065ed1a92a4cab1b7') - version('0.12.15', 'bebac0782862c15c2944764343e55582') - version('0.12.14', '89a3dbad0aa3e345b9d0b862fa1fc56a') - version('0.12.13', '5186d119132bfe07f66da74c50b190a4') - version('0.12.12', '97b36a3b567e3438067c4a7d0075fd90') - version('0.12.11', 'ea1710213cbb1d91b1d0318e6fa9aa37') - version('0.12.9', '691c49b12794507288b728ede03668a5') - version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b') - version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') + version('0.12.16', sha256='d4e1636e53e2b656e173b49085b7abbb627981787cd63d63df325c713c83a8e6') + version('0.12.15', sha256='bb6fddf67c888ec4e28cdf72539663cdbda8df5861e5579f4fc6b64da836dbde') + version('0.12.14', sha256='da28fcfc3fe7c48d02f9f3e309b56f4be52b14a01216a23e3de8f9d6deeb7e63') + version('0.12.13', sha256='a570ad88282fb961ba32c867c49dbd3dce6f4dfc7b59ab1fbde510449827a8ae') + version('0.12.12', sha256='9f3eb1e6154f4d56b52ab550a22e522e9999c7998388fdc235e48af5e8c6deaf') + version('0.12.11', sha256='bd8cae275bb45cf98f3e3c6e1b5189bdd9c02e74b25241419ed3e4851d859c7f') + version('0.12.9', sha256='f0bd0df28ded09cb3cb5c2a348e2f81d1a2bf0b2248e9aecd67aeeeaeabbcd5e') + version('0.12.6', sha256='1bb54e03b817a3d6ab5917f1bbf5250c6b33f61e466628a378022ed65a010141') + version('0.12.5', sha256='13449481c91b5271b34d81f462864864c1905bb05021781eee11c36fdafa80ef') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py index 55f412a45c9..62504685729 100644 --- a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py +++ b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py @@ -16,7 +16,7 @@ class RRcpparmadillo(RPackage): version('0.9.600.4.0', sha256='2057b7aa965a4c821dd734276d8e6a01cd59a1b52536b65cb815fa7e8c114f1e') version('0.9.400.3.0', sha256='56936d501fe8e6f8796ae1a6badb9294d7dad98a0b557c3b3ce6bd4ecaad13b0') - version('0.8.100.1.0', 'a79c0ee967f502702414bc3c80c88f56') + version('0.8.100.1.0', sha256='97ca929b34d84d99d7cadc3612b544632cdd0c43ed962933a3d47caa27854fa7') depends_on('r@3.3.0:', when='@0.8.500.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppblaze/package.py b/var/spack/repos/builtin/packages/r-rcppblaze/package.py index e9af43aded0..b043f054eba 100644 --- a/var/spack/repos/builtin/packages/r-rcppblaze/package.py +++ b/var/spack/repos/builtin/packages/r-rcppblaze/package.py @@ -38,7 +38,7 @@ class RRcppblaze(RPackage): url = "https://cloud.r-project.org/src/contrib/RcppBlaze_0.2.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppBlaze" - version('0.2.2', '22ecae73cf1bebce06ed6387d49f2c77') + version('0.2.2', sha256='67550ed8aea12a219047af61b41e5b9f991608a21ce9a8fbf7ac55da0f7c2742') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppcctz/package.py b/var/spack/repos/builtin/packages/r-rcppcctz/package.py index d4f48d3a5c1..7948218f5ea 100644 --- a/var/spack/repos/builtin/packages/r-rcppcctz/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcctz/package.py @@ -19,6 +19,6 @@ class RRcppcctz(RPackage): version('0.2.6', sha256='0e9a76055d29da24cd4c4069c78c1f44998f3461be60c7a6c3e7a35059fb79ae') version('0.2.4', sha256='98b6867d38abe03957fe803e88b6cc2d122b85a68ef07fa86f7e1009d6c00819') - version('0.2.3', '7635014a1cc696a3f00a7619fb5d7008') + version('0.2.3', sha256='0fefcc98387b2c1a5907e5230babb46e2cc11b603424f458f515e445a3236031') depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py index dc517e90603..822092a1034 100644 --- a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py @@ -14,7 +14,7 @@ class RRcppcnpy(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppCNPy" version('0.2.10', sha256='77d6fbc86520a08da40d44c0b82767099f8f719ca95870d91efff1a9cab1ab9c') - version('0.2.9', '7f63354d15928b6716830c2975b3baf0') + version('0.2.9', sha256='733f004ad1a8b0e5aafbf547c4349d2df3118afd57f1ff99f20e39135c6edb30') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index 221a998383d..1095229c213 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -27,9 +27,9 @@ class RRcppeigen(RPackage): version('0.3.3.5.0', sha256='e5c6af17770c5f57b7cf2fba04ad1a519901b446e8138bfff221952458207f05') version('0.3.3.4.0', sha256='11020c567b299b1eac95e8a4d57abf0315931286907823dc7b66c44d0dd6dad4') - version('0.3.3.3.1', '1a5ae17828813e40e6b3e7400e408a2b') - version('0.3.2.9.0', '14a7786882a5d9862d53c4b2217df318') - version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') + version('0.3.3.3.1', sha256='14fdd2cb764d0a822e11b8f09dcf1c3c8580d416f053404732064d8f2b176f24') + version('0.3.2.9.0', sha256='25affba9065e3c12d67b1934d1ce97a928a4011a7738f7b90f0e9830409ec93b') + version('0.3.2.8.1', sha256='ceccb8785531c5c23f9232b594e5372c214a114a08ec759115e946badd08d681') depends_on('r@2.15.1:', type=('build', 'run')) depends_on('r-matrix@1.1-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppprogress/package.py b/var/spack/repos/builtin/packages/r-rcppprogress/package.py index 4680b00964e..618bd87ece9 100644 --- a/var/spack/repos/builtin/packages/r-rcppprogress/package.py +++ b/var/spack/repos/builtin/packages/r-rcppprogress/package.py @@ -17,9 +17,9 @@ class RRcppprogress(RPackage): version('0.4.1', sha256='11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a') version('0.4', sha256='706e14360dbc5976db05c2ac6692c3279c0f8c95e72bf9d4becd9e1348025e3e') - version('0.3', '3cd527af84bc6fcb3c77422e0ff09dba') - version('0.2.1', 'c9cd69759ff457acfee0b52353f9af1b') - version('0.2', '9522c962ecddd4895b5636e7a499bda5') - version('0.1', '34afefe0580ca42b6353533fe758d5bf') + version('0.3', sha256='3de5dc47cc2f9e839f92355c463289531e8c13806e54c7438f63c7c34378261d') + version('0.2.1', sha256='cf121d34766344d05dea77895cd2e48a977ebb28ccf7af14bb46c3744c4a50b5') + version('0.2', sha256='ca32624739058f1b5aab18b09dc4c613ecfd18a3ace39f3b97790232db829481') + version('0.1', sha256='04f71d3391b7dfab997afadf7ffdd87b88037f7fbc751bea544ad2a65e2872bf') depends_on('r-rcpp@0.9.4:', when='@:0.4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcurl/package.py b/var/spack/repos/builtin/packages/r-rcurl/package.py index 0af3d5275ea..3014977be62 100644 --- a/var/spack/repos/builtin/packages/r-rcurl/package.py +++ b/var/spack/repos/builtin/packages/r-rcurl/package.py @@ -23,7 +23,7 @@ class RRcurl(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/RCurl" version('1.95-4.12', sha256='393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4') - version('1.95-4.8', '9c8aaff986eb2792c89dd3ae54d21580') + version('1.95-4.8', sha256='e72243251bbbec341bc5864305bb8cc23d311d19c5d0d9310afec7eb35aa2bfb') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-bitops', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rda/package.py b/var/spack/repos/builtin/packages/r-rda/package.py index 4cdbe65ac05..f5d0a08bf65 100644 --- a/var/spack/repos/builtin/packages/r-rda/package.py +++ b/var/spack/repos/builtin/packages/r-rda/package.py @@ -16,6 +16,6 @@ class RRda(RPackage): version('1.0.2-2.1', sha256='6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8') version('1.0.2-2', sha256='52ee41249b860af81dc692eee38cd4f8f26d3fbe34cb274f4e118de0013b58bc') - version('1.0.2-1', '78060c5e054a63a2df4ae4002d7247bc') + version('1.0.2-1', sha256='e5b96610ec9e82f12efe5dbb9a3ec9ecba9aaddfad1d6ab3f8c37d15fc2b42b7') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-readr/package.py b/var/spack/repos/builtin/packages/r-readr/package.py index 586d0d95285..7020c1e2fca 100644 --- a/var/spack/repos/builtin/packages/r-readr/package.py +++ b/var/spack/repos/builtin/packages/r-readr/package.py @@ -17,7 +17,7 @@ class RReadr(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/readr" version('1.3.1', sha256='33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3') - version('1.1.1', 'cffb6669664f6a0f6fe172542e64cb47') + version('1.1.1', sha256='1a29b99009a06f2cee18d08bc6201fd4985b6d45c76cefca65084dcc1a2f7cb3') depends_on('r@3.0.2:', when='@:1.2.1', type=('build', 'run')) depends_on('r@3.1:', when='@1.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-readxl/package.py b/var/spack/repos/builtin/packages/r-readxl/package.py index 599534113d3..6d97196aa25 100644 --- a/var/spack/repos/builtin/packages/r-readxl/package.py +++ b/var/spack/repos/builtin/packages/r-readxl/package.py @@ -20,7 +20,7 @@ class RReadxl(RPackage): version('1.3.1', sha256='24b441713e2f46a3e7c6813230ad6ea4d4ddf7e0816ad76614f33094fbaaaa96') version('1.3.0', sha256='8379d1026dcfc662d073eb1c69ed1d90aa6439d6cb3c6fc1b5d1db4f51b3fadc') version('1.1.0', sha256='b63d21fc6510acb373e96deaec45e966a523ec75cbec75a089529297ed443116') - version('1.0.0', '030c47ae1af5dd4168087160c29131e4') + version('1.0.0', sha256='fbd62f07fed7946363698a57be88f4ef3fa254ecf456ef292535849c787fc7ad') depends_on('r-tibble@1.3.1:', type=('build', 'run')) depends_on('r-rcpp@0.12.18:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py index 457908f4dfd..f8f204f0a19 100644 --- a/var/spack/repos/builtin/packages/r-registry/package.py +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -15,6 +15,6 @@ class RRegistry(RPackage): version('0.5-1', sha256='dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc') version('0.5', sha256='5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb') - version('0.3', '85345b334ec81eb3da6edcbb27c5f421') + version('0.3', sha256='58a5c43b8012ca5e509fa29a8daf6f24f097b8eb021a723f6a9c33db1dd3f430') depends_on('r@2.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rematch/package.py b/var/spack/repos/builtin/packages/r-rematch/package.py index 2887630876a..d4172c70da0 100644 --- a/var/spack/repos/builtin/packages/r-rematch/package.py +++ b/var/spack/repos/builtin/packages/r-rematch/package.py @@ -15,4 +15,4 @@ class RRematch(RPackage): url = "https://cloud.r-project.org/src/contrib/rematch_1.0.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rematch" - version('1.0.1', '5271666295e232931f21499522489dd3') + version('1.0.1', sha256='a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578') diff --git a/var/spack/repos/builtin/packages/r-reordercluster/package.py b/var/spack/repos/builtin/packages/r-reordercluster/package.py index 5d63690aa80..3c85ee3503b 100644 --- a/var/spack/repos/builtin/packages/r-reordercluster/package.py +++ b/var/spack/repos/builtin/packages/r-reordercluster/package.py @@ -15,7 +15,7 @@ class RReordercluster(RPackage): url = "https://cloud.r-project.org/src/contrib/ReorderCluster_1.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/ReorderCluster" - version('1.0', '67ba34acb15dda75389a822bd2fdd31a') + version('1.0', sha256='a87898faa20380aac3e06a52eedcb2f0eb2b35ab74fdc3435d40ee9f1d28476b') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-gplots', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py index 90da8713f61..925ab477eaf 100644 --- a/var/spack/repos/builtin/packages/r-repr/package.py +++ b/var/spack/repos/builtin/packages/r-repr/package.py @@ -17,7 +17,7 @@ class RRepr(RPackage): version('1.0.1', sha256='ecde22c17fd800e1ff5c2b2962689119aa486fba40fbc6f2c50e8d4cc61bc44b') version('1.0.0', sha256='98b2eb1058c1cb2caa8f98708b63726f5564b45de03d38b95ff6b963a8261f49') - version('0.9', 'db5ff74893063b492f684e42283070bd') + version('0.9', sha256='24cac6e98f2a7e5483cf87aaffcb37611702099b63d3783e319441b4ecd0264b') depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-htmltools', when='@0.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reprex/package.py b/var/spack/repos/builtin/packages/r-reprex/package.py index 7a0f5063891..9c9206e9a65 100644 --- a/var/spack/repos/builtin/packages/r-reprex/package.py +++ b/var/spack/repos/builtin/packages/r-reprex/package.py @@ -21,7 +21,7 @@ class RReprex(RPackage): version('0.3.0', sha256='203c2ae6343f6ff887e7a5a3f5d20bae465f6e8d9745c982479f5385f4effb6c') version('0.2.1', sha256='5d234ddfbcadc5a5194a58eb88973c51581e7e2e231f146974af8f42747b45f3') - version('0.1.1', 'fcd89995d7b35a2ddd4269973937bde3') + version('0.1.1', sha256='919ae93039b2d8fb8eace98da9376c031d734d9e75c237efb24d047f35b5ba4b') depends_on('r@3.0.2:', when='@:0.1.2', type=('build', 'run')) depends_on('r@3.1:', when='@0.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reshape/package.py b/var/spack/repos/builtin/packages/r-reshape/package.py index ed783c9def9..9ef32d2fb65 100644 --- a/var/spack/repos/builtin/packages/r-reshape/package.py +++ b/var/spack/repos/builtin/packages/r-reshape/package.py @@ -15,7 +15,7 @@ class RReshape(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/reshape" version('0.8.8', sha256='4d5597fde8511e8fe4e4d1fd7adfc7ab37ff41ac68c76a746f7487d7b106d168') - version('0.8.7', '0b0eececc5eb74dea9d59a985bce6211') + version('0.8.7', sha256='2fa6c87d1e89f182e51bc5a4fcda3d42d83b8fb4474ca525fa7a8db5081f3992') depends_on('r@2.6.1:', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index 0a04e1b4edf..4feabd2e1dc 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -15,8 +15,8 @@ class RReshape2(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/reshape2" version('1.4.3', sha256='8aff94c935e75032344b52407593392ddd4e16a88bb206984340c816d42c710e') - version('1.4.2', 'c851a0312191b8c5bab956445df7cf5f') - version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') + version('1.4.2', sha256='6d3783610379be4c5676d9236cf66276a166b5b96c18f2759e9b219758959b6b') + version('1.4.1', sha256='fbd49f75a5b0b7266378515af98db310cf6c772bf6e68bed01f38ee99b408042') depends_on('r@3.1:', when='@1.4.3:', type=('build', 'run')) depends_on('r-plyr@1.8.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rex/package.py b/var/spack/repos/builtin/packages/r-rex/package.py index 54d124d84a3..168aced5302 100644 --- a/var/spack/repos/builtin/packages/r-rex/package.py +++ b/var/spack/repos/builtin/packages/r-rex/package.py @@ -13,7 +13,7 @@ class RRex(RPackage): url = "https://cloud.r-project.org/src/contrib/rex_1.1.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rex" - version('1.1.2', '8820b4d4fe3718f275847b6f2cf83689') + version('1.1.2', sha256='bd3c74ceaf335336f5dd04314d0a791f6311e421a2158f321f5aab275f539a2a') depends_on('r-lazyeval', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgdal/package.py b/var/spack/repos/builtin/packages/r-rgdal/package.py index 39c95f3cb5f..156781d24a8 100644 --- a/var/spack/repos/builtin/packages/r-rgdal/package.py +++ b/var/spack/repos/builtin/packages/r-rgdal/package.py @@ -23,7 +23,7 @@ class RRgdal(RPackage): version('1.4-4', sha256='2532e76e0af27d145f799d70006a5dbecb2d3be698e3d0bbf580f4c41a34c5d7') version('1.3-9', sha256='3e44f88d09894be4c0abd8874d00b40a4a5f4542b75250d098ffbb3ba41e2654') - version('1.2-16', 'de83bf08519a53de68a7632ecb7f2dc9') + version('1.2-16', sha256='017fefea4f9a6d4540d128c707197b7025b55e4aff98fc763065366b025b03c9') depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-sp@1.1-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgenoud/package.py b/var/spack/repos/builtin/packages/r-rgenoud/package.py index f5cc12720d0..46875cffeb4 100644 --- a/var/spack/repos/builtin/packages/r-rgenoud/package.py +++ b/var/spack/repos/builtin/packages/r-rgenoud/package.py @@ -15,6 +15,6 @@ class RRgenoud(RPackage): version('5.8-3.0', sha256='9beb11b5edab3ab3aa6001daa39668b240a8e0328be9d55db4e23ff88ce3235d') version('5.8-2.0', sha256='106c4f6a6df5159578e929a0141b3cfbaa88141a70703ff59a1fc48a27e2d239') - version('5.8-1.0', '85801093d2f1e6789683b46ab4a7d70f') + version('5.8-1.0', sha256='9deca354be6887f56bf9f4ca9a7291296050e51149ae9a3b757501704126c38a') depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgeos/package.py b/var/spack/repos/builtin/packages/r-rgeos/package.py index fd982f99968..248a5b1760e 100644 --- a/var/spack/repos/builtin/packages/r-rgeos/package.py +++ b/var/spack/repos/builtin/packages/r-rgeos/package.py @@ -18,7 +18,7 @@ class RRgeos(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/rgeos" version('0.5-1', sha256='8408973e7fe5648e39aa53f3d4bfe800638021a146a4e06f86496c0132e05488') - version('0.3-26', '7d10a28011b49f68c5817b6fbca132df') + version('0.3-26', sha256='98524a0b8113abe6c3d0ecc1f2f66e7ab6d40c783a76158cfc017e1ab1e3f433') depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-sp@1.1-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgl/package.py b/var/spack/repos/builtin/packages/r-rgl/package.py index 2195923a6e0..fcd18eb22fb 100644 --- a/var/spack/repos/builtin/packages/r-rgl/package.py +++ b/var/spack/repos/builtin/packages/r-rgl/package.py @@ -21,7 +21,7 @@ class RRgl(RPackage): version('0.100.26', sha256='e1889c2723ad458b39fdf9366fdaf590d7657d3762748f8534a8491ef754e740') version('0.100.24', sha256='1233a7bdc5a2b908fc64d5f56e92a0e123e8f7c0b9bac93dfd005608b78fa35a') version('0.99.16', sha256='692a545ed2ff0f5e15289338736f0e3c092667574c43ac358d8004901d7a1a61') - version('0.98.1', 'bd69e1d33f1590feb4b6dc080b133e5b') + version('0.98.1', sha256='5f49bed9e092e672f73c8a1a5365cdffcda06db0315ac087e95ab9c9c71a6986') depends_on('r@3.2:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py index 1c615f7e777..bd24f770568 100644 --- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -18,7 +18,7 @@ class RRgooglemaps(RPackage): version('1.4.3', sha256='44cb62bcd23e5b4807e91c5825352eb8d38aaaeb3b38a8271ca9f21c1e1d4b19') version('1.4.2', sha256='b479996fcb72f067644a7ea7f00325e44e76efd202e84aaab022753c4a6d5584') - version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5') + version('1.2.0.7', sha256='9c268a5a554ad6da69fb560d88dea9c86ec9e9a56b691f1b63faedfe20826712') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py index 5681e87113f..f540a83bf80 100644 --- a/var/spack/repos/builtin/packages/r-rinside/package.py +++ b/var/spack/repos/builtin/packages/r-rinside/package.py @@ -26,9 +26,9 @@ class RRinside(RPackage): url = "https://cloud.r-project.org/src/contrib/RInside_0.2.15.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/RInside" - version('0.2.15', '3b8c13dc53c6958c1f82c0a25dd6c211') - version('0.2.14', 'fc72761e22b1f597433eb53d6eb122ff') - version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88') + version('0.2.15', sha256='1e1d87a3584961f3aa4ca6acd4d2f3cda26abdab027ff5be2fd5cd76a98af02b') + version('0.2.14', sha256='8de5340993fe879ca00fa559c5b1b27b408ba78bfc5f67d36d6f0b8d8e8649cf') + version('0.2.13', sha256='be1da861f4f8c1292f0691bce05978e409a081f24ad6006ae173a6a89aa4d031') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rjags/package.py b/var/spack/repos/builtin/packages/r-rjags/package.py index 0b86c0e8e67..c2a70c8dc33 100644 --- a/var/spack/repos/builtin/packages/r-rjags/package.py +++ b/var/spack/repos/builtin/packages/r-rjags/package.py @@ -16,7 +16,7 @@ class RRjags(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/rjags/" version('4-8', sha256='1529827ab11493fb5f05552e239d700ae2f818995d86d3c9e4c92523f594b59f') - version('4-6', 'c26b7cc8e8ddcdb55e14cba28df39f4c') + version('4-6', sha256='cf24bb1e7c8445bafb49097089ad33e5bd5d8efbccf16fc7e32ad230f05f89ad') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-coda@0.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index cc6bb3cdfba..59cbde505f5 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -15,7 +15,7 @@ class RRjava(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/rJava" version('0.9-11', sha256='c28ae131456a98f4d3498aa8f6eac9d4df48727008dacff1aa561fc883972c69') - version('0.9-8', '51ae0d690ceed056ebe7c4be71fc6c7a') + version('0.9-8', sha256='dada5e031414da54eb80b9024d51866c20b92d41d68da65789fe0130bc54bd8a') depends_on('r@2.5:', type=('build', 'run')) depends_on('java@1.2:') diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py index 9c2c7a14095..ae0dbac3f49 100644 --- a/var/spack/repos/builtin/packages/r-rjson/package.py +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -15,6 +15,6 @@ class RRjson(RPackage): version('0.2.20', sha256='3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c') version('0.2.19', sha256='5c2672461986f2b715416cab92ed262abe9875f31299bc8a1a072ef7c6dd49bc') - version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9') + version('0.2.15', sha256='77d00d8f6a1c936329b46f3b8b0be79a165f8c5f1989497f942ecc53dcf6f2ef') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py index b981fa80fe0..17a6b7251e7 100644 --- a/var/spack/repos/builtin/packages/r-rjsonio/package.py +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -29,4 +29,4 @@ class RRjsonio(RPackage): version('1.3-1.2', sha256='550e18f7c04186376d67747b8258f529d205bfc929da9194fe45ec384e092d7e') version('1.3-1.1', sha256='c72493b441758cd1e3e9d91296b9ea31068e71104649f46ad84c854a02c09693') - version('1.3-0', '72c395622ba8d1435ec43849fd32c830') + version('1.3-0', sha256='119334b7761c6c1c3cec52fa17dbc1b72eaebb520c53e68d873dea147cf48fb7') diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py index f7a5344ba42..5136c13061e 100644 --- a/var/spack/repos/builtin/packages/r-rlang/package.py +++ b/var/spack/repos/builtin/packages/r-rlang/package.py @@ -19,10 +19,10 @@ class RRlang(RPackage): version('0.3.1', sha256='30427b2be2288e88acd30c4ea348ee06043a649fd73623a63148b1ad96317151') version('0.3.0.1', sha256='29451db0a3cabd75761d32df47a5d43ccadbde07ecb693ffdd73f122a0b9f348') version('0.3.0', sha256='9ab10ea3e19b2d60a289602ebbefa83509f430db1c8161e523896c374241b893') - version('0.2.2', 'df2abf3a1936c503ed1edd4350ffb5f0') - version('0.1.4', 'daed5104d557c0cbfb4a654ec8ffb579') - version('0.1.2', '170f8cf7b61898040643515a1746a53a') - version('0.1.1', '38a51a0b8f8487eb52b4f3d986313682') + version('0.2.2', sha256='c9119420ff0caeb6b0fcee8800e2fb1ec072e291e0e53b8acea3c4cf49420d33') + version('0.1.4', sha256='8d9b6c962ae81b96c96ada9614c6a1ffb9eda12dd407e2aff634f7d335e7b9f4') + version('0.1.2', sha256='90cfcd88cae6fff044fca64b24a8e6bdc09fc276163b518ff2d90268b0c785f9') + version('0.1.1', sha256='5901f95d68728a7d9bb1c2373a20ce6e4ad222f66e397e7735e9eff987c73c3f') depends_on('r@3.1.0:', when='@:0.3.4', type=('build', 'run')) depends_on('r@3.2.0:', when='@0.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py index aec117f37a7..c059b57ce54 100644 --- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py +++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py @@ -16,8 +16,8 @@ class RRmarkdown(RPackage): version('1.14', sha256='f636b1048c5be56e06aa0b2b4342ad5c8192734f1e9b27468fef62be672edc61') version('1.13', sha256='96fb6b08d27bbb8054145e0a55721f905341941d4f6691480a2a234e2d5a63ef') - version('1.7', '477c50840581ba7947b3d905c67a511b') - version('1.0', '264aa6a59e9680109e38df8270e14c58') + version('1.7', sha256='c3191db65b9ad41b6dbb77aff53487701032d306e92b208ef7515b747931fe63') + version('1.0', sha256='ff1ecb74ebc444b9b0b7b547adc512daefe1ee08d06bc0e3ee4eb68e58d2ef30') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-knitr@1.22:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py index 92b99dd9f7d..84f86a813df 100644 --- a/var/spack/repos/builtin/packages/r-rminer/package.py +++ b/var/spack/repos/builtin/packages/r-rminer/package.py @@ -15,7 +15,7 @@ class RRminer(RPackage): url = "https://cloud.r-project.org/src/contrib/rminer_1.4.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rminer" - version('1.4.2', '7d5d90f4ae030cf647d67aa962412c05') + version('1.4.2', sha256='64444dcedcd17f2f26129819d6bd2f84d4bb59c8f65328b6054ef32cb9624fc2') depends_on('r-plotrix', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py index 840a4f3f205..72e232adc13 100644 --- a/var/spack/repos/builtin/packages/r-rmpfr/package.py +++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py @@ -19,7 +19,7 @@ class RRmpfr(RPackage): version('0.7-2', sha256='ec1da6ec5292ea6ac95495c6a299591d367e520ae324719817fb884c865603ff') version('0.7-1', sha256='9b3021617a22b0710b0f1acc279290762317ff123fd9e8fd03f1449f4bbfe204') - version('0.6-1', '55d4ec257bd2a9233bafee9e444d0265') + version('0.6-1', sha256='bf50991055e9336cd6a110d711ae8a91a0551b96f9eaab5fef8c05f578006e1c') depends_on('r@3.0.1:', when='@:0.6-1', type=('build', 'run')) depends_on('r@3.1.0:', when='@0.7-0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rmpi/package.py b/var/spack/repos/builtin/packages/r-rmpi/package.py index fe43add7b86..a029dfba279 100644 --- a/var/spack/repos/builtin/packages/r-rmpi/package.py +++ b/var/spack/repos/builtin/packages/r-rmpi/package.py @@ -16,7 +16,7 @@ class RRmpi(RPackage): version('0.6-9', sha256='b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6') version('0.6-8', sha256='9b453ce3bd7284eda33493a0e47bf16db6719e3c48ac5f69deac6746f5438d96') - version('0.6-6', 'a6fa2ff5e1cd513334b4e9e9e7a2286f') + version('0.6-6', sha256='d8fc09ad38264697caa86079885a7a1098921a3116d5a77a62022b9508f8a63a') depends_on('r@2.15.1:', type=('build', 'run')) depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 6739bdb1043..6f02466d066 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -14,7 +14,7 @@ class RRmysql(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/RMySQL" version('0.10.17', sha256='754df4fce159078c1682ef34fc96aa5ae30981dc91f4f2bada8d1018537255f5') - version('0.10.9', '3628200a1864ac3005cfd55cc7cde17a') + version('0.10.9', sha256='41289c743dc8ee2e0dea8b8f291d65f0a7cd11e799b713d94840406ff296fd42') depends_on('r-dbi@0.4:', type=('build', 'run')) depends_on('mariadb@:5.5') diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index ea11d03f0fb..9269273cf87 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -20,7 +20,7 @@ class RRngtools(RPackage): version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') version('1.3.1.1', sha256='99e1a8fde6b81128d0946746c1ef84ec5b6c2973ad843a080098baf73aa3364c') version('1.3.1', sha256='763fc493cb821a4d3e514c0dc876d602a692c528e1d67f295dde70c77009e224') - version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') + version('1.2.4', md5='715967f8b3af2848a76593a7c718c1cd') depends_on('r@3.0.0:', when='@:1.3.1', type=('build', 'run')) depends_on('r@3.6.0:', when='@1.3.1.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py index 6b8c510639d..84bbafc83fc 100644 --- a/var/spack/repos/builtin/packages/r-robustbase/package.py +++ b/var/spack/repos/builtin/packages/r-robustbase/package.py @@ -19,7 +19,7 @@ class RRobustbase(RPackage): version('0.93-5', sha256='bde564dbd52f04ab32f9f2f9dd09b9578f3ccd2541cf5f8ff430da42a55e7f56') version('0.93-4', sha256='ea9e03d484ef52ea805803477ffc48881e4c8c86ffda4eea56109f8b23f0a6e0') - version('0.92-7', 'db3c8d12f9729b35bad17abf09e80b72') + version('0.92-7', sha256='fcbd6ccbb0291b599fe6a674a91344511e0a691b9cadba0a9d40037faa22bf8f') depends_on('r@3.0.2:', when='@:0.93-1.1', type=('build', 'run')) depends_on('r@3.1.0:', when='@0.93-2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rocr/package.py b/var/spack/repos/builtin/packages/r-rocr/package.py index 4952136ac5d..f7df3a08364 100644 --- a/var/spack/repos/builtin/packages/r-rocr/package.py +++ b/var/spack/repos/builtin/packages/r-rocr/package.py @@ -27,5 +27,5 @@ class RRocr(RPackage): url = "https://cloud.r-project.org/src/contrib/ROCR_1.0-7.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/ROCR" - version('1.0-7', '46cbd43ae87fc4e1eff2109529a4820e') + version('1.0-7', sha256='e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9') depends_on('r-gplots', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index a21269c1ef6..187d2185837 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -14,7 +14,7 @@ class RRodbc(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/RODBC/" version('1.3-15', sha256='c43e5a2f0aa2f46607e664bfc0bb3caa230bbb779f4ff084e01727642da136e1') - version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e') + version('1.3-13', sha256='e8ea7eb77a07be36fc2d824c28bb426334da7484957ffbc719140373adf1667c') depends_on('unixodbc') diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py index 3958ab12984..e686f380c57 100644 --- a/var/spack/repos/builtin/packages/r-roxygen2/package.py +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -15,7 +15,7 @@ class RRoxygen2(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/roxygen2" version('6.1.1', sha256='ed46b7e062e0dfd8de671c7a5f6d120fb2b720982e918dbeb01e6985694c0273') - version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7') + version('5.0.1', sha256='9f755ddd08358be436f08b02df398e50e7508b856131aeeed235099bb3a7eba5') depends_on('r@3.0.2:', when='@:6.0.1', type=('build', 'run')) depends_on('r@3.1:', when='@6.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpart-plot/package.py b/var/spack/repos/builtin/packages/r-rpart-plot/package.py index 4671e1078a1..cf854fce3eb 100644 --- a/var/spack/repos/builtin/packages/r-rpart-plot/package.py +++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py @@ -16,7 +16,7 @@ class RRpartPlot(RPackage): version('3.0.7', sha256='04e7fcadfa907507b74529c3ecfae4a0c782badf55e87d9c62dbd9a536ea9144') version('3.0.6', sha256='1c584290c8f58ded5c3f0638790a0da63408eca3ecd5d5c4d8c46954de9f4b02') - version('2.1.0', 'fb0f8edfe22c464683ee82aa429136f9') + version('2.1.0', sha256='17686da1883f97cb8f44be0d9cb915b366a3cb7313cd131b96497ab09f727436') depends_on('r@3.2.0:', when='@2.1.2:3.0.6', type=('build', 'run')) depends_on('r@3.4.0:', when='@3.0.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpart/package.py b/var/spack/repos/builtin/packages/r-rpart/package.py index 4c309ba4ab3..ef57ad9b3ca 100644 --- a/var/spack/repos/builtin/packages/r-rpart/package.py +++ b/var/spack/repos/builtin/packages/r-rpart/package.py @@ -16,7 +16,7 @@ class RRpart(RPackage): version('4.1-15', sha256='2b8ebe0e9e11592debff893f93f5a44a6765abd0bd956b0eb1f70e9394cfae5c') version('4.1-13', sha256='8e11a6552224e0fbe23a85aba95acd21a0889a3fe48277f3d345de3147c7494c') - version('4.1-11', 'f77b37cddf7e9a7b5993a52a750b8817') - version('4.1-10', '15873cded4feb3ef44d63580ba3ca46e') + version('4.1-11', sha256='38ab80959f59bcdd2c4c72860e8dd0deab0307668cbbf24f96014d7a2496ad98') + version('4.1-10', sha256='c5ddaed288d38118876a94c7aa5000dce0070b8d736dba12de64a9cb04dc2d85') depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index a5c9e119745..08417089cc8 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -22,7 +22,7 @@ class RRpostgresql(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/RPostgreSQL" version('0.6-2', sha256='080118647208bfa2621bcaac0d324891cc513e07618fa22e3c50ec2050e1b0d5') - version('0.4-1', 'e7b22e212afbb2cbb88bab937f93e55a') + version('0.4-1', sha256='6292e37fa841670a3fb1a0950ceb83d15beb4631c3c532c8ce279d1c0d10bf79') depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-dbi@0.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rprojroot/package.py b/var/spack/repos/builtin/packages/r-rprojroot/package.py index b1ec14200d8..5388cff895b 100644 --- a/var/spack/repos/builtin/packages/r-rprojroot/package.py +++ b/var/spack/repos/builtin/packages/r-rprojroot/package.py @@ -16,7 +16,7 @@ class RRprojroot(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/rprojroot" version('1.3-2', sha256='df5665834941d8b0e377a8810a04f98552201678300f168de5f58a587b73238b') - version('1.2', 'c1a0574aaac2a43a72f804abbaea19c3') + version('1.2', sha256='28b4d235ce67314528a0c1cc7e98faed42437b42e07fca18a59a80fdc3eefeb9') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-backports', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py index 1fdc9326525..c6df54a4813 100644 --- a/var/spack/repos/builtin/packages/r-rsnns/package.py +++ b/var/spack/repos/builtin/packages/r-rsnns/package.py @@ -22,7 +22,7 @@ class RRsnns(RPackage): version('0.4-11', sha256='87943126e98ae47f366e3025d0f3dc2f5eb0aa2924508fd9ee9a0685d7cb477c') version('0.4-10.1', sha256='38bb3d172390bd01219332ec834744274b87b01f94d23b29a9d818c2bca04071') - version('0.4-7', 'ade7736611c456effb5f72e0ce0a1e6f') + version('0.4-7', sha256='ec941dddda55e4e29ed281bd8768a93d65e0d86d56ecab0f2013c64c8d1a4994') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-rcpp@0.8.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py index 03c24b0b468..891c70632eb 100644 --- a/var/spack/repos/builtin/packages/r-rsolnp/package.py +++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py @@ -14,7 +14,7 @@ class RRsolnp(RPackage): url = "https://cloud.r-project.org/src/contrib/Rsolnp_1.16.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/Rsolnp" - version('1.16', '507e1e1a64f5f1d32b7e4e12ed19599f') + version('1.16', sha256='3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-truncnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index d9e018304d2..c84e712ba54 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -17,7 +17,7 @@ class RRsqlite(RPackage): version('2.1.2', sha256='66dad425d22b09651c510bf84b7fc36375ce537782f02585cf1c6856ae82d9c6') version('2.1.0', sha256='ad6081be2885be5921b1a44b1896e6a8568c8cff40789f43bfaac9f818767642') - version('2.0', '63842410e78ccdfc52d4ee97992521d5') + version('2.0', sha256='7f0fe629f34641c6af1e8a34412f3089ee2d184853843209d97ffe29430ceff6') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-dbi@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 6e8bc944586..30df716358d 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -23,8 +23,8 @@ class RRstan(RPackage): version('2.19.2', sha256='31e4ceb9c327cd62873225097ffa538c2ac4cb0547c52271e52e4c7652d508da') version('2.18.2', sha256='4d75dad95610d5a1d1c89a4ddbaf4326462e4ffe0ad28aed2129f2d9292e70ff') - version('2.17.2', '60f4a0284c58f5efc1b1cbf488d7edda') - version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a') + version('2.17.2', sha256='a7b197e6e42f8f0c302da9205afc19a0261eaf6af1425854303d2ce6cbd36729') + version('2.10.1', sha256='4d2040742607f8675633c6b8c0a2e810f2fe3077f9242b1edfd42642613a8294') depends_on('r@3.0.2:', when='@:2.17.3', type=('build', 'run')) depends_on('r@3.4.0:', when='@2.18.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index 9a7779f063e..a14069e90c9 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -16,6 +16,6 @@ class RRstudioapi(RPackage): version('0.10', sha256='80c5aa3063bcab649904cb92f0b164edffa2f6b0e6a8f7ea28ae317b80e1ab96') version('0.9.0', sha256='5149a2830ae7134c396ce64764b263cf9f348d4399f53da3804f40d7d5bec13e') - version('0.7', 'ee4ab567a7a9fdfac1a6fd01fe38de4a') - version('0.6', 'fdb13bf46aab02421557e713fceab66b') - version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') + version('0.7', sha256='a541bc76ef082d2c27e42fd683f8262cb195b1497af3509178d2642870397a8c') + version('0.6', sha256='da24c6cdb13af1bdf4261671a065dcca4c1b7af1412cb810eb805bf3c5f97bfe') + version('0.5', sha256='d5f35bf9614ca2a4bc5333bac7a494d81fbe72b34783304f811f8e0abac3f669') diff --git a/var/spack/repos/builtin/packages/r-rtsne/package.py b/var/spack/repos/builtin/packages/r-rtsne/package.py index be053b293f4..be9dc733368 100644 --- a/var/spack/repos/builtin/packages/r-rtsne/package.py +++ b/var/spack/repos/builtin/packages/r-rtsne/package.py @@ -15,8 +15,8 @@ class RRtsne(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/Rtsne" version('0.15', sha256='56376e4f0a382fad3d3d40e2cb0562224be5265b827622bcd235e8fc63df276c') - version('0.13', 'ea1d2ef2bda16735bbf219ffda5b0661') - version('0.11', '9a1eaa9b71d67cc27a55780e6e9df733') - version('0.10', 'c587e1b76fdcea2629424f74c6e92340') + version('0.13', sha256='1c3bffe3bd11733ee4fe01749c293669daafda1af2ec74f9158f6080625b999d') + version('0.11', sha256='1e2e7368f3de870b9270f70b207ba9e8feea67f9b061cb6abb2fec785fb7247e') + version('0.10', sha256='c54371f4a935520e7e7ab938ef8f5f7f9ad2a829123b9513ae715c07de034790') depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rvcheck/package.py b/var/spack/repos/builtin/packages/r-rvcheck/package.py index 9adfd8d31d2..b0727ab380a 100644 --- a/var/spack/repos/builtin/packages/r-rvcheck/package.py +++ b/var/spack/repos/builtin/packages/r-rvcheck/package.py @@ -15,7 +15,7 @@ class RRvcheck(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/rvcheck" version('0.1.3', sha256='0b59986c1ccc5b89f8aca8fa7cf62d0b875719addb40e08dbda1791cfd334fc4') - version('0.0.9', '7e9821de754577f94fdcbf7b02a20edc') + version('0.0.9', sha256='6e7be7b029d28181a1b57ebd4d25978f3459722ffdb45a3698157a7f943bea92') depends_on('r@3.3.0:', when='@:0.1.1', type=('build', 'run')) depends_on('r@3.4.0:', when='@0.1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rvest/package.py b/var/spack/repos/builtin/packages/r-rvest/package.py index 1872315f773..ede298ee4c3 100644 --- a/var/spack/repos/builtin/packages/r-rvest/package.py +++ b/var/spack/repos/builtin/packages/r-rvest/package.py @@ -16,7 +16,7 @@ class RRvest(RPackage): version('0.3.4', sha256='413e171b9e89b7dc4e8b41165027cf19eb97cd73e149c252237bbdf0d0a4254a') version('0.3.3', sha256='b10a87fa2d733f7c0fc567242ef0ab10a1a77d58d51796996cc0fd81381a556f') - version('0.3.2', '78c88740850e375fc5da50d37734d1b2') + version('0.3.2', sha256='0d6e8837fb1df79b1c83e7b48d8f1e6245f34a10c4bb6952e7bec7867e4abb12') depends_on('r@3.0.1:', when='@:0.3.2', type=('build', 'run')) depends_on('r@3.1:', when='@0.3.3', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index 8b800c4b5fb..aeaa990a459 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -16,7 +16,7 @@ class RRzmq(RPackage): version('0.9.6', sha256='80a3fc6eb6f7851224c4cd5e219ca4db0286551ad429359d4df853ccb9234316') version('0.9.4', sha256='03fbda756d823c11fba359b94a6213c3440e61973331668eaac35779717f73ad') - version('0.7.7', '8ba18fd1c222d1eb25bb622ccd2897e0') + version('0.7.7', sha256='bdbaf77a0e04c5b6d6ce79ab2747848a5044355eed2e2c4d39c4ba16f97dc83d') depends_on('r@3.1.0:', when='@0.9.0:', type=('build', 'run')) depends_on('zeromq@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-samr/package.py b/var/spack/repos/builtin/packages/r-samr/package.py index 5ebc81a468e..98171dfcb4a 100644 --- a/var/spack/repos/builtin/packages/r-samr/package.py +++ b/var/spack/repos/builtin/packages/r-samr/package.py @@ -13,7 +13,7 @@ class RSamr(RPackage): url = "https://cloud.r-project.org/src/contrib/samr_2.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/samr" version('3.0', sha256='25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506') - version('2.0', 'e8f50b8b25069d03d42c2c61c72b0da0') + version('2.0', sha256='090b5becd91d60f4bb8269df5c9bc19a03c09917d327b28e75b0ee7b80624e67') depends_on('r-impute', type=('build', 'run')) depends_on('r-matrixstats', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index d303fe56cf2..00f508c0e5b 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -16,7 +16,7 @@ class RSandwich(RPackage): version('2.5-1', sha256='dbef6f4d12b83e166f9a2508b7c732b04493641685d6758d29f3609e564166d6') version('2.5-0', sha256='6cc144af20739eb23e5539010d3833d7c7fc53cbca2addb583ab933167c11399') - version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') + version('2.3-4', sha256='2052f7e3d19a05c372f422c5480f1058a4107e420cd038a9bd7240c4f0746d4d') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index 0ea8442689f..46fcef15b05 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -15,9 +15,9 @@ class RScales(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/scales" version('1.0.0', sha256='0c1f4a14edd336a404da34a3cc71a6a9d0ca2040ba19360c41a79f36e06ca30c') - version('0.5.0', '435f6bd826c5cf8df703ffb8a6750fd1') - version('0.4.1', '3fb2218866a7fe4c1f6e66790876f85a') - version('0.4.0', '7b5602d9c55595901192248bca25c099') + version('0.5.0', sha256='dbfcc0817c4ab8b8777ec7d68ebfe220177c193cfb5bd0e8ba5d365dbfe3e97d') + version('0.4.1', sha256='642b88fb1fce7bac72a0038ce532b65b8a79dffe826fec25033cf386ab630cd3') + version('0.4.0', sha256='851ef6136339b361b3f843fb73ea89f9112279b9cc126bdb38acde8d24c1c6a7') depends_on('r@2.13:', when='@:0.5.0', type=('build', 'run')) depends_on('r@3.1:', when='@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py index e4bb9abbc6e..1772ff50143 100644 --- a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py +++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py @@ -14,6 +14,6 @@ class RScatterplot3d(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/scatterplot3d" version('0.3-41', sha256='4c8326b70a3b2d37126ca806771d71e5e9fe1201cfbe5b0d5a0a83c3d2c75d94') - version('0.3-40', '67b9ab6131d244d7fc1db39dcc911dfe') + version('0.3-40', sha256='8249118aa29199017a6686d8245fed5343dabcf049b1588141a7cf83245b6a29') depends_on('r@2.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sdmtools/package.py b/var/spack/repos/builtin/packages/r-sdmtools/package.py index e6dd23d74d9..bf1d228b584 100644 --- a/var/spack/repos/builtin/packages/r-sdmtools/package.py +++ b/var/spack/repos/builtin/packages/r-sdmtools/package.py @@ -18,10 +18,10 @@ class RSdmtools(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/SDMTools" version('1.1-221.1', sha256='3825856263bdb648ca018b27dc6ab8ceaef24691215c197f8d5cd17718b54fbb') - version('1.1-221', '3604da1783d0c6081b62b29d35a32c3c') - version('1.1-20', '27cc8de63cfdd86d4ba9983012121c58') - version('1.1-13', '0d6a14d985988a81b9ff06c635675143') - version('1.1-12', 'a13d75e4024d908a57ea462112d8a437') - version('1.1-11', 'cb890ee06eb862f97141b73c7390a0a9') + version('1.1-221', sha256='a6da297a670f756ee964ffd99c3b212c55c297d385583fd0e767435dd5cd4ccd') + version('1.1-20', sha256='d6a261ce8f487d5d03b1931039f528f2eb50fb9386e7aae40045c966ff6d4182') + version('1.1-13', sha256='02d94977bfa2f41f1db60e619335ac0ea8109dd98108ff9d21a412f7c4a14a2e') + version('1.1-12', sha256='6dc4a8a046e7fced190402f39a9bae6f863e08c320f0881367c022b2f220f14b') + version('1.1-11', sha256='1caf8fa1914ad6921d76e7b22a8c25cfe55892b0d21aef3b2a7b8f5b79b9388b') depends_on('r-r-utils', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py index 748d8811ef9..c6e8e2616a9 100644 --- a/var/spack/repos/builtin/packages/r-segmented/package.py +++ b/var/spack/repos/builtin/packages/r-segmented/package.py @@ -17,5 +17,5 @@ class RSegmented(RPackage): version('1.0-0', sha256='eeadc89b4bb4744bbd1e4e6c3b6536ff96fc7ee09016228dfdc0a8ebdc74fac5') version('0.5-4.0', sha256='7ff63a19915cbd1e190d3a4875892b4c7bd97890b0dc2909126348a19aec4071') - version('0.5-2.2', '1511ec365aea289d5f0a574f6d10d2d6') - version('0.5-1.4', 'f9d76ea9e22ef5f40aa126b697351cae') + version('0.5-2.2', sha256='3aa7136370dd77911ba8e061b5215560d120bc71f355eeadc0856389dfecb2f1') + version('0.5-1.4', sha256='b1dc5f79ccc076c2943b15fe4f339368afa241797b7e80c91b62132cfa66809c') diff --git a/var/spack/repos/builtin/packages/r-selectr/package.py b/var/spack/repos/builtin/packages/r-selectr/package.py index 628ee221f99..f26c7069749 100644 --- a/var/spack/repos/builtin/packages/r-selectr/package.py +++ b/var/spack/repos/builtin/packages/r-selectr/package.py @@ -20,7 +20,7 @@ class RSelectr(RPackage): version('0.4-1', sha256='8bd42f167629344e485e586f9b05fed342746132489079084d82133d7b3ee2ca') version('0.4-0', sha256='40cd51bfe499954b300742c49f92167a68964b974268a7f47ca8864f32020ece') - version('0.3-1', '7190fcdea1823ad7ef429cab6938e960') + version('0.3-1', sha256='db4f7ceea4b522a54c3ae7709787b0b7fcf389c5d945c5a278e3625388218949') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py index ab7685fc475..7bba7601ebe 100644 --- a/var/spack/repos/builtin/packages/r-seqinr/package.py +++ b/var/spack/repos/builtin/packages/r-seqinr/package.py @@ -15,8 +15,8 @@ class RSeqinr(RPackage): url = "https://cloud.r-project.org/src/contrib/seqinr_3.3-6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/seqinr" - version('3.4-5', 'd550525dcea754bbd5b83cb46b4124cc') - version('3.3-6', '73023d627e72021b723245665e1ad055') + version('3.4-5', sha256='162a347495fd52cbb62e8187a4692e7c50b9fa62123c5ef98f2744c98a05fb9f') + version('3.3-6', sha256='42a3ae01331db744d67cc9c5432ce9ae389bed465af826687b9c10216ac7a08d') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-ade4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-seurat/package.py b/var/spack/repos/builtin/packages/r-seurat/package.py index c3e5de9dce2..a00cc72c999 100644 --- a/var/spack/repos/builtin/packages/r-seurat/package.py +++ b/var/spack/repos/builtin/packages/r-seurat/package.py @@ -17,8 +17,8 @@ class RSeurat(RPackage): version('3.1.0', sha256='d8d3fad2950a8f791376e3d20c72ea07c68bf8d82d800661cab5ce696db39d45') version('3.0.2', sha256='16df5dec6b41d49320c5bf5ce30eb3b7dedeea69b054b55b77528f2f2b7bce04') version('3.0.1', sha256='8c467bdbfdb9aff51bde6a897ff98a7389941f688639d8f1d36c71dde076a257') - version('2.1.0', '46427837bb739883f9b7addd08fccee5') - version('2.0.1', 'a77794891e93b9fa1ef41735fe8424ea') + version('2.1.0', sha256='7d20d231b979a4aa63cd7dae7e725405212e8975889f12b8d779c6c896c10ac3') + version('2.0.1', sha256='6aa33aa3afb29a8be364ab083c7071cfbc56ad042a019bcf6f939e0c8c7744f0') depends_on('r@3.2.0:', when='@:2.3.0', type=('build', 'run')) depends_on('r@3.4.0:', when='@2.3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sf/package.py b/var/spack/repos/builtin/packages/r-sf/package.py index bd79b7a4fd5..b9b382d7dfb 100644 --- a/var/spack/repos/builtin/packages/r-sf/package.py +++ b/var/spack/repos/builtin/packages/r-sf/package.py @@ -18,7 +18,7 @@ class RSf(RPackage): version('0.7-7', sha256='d1780cb46a285b30c7cc41cae30af523fbc883733344e53f7291e2d045e150a4') version('0.7-5', sha256='53ed0567f502216a116c4848f5a9262ca232810f82642df7b98e0541a2524868') - version('0.5-5', '53ff32d0c9bf2844666c68ce7d75beb2') + version('0.5-5', sha256='82ad31f98243b6982302fe245ee6e0d8d0546e5ff213ccc00ec3025dfec62229') depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-rcpp@0.12.18:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sfsmisc/package.py b/var/spack/repos/builtin/packages/r-sfsmisc/package.py index 779d13959c6..86d2b0267b5 100644 --- a/var/spack/repos/builtin/packages/r-sfsmisc/package.py +++ b/var/spack/repos/builtin/packages/r-sfsmisc/package.py @@ -17,7 +17,7 @@ class RSfsmisc(RPackage): version('1.1-4', sha256='44b6a9c859922e86b7182e54eb781d3264f3819f310343518ebc66f54f305c7d') version('1.1-3', sha256='58eff7d4a9c79212321858efe98d2a6153630e263ff0218a31d5e104b8b545f8') - version('1.1-0', '1ba4303076e2bbf018f7eecc7d04e178') + version('1.1-0', sha256='7f430cf3ebb95bac806fbf093fb1e2112deba47416a93be8d5d1064b76bc0015') depends_on('r@3.0.1:', when='@:1.1-1', type=('build', 'run')) depends_on('r@3.2.0:', when='@1.1-2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shape/package.py b/var/spack/repos/builtin/packages/r-shape/package.py index 67851868f13..7ee99402898 100644 --- a/var/spack/repos/builtin/packages/r-shape/package.py +++ b/var/spack/repos/builtin/packages/r-shape/package.py @@ -15,7 +15,7 @@ class RShape(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/shape" version('1.4.4', sha256='f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41') - version('1.4.3', '2a807bf95e7decc71478f805221852da') - version('1.4.2', '75557c43a385b9cc0c4dff361af6e06c') + version('1.4.3', sha256='720f6ca9c70a39a3900af9d074bff864b18ac58013b21d48b779047481b93ded') + version('1.4.2', sha256='c6c08ba9cc2e90e5c9d3d5223529b57061a041f637886ad7665b9fa27465637a') depends_on('r@2.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index 3c1c3bcb478..a35f37a4b49 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -17,8 +17,8 @@ class RShiny(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/shiny" version('1.3.2', sha256='28b851ae6c196ca845f6e815c1379247595ac123a4faa10a16533d1a9ce0c24f') - version('1.0.5', '419dd5d3ea0bd87a07f8f0b1ef14fc13') - version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611') + version('1.0.5', sha256='20e25f3f72f3608a2151663f7836f2e0c6da32683a555d7541063ae7a935fa42') + version('0.13.2', sha256='0fe7e952f468242d7c43ae49afcc764788f7f2fd5436d18c3d20a80db7296231') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-httpuv@1.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shinydashboard/package.py b/var/spack/repos/builtin/packages/r-shinydashboard/package.py index 23733e9576e..8958f7bb1ab 100644 --- a/var/spack/repos/builtin/packages/r-shinydashboard/package.py +++ b/var/spack/repos/builtin/packages/r-shinydashboard/package.py @@ -14,8 +14,8 @@ class RShinydashboard(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/shinydashboard" version('0.7.1', sha256='51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e') - version('0.7.0', 'a572695884e3b45320b0ab5a7b364ffd') - version('0.6.1', '0f6ad0448237e10d53d4d27ade1c6863') + version('0.7.0', sha256='0b7b102e9e5bea78ddc4da628d072a358270f2db9b63a6ebe4d8bdce3066d883') + version('0.6.1', sha256='1ee38f257433d24455426bc9d85c36f588735a54fbf6143935fed9cccb3bf193') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-htmltools@0.2.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-smoof/package.py b/var/spack/repos/builtin/packages/r-smoof/package.py index 60520006b8c..1214c8f5ef7 100644 --- a/var/spack/repos/builtin/packages/r-smoof/package.py +++ b/var/spack/repos/builtin/packages/r-smoof/package.py @@ -17,8 +17,8 @@ class RSmoof(RPackage): url = "https://cloud.r-project.org/src/contrib/smoof_1.5.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/smoof" - version('1.5.1', 'c3e3b5dafed34608f933ae255cf49054') - version('1.5', 'b371bde2724eade5a6d4d808fa3ad269') + version('1.5.1', sha256='cfb6f6460e9593351428656b225b5ba3867a216d35a05f2babdb20db6ba35306') + version('1.5', sha256='9b73ad5bfc8e1120c9651539ea52b1468f316cc7fc5fef8afd6d357adf01504c') depends_on('r-paramhelpers@1.8:', type=('build', 'run')) depends_on('r-bbmisc@1.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sn/package.py b/var/spack/repos/builtin/packages/r-sn/package.py index 61d84c1df29..8f15910324b 100644 --- a/var/spack/repos/builtin/packages/r-sn/package.py +++ b/var/spack/repos/builtin/packages/r-sn/package.py @@ -18,11 +18,11 @@ class RSn(RPackage): version('1.5-4', sha256='46677ebc109263a68f62b5cf53ec59916cda490e5bc5bbb08276757a677f8674') version('1.5-3', sha256='cc21b97ddd674c9b1296260f2a72ffb085cdcb877c8332f0bfa96ff028517183') - version('1.5-0', 'a3349773be950199d7f4c17954be56d1') - version('1.4-0', 'cfa604317ea54224b06abd1cec179375') - version('1.3-0', '84d02ba2ab5ca6f3644626013e7ce36d') - version('1.2-4', 'bf3a47b05016326e910fdb4cc4967e4d') - version('1.2-3', '290ae511d974a6beb4c3c79c0106858f') + version('1.5-0', sha256='0164f7cffbf9e2a0f03f9bed3b96388b08d8a8ca476bbb686aa88be6b4ec073a') + version('1.4-0', sha256='d363ae1662bc765e491b98c925901fa9d2d3d6cc760987444db35dbe325aefc0') + version('1.3-0', sha256='926fc4cde1079860572c2829efc83503f3e1f157b8448b6a40450ca7f5470503') + version('1.2-4', sha256='a812f754abd1ecdbc9de4e5c8b8f5526c08c06a710d390b1fff2a09328637fb6') + version('1.2-3', sha256='1af8ced9ed33680d731ab5132be4674d170d76c64a3059ff56c33159d8396154') depends_on('r@2.15.3:', type=('build', 'run')) depends_on('r-mnormt@1.5-4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py index e7173b4c356..ac4d2a3b4b7 100644 --- a/var/spack/repos/builtin/packages/r-snow/package.py +++ b/var/spack/repos/builtin/packages/r-snow/package.py @@ -14,6 +14,6 @@ class RSnow(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/snow" version('0.4-3', sha256='8512537daf334ea2b8074dbb80cf5e959a403a78d68bc1e97664e8a4f64576d8') - version('0.4-2', 'afc7b0dfd4518aedb6fc81712fd2ac70') + version('0.4-2', sha256='ee070187aea3607c9ca6235399b3db3e181348692405d038e962e06aefccabd7') depends_on('r@2.13.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snowfall/package.py b/var/spack/repos/builtin/packages/r-snowfall/package.py index fbc86513af7..36cb71c9a24 100644 --- a/var/spack/repos/builtin/packages/r-snowfall/package.py +++ b/var/spack/repos/builtin/packages/r-snowfall/package.py @@ -17,7 +17,7 @@ class RSnowfall(RPackage): url = "https://cloud.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/snowfall" - version('1.84-6.1', '5ec38116aa9cac237d56f59ba5bd60e3') + version('1.84-6.1', sha256='5c446df3a931e522a8b138cf1fb7ca5815cc82fcf486dbac964dcbc0690e248d') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-snow', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py index f87b92c3675..0be184ed1e1 100644 --- a/var/spack/repos/builtin/packages/r-som/package.py +++ b/var/spack/repos/builtin/packages/r-som/package.py @@ -13,10 +13,10 @@ class RSom(RPackage): url = "https://cloud.r-project.org/src/contrib/som_0.3-5.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/som" - version('0.3-5.1', '802a5a80902579354ce3420faeeeb756') - version('0.3-5', '72717499794c7aa945a768b742af8895') - version('0.3-4', '1e25572e446409f5e32c5da5f1af98e6') - version('0.3-3', 'd4ac444be24f71d08b99974c2f4b96e5') - version('0.3-2', '4ce28f46df68fbb73905711ba2416fac') + version('0.3-5.1', sha256='a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9') + version('0.3-5', sha256='f7672afaaffcf41a8b2dd50e4c76b3a640ea2ad099f18b5dfcf00389abf6ba07') + version('0.3-4', sha256='679e3d3f0af6e56da3b0a4d8577334e03ad45fe76916bbc2592548f85b6b1c84') + version('0.3-3', sha256='434e2210df3e6a459a8588606676c02494f58c5b52e25291d142121b7b9be5c7') + version('0.3-2', sha256='b46ecb79c08f3d4cf9527d5c7f85a235808dda45dae7f50909b2df90e7b9e543') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sourcetools/package.py b/var/spack/repos/builtin/packages/r-sourcetools/package.py index 2df62d25d86..404c04c8b66 100644 --- a/var/spack/repos/builtin/packages/r-sourcetools/package.py +++ b/var/spack/repos/builtin/packages/r-sourcetools/package.py @@ -14,7 +14,7 @@ class RSourcetools(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/sourcetools" version('0.1.7', sha256='47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca') - version('0.1.6', 'c78a816384b168d04af41bd7ff4d909d') - version('0.1.5', 'b4d7902ffafd9802e8fbff5ce824bb28') + version('0.1.6', sha256='c9f48d2f0b7f7ed0e7fecdf8e730b0b80c4d567f0e1e880d118b0944b1330c51') + version('0.1.5', sha256='c2373357ad76eaa7d03f9f01c19b5001a3e4db788acbca068b0abbe7a99ea64b') depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py index 2cdbaf6ffd5..1a953994d67 100644 --- a/var/spack/repos/builtin/packages/r-sp/package.py +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -18,7 +18,7 @@ class RSp(RPackage): version('1.3-1', sha256='57988b53ba8acc35f3912d62feba4b929a0f757c6b54080c623c5d805e0cb59f') version('1.2-7', sha256='6d60e03e1abd30a7d4afe547d157ce3dd7a8c166fc5e407fd6d62ae99ff30460') - version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1') + version('1.2-3', sha256='58b3a9e395ca664ee61b20b480be4eb61576daca44c3d3f6f9a943bb0155879a') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index e5974e19afc..15ca85f5448 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -17,7 +17,7 @@ class RSparsem(RPackage): version('1.77', sha256='a9329fef14ae4fc646df1f4f6e57efb0211811599d015f7bc04c04285495d45c') version('1.76', sha256='c2c8e44376936a5fe6f09a37f3668016e66cbc687519cc952aa346a658a2b69b') - version('1.74', 'a16c9b7db172dfd2b7b6508c48e81a5d') - version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') + version('1.74', sha256='4712f0c80e9f3cb204497f146ba60b15e75976cdb7798996a7c51f841a85eeba') + version('1.7', sha256='df61550b267f8ee9b9d3b17acbadd57a428b43e5e13a6b1c56ed4c38cb523369') depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py index 2c0f9bc47b1..24073cbcde8 100644 --- a/var/spack/repos/builtin/packages/r-spdep/package.py +++ b/var/spack/repos/builtin/packages/r-spdep/package.py @@ -28,7 +28,7 @@ class RSpdep(RPackage): version('1.1-2', sha256='ba0ca3a0ad6b9cc1dc46cadd9e79259949ad38c88f738e98e482d6c06640b31a') version('1.0-2', sha256='6f9efa4347d5c13b49922b75481ac403431c3c76a65a109af29954aa7bb138b2') - version('0.6-13', 'bfc68b3016b4894b152ecec4b86f85d1') + version('0.6-13', sha256='ed345f4c7ea7ba064b187eb6b25f0ac46f17616f3b56ab89978935cdc67df1c4') depends_on('r@3.0.0:', when='@:0.7-7', type=('build', 'run')) depends_on('r@3.3.0:', when='@0.7-8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-speedglm/package.py b/var/spack/repos/builtin/packages/r-speedglm/package.py index 2371b3090e5..d3b87fd29df 100644 --- a/var/spack/repos/builtin/packages/r-speedglm/package.py +++ b/var/spack/repos/builtin/packages/r-speedglm/package.py @@ -14,7 +14,7 @@ class RSpeedglm(RPackage): url = "https://cloud.r-project.org/src/contrib/speedglm_0.3-2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/speedglm" - version('0.3-2', 'c4874d4c2a677d657a335186ebb63131') + version('0.3-2', sha256='5fcaf18324dc754152f528a44894944063303f780d33e58569ea7c306bfc45ac') depends_on('r-mass', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-splancs/package.py b/var/spack/repos/builtin/packages/r-splancs/package.py index 4ef99ef42ca..9b3726a2b7d 100644 --- a/var/spack/repos/builtin/packages/r-splancs/package.py +++ b/var/spack/repos/builtin/packages/r-splancs/package.py @@ -13,7 +13,7 @@ class RSplancs(RPackage): url = "https://cloud.r-project.org/src/contrib/splancs_2.01-40.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/splancs" - version('2.01-40', 'dc08a5c9a1fd2098d78459152f4917ce') + version('2.01-40', sha256='79744381ebc4a361740a36dca3c9fca9ae015cfe0bd585b7856a664a3da74363') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-sp@0.9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-splitstackshape/package.py b/var/spack/repos/builtin/packages/r-splitstackshape/package.py index a314d22134a..d4ce79870fc 100644 --- a/var/spack/repos/builtin/packages/r-splitstackshape/package.py +++ b/var/spack/repos/builtin/packages/r-splitstackshape/package.py @@ -24,7 +24,7 @@ class RSplitstackshape(RPackage): version('1.4.8', sha256='656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56') version('1.4.6', sha256='b9888f9508babdb8e09f57674facaa8b158a06255ef1e61c8df813f58881860f') - version('1.4.4', '54d2554fe92dfc4670a000b45baacc28') + version('1.4.4', sha256='78c27fb55459b0cc858cef5c2201a10ae2472a1a0be179e05df05ced2f590f6e') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-data-table@1.9.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sqldf/package.py b/var/spack/repos/builtin/packages/r-sqldf/package.py index da7d95aa310..c7ffa1786cf 100644 --- a/var/spack/repos/builtin/packages/r-sqldf/package.py +++ b/var/spack/repos/builtin/packages/r-sqldf/package.py @@ -22,7 +22,7 @@ class RSqldf(RPackage): url = "https://cloud.r-project.org/src/contrib/sqldf_0.4-11.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/sqldf" - version('0.4-11', '85def6fe2418569370c24e53522d2c2d') + version('0.4-11', sha256='cee979d4e8c67b4924655365d925a8d67104e62adf71741f645cdc5196de2260') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-gsubfn@0.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-squash/package.py b/var/spack/repos/builtin/packages/r-squash/package.py index f38963c8d01..fbd4ac15452 100644 --- a/var/spack/repos/builtin/packages/r-squash/package.py +++ b/var/spack/repos/builtin/packages/r-squash/package.py @@ -13,5 +13,5 @@ class RSquash(RPackage): url = "https://cloud.r-project.org/src/contrib/squash_1.0.8.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/squash" - version('1.0.8', '50d5743d306fa11cfa1a3c4daa75e508') - version('1.0.7', '4ac381b17d4d7b77bdaa6f824fbb03ab') + version('1.0.8', sha256='e6932c0a461d5c85f7180a31d18a3eb4f28afd6769efe251075a4de12de039f4') + version('1.0.7', sha256='d2d7182a72dfd93b8b65e775bea11e891c38598fa49a3ed4f92ec1159ffab6f1') diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py index 2cac7d0963c..374cd8e67f1 100644 --- a/var/spack/repos/builtin/packages/r-stanheaders/package.py +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -29,8 +29,8 @@ class RStanheaders(RPackage): version('2.18.1-10', sha256='8a9f7e22105428e97d14f44f75395c37cf8c809de148d279c620024452b3565a') version('2.18.1', sha256='ce0d609a7cd11725b1203bdeae92acc54da3a48b8266eb9dbdb9d95b14df9209') - version('2.17.1', '11d8770277dd18e563852852633c6c25') - version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57') + version('2.17.1', sha256='4300a1910a2eb40d7a6ecabea3c1e26f0aa9421eeb3000689272a0f62cb80d97') + version('2.10.0-2', sha256='ce4e335172bc65da874699302f6ba5466cdbcf69458c11954c0f131fc78b59b7') depends_on('r@3.4.0:', when='@2.18.0:', type=('build', 'run')) depends_on('pandoc', type='build') diff --git a/var/spack/repos/builtin/packages/r-statmod/package.py b/var/spack/repos/builtin/packages/r-statmod/package.py index ceee29fceb4..14b8c62feb2 100644 --- a/var/spack/repos/builtin/packages/r-statmod/package.py +++ b/var/spack/repos/builtin/packages/r-statmod/package.py @@ -21,6 +21,6 @@ class RStatmod(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/statmod" version('1.4.32', sha256='2f67a1cfa66126e6345f8a40564a3077d08f1748f17cb8c8fb05c94ed0f57e20') - version('1.4.30', '34e60132ce3df38208f9dc0db0479151') + version('1.4.30', sha256='9d2c1722a85f53623a9ee9f73d835119ae22ae2b8ec7b50d675401e314ea641f') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-statnet-common/package.py b/var/spack/repos/builtin/packages/r-statnet-common/package.py index 7ad4104329e..5c032da3530 100644 --- a/var/spack/repos/builtin/packages/r-statnet-common/package.py +++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py @@ -16,7 +16,7 @@ class RStatnetCommon(RPackage): version('4.3.0', sha256='834a3359eac967df0420eee416ae4983e3b502a3de56bb24f494a7ca4104e959') version('4.2.0', sha256='1176c3303436ebe858d02979cf0a0c33e4e2d1f3637516b4761d573ccd132461') - version('3.3.0', '36bc11098dcd3652a4beb05c156ad6c8') + version('3.3.0', sha256='d714c4e7b0cbf71b7a628af443f5be530e74ad1e21f6b04f1b1087f6d7e40fa4') depends_on('r@3.5:', when='@4.2.0:', type=('build', 'run')) depends_on('r-coda', when='@4.1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index 8c44256da8e..3ddca99716c 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -23,10 +23,10 @@ class RStringi(RPackage): version('1.4.3', sha256='13cecb396b700f81af38746e97b550a1d9fda377ca70c78f6cdfc770d33379ed') version('1.3.1', sha256='32df663bb6e9527e1ac265eec2116d26f7b7e62ea5ae7cc5de217cbb8defc362') - version('1.1.5', '0d5ec30ae368ab1b87a36fee3e228e7b') - version('1.1.3', '3b89cee3b5ef7c031077cd7707718e07') - version('1.1.2', '0ec2faa62643e1900734c0eaf5096648') - version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') + version('1.1.5', sha256='651e85fc4ec6cf71ad8a4347f2bd4b00a490cf9eec20921a83bf5222740402f2') + version('1.1.3', sha256='9ef22062e4be797c1cb6c2c8822ad5c237edb08b0318a96be8bd1930191af389') + version('1.1.2', sha256='e50b7162ceb7ebae403475f6f8a76a39532a2abc82112db88661f48aa4b9218e') + version('1.1.1', sha256='243178a138fe68c86384feb85ead8eb605e8230113d638da5650bca01e24e165') depends_on('r@2.14:', type=('build', 'run')) depends_on('icu4c@52:') diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index aa6bee349d5..cc1812e7bb8 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -19,9 +19,9 @@ class RStringr(RPackage): version('1.4.0', sha256='87604d2d3a9ad8fd68444ce0865b59e2ffbdb548a38d6634796bbd83eeb931dd') version('1.3.1', sha256='7a8b8ea038e45978bd797419b16793f44f10c5355ad4c64b74d15276fef20343') - version('1.2.0', '9054b1de91c578cc5cf454d656e9c697') - version('1.1.0', '47973a33944c6d5db9524b1e835b8a5d') - version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') + version('1.2.0', sha256='61d0b30768bbfd7c0bb89310e2de5b7b457ac504538acbcca50374b46b16129a') + version('1.1.0', sha256='ccb1f0e0f3e9524786f6cbae705c42eedf3874d0e641564e5e00517d892c5a33') + version('1.0.0', sha256='f8267db85b83c0fc8904009719c93296934775b0d6890c996ec779ec5336df4a') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-stringi@1.1.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-strucchange/package.py b/var/spack/repos/builtin/packages/r-strucchange/package.py index 8e111a58d7d..debf0a73b98 100644 --- a/var/spack/repos/builtin/packages/r-strucchange/package.py +++ b/var/spack/repos/builtin/packages/r-strucchange/package.py @@ -14,7 +14,7 @@ class RStrucchange(RPackage): url = "https://cloud.r-project.org/src/contrib/strucchange_1.5-1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/strucchange" - version('1.5-1', 'fc751fc011df9c8df82d577298cb8395') + version('1.5-1', sha256='740e2e20477b9fceeef767ae1002adc5ec397cb0f7daba5289a2c23b0dddaf31') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-subplex/package.py b/var/spack/repos/builtin/packages/r-subplex/package.py index 2ddbb19bf34..1d057dc046d 100644 --- a/var/spack/repos/builtin/packages/r-subplex/package.py +++ b/var/spack/repos/builtin/packages/r-subplex/package.py @@ -15,6 +15,6 @@ class RSubplex(RPackage): version('1.5-4', sha256='ff94cf6b1560f78c31712c05bc2bc1b703339e09c7fc777ee94abf15fa7a8b81') version('1.5-2', sha256='6f8c3ccadf1ccd7f11f3eae28cec16eed3695f14e351b864d807dbaba6cd3ded') - version('1.4-1', '2ed963dbbb1dbef47ebec7003f39a117') + version('1.4-1', sha256='94b7b961aaa229a6f025151191ed50272af1394be69f1c41146b9e8c786caec6') depends_on('r@2.5.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py index a3f22495213..e3a2c69b1b3 100644 --- a/var/spack/repos/builtin/packages/r-survey/package.py +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -21,7 +21,7 @@ class RSurvey(RPackage): version('3.36', sha256='90f32e9d2b52eacf881e6717a4b5edfc5a3beb5da516f8372293549589d79475') version('3.35-1', sha256='11e5ddde9c8c21dfaed0b1247036e068ad32782c76ff71f7937eb7585dd364db') - version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0') + version('3.30-3', sha256='be45d00b22d857e66905789031f2db1037505f80ce15d4b0ea84dabb03bc9e6d') depends_on('r@2.14.0:', when='@:3.31-5', type=('build', 'run')) depends_on('r@2.16.0:', when='@3.32:3.34', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py index 34c23beca0a..bea175b3ec3 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -17,9 +17,9 @@ class RSurvival(RPackage): version('2.44-1.1', sha256='55b151e15fcd24ccb3acf60331c9a7ad82bc10f3841ab3be9bc2a37e9ee751b9') version('2.44-1', sha256='82c44afa41fe4504295855f1da4a5940c3289dfd61bc664bf211bb67c051a909') - version('2.41-3', '6edb8093d1177775685dc26f3ce78d73') - version('2.40-1', 'a2474b656cd723791268e3114481b8a7') - version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') + version('2.41-3', sha256='f3797c344de93abd2ba8c89568770a13524a8b2694144ae55adec46921c8961d') + version('2.40-1', sha256='91d5217847e39bebcbce4f0a2e295304e5816b1270e71f5f2ed39807f004ee82') + version('2.39-5', sha256='607170ebe36080d102e884cf13c3b29df01d6bb3b593258afffa67fee2a0ada7') depends_on('r@2.13.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py index 3637255bf1b..a219d3b5c5b 100644 --- a/var/spack/repos/builtin/packages/r-tarifx/package.py +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -14,7 +14,7 @@ class RTarifx(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/taRifx" version('1.0.6.1', sha256='d4c832b26d476a395ddf8349c42613270023c8bbf52a274d280be6284c11d7e2') - version('1.0.6', '7e782e04bd69d929b29f91553382e6a2') + version('1.0.6', sha256='3dc70ac9c828d904cbac9fc9465918cd58cb5e9e35e92fe0cf38f436a1017782') depends_on('r-reshape2', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tclust/package.py b/var/spack/repos/builtin/packages/r-tclust/package.py index e0534329818..5f6d169c9c4 100644 --- a/var/spack/repos/builtin/packages/r-tclust/package.py +++ b/var/spack/repos/builtin/packages/r-tclust/package.py @@ -14,10 +14,10 @@ class RTclust(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/tclust" version('1.4-1', sha256='4b0be612c8ecd7b4eb19a44ab6ac8f5d40515600ae1144c55989b6b41335ad9e') - version('1.3-1', '5415d74682588d4a6fb8ce166fc75661') - version('1.2-7', 'e32cd02819682cc944c7baaac3b6f2b7') - version('1.2-3', '922abc1abd8da4c6ac9830e1f2f71e84') - version('1.1-03', 'f1cc9278bdb068acce4623a9d98b7b62') - version('1.1-02', '6f206501b0341fb5623208d145984f5a') + version('1.3-1', sha256='fe4479a73b947d8f6c1cc63587283a8b6223d430d39eee4e5833a06d3d1726d2') + version('1.2-7', sha256='7d2cfa35bbd44086af45be842e6c4743380c7cc8a0f985d2bb7c1a0690c878d7') + version('1.2-3', sha256='d749d4e4107b876a22ca2c0299e30e2c77cb04f53f7e5658348e274aae3f2b28') + version('1.1-03', sha256='b8a62a1d27e69ac7e985ba5ea2ae5d182d2e51665bfbfb178e22b63041709270') + version('1.1-02', sha256='f73c0d7a495552f901b710cf34e114c0ba401d5a17c48156313245904bcccad4') depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tensora/package.py b/var/spack/repos/builtin/packages/r-tensora/package.py index 4330b8c9651..fdcd0573650 100644 --- a/var/spack/repos/builtin/packages/r-tensora/package.py +++ b/var/spack/repos/builtin/packages/r-tensora/package.py @@ -16,6 +16,6 @@ class RTensora(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/tensorA" version('0.36.1', sha256='c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c') - version('0.36', '01c0613491d9b46600bf403d7e3bdd80') + version('0.36', sha256='97b3e72f26ca3a756d045008764d787a32c68f0a276fb7a29b6e1b4592fdecf6') depends_on('r@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py index e4a9ae9db79..ed72ba336fb 100644 --- a/var/spack/repos/builtin/packages/r-testit/package.py +++ b/var/spack/repos/builtin/packages/r-testit/package.py @@ -17,5 +17,5 @@ class RTestit(RPackage): version('0.9', sha256='9cf6b3df9b2c700e4e7dcbd5b8cb64fabefe674e1f40346ccaf39fe7feda5e55') version('0.8', sha256='08a9c19c962eae60f4ab58885a23e0bc239efc39da682290be436c066f8d97f7') - version('0.7', 'cfc5f5c66aa644fbf53efc4b29d18e8c') - version('0.5', 'f206d3cbdc5174e353d2d05ba6a12e59') + version('0.7', sha256='03332889bffe8b69d36e696e3a6a1a29713cdcbccf1efced6cddbf061fb41a1f') + version('0.5', sha256='1416fd69b324e5049be5adfaebde159252a119e8e987562e48b4b28cc9af69ec') diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py index baf7fced96d..a9128acb3ec 100644 --- a/var/spack/repos/builtin/packages/r-testthat/package.py +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -16,7 +16,7 @@ class RTestthat(RPackage): version('2.2.1', sha256='67ee0512bb312695c81fd74338bb8ce9e2e58763681ddbcdfdf35f52dfdb0b78') version('2.1.0', sha256='cf5fa7108111b32b86e70819352f86b57ab4e835221bb1e83642d52a1fdbcdd4') - version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc') + version('1.0.2', sha256='0ef7df0ace1fddf821d329f9d9a5d42296085350ae0d94af62c45bd203c8415e') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py index 8631d5d7269..52597e61530 100644 --- a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py +++ b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py @@ -20,7 +20,7 @@ class RTfmpvalue(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/TFMPvalue" version('0.0.8', sha256='6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841') - version('0.0.6', '69fdf4f9b9a0f408a5cee9ce34bea261') + version('0.0.6', sha256='cee3aa2d4e22856865d820f695e29a5f23486e5e08cd42cb95a0728f5f9522a1') depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-rcpp@0.11.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-th-data/package.py b/var/spack/repos/builtin/packages/r-th-data/package.py index 593cb7e6ae2..20c163164ec 100644 --- a/var/spack/repos/builtin/packages/r-th-data/package.py +++ b/var/spack/repos/builtin/packages/r-th-data/package.py @@ -15,8 +15,8 @@ class RThData(RPackage): version('1.0-10', sha256='618a1c67a30536d54b1e48ba3af46a6edcd6c2abef17935b5d4ba526a43aff55') version('1.0-9', sha256='d8318a172ce2b9f7f284dc297c8a8d5093de8eccbb566c8e7580e70938dfae0f') - version('1.0-8', '2cc20acc8b470dff1202749b4bea55c4') - version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') + version('1.0-8', sha256='478f109fcc1226500ead8e3bd6e047cecde2294fde4df8ec216d38313db79a9d') + version('1.0-7', sha256='29e126344daccbebc7df68924730ae4159a0faad77f86302070920684ba6070e') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py index 604bbb9c2a5..a6e2c603e73 100644 --- a/var/spack/repos/builtin/packages/r-threejs/package.py +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -15,7 +15,7 @@ class RThreejs(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/threejs" version('0.3.1', sha256='71750b741672a435ecf749b69c72f0681aa8bb795e317f4e3056d5e33f6d79e8') - version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b') + version('0.2.2', sha256='41fe949490fbe0f71e39b0a144791da427bd7361d027579cb4a002ed53520cc5') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-htmlwidgets@0.3.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 9e2aa5cebbd..950f336df2d 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -19,9 +19,9 @@ class RTibble(RPackage): version('2.0.0', sha256='05ad2d62e949909548c4bb8ac596810321f11b330afa9717d0889dc35edd99ba') version('1.4.2', sha256='11670353ff7059a55066dd075d1534d6a27bc5c3583fb9bc291bf750a75c5b17') version('1.4.1', sha256='32267fae1ca86abdd37c4683f9d2b1a47b8b65e1977ea3900aa197066c57aa29') - version('1.3.4', '298e81546f999fb0968625698511b8d3') - version('1.2', 'bdbc3d67aa16860741add6d6ec20ea13') - version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') + version('1.3.4', sha256='a7eef7018a68fc07c17c583fb7821a08d6bc381f5961258bffaa6ef6b137760b') + version('1.2', sha256='ed8a8bd0591223f742be80fd1cd8c4a9618d0f04011ec95c272b61ea45193104') + version('1.1', sha256='10ea18890e5514faa4c2c05fa231a6e2bbb7689f3800850cead214306414c88e') depends_on('r@3.1.0:', when='@1.3.0:', type=('build', 'run')) depends_on('r@3.1.2:', when='@:1.2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidycensus/package.py b/var/spack/repos/builtin/packages/r-tidycensus/package.py index c6c52e3bd11..87cc13bd5c6 100644 --- a/var/spack/repos/builtin/packages/r-tidycensus/package.py +++ b/var/spack/repos/builtin/packages/r-tidycensus/package.py @@ -18,7 +18,7 @@ class RTidycensus(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/tidycensus" version('0.9.2', sha256='2454525301caff9eaaf6ebe14f58706ece1fbace6187ce8bf3fff04c842b9536') - version('0.3.1', '420d046b5a408d321e775c3d410e7699') + version('0.3.1', sha256='d03cbee7abbf87bb4ce2e649726bdd143d47b549f30b5a11aaaa6c4aff78e778') depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index 456a6b79314..5f3b471b581 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -17,8 +17,8 @@ class RTidyr(RPackage): version('0.8.3', sha256='a18f54ec35124110058ab23f7e0a3c037a8d50f0405520cf5cc5443ec022cc37') version('0.8.2', sha256='99a508d0539390364789c5f4835b36c4a383927f0ec1648e2a4636c1cc6e490f') - version('0.7.2', '42d723bf04c5c1c59e27a8be14f3a6b6') - version('0.5.1', '3cadc869510c054ed93d374ab44120bd') + version('0.7.2', sha256='062cea2e2b57fffd500e4ce31cba6d593e65684fc0897ea49ea38d257c76009c') + version('0.5.1', sha256='dbab642ac7231cbfe3e2a0d4553fb4ffb3699c6d6b432be2bb5812dfbbdbdace') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyselect/package.py b/var/spack/repos/builtin/packages/r-tidyselect/package.py index 89eba20d6d9..ef330423305 100644 --- a/var/spack/repos/builtin/packages/r-tidyselect/package.py +++ b/var/spack/repos/builtin/packages/r-tidyselect/package.py @@ -17,7 +17,7 @@ class RTidyselect(RPackage): version('0.2.5', sha256='5ce2e86230fa35cfc09aa71dcdd6e05e1554a5739c863ca354d241bfccb86c74') version('0.2.4', sha256='5cb30e56ad5c1ac59786969edc8d542a7a1735a129a474f585a141aefe6a2295') - version('0.2.3', 'c9dbd895ad7ce209bacfad6d19de91c9') + version('0.2.3', sha256='0c193abc8251a60e1d2a32a99c77651c336bc185e3c2a72e5f8781813d181c2c') depends_on('r@3.1:', type=('build', 'run')) depends_on('r-glue@1.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyverse/package.py b/var/spack/repos/builtin/packages/r-tidyverse/package.py index 83027d7ff22..671d8a78560 100644 --- a/var/spack/repos/builtin/packages/r-tidyverse/package.py +++ b/var/spack/repos/builtin/packages/r-tidyverse/package.py @@ -16,7 +16,7 @@ class RTidyverse(RPackage): url = "https://cloud.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/tidyverse" - version('1.2.1', '7e2ca0b72ab668342c02fd0f52c082e1') + version('1.2.1', sha256='ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b') depends_on('r-broom@0.4.2:', type=('build', 'run')) depends_on('r-cli@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tiff/package.py b/var/spack/repos/builtin/packages/r-tiff/package.py index b74693ac46e..44779dde906 100644 --- a/var/spack/repos/builtin/packages/r-tiff/package.py +++ b/var/spack/repos/builtin/packages/r-tiff/package.py @@ -15,7 +15,7 @@ class RTiff(RPackage): url = "https://cloud.r-project.org/src/contrib/tiff_0.1-5.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/tiff" - version('0.1-5', '5052990b8647c77d3e27bc0ecf064e0b') + version('0.1-5', sha256='9514e6a9926fcddc29ce1dd12b1072ad8265900373f738de687ef4a1f9124e2b') depends_on('r@2.9.0:', type=('build', 'run')) depends_on("jpeg") diff --git a/var/spack/repos/builtin/packages/r-tigris/package.py b/var/spack/repos/builtin/packages/r-tigris/package.py index 19c1cef79a1..3d7bd60769d 100644 --- a/var/spack/repos/builtin/packages/r-tigris/package.py +++ b/var/spack/repos/builtin/packages/r-tigris/package.py @@ -15,7 +15,7 @@ class RTigris(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/tigris" version('0.8.2', sha256='ed8d6ab25332c2cc800858d58324bd8264772d8a916a3f0a8d489250a7e7140e') - version('0.5.3', 'c11cb459bf134d3deb1a641a60c86413') + version('0.5.3', sha256='6ecf76f82216798465cd9704acb432caea47469ffc4953f1aaefa4d642a28445') depends_on('r@3.0.0:', when='@:0.5.3', type=('build', 'run')) depends_on('r@3.3.0:', when='@0.6.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-timedate/package.py b/var/spack/repos/builtin/packages/r-timedate/package.py index 2025d4af64f..bb5fb25a0ac 100644 --- a/var/spack/repos/builtin/packages/r-timedate/package.py +++ b/var/spack/repos/builtin/packages/r-timedate/package.py @@ -16,6 +16,6 @@ class RTimedate(RPackage): version('3043.102', sha256='377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473') version('3042.101', sha256='6c8d4c7689b31c6a43555d9c7258516556ba03b132e5643691e3e317b89a8c6d') - version('3012.100', '9f69d3724efbf0e125e6b8e6d3475fe4') + version('3012.100', sha256='6262ef7ca9f5eeb9db8229d6bb7a51d46d467a4fa73e2ccc5b4b78e18780c432') depends_on('r@2.15.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-trimcluster/package.py b/var/spack/repos/builtin/packages/r-trimcluster/package.py index df73e3bf94e..ccd0d8980da 100644 --- a/var/spack/repos/builtin/packages/r-trimcluster/package.py +++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py @@ -14,6 +14,6 @@ class RTrimcluster(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/trimcluster" version('0.1-2.1', sha256='b64a872a6c2ad677dfeecc776c9fe5aff3e8bab6bc6a8c86957b5683fd5d2300') - version('0.1-2', '7617920e224bd18f5b87db38a3116ec2') + version('0.1-2', sha256='622fb61580cc19b9061c6ee28ffd751250a127f07904b45a0e1c5438d25b4f53') depends_on('r@1.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py index 19d76beb064..d307bccdb54 100644 --- a/var/spack/repos/builtin/packages/r-truncnorm/package.py +++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py @@ -14,6 +14,6 @@ class RTruncnorm(RPackage): url = "https://cloud.r-project.org/src/contrib/truncnorm_1.0-8.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/truncnorm" - version('1.0-8', 'c60cd6555be0dd2ea91e61757439282d') + version('1.0-8', sha256='49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e') depends_on('r@3.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py index 221be990b55..3acc3c47967 100644 --- a/var/spack/repos/builtin/packages/r-trust/package.py +++ b/var/spack/repos/builtin/packages/r-trust/package.py @@ -14,6 +14,6 @@ class RTrust(RPackage): url = "https://cloud.r-project.org/src/contrib/trust_0.1-7.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/trust" - version('0.1-7', '7e218b3a6b33bd77bd7e86dc6360418d') + version('0.1-7', sha256='e3d15aa84a71becd2824253d4a8156bdf1ab9ac3b72ced0cd53f3bb370ac6f04') depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tseries/package.py b/var/spack/repos/builtin/packages/r-tseries/package.py index e55c8c3b1a8..ef00918fb7f 100644 --- a/var/spack/repos/builtin/packages/r-tseries/package.py +++ b/var/spack/repos/builtin/packages/r-tseries/package.py @@ -15,7 +15,7 @@ class RTseries(RPackage): version('0.10-47', sha256='202377df56806fe611c2e12c4d9732c71b71220726e2defa7e568d2b5b62fb7b') version('0.10-46', sha256='12940afd1d466401160e46f993ed4baf28a42cef98d3757b66ee15e916e07222') - version('0.10-42', '3feaa5c463bc967d749323163d9bc836') + version('0.10-42', sha256='827f79858715c700e8cabd2c27853ba88ad0e05eb043bc94e126b155a75546c4') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-quadprog', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tsne/package.py b/var/spack/repos/builtin/packages/r-tsne/package.py index a65ae8cfa20..1ef92be922a 100644 --- a/var/spack/repos/builtin/packages/r-tsne/package.py +++ b/var/spack/repos/builtin/packages/r-tsne/package.py @@ -13,6 +13,6 @@ class RTsne(RPackage): url = "https://cloud.r-project.org/src/contrib/tsne_0.1-3.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/tnse" - version('0.1-3', '00974d4b3fd5f1100d0ebd24e03b0af9') - version('0.1-2', 'd96d8dce6ffeda68e2b25ec1ff52ea61') - version('0.1-1', '8197e5c61dec916b7a31b74e658b632d') + version('0.1-3', sha256='66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69') + version('0.1-2', sha256='c6c3455e0f0f5dcac14299b3dfeb1a5f1bfe5623cdaf602afc892491d3d1058b') + version('0.1-1', sha256='c953991215a660cf144e55848d2507bcf7932618e164b0e56901fb33831fd1d3') diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py index 08583bb6dbe..a137c21bd5b 100644 --- a/var/spack/repos/builtin/packages/r-ttr/package.py +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -15,7 +15,7 @@ class RTtr(RPackage): version('0.23-4', sha256='eb17604da986213b3b924f0af65c3d089502a658a253ee34f6b8f6caccf6bfa2') version('0.23-3', sha256='2136032c7a2cd2a82518a4412fc655ecb16597b123dbdebe5684caef9f15261f') - version('0.23-1', '35f693ac0d97e8ec742ebea2da222986') + version('0.23-1', sha256='699798f06ceae9663da47b67d1bc8679fc1c0776d12afd054d6ac4d19e05b2ae') depends_on('r-xts@0.10-0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py index 0adfcef4b3b..551455471fe 100644 --- a/var/spack/repos/builtin/packages/r-udunits2/package.py +++ b/var/spack/repos/builtin/packages/r-udunits2/package.py @@ -13,7 +13,7 @@ class RUdunits2(RPackage): url = "https://cloud.r-project.org/src/contrib/udunits2_0.13.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/udunits2" - version('0.13', 'c8717808c740ef70eed7aea93c7c4c7d') + version('0.13', sha256='d155d3c07f6202b65dec4075ffd1e1c3f4f35f5fdece8cfb319d39256a3e5b79') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('udunits2') diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py index 49ae88dcba8..c6b4ce8f193 100644 --- a/var/spack/repos/builtin/packages/r-units/package.py +++ b/var/spack/repos/builtin/packages/r-units/package.py @@ -20,7 +20,7 @@ class RUnits(RPackage): version('0.6-3', sha256='03de88d9dcfe80d22dd3813413f33657c576aed24a8091dbfc7f68602020a64f') version('0.6-2', sha256='5e286775d0712c8e15b6ae3a533d4c4349b0f6410c2d9d897ca519c3d0e5f170') - version('0.4-6', '0bb90dde5dad7608fa6feb1599381bf2') + version('0.4-6', sha256='db383c9b7ec221a5da29a2ddf4f74f9064c44ea2102ea7e07cc1cc5bb30fa1ef') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-udunits2@0.13:', when='@:0.5-1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py index d68b08fc994..2e502658cca 100644 --- a/var/spack/repos/builtin/packages/r-uuid/package.py +++ b/var/spack/repos/builtin/packages/r-uuid/package.py @@ -15,6 +15,6 @@ class RUuid(RPackage): url = "https://cloud.r-project.org/src/contrib/uuid_0.1-2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/uuid" - version('0.1-2', 'f97d000c0b16bca455fb5bf2cd668ddf') + version('0.1-2', sha256='dd71704dc336b0857981b92a75ed9877d4ca47780b1682def28839304cd3b1be') depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-varselrf/package.py b/var/spack/repos/builtin/packages/r-varselrf/package.py index 03fedb632aa..090d6d90bb3 100644 --- a/var/spack/repos/builtin/packages/r-varselrf/package.py +++ b/var/spack/repos/builtin/packages/r-varselrf/package.py @@ -18,7 +18,7 @@ class RVarselrf(RPackage): url = "https://cloud.r-project.org/src/contrib/varSelRF_0.7-8.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/varSelRF" - version('0.7-8', '103c460d0734bd38ae13496c839d3435') + version('0.7-8', sha256='719487fb560cb4733816bafe4cbc958a132674825e3b9d4f82ce8f2003cd8940') depends_on('r@2.0.0:', type=('build', 'run')) depends_on('r-randomforest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py index f342ec57700..150adb92480 100644 --- a/var/spack/repos/builtin/packages/r-vcd/package.py +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -20,7 +20,7 @@ class RVcd(RPackage): version('1.4-4', sha256='a561adf120b5ce41b66e0c0c321542fcddc772eb12b3d7020d86e9cd014ce9d2') version('1.4-3', sha256='17ce89927421d9cd01285b6093eeaaecb1e7252388007f66d3b9222e58cc5f15') - version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02') + version('1.4-1', sha256='af4c77522efef28271afab7d90679824826132c6bc61abe17df763ed1fc24994') depends_on('r@2.4.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py index 2248bfd9e1e..59c851dbabd 100644 --- a/var/spack/repos/builtin/packages/r-vegan/package.py +++ b/var/spack/repos/builtin/packages/r-vegan/package.py @@ -16,7 +16,7 @@ class RVegan(RPackage): version('2.5-5', sha256='876b5266f29f3034fed881020d16f476e62d145a00cb450a1a213e019e056971') version('2.5-4', sha256='5116a440111fca49b5f95cfe888b180ff29a112e6301d5e2ac5cae0e628493e0') - version('2.4-3', 'db17d4c4b9a4d421246abd5b36b00fec') + version('2.4-3', sha256='2556b1281a62e53f32bb57539bc600c00a599d0699867912220535d1a3ebec97') depends_on('r@3.0.0:', when='@:2.4-6', type=('build', 'run')) depends_on('r@3.1.0:', when='@2.5-1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vgam/package.py b/var/spack/repos/builtin/packages/r-vgam/package.py index 3039bbbd6cc..d496816056c 100644 --- a/var/spack/repos/builtin/packages/r-vgam/package.py +++ b/var/spack/repos/builtin/packages/r-vgam/package.py @@ -16,11 +16,11 @@ class RVgam(RPackage): version('1.1-1', sha256='de192bd65a7e8818728008de8e60e6dd3b61a13616c887a43e0ccc8147c7da52') version('1.0-6', sha256='121820a167411e847b41bdcb0028b55842d0ccc0c3471755c67449837e0fe3b9') - version('1.0-4', '9d30736842db6d9dcec83df49f11d3c1') - version('1.0-3', 'a158cd0a6ff956b4bf21d610df361b18') - version('1.0-2', '813b303d5d956914cf8910db3fa1ba14') - version('1.0-1', '778182585c774036ac3d10240cf63b40') - version('1.0-0', '81da7b3a797b5e26b9e859dc2f373b7b') + version('1.0-4', sha256='e581985f78ef8b866d0e810b2727061bb9c9bc177b2c9090aebb3a35ae87a964') + version('1.0-3', sha256='23bb6690ae15e9ede3198ef55d5d3236c279aa8fa6bd4f7350242379d9d72673') + version('1.0-2', sha256='03561bf484f97b616b1979132c759c5faa69c5d5a4cfd7aea2ea6d3612ac0961') + version('1.0-1', sha256='c066864e406fcee23f383a28299dba3cf83356e5b68df16324885afac87a05ea') + version('1.0-0', sha256='6acdd7db49c0987c565870afe593160ceba72a6ca4a84e6da3cf6f74d1fa02e1') depends_on('r@3.0.0:', when='@:1.0-1', type=('build', 'run')) depends_on('r@3.1.0:', when='@1.0-2:1.0-3', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vipor/package.py b/var/spack/repos/builtin/packages/r-vipor/package.py index e4deb92f860..a4fe8257f17 100644 --- a/var/spack/repos/builtin/packages/r-vipor/package.py +++ b/var/spack/repos/builtin/packages/r-vipor/package.py @@ -13,7 +13,7 @@ class RVipor(RPackage): url = "https://cloud.r-project.org/src/contrib/vipor_0.4.5.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/vipor" - version('0.4.5', 'd08bc95b3aaf1574bf41b7eb41b67ce4') - version('0.4.4', '834212e3971787809ba9737744d54dee') + version('0.4.5', sha256='7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84') + version('0.4.4', sha256='5abfd7869dae42ae2e4f52206c23433a43b485b1220685e445877ee5864a3f5c') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py index 82f5578b1a6..50b6683a8db 100644 --- a/var/spack/repos/builtin/packages/r-viridis/package.py +++ b/var/spack/repos/builtin/packages/r-viridis/package.py @@ -15,7 +15,7 @@ class RViridis(RPackage): version('0.5.1', sha256='ddf267515838c6eb092938133035cee62ab6a78760413bfc28b8256165701918') version('0.5.0', sha256='fea477172c1e11be40554545260b36d6ddff3fe6bc3bbed87813ffb77c5546cd') - version('0.4.0', 'f874384cbedf459f6c309ddb40b354ea') + version('0.4.0', sha256='93d2ded68ed7cec5633c260dbc47051416147aae074f29ebe135cc329250b00e') depends_on('r@2.10:', type=('build', 'run')) depends_on('r-viridislite@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-viridislite/package.py b/var/spack/repos/builtin/packages/r-viridislite/package.py index 5ff479d2f49..e81c7b2ef0f 100644 --- a/var/spack/repos/builtin/packages/r-viridislite/package.py +++ b/var/spack/repos/builtin/packages/r-viridislite/package.py @@ -14,6 +14,6 @@ class RViridislite(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/viridisLite" version('0.3.0', sha256='780ea12e7c4024d5ba9029f3a107321c74b8d6d9165262f6e64b79e00aa0c2af') - version('0.2.0', '04a04415cf651a2b5f964b261896c0fb') + version('0.2.0', sha256='2d4d909f21c51e720bd685f05041ba158294e0a4064e0946d0bd916709818694') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py index bbf78d73723..5c68597a7f7 100644 --- a/var/spack/repos/builtin/packages/r-visnetwork/package.py +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -16,7 +16,7 @@ class RVisnetwork(RPackage): version('2.0.7', sha256='15ad01636a3a19e1901be6743052805a5b6a9ac1240fb3dab765252b1e865128') version('2.0.6', sha256='ec2478e6a2af446569ef2d5210a2bc6b2600bcb7fd9908cef8f8c80b01e9c8aa') - version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7') + version('1.0.1', sha256='13aacf58d3bf9e78c7fb3af180062762bf22aec1777c829715c5b00396639a70') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py index 951e64faba5..3a1f67657ca 100644 --- a/var/spack/repos/builtin/packages/r-whisker/package.py +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -14,4 +14,4 @@ class RWhisker(RPackage): url = "https://cloud.r-project.org/src/contrib/whisker_0.3-2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/whisker" - version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6') + version('0.3-2', sha256='484836510fcf123a66ddd13cdc8f32eb98e814cad82ed30c0294f55742b08c7c') diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index f1e50a2ec43..b8f6606ea3f 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -17,7 +17,7 @@ class RWithr(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/withr" version('2.1.2', sha256='41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686') - version('1.0.2', 'ca52b729af9bbaa14fc8b7bafe38663c') - version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') + version('1.0.2', sha256='2391545020adc4256ee7c2e31c30ff6f688f0b6032e355e1ce8f468cab455f10') + version('1.0.1', sha256='7e245fdd17d290ff9e7c237159804dd06e1c6a3efe7855ed641eb0765a1e727d') depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py index 13cc2d6139f..50b7c0f880f 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -23,8 +23,8 @@ class RXgboost(RPackage): version('0.90.0.2', sha256='240584c1b4d54a95b4fef9074480752fae9a5b096e8f84747457d641decfc9bf') version('0.81.0.1', sha256='3e7ada32e66881ea5c90aeafdab948927014c76cfff60a8e3d7f9e1f8a9ed7ce') - version('0.6-4', '86e517e3ce39f8a01de796920f6b425e') - version('0.4-4', 'c24d3076058101a71de4b8af8806697c') + version('0.6-4', sha256='9fc51dd1b910c70930357f617d1ac7a74c5056e8847d4188175db27c09f9d1ed') + version('0.4-4', sha256='b955fc3352fcdc4894178c82fd62fbaf5e099c9d794f1e9daa2dd7b3494b61ff') depends_on('r@2.10:', when='@:0.4-4', type=('build', 'run')) depends_on('r@2.15.1:', when='@0.6-0:0.6-2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index a6b1d4619db..33cce26177d 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -16,8 +16,8 @@ class RXlconnect(RPackage): version('0.2-15', sha256='26e1d8db65974719adbc25f1327c584003eb562dc1bb2121bffc2550cf3178b3') version('0.2-14', sha256='d1013ed26947572bad97d62a3d66346f74993cf96c6408d21d5b6ee567468819') - version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') - version('0.2-11', '9d1769a103cda05665df399cc335017d') + version('0.2-12', sha256='500624f078fb27338aa91d8710daaf38633659a9b17f7cb713232a3d66f9f62c') + version('0.2-11', sha256='17c5eddd00b933fd7a2ab9d942c813046d45f0af487f8d5b11011a004db69d0b') depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-xlconnectjars@0.2-15', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index 57edc703aeb..0dce0584cf3 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -15,8 +15,8 @@ class RXlconnectjars(RPackage): version('0.2-15', sha256='bd6f48a72c3a02b7a5e9373bcfc671614bc793f41d7bb8f4f34115a89ff4f8c6') version('0.2-14', sha256='c675f0ccff0c3e56b2b1cc00d4d28bf8fdfa508266ac0ffab5c0641151dd7332') - version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') - version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') + version('0.2-12', sha256='676bf430ec118355142b3ebe8ecdadcd0019f6e9ac17c7b79b770668eace6df2') + version('0.2-9', sha256='e31dd189f24afad84abb8bd865c2353b0eccee60ac74ce9030b846789248474b') depends_on('r-rjava', type=('build', 'run')) depends_on('java@6:') diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index 06f3b7e916a..cdc2f237a5e 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -15,7 +15,7 @@ class RXlsx(RPackage): listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') - version('0.5.7', '36b1b16f29c54b6089b1dae923180dd5') + version('0.5.7', md5='36b1b16f29c54b6089b1dae923180dd5') depends_on('r-rjava', type=('build', 'run')) depends_on('r-xlsxjars', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index ad383b3fef4..0de4e08d240 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -14,6 +14,6 @@ class RXlsxjars(RPackage): url = "https://cloud.r-project.org/src/contrib/xlsxjars_0.6.1.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/xlsxjars" - version('0.6.1', '5a1721d5733cb42f3a29e3f353e39166') + version('0.6.1', sha256='37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6') depends_on('r-rjava', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py index 954c1c76334..ebe512ea638 100644 --- a/var/spack/repos/builtin/packages/r-xml/package.py +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -17,9 +17,9 @@ class RXml(RPackage): version('3.98-1.20', sha256='46af86376ea9a0fb1b440cf0acdf9b89178686a05c4b77728fcff1f023aa4858') version('3.98-1.19', sha256='81b1c4a2df24c5747fa8b8ec2d76b4e9c3649b56ca94f6c93fbd106c8a72beab') - version('3.98-1.9', '70dd9d711cf3cbd218eb2b870aee9503') - version('3.98-1.5', 'd1cfcd56f7aec96a84ffca91aea507ee') - version('3.98-1.4', '1a7f3ce6f264eeb109bfa57bedb26c14') + version('3.98-1.9', sha256='a3b70169cb2fbd8d61a41ff222d27922829864807e9ecad373f55ba0df6cf3c3') + version('3.98-1.5', sha256='deaff082e4d37931d2dabea3a60c3d6916d565821043b22b3f9522ebf3918d35') + version('3.98-1.4', sha256='9c0abc75312f66aac564266b6b79222259c678aedee9fc347462978354f11126') depends_on('r@2.13.0:', type=('build', 'run')) depends_on('libxml2@2.6.3:') diff --git a/var/spack/repos/builtin/packages/r-xml2/package.py b/var/spack/repos/builtin/packages/r-xml2/package.py index cf355c7f6ff..5ade615aef8 100644 --- a/var/spack/repos/builtin/packages/r-xml2/package.py +++ b/var/spack/repos/builtin/packages/r-xml2/package.py @@ -16,7 +16,7 @@ class RXml2(RPackage): version('1.2.2', sha256='3050f147c4335be2925a576557bbda36bd52a5bba3110d47b740a2dd811a78f4') version('1.2.1', sha256='5615bbc94607efc3bc192551992b349091df802ae34b855cfa817733f2690605') - version('1.1.1', '768f7edc39c4baab6b6b9e7c7ec79fee') + version('1.1.1', sha256='00f3e3b66b76760c19da5f6dddc98e6f30de36a96b211e59e1a3f4ff58763116') depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-rcpp@0.12.12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py index 96eeedcaba6..68a11ea0f56 100644 --- a/var/spack/repos/builtin/packages/r-xtable/package.py +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -15,6 +15,6 @@ class RXtable(RPackage): version('1.8-4', sha256='5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c') version('1.8-3', sha256='53b2b0fff8d7a8bba434063c2a01b867f510a4389ded2691fbedbc845f08c325') - version('1.8-2', '239e4825cd046156a67efae3aac01d86') + version('1.8-2', sha256='1623a1cde2e130fedb46f98840c3a882f1cbb167b292ef2bd86d70baefc4280d') depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py index d698110be7f..95732f19a32 100644 --- a/var/spack/repos/builtin/packages/r-xts/package.py +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -17,6 +17,6 @@ class RXts(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/xts" version('0.11-2', sha256='12772f6a66aab5b84b0665c470f11a3d8d8a992955c027261cfe8e6077ee13b8') - version('0.9-7', 'a232e94aebfa654653a7d88a0503537b') + version('0.9-7', sha256='f11f7cb98f4b92b7f6632a2151257914130880c267736ef5a264b5dc2dfb7098') depends_on('r-zoo@1.7-12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py index 9454402e20c..260e3d82bf9 100644 --- a/var/spack/repos/builtin/packages/r-yaml/package.py +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -16,5 +16,5 @@ class RYaml(RPackage): version('2.2.0', sha256='55bcac87eca360ab5904914fcff473a6981a1f5e6d2215d2634344d0ac30c546') version('2.1.19', sha256='e5db035693ac765e4b5fe1fc2e9711f8ca73e398e3f2bf27cc60def59ccd7f11') - version('2.1.14', '2de63248e6a122c368f8e4537426e35c') - version('2.1.13', 'f2203ea395adaff6bd09134666191d9a') + version('2.1.14', sha256='41a559846f6d44cc2dbcb3fc0becbc50d2766d3dc2aad7cfb97c1f9759ec0875') + version('2.1.13', sha256='26f69aa2008bcacf3b2f95ef82a4667eaec2f2da8487646f71f1e2635d2d7fa2') diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index fe845adea54..43a4069adfc 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -19,8 +19,8 @@ class RZoo(RPackage): version('1.8-6', sha256='2217a4f362f2201443b5fdbfd9a77d9a6caeecb05f02d703ee8b3b9bf2af37cc') version('1.8-5', sha256='8773969973d28d7d1a48f74b73be1dbd97acb3b22a4668a102e8bb585a7de826') - version('1.7-14', '8c577a7c1e535c899ab14177b1039c32') - version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') + version('1.7-14', sha256='4858675fed056a4329c4998517cc944db386447483390bd342de719e0509f598') + version('1.7-13', sha256='0ca5264d6077c785963705e462aec3e57e0d0651379f9bf4ee32e4f3b25dc754') depends_on('r@2.10.0:', when='@:1.8-1', type=('build', 'run')) depends_on('r@3.1.0:', when='@1.8-2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index e179e37a6e4..6d68e72bc3e 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -26,23 +26,23 @@ class R(AutotoolsPackage): version('3.5.3', sha256='2bfa37b7bd709f003d6b8a172ddfb6d03ddd2d672d6096439523039f7a8e678c') version('3.5.2', sha256='e53d8c3cf20f2b8d7a9c1631b6f6a22874506fb392034758b3bb341c586c5b62') version('3.5.1', sha256='0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed') - version('3.5.0', 'c0455dbfa76ca807e4dfa93d49dcc817') - version('3.4.4', '9d6f73be072531e95884c7965ff80cd8') - version('3.4.3', 'bc55db54f992fda9049201ca62d2a584') - version('3.4.2', '1cd6d37850188e7f190f1eb94a24ca1f') - version('3.4.1', '3a79c01dc0527c62e80ffb1c489297ea') - version('3.4.0', '75083c23d507b9c16d5c6afbd7a827e7') - version('3.3.3', '0ac211ec15e813a24f8f4a5a634029a4') - version('3.3.2', '2437014ef40641cdc9673e89c040b7a8') - version('3.3.1', 'f50a659738b73036e2f5635adbd229c5') - version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') - version('3.2.5', '7b23ee70cfb383be3bd4360e3c71d8c3') - version('3.2.3', '1ba3dac113efab69e706902810cc2970') - version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') - version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3') - version('3.2.0', '66fa17ad457d7e618191aa0f52fc402e') - version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4') - version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74') + version('3.5.0', sha256='fd1725535e21797d3d9fea8963d99be0ba4c3aecadcf081b43e261458b416870') + version('3.4.4', sha256='b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337') + version('3.4.3', sha256='7a3cb831de5b4151e1f890113ed207527b7d4b16df9ec6b35e0964170007f426') + version('3.4.2', sha256='971e30c2436cf645f58552905105d75788bd9733bddbcb7c4fbff4c1a6d80c64') + version('3.4.1', sha256='02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78') + version('3.4.0', sha256='288e9ed42457c47720780433b3d5c3c20983048b789291cc6a7baa11f9428b91') + version('3.3.3', sha256='5ab768053a275084618fb669b4fbaadcc39158998a87e8465323829590bcfc6c') + version('3.3.2', sha256='d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c') + version('3.3.1', sha256='3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2') + version('3.3.0', sha256='9256b154b1a5993d844bee7b1955cd49c99ad72cef03cce3cd1bdca1310311e4') + version('3.2.5', sha256='60745672dce5ddc201806fa59f6d4e0ba6554d8ed78d0f9f0d79a629978f80b5') + version('3.2.3', sha256='b93b7d878138279234160f007cb9b7f81b8a72c012a15566e9ec5395cfd9b6c1') + version('3.2.2', sha256='9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d') + version('3.2.1', sha256='d59dbc3f04f4604a5cf0fb210b8ea703ef2438b3ee65fd5ab536ec5234f4c982') + version('3.2.0', sha256='f5ae953f18ba6f3d55b46556bbbf73441350f9fd22625402b723a2b81ff64f35') + version('3.1.3', sha256='07e98323935baa38079204bfb9414a029704bb9c0ca5ab317020ae521a377312') + version('3.1.2', sha256='bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a') variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK') diff --git a/var/spack/repos/builtin/packages/racon/package.py b/var/spack/repos/builtin/packages/racon/package.py index 40ad514689f..50b92e668a9 100644 --- a/var/spack/repos/builtin/packages/racon/package.py +++ b/var/spack/repos/builtin/packages/racon/package.py @@ -16,8 +16,8 @@ class Racon(CMakePackage): version('1.3.2', sha256='7c99380a0f1091f5ee138b559e318d7e9463d3145eac026bf236751c2c4b92c7') version('1.3.1', sha256='7ce3b1ce6abdb6c6a63d50755b1fc55d5a4d2ab8f86a1df81890d4a7842d9b75') - version('1.3.0', 'e00d61f391bce2af20ebd2a3aee1e05a') - version('1.2.1', '7bf273b965a5bd0f41342a9ffe5c7639') + version('1.3.0', sha256='f2331fb88eae5c54227dc16651607af6f045ae1ccccc1d117011762927d4606a') + version('1.2.1', sha256='6e4b752b7cb6ab13b5e8cb9db58188cf1a3a61c4dcc565c8849bf4868b891bf8') depends_on('cmake@3.2:', type='build') depends_on('python', type='build') diff --git a/var/spack/repos/builtin/packages/ragel/package.py b/var/spack/repos/builtin/packages/ragel/package.py index 919b70873a3..586bbac28c9 100644 --- a/var/spack/repos/builtin/packages/ragel/package.py +++ b/var/spack/repos/builtin/packages/ragel/package.py @@ -19,6 +19,6 @@ class Ragel(AutotoolsPackage): git = "git://colm.net/ragel.git" url = "http://www.colm.net/files/ragel/ragel-6.10.tar.gz" - version('6.10', '748cae8b50cffe9efcaa5acebc6abf0d') + version('6.10', sha256='5f156edb65d20b856d638dd9ee2dfb43285914d9aa2b6ec779dac0270cd56c3f') depends_on('colm', type='build') diff --git a/var/spack/repos/builtin/packages/randfold/package.py b/var/spack/repos/builtin/packages/randfold/package.py index acabe87f5c5..b28035d1951 100644 --- a/var/spack/repos/builtin/packages/randfold/package.py +++ b/var/spack/repos/builtin/packages/randfold/package.py @@ -12,7 +12,7 @@ class Randfold(MakefilePackage): homepage = "http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/" url = "http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.1.tar.gz" - version('2.0.1', 'c9ebf7dc9d62fa4554a738a15fe1ded8') + version('2.0.1', sha256='b286145deb9ac6197062d98e209da095f00c45a5a615616bcf2b2a6609ed113f') depends_on('squid') diff --git a/var/spack/repos/builtin/packages/random123/package.py b/var/spack/repos/builtin/packages/random123/package.py index 0a8b25601a2..6afd7a3168a 100644 --- a/var/spack/repos/builtin/packages/random123/package.py +++ b/var/spack/repos/builtin/packages/random123/package.py @@ -15,7 +15,7 @@ class Random123(Package): homepage = "http://www.deshawresearch.com/resources_random123.html" url = "http://www.deshawresearch.com/downloads/download_random123.cgi/Random123-1.09.tar.gz" - version('1.09', '67ae45ff94b12acea590a6aa04ed1123') + version('1.09', sha256='cf6abf623061bcf3d17e5e49bf3f3f0ae400ee89ae2e97c8cb8dcb918b1ebabe') patch('ibmxl.patch', when='@1.09') patch('arm-gcc.patch', when='@1.09') diff --git a/var/spack/repos/builtin/packages/randrproto/package.py b/var/spack/repos/builtin/packages/randrproto/package.py index 888ad2f7a8f..6b6a2de5af3 100644 --- a/var/spack/repos/builtin/packages/randrproto/package.py +++ b/var/spack/repos/builtin/packages/randrproto/package.py @@ -16,7 +16,7 @@ class Randrproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/randrproto" url = "https://www.x.org/archive/individual/proto/randrproto-1.5.0.tar.gz" - version('1.5.0', '863d6ee3e0b2708f75d968470ed31eb9') + version('1.5.0', sha256='8f8a716d6daa6ba05df97d513960d35a39e040600bf04b313633f11679006fab') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/rapidjson/package.py b/var/spack/repos/builtin/packages/rapidjson/package.py index 93306f8b793..028b1b007f6 100644 --- a/var/spack/repos/builtin/packages/rapidjson/package.py +++ b/var/spack/repos/builtin/packages/rapidjson/package.py @@ -12,10 +12,10 @@ class Rapidjson(CMakePackage): homepage = "http://rapidjson.org" url = "https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" - version('1.1.0', 'badd12c511e081fec6c89c43a7027bce') - version('1.0.2', '97cc60d01282a968474c97f60714828c') - version('1.0.1', '48cc188df49617b859d13d31344a50b8') - version('1.0.0', '08247fbfa464d7f15304285f04b4b228') + version('1.1.0', sha256='bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e') + version('1.0.2', sha256='c3711ed2b3c76a5565ee9f0128bb4ec6753dbcc23450b713842df8f236d08666') + version('1.0.1', sha256='a9003ad5c6384896ed4fd1f4a42af108e88e1b582261766df32d717ba744ee73') + version('1.0.0', sha256='4189b32b9c285f34b37ffe4c0fd5627c1e59c2444daacffe5a96fdfbf08d139b') # released versions compile with -Werror and fail with gcc-7 # branch-fall-through warnings diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py index f584b9621f3..43fb415ff43 100644 --- a/var/spack/repos/builtin/packages/ravel/package.py +++ b/var/spack/repos/builtin/packages/ravel/package.py @@ -13,7 +13,7 @@ class Ravel(CMakePackage): homepage = "https://github.com/llnl/ravel" url = 'https://github.com/llnl/ravel/archive/v1.0.0.tar.gz' - version('1.0.0', 'b25fece58331c2adfcce76c5036485c2') + version('1.0.0', sha256='e1e1ac6d70c9aae915623d81a8f1258488fd26f880612fe21f2e032827aa93eb') depends_on('cmake@2.8.9:', type='build') diff --git a/var/spack/repos/builtin/packages/raxml/package.py b/var/spack/repos/builtin/packages/raxml/package.py index 84a63fbd2cb..ec4a3b56802 100644 --- a/var/spack/repos/builtin/packages/raxml/package.py +++ b/var/spack/repos/builtin/packages/raxml/package.py @@ -14,7 +14,7 @@ class Raxml(Package): homepage = "https://sco.h-its.org/exelixis/web/software/raxml" url = "https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz" - version('8.2.11', '6bd5c4e1f93003ccf13c9b59a5d080ab') + version('8.2.11', sha256='08cda74bf61b90eb09c229e39b1121c6d95caf182708e8745bd69d02848574d7') variant('mpi', default=True, description='Enable MPI parallel support') variant('pthreads', default=False, description='Enable pthreads version') diff --git a/var/spack/repos/builtin/packages/ray/package.py b/var/spack/repos/builtin/packages/ray/package.py index 5b9d7946747..6c7a9c463ee 100644 --- a/var/spack/repos/builtin/packages/ray/package.py +++ b/var/spack/repos/builtin/packages/ray/package.py @@ -12,7 +12,7 @@ class Ray(CMakePackage): homepage = "http://denovoassembler.sourceforge.net/" url = "https://downloads.sourceforge.net/project/denovoassembler/Ray-2.3.1.tar.bz2" - version('2.3.1', '82f693c4db60af4328263c9279701009') + version('2.3.1', sha256='3122edcdf97272af3014f959eab9a0f0e5a02c8ffc897d842b06b06ccd748036') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/rdp-classifier/package.py b/var/spack/repos/builtin/packages/rdp-classifier/package.py index 2faf86fb500..f2f0f254fb3 100644 --- a/var/spack/repos/builtin/packages/rdp-classifier/package.py +++ b/var/spack/repos/builtin/packages/rdp-classifier/package.py @@ -14,7 +14,7 @@ class RdpClassifier(Package): homepage = "http://rdp.cme.msu.edu/" url = "https://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.12.zip" - version('2.12', '7fdfa33512629810f0ff06b905642ddd') + version('2.12', sha256='977896248189a1ce2146dd3a61d203c3c6bc9aa3982c60332d463832922f7d0a') depends_on('java', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/re2c/package.py b/var/spack/repos/builtin/packages/re2c/package.py index 31bb2cb1ce6..580e2704ac9 100644 --- a/var/spack/repos/builtin/packages/re2c/package.py +++ b/var/spack/repos/builtin/packages/re2c/package.py @@ -13,8 +13,8 @@ class Re2c(AutotoolsPackage): homepage = "http://re2c.org/index.html" url = "https://github.com/skvadrik/re2c/releases/download/1.2.1/re2c-1.2.1.tar.xz" - version('1.2.1', '8b5d7dfc5a709c7220714889fa24ed32') - version('1.0.3', '8f575e2bf2efd3c685c87042f279ae4f') + version('1.2.1', sha256='1a4cd706b5b966aeffd78e3cf8b24239470ded30551e813610f9cd1a4e01b817') + version('1.0.3', md5='8f575e2bf2efd3c685c87042f279ae4f') def configure_args(self): args = ['--disable-dependency-tracking'] diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py index 906b26c3ef1..74cd4b661bb 100644 --- a/var/spack/repos/builtin/packages/readline/package.py +++ b/var/spack/repos/builtin/packages/readline/package.py @@ -19,8 +19,8 @@ class Readline(AutotoolsPackage): url = "http://ftpmirror.gnu.org/readline/readline-8.0.tar.gz" version('8.0', sha256='e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461') - version('7.0', '205b03a87fc83dab653b628c59b9fc91') - version('6.3', '33c8fb279e981274f485fd91da77e94a') + version('7.0', sha256='750d437185286f40a369e1e4f4764eda932b9459b5ec9a731628393dd3d32334') + version('6.3', sha256='56ba6071b9462f980c5a72ab0023893b65ba6debb4eeb475d7a563dc65cafd43') depends_on('ncurses') # from url=http://www.linuxfromscratch.org/patches/downloads/readline/readline-6.3-upstream_fixes-1.patch diff --git a/var/spack/repos/builtin/packages/recordproto/package.py b/var/spack/repos/builtin/packages/recordproto/package.py index 86cfe400219..30eb2229368 100644 --- a/var/spack/repos/builtin/packages/recordproto/package.py +++ b/var/spack/repos/builtin/packages/recordproto/package.py @@ -15,7 +15,7 @@ class Recordproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/recordproto" url = "https://www.x.org/archive/individual/proto/recordproto-1.14.2.tar.gz" - version('1.14.2', '868235e1e150e68916d5a316ebc4ccc4') + version('1.14.2', sha256='485f792570dd7afe49144227f325bf2827bc7d87aae6a8ab6c1de2b06b1c68c5') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/redundans/package.py b/var/spack/repos/builtin/packages/redundans/package.py index bf17cfb812a..88cfdbc5107 100644 --- a/var/spack/repos/builtin/packages/redundans/package.py +++ b/var/spack/repos/builtin/packages/redundans/package.py @@ -15,7 +15,7 @@ class Redundans(Package): git = "https://github.com/Gabaldonlab/redundans.git" version('0.14a', commit='a20215a862aed161cbfc79df9133206156a1e9f0') - version('0.13c', '2003fb7c70521f5e430553686fd1a594') + version('0.13c', sha256='26d48f27a32678d94c1d00cb3b8991d74891d6cad64a94569901ff9607a7a736') depends_on('python', type=('build', 'run')) depends_on('py-pyscaf', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/rempi/package.py b/var/spack/repos/builtin/packages/rempi/package.py index 7f2997f5589..4668b3aaaed 100644 --- a/var/spack/repos/builtin/packages/rempi/package.py +++ b/var/spack/repos/builtin/packages/rempi/package.py @@ -11,8 +11,8 @@ class Rempi(AutotoolsPackage): homepage = "https://github.com/PRUNERS/ReMPI" url = "https://github.com/PRUNERS/ReMPI/releases/download/v1.0.0/ReMPI-1.0.0.tar.gz" - version("1.1.0", "05b872a6f3e2f49a2fc6112a844c7f43") - version("1.0.0", "32c780a6a74627b5796bea161d4c4733") + version("1.1.0", sha256="4fd94fca52311fd19dc04a32547841e6c1c1656b7999b2f76f537d6ec24efccc") + version("1.0.0", sha256="1cb21f457cf8a04632150156a2ba699dd0c3f81d47e8881a9b943b9bf575fa01") depends_on("mpi") depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/rename/package.py b/var/spack/repos/builtin/packages/rename/package.py index 03f27657cb4..2b777a42880 100644 --- a/var/spack/repos/builtin/packages/rename/package.py +++ b/var/spack/repos/builtin/packages/rename/package.py @@ -12,7 +12,7 @@ class Rename(Package): homepage = "http://plasmasturm.org/code/rename" url = "https://github.com/ap/rename/archive/v1.600.tar.gz" - version('1.600', '91beb555c93d407420b5dad191069bb3') + version('1.600', sha256='538fa908c9c2c4e7a08899edb6ddb47f7cbeb9b1a1d04e003d3c19b56fcc7f88') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/rendercheck/package.py b/var/spack/repos/builtin/packages/rendercheck/package.py index 038e3b23078..bf3de64fef9 100644 --- a/var/spack/repos/builtin/packages/rendercheck/package.py +++ b/var/spack/repos/builtin/packages/rendercheck/package.py @@ -13,7 +13,7 @@ class Rendercheck(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/rendercheck" url = "https://www.x.org/archive/individual/app/rendercheck-1.5.tar.gz" - version('1.5', '92ddef6d01f02529521af103f9b9bf60') + version('1.5', sha256='1553fef61c30f2524b597c3758cc8d3f8dc1f52eb8137417fa0667b0adc8a604') depends_on('libxrender') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/renderproto/package.py b/var/spack/repos/builtin/packages/renderproto/package.py index 54ea6599673..e189368b0bf 100644 --- a/var/spack/repos/builtin/packages/renderproto/package.py +++ b/var/spack/repos/builtin/packages/renderproto/package.py @@ -15,7 +15,7 @@ class Renderproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/renderproto" url = "https://www.x.org/archive/individual/proto/renderproto-0.11.1.tar.gz" - version('0.11.1', '9b103359123e375bb7760f7dbae3dece') + version('0.11.1', sha256='a0a4be3cad9381ae28279ba5582e679491fc2bec9aab8a65993108bf8dbce5fe') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index e1c49d2cb09..f5b2e69f429 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -15,7 +15,7 @@ class Repeatmasker(Package): url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz" version('4.0.9', sha256='8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5') - version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6') + version('4.0.7', sha256='16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166') variant('crossmatch', description='Enable CrossMatch search engine', default=False) diff --git a/var/spack/repos/builtin/packages/resourceproto/package.py b/var/spack/repos/builtin/packages/resourceproto/package.py index 454427212d2..d7b0fb5b0d4 100644 --- a/var/spack/repos/builtin/packages/resourceproto/package.py +++ b/var/spack/repos/builtin/packages/resourceproto/package.py @@ -15,7 +15,7 @@ class Resourceproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/resourceproto" url = "https://www.x.org/archive/individual/proto/resourceproto-1.2.0.tar.gz" - version('1.2.0', '33091d5358ec32dd7562a1aa225a70aa') + version('1.2.0', sha256='469029d14fdeeaa7eed1be585998ff4cb92cf664f872d1d69c04140815b78734') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py index ac21ee64a9a..43ac1e72161 100644 --- a/var/spack/repos/builtin/packages/revbayes/package.py +++ b/var/spack/repos/builtin/packages/revbayes/package.py @@ -15,7 +15,7 @@ class Revbayes(CMakePackage): version('1.0.11', sha256='7e81b1952e3a63cb84617fa632f4ccdf246b4d79e7d537a423540de047dadf50') version('1.0.10', sha256='95e9affe8ca8d62880cf46778b6ec9dd8726e62a185670ebcbadf2eb2bb79f93') - version('1.0.4', '5d6de96bcb3b2686b270856de3555a58', + version('1.0.4', md5='5d6de96bcb3b2686b270856de3555a58', url='https://github.com/revbayes/revbayes/archive/v1.0.4-release.tar.gz') variant('mpi', default=True, description='Enable MPI parallel support') diff --git a/var/spack/repos/builtin/packages/rgb/package.py b/var/spack/repos/builtin/packages/rgb/package.py index 5183050bcef..4d316373f1e 100644 --- a/var/spack/repos/builtin/packages/rgb/package.py +++ b/var/spack/repos/builtin/packages/rgb/package.py @@ -18,7 +18,7 @@ class Rgb(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/rgb" url = "https://www.x.org/archive/individual/app/rgb-1.0.6.tar.gz" - version('1.0.6', '9759d058108f39066bbdf1d5d6de048c') + version('1.0.6', sha256='cb998035e08b9f58ad3150cab60461c3225bdd075238cffc665e24da40718933') depends_on('xorg-server') diff --git a/var/spack/repos/builtin/packages/rhash/package.py b/var/spack/repos/builtin/packages/rhash/package.py index 29ad1859cf3..a5d63c204fe 100644 --- a/var/spack/repos/builtin/packages/rhash/package.py +++ b/var/spack/repos/builtin/packages/rhash/package.py @@ -16,7 +16,7 @@ class Rhash(MakefilePackage): homepage = "https://sourceforge.net/projects/rhash/" url = "https://github.com/rhash/RHash/archive/v1.3.5.tar.gz" - version('1.3.5', 'f586644019c10c83c6b6835de4b99e74') + version('1.3.5', sha256='98e0688acae29e68c298ffbcdbb0f838864105f9b2bd8857980664435b1f1f2e') # For macOS build instructions, see: # https://github.com/Homebrew/homebrew-core/blob/master/Formula/rhash.rb diff --git a/var/spack/repos/builtin/packages/rlwrap/package.py b/var/spack/repos/builtin/packages/rlwrap/package.py index 136804a8993..04e2cf7df8e 100644 --- a/var/spack/repos/builtin/packages/rlwrap/package.py +++ b/var/spack/repos/builtin/packages/rlwrap/package.py @@ -13,6 +13,6 @@ class Rlwrap(AutotoolsPackage): homepage = "https://github.com/hanslub42/rlwrap" url = "https://github.com/hanslub42/rlwrap/releases/download/v0.43/rlwrap-0.43.tar.gz" - version('0.43', 'b993e83d3a292464de70719b32f83a34') + version('0.43', sha256='8e86d0b7882d9b8a73d229897a90edc207b1ae7fa0899dca8ee01c31a93feb2f') depends_on('readline@4.2:') diff --git a/var/spack/repos/builtin/packages/rna-seqc/package.py b/var/spack/repos/builtin/packages/rna-seqc/package.py index 6b34b588cf9..a33762a9b63 100644 --- a/var/spack/repos/builtin/packages/rna-seqc/package.py +++ b/var/spack/repos/builtin/packages/rna-seqc/package.py @@ -14,11 +14,11 @@ class RnaSeqc(Package): homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc" url = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar" - version('1.1.8', '71d7b5d3b3dcc1893cdc7f6819185d41', expand=False) - version('1.1.7', '2d0b8ecac955af2f9bc1b185fdfb6b45', expand=False) - version('1.1.6', 'fa9c9885081ae2e47f285c7c0f596a14', expand=False) - version('1.1.5', '4b875671e906f708cbb8fd9bcf0e958d', expand=False) - version('1.1.4', 'b04d06947c48cb2dc1b0ba29c8232db5', expand=False) + version('1.1.8', sha256='0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793', expand=False) + version('1.1.7', sha256='78e043a2973fed8d567e16bd1f68b1bd78dafe536a41cee07c32e3148e1f1ff3', expand=False) + version('1.1.6', sha256='76f1497b275c801d18a1b403336569552853dd248d94aa625862ea08c6ba25f6', expand=False) + version('1.1.5', sha256='1da100182037f46c61f93a063083e3be579da2678b0441fbc3fc8b58120e52c9', expand=False) + version('1.1.4', sha256='eac437061157036dddf496be8e05fe62b011fb95d34e9079c93ee4001710f1c6', expand=False) depends_on('jdk@8:', type='run') diff --git a/var/spack/repos/builtin/packages/rngstreams/package.py b/var/spack/repos/builtin/packages/rngstreams/package.py index c5915dedb6f..3fdaff3b044 100644 --- a/var/spack/repos/builtin/packages/rngstreams/package.py +++ b/var/spack/repos/builtin/packages/rngstreams/package.py @@ -12,4 +12,4 @@ class Rngstreams(AutotoolsPackage): homepage = "http://statmath.wu.ac.at/software/RngStreams" url = "http://statmath.wu.ac.at/software/RngStreams/rngstreams-1.0.1.tar.gz" - version('1.0.1', '6d9d842247cd1d4e9e60440406858a69') + version('1.0.1', sha256='966195febb9fb9417e4e361948843425aee12efc8b4e85332acbcd011ff2d9b0') diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index c686827db14..e462fd70bd8 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -26,9 +26,9 @@ class Rose(AutotoolsPackage): "0.9.10.0", sha256="7b53b6913fd6ca0c5050b630dae380f3e6b0897cde6148172ba01095f71cbaca", ) - version("0.9.9.104", "b01cf9d2fd440fc0fe77a713c5f7831e") - version("0.9.9.0", "8f47fb8aa803d019657bd42c8b892cce") - version("0.9.7.0", "be0d0941ba4c0349a20d6394c20d16d7") + version("0.9.9.104", md5="b01cf9d2fd440fc0fe77a713c5f7831e") + version("0.9.9.0", md5="8f47fb8aa803d019657bd42c8b892cce") + version("0.9.7.0", md5="be0d0941ba4c0349a20d6394c20d16d7") version( "0.9.9.52", commit="bd4fc0cc332ce62d9fa54db19879507d9e4f239b", diff --git a/var/spack/repos/builtin/packages/rr/package.py b/var/spack/repos/builtin/packages/rr/package.py index 18e3e2f5e65..5fa46341af5 100644 --- a/var/spack/repos/builtin/packages/rr/package.py +++ b/var/spack/repos/builtin/packages/rr/package.py @@ -11,9 +11,9 @@ class Rr(CMakePackage): homepage = "http://rr-project.org/" url = "https://github.com/mozilla/rr/archive/4.5.0.tar.gz" - version('4.5.0', '1ec0aed0559b81143f59a200eeb302ef') - version('4.4.0', '6d1cbb4fafbf6711114369907cf1efb1') - version('4.3.0', '31470564e8b7eb317f619e4ef2244082') + version('4.5.0', sha256='19f28259c0aa562c9518ae51207377fa93071a7dc270a0738d8d39e45ae2b1c0') + version('4.4.0', sha256='b2b24a3f67df47576126421746cd2942a458d2825faa76e8bb3ca43edffa03d3') + version('4.3.0', sha256='46933cdd706d71c3de05b55937c85ee055c08e67e5c1e6a1278c7feb187ca37a') depends_on('gdb') depends_on('git') diff --git a/var/spack/repos/builtin/packages/rsbench/package.py b/var/spack/repos/builtin/packages/rsbench/package.py index 25544327d8e..cb71349e214 100644 --- a/var/spack/repos/builtin/packages/rsbench/package.py +++ b/var/spack/repos/builtin/packages/rsbench/package.py @@ -14,8 +14,8 @@ class Rsbench(MakefilePackage): homepage = "https://github.com/ANL-CESAR/RSBench" url = "https://github.com/ANL-CESAR/RSBench/archive/v2.tar.gz" - version('2', '15a3ac5ea72529ac1ed9ed016ee68b4f') - version('0', '3427634dc5e7cd904d88f9955b371757') + version('2', sha256='1e97a38a863836e98cedc5cc669f8fdcaed905fafdc921d2bce32319b3e157ff') + version('0', sha256='95c06cf4cb6f396f9964d5e4b58a477bf9d7131cd39804480f1cb74e9310b271') tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/rsem/package.py b/var/spack/repos/builtin/packages/rsem/package.py index b2aff252691..eb8b6cb3145 100644 --- a/var/spack/repos/builtin/packages/rsem/package.py +++ b/var/spack/repos/builtin/packages/rsem/package.py @@ -14,7 +14,7 @@ class Rsem(MakefilePackage): url = "https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz" version('1.3.1', sha256='93c749a03ac16e94b1aab94d032d4fd5687d3261316ce943ecb89d3ae3ec2e11') - version('1.3.0', '273fd755e23d349cc38a079b81bb03b6') + version('1.3.0', sha256='ecfbb79c23973e1c4134f05201f4bd89b0caf0ce4ae1ffd7c4ddc329ed4e05d2') depends_on('r', type=('build', 'run')) depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/rstart/package.py b/var/spack/repos/builtin/packages/rstart/package.py index 168e8717619..50e3838efd3 100644 --- a/var/spack/repos/builtin/packages/rstart/package.py +++ b/var/spack/repos/builtin/packages/rstart/package.py @@ -17,7 +17,7 @@ class Rstart(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/rstart" url = "https://www.x.org/archive/individual/app/rstart-1.0.5.tar.gz" - version('1.0.5', '32db3625cb5e841e17d6bc696f21edfb') + version('1.0.5', sha256='5271c0c2675b4ad09aace7edddfdd137af10fc754afa6260d8eb5d0bba7098c7') depends_on('xproto', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/rsync/package.py b/var/spack/repos/builtin/packages/rsync/package.py index 74281fbca3d..919100cb03d 100644 --- a/var/spack/repos/builtin/packages/rsync/package.py +++ b/var/spack/repos/builtin/packages/rsync/package.py @@ -11,6 +11,6 @@ class Rsync(AutotoolsPackage): homepage = "https://rsync.samba.org" url = "https://download.samba.org/pub/rsync/src/rsync-3.1.2.tar.gz" - version('3.1.3', '1581a588fde9d89f6bc6201e8129afaf') - version('3.1.2', '0f758d7e000c0f7f7d3792610fad70cb') - version('3.1.1', '43bd6676f0b404326eee2d63be3cdcfe') + version('3.1.3', sha256='55cc554efec5fdaad70de921cd5a5eeb6c29a95524c715f3bbf849235b0800c0') + version('3.1.2', sha256='ecfa62a7fa3c4c18b9eccd8c16eaddee4bd308a76ea50b5c02a5840f09c0a1c2') + version('3.1.1', sha256='7de4364fcf5fe42f3bdb514417f1c40d10bbca896abe7e7f2c581c6ea08a2621') diff --git a/var/spack/repos/builtin/packages/rtags/package.py b/var/spack/repos/builtin/packages/rtags/package.py index 8190a1b519c..54f55884a47 100644 --- a/var/spack/repos/builtin/packages/rtags/package.py +++ b/var/spack/repos/builtin/packages/rtags/package.py @@ -12,8 +12,8 @@ class Rtags(CMakePackage): homepage = "https://github.com/Andersbakken/rtags/" url = "https://andersbakken.github.io/rtags-releases/rtags-2.17.tar.gz" - version('2.17', '95b24d7729678645a027d83be114d624') - # version('2.12', '84988aaff27915a79d4b4b57299f9a51') # no available + version('2.17', sha256='cde8882aceb09d65690007e214cc1979e0105842beb7747d49f79e33ed37d383') + # version('2.12', md5='84988aaff27915a79d4b4b57299f9a51') # no available depends_on("llvm@3.3: +clang") depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/rtax/package.py b/var/spack/repos/builtin/packages/rtax/package.py index 4955228d37c..df47eac7f48 100644 --- a/var/spack/repos/builtin/packages/rtax/package.py +++ b/var/spack/repos/builtin/packages/rtax/package.py @@ -13,7 +13,7 @@ class Rtax(Package): homepage = "https://github.com/davidsoergel/rtax" url = "http://static.davidsoergel.com/rtax-0.984.tgz" - version('0.984', 'e9dbbe4b3c26b0f0f6c14a5fb46aa587') + version('0.984', sha256='92ad9a881ca1d17221794b4313654291b30df6a9edcd0453034a090ae13a3442') depends_on('usearch') diff --git a/var/spack/repos/builtin/packages/ruby-gnuplot/package.py b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py index aeb7a44b99f..1ba329e4825 100644 --- a/var/spack/repos/builtin/packages/ruby-gnuplot/package.py +++ b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py @@ -12,7 +12,7 @@ class RubyGnuplot(Package): homepage = "https://rubygems.org/gems/gnuplot/versions/2.6.2" url = "https://rubygems.org/downloads/gnuplot-2.6.2.gem" - version('2.6.2', 'ff36a37cf71b9cd6273fcd14bbfd82df', expand=False) + version('2.6.2', sha256='d2c28d4a55867ef6f0a5725ce157581917b4d27417bc3767c7c643a828416bb3', expand=False) depends_on('gnuplot+X') diff --git a/var/spack/repos/builtin/packages/ruby-ronn/package.py b/var/spack/repos/builtin/packages/ruby-ronn/package.py index 1d69dddbdaa..d11957a3d9f 100644 --- a/var/spack/repos/builtin/packages/ruby-ronn/package.py +++ b/var/spack/repos/builtin/packages/ruby-ronn/package.py @@ -13,8 +13,8 @@ class RubyRonn(Package): homepage = "https://rubygems.org/gems/ronn" url = "https://github.com/rtomayko/ronn/archive/0.7.3.tar.gz" - version('0.7.3', '90cdedb42920c8c2a74e2d177e9535b6') - version('0.7.0', '34ad78510a75e46904629631f5335e06') + version('0.7.3', sha256='808aa6668f636ce03abba99c53c2005cef559a5099f6b40bf2c7aad8e273acb4') + version('0.7.0', sha256='ea14337093de8707aa8a67b97357332fa8a03b0df722bdbf4f027fbe4379b185') extends('ruby') diff --git a/var/spack/repos/builtin/packages/ruby-rubyinline/package.py b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py index 576c0517220..55bbe3be345 100644 --- a/var/spack/repos/builtin/packages/ruby-rubyinline/package.py +++ b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py @@ -12,7 +12,7 @@ class RubyRubyinline(Package): homepage = "https://rubygems.org/gems/RubyInline" url = "https://rubygems.org/downloads/RubyInline-3.12.4.gem" - version('3.12.4', '3058f4c48e62baef811b127f4925ee70', expand=False) + version('3.12.4', sha256='205bbc14c02d3d55e1b497241ede832ab87f3d981f92f3bda98b75e8144103e0', expand=False) extends('ruby') diff --git a/var/spack/repos/builtin/packages/ruby-svn2git/package.py b/var/spack/repos/builtin/packages/ruby-svn2git/package.py index 0202a3b9e98..32e71201733 100644 --- a/var/spack/repos/builtin/packages/ruby-svn2git/package.py +++ b/var/spack/repos/builtin/packages/ruby-svn2git/package.py @@ -17,7 +17,7 @@ class RubySvn2git(Package): homepage = "https://github.com/nirvdrum/svn2git/" url = "https://github.com/nirvdrum/svn2git/archive/v2.4.0.tar.gz" - version('2.4.0', 'f19ac6eb0634aa1fed31a1e40a2aeaa2') + version('2.4.0', sha256='81d0a3eff5b12b729d0fe8ad117db386954c635067f1c86007360c6c76dec253') depends_on('git') depends_on('subversion+perl') diff --git a/var/spack/repos/builtin/packages/ruby-terminal-table/package.py b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py index bb75c0b0955..cea27b4de2b 100644 --- a/var/spack/repos/builtin/packages/ruby-terminal-table/package.py +++ b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py @@ -12,7 +12,7 @@ class RubyTerminalTable(Package): homepage = "https://rubygems.org/gems/terminal-table" url = "https://rubygems.org/downloads/terminal-table-1.8.0.gem" - version('1.8.0', 'd78db9d71f70aaadd7e689641078e7e7', expand=False) + version('1.8.0', sha256='13371f069af18e9baa4e44d404a4ada9301899ce0530c237ac1a96c19f652294', expand=False) extends('ruby') diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 3c34f3f2b5c..2fbbc0c5377 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -15,9 +15,9 @@ class Ruby(AutotoolsPackage): list_url = "http://cache.ruby-lang.org/pub/ruby/" list_depth = 1 - version('2.6.2', 'a0405d2bf2c2d2f332033b70dff354d224a864ab0edd462b7a413420453b49ab') - version('2.5.3', '9828d03852c37c20fa333a0264f2490f07338576734d910ee3fd538c9520846c') - version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852') + version('2.6.2', sha256='a0405d2bf2c2d2f332033b70dff354d224a864ab0edd462b7a413420453b49ab') + version('2.5.3', sha256='9828d03852c37c20fa333a0264f2490f07338576734d910ee3fd538c9520846c') + version('2.2.0', sha256='7671e394abfb5d262fbcd3b27a71bf78737c7e9347fa21c39e58b0bb9c4840fc') variant('openssl', default=True, description="Enable OpenSSL support") variant('readline', default=False, description="Enable Readline support") diff --git a/var/spack/repos/builtin/packages/rust-bindgen/package.py b/var/spack/repos/builtin/packages/rust-bindgen/package.py index 3c44e9d0828..fb5d7ca7bee 100644 --- a/var/spack/repos/builtin/packages/rust-bindgen/package.py +++ b/var/spack/repos/builtin/packages/rust-bindgen/package.py @@ -12,7 +12,7 @@ class RustBindgen(Package): homepage = "http://www.rust-lang.org" url = "https://github.com/servo/rust-bindgen/archive/v0.20.5.tar.gz" - version('0.20.5', '3e4d70a5bec540324fdd95bc9e82bebc') + version('0.20.5', sha256='4f5236e7979d262c43267afba365612b1008b91b8f81d1efc6a8a2199d52bb37') extends("rust") depends_on("llvm") diff --git a/var/spack/repos/builtin/packages/sailfish/package.py b/var/spack/repos/builtin/packages/sailfish/package.py index fcc57a4d863..2a87a2c4ed0 100644 --- a/var/spack/repos/builtin/packages/sailfish/package.py +++ b/var/spack/repos/builtin/packages/sailfish/package.py @@ -12,7 +12,7 @@ class Sailfish(CMakePackage): homepage = "http://www.cs.cmu.edu/~ckingsf/software/sailfish" url = "https://github.com/kingsfordgroup/sailfish/archive/v0.10.1.tar.gz" - version('0.10.1', 'e6dab4cf3a39f346df7c28f40eb58cad') + version('0.10.1', sha256='a0d6d944382f2e07ffbfd0371132588e2f22bb846ecfc3d3435ff3d81b30d6c6') depends_on('boost@1.55:') depends_on('tbb') diff --git a/var/spack/repos/builtin/packages/salmon/package.py b/var/spack/repos/builtin/packages/salmon/package.py index 487c749025b..bc24483e019 100644 --- a/var/spack/repos/builtin/packages/salmon/package.py +++ b/var/spack/repos/builtin/packages/salmon/package.py @@ -15,8 +15,8 @@ class Salmon(CMakePackage): version('0.14.1', sha256='05289170e69b5f291a8403b40d6b9bff54cc38825e9f721c210192b51a19273e') version('0.12.0', sha256='91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3') - version('0.9.1', '1277b8ed65d2c6982ed176a496a2a1e3') - version('0.8.2', 'ee512697bc44b13661a16d4e14cf0a00') + version('0.9.1', sha256='3a32c28d217f8f0af411c77c04144b1fa4e6fd3c2f676661cc875123e4f53520') + version('0.8.2', sha256='299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91') depends_on('tbb') depends_on('boost@:1.66.0') diff --git a/var/spack/repos/builtin/packages/samblaster/package.py b/var/spack/repos/builtin/packages/samblaster/package.py index 8bc611dc0f5..bc69c0b78f0 100644 --- a/var/spack/repos/builtin/packages/samblaster/package.py +++ b/var/spack/repos/builtin/packages/samblaster/package.py @@ -13,8 +13,8 @@ class Samblaster(MakefilePackage): homepage = "https://github.com/GregoryFaust/samblaster" url = "https://github.com/GregoryFaust/samblaster/archive/v.0.1.24.tar.gz" - version('0.1.24', '885d5782cc277865dfb086fc0a20243e') - version('0.1.23', '95d33b6fcceaa38a9bd79014446b4545') + version('0.1.24', sha256='72c42e0a346166ba00152417c82179bd5139636fea859babb06ca855af93d11f') + version('0.1.23', sha256='0d35ce629771946e3d6fc199025747054e5512bffa1ba4446ed81160fffee57a') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/samrai/package.py b/var/spack/repos/builtin/packages/samrai/package.py index b047d6932b1..9843f2a0e47 100644 --- a/var/spack/repos/builtin/packages/samrai/package.py +++ b/var/spack/repos/builtin/packages/samrai/package.py @@ -18,24 +18,24 @@ class Samrai(AutotoolsPackage): url = "https://computing.llnl.gov/projects/samrai/download/SAMRAI-v3.11.2.tar.gz" list_url = homepage - version('3.12.0', '07364f6e209284e45ac0e9caf1d610f6') - version('3.11.5', '4359a03145c03501b230777f92b62104') - version('3.11.4', '473d6796772f5926b1c0d1cf8f3f8c99') + version('3.12.0', sha256='b8334aa22330a7c858e09e000dfc62abbfa3c449212b4993ec3c4035bed6b832') + version('3.11.5', sha256='6ec1f4cf2735284fe41f74073c4f1be87d92184d79401011411be3c0671bd84c') + version('3.11.4', sha256='fa87f6cc1cb3b3c4856bc3f4d7162b1f9705a200b68a5dc173484f7a71c7ea0a') # Version 3.11.3 permissions don't allow downloading - version('3.11.2', 'd5f59f8efd755b23b797e46349428206') - version('3.11.1', '19a2398a7448ec0f0f0c5e8fc6f80478') - version('3.10.0', 'ff5f5b8b4a35b52a1b7e37a74166c65a') - version('3.9.1', '232d04d0c995f5abf20d94350befd0b2') - version('3.8.0', 'c18fcffa706346bfa5828b36787ce5fe') - version('3.7.3', '12d574eacadf8c9a70f1bb4cd1a69df6') - version('3.7.2', 'f6a716f171c9fdbf3cb12f71fa6e2737') - version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce') - version('3.5.2-beta', 'd072d9d681eeb9ada15ce91bea784274') - version('3.5.0-beta', '1ad18a319fc573e12e2b1fbb6f6b0a19') - version('3.4.1-beta', '00814cbee2cb76bf8302aff56bbb385b') - version('3.3.3-beta', '1db3241d3e1cab913dc310d736c34388') - version('3.3.2-beta', 'e598a085dab979498fcb6c110c4dd26c') - version('2.4.4', '04fb048ed0efe7c531ac10c81cc5f6ac') + version('3.11.2', sha256='fd9518cc9fd8c8f6cdd681484c6eb42114aebf2a6ba4c8e1f12b34a148dfdefb') + version('3.11.1', sha256='14317938e55cb7dc3eca21d9b7667a256a08661c6da988334f7af566a015b327') + version('3.10.0', sha256='8d6958867f7165396459f4556e439065bc2cd2464bcfe16195a2a68345d56ea7') + version('3.9.1', sha256='ce0aa9bcb3accbd39c09dd32cbc9884dc00e7a8d53782ba46b8fe7d7d60fc03f') + version('3.8.0', sha256='0fc811ca83bd72d238f0efb172d466e80e5091db0b78ad00ab6b93331a1fe489') + version('3.7.3', sha256='19eada4f351a821abccac0779fde85e2ad18b931b6a8110510a4c21707c2f5ce') + version('3.7.2', sha256='c20c5b12576b73a1a095d8ef54536c4424517adaf472d55d48e57455eda74f2d') + version('3.6.3-beta', sha256='7d9202355a66b8850333484862627f73ea3d7620ca84cde757dee629ebcb61bb') + version('3.5.2-beta', sha256='9a591fc962edd56ea073abd13d03027bd530f1e61df595fae42dd9a7f8b9cc3a') + version('3.5.0-beta', sha256='3e10c55d7b652b6feca902ce782751d4b16c8ad9d4dd8b9e2e9ec74dd64f30da') + version('3.4.1-beta', sha256='5aadc813b75b65485f221372e174a2691e184e380f569129e7aa4484ca4047f8') + version('3.3.3-beta', sha256='c07b5dc8d56a8f310239d1ec6be31182a6463fea787a0e10b54a3df479979cac') + version('3.3.2-beta', sha256='430ea1a77083c8990a3c996572ed15663d9b31c0f8b614537bd7065abd6f375f') + version('2.4.4', sha256='33242e38e6f4d35bd52f4194bd99a014485b0f3458b268902f69f6c02b35ee5c') # Debug mode reduces optimization, includes assertions, debug symbols # and more print statements diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index c2abdce85d1..e4624d46e4e 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -14,14 +14,14 @@ class Samtools(Package): homepage = "www.htslib.org" url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" - version('1.9', 'cca9a40d9b91b007af2ff905cb8b5924') - version('1.8', 'c6e981c92ca00a44656a708c4b52aba3') - version('1.7', '2240175242b5183bfa6baf1483f68023') - version('1.6', 'b756f05fd5d1a7042074417edb8c9aea') + version('1.9', sha256='083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482') + version('1.8', sha256='c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16') + version('1.7', sha256='e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1') + version('1.6', sha256='ee5cd2c8d158a5969a6db59195ff90923c662000816cc0c41a190b2964dbe49e') version('1.5', sha256='8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6') - version('1.4', '8cbd7d2a0ec16d834babcd6c6d85d691') - version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88') - version('1.2', '988ec4c3058a6ceda36503eebecd4122') + version('1.4', sha256='9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4') + version('1.3.1', sha256='6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e') + version('1.2', sha256='420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa') depends_on('ncurses') # htslib became standalone @1.3.1, must use corresponding version diff --git a/var/spack/repos/builtin/packages/sandbox/package.py b/var/spack/repos/builtin/packages/sandbox/package.py index 41106f3cbfa..37f48f2080c 100644 --- a/var/spack/repos/builtin/packages/sandbox/package.py +++ b/var/spack/repos/builtin/packages/sandbox/package.py @@ -12,4 +12,4 @@ class Sandbox(AutotoolsPackage): homepage = "https://www.gentoo.org/proj/en/portage/sandbox/" url = "https://dev.gentoo.org/~mgorny/dist/sandbox-2.12.tar.xz" - version('2.12', 'be97a391dd0696ab1813ca7aad455471') + version('2.12', sha256='265a490a8c528237c55ad26dfd7f62336fa5727c82358fc9cfbaa2e52c47fc50') diff --git a/var/spack/repos/builtin/packages/sas/package.py b/var/spack/repos/builtin/packages/sas/package.py index 920f70ebf17..39e25b97ae6 100644 --- a/var/spack/repos/builtin/packages/sas/package.py +++ b/var/spack/repos/builtin/packages/sas/package.py @@ -13,9 +13,9 @@ class Sas(CMakePackage): homepage = "https://github.com/dpiparo/SAS" url = "https://github.com/dpiparo/SAS/archive/0.1.3.tar.gz" - version('0.2.0', 'e6fecfb71d9cdce342c8593f4728c9f0') - version('0.1.4', '20d7311258f2a59c9367ae1576c392b6') - version('0.1.3', '1e6572afcc03318d16d7321d40eec0fd') + version('0.2.0', sha256='a369e56f8edc61dbf59ae09dbb11d98bc05fd337c5e47e13af9c913bf7bfc538') + version('0.1.4', sha256='9b2a3436efe3c8060ee4882f3ed37d848ee79a63d6055a71a23fad6409559f40') + version('0.1.3', sha256='93c3194bb7d518c215e79436bfb43304683832b3cc66bfc838f6195ce4574943') depends_on('python@2.7:') depends_on('llvm@3.5:') diff --git a/var/spack/repos/builtin/packages/sbt/package.py b/var/spack/repos/builtin/packages/sbt/package.py index 1b2e7233de8..4af58b0ceb1 100644 --- a/var/spack/repos/builtin/packages/sbt/package.py +++ b/var/spack/repos/builtin/packages/sbt/package.py @@ -12,10 +12,10 @@ class Sbt(Package): homepage = 'http://www.scala-sbt.org' url = "https://github.com/sbt/sbt/releases/download/v1.1.4/sbt-1.1.4.tgz" - version('1.1.6', 'd307b131ed041c783ac5ed7bbb4768dc') - version('1.1.5', 'b771480feb07f98fa8cd6d787c8d4485') - version('1.1.4', 'c71e5fa846164d14d4cd450520d66c6a') - version('0.13.17', 'c52c6152cc7aadfd1f0736a1a5d0a5b8') + version('1.1.6', sha256='f545b530884e3abbca026df08df33d5a15892e6d98da5b8c2297413d1c7b68c1') + version('1.1.5', sha256='8303d7496bc70eb441e8136bd29ffc295c629dadecefa4e7a475176ab4d282d5') + version('1.1.4', sha256='2fbd592b1cfd7bc3612154a32925d5843b602490e8c8977a53fa86b35e308341') + version('0.13.17', sha256='25f782ccb2ad6d54e13ce6cec0afa3d2328874c508d68ee34e2f742e99f2c847') depends_on('java') diff --git a/var/spack/repos/builtin/packages/scala/package.py b/var/spack/repos/builtin/packages/scala/package.py index 68bb6006c43..9d990009cba 100644 --- a/var/spack/repos/builtin/packages/scala/package.py +++ b/var/spack/repos/builtin/packages/scala/package.py @@ -17,10 +17,10 @@ class Scala(Package): homepage = "https://www.scala-lang.org/" url = "https://downloads.lightbend.com/scala/2.12.1/scala-2.12.1.tgz" - version('2.12.5', '25cf4989d061c585bd0a3fa357ccf0a6') - version('2.12.1', '3eaecbce019b0fa3067503846e292b32') - version('2.11.11', '3f5b76001f60cbc31111ddb81de5ea07') - version('2.10.6', 'd79dc9fdc627b73289306bdaec81ca98') + version('2.12.5', sha256='b261ffe9a495b12e9dda2ed37331e579547e4d1b8b5810161b6c3b39ac806aa1') + version('2.12.1', sha256='4db068884532a3e27010df17befaca0f06ea50f69433d58e06a5e63c7a3cc359') + version('2.11.11', sha256='12037ca64c68468e717e950f47fc77d5ceae5e74e3bdca56f6d02fd5bfd6900b') + version('2.10.6', sha256='54adf583dae6734d66328cafa26d9fa03b8c4cf607e27b9f3915f96e9bcd2d67') depends_on('java') diff --git a/var/spack/repos/builtin/packages/scalasca/package.py b/var/spack/repos/builtin/packages/scalasca/package.py index c7d0278610d..ec6d0d9bb7c 100644 --- a/var/spack/repos/builtin/packages/scalasca/package.py +++ b/var/spack/repos/builtin/packages/scalasca/package.py @@ -21,10 +21,10 @@ class Scalasca(AutotoolsPackage): list_url = "https://scalasca.org/scalasca/front_content.php?idart=1072" version('2.5', sha256='7dfa01e383bfb8a4fd3771c9ea98ff43772e415009d9f3c5f63b9e05f2dde0f6') - version('2.4', '4a895868258030f700a635eac93d36764f60c8c63673c7db419ea4bcc6b0b760') - version('2.3.1', 'a83ced912b9d2330004cb6b9cefa7585') - version('2.2.2', '2bafce988b0522d18072f7771e491ab9') - version('2.1', 'bab9c2b021e51e2ba187feec442b96e6') + version('2.4', sha256='4a895868258030f700a635eac93d36764f60c8c63673c7db419ea4bcc6b0b760') + version('2.3.1', sha256='8ff485d03ab2c02a5852d346ae041a191c60b4295f8f9b87fe58cd36977ba558') + version('2.2.2', sha256='909567ca294366119bbcb7e8122b94f43982cbb328e18c6f6ce7a722d72cd6d4') + version('2.1', sha256='fefe43f10becf7893863380546c80ac8db171a3b1ebf97d0258602667572c2fc') depends_on("mpi") diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py index f521a960aab..db1861e5aaa 100644 --- a/var/spack/repos/builtin/packages/scalpel/package.py +++ b/var/spack/repos/builtin/packages/scalpel/package.py @@ -15,7 +15,7 @@ class Scalpel(MakefilePackage): homepage = "http://scalpel.sourceforge.net/index.html" url = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz" - version('0.5.3', '682c9f1cd6ab2cb11c6866f303c673f0') + version('0.5.3', sha256='d45b569fe3aa5934883bc7216c243d53168351c23e020d96a46fa77a1563b65e') depends_on('perl@5.10.0:') diff --git a/var/spack/repos/builtin/packages/scan-for-matches/package.py b/var/spack/repos/builtin/packages/scan-for-matches/package.py index 6b2e7f2d704..10cb9b71798 100644 --- a/var/spack/repos/builtin/packages/scan-for-matches/package.py +++ b/var/spack/repos/builtin/packages/scan-for-matches/package.py @@ -13,7 +13,7 @@ class ScanForMatches(Package): homepage = "http://blog.theseed.org/servers/2010/07/scan-for-matches.html" url = "http://www.theseed.org/servers/downloads/scan_for_matches.tgz" - version('2010-7-16', 'f64c9cfb385984ded2a7ad9ad2253d83') + version('2010-7-16', sha256='c6b17930efbdfbac28b57c3a0b4f8c26effb36c48988d82e41c81c6962e2d68f') def install(self, spec, prefix): cc = Executable(self.compiler.cc) diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py index a4f89ad5a63..8a898f69665 100644 --- a/var/spack/repos/builtin/packages/scons/package.py +++ b/var/spack/repos/builtin/packages/scons/package.py @@ -15,9 +15,9 @@ class Scons(PythonPackage): version('3.1.0', sha256='94e0d0684772d3e6d9368785296716e0ed6ce757270b3ed814e5aa72d3163890') version('3.0.5', sha256='e95eaae17d9e490cf12cd37f091a6cbee8a628b5c8dbd3cab1f348f602f46462') version('3.0.4', sha256='72c0b56db84f40d3558f351918a0ab98cb4345e8696e879d3e271f4df4a5913c') - version('3.0.1', 'b6a292e251b34b82c203b56cfa3968b3') - version('2.5.1', '3eac81e5e8206304a9b4683c57665aa4') - version('2.5.0', 'bda5530a70a41a7831d83c8b191c021e') + version('3.0.1', sha256='24475e38d39c19683bc88054524df018fe6949d70fbd4c69e298d39a0269f173') + version('2.5.1', sha256='c8de85fc02ed1a687b1f2ac791eaa0c1707b4382a204f17d782b5b111b9fdf07') + version('2.5.0', sha256='01f1b3d6023516a8e1b5e77799e5a82a23b32953b1102d339059ffeca8600493') # Python 3 support was added in SCons 3.0.0 depends_on('python@:2', when='@:2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py index 0e2d538a33b..df44111cb71 100644 --- a/var/spack/repos/builtin/packages/scorep/package.py +++ b/var/spack/repos/builtin/packages/scorep/package.py @@ -15,15 +15,15 @@ class Scorep(AutotoolsPackage): homepage = "http://www.vi-hps.org/projects/score-p" url = "https://www.vi-hps.org/cms/upload/packages/scorep/scorep-4.1.tar.gz" - version('6.0', '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8') - version('5.0', '0651614eacfc92ffbe5264a3efebd0803527ae6e8b11f7df99a56a02c37633e1') - version('4.1', '7bb6c1eecdd699b4a3207caf202866778ee01f15ff39a9ec198fcd872578fe63') - version('4.0', 'f04478e0407d67eeb8c49c3c51d91e12') - version('3.1', '065bf8eb08398e8146c895718ddb9145') - version('3.0', '44da8beaa3f71436a5f6fe51938aab2f') - version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888') - version('1.4.2', '3b9a042b13bdd5836452354e6567f71e') - version('1.3', '9db6f957b7f51fa01377a9537867a55c') + version('6.0', sha256='5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8') + version('5.0', sha256='0651614eacfc92ffbe5264a3efebd0803527ae6e8b11f7df99a56a02c37633e1') + version('4.1', sha256='7bb6c1eecdd699b4a3207caf202866778ee01f15ff39a9ec198fcd872578fe63') + version('4.0', sha256='c050525606965950ad9b35c14077b88571bcf9bfca08599279a3d8d1bb00e655') + version('3.1', sha256='49efe8a4e02afca752452809e1b21cba42e8ccb0a0772f936d4459d94e198540') + version('3.0', sha256='c9e7fe0a8239b3bbbf7628eb15f7e90de9c36557818bf3d01aecce9fec2dc0be') + version('2.0.2', sha256='d19498408781048f0e9039a1a245bce6b384f09fbe7d3643105b4e2981ecd610') + version('1.4.2', sha256='d7f3fcca2efeb2f5d5b5f183b3b2c4775e66cbb3400ea2da841dd0428713ebac') + version('1.3', sha256='dcfd42bd05f387748eeefbdf421cb3cd98ed905e009303d70b5f75b217fd1254') patch('gcc7.patch', when='@:3') diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index abf5009663a..935de81075a 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -14,12 +14,12 @@ class Scotch(Package): url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.4.tar.gz" list_url = "http://gforge.inria.fr/frs/?group_id=248" - version('6.0.6', 'ef676a3118b5590c416176e402fac248') - version('6.0.5a', '8430dff7175a1dfd5a3258e75260cf71') - version('6.0.4', 'd58b825eb95e1db77efe8c6ff42d329f') - version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc') - version('6.0.0', 'c50d6187462ba801f9a82133ee666e8e') - version('5.1.10b', 'f587201d6cf5cf63527182fbfba70753') + version('6.0.6', sha256='686f0cad88d033fe71c8b781735ff742b73a1d82a65b8b1586526d69729ac4cf') + version('6.0.5a', sha256='5b21b95e33acd5409d682fa7253cefbdffa8db82875549476c006d8cbe7c556f') + version('6.0.4', sha256='f53f4d71a8345ba15e2dd4e102a35fd83915abf50ea73e1bf6efe1bc2b4220c7') + version('6.0.3', sha256='6461cc9f28319a9dbe6cc10e28c0cbe90b4b25e205723c3edcde9a3ff974d6d8') + version('6.0.0', sha256='8206127d038bda868dda5c5a7f60ef8224f2e368298fbb01bf13fa250e378dd4') + version('5.1.10b', sha256='54c9e7fafefd49d8b2017d179d4f11a655abe10365961583baaddc4eeb6a9add') variant('mpi', default=True, description='Activate the compilation of parallel libraries') diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py index a0fa2fd3331..e038def9f36 100644 --- a/var/spack/repos/builtin/packages/scr/package.py +++ b/var/spack/repos/builtin/packages/scr/package.py @@ -20,7 +20,7 @@ class Scr(CMakePackage): # NOTE: scr-v1.1.8 is built with autotools and is not properly build here. # scr-v1.1.8 will be deprecated with the upcoming release of v1.2.0 # url = "https://github.com/LLNL/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz" - # version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e') + # version('1.1.8', md5='6a0f11ad18e27fcfc00a271ff587b06e') version('master', branch='master') version('1.2.2', sha256='764a85638a9e8762667ec1f39fa5f7da7496fca78de379a22198607b3e027847') diff --git a/var/spack/repos/builtin/packages/screen/package.py b/var/spack/repos/builtin/packages/screen/package.py index f7bcc5e4d3c..100f5479aca 100644 --- a/var/spack/repos/builtin/packages/screen/package.py +++ b/var/spack/repos/builtin/packages/screen/package.py @@ -14,22 +14,22 @@ class Screen(AutotoolsPackage): homepage = "https://www.gnu.org/software/screen/" url = "https://ftpmirror.gnu.org/screen/screen-4.3.1.tar.gz" - version('4.6.2', 'a0f529d3333b128dfaa324d978ba73a8') - version('4.3.1', '5bb3b0ff2674e29378c31ad3411170ad') - version('4.3.0', 'f76d28eadc4caaf6cdff00685ae6ad46') - version('4.2.1', '419a0594e2b25039239af8b90eda7d92') - version('4.2.0', 'e5199156a8ac863bbf92495a7638b612') - version('4.0.3', '8506fd205028a96c741e4037de6e3c42') - version('4.0.2', 'ed68ea9b43d9fba0972cb017a24940a1') - version('3.9.15', '0dff6fdc3fbbceabf25a43710fbfe75f') - version('3.9.11', '19572f92404995e7b2dea8117204dd67') - version('3.9.10', 'bbe271715d1dee038b3cd72d6d2f05fb') - version('3.9.9', '9a8b1d6c7438c64b884c4f7d7662afdc') - version('3.9.8', '8ddfebe32c2d45410ce89ea9779bb1cf') - version('3.9.4', '7de72cd18f7adcdf993ecc6764d0478a') - version('3.7.6', '9a353b828d79c3c143109265cae663a7') - version('3.7.4', 'c5ab40b068968075e41e25607dfce543') - version('3.7.2', '2d6db5de7fb0cf849cc5a6f94203f029') - version('3.7.1', '27cdd29318446561ef7c966041cbd2c9') + version('4.6.2', sha256='1b6922520e6a0ce5e28768d620b0f640a6631397f95ccb043b70b91bb503fa3a') + version('4.3.1', sha256='fa4049f8aee283de62e283d427f2cfd35d6c369b40f7f45f947dbfd915699d63') + version('4.3.0', sha256='5164e89bcc60d7193177e6e02885cc42411d1d815c839e174fb9abafb9658c46') + version('4.2.1', sha256='5468545047e301d2b3579f9d9ce00466d14a7eec95ce806e3834a3d6b0b9b080') + version('4.2.0', sha256='7dc1b7a3e7669eefe7e65f32e201704d7a11cc688244fcf71757f7792a5ff413') + version('4.0.3', sha256='78f0d5b1496084a5902586304d4a73954b2bfe33ea13edceecf21615c39e6c77') + version('4.0.2', sha256='05d087656d232b38c82379dfc66bf526d08e75e1f4c626acea4a2dda1ebcc845') + version('3.9.15', sha256='11ea131c224fa759feee3bc6ee2e3d6915a97d2d6da46db968dc24b41de054db') + version('3.9.11', sha256='f0d6d2eae538688766381c1658e3d4a64c8b4afb3682c2bb33ce96edc840a261') + version('3.9.10', sha256='3e8df4e1888e59267c37d2a24fa8365cd4d2081392f719579a347a2c6d1386a8') + version('3.9.9', sha256='8e40931ee93387c6897307419befb9d9c39bf66cd42261231f6160ef6c54dccb') + version('3.9.8', sha256='7c0593b5eec5191897e4293832cece08e4cbf362a2cf056d7d30e22727e7156b') + version('3.9.4', sha256='a3d84f7e2ae97e6264a52bcc7e0717bc9cf6bb9dbbab8d1acd1e78eb35233f42') + version('3.7.6', sha256='f30251dec5e23fac0d77922b5064e0b4db6d4d22a2a6534ebe4f3bae5ce22523') + version('3.7.4', sha256='65d33ad60c7e18f0c527654574ba1e630a8d4da106f377264a0ec3fa953d22cf') + version('3.7.2', sha256='6a882385d2810b8220b9e03c75c5fa184dcbd1afdb95974bbac396bb749a6cc0') + version('3.7.1', sha256='0cd5b1a2cbba6bb2f2bc2145aec650abf02541fd3a2071117a99e4982f6e01da') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/scripts/package.py b/var/spack/repos/builtin/packages/scripts/package.py index bad43e68eef..93387b06c46 100644 --- a/var/spack/repos/builtin/packages/scripts/package.py +++ b/var/spack/repos/builtin/packages/scripts/package.py @@ -12,7 +12,7 @@ class Scripts(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/scripts" url = "https://www.x.org/archive/individual/app/scripts-1.0.1.tar.gz" - version('1.0.1', '1e8294a126a2a7556b21025a8d933e8b') + version('1.0.1', sha256='0ed6dabdbe821944d61830489ad5f21bd934550456b9157a1cd8a32f76e08279') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/scrnsaverproto/package.py b/var/spack/repos/builtin/packages/scrnsaverproto/package.py index aa78b6199e9..d337db7b893 100644 --- a/var/spack/repos/builtin/packages/scrnsaverproto/package.py +++ b/var/spack/repos/builtin/packages/scrnsaverproto/package.py @@ -15,7 +15,7 @@ class Scrnsaverproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/scrnsaverproto" url = "https://www.x.org/archive/individual/proto/scrnsaverproto-1.2.2.tar.gz" - version('1.2.2', '21704f1bad472d94abd22fea5704bb48') + version('1.2.2', sha256='d8dee19c52977f65af08fad6aa237bacee11bc5a33e1b9b064e8ac1fd99d6e79') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/sctk/package.py b/var/spack/repos/builtin/packages/sctk/package.py index 4e6655d0800..c530a1fe962 100644 --- a/var/spack/repos/builtin/packages/sctk/package.py +++ b/var/spack/repos/builtin/packages/sctk/package.py @@ -16,13 +16,13 @@ class Sctk(Package): homepage = "https://www.nist.gov/itl/iad/mig/tools" url = "http://www.openslr.org/resources/4/sctk-2.4.10-20151007-1312Z.tar.bz2" - version('2.4.10', 'dd01ad49a33486a4754655d06177f646', + version('2.4.10', sha256='9cef424ce3a899f83b9527dc6fa83badf1bb14151529a78580301dd248bd2bf9', url='http://www.openslr.org/resources/4/sctk-2.4.10-20151007-1312Z.tar.bz2') - version('2.4.9', '8cdab2a1263fe103481e23776e2178a1', + version('2.4.9', sha256='262c92cca47755539dfa28add6120aa3ec4983b44b51f053f601e601c064617c', url='http://www.openslr.org/resources/4/sctk-2.4.9-20141015-1634Z.tar.bz2') - version('2.4.8', '2385209185b584e28dc42ea2cd324478', + version('2.4.8', sha256='ca9c5164cd06439ff85e681bc94a02a67139c7111591c628667151d386a02d5b', url='http://www.openslr.org/resources/4/sctk-2.4.8-20130429-2145.tar.bz2') - version('2.4.0', '77912e75304098ffcc6850ecf641d1a4', + version('2.4.0', sha256='73886bf3b879882a132141967ffe6b365178a2226390d2212f51a63e5df066e2', url='http://www.openslr.org/resources/4/sctk-2.4.0-20091110-0958.tar.bz2') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/sdl2-image/package.py b/var/spack/repos/builtin/packages/sdl2-image/package.py index 89cebb7d4e3..76356d708e6 100644 --- a/var/spack/repos/builtin/packages/sdl2-image/package.py +++ b/var/spack/repos/builtin/packages/sdl2-image/package.py @@ -13,6 +13,6 @@ class Sdl2Image(AutotoolsPackage): homepage = "http://sdl.beuc.net/sdl.wiki/SDL_image" url = "https://www.libsdl.org/projects/SDL_image/release/SDL2_image-2.0.1.tar.gz" - version('2.0.1', 'd94b94555ba022fa249a53a021dc3606') + version('2.0.1', sha256='3a3eafbceea5125c04be585373bfd8b3a18f259bd7eae3efc4e6d8e60e0d7f64') depends_on('sdl2') diff --git a/var/spack/repos/builtin/packages/sdl2/package.py b/var/spack/repos/builtin/packages/sdl2/package.py index 25c6bd2b3a4..06a083a73ad 100644 --- a/var/spack/repos/builtin/packages/sdl2/package.py +++ b/var/spack/repos/builtin/packages/sdl2/package.py @@ -14,7 +14,7 @@ class Sdl2(CMakePackage): homepage = "https://wiki.libsdl.org/FrontPage" url = "https://libsdl.org/release/SDL2-2.0.5.tar.gz" - version('2.0.5', 'd4055424d556b4a908aa76fad63abd3c') + version('2.0.5', sha256='442038cf55965969f2ff06d976031813de643af9c9edc9e331bd761c242e8785') depends_on('cmake@2.8.5:', type='build') depends_on('libxext', type='link') diff --git a/var/spack/repos/builtin/packages/sed/package.py b/var/spack/repos/builtin/packages/sed/package.py index 98d6b2b0e21..b9af55888f8 100644 --- a/var/spack/repos/builtin/packages/sed/package.py +++ b/var/spack/repos/builtin/packages/sed/package.py @@ -11,4 +11,4 @@ class Sed(AutotoolsPackage): homepage = "http://www.gnu.org/software/sed/" url = "https://ftpmirror.gnu.org/sed/sed-4.2.2.tar.bz2" - version('4.2.2', '7ffe1c7cdc3233e1e0c4b502df253974') + version('4.2.2', sha256='f048d1838da284c8bc9753e4506b85a1e0cc1ea8999d36f6995bcb9460cddbd7') diff --git a/var/spack/repos/builtin/packages/seqan/package.py b/var/spack/repos/builtin/packages/seqan/package.py index 4bf11faf691..96b4799efb8 100644 --- a/var/spack/repos/builtin/packages/seqan/package.py +++ b/var/spack/repos/builtin/packages/seqan/package.py @@ -18,7 +18,7 @@ class Seqan(CMakePackage): homepage = "https://www.seqan.de" url = "https://github.com/seqan/seqan/archive/seqan-v2.4.0.tar.gz" - version('2.4.0', 'd899821e295fed0a22e08099f40cbc17') + version('2.4.0', sha256='d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7') depends_on('cmake@3.4.0:', type='build') depends_on('python@2.7.0:', type='build') diff --git a/var/spack/repos/builtin/packages/seqprep/package.py b/var/spack/repos/builtin/packages/seqprep/package.py index 738091d5e74..cdb4b1fcb24 100644 --- a/var/spack/repos/builtin/packages/seqprep/package.py +++ b/var/spack/repos/builtin/packages/seqprep/package.py @@ -13,7 +13,7 @@ class Seqprep(MakefilePackage): homepage = "https://github.com/jstjohn/SeqPrep" url = "https://github.com/jstjohn/SeqPrep/archive/v1.3.2.tar.gz" - version('1.3.2', 'b6a4f5491dfdb0ce38bf791454151468') + version('1.3.2', sha256='2b8a462a0e0a3e51f70be7730dc77b1f2bb69e74845dd0fbd2110a921c32265a') depends_on('zlib', type='link') diff --git a/var/spack/repos/builtin/packages/seqtk/package.py b/var/spack/repos/builtin/packages/seqtk/package.py index ec887f91752..1e32dc69113 100644 --- a/var/spack/repos/builtin/packages/seqtk/package.py +++ b/var/spack/repos/builtin/packages/seqtk/package.py @@ -13,8 +13,8 @@ class Seqtk(Package): url = "https://github.com/lh3/seqtk/archive/v1.1.tar.gz" version('1.3', sha256='5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563') - version('1.2', '255ffe05bf2f073dc57abcff97f11a37') - version('1.1', 'ebf5cc57698a217150c2250494e039a2') + version('1.2', sha256='bd53316645ab10f0aaba59e1e72c28442ee4c9c37fddaacce5e24757eff78d7b') + version('1.1', sha256='f01b9f9af6e443673a0105a7536a01957a4fc371826385a1f3dd1e417aa91d52') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py index a847401381d..7f2c10b084f 100644 --- a/var/spack/repos/builtin/packages/serf/package.py +++ b/var/spack/repos/builtin/packages/serf/package.py @@ -13,8 +13,8 @@ class Serf(SConsPackage): homepage = 'https://serf.apache.org/' url = 'https://archive.apache.org/dist/serf/serf-1.3.9.tar.bz2' - version('1.3.9', '26015c63e3bbb108c1689bf2090e4c26351db674') - version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446') + version('1.3.9', sha256='549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc') + version('1.3.8', sha256='e0500be065dbbce490449837bb2ab624e46d64fc0b090474d9acaa87c82b2590') variant('debug', default=False, description='Enable debugging info and strict compile warnings') diff --git a/var/spack/repos/builtin/packages/sessreg/package.py b/var/spack/repos/builtin/packages/sessreg/package.py index 3d1e02fc6f9..bcdaf360008 100644 --- a/var/spack/repos/builtin/packages/sessreg/package.py +++ b/var/spack/repos/builtin/packages/sessreg/package.py @@ -14,7 +14,7 @@ class Sessreg(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/sessreg" url = "https://www.x.org/archive/individual/app/sessreg-1.1.0.tar.gz" - version('1.1.0', '5d7eb499043c7fdd8d53c5ba43660312') + version('1.1.0', sha256='e561edb48dfc3b0624554169c15f9dd2c3139e83084cb323b0c712724f2b6043') depends_on('xproto@7.0.25:', type='build') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/setxkbmap/package.py b/var/spack/repos/builtin/packages/setxkbmap/package.py index 5f226bbaa8b..5ab188da5ce 100644 --- a/var/spack/repos/builtin/packages/setxkbmap/package.py +++ b/var/spack/repos/builtin/packages/setxkbmap/package.py @@ -14,7 +14,7 @@ class Setxkbmap(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/setxkbmap" url = "https://www.x.org/archive/individual/app/setxkbmap-1.3.1.tar.gz" - version('1.3.1', 'fdfc0fc643a50fb0b5fa7546e4d28868') + version('1.3.1', sha256='e24a73669007fa3b280eba4bdc7f75715aeb2e394bf2d63f5cc872502ddde264') depends_on('libxkbfile') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/sga/package.py b/var/spack/repos/builtin/packages/sga/package.py index 3a55703e428..1a6eb2886b6 100644 --- a/var/spack/repos/builtin/packages/sga/package.py +++ b/var/spack/repos/builtin/packages/sga/package.py @@ -14,15 +14,15 @@ class Sga(AutotoolsPackage): homepage = "https://www.msi.umn.edu/sw/sga" url = "https://github.com/jts/sga/archive/v0.10.15.tar.gz" - version('0.10.15', '990aed1593f8072650c6366e5cf32519') - version('0.10.14', '211edb372898d6515dcde98d17078b7b') - version('0.10.13', 'd4f6aefc48c940dba96cc6513649ecdd') - version('0.10.12', '993bc165b4c77b75a5a2fe01c200c0da') - version('0.10.11', 'b649da5471209f50df2d53f0f2bfa0ed') - version('0.10.10', '494ff18d82b34cdaf8432b48b0356aae') - version('0.10.9', 'c2111bfd278d8faaab19732aec79fa78') - version('0.10.8', '4d75f836eaae6018d993a0b75326014a') - version('0.10.3', 'b12d35b24ca8a63c4dcc9f5d7e7c4133') + version('0.10.15', sha256='1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b') + version('0.10.14', sha256='763c011b302e1085048c93d917f081ea9348a8470e222dfd369064548e8b3994') + version('0.10.13', sha256='77859ab233980594941aa4c4cb5c2cbe1f5c43f2519f329c3a88a97865dee599') + version('0.10.12', sha256='f27f13ce1e7c1a3f35f9f4eed6c1896f3b92471bc4acc7f2364a12ce098e9779') + version('0.10.11', sha256='4704ad74705931311ed66a0886453e57616798147d149e16e13ac5acd9b5b87c') + version('0.10.10', sha256='5a75a81d405d22d51f3b7388c42d5baced4388110d39e5d77249bf3eac76a83a') + version('0.10.9', sha256='34573cb7423affd5e15c1175d9af69f7495b094b60ddfcbafd910fd703c25006') + version('0.10.8', sha256='55c5e0e425e14902e83d68cfb8cee4c86ee186459e54113a484b2a1b06d223c8') + version('0.10.3', sha256='c000823a58428d9db2979b30a571ad89aec78a8cb1af60bae1ce252dd4e8adac') depends_on('zlib') depends_on('sparsehash') diff --git a/var/spack/repos/builtin/packages/shapeit/package.py b/var/spack/repos/builtin/packages/shapeit/package.py index e12c94afa44..9eb398aa747 100644 --- a/var/spack/repos/builtin/packages/shapeit/package.py +++ b/var/spack/repos/builtin/packages/shapeit/package.py @@ -13,7 +13,7 @@ class Shapeit(Package): homepage = "https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html" url = "https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.12.Linux.dynamic.tgz" - version('2.837', '895873bb655a0a985cbfd870fdd1dd60') + version('2.837', sha256='ec2ce728dd754452423ff5a8f7ed39c1c1218a11cedb93fab0c18428e3211874') def url_for_version(self, version): url = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v{0}.r{1}.GLIBCv2.12.Linux.dynamic.tgz' diff --git a/var/spack/repos/builtin/packages/shared-mime-info/package.py b/var/spack/repos/builtin/packages/shared-mime-info/package.py index 33dcd78403b..c6cabe1d488 100644 --- a/var/spack/repos/builtin/packages/shared-mime-info/package.py +++ b/var/spack/repos/builtin/packages/shared-mime-info/package.py @@ -13,8 +13,8 @@ class SharedMimeInfo(AutotoolsPackage): homepage = "https://freedesktop.org/wiki/Software/shared-mime-info" url = "http://freedesktop.org/~hadess/shared-mime-info-1.8.tar.xz" - version('1.9', '45103889b91242850aa47f09325e798b') - version('1.8', 'f6dcadce764605552fc956563efa058c') + version('1.9', sha256='5c0133ec4e228e41bdf52f726d271a2d821499c2ab97afd3aa3d6cf43efcdc83') + version('1.8', sha256='2af55ef1a0319805b74ab40d331a3962c905477d76c086f49e34dc96363589e9') parallel = False diff --git a/var/spack/repos/builtin/packages/shiny-server/package.py b/var/spack/repos/builtin/packages/shiny-server/package.py index 142f13b73c6..d26ece50b1f 100644 --- a/var/spack/repos/builtin/packages/shiny-server/package.py +++ b/var/spack/repos/builtin/packages/shiny-server/package.py @@ -23,7 +23,7 @@ class ShinyServer(CMakePackage): homepage = "https://www.rstudio.com/products/shiny/shiny-server/" url = "https://github.com/rstudio/shiny-server/archive/v1.5.3.838.tar.gz" - version('1.5.3.838', '96f20fdcdd94c9e9bb851baccb82b97f') + version('1.5.3.838', sha256='6fd1b12cd1cbe5c64cacbec4accefe955353f9c675e5feff809c0e911a382141') depends_on('python@:2.8') # docs say: "Really. 3.x will not work" depends_on('cmake@2.8.10:') diff --git a/var/spack/repos/builtin/packages/shocklibs/package.py b/var/spack/repos/builtin/packages/shocklibs/package.py index 2e48c73a6c7..55395897f52 100644 --- a/var/spack/repos/builtin/packages/shocklibs/package.py +++ b/var/spack/repos/builtin/packages/shocklibs/package.py @@ -12,7 +12,7 @@ class Shocklibs(Package): homepage = "https://github.com/MG-RAST/Shock" url = "https://github.com/MG-RAST/Shock/archive/v0.9.24.tar.gz" - version('0.9.24', '98b2e91e2726c7165f75afaf0ca51a5b') + version('0.9.24', sha256='465d06f33df2570eaf3ffd535a38fc464084ac95a2f145ead5c71f34beeb0a35') def install(self, spec, prefix): install_tree('libs', prefix.libs) diff --git a/var/spack/repos/builtin/packages/shoremap/package.py b/var/spack/repos/builtin/packages/shoremap/package.py index 5c626c6501d..d7b51dafff4 100644 --- a/var/spack/repos/builtin/packages/shoremap/package.py +++ b/var/spack/repos/builtin/packages/shoremap/package.py @@ -19,7 +19,7 @@ class Shoremap(MakefilePackage): homepage = "http://bioinfo.mpipz.mpg.de/shoremap/" url = "http://bioinfo.mpipz.mpg.de/shoremap/SHOREmap_v3.6.tar.gz" - version('3.6', 'ccc9331189705a139d50f2c161178cb1') + version('3.6', sha256='0da4179e92cbc68434a9d8eff7bd5fff55c89fd9a543a2db6bd0f69074f2ec70') depends_on('dislin') diff --git a/var/spack/repos/builtin/packages/shortbred/package.py b/var/spack/repos/builtin/packages/shortbred/package.py index 21e2c914178..d94bf8c36ce 100644 --- a/var/spack/repos/builtin/packages/shortbred/package.py +++ b/var/spack/repos/builtin/packages/shortbred/package.py @@ -13,7 +13,7 @@ class Shortbred(Package): homepage = "https://huttenhower.sph.harvard.edu/shortbred" url = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz" - version('0.9.4', 'ad3dff344cbea3713e78b384afad28fd') + version('0.9.4', sha256='a85e5609db79696d3f2d478408fc6abfeea7628de9f533c4e1e0ea3622b397ba') depends_on('blast-plus@2.2.28:') depends_on('cdhit@4.6:') diff --git a/var/spack/repos/builtin/packages/shortstack/package.py b/var/spack/repos/builtin/packages/shortstack/package.py index 660acdbfa6c..315b1fb5a17 100644 --- a/var/spack/repos/builtin/packages/shortstack/package.py +++ b/var/spack/repos/builtin/packages/shortstack/package.py @@ -14,7 +14,7 @@ class Shortstack(Package): homepage = "http://sites.psu.edu/axtell/software/shortstack/" url = "https://github.com/MikeAxtell/ShortStack/archive/v3.8.3.tar.gz" - version('3.8.3', '3f21f494f799039f3fa88ea343f2d20d') + version('3.8.3', sha256='7c76f51ed949ca95ec5df7cb54803ae2350658fd64c75909351d5a856abb0dbe') depends_on('perl', type=('build', 'run')) depends_on('samtools') diff --git a/var/spack/repos/builtin/packages/showfont/package.py b/var/spack/repos/builtin/packages/showfont/package.py index 189badf70bf..ff3c7b8ae81 100644 --- a/var/spack/repos/builtin/packages/showfont/package.py +++ b/var/spack/repos/builtin/packages/showfont/package.py @@ -14,7 +14,7 @@ class Showfont(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/showfont" url = "https://www.x.org/archive/individual/app/showfont-1.0.5.tar.gz" - version('1.0.5', 'cea973363df01fb27a87e939600137fd') + version('1.0.5', sha256='566e34a145ea73397724d46e84f6a9b3691cf55d0fcb96ec7f917b2b39265ebb') depends_on('libfs') diff --git a/var/spack/repos/builtin/packages/sickle/package.py b/var/spack/repos/builtin/packages/sickle/package.py index 27780536c9c..2ccb2d54cfc 100644 --- a/var/spack/repos/builtin/packages/sickle/package.py +++ b/var/spack/repos/builtin/packages/sickle/package.py @@ -15,7 +15,7 @@ class Sickle(MakefilePackage): homepage = "https://github.com/najoshi/sickle" url = "https://github.com/najoshi/sickle/archive/v1.33.tar.gz" - version('1.33', '9e2ba812183e1515198c9e15c4cd2cd7') + version('1.33', sha256='eab271d25dc799e2ce67c25626128f8f8ed65e3cd68e799479bba20964624734') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/siesta/package.py b/var/spack/repos/builtin/packages/siesta/package.py index 949308df3ba..70d52a2607c 100644 --- a/var/spack/repos/builtin/packages/siesta/package.py +++ b/var/spack/repos/builtin/packages/siesta/package.py @@ -14,8 +14,8 @@ class Siesta(Package): homepage = "https://departments.icmab.es/leem/siesta/" - version('4.0.1', '5cb60ce068f2f6e84fa9184ffca94c08', url='https://launchpad.net/siesta/4.0/4.0.1/+download/siesta-4.0.1.tar.gz') - version('3.2-pl-5', '27a300c65eb2a25d107d910d26aaf81a', url='http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz') + version('4.0.1', sha256='bfb9e4335ae1d1639a749ce7e679e739fdead5ee5766b5356ea1d259a6b1e6d1', url='https://launchpad.net/siesta/4.0/4.0.1/+download/siesta-4.0.1.tar.gz') + version('3.2-pl-5', sha256='e438bb007608e54c650e14de7fa0b5c72562abb09cbd92dcfb5275becd929a23', url='http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz') patch('configure.patch', when='@:4.0') diff --git a/var/spack/repos/builtin/packages/signify/package.py b/var/spack/repos/builtin/packages/signify/package.py old mode 100755 new mode 100644 index 2b11aaed0c7..4c44ec83913 --- a/var/spack/repos/builtin/packages/signify/package.py +++ b/var/spack/repos/builtin/packages/signify/package.py @@ -12,7 +12,7 @@ class Signify(MakefilePackage): homepage = "https://github.com/aperezdc/signify" url = "https://github.com/aperezdc/signify/archive/v23.tar.gz" - version('23', '0552295572a172740ae8427eb018ede8') + version('23', sha256='1c690bf0e4283e0764a4a9dd784cb3debf4bb456b975b275dd1aaac7d5afe030') depends_on('libbsd@0.8:') diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index 3023a144c4e..a8588acc2ef 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -13,11 +13,11 @@ class Silo(AutotoolsPackage): homepage = "http://wci.llnl.gov/simulation/computer-codes/silo" url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2.tar.gz" - version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8', preferred=True) - version('4.10.2-bsd', '60fef9ce373daf1e9cc8320cfa509bc5', + version('4.10.2', sha256='3af87e5f0608a69849c00eb7c73b11f8422fa36903dd14610584506e7f68e638', preferred=True) + version('4.10.2-bsd', sha256='4b901dfc1eb4656e83419a6fde15a2f6c6a31df84edfad7f1dc296e01b20140e', url="https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2-bsd.tar.gz") - version('4.9', 'a83eda4f06761a86726e918fc55e782a') - version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9') + version('4.9', sha256='90f3d069963d859c142809cfcb034bc83eb951f61ac02ccb967fc8e8d0409854') + version('4.8', sha256='c430c1d33fcb9bc136a99ad473d535d6763bd1357b704a915ba7b1081d58fb21') variant('fortran', default=True, description='Enable Fortran support') variant('shared', default=True, description='Build shared libraries') diff --git a/var/spack/repos/builtin/packages/simgrid/package.py b/var/spack/repos/builtin/packages/simgrid/package.py index 56071a8e61e..70869c7922b 100644 --- a/var/spack/repos/builtin/packages/simgrid/package.py +++ b/var/spack/repos/builtin/packages/simgrid/package.py @@ -14,27 +14,27 @@ class Simgrid(CMakePackage): url = "https://gforge.inria.fr/frs/download.php/file/37758/SimGrid-3.21.tar.gz" git = 'https://scm.gforge.inria.fr/anonscm/git/simgrid/simgrid.git' - version('3.21', '6a5664f20433f64ebc988455d988bb75', + version('3.21', sha256='d2a6e9021016dd39a2b6f8d5d18c8223f6885746c5269550d19ba29c47c0c6a0', url='https://gforge.inria.fr/frs/download.php/file/37758/SimGrid-3.21.tar.gz') - version('3.20', 'df65463394f0f4a8e02758bf558eeb3f', + version('3.20', sha256='4d4757eb45d87cf18d990d589c31d223b0ea8cf6fcd8c94fca4d38162193cef6', url='https://gforge.inria.fr/frs/download.php/file/37602/SimGrid-3.20.tar.gz') - version('3.19', 'e6e1a56685505595617dacd5e617868e', + version('3.19', sha256='64a3b82fdf0a65bb8b7c8e9feb01694360edaf38070097bf28aa181eccb86ea7', url='https://gforge.inria.fr/frs/download.php/file/37452/SimGrid-3.19.tar.gz') - version('3.18', 'a3f457f70eb9ef095c275672b21247f4', + version('3.18', sha256='dc8f6223d89326b6a21c99eabc90598fa153d6b0818a63ff5c3ec8726e2257b2', url='https://gforge.inria.fr/frs/download.php/file/37294/SimGrid-3.18.tar.gz') - version('3.17', '0abf5a7265931bf0ce269399f26b6fc1', + version('3.17', sha256='f5e44f41983e83f65261598ab0de1909d3a8a3feb77f28e37d38f04631dbb908', url='https://gforge.inria.fr/frs/download.php/file/37148/SimGrid-3.17.tar.gz') - version('3.16', '7a2529d8769dd7ae1b088d7bcc6fcc14', + version('3.16', sha256='51782534fec87eed9da345319ead699b13d7dad4be7ac89984a0446cb385d3fa', url='https://gforge.inria.fr/frs/download.php/file/36900/SimGrid-3.16.tar.gz') - version('3.15', 'e196d30e80350dce8cd41b0af468c4fc', + version('3.15', sha256='d1e411cdbfa953c018411b842727339ede6b82efcd5d3f6adc13a24f182fa9e8', url='https://gforge.inria.fr/frs/download.php/file/36621/SimGrid-3.15.tar.gz') - version('3.14.159', 'a23be064ceb59714055199167efa0828', + version('3.14.159', sha256='2d93db245c6ec8039ffe332a77531b836ad093d57f18ec3f7920fe98e3719f48', url='http://gforge.inria.fr/frs/download.php/file/36384/SimGrid-3.14.159.tar.gz') - version('3.13', '8ace1684972a01429d5f1c5db8966709', + version('3.13', sha256='7bcedd19492f9a32cc431840ad2688d0d6e4121982d6d26e0174b5c92b086121', url='http://gforge.inria.fr/frs/download.php/file/35817/SimGrid-3.13.tar.gz') - version('3.12', 'd73faaf81d7a9eb0d309cfd72532c5f1', + version('3.12', sha256='d397ee0273395dc687fbcd2601515e7142559801a3db387454d77e0e18cd7878', url='http://gforge.inria.fr/frs/download.php/file/35215/SimGrid-3.12.tar.gz') - version('3.11', '358ed81042bd283348604eb1beb80224', + version('3.11', sha256='6efb006e028e37f74a34fc37d585a8cb296720020cabad361d65662533f1600b', url='http://gforge.inria.fr/frs/download.php/file/33683/SimGrid-3.11.tar.gz') version('git', branch='master') diff --git a/var/spack/repos/builtin/packages/simul/package.py b/var/spack/repos/builtin/packages/simul/package.py index 4ee7f781885..5d99fd021eb 100644 --- a/var/spack/repos/builtin/packages/simul/package.py +++ b/var/spack/repos/builtin/packages/simul/package.py @@ -13,10 +13,10 @@ class Simul(Package): homepage = "https://github.com/LLNL/simul" url = "https://github.com/LLNL/simul/archive/1.16.tar.gz" - version('1.16', 'd616c1046a170c1e1b7956c402d23a95') - version('1.15', 'a5744673c094a87c05c6f0799d1f496f') - version('1.14', 'f8c14f0bac15741e2af354e3f9a0e30f') - version('1.13', '8a80a62d569557715d6c9c326e39a8ef') + version('1.16', sha256='63fce55346b22113f05efe3d1ca6ddbaea5abb959e28b24c6821bce949859a9b') + version('1.15', sha256='39a2458cd31c9266c58effd598611c610c5a2616ca6a7318f76830d203f3783f') + version('1.14', sha256='cbc70881b2a03e9a5076dbdf82b6fdfa48351ab381e379935b9c7db0ee315c92') + version('1.13', sha256='42a67258181fbf723cfe13d4d2dabc5aed0d0daa606b9d817108c354e37d1c64') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/simulationio/package.py b/var/spack/repos/builtin/packages/simulationio/package.py index 2d2993f6d1b..400eb7d2ba9 100644 --- a/var/spack/repos/builtin/packages/simulationio/package.py +++ b/var/spack/repos/builtin/packages/simulationio/package.py @@ -16,8 +16,8 @@ class Simulationio(CMakePackage): version('develop', branch='master') version('9.0.1', sha256='c2f6c99417165f6eb8cbb9c44822d119586675abb34eabd553eb80f44b53e0c8') - version('1.0.0', '5cbf1d0084eb436d861ffcdd297eaa08') - version('0.1.0', '00f7dabc08ed1ab77858785ce0809f50') + version('1.0.0', md5='5cbf1d0084eb436d861ffcdd297eaa08') + version('0.1.0', md5='00f7dabc08ed1ab77858785ce0809f50') variant('julia', default=False) variant('python', default=True) diff --git a/var/spack/repos/builtin/packages/singularity-legacy/package.py b/var/spack/repos/builtin/packages/singularity-legacy/package.py index 52caa534509..c8f40f46ce4 100644 --- a/var/spack/repos/builtin/packages/singularity-legacy/package.py +++ b/var/spack/repos/builtin/packages/singularity-legacy/package.py @@ -22,7 +22,7 @@ class SingularityLegacy(AutotoolsPackage): version('2.6-release', branch='vault/2.6-release') version('2.6.1', sha256='f38d46a225e8368eb4693137806d2dc96e925a50bdf7f6983662848831041df2') version('2.6.0', sha256='7c425211a099f6fa6f74037e6e17be58fb5923b0bd11aea745e48ef83c488b49') - version('2.5.2', '2edc1a8ac9a4d7d26fba6244f1c5fd95') + version('2.5.2', sha256='eca09dbf4de5e971404a31f24d6c90081aef77075f51be8b3eb15b8715d6805e') depends_on('libarchive', when='@2.5.2:') # these are only needed if we're grabbing the unreleased tree diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py index ed6322304fc..43e40ac039e 100644 --- a/var/spack/repos/builtin/packages/singularity/package.py +++ b/var/spack/repos/builtin/packages/singularity/package.py @@ -31,7 +31,7 @@ class Singularity(MakefilePackage): version('3.4.0', sha256='eafb27f1ffbed427922ebe2b5b95d1c9c09bfeb897518867444fe230e3e35e41') version('3.3.0', sha256='070530a472e7e78492f1f142c8d4b77c64de4626c4973b0589f0d18e1fcf5b4f') version('3.2.1', sha256='d4388fb5f7e0083f0c344354c9ad3b5b823e2f3f27980e56efa7785140c9b616') - version('3.1.1', '158f58a79db5337e1d655ee0159b641e42ea7435') + version('3.1.1', sha256='7f0df46458d8894ba0c2071b0848895304ae6b1137d3d4630f1600ed8eddf1a4') depends_on('go') depends_on('libuuid') diff --git a/var/spack/repos/builtin/packages/sleef/package.py b/var/spack/repos/builtin/packages/sleef/package.py index 870e62b763a..8718026346e 100644 --- a/var/spack/repos/builtin/packages/sleef/package.py +++ b/var/spack/repos/builtin/packages/sleef/package.py @@ -13,4 +13,4 @@ class Sleef(CMakePackage): homepage = "http://sleef.org" url = "https://github.com/shibatch/sleef/archive/3.2.tar.gz" - version('3.2', '459215058f2c8d55cd2b644d56c8c4f0') + version('3.2', sha256='3130c5966e204e6d6a3ace81e543d12b5b21f60897f1c185bfa587c1bd77bee2') diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index 1dc1c7d615b..dd9774a2eaf 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -18,23 +18,23 @@ class Slepc(Package): maintainers = ['joseeroman', 'balay'] version('develop', branch='master') - version('3.12.0', '872831d961cf76389fafb7553231ae1a6676555850c98ea0e893c06f596b2e9e') - version('3.11.2', 'cd6a73ac0c9f689c12f2987000a7a28fa7df53fdc069fb59a2bb148699e741dd') - version('3.11.1', '4816070d4ecfeea6212c6944cee22dc7b4763df1eaf6ab7847cc5ac5132608fb') - version('3.11.0', 'bf29043c311fe2c549a25e2b0835095723a3eebc1dff288a233b32913b5762a2') - version('3.10.2', '0594972293f6586458a54b7c1e1121b311a9c9449060355d52bb3bf09ad6812b') - version('3.10.1', 'f64787c8c2ab3d2f6db3c67d2bfe6ee84f741ce3dfde1d2f8221e131820a12a1') - version('3.10.0', '069d7a579995e0be1567c5bc869251e29c00044369a786933ca3040149d0412a') - version('3.9.2', '247585b3f8c10bf50b9464cb8ef7b5f22bead6f96524384897a37ec4146eb03e') - version('3.9.1', 'e174ea7c127d9161eef976b0288f0c56d443a58d6ab2dc8af1e8bd66f156ce17') - version('3.9.0', '1f3930db56b4065aaf214ea758ddff1a70bf19d45544cbdfd19d2787db4bfe0b') - version('3.8.2', '1e7d20d20eb26da307d36017461fe4a55f40e947e232739179dbe6412e22ed13') - version('3.8.0', 'c58ccc4e852d1da01112466c48efa41f0839649f3a265925788237d76cd3d963') - version('3.7.4', '2fb782844e3bc265a8d181c3c3e2632a4ca073111c874c654f1365d33ca2eb8a') - version('3.7.3', '3ef9bcc645a10c1779d56b3500472ceb66df692e389d635087d30e7c46424df9') - version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2') - version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876') - version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df') + version('3.12.0', sha256='872831d961cf76389fafb7553231ae1a6676555850c98ea0e893c06f596b2e9e') + version('3.11.2', sha256='cd6a73ac0c9f689c12f2987000a7a28fa7df53fdc069fb59a2bb148699e741dd') + version('3.11.1', sha256='4816070d4ecfeea6212c6944cee22dc7b4763df1eaf6ab7847cc5ac5132608fb') + version('3.11.0', sha256='bf29043c311fe2c549a25e2b0835095723a3eebc1dff288a233b32913b5762a2') + version('3.10.2', sha256='0594972293f6586458a54b7c1e1121b311a9c9449060355d52bb3bf09ad6812b') + version('3.10.1', sha256='f64787c8c2ab3d2f6db3c67d2bfe6ee84f741ce3dfde1d2f8221e131820a12a1') + version('3.10.0', sha256='069d7a579995e0be1567c5bc869251e29c00044369a786933ca3040149d0412a') + version('3.9.2', sha256='247585b3f8c10bf50b9464cb8ef7b5f22bead6f96524384897a37ec4146eb03e') + version('3.9.1', sha256='e174ea7c127d9161eef976b0288f0c56d443a58d6ab2dc8af1e8bd66f156ce17') + version('3.9.0', sha256='1f3930db56b4065aaf214ea758ddff1a70bf19d45544cbdfd19d2787db4bfe0b') + version('3.8.2', sha256='1e7d20d20eb26da307d36017461fe4a55f40e947e232739179dbe6412e22ed13') + version('3.8.0', sha256='c58ccc4e852d1da01112466c48efa41f0839649f3a265925788237d76cd3d963') + version('3.7.4', sha256='2fb782844e3bc265a8d181c3c3e2632a4ca073111c874c654f1365d33ca2eb8a') + version('3.7.3', sha256='3ef9bcc645a10c1779d56b3500472ceb66df692e389d635087d30e7c46424df9') + version('3.7.1', sha256='670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2') + version('3.6.3', sha256='384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876') + version('3.6.2', sha256='2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df') variant('arpack', default=True, description='Enables Arpack wrappers') variant('blopex', default=False, description='Enables BLOPEX wrappers') diff --git a/var/spack/repos/builtin/packages/slurm/package.py b/var/spack/repos/builtin/packages/slurm/package.py index d635e48a0f3..94a1c90a805 100644 --- a/var/spack/repos/builtin/packages/slurm/package.py +++ b/var/spack/repos/builtin/packages/slurm/package.py @@ -26,7 +26,7 @@ class Slurm(AutotoolsPackage): version('18-08-0-1', sha256='62129d0f2949bc8a68ef86fe6f12e0715cbbf42f05b8da6ef7c3e7e7240b50d9') version('17-11-9-2', sha256='6e34328ed68262e776f524f59cca79ac75bcd18030951d45ea545a7ba4c45906') - version('17-02-6-1', '8edbb9ad41819464350d9de013367020') + version('17-02-6-1', sha256='97b3a3639106bd6d44988ed018e2657f3d640a3d5c105413d05b4721bc8ee25e') variant('gtk', default=False, description='Enable GTK+ support') variant('mariadb', default=False, description='Use MariaDB instead of MySQL') diff --git a/var/spack/repos/builtin/packages/smalt/package.py b/var/spack/repos/builtin/packages/smalt/package.py index ba3573321a3..54d968db71c 100644 --- a/var/spack/repos/builtin/packages/smalt/package.py +++ b/var/spack/repos/builtin/packages/smalt/package.py @@ -12,4 +12,4 @@ class Smalt(AutotoolsPackage): homepage = "http://www.sanger.ac.uk/science/tools/smalt-0" url = "https://downloads.sourceforge.net/project/smalt/smalt-0.7.6.tar.gz" - version('0.7.6', 'c3215d70ba960c8fdc8e80191695c60b') + version('0.7.6', sha256='89ccdfe471edba3577b43de9ebfdaedb5cd6e26b02bf4000c554253433796b31') diff --git a/var/spack/repos/builtin/packages/smproxy/package.py b/var/spack/repos/builtin/packages/smproxy/package.py index d68fedcfbbf..24652e99c60 100644 --- a/var/spack/repos/builtin/packages/smproxy/package.py +++ b/var/spack/repos/builtin/packages/smproxy/package.py @@ -13,7 +13,7 @@ class Smproxy(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/smproxy" url = "https://www.x.org/archive/individual/app/smproxy-1.0.6.tar.gz" - version('1.0.6', '012c259f5a89e5c636037446d44eb354') + version('1.0.6', sha256='a01374763426a5fdcbc7a65edc54e2070cdbca4df41dddd3051c7586e4c814c9') depends_on('libsm') depends_on('libice') diff --git a/var/spack/repos/builtin/packages/snakemake/package.py b/var/spack/repos/builtin/packages/snakemake/package.py index 3f84a7aa403..5ccca9bbc39 100644 --- a/var/spack/repos/builtin/packages/snakemake/package.py +++ b/var/spack/repos/builtin/packages/snakemake/package.py @@ -12,7 +12,7 @@ class Snakemake(PythonPackage): homepage = "https://snakemake.readthedocs.io/en/stable/" url = "https://pypi.io/packages/source/s/snakemake/snakemake-3.11.2.tar.gz" - version('3.11.2', '6bf834526078522b38d271fdf73e6b22') + version('3.11.2', sha256='f7a3b586bc2195f2dce4a4817b7ec828b6d2a0cff74a04e0f7566dcd923f9761') depends_on('python@3.3:') depends_on('py-requests', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/snap-berkeley/package.py b/var/spack/repos/builtin/packages/snap-berkeley/package.py index 06e7cc1c50a..51694c94b35 100644 --- a/var/spack/repos/builtin/packages/snap-berkeley/package.py +++ b/var/spack/repos/builtin/packages/snap-berkeley/package.py @@ -15,8 +15,8 @@ class SnapBerkeley(MakefilePackage): homepage = "http://snap.cs.berkeley.edu/" url = "https://github.com/amplab/snap/archive/v1.0beta.18.tar.gz" - version('1.0beta.18', '41e595fffa482e9eda1c3f69fb5dedeb') - version('0.15', 'a7d87cc822f052665a347ab0aa84d4de', preferred=True) + version('1.0beta.18', sha256='9e8a8dc3f17e3f533d34011afe98316c19cbd70cc8b4830375611e003697daee') + version('0.15', sha256='bea0174c8d01907023494d7ffd2a6dab9c38d248cfe4d3c26feedf9d5becce9a', preferred=True) depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/snap-korf/package.py b/var/spack/repos/builtin/packages/snap-korf/package.py index 8cc4731e175..930d8c28e76 100644 --- a/var/spack/repos/builtin/packages/snap-korf/package.py +++ b/var/spack/repos/builtin/packages/snap-korf/package.py @@ -14,7 +14,7 @@ class SnapKorf(MakefilePackage): homepage = "http://korflab.ucdavis.edu/software.html" url = "http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz" - version('2013-11-29', 'dfdf48e37cdb32af4eecd9201506b6e3') + version('2013-11-29', sha256='e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a') depends_on('perl', type=('build', 'run')) depends_on('boost') diff --git a/var/spack/repos/builtin/packages/snappy/package.py b/var/spack/repos/builtin/packages/snappy/package.py index f50f3699a12..460cc219638 100644 --- a/var/spack/repos/builtin/packages/snappy/package.py +++ b/var/spack/repos/builtin/packages/snappy/package.py @@ -12,7 +12,7 @@ class Snappy(CMakePackage): homepage = "https://github.com/google/snappy" url = "https://github.com/google/snappy/archive/1.1.7.tar.gz" - version('1.1.7', 'ee9086291c9ae8deb4dac5e0b85bf54a') + version('1.1.7', sha256='3dfa02e873ff51a11ee02b9ca391807f0c8ea0529a4924afa645fbf97163f9d4') variant('shared', default=True, description='Build shared libraries') variant('pic', default=True, description='Build position independent code') diff --git a/var/spack/repos/builtin/packages/sniffles/package.py b/var/spack/repos/builtin/packages/sniffles/package.py index 66cd9648284..03da487df18 100644 --- a/var/spack/repos/builtin/packages/sniffles/package.py +++ b/var/spack/repos/builtin/packages/sniffles/package.py @@ -12,8 +12,8 @@ class Sniffles(CMakePackage): homepage = "https://github.com/fritzsedlazeck/Sniffles/wiki" url = "https://github.com/fritzsedlazeck/Sniffles/archive/v1.0.5.tar.gz" - version('1.0.7', '83bd93c5ab5dad3a6dc776f11d3a880e') - version('1.0.5', 'c2f2350d00418ba4d82c074e7f0b1832') + version('1.0.7', sha256='03fa703873bdf9c32055c584448e1eece45f94b4bc68e60c9624cf3841e6d8a9') + version('1.0.5', sha256='386c6536bdaa4637579e235bac48444c08297337c490652d1e165accd34b258f') # the build process doesn't actually install anything, do it by hand def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/snphylo/package.py b/var/spack/repos/builtin/packages/snphylo/package.py index 40c11ce7e95..ae406850664 100644 --- a/var/spack/repos/builtin/packages/snphylo/package.py +++ b/var/spack/repos/builtin/packages/snphylo/package.py @@ -12,7 +12,7 @@ class Snphylo(Package): homepage = "http://chibba.pgml.uga.edu/snphylo/" url = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz" - version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6') + version('2016-02-04', sha256='d9e144021c83dbef97bebf743b92109ad0afcfe70f37c244059b43f11b8a50da') depends_on('python', type=('build', 'run')) depends_on('r', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/snptest/package.py b/var/spack/repos/builtin/packages/snptest/package.py index 9d315508f07..ae41ac24ceb 100644 --- a/var/spack/repos/builtin/packages/snptest/package.py +++ b/var/spack/repos/builtin/packages/snptest/package.py @@ -13,7 +13,7 @@ class Snptest(Package): homepage = "https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html" url = "http://www.well.ox.ac.uk/~gav/resources/snptest_v2.5.2_linux_x86_64_dynamic.tgz" - version('2.5.2', 'e3f2cc0351f260cf29369dc4f79a660a') + version('2.5.2', sha256='1ffa3ebafa2c5db4866a38e01bb09f43df7973d053423ce67221cb3f8acb30f6') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/soapdenovo-trans/package.py b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py index 6a05c53e3c5..f21b371a44c 100644 --- a/var/spack/repos/builtin/packages/soapdenovo-trans/package.py +++ b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py @@ -14,7 +14,7 @@ class SoapdenovoTrans(MakefilePackage): homepage = "http://soap.genomics.org.cn/SOAPdenovo-Trans.html" url = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz" - version('1.0.4', 'a3b00b0f743b96141c4d5f1b49f2918c') + version('1.0.4', sha256='378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795') build_directory = 'src' diff --git a/var/spack/repos/builtin/packages/soapdenovo2/package.py b/var/spack/repos/builtin/packages/soapdenovo2/package.py index d0ac15d8f77..65a8210ddfa 100644 --- a/var/spack/repos/builtin/packages/soapdenovo2/package.py +++ b/var/spack/repos/builtin/packages/soapdenovo2/package.py @@ -16,7 +16,7 @@ class Soapdenovo2(MakefilePackage): homepage = "https://github.com/aquaskyline/SOAPdenovo2" url = "https://github.com/aquaskyline/SOAPdenovo2/archive/r240.tar.gz" - version('240', '3bc6b63edf87bb47874bb6f126e43cd4') + version('240', sha256='cc9e9f216072c0bbcace5efdead947e1c3f41f09baec5508c7b90f933a090909') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/sofa-c/package.py b/var/spack/repos/builtin/packages/sofa-c/package.py index cc67527b553..5b926c33ef6 100644 --- a/var/spack/repos/builtin/packages/sofa-c/package.py +++ b/var/spack/repos/builtin/packages/sofa-c/package.py @@ -12,7 +12,7 @@ class SofaC(MakefilePackage): homepage = "http://www.iausofa.org/current_C.html" url = "http://www.iausofa.org/2018_0130_C/sofa_c-20180130.tar.gz" - version('20180130', '9d6903c7690e84a788b622fba6f10146') + version('20180130', sha256='de09807198c977e1c58ea1d0c79c40bdafef84f2072eab586a7ac246334796db') @property def build_directory(self): diff --git a/var/spack/repos/builtin/packages/somatic-sniper/package.py b/var/spack/repos/builtin/packages/somatic-sniper/package.py index e6a125be288..a148459687a 100644 --- a/var/spack/repos/builtin/packages/somatic-sniper/package.py +++ b/var/spack/repos/builtin/packages/somatic-sniper/package.py @@ -12,7 +12,7 @@ class SomaticSniper(CMakePackage): homepage = "http://gmt.genome.wustl.edu/packages/somatic-sniper" url = "https://github.com/genome/somatic-sniper/archive/v1.0.5.0.tar.gz" - version('1.0.5.0', '64bc2b001c9a8089f2a05900f8a0abfe') + version('1.0.5.0', sha256='fc41e90237b059fcc591e404830c4b1be678642dd5afd76ce545b97b4b7b3de1') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/sowing/package.py b/var/spack/repos/builtin/packages/sowing/package.py index ee1da00f25f..7721c034752 100644 --- a/var/spack/repos/builtin/packages/sowing/package.py +++ b/var/spack/repos/builtin/packages/sowing/package.py @@ -15,8 +15,8 @@ class Sowing(AutotoolsPackage): homepage = "http://www.mcs.anl.gov/petsc/index.html" url = "http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz" - version('1.1.25-p1', 'fc5e5664b80e606ad71ba9b85f4c86b9') - version('1.1.23-p1', '65aaf3ae2a4c0f30d532fec291702e16') + version('1.1.25-p1', sha256='c3a5bb170fffeeb1405ec4c3a048744a528d2bef24de29b6ac5e970cfeaddab5') + version('1.1.23-p1', sha256='3e36f59e06fccbbf7b78d185c5654edaf70cf76f1c584bcbf08c39d7f29125e8') def build(self, spec, prefix): make('ALL', parallel=False) diff --git a/var/spack/repos/builtin/packages/sox/package.py b/var/spack/repos/builtin/packages/sox/package.py index 2a92660baa7..98e4ade490f 100644 --- a/var/spack/repos/builtin/packages/sox/package.py +++ b/var/spack/repos/builtin/packages/sox/package.py @@ -12,7 +12,7 @@ class Sox(AutotoolsPackage): homepage = "http://sox.sourceforge.net/Main/HomePage" url = "https://downloads.sourceforge.net/project/sox/sox/14.4.2/sox-14.4.2.tar.bz2" - version('14.4.2', 'ba804bb1ce5c71dd484a102a5b27d0dd') + version('14.4.2', sha256='81a6956d4330e75b5827316e44ae381e6f1e8928003c6aa45896da9041ea149c') variant('mp3', default=False, diff --git a/var/spack/repos/builtin/packages/spades/package.py b/var/spack/repos/builtin/packages/spades/package.py index 9df7dbafbb2..b032d1f210e 100644 --- a/var/spack/repos/builtin/packages/spades/package.py +++ b/var/spack/repos/builtin/packages/spades/package.py @@ -13,10 +13,10 @@ class Spades(CMakePackage): homepage = "http://cab.spbu.ru/software/spades/" url = "http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1.tar.gz" - version('3.13.0', 'c63442248c4c712603979fa70503c2bff82354f005acda2abc42dd5598427040') - version('3.12.0', '15b48a3bcbbe6a8ad58fd04ba5d3f1015990fbfd9bdf4913042803b171853ac7') - version('3.11.1', '478677b560e2f98db025e8efd5245cdf') - version('3.10.1', 'dcab7d145af81b59cc867562f27536c3') + version('3.13.0', sha256='c63442248c4c712603979fa70503c2bff82354f005acda2abc42dd5598427040') + version('3.12.0', sha256='15b48a3bcbbe6a8ad58fd04ba5d3f1015990fbfd9bdf4913042803b171853ac7') + version('3.11.1', sha256='3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474') + version('3.10.1', sha256='d49dd9eb947767a14a9896072a1bce107fb8bf39ed64133a9e2f24fb1f240d96') depends_on('python', type=('build', 'run')) depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py index 9ca6a5aa26f..9b05e3b4bfd 100644 --- a/var/spack/repos/builtin/packages/spark/package.py +++ b/var/spack/repos/builtin/packages/spark/package.py @@ -22,13 +22,13 @@ class Spark(Package): depends_on('java', type=('build', 'run')) depends_on('hadoop', when='+hadoop', type=('build', 'run')) - version('2.3.0', 'db21021b8e877b219ab886097ef42344') - version('2.1.0', '21d4471e78250775b1fa7c0e6c3a1326') - version('2.0.2', '32110c1bb8f081359738742bd26bced1') - version('2.0.0', '8a5307d973da6949a385aefb6ff747bb') - version('1.6.2', '304394fbe2899211217f0cd9e9b2b5d9') - version('1.6.1', 'fcf4961649f15af1fea78c882e65b001') - version('1.6.0', '2c28edc89ca0067e63e525c04f7b1d89') + version('2.3.0', sha256='a7e29e78bd43aa6d137f0bb0afd54a3017865d471456c6d436ae79475bbeb161') + version('2.1.0', sha256='3ca4ecb0eb9a00de5099cc2564ed957433a2d15d9d645a60470324621853c5ae') + version('2.0.2', sha256='122ec1af0fcb23c0345f20f77d33cf378422ffe966efe4b9ef90e55cf7a46a3c') + version('2.0.0', sha256='7c90bc4b7689df30f187e00845db8c7c9fb4045a0bcf2fa70a4954cc17d2c0d1') + version('1.6.2', sha256='f6b43333ca80629bacbbbc2e460d21064f53f50880f3f0a3f68745fdf8b3137e') + version('1.6.1', sha256='3d67678c5cb5eeba1cab125219fa2f9f17609368ea462e3993d2eae7c8f37207') + version('1.6.0', sha256='9f62bc1d1f7668becd1fcedd5ded01ad907246df287d2525cfc562d88a3676da') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/sparsehash/package.py b/var/spack/repos/builtin/packages/sparsehash/package.py index 795529cde04..4a1d3d706b3 100644 --- a/var/spack/repos/builtin/packages/sparsehash/package.py +++ b/var/spack/repos/builtin/packages/sparsehash/package.py @@ -11,4 +11,4 @@ class Sparsehash(AutotoolsPackage): homepage = "https://github.com/sparsehash/sparsehash" url = "https://github.com/sparsehash/sparsehash/archive/sparsehash-2.0.3.tar.gz" - version('2.0.3', 'd8d5e2538c1c25577b3f066d7a55e99e') + version('2.0.3', sha256='05e986a5c7327796dad742182b2d10805a8d4f511ad090da0490f146c1ff7a8c') diff --git a/var/spack/repos/builtin/packages/sparta/package.py b/var/spack/repos/builtin/packages/sparta/package.py index e6a7f7e8370..e72eb9a8502 100644 --- a/var/spack/repos/builtin/packages/sparta/package.py +++ b/var/spack/repos/builtin/packages/sparta/package.py @@ -14,7 +14,7 @@ class Sparta(Package): homepage = "https://github.com/atulkakrana/sPARTA.github" url = "https://github.com/atulkakrana/sPARTA/archive/1.25.tar.gz" - version('1.25', '50fda66bf860f63ae8aef5e8fb997a75') + version('1.25', sha256='007997b9bf5041ae35c9bb79455d533c0f0773f9dd3ba4e5ddf306139625681f') depends_on('bowtie2') depends_on('python@3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/spdlog/package.py b/var/spack/repos/builtin/packages/spdlog/package.py index 2bf342f38b2..962131ff28a 100644 --- a/var/spack/repos/builtin/packages/spdlog/package.py +++ b/var/spack/repos/builtin/packages/spdlog/package.py @@ -25,9 +25,9 @@ class Spdlog(CMakePackage): version('0.14.0', sha256='eb5beb4e53f4bfff5b32eb4db8588484bdc15a17b90eeefef3a9fc74fec1d83d') version('0.13.0', sha256='d798a6ca19165f0a18a43938859359269f5a07fd8e0eb83ab8674739c9e8f361') version('0.12.0', sha256='5cfd6a0b3182a88e1eb35bcb65a7ef9035140d7c73b16ba6095939dbf07325b9') - version('0.11.0', '08232203f18a6f9ff47e083cc7a141a050805d3b') - version('0.10.0', '57b471ef97a23cc29c38b62e00e89a411a87ea7f') - version('0.9.0', 'dda741ef8e12d57d91f778d85e95a27d84a82ac4') + version('0.11.0', sha256='8c0f1810fb6b7d23fef70c2ea8b6fa6768ac8d18d6e0de39be1f48865e22916e') + version('0.10.0', sha256='fbbc53c1cc09b93b4c3d76b683bbe9315e2efe3727701227374dce6aa4264075') + version('0.9.0', sha256='bbbe5a855c8b309621352921d650449eb2f741d35d55ec50fb4d8122ddfb8f01') variant('shared', default=True, description='Build shared libraries (v1.4.0+)') diff --git a/var/spack/repos/builtin/packages/speex/package.py b/var/spack/repos/builtin/packages/speex/package.py index 630a69c833b..ae9cfd02c90 100644 --- a/var/spack/repos/builtin/packages/speex/package.py +++ b/var/spack/repos/builtin/packages/speex/package.py @@ -13,4 +13,4 @@ class Speex(AutotoolsPackage): homepage = "https://speex.org" url = "http://downloads.us.xiph.org/releases/speex/speex-1.2.0.tar.gz" - version('1.2.0', '8ab7bb2589110dfaf0ed7fa7757dc49c') + version('1.2.0', sha256='eaae8af0ac742dc7d542c9439ac72f1f385ce838392dc849cae4536af9210094') diff --git a/var/spack/repos/builtin/packages/spglib/package.py b/var/spack/repos/builtin/packages/spglib/package.py index efe4cb662c2..981d30fb83f 100644 --- a/var/spack/repos/builtin/packages/spglib/package.py +++ b/var/spack/repos/builtin/packages/spglib/package.py @@ -16,5 +16,5 @@ class Spglib(CMakePackage): # patch by Krishnendu Ghosh patch('fix_cpp.patch', when='@:1.10.3') - version('1.10.3', 'f6ef0554fa528ffa49d8eaee18a2b7b9') - version('1.10.0', '0ad9330ae8a511d25e2e26cb9bf02808') + version('1.10.3', sha256='43776b5fb220b746d53c1aa39d0230f304687ec05984671392bccaf850d9d696') + version('1.10.0', sha256='117fff308731784bea2ddaf3d076f0ecbf3981b31ea1c1bfd5ce4f057a5325b1') diff --git a/var/spack/repos/builtin/packages/sph2pipe/package.py b/var/spack/repos/builtin/packages/sph2pipe/package.py index 969ef82ba9e..2581312641c 100644 --- a/var/spack/repos/builtin/packages/sph2pipe/package.py +++ b/var/spack/repos/builtin/packages/sph2pipe/package.py @@ -13,6 +13,6 @@ class Sph2pipe(CMakePackage): homepage = "https://www.ldc.upenn.edu/language-resources/tools/sphere-conversion-tools" url = "https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/ctools/sph2pipe_v2.5.tar.gz" - version('2.5', '771d9143e9aec0a22c6a14e138974be2') + version('2.5', sha256='5be236dc94ed0a301c5c8a369f849f76799ec7e70f25dfc0521068d9d1d4d3e3') patch('cmake.patch') diff --git a/var/spack/repos/builtin/packages/spherepack/package.py b/var/spack/repos/builtin/packages/spherepack/package.py index 79f3f62370d..f638ea91d4f 100644 --- a/var/spack/repos/builtin/packages/spherepack/package.py +++ b/var/spack/repos/builtin/packages/spherepack/package.py @@ -13,7 +13,7 @@ class Spherepack(Package): homepage = "https://www2.cisl.ucar.edu/resources/legacy/spherepack" url = "https://www2.cisl.ucar.edu/sites/default/files/spherepack3.2.tar" - version('3.2', '283627744f36253b4260efd7dfb7c762') + version('3.2', sha256='d58ef8cbc45cf2ad24f73a9f73f5f9d4fbe03cd9e2e7722e526fffb68be581ba') def install(self, spec, prefix): if self.compiler.fc is None: diff --git a/var/spack/repos/builtin/packages/spindle/package.py b/var/spack/repos/builtin/packages/spindle/package.py index aab49983a73..8106bc92064 100644 --- a/var/spack/repos/builtin/packages/spindle/package.py +++ b/var/spack/repos/builtin/packages/spindle/package.py @@ -15,6 +15,6 @@ class Spindle(AutotoolsPackage): homepage = "https://computing.llnl.gov/project/spindle/" url = "https://github.com/hpc/Spindle/archive/v0.8.1.tar.gz" - version('0.8.1', 'f11793a6b9d8df2cd231fccb2857d912') + version('0.8.1', sha256='c1e099e913faa8199be5811dc7b8be0266f0d1fd65f0a3a25bb46fbc70954ed6') depends_on("launchmon") diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py index 71b8455c875..fe0def9622a 100644 --- a/var/spack/repos/builtin/packages/spot/package.py +++ b/var/spack/repos/builtin/packages/spot/package.py @@ -12,8 +12,8 @@ class Spot(AutotoolsPackage): homepage = "https://spot.lrde.epita.fr/" url = "http://www.lrde.epita.fr/dload/spot/spot-1.99.3.tar.gz" - version('1.99.3', 'd53adcb2d0fe7c69f45d4e595a58254e') - version('1.2.6', '799bf59ccdee646d12e00f0fe6c23902') + version('1.99.3', sha256='86964af559994af4451a8dca663a9e1db6e869ed60e747ab60ce72dddc31b61b') + version('1.2.6', sha256='360678c75f6741f697e8e56cdbc9937f104eb723a839c3629f0dc5dc6de11bfc') variant('python', default=True, description='Enable python API') diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py index 2be29341d85..6cec0162d0f 100644 --- a/var/spack/repos/builtin/packages/sqlite/package.py +++ b/var/spack/repos/builtin/packages/sqlite/package.py @@ -20,7 +20,7 @@ class Sqlite(AutotoolsPackage): version('3.27.2', sha256='50c39e85ea28b5ecfdb3f9e860afe9ba606381e21836b2849efca6a0bfe6ef6e') version('3.27.1', sha256='54a92b8ff73ff6181f89b9b0c08949119b99e8cccef93dbef90e852a8b10f4f8') version('3.27.0', sha256='dbfb0fb4fc32569fa427d3658e888f5e3b84a0952f706ccab1fd7c62a54f10f0') - version('3.26.0', '9af2df1a6da5db6e2ecf3f463625f16740e036e9') + version('3.26.0', sha256='5daa6a3fb7d1e8c767cd59c4ded8da6e4b00c61d3b466d0685e35c4dd6d7bf5d') # All versions prior to 3.26.0 are vulnerable to Magellan when FTS # is enabled, see https://blade.tencent.com/magellan/index_en.html @@ -44,7 +44,7 @@ class Sqlite(AutotoolsPackage): resource(name='extension-functions', url='https://sqlite.org/contrib/download/extension-functions.c/download/extension-functions.c?get=25', - md5='3a32bfeace0d718505af571861724a43', + sha256='991b40fe8b2799edc215f7260b890f14a833512c9d9896aa080891330ffe4052', expand=False, placement={'extension-functions.c?get=25': 'extension-functions.c'}, diff --git a/var/spack/repos/builtin/packages/sqlitebrowser/package.py b/var/spack/repos/builtin/packages/sqlitebrowser/package.py index df973e1ff3e..2b89b4d6f8b 100644 --- a/var/spack/repos/builtin/packages/sqlitebrowser/package.py +++ b/var/spack/repos/builtin/packages/sqlitebrowser/package.py @@ -14,7 +14,7 @@ class Sqlitebrowser(CMakePackage): homepage = "https://sqlitebrowser.org" url = "https://github.com/sqlitebrowser/sqlitebrowser/archive/v3.10.1.tar.gz" - version('3.10.1', '66cbe41f9da5be80067942ed3816576c') + version('3.10.1', sha256='36eb53bc75192c687dce298c79f1532c410ce4ecbeeacfb07b9d02a307f16bef') msg = 'sqlitebrowser requires C++11 support' conflicts('%gcc@:4.8.0', msg=msg) diff --git a/var/spack/repos/builtin/packages/squashfs/package.py b/var/spack/repos/builtin/packages/squashfs/package.py index 30ba0bae583..1e148da95c3 100644 --- a/var/spack/repos/builtin/packages/squashfs/package.py +++ b/var/spack/repos/builtin/packages/squashfs/package.py @@ -13,10 +13,10 @@ class Squashfs(MakefilePackage): url = 'https://downloads.sourceforge.net/project/squashfs/squashfs/squashfs4.3/squashfs4.3.tar.gz' # version sha1 - version('4.3', 'a615979db9cee82e4a934a1455577f597d290b41') - version('4.2', 'e0944471ff68e215d3fecd464f30ea6ceb635fd7') - version('4.1', '7f9b1f9839b3638882f636fd170fd817d650f856') - version('4.0', '3efe764ac27c507ee4a549fc6507bc86ea0660dd') + version('4.3', sha256='0d605512437b1eb800b4736791559295ee5f60177e102e4d4ccd0ee241a5f3f6') + version('4.2', sha256='d9e0195aa922dbb665ed322b9aaa96e04a476ee650f39bbeadb0d00b24022e96') + version('4.1', sha256='3a870d065a25b3f5467bc6d9ed34340befab51a3f9e4b7e3792ea0ff4e06046a') + version('4.0', sha256='18948edbe06bac2c4307eea99bfb962643e4b82e5b7edd541b4d743748e12e21') depends_on('m4', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/squid/package.py b/var/spack/repos/builtin/packages/squid/package.py index c6f9fddcd3d..a039bbedc5b 100644 --- a/var/spack/repos/builtin/packages/squid/package.py +++ b/var/spack/repos/builtin/packages/squid/package.py @@ -11,4 +11,4 @@ class Squid(AutotoolsPackage): homepage = "http://eddylab.org/software.html" - version('1.9g', 'b9bf480c65d01417b7894c82d094ce07', url='http://eddylab.org/software/squid/squid.tar.gz') + version('1.9g', sha256='302f42e8794aa4dbcfa0996c14fb7a70a7c4397fc45c2bbd2748055460d8dca7', url='http://eddylab.org/software/squid/squid.tar.gz') diff --git a/var/spack/repos/builtin/packages/sst-dumpi/package.py b/var/spack/repos/builtin/packages/sst-dumpi/package.py index c3eeeabe6b3..1acd67b6fb3 100644 --- a/var/spack/repos/builtin/packages/sst-dumpi/package.py +++ b/var/spack/repos/builtin/packages/sst-dumpi/package.py @@ -23,7 +23,7 @@ class SstDumpi(AutotoolsPackage): git = "https://github.com/sstsimulator/sst-dumpi.git" version('master', branch='master') - version('6.1.0', '31c3f40a697dc85bf23dd34270982319') + version('6.1.0', sha256='d4f6afcff5ba67fcc3a29f461afbb59855053840f5f320552a77b4e14c687bb6') depends_on('autoconf@1.68:', type='build') depends_on('automake@1.11.1:', type='build') diff --git a/var/spack/repos/builtin/packages/sst-macro/package.py b/var/spack/repos/builtin/packages/sst-macro/package.py index 9f13b6922aa..1c591eb9c4e 100644 --- a/var/spack/repos/builtin/packages/sst-macro/package.py +++ b/var/spack/repos/builtin/packages/sst-macro/package.py @@ -21,7 +21,7 @@ class SstMacro(AutotoolsPackage): version('develop', branch='devel') version('8.0.0', sha256='8618a259e98ede9a1a2ce854edd4930628c7c5a770c3915858fa840556c1861f') - version('6.1.0', '98b737be6326b8bd711de832ccd94d14') + version('6.1.0', sha256='930b67313b594148d6356e550ca370214a9283858235321d3ef974191eb028d6') depends_on('boost@1.59:', when='@:6.1.0') diff --git a/var/spack/repos/builtin/packages/stacks/package.py b/var/spack/repos/builtin/packages/stacks/package.py index 795f46d77fe..0245fb1d8cf 100644 --- a/var/spack/repos/builtin/packages/stacks/package.py +++ b/var/spack/repos/builtin/packages/stacks/package.py @@ -14,7 +14,7 @@ class Stacks(AutotoolsPackage): url = "http://catchenlab.life.illinois.edu/stacks/source/stacks-1.46.tar.gz" version('2.3b', sha256='a46786d8811a730ebcdc17891e89f50d4f4ae196734439dac86091f45c92ac72') - version('1.46', '18b0568a4bba44fb4e5be0eb7ee2c08d') + version('1.46', sha256='45a0725483dc0c0856ad6b1f918e65d91c1f0fe7d8bf209f76b93f85c29ea28a') variant('sparsehash', default=True, description='Improve Stacks memory usage with SparseHash') diff --git a/var/spack/repos/builtin/packages/staden-io-lib/package.py b/var/spack/repos/builtin/packages/staden-io-lib/package.py index 6345b3258e9..4b5c56be28c 100644 --- a/var/spack/repos/builtin/packages/staden-io-lib/package.py +++ b/var/spack/repos/builtin/packages/staden-io-lib/package.py @@ -13,6 +13,6 @@ class StadenIoLib(AutotoolsPackage): homepage = "http://staden.sourceforge.net/" url = "https://sourceforge.net/projects/staden/files/io_lib/1.14.8/io_lib-1.14.8.tar.gz/download" - version('1.14.8', 'fe5ee6aaec8111a5bc3ac584a0c0c0c7') + version('1.14.8', sha256='3bd560309fd6d70b14bbb8230e1baf8706b804eb6201220bb6c3d6db72003d1b') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/star/package.py b/var/spack/repos/builtin/packages/star/package.py index 6bc32880fee..f63132951cd 100644 --- a/var/spack/repos/builtin/packages/star/package.py +++ b/var/spack/repos/builtin/packages/star/package.py @@ -24,7 +24,7 @@ class Star(Package): version('2.5.3a', sha256='2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04') version('2.5.2b', sha256='f88b992740807ab10f2ac3b83781bf56951617f210001fab523f6480d0b546d9') version('2.5.2a', sha256='2a372d9bcab1dac8d35cbbed3f0ab58291e4fbe99d6c1842b094ba7449d55476') - version('2.4.2a', '8b9345f2685a5ec30731e0868e86d506', url='https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz') + version('2.4.2a', sha256='ac166d190c0fd34bf3418a5640050b0e7734d279813e02daa013d0924fb579b0', url='https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/startup-notification/package.py b/var/spack/repos/builtin/packages/startup-notification/package.py index ee1130b22ff..1d1fdc64465 100644 --- a/var/spack/repos/builtin/packages/startup-notification/package.py +++ b/var/spack/repos/builtin/packages/startup-notification/package.py @@ -13,7 +13,7 @@ class StartupNotification(AutotoolsPackage): homepage = "https://www.freedesktop.org/wiki/Software/startup-notification/" url = "http://www.freedesktop.org/software/startup-notification/releases/startup-notification-0.12.tar.gz" - version('0.12', '2cd77326d4dcaed9a5a23a1232fb38e9') + version('0.12', sha256='3c391f7e930c583095045cd2d10eb73a64f085c7fde9d260f2652c7cb3cfbe4a') depends_on('libx11') depends_on('libxcb') diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py index 10b39690210..f8d9dd2bab9 100644 --- a/var/spack/repos/builtin/packages/stat/package.py +++ b/var/spack/repos/builtin/packages/stat/package.py @@ -14,17 +14,17 @@ class Stat(AutotoolsPackage): git = "https://github.com/llnl/stat.git" version('develop', branch='develop') - version('4.0.1', '3e21b48e7932d9a4a9efb300f0b97fa2', + version('4.0.1', sha256='ae3fbd6946003fb16233d82d40285780a9a802da5fe30d09adb8a8b2a2cc4ad6', url='https://github.com/LLNL/STAT/files/2489327/stat-4.0.1.tar.gz') - version('4.0.0', 'b357160662ced251bc55cb1b884c3407', + version('4.0.0', sha256='1c4f62686645f6dc1d9ef890acc9c2839c150789dc220718775878feb41bdabf', url='https://github.com/LLNL/STAT/releases/download/v4.0.0/stat-4.0.0.tar.gz') - version('3.0.1', 'dac6f23c3639a0b21f923dc6219ba385', + version('3.0.1', sha256='540916ffb92026ca7aa825a2320095a89b9b4fd3426ee7657b44ac710618947e', url='https://github.com/LLNL/STAT/files/911503/stat-3.0.1.zip') - version('3.0.0', 'a97cb235c266371c4a26329112de48a2', + version('3.0.0', sha256='b95cac82989e273e566f16ba17a75526374ee8e0ef066a411977e1935967df57', url='https://github.com/LLNL/STAT/releases/download/v3.0.0/STAT-3.0.0.tar.gz') - version('2.2.0', '26bd69dd57a15afdd5d0ebdb0b7fb6fc') - version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91') - version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b') + version('2.2.0', sha256='ed4732bfbe942ca8e29342f24f48e0c295989b0639a548febe7a1c1390ae1993') + version('2.1.0', sha256='497ed2bd1127cb2e97b32a30a4f62b6b298d18f3313c0278dd908c6ecba64f43') + version('2.0.0', sha256='b19587c2166b5d4d3a89a0ec5433ac61335aa7ad5cfa5a3b4406f5ea6c0bf0ac') # TODO: dysect requires Dyninst patch for version 3.0.0b variant('dysect', default=False, description="enable DySectAPI") diff --git a/var/spack/repos/builtin/packages/stc/package.py b/var/spack/repos/builtin/packages/stc/package.py index 77d2bde13d3..ce52a418f26 100644 --- a/var/spack/repos/builtin/packages/stc/package.py +++ b/var/spack/repos/builtin/packages/stc/package.py @@ -15,8 +15,8 @@ class Stc(AutotoolsPackage): git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') - version('0.8.3', '1d7eee78d3531b7c1901c5aec5703721') - version('0.8.2', '883b0657f1aac9b81158ef0a8989be4c') + version('0.8.3', sha256='d61ca80137a955b12e84e41cb8a78ce1a58289241a2665076f12f835cf68d798') + version('0.8.2', sha256='13f0f03fdfcca3e63d2d58d7e7dbdddc113d5b9826c9357ab0713b63e8e42c5e') depends_on('java', type=('build', 'run')) depends_on('ant', type='build') diff --git a/var/spack/repos/builtin/packages/stow/package.py b/var/spack/repos/builtin/packages/stow/package.py index 5a0b4d5a433..508b30d715d 100644 --- a/var/spack/repos/builtin/packages/stow/package.py +++ b/var/spack/repos/builtin/packages/stow/package.py @@ -17,11 +17,11 @@ class Stow(AutotoolsPackage): homepage = "https://www.gnu.org/software/stow/" url = "https://ftpmirror.gnu.org/stow/stow-2.2.2.tar.bz2" - version('2.2.2', 'af1e1de9d973c835bee80c745b5ee849') - version('2.2.0', '5bb56592eff9aaf9dfb6c975b3004240') - version('2.1.3', '533651c25b29c3630f01d0be33849a7c') - version('2.1.2', '0b8154a2165e4004ddc9579e3499af98') - version('2.1.1', '882d2490d05723b4b78029c2973775d3') - version('2.1.0', 'aa3a2389b6cbf3bd555e15c80a0be6ab') + version('2.2.2', sha256='a0022034960e47a8d23dffb822689f061f7a2d9101c9835cf11bf251597aa6fd') + version('2.2.0', sha256='86bc30fe1d322a5c80ff3bd7580c2758149aad7c3bbfa18b48a9d95c25d66b05') + version('2.1.3', sha256='2dff605c801fee9fb7d0fef6988bbb8a0511fad469129b20cae60e0544ba1443') + version('2.1.2', sha256='dda4231dab409d906c5de7f6a706a765e6532768ebbffe34e1823e3371f891f9') + version('2.1.1', sha256='8bdd21bb2ef6edf5812bf671e64cdd584d92d547d932406cef179646ea6d1998') + version('2.1.0', sha256='f0e909034fd072b1f5289abb771133d5c4e88d82d4da84195891c53d9b0de5ca') depends_on('perl@5.6.1:') diff --git a/var/spack/repos/builtin/packages/strace/package.py b/var/spack/repos/builtin/packages/strace/package.py index 510f65c7a94..f3573480b44 100644 --- a/var/spack/repos/builtin/packages/strace/package.py +++ b/var/spack/repos/builtin/packages/strace/package.py @@ -20,7 +20,7 @@ class Strace(AutotoolsPackage): version('5.2', sha256='d513bc085609a9afd64faf2ce71deb95b96faf46cd7bc86048bc655e4e4c24d2') version('5.1', sha256='f5a341b97d7da88ee3760626872a4899bf23cf8dee56901f114be5b1837a9a8b') version('5.0', sha256='3b7ad77eb2b81dc6078046a9cc56eed5242b67b63748e7fc28f7c2daf4e647da') - version('4.21', '785b679a75e9758ebeb66816f315b9fe') + version('4.21', sha256='5c7688db44073e94c59a5627744e5699454419824cc8166e8bcfd7ec58375c37') def configure_args(self): args = [] diff --git a/var/spack/repos/builtin/packages/strelka/package.py b/var/spack/repos/builtin/packages/strelka/package.py index 6cce7296da2..3481643fb5f 100644 --- a/var/spack/repos/builtin/packages/strelka/package.py +++ b/var/spack/repos/builtin/packages/strelka/package.py @@ -13,7 +13,7 @@ class Strelka(CMakePackage): homepage = "https://github.com/Illumina/strelka" url = "https://github.com/Illumina/strelka/releases/download/v2.8.2/strelka-2.8.2.release_src.tar.bz2" - version('2.8.2', 'c48753997fcf2e4edac4e9854495721e') + version('2.8.2', sha256='27415f7c14f92e0a6b80416283a0707daed121b8a3854196872981d132f1496b') depends_on('python@2.4:') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/stringtie/package.py b/var/spack/repos/builtin/packages/stringtie/package.py index 419c2e47555..6e92476e6d6 100644 --- a/var/spack/repos/builtin/packages/stringtie/package.py +++ b/var/spack/repos/builtin/packages/stringtie/package.py @@ -13,9 +13,9 @@ class Stringtie(MakefilePackage): homepage = "https://ccb.jhu.edu/software/stringtie" url = "https://github.com/gpertea/stringtie/archive/v1.3.3b.tar.gz" - version('1.3.4d', '0134c0adc264efd31a1df4301b33bfcf3b3fe96bd3990ce3df90819bad9af968') - version('1.3.4a', '2a191ef6512242a3a5778cf7718bb6af') - version('1.3.3b', '11a43260b18e4272182380e922445d88') + version('1.3.4d', sha256='0134c0adc264efd31a1df4301b33bfcf3b3fe96bd3990ce3df90819bad9af968') + version('1.3.4a', sha256='6164a5fa9bf8807ef68ec89f47e3a61fe57fa07fe858f52fb6627f705bf71add') + version('1.3.3b', sha256='30e8a3a29b474f0abeef1540d9b4624a827d8b29d7347226d86a38afea28bc0f') depends_on('samtools') diff --git a/var/spack/repos/builtin/packages/structure/package.py b/var/spack/repos/builtin/packages/structure/package.py index 595cdd6b9e7..0ab0bfad586 100644 --- a/var/spack/repos/builtin/packages/structure/package.py +++ b/var/spack/repos/builtin/packages/structure/package.py @@ -13,7 +13,7 @@ class Structure(MakefilePackage): homepage = "http://web.stanford.edu/group/pritchardlab/structure.html" url = "http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/structure_kernel_source.tar.gz" - version('2.3.4', '4e0591678cdbfe79347d272b5dceeda1') + version('2.3.4', sha256='f2b72b9189a514f53e921bbdc1aa3dbaca7ac34a8467af1f972c7e4fc9c0bb37') depends_on('jdk', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py index e3f89592b73..3f22f4fddaf 100644 --- a/var/spack/repos/builtin/packages/sublime-text/package.py +++ b/var/spack/repos/builtin/packages/sublime-text/package.py @@ -15,9 +15,9 @@ class SublimeText(Package): version('3.2.2.3211', sha256='0b3c8ca5e6df376c3c24a4b9ac2e3b391333f73b229bc6e87d0b4a5f636d74ee') version('3.2.1.3207', sha256='acb64f1de024a0f004888096afa101051e48d96c7a3e7fe96e11312d524938c4') - version('3.1.1.3176', '7d4c8c5167224888d901e8cbafb6ec7f') - version('3.0.3126', 'acc34252b0ea7dff1f581c5db1564dcb') - version('2.0.2', '699cd26d7fe0bada29eb1b2cd7b50e4b') + version('3.1.1.3176', sha256='74f17c1aec4ddec9d4d4c39f5aec0414a4755d407a05efa571e8892e0b9cf732') + version('3.0.3126', sha256='18db132e9a305fa3129014b608628e06f9442f48d09cfe933b3b1a84dd18727a') + version('2.0.2', sha256='01baed30d66432e30002a309ff0393967be1daba5cce653e43bba6bd6c38ab84') # Sublime text comes as a pre-compiled binary. # Since we can't link to Spack packages, we'll just have to diff --git a/var/spack/repos/builtin/packages/subread/package.py b/var/spack/repos/builtin/packages/subread/package.py index f126c03d415..f286d03b52e 100644 --- a/var/spack/repos/builtin/packages/subread/package.py +++ b/var/spack/repos/builtin/packages/subread/package.py @@ -15,9 +15,9 @@ class Subread(MakefilePackage): url = "https://downloads.sourceforge.net/project/subread/subread-1.5.2/subread-1.5.2-source.tar.gz" version('1.6.4', sha256='b7bd0ee3b0942d791aecce6454d2f3271c95a010beeeff2daf1ff71162e43969') - version('1.6.2', '70125531737fe9ba2be83622ca236e5e') - version('1.6.0', 'ed7e32c56bda1e769703e0a4db5a89a7') - version('1.5.2', '817d2a46d87fcef885c8832475b8b247') + version('1.6.2', sha256='77b4896c1c242967c5883a06c0a5576a5ff220008a12aa60af9669d2f9a87d7a') + version('1.6.0', sha256='31251ec4c134e3965d25ca3097890fb37e2c7a4163f6234515534fd325b1002a') + version('1.5.2', sha256='a8c5f0e09ed3a105f01866517a89084c7302ff70c90ef8714aeaa2eab181a0aa') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index a53177766b8..29c897ecfb7 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -11,12 +11,12 @@ class Subversion(Package): homepage = 'https://subversion.apache.org/' url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz' - version('1.9.7', '1a5f48acf9d0faa60e8c7aea96a9b29ab1d4dcac') - version('1.9.6', '89e1b3f9d79422c094ccb95769360d5fe7df2bb1') - version('1.9.5', 'ac9f8ee235f1b667dd6506864af8035aaedfc2d9') - version('1.9.3', 'a92bcfaec4e5038f82c74a7b5bbd2f46') - version('1.8.17', 'd1f8d45f97168d6271c58c5b25421cc32954c81b') - version('1.8.13', '8065b3698d799507fb72dd7926ed32b6') + version('1.9.7', sha256='c72a209c883e20245f14c4e644803f50ae83ae24652e385ff5e82300a0d06c3c') + version('1.9.6', sha256='a400cbc46d05cb29f2d7806405bb539e9e045b24013b0f12f8f82688513321a7') + version('1.9.5', sha256='280ba586c5d51d7b976b65d22d5e8e42f3908ed1c968d71120dcf534ce857a83') + version('1.9.3', sha256='74cd21d2f8a2a54e4dbd2389fe1605a19dbda8ba88ffc4bb0edc9a66e143cc93') + version('1.8.17', sha256='1b2cb9a0ca454035e55b114ee91c6433b9ede6c2893f2fb140939094d33919e4') + version('1.8.13', sha256='17e8900a877ac9f0d5ef437c20df437fec4eb2c5cb9882609d2277e2312da52c') variant('perl', default=False, description='Build with Perl bindings') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 1d375acdfac..6c0896b5b1e 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -14,12 +14,12 @@ class SuiteSparse(Package): url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.2.0.tar.gz' version('5.3.0', sha256='90e69713d8c454da5a95a839aea5d97d8d03d00cc1f667c4bdfca03f640f963d') - version('5.2.0', '8e625539dbeed061cc62fbdfed9be7cf') - version('5.1.0', '9c34d7c07ad5ce1624b8187faa132046') - version('4.5.5', '0a5b38af0016f009409a9606d2f1b555') - version('4.5.4', 'f6ab689442e64a1624a47aa220072d1b') - version('4.5.3', '8ec57324585df3c6483ad7f556afccbd') - version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + version('5.2.0', sha256='3c46c035ea8217649958a0f73360e825b0c9dcca4e32a9349d2c7678c0d48813') + version('5.1.0', sha256='1b1371074224c6844697f3a55024d185b7ff6ffa49ac141d433fbb1aadf426f5') + version('4.5.5', sha256='b9a98de0ddafe7659adffad8a58ca3911c1afa8b509355e7aa58b02feb35d9b6') + version('4.5.4', sha256='698b5c455645bb1ad29a185f0d52025f3bd7cb7261e182c8878b0eb60567a714') + version('4.5.3', sha256='6199a3a35fbce82b155fd2349cf81d2b7cddaf0dac218c08cb172f9bc143f37a') + version('4.5.1', sha256='ac4524b9f69c4f8c2652d720b146c92a414c1943f86d46df49b4ff8377ae8752') variant('tbb', default=False, description='Build with Intel TBB') variant('pic', default=True, description='Build position independent code (required to link with shared libraries)') diff --git a/var/spack/repos/builtin/packages/sumaclust/package.py b/var/spack/repos/builtin/packages/sumaclust/package.py index 1d061975657..9c90fe15648 100644 --- a/var/spack/repos/builtin/packages/sumaclust/package.py +++ b/var/spack/repos/builtin/packages/sumaclust/package.py @@ -12,7 +12,7 @@ class Sumaclust(MakefilePackage): homepage = "https://git.metabarcoding.org/obitools/sumaclust" - version('1.0.20', '31c7583fbe2e3345d5fe3e9431d9b30c', + version('1.0.20', sha256='b697495f9a2b93fe069ecdb3bc6bba75b07ec3ef9f01ed66c4dd69587a40cfc1', url="https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/sumaclust_v1.0.20.tar.gz") def build(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 75b9c32856b..c49a624b17f 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -18,17 +18,17 @@ class SuperluDist(CMakePackage): version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') - version('6.1.1', '35d25cff592c724439870444ed45e1d1d15ca2c65f02ccd4b83a6d3c9d220bd1') - version('6.1.0', '92c6d1424dd830ee2d1e7396a418a5f6645160aea8472e558c4e4bfe006593c4') - version('6.0.0', 'ff6cdfa0263d595708bbb6d11fb780915d8cfddab438db651e246ea292f37ee4') - version('5.4.0', '3ac238fe082106a2c4dbaf0c22af1ff1247308ffa8f053de9d78c3ec7dd0d801') - version('5.3.0', '49ed110bdef1e284a0181d6c7dd1fae3aa110cb45f67c6aa5cb791070304d670') - version('5.2.2', '65cfb9ace9a81f7affac4ad92b9571badf0f10155b3468531b0fffde3bd8e727') - version('5.2.1', '67cf3c46cbded4cee68e2a9d601c30ab13b08091c8cdad95b0a8e018b6d5d1f1') - version('5.1.3', '58e3dfdb4ae6f8e3f6f3d5ee5e851af59b967c4483cdb3b15ccd1dbdf38f44f9') - version('5.1.2', 'e34865ad6696ee6a6d178b4a01c8e19103a7d241ba9de043603970d63b0ee1e2') - version('5.1.0', '73f292ab748b590b6dd7469e6986aeb95d279b8b8b3da511c695a396bdbc996c') - version('5.0.0', '78d1d6460ff16b3f71e4bcd7306397574d54d421249553ccc26567f00a10bfc6') + version('6.1.1', sha256='35d25cff592c724439870444ed45e1d1d15ca2c65f02ccd4b83a6d3c9d220bd1') + version('6.1.0', sha256='92c6d1424dd830ee2d1e7396a418a5f6645160aea8472e558c4e4bfe006593c4') + version('6.0.0', sha256='ff6cdfa0263d595708bbb6d11fb780915d8cfddab438db651e246ea292f37ee4') + version('5.4.0', sha256='3ac238fe082106a2c4dbaf0c22af1ff1247308ffa8f053de9d78c3ec7dd0d801') + version('5.3.0', sha256='49ed110bdef1e284a0181d6c7dd1fae3aa110cb45f67c6aa5cb791070304d670') + version('5.2.2', sha256='65cfb9ace9a81f7affac4ad92b9571badf0f10155b3468531b0fffde3bd8e727') + version('5.2.1', sha256='67cf3c46cbded4cee68e2a9d601c30ab13b08091c8cdad95b0a8e018b6d5d1f1') + version('5.1.3', sha256='58e3dfdb4ae6f8e3f6f3d5ee5e851af59b967c4483cdb3b15ccd1dbdf38f44f9') + version('5.1.2', sha256='e34865ad6696ee6a6d178b4a01c8e19103a7d241ba9de043603970d63b0ee1e2') + version('5.1.0', sha256='73f292ab748b590b6dd7469e6986aeb95d279b8b8b3da511c695a396bdbc996c') + version('5.0.0', sha256='78d1d6460ff16b3f71e4bcd7306397574d54d421249553ccc26567f00a10bfc6') variant('int64', default=False, description='Build with 64 bit integers') variant('openmp', default=False, description='Build with OpenMP support (needs a good multithreaded BLAS implementation for good performance)') diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py index 0c1a4f2b1f6..74bf6e9c0f6 100644 --- a/var/spack/repos/builtin/packages/superlu-mt/package.py +++ b/var/spack/repos/builtin/packages/superlu-mt/package.py @@ -16,7 +16,7 @@ class SuperluMt(Package): homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt" url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_mt_3.1.tar.gz" - version('3.1', '06ac62f1b4b7d17123fffa0d0c315e91') + version('3.1', sha256='407b544b9a92b2ed536b1e713e80f986824cf3016657a4bfc2f3e7d2a76ecab6') variant('blas', default=True, description='Build with external BLAS library') diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py index edd55b70508..dfc81f662ba 100644 --- a/var/spack/repos/builtin/packages/superlu/package.py +++ b/var/spack/repos/builtin/packages/superlu/package.py @@ -16,8 +16,8 @@ class Superlu(Package): homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu" url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_5.2.1.tar.gz" - version('5.2.1', '3a1a9bff20cb06b7d97c46d337504447') - version('4.3', 'b72c6309f25e9660133007b82621ba7c') + version('5.2.1', sha256='28fb66d6107ee66248d5cf508c79de03d0621852a0ddeba7301801d3d859f463') + version('4.3', sha256='169920322eb9b9c6a334674231479d04df72440257c17870aaa0139d74416781') variant('pic', default=True, description='Build with position independent code') diff --git a/var/spack/repos/builtin/packages/sw4lite/package.py b/var/spack/repos/builtin/packages/sw4lite/package.py index 8a9bf6d68c4..a6378dd5693 100644 --- a/var/spack/repos/builtin/packages/sw4lite/package.py +++ b/var/spack/repos/builtin/packages/sw4lite/package.py @@ -19,7 +19,7 @@ class Sw4lite(MakefilePackage): version('develop', branch='master') version('1.1', sha256='34b5f7b56f9e40474c14abebcaa024192de018de6beb6dafee53d3db5b07c6d3') - version('1.0', '3d911165f4f2ff6d5f9c1bd56ab6723f') + version('1.0', sha256='2ed7784fe0564b33879c280d3a8d54d963f2f45cd7f61215b8077fcc4ce8a608') variant('openmp', default=True, description='Build with OpenMP support') variant('precision', default='double', values=('float', 'double'), diff --git a/var/spack/repos/builtin/packages/swap-assembler/package.py b/var/spack/repos/builtin/packages/swap-assembler/package.py index 1ef2a1f427a..f8cca4ca62a 100644 --- a/var/spack/repos/builtin/packages/swap-assembler/package.py +++ b/var/spack/repos/builtin/packages/swap-assembler/package.py @@ -12,7 +12,7 @@ class SwapAssembler(MakefilePackage): homepage = "https://sourceforge.net/projects/swapassembler/" url = "https://sourceforge.net/projects/swapassembler/files/SWAP_Assembler-0.4.tar.bz2/download" - version('0.4', '944f2aeae4f451be81160bb625304fc3') + version('0.4', sha256='45632e25578aacfbacd76df9697cbc798e09ac92284d9c9c07be15e0eb348e0d') depends_on('mpich') diff --git a/var/spack/repos/builtin/packages/swarm/package.py b/var/spack/repos/builtin/packages/swarm/package.py index 6f57ae89d70..9bb73e805ba 100644 --- a/var/spack/repos/builtin/packages/swarm/package.py +++ b/var/spack/repos/builtin/packages/swarm/package.py @@ -12,7 +12,7 @@ class Swarm(MakefilePackage): homepage = "https://github.com/torognes/swarm" url = "https://github.com/torognes/swarm/archive/v2.1.13.tar.gz" - version('2.1.13', 'ab6aff0ba5d20a53b9f13f8f3d85839f') + version('2.1.13', sha256='ec4b22cc1874ec6d2c89fe98e23a2fb713aec500bc4a784f0556389d22c02650') build_directory = 'src' diff --git a/var/spack/repos/builtin/packages/swfft/package.py b/var/spack/repos/builtin/packages/swfft/package.py index 76708b5dfb7..ea23a67038b 100644 --- a/var/spack/repos/builtin/packages/swfft/package.py +++ b/var/spack/repos/builtin/packages/swfft/package.py @@ -15,7 +15,7 @@ class Swfft(MakefilePackage): url = "https://xgitlab.cels.anl.gov/api/v4/projects/hacc%2FSWFFT/repository/archive.tar.gz?sha=v1.0" git = "https://xgitlab.cels.anl.gov/hacc/SWFFT.git" - version('1.0', '0fbc34544b97ba9c3fb19ef2d7a0f076') + version('1.0', sha256='d0eba8446a89285e4e43cba787fec6562a360079a99d56f3af5001cc7e66d5dc') version('develop', branch='master') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index a6f94823ae8..cf538d24c03 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -16,8 +16,8 @@ class Swiftsim(AutotoolsPackage): homepage = 'http://icc.dur.ac.uk/swift/' url = 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0' - version('0.7.0', '1c703d7e20a31a3896e1c291bddd71ab') - version('0.3.0', '162ec2bdfdf44a31a08b3fcee23a886a') + version('0.7.0', sha256='d570e83e1038eb31bc7ae95d1903a2371fffbca90d08f60b6b32bb0fd8a6f516') + version('0.3.0', sha256='dd26075315cb2754dc1292e8d838bbb83739cff7f068a98319b80b9c2b0f84bc') variant('mpi', default=True, description='Enable distributed memory parallelism') diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index 789170a6850..a716916865b 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -23,15 +23,15 @@ class Swig(AutotoolsPackage): url = "http://prdownloads.sourceforge.net/swig/swig-3.0.12.tar.gz" version('master', git='https://github.com/swig/swig.git') - version('4.0.0', 'e8a39cd6437e342cdcbd5af27a9bf11b62dc9efec9248065debcb8276fcbb925') - version('3.0.12', '82133dfa7bba75ff9ad98a7046be687c') - version('3.0.11', '13732eb0f1ab2123d180db8425c1edea') - version('3.0.10', 'bb4ab8047159469add7d00910e203124') - version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97') - version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') - version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4') - version('2.0.2', 'eaf619a4169886923e5f828349504a29') - version('1.3.40', '2df766c9e03e02811b1ab4bba1c7b9cc') + version('4.0.0', sha256='e8a39cd6437e342cdcbd5af27a9bf11b62dc9efec9248065debcb8276fcbb925') + version('3.0.12', sha256='7cf9f447ae7ed1c51722efc45e7f14418d15d7a1e143ac9f09a668999f4fc94d') + version('3.0.11', sha256='d9031d531d7418829a54d0d51c4ed9007016b213657ec70be44031951810566e') + version('3.0.10', sha256='2939aae39dec06095462f1b95ce1c958ac80d07b926e48871046d17c0094f44c') + version('3.0.8', sha256='58a475dbbd4a4d7075e5fe86d4e54c9edde39847cdb96a3053d87cb64a23a453') + version('3.0.2', sha256='a2669657cabcedc371f63c0457407a183e0b6b2ef4e7e303c1ec9a3964cc7813') + version('2.0.12', sha256='65e13f22a60cecd7279c59882ff8ebe1ffe34078e85c602821a541817a4317f7') + version('2.0.2', sha256='6e6b5e8db2bbf2761ff789a3109e4f12ca664ec178d3a164ed0dc273d346c11f') + version('1.3.40', sha256='1945b3693bcda6777bd05fef1015a0ad1a4604cde4a4a0a368b61ccfd143ac09') version('fortran', branch='master', git='https://github.com/swig-fortran/swig.git') diff --git a/var/spack/repos/builtin/packages/symengine/package.py b/var/spack/repos/builtin/packages/symengine/package.py index 2e7bd946ee4..e2cc2cef7ff 100644 --- a/var/spack/repos/builtin/packages/symengine/package.py +++ b/var/spack/repos/builtin/packages/symengine/package.py @@ -15,10 +15,10 @@ class Symengine(CMakePackage): git = "https://github.com/symengine/symengine.git" version('develop', branch='master') - version('0.4.0', 'fd9ae3e98258291ef35b6392faa72ace') - version('0.3.0', 'e61d7513cca4963cd062616891de54c6') - version('0.2.0', '45401561add36a13c1f0b0c5f8d7422d') - version('0.1.0', '41ad7daed61fc5a77c285eb6c7303425') + version('0.4.0', sha256='dd755901a9e2a49e53ba3bbe3f565f94265af05299e57a7b592186dd35916a1b') + version('0.3.0', sha256='591463cb9e741d59f6dfd39a7943e3865d3afe9eac47d1a9cbf5ca74b9c49476') + version('0.2.0', sha256='64d050b0b9decd12bf4ea3b7d18d3904dd7cb8baaae9fbac1b8068e3c59709be') + version('0.1.0', sha256='daba3ba0ae91983a772f66bf755b1953c354fe6dc353588b23705d9a79b011fc') variant('boostmp', default=False, description='Compile with Boost multi-precision integer library') diff --git a/var/spack/repos/builtin/packages/sympol/package.py b/var/spack/repos/builtin/packages/sympol/package.py index e249791e25e..ed9623c74c2 100644 --- a/var/spack/repos/builtin/packages/sympol/package.py +++ b/var/spack/repos/builtin/packages/sympol/package.py @@ -12,7 +12,7 @@ class Sympol(CMakePackage): homepage = "http://www.math.uni-rostock.de/~rehn/software/sympol.html" url = "http://www.math.uni-rostock.de/~rehn/software/sympol-0.1.8.tar.gz" - version('0.1.8', '7cba1997f8532c754cb7259bf70caacb') + version('0.1.8', sha256='8f4c013fa563e696fc8c27c408fd1f3d47783639815e8141e3a99826f1f3d54f') depends_on("cmake@2.6:", type="build") diff --git a/var/spack/repos/builtin/packages/sz/package.py b/var/spack/repos/builtin/packages/sz/package.py index 03aaa6c7508..955503bfbfa 100644 --- a/var/spack/repos/builtin/packages/sz/package.py +++ b/var/spack/repos/builtin/packages/sz/package.py @@ -25,9 +25,9 @@ class Sz(AutotoolsPackage): version('1.4.12.3', sha256='c1413e1c260fac7a48cb11c6dd705730525f134b9f9b244af59885d564ac7a6f') version('1.4.12.1', sha256='98289d75481a6e407e4027b5e23013ae83b4aed88b3f150327ea711322cd54b6') version('1.4.11.1', sha256='6cbc5b233a3663a166055f1874f17c96ba29aa5a496d352707ab508288baa65c') - version('1.4.11.0', '10dee28b3503821579ce35a50e352cc6') - version('1.4.10.0', '82e23dc5a51bcce1f70ba7e3b68a5965') - version('1.4.9.2', '028ce90165b7a4c4051d4c0189f193c0') + version('1.4.11.0', sha256='52ff03c688522ebe085caa7a5f73ace28d8eaf0eb9a161a34a9d90cc5672ff8c') + version('1.4.10.0', sha256='cf23cf1ffd7c69c3d3128ae9c356b6acdc03a38f92c02db5d9bfc04f3fabc506') + version('1.4.9.2', sha256='9dc785274d068d04c2836955fc93518a9797bfd409b46fea5733294b7c7c18f8') variant('fortran', default=False, description='Enable fortran compilation') diff --git a/var/spack/repos/builtin/packages/talloc/package.py b/var/spack/repos/builtin/packages/talloc/package.py index 3f26dff9495..b7c81bdc60b 100644 --- a/var/spack/repos/builtin/packages/talloc/package.py +++ b/var/spack/repos/builtin/packages/talloc/package.py @@ -13,4 +13,4 @@ class Talloc(AutotoolsPackage): homepage = "https://talloc.samba.org" url = "https://www.samba.org/ftp/talloc/talloc-2.1.9.tar.gz" - version('2.1.9', '19ba14eba97d79a169fa92ea824d2b9e') + version('2.1.9', sha256='f0aad4cb88a3322207c82136ddc07bed48a37c2c21f82962d6c5ccb422711062') diff --git a/var/spack/repos/builtin/packages/tantan/package.py b/var/spack/repos/builtin/packages/tantan/package.py index b72c51490d0..f4dc72643a7 100644 --- a/var/spack/repos/builtin/packages/tantan/package.py +++ b/var/spack/repos/builtin/packages/tantan/package.py @@ -13,7 +13,7 @@ class Tantan(MakefilePackage): homepage = "http://cbrc3.cbrc.jp/~martin/tantan" url = "http://cbrc3.cbrc.jp/~martin/tantan/tantan-13.zip" - version('13', '90a30284a7d0cd04d797527d47bc8bd0') + version('13', sha256='3f7ba7d8d04a32c3716ea3e4e2f0798942fb93e5123574ce01c9436e1854a518') def install(self, spec, prefix): make('prefix={0}'.format(self.prefix), 'install') diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py index 6c00cdd6893..3ef16bbfcdf 100644 --- a/var/spack/repos/builtin/packages/tar/package.py +++ b/var/spack/repos/builtin/packages/tar/package.py @@ -15,9 +15,9 @@ class Tar(AutotoolsPackage): version('1.32', sha256='b59549594d91d84ee00c99cf2541a3330fed3a42c440503326dab767f2fbb96c') version('1.31', sha256='b471be6cb68fd13c4878297d856aebd50551646f4e3074906b1a74549c40d5a2') - version('1.30', 'e0c5ed59e4dd33d765d6c90caadd3c73') + version('1.30', sha256='4725cc2c2f5a274b12b39d1f78b3545ec9ebb06a6e48e8845e1995ac8513b088') version('1.29', sha256='cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0') - version('1.28', '6ea3dbea1f2b0409b234048e021a9fd7') + version('1.28', sha256='6a6b65bac00a127a508533c604d5bf1a3d40f82707d56f20cefd38a05e8237de') depends_on('libiconv') diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py index 8db5943e9d4..3aa1722eef4 100644 --- a/var/spack/repos/builtin/packages/task/package.py +++ b/var/spack/repos/builtin/packages/task/package.py @@ -11,8 +11,8 @@ class Task(CMakePackage): homepage = "http://www.taskwarrior.org" url = "http://taskwarrior.org/download/task-2.4.4.tar.gz" - version('2.5.1', 'bcd984a00d6d1eb6b40faf567419f784') - version('2.4.4', '517450c4a23a5842df3e9905b38801b3') + version('2.5.1', sha256='d87bcee58106eb8a79b850e9abc153d98b79e00d50eade0d63917154984f2a15') + version('2.4.4', sha256='7ff406414e0be480f91981831507ac255297aab33d8246f98dbfd2b1b2df8e3b') depends_on('cmake@2.8:', type='build') depends_on('gnutls') diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py index d43feea5231..4d038cd18b1 100644 --- a/var/spack/repos/builtin/packages/taskd/package.py +++ b/var/spack/repos/builtin/packages/taskd/package.py @@ -12,7 +12,7 @@ class Taskd(CMakePackage): homepage = "http://www.taskwarrior.org" url = "http://taskwarrior.org/download/taskd-1.1.0.tar.gz" - version('1.1.0', 'ac855828c16f199bdbc45fbc227388d0') + version('1.1.0', sha256='7b8488e687971ae56729ff4e2e5209ff8806cf8cd57718bfd7e521be130621b4') depends_on('libuuid') depends_on('gnutls') diff --git a/var/spack/repos/builtin/packages/tasmanian/package.py b/var/spack/repos/builtin/packages/tasmanian/package.py index e8dbe58113d..3b4a7682d3a 100644 --- a/var/spack/repos/builtin/packages/tasmanian/package.py +++ b/var/spack/repos/builtin/packages/tasmanian/package.py @@ -19,11 +19,11 @@ class Tasmanian(CMakePackage): version('develop', branch='master') - version('7.0', '60916a3dee3d23c1c41ca8005238f66e') # use for xsdk-0.5.0 - version('6.0', '43dcb1d2bcb2f2c829ad046d0e91e83d') # use for xsdk-0.4.0 - version('5.1', '5d904029a24470a6acf4a87d3339846e') + version('7.0', sha256='4094ba4ee2f1831c575d00368c8471d3038f813398be2e500739cef5c7c4a47b') # use for xsdk-0.5.0 + version('6.0', sha256='ceab842e9fbce2f2de971ba6226967caaf1627b3e5d10799c3bd2e7c3285ba8b') # use for xsdk-0.4.0 + version('5.1', sha256='b0c1be505ce5f8041984c63edca9100d81df655733681858f5cc10e8c0c72711') - version('5.0', '4bf131841d786033863d271739be0f7a', + version('5.0', sha256='2540bb63dea987ab205f7b375aff41f320b1de9bd7f1d1064ef96b22eeda1251', url='http://tasmanian.ornl.gov/documents/Tasmanian_v5.0.zip') variant('xsdkflags', default=False, diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py index 0cfd580a7b8..50c826b6109 100644 --- a/var/spack/repos/builtin/packages/tau/package.py +++ b/var/spack/repos/builtin/packages/tau/package.py @@ -23,21 +23,21 @@ class Tau(Package): git = "https://github.com/UO-OACISS/tau2" version('develop', branch='master') - version('2.28.2', '64e129a482056755012b91dae2fb4f728dbf3adbab53d49187eca952891c5457') - version('2.28.1', '4e48fb477250f201ab00381cb43afea6') - version('2.28', '68c6f13ae748d12c921456e494006796ca2b0efebdeef76ee7c898c81592883e') - version('2.27.2p1', 'b9cc42ee8afdcfefe5104ab0a8f23a23') - version('2.27.2', 'b264ab0df78112f9a529e59a5f4dc191') - version('2.27.1', '4f98ff67ae5ab1ff2712f694bdec1fa9') - version('2.27', '76602d35fc96f546b5b9dcaf09158651') - version('2.26.3', '4ec14e85b8f3560b58628512c7b49e17') - version('2.26.2', '8a5908c35dac9406c9220b8098c70c1c') - version('2.26.1', 'cc13df9d6ad19bca9a8e55a9e7d0341e') - version('2.26', '2af91f02ad26d5bf0954146c56a8cdfa') - version('2.25', '46cd48fa3f3c4ce0197017b3158a2b43') - version('2.24.1', '6635ece6d1f08215b02f5d0b3c1e971b') - version('2.24', '57ce33539c187f2e5ec68f0367c76db4') - version('2.23.1', '6593b47ae1e7a838e632652f0426fe72') + version('2.28.2', sha256='64e129a482056755012b91dae2fb4f728dbf3adbab53d49187eca952891c5457') + version('2.28.1', sha256='b262e5c9977471e9f5a8d729b3db743012df9b0ab8244da2842039f8a3b98b34') + version('2.28', sha256='68c6f13ae748d12c921456e494006796ca2b0efebdeef76ee7c898c81592883e') + version('2.27.2p1', sha256='3256771fb71c2b05932b44d0650e6eadc712f1bdedf4c0fb2781db3b266225dd') + version('2.27.2', sha256='d319a4588ad303b71082254f4f40aa76f6183a01b5bc4bd987f76e1a6026efa1') + version('2.27.1', sha256='315babab4da25dd08633ad8dbf33d93db77f57d240bcbd3527ed5b8710cb9d8f') + version('2.27', sha256='d48fdca49cda2d9f25a0cf5dbd961201c8a2b1f025bcbb121d96ad43f211f1a7') + version('2.26.3', sha256='bd785ed47f20e6b8b2a1d99ce383d292f70b1fb9e2eaab21f5eaf8e64b28e990') + version('2.26.2', sha256='92ca68db51fd5bd026187e70b397bcd1db9bfb07008d7e8bc935411a97978834') + version('2.26.1', sha256='d084ff87e5f9fe640a3fc48aa5c8c52f586e7b739787f2bb9a4249005e459896') + version('2.26', sha256='458228646a13a228841d4133f24af14cc182f4978eb15ef6244d71735abe8d16') + version('2.25', sha256='ab8a8c15a075af69aa23b4790b4e2d9dffc3b880fc1ff806c21535ab69b6a088') + version('2.24.1', sha256='bc27052c36377e4b8fc0bbb4afaa57eaa8bcb3f5e5066e576b0f40d341c28a0e') + version('2.24', sha256='5d28e8b26561c7cd7d0029b56ec0f95fc26803ac0b100c98e00af0b02e7f55e2') + version('2.23.1', sha256='31a4d0019cec6ef57459a9cd18a220f0130838a5f1a0b5ea7879853f5a38cf88') # Disable some default dependencies on Darwin/OSX darwin_default = False diff --git a/var/spack/repos/builtin/packages/tcl-itcl/package.py b/var/spack/repos/builtin/packages/tcl-itcl/package.py index 585728046a4..ec6457e69de 100644 --- a/var/spack/repos/builtin/packages/tcl-itcl/package.py +++ b/var/spack/repos/builtin/packages/tcl-itcl/package.py @@ -14,7 +14,7 @@ class TclItcl(AutotoolsPackage): homepage = "https://sourceforge.net/projects/incrtcl/" url = "https://sourceforge.net/projects/incrtcl/files/%5Bincr%20Tcl_Tk%5D-4-source/itcl%204.0.4/itcl4.0.4.tar.gz" - version('4.0.4', 'c9c52afdd9435490e2db17c3c6c95ab4') + version('4.0.4', sha256='63860438ca22f70049aecff70dc607b31bb1bea0edcc736e36ac6e36c24aecde') extends('tcl') diff --git a/var/spack/repos/builtin/packages/tcl-tcllib/package.py b/var/spack/repos/builtin/packages/tcl-tcllib/package.py index 2a8b7bacbf2..ea985d3b9d1 100644 --- a/var/spack/repos/builtin/packages/tcl-tcllib/package.py +++ b/var/spack/repos/builtin/packages/tcl-tcllib/package.py @@ -18,11 +18,11 @@ class TclTcllib(AutotoolsPackage): list_url = "https://sourceforge.net/projects/tcllib/files/tcllib/" list_depth = 1 - version('1.19', '8d3990d01e3fb66480d441d18a7a7d0d') - version('1.18', '219361e6bdf9d9c0d79edbd1ab3e8080') - version('1.17', '4c75fbfbb518f8990fcd4686b976bd70') - version('1.16', 'e65e91f5ca188648019fdbe15fbfb9bf') - version('1.15', '7a0525912e8863f8d4360ab10e5450f8') - version('1.14', '55bac9afce54c3328f368918cc2d7a4b') + version('1.19', sha256='01fe87cf1855b96866cf5394b6a786fd40b314022714b34110aeb6af545f6a9c') + version('1.18', sha256='72667ecbbd41af740157ee346db77734d1245b41dffc13ac80ca678dd3ccb515') + version('1.17', sha256='00c16aa28512ff6a67f199ffa5e04acaeb7b8464b2b7dc70ad8d00ce4c8d25ce') + version('1.16', sha256='0b3a87577bf1ea79c70479be5230f0ba466587b4621828ec4941c4840fa1b2e8') + version('1.15', sha256='6d308980d9dace24c6252b96223c1646e83795ba03dbf996525ad27e1b56bffd') + version('1.14', sha256='dd149fcb37ceb04da83531276a9d7563827807dcee49f9b9f63bedea9e130584') extends('tcl') diff --git a/var/spack/repos/builtin/packages/tcl-tclxml/package.py b/var/spack/repos/builtin/packages/tcl-tclxml/package.py index 160ab826339..a11268bfb3a 100644 --- a/var/spack/repos/builtin/packages/tcl-tclxml/package.py +++ b/var/spack/repos/builtin/packages/tcl-tclxml/package.py @@ -17,8 +17,8 @@ class TclTclxml(AutotoolsPackage): list_url = "https://sourceforge.net/projects/tclxml/files/TclXML/" list_depth = 1 - version('3.2', '9d1605246c899eff7db591bca3c23200') - version('3.1', '35de63a4ceba7a6fdb85dd1a62f2e881') + version('3.2', sha256='f4116b6680b249ce74b856a121762361ca09e6256f0c8ad578d1c661b822cb39') + version('3.1', sha256='9b017f29c7a06fa1a57d1658bd1d3867297c26013604bdcc4d7b0ca2333552c9') extends('tcl') diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py index 4b07d9d21b8..a76c748262b 100644 --- a/var/spack/repos/builtin/packages/tcl/package.py +++ b/var/spack/repos/builtin/packages/tcl/package.py @@ -20,12 +20,12 @@ class Tcl(AutotoolsPackage): homepage = "http://www.tcl.tk" url = "http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz" - version('8.6.8', '81656d3367af032e0ae6157eff134f89') - version('8.6.6', '5193aea8107839a79df8ac709552ecb7') - version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326') - version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304') - version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f') - version('8.5.19', '4f4e1c919f6a6dbb37e9a12d429769a6') + version('8.6.8', sha256='c43cb0c1518ce42b00e7c8f6eaddd5195c53a98f94adc717234a65cbcfd3f96a') + version('8.6.6', sha256='a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07') + version('8.6.5', sha256='ce26d5b9c7504fc25d2f10ef0b82b14cf117315445b5afa9e673ed331830fb53') + version('8.6.4', sha256='9e6ed94c981c1d0c5f5fefb8112d06c6bf4d050a7327e95e71d417c416519c8d') + version('8.6.3', sha256='6ce0778de0d50daaa9c345d7c1fd1288fb658f674028812e7eeee992e3051005') + version('8.5.19', sha256='d3f04456da873d17f02efc30734b0300fb6c3b85028d445fe284b83253a6db18') extendable = True diff --git a/var/spack/repos/builtin/packages/tclap/package.py b/var/spack/repos/builtin/packages/tclap/package.py index 3e39bd6bc2c..39e4386f31a 100644 --- a/var/spack/repos/builtin/packages/tclap/package.py +++ b/var/spack/repos/builtin/packages/tclap/package.py @@ -12,5 +12,5 @@ class Tclap(AutotoolsPackage): homepage = "http://tclap.sourceforge.net" url = "https://downloads.sourceforge.net/project/tclap/tclap-1.2.2.tar.gz" - version('1.2.2', '6f35665814dca292eceda007d7e13bcb') - version('1.2.1', 'eb0521d029bf3b1cc0dcaa7e42abf82a') + version('1.2.2', sha256='f5013be7fcaafc69ba0ce2d1710f693f61e9c336b6292ae4f57554f59fde5837') + version('1.2.1', sha256='9f9f0fe3719e8a89d79b6ca30cf2d16620fba3db5b9610f9b51dd2cd033deebb') diff --git a/var/spack/repos/builtin/packages/tcptrace/package.py b/var/spack/repos/builtin/packages/tcptrace/package.py index 8797b649d6e..97d5321b705 100644 --- a/var/spack/repos/builtin/packages/tcptrace/package.py +++ b/var/spack/repos/builtin/packages/tcptrace/package.py @@ -16,7 +16,7 @@ class Tcptrace(AutotoolsPackage): homepage = "http://www.tcptrace.org/" url = "http://www.tcptrace.org/download/tcptrace-6.6.7.tar.gz" - version('6.6.7', '68128dc1817b866475e2f048e158f5b9') + version('6.6.7', sha256='63380a4051933ca08979476a9dfc6f959308bc9f60d45255202e388eb56910bd') depends_on('bison', type='build') depends_on('flex', type='build') diff --git a/var/spack/repos/builtin/packages/tealeaf/package.py b/var/spack/repos/builtin/packages/tealeaf/package.py index 4a720fa115e..834f99db380 100644 --- a/var/spack/repos/builtin/packages/tealeaf/package.py +++ b/var/spack/repos/builtin/packages/tealeaf/package.py @@ -20,7 +20,7 @@ class Tealeaf(MakefilePackage): tags = ['proxy-app'] - version('1.0', '02a907281ad2d09e70ca0a17551c6d79') + version('1.0', sha256='e11799d1a3fbe76041333ba98858043b225c5d65221df8c600479bc55e7197ce') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py index 38c9052b128..34926fabac1 100644 --- a/var/spack/repos/builtin/packages/tetgen/package.py +++ b/var/spack/repos/builtin/packages/tetgen/package.py @@ -17,8 +17,8 @@ class Tetgen(Package): homepage = "http://wias-berlin.de/software/tetgen/" - version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') - version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18', url='http://www.tetgen.org/files/tetgen1.4.3.tar.gz') + version('1.5.0', sha256='4d114861d5ef2063afd06ef38885ec46822e90e7b4ea38c864f76493451f9cf3', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') + version('1.4.3', sha256='952711bb06b7f64fd855eb24c33f08e3faf40bdd54764de10bbe5ed5b0dce034', url='http://www.tetgen.org/files/tetgen1.4.3.tar.gz') variant('debug', default=False, description='Builds the library in debug mode.') variant('except', default=False, description='Replaces asserts with exceptions for better C++ compatibility.') diff --git a/var/spack/repos/builtin/packages/tethex/package.py b/var/spack/repos/builtin/packages/tethex/package.py index 50e0d253d23..3b78e89d7de 100644 --- a/var/spack/repos/builtin/packages/tethex/package.py +++ b/var/spack/repos/builtin/packages/tethex/package.py @@ -18,7 +18,7 @@ class Tethex(CMakePackage): git = "https://github.com/martemyev/tethex.git" version('develop', branch='master') - version('0.0.7', '6c9e4a18a6637deb4400c6d77ec03184') + version('0.0.7', sha256='5f93f434c6d110be3d8d0eba69336864d0e5a26aba2d444eb25adbd2caf73645') variant('build_type', default='Release', description='The build type to build', diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py index ccfb88affe8..155c138b45d 100644 --- a/var/spack/repos/builtin/packages/texinfo/package.py +++ b/var/spack/repos/builtin/packages/texinfo/package.py @@ -17,11 +17,11 @@ class Texinfo(AutotoolsPackage): homepage = "https://www.gnu.org/software/texinfo/" url = "https://ftpmirror.gnu.org/texinfo/texinfo-6.0.tar.gz" - version('6.5', '94e8f7149876793030e5518dd8d6e956') - version('6.3', '9b08daca9bf8eccae9b0f884aba41f9e') - version('6.0', 'e1a2ef5dce5018b53f0f6eed45b247a7') - version('5.2', '1b8f98b80a8e6c50422125e07522e8db') - version('5.1', '54e250014fe698fb4832016158747c03') - version('5.0', '918432285abe6fe96c98355594c5656a') + version('6.5', sha256='d34272e4042c46186ddcd66bd5d980c0ca14ff734444686ccf8131f6ec8b1427') + version('6.3', sha256='300a6ba4958c2dd4a6d5ce60f0a335daf7e379f5374f276f6ba31a221f02f606') + version('6.0', sha256='83d3183290f34e7f958d209d0b20022c6fe9e921eb6fe94c27d988827d4878d2') + version('5.2', sha256='6b8ca30e9b6f093b54fe04439e5545e564c63698a806a48065c0bba16994cf74') + version('5.1', sha256='50e8067f9758bb2bf175b69600082ac4a27c464cb4bcd48a578edd3127216600') + version('5.0', sha256='2c579345a39a2a0bb4b8c28533f0b61356504a202da6a25d17d4d866af7f5803') depends_on('perl') diff --git a/var/spack/repos/builtin/packages/texstudio/package.py b/var/spack/repos/builtin/packages/texstudio/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/the-silver-searcher/package.py b/var/spack/repos/builtin/packages/the-silver-searcher/package.py index 8c7ec21d2b7..72fb8ded9d1 100644 --- a/var/spack/repos/builtin/packages/the-silver-searcher/package.py +++ b/var/spack/repos/builtin/packages/the-silver-searcher/package.py @@ -12,9 +12,9 @@ class TheSilverSearcher(AutotoolsPackage): homepage = "http://geoff.greer.fm/ag/" url = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz" - version('2.1.0', '3e7207b060424174323236932bf76ec2') - version('0.32.0', '3fdfd5836924246073d5344257a06823') - version('0.30.0', '95e2e7859fab1156c835aff7413481db') + version('2.1.0', sha256='d4652bd91c3a05e87a15809c5f3f14ad2e5e1f80185af510e3fa4ad2038c15d4') + version('0.32.0', sha256='944ca77e498f344b2bfbd8df6d5d8df7bbc1c7e080b50c0bab3d1a9a55151b60') + version('0.30.0', sha256='b4bf9e50bf48bc5fde27fc386f7bcad8644ef15a174c862a10813e81bd127e69') depends_on('pcre') depends_on('xz') diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index c23668a0073..5c56f651d04 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -19,10 +19,10 @@ class Thrift(Package): homepage = "http://thrift.apache.org" url = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz" - version('0.11.0', '0be59730ebce071eceaf6bfdb8d3a20e') - version('0.10.0', '795c5dd192e310ffff38cfd9430d6b29') - version('0.9.3', '88d667a8ae870d5adeca8cb7d6795442') - version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678') + version('0.11.0', sha256='c4ad38b6cb4a3498310d405a91fef37b9a8e79a50cd0968148ee2524d2fa60c2') + version('0.10.0', sha256='2289d02de6e8db04cbbabb921aeb62bfe3098c4c83f36eec6c31194301efa10b') + version('0.9.3', sha256='b0740a070ac09adde04d43e852ce4c320564a292f26521c46b78e0641564969e') + version('0.9.2', md5='89f63cc4d0100912f4a1f8a9dee63678') # Currently only support for c-family and python variant('c', default=True, diff --git a/var/spack/repos/builtin/packages/thrust/package.py b/var/spack/repos/builtin/packages/thrust/package.py index 39166d2a85f..59152487c0f 100644 --- a/var/spack/repos/builtin/packages/thrust/package.py +++ b/var/spack/repos/builtin/packages/thrust/package.py @@ -18,7 +18,7 @@ class Thrust(Package): version('1.9.2', sha256='1fb1272be9e8c28973f5c39eb230d1914375ef38bcaacf09a3fa51c6b710b756') version('1.9.1', sha256='7cf59bf42a7b05bc6799c88269bf41eb637ca2897726a5ade334a1b8b4579ef1') version('1.9.0', sha256='a98cf59fc145dd161471291d4816f399b809eb0db2f7085acc7e3ebc06558b37') - version('1.8.2', 'fc7fc807cba98640c816463b511fb53f') + version('1.8.2', sha256='83bc9e7b769daa04324c986eeaf48fcb53c2dda26bcc77cb3c07f4b1c359feb8') def install(self, spec, prefix): install_tree('doc', join_path(prefix, 'doc')) diff --git a/var/spack/repos/builtin/packages/tig/package.py b/var/spack/repos/builtin/packages/tig/package.py index cb353a319a0..dd78e875611 100644 --- a/var/spack/repos/builtin/packages/tig/package.py +++ b/var/spack/repos/builtin/packages/tig/package.py @@ -12,6 +12,6 @@ class Tig(AutotoolsPackage): homepage = "https://jonas.github.io/tig/" url = "https://github.com/jonas/tig/releases/download/tig-2.2.2/tig-2.2.2.tar.gz" - version('2.2.2', '3b4a9f0fd8d18c1039863e6c4ace6e46') + version('2.2.2', sha256='316214d87f7693abc0cbe8ebbb85decdf5e1b49d7ad760ac801af3dd73385e35') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/tinyxml/package.py b/var/spack/repos/builtin/packages/tinyxml/package.py index aaebbae8692..22bc9bba8c1 100644 --- a/var/spack/repos/builtin/packages/tinyxml/package.py +++ b/var/spack/repos/builtin/packages/tinyxml/package.py @@ -13,7 +13,7 @@ class Tinyxml(CMakePackage): homepage = "http://grinninglizard.com/tinyxml/" url = "https://downloads.sourceforge.net/project/tinyxml/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz" - version('2.6.2', 'cba3f50dd657cb1434674a03b21394df9913d764') + version('2.6.2', sha256='15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593') variant('shared', default=True, description='Build a shared library') diff --git a/var/spack/repos/builtin/packages/tinyxml2/package.py b/var/spack/repos/builtin/packages/tinyxml2/package.py index 42726583f48..a17634158de 100644 --- a/var/spack/repos/builtin/packages/tinyxml2/package.py +++ b/var/spack/repos/builtin/packages/tinyxml2/package.py @@ -12,9 +12,9 @@ class Tinyxml2(CMakePackage): homepage = "http://grinninglizard.com/tinyxml2/" url = "https://github.com/leethomason/tinyxml2/archive/3.0.0.tar.gz" - version('4.0.1', '08570d385788f6b02f50f5fd9df32a9d4f8482cc') - version('4.0.0', '7a6f0858d75f360922f3ca272f7067e8cdf00489') - version('3.0.0', '07acaae49f7dd3dab790da4fe72d0c7ef0d116d1') - version('2.2.0', '7869aa08241ce16f93ba3732c1cde155b1f2b6a0') - version('2.1.0', '70ef3221bdc190fd8fc50cdd4a6ef440f44b74dc') - version('2.0.2', 'c78a4de58540e2a35f4775fd3e577299ebd15117') + version('4.0.1', sha256='14b38ef25cc136d71339ceeafb4856bb638d486614103453eccd323849267f20') + version('4.0.0', sha256='90add44f06de081047d431c08d7269c25b4030e5fe19c3bc8381c001ce8f258c') + version('3.0.0', sha256='128aa1553e88403833e0cccf1b651f45ce87bc207871f53fdcc8e7f9ec795747') + version('2.2.0', sha256='f891224f32e7a06bf279290619cec80cc8ddc335c13696872195ffb87f5bce67') + version('2.1.0', sha256='4bdd6569fdce00460bf9cda0ff5dcff46d342b4595900d849cc46a277a74cce6') + version('2.0.2', sha256='3cc3aa09cd1ce77736f23488c7cb24e65e11daed4e870ddc8d352aa4070c7c74') diff --git a/var/spack/repos/builtin/packages/tix/package.py b/var/spack/repos/builtin/packages/tix/package.py index 1eb4d9e4f72..47dfc425fac 100644 --- a/var/spack/repos/builtin/packages/tix/package.py +++ b/var/spack/repos/builtin/packages/tix/package.py @@ -12,7 +12,7 @@ class Tix(AutotoolsPackage): homepage = "https://sourceforge.net/projects/tix/" url = "https://sourceforge.net/projects/tix/files/tix/8.4.3/Tix8.4.3-src.tar.gz/download" - version('8.4.3', '2b8bf4b10a852264678182652f477e59') + version('8.4.3', sha256='562f040ff7657e10b5cffc2c41935f1a53c6402eb3d5f3189113d734fd6c03cb') extends('tcl') depends_on('tk@:8.5.99') diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py index 2a09333740a..0533e54e055 100644 --- a/var/spack/repos/builtin/packages/tk/package.py +++ b/var/spack/repos/builtin/packages/tk/package.py @@ -17,11 +17,11 @@ class Tk(AutotoolsPackage): homepage = "http://www.tcl.tk" url = "http://prdownloads.sourceforge.net/tcl/tk8.6.5-src.tar.gz" - version('8.6.8', '5e0faecba458ee1386078fb228d008ba') - version('8.6.6', 'dd7dbb3a6523c42d05f6ab6e86096e99') - version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4') - version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221') - version('8.5.19', 'e89df710447cce0fc0bde65667c12f85') + version('8.6.8', sha256='49e7bca08dde95195a27f594f7c850b088be357a7c7096e44e1158c7a5fd7b33') + version('8.6.6', sha256='d62c371a71b4744ed830e3c21d27968c31dba74dd2c45f36b9b071e6d88eb19d') + version('8.6.5', sha256='fbbd93541b4cd467841208643b4014c4543a54c3597586727f0ab128220d7946') + version('8.6.3', sha256='ba15d56ac27d8c0a7b1a983915a47e0f635199b9473cf6e10fbce1fc73fd8333') + version('8.5.19', sha256='407af1de167477d598bd6166d84459a3bdccc2fb349360706154e646a9620ffa') variant('xft', default=True, description='Enable X FreeType') diff --git a/var/spack/repos/builtin/packages/tmalign/package.py b/var/spack/repos/builtin/packages/tmalign/package.py index 73e6b646727..d2137f3419d 100644 --- a/var/spack/repos/builtin/packages/tmalign/package.py +++ b/var/spack/repos/builtin/packages/tmalign/package.py @@ -13,7 +13,7 @@ class Tmalign(Package): homepage = "http://zhanglab.ccmb.med.umich.edu/TM-align" url = "http://zhanglab.ccmb.med.umich.edu/TM-align/TM-align-C/TMalignc.tar.gz" - version('2016-05-25', 'c1027e4b65c07d1c5df9717de7417118') + version('2016-05-25', sha256='ce7f68289f3766d525afb0a58e3acfc28ae05f538d152bd33d57f8708c60e2af') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py index b65a067d452..39884d2956b 100644 --- a/var/spack/repos/builtin/packages/tmux/package.py +++ b/var/spack/repos/builtin/packages/tmux/package.py @@ -18,14 +18,14 @@ class Tmux(AutotoolsPackage): url = "https://github.com/tmux/tmux/releases/download/2.6/tmux-2.6.tar.gz" version('2.8', sha256='7f6bf335634fafecff878d78de389562ea7f73a7367f268b66d37ea13617a2ba') - version('2.7', 'bcdfcf910c94c3e02ce6b1c035880306') - version('2.6', 'd541ff392249f94c4f3635793556f827') - version('2.5', '4a5d73d96d8f11b0bdf9b6f15ab76d15') - version('2.4', '6165d3aca811a3225ef8afbd1afcf1c5') - version('2.3', 'fcfd1611d705d8b31df3c26ebc93bd3e') - version('2.2', 'bd95ee7205e489c62c616bb7af040099') - version('2.1', '74a2855695bccb51b6e301383ad4818c') - version('1.9a', 'b07601711f96f1d260b390513b509a2d') + version('2.7', sha256='9ded7d100313f6bc5a87404a4048b3745d61f2332f99ec1400a7c4ed9485d452') + version('2.6', sha256='b17cd170a94d7b58c0698752e1f4f263ab6dc47425230df7e53a6435cc7cd7e8') + version('2.5', sha256='ae135ec37c1bf6b7750a84e3a35e93d91033a806943e034521c8af51b12d95df') + version('2.4', sha256='757d6b13231d0d9dd48404968fc114ac09e005d475705ad0cd4b7166f799b349') + version('2.3', sha256='55313e132f0f42de7e020bf6323a1939ee02ab79c48634aa07475db41573852b') + version('2.2', sha256='bc28541b64f99929fe8e3ae7a02291263f3c97730781201824c0f05d7c8e19e4') + version('2.1', sha256='31564e7bf4bcef2defb3cb34b9e596bd43a3937cad9e5438701a81a5a9af6176') + version('1.9a', sha256='c5e3b22b901cf109b20dab54a4a651f0471abd1f79f6039d79b250d21c2733f5') depends_on('libevent') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py index f9b2373e08b..a3d602e3aea 100644 --- a/var/spack/repos/builtin/packages/tophat/package.py +++ b/var/spack/repos/builtin/packages/tophat/package.py @@ -12,8 +12,8 @@ class Tophat(AutotoolsPackage): homepage = "http://ccb.jhu.edu/software/tophat/index.shtml" url = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz" - version('2.1.2', 'db844fd7f53c519e716cd6222e6195b2') - version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f') + version('2.1.2', sha256='15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1') + version('2.1.1', sha256='991b1b7c840a5f5c4e9a15b2815983257d2b0748246af0b9094c7d07552b023e') depends_on('autoconf', type='build') # 2.1.1 only builds with automake@1.15.1. There's a patch here: diff --git a/var/spack/repos/builtin/packages/tppred/package.py b/var/spack/repos/builtin/packages/tppred/package.py index abc8303b237..a4ae0997332 100644 --- a/var/spack/repos/builtin/packages/tppred/package.py +++ b/var/spack/repos/builtin/packages/tppred/package.py @@ -13,7 +13,7 @@ class Tppred(Package): homepage = "https://tppred2.biocomp.unibo.it/tppred2/default/software" url = "http://biocomp.unibo.it/savojard/tppred2.tar.gz" - version('2.0', 'cd848569f6a8aa51d18fbe55fe45d624') + version('2.0', sha256='0e180d5ce1f0bccfdbc3dbf9981b3fbe2101c85491c58c58c88856861688a4f5') depends_on('python@2.7:2.999', type='run') depends_on('py-scikit-learn@0.13.1', type='run') diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py index b30f3689338..85cf56bd858 100644 --- a/var/spack/repos/builtin/packages/transabyss/package.py +++ b/var/spack/repos/builtin/packages/transabyss/package.py @@ -12,7 +12,7 @@ class Transabyss(Package): homepage = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss" url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/1.5.5/transabyss-1.5.5.zip" - version('1.5.5', '9ebe0394243006f167135cac4df9bee6') + version('1.5.5', sha256='7804961c13296c587a1b22180dd3f02091a4494cbbd04fc33c2060599caadb0b') depends_on('abyss@1.5.2') depends_on('python@2.7.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py index 26cb4f8f715..b49b67ae9bf 100644 --- a/var/spack/repos/builtin/packages/transdecoder/package.py +++ b/var/spack/repos/builtin/packages/transdecoder/package.py @@ -16,7 +16,7 @@ class Transdecoder(MakefilePackage): url = "https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.5.0.tar.gz" version('5.5.0', sha256='c800d9226350817471e9f51267c91f7cab99dbc9b26c980527fc1019e7d90a76') - version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300', + version('3.0.1', sha256='753a5fac5bfd04466aeabff48053c92e876cece8906b96de3b72f23f86fafae7', url='https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/transposome/package.py b/var/spack/repos/builtin/packages/transposome/package.py index 587eae343ec..48bd94ff0a8 100644 --- a/var/spack/repos/builtin/packages/transposome/package.py +++ b/var/spack/repos/builtin/packages/transposome/package.py @@ -13,6 +13,6 @@ class Transposome(PerlPackage): homepage = "https://sestaton.github.io/Transposome/" url = "https://github.com/sestaton/Transposome/archive/v0.11.2.tar.gz" - version('0.11.2', '157c1fc090b0aa30050d03df885dcde0') + version('0.11.2', sha256='f0bfdb33c34ada726b36c7b7ed6defa8540a7f8abe08ad46b3ccfec5dcd4720d') depends_on('blast-plus') diff --git a/var/spack/repos/builtin/packages/transset/package.py b/var/spack/repos/builtin/packages/transset/package.py index c9fc487eb08..725d13e1988 100644 --- a/var/spack/repos/builtin/packages/transset/package.py +++ b/var/spack/repos/builtin/packages/transset/package.py @@ -12,7 +12,7 @@ class Transset(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/transset" url = "https://www.x.org/archive/individual/app/transset-1.0.1.tar.gz" - version('1.0.1', '4bbee6f6ea6fbd403280b4bb311db6dc') + version('1.0.1', sha256='87c560e69e05ae8a5bad17ff62ac31cda43a5065508205b109c756c0ab857d55') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/trapproto/package.py b/var/spack/repos/builtin/packages/trapproto/package.py index 3866ed90701..27c5e46e5ee 100644 --- a/var/spack/repos/builtin/packages/trapproto/package.py +++ b/var/spack/repos/builtin/packages/trapproto/package.py @@ -12,4 +12,4 @@ class Trapproto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/trapproto" url = "https://www.x.org/archive/individual/proto/trapproto-3.4.3.tar.gz" - version('3.4.3', '1344759ae8d7d923e64f5eec078a679b') + version('3.4.3', sha256='abfb930b5703b5a6ebafe84d0246bd8c6b099ca4a4eab06d1dc0776a8a9b87c1') diff --git a/var/spack/repos/builtin/packages/tree/package.py b/var/spack/repos/builtin/packages/tree/package.py index 7b9ca1f7625..d4cf705bfd4 100644 --- a/var/spack/repos/builtin/packages/tree/package.py +++ b/var/spack/repos/builtin/packages/tree/package.py @@ -18,7 +18,7 @@ class Tree(Package): homepage = "http://mama.indstate.edu/users/ice/tree/" url = "http://mama.indstate.edu/users/ice/tree/src/tree-1.7.0.tgz" - version('1.7.0', 'abe3e03e469c542d8e157cdd93f4d8a6') + version('1.7.0', sha256='6957c20e82561ac4231638996e74f4cfa4e6faabc5a2f511f0b4e3940e8f7b12') def install(self, spec, prefix): objs = [ diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py index 8414e875106..ba0ce5a3ef0 100644 --- a/var/spack/repos/builtin/packages/triangle/package.py +++ b/var/spack/repos/builtin/packages/triangle/package.py @@ -16,7 +16,7 @@ class Triangle(Package): homepage = "http://www.cs.cmu.edu/~quake/triangle.html" url = "http://www.netlib.org/voronoi/triangle.zip" - version('1.6', '10aff8d7950f5e0e2fb6dd2e340be2c9') + version('1.6', sha256='1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480') def install(self, spec, prefix): make() diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index b484599c66b..47e1fb1936f 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -35,20 +35,20 @@ class Trilinos(CMakePackage): version('xsdk-0.2.0', tag='xsdk-0.2.0') version('develop', branch='develop') version('master', branch='master') - version('12.14.1', '52a4406cca2241f5eea8e166c2950471dd9478ad6741cbb2a7fc8225814616f0') - version('12.12.1', 'ecd4606fa332212433c98bf950a69cc7') - version('12.10.1', '667333dbd7c0f031d47d7c5511fd0810') - version('12.8.1', '9f37f683ee2b427b5540db8a20ed6b15') - version('12.6.4', 'e11fff717d0e4565779f75a47feecbb2') - version('12.6.3', '9ce30b6ab956bfc41730479a9ef05d05') - version('12.6.2', '0237d32feedd979a6fbb139aa5df8500') - version('12.6.1', '14ab8f7e74b66c33d5731cbf68b8cb82') - version('12.4.2', '98880f414752220e60feaeb36b023f60') - version('12.2.1', '8b344a9e9e533126dfd96db58ce69dde') - version('12.0.1', 'b8263f7037f7c688091d0da19d169709') - version('11.14.3', 'ff31ad49d633ab28369c228784055c85') - version('11.14.2', '1fdf15a5b4494f832b414f9c447ab685') - version('11.14.1', '478d0438d935294a7c94347c94a7c8cb') + version('12.14.1', sha256='52a4406cca2241f5eea8e166c2950471dd9478ad6741cbb2a7fc8225814616f0') + version('12.12.1', sha256='5474c5329c6309224a7e1726cf6f0d855025b2042959e4e2be2748bd6bb49e18') + version('12.10.1', sha256='ab81d917196ffbc21c4927d42df079dd94c83c1a08bda43fef2dd34d0c1a5512') + version('12.8.1', sha256='d20fe60e31e3ba1ef36edecd88226240a518f50a4d6edcc195b88ee9dda5b4a1') + version('12.6.4', sha256='1c7104ba60ee8cc4ec0458a1c4f6a26130616bae7580a7b15f2771a955818b73') + version('12.6.3', sha256='4d28298bb4074eef522db6cd1626f1a934e3d80f292caf669b8846c0a458fe81') + version('12.6.2', sha256='8be7e3e1166cc05aea7f856cc8033182e8114aeb8f87184cb38873bfb2061779') + version('12.6.1', sha256='4b38ede471bed0036dcb81a116fba8194f7bf1a9330da4e29c3eb507d2db18db') + version('12.4.2', sha256='fd2c12e87a7cedc058bcb8357107ffa2474997aa7b17b8e37225a1f7c32e6f0e') + version('12.2.1', sha256='088f303e0dc00fb4072b895c6ecb4e2a3ad9a2687b9c62153de05832cf242098') + version('12.0.1', sha256='eee7c19ca108538fa1c77a6651b084e06f59d7c3307dae77144136639ab55980') + version('11.14.3', sha256='e37fa5f69103576c89300e14d43ba77ad75998a54731008b25890d39892e6e60') + version('11.14.2', sha256='f22b2b0df7b88e28b992e19044ba72b845292b93cbbb3a948488199647381119') + version('11.14.1', sha256='f10fc0a496bf49427eb6871c80816d6e26822a39177d850cc62cf1484e4eec07') # ###################### Variants ########################## diff --git a/var/spack/repos/builtin/packages/trimgalore/package.py b/var/spack/repos/builtin/packages/trimgalore/package.py index 04df207971d..fd26b945ed0 100644 --- a/var/spack/repos/builtin/packages/trimgalore/package.py +++ b/var/spack/repos/builtin/packages/trimgalore/package.py @@ -16,8 +16,8 @@ class Trimgalore(Package): version('0.6.1', sha256='658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0') version('0.6.0', sha256='f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec') - version('0.4.5', 'c71756042b2a65c34d483533a29dc206') - version('0.4.4', 'aae1b807b48e38bae7074470203997bb') + version('0.4.5', sha256='a6b97e554944ddc6ecd50e78df486521f17225d415aad84e9911163faafe1f3c') + version('0.4.4', sha256='485a1357e08eadeb5862bbb796022a25a6ace642c4bc13bbaf453b7dc7cff8e2') depends_on('perl', type=('build', 'run')) depends_on('py-cutadapt', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/trimmomatic/package.py b/var/spack/repos/builtin/packages/trimmomatic/package.py index d9cf5ffda23..b75fcd802f2 100644 --- a/var/spack/repos/builtin/packages/trimmomatic/package.py +++ b/var/spack/repos/builtin/packages/trimmomatic/package.py @@ -16,8 +16,8 @@ class Trimmomatic(Package): # Older version aren't explicitly made available, but the URL # works as we'd like it to, so... version('0.38', sha256='d428af42b6c400a2e7ee5e6b4cab490eddc621f949b086bd7dddb698dcf1647c') - version('0.36', '8549130d86b6f0382b1a71a2eb45de39') - version('0.33', '924fc8eb38fdff71740a0e05d32d6a2b') + version('0.36', sha256='4846c42347b663b9d6d3a8cef30da2aec89fc718bf291392c58e5afcea9f70fe') + version('0.33', sha256='6968583a6c5854a44fff7d427e7ccdcb8dc17f4616082dd390a0633f87a09e3d') depends_on('java@8', type='run') diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py index 3bfb35b61ee..997e36c0efd 100644 --- a/var/spack/repos/builtin/packages/trinity/package.py +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -22,7 +22,7 @@ class Trinity(MakefilePackage): homepage = "http://trinityrnaseq.github.io/" url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz" - version('2.6.6', 'b7472e98ab36655a6d9296d965471a56') + version('2.6.6', sha256='868dfadeefaf2d3c6150a88d5e86fbc09466d69bbf4a65f70b4f5a7485668984') depends_on("java@8:", type=("build", "run")) depends_on("bowtie2") diff --git a/var/spack/repos/builtin/packages/trnascan-se/package.py b/var/spack/repos/builtin/packages/trnascan-se/package.py index 55a58946080..1f9509556c9 100644 --- a/var/spack/repos/builtin/packages/trnascan-se/package.py +++ b/var/spack/repos/builtin/packages/trnascan-se/package.py @@ -12,4 +12,4 @@ class TrnascanSe(AutotoolsPackage): homepage = "http://lowelab.ucsc.edu/tRNAscan-SE/" url = "http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz" - version('2.0.0', '36d2b53bcb281efbae09e0305346e544') + version('2.0.0', sha256='0dde1c07142e4bf77b21d53ddf3eeb1ef8c52248005a42323d13f8d7c798100c') diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py index 07a575c126f..8ec3b9de39f 100644 --- a/var/spack/repos/builtin/packages/turbine/package.py +++ b/var/spack/repos/builtin/packages/turbine/package.py @@ -18,9 +18,9 @@ class Turbine(AutotoolsPackage): configure_directory = 'turbine/code' version('master', branch='master') - version('1.2.3', '028f6f4f5041e5ffbbf3ab8008e3b781') - version('1.2.1', 'c8976b22849aafe02a8fb4259dfed434') - version('1.1.0', '9a347cf16df02707cb529f96c265a082') + version('1.2.3', sha256='a3156c7e0b39e166da3de8892f55fa5d535b0c99c87a9add067c801098fe51ba') + version('1.2.1', md5='c8976b22849aafe02a8fb4259dfed434') + version('1.1.0', sha256='98fad47597935a04d15072e42bf85411d55ef00cb6f953e9f14d6de902e33209') variant('python', default=False, description='Enable calling python') diff --git a/var/spack/repos/builtin/packages/tut/package.py b/var/spack/repos/builtin/packages/tut/package.py index 01f435152c5..286e813c6dc 100644 --- a/var/spack/repos/builtin/packages/tut/package.py +++ b/var/spack/repos/builtin/packages/tut/package.py @@ -12,7 +12,7 @@ class Tut(WafPackage): homepage = "http://mrzechonek.github.io/tut-framework/" url = "https://github.com/mrzechonek/tut-framework/tarball/2016-12-19" - version('2016-12-19', '8b1967fa295ae1ce4d4431c2f811e521') + version('2016-12-19', sha256='9fc0325d6db9709cc5213773bf4fd84f2a95154f18f7f8a553e1e52392e15691') patch('python3-octal.patch', when='@2016-12-19') diff --git a/var/spack/repos/builtin/packages/twm/package.py b/var/spack/repos/builtin/packages/twm/package.py index fbd267cbc89..64c80ec3ebb 100644 --- a/var/spack/repos/builtin/packages/twm/package.py +++ b/var/spack/repos/builtin/packages/twm/package.py @@ -15,7 +15,7 @@ class Twm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/twm" url = "https://www.x.org/archive/individual/app/twm-1.0.9.tar.gz" - version('1.0.9', 'e98fcb32f774ac1ff7bf82101b79f61e') + version('1.0.9', sha256='1c325e8456a200693c816baa27ceca9c5e5e0f36af63d98f70a335853a0039e8') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/typhon/package.py b/var/spack/repos/builtin/packages/typhon/package.py index c0b05e1bb05..d29fdab8b0e 100644 --- a/var/spack/repos/builtin/packages/typhon/package.py +++ b/var/spack/repos/builtin/packages/typhon/package.py @@ -19,7 +19,7 @@ class Typhon(CMakePackage): version('develop', branch='develop') version('3.0.2', sha256='28087eb07bf91d23792900214728b5eea61b5e81aa33df28c032dadd6d89b76e') - version('3.0.1', '89045decfba5fd468ef05ad4c924df8c') - version('3.0', 'ec67cd1aa585ce2410d4fa50514a916f') + version('3.0.1', sha256='8d6e19192e52eadf92175423ae0efd8a1a343c2ea2bc48aacb9028074447c2bb') + version('3.0', sha256='b9736269ebe9c0fd7efabc4716b0543144780ed26ddaf595083354113aa2efd7') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/typhonio/package.py b/var/spack/repos/builtin/packages/typhonio/package.py index c82de115f5d..92e96acd1f1 100644 --- a/var/spack/repos/builtin/packages/typhonio/package.py +++ b/var/spack/repos/builtin/packages/typhonio/package.py @@ -15,7 +15,7 @@ class Typhonio(CMakePackage): git = "https://github.com/UK-MAC/typhonio.git" version('develop', branch='cmake_build') - version('1.6_CMake', '8e8b2940a57874205e6d451856db5c2755884bf9') + version('1.6_CMake', sha256='c9b7b2a7f4fa0b786f6b69c6426b67f42efc4ea6871323139d52cd44f4d0ff7c') variant('build_type', default='Release', description='The build type to build', values=('Debug', 'Release')) diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py index 65af923e3fa..c3b5729f1cb 100644 --- a/var/spack/repos/builtin/packages/uberftp/package.py +++ b/var/spack/repos/builtin/packages/uberftp/package.py @@ -12,8 +12,8 @@ class Uberftp(AutotoolsPackage): homepage = "http://toolkit.globus.org/grid_software/data/uberftp.php" url = "https://github.com/JasonAlt/UberFTP/archive/Version_2_8.tar.gz" - version('2_8', 'bc7a159955a9c4b9f5f42f3d2b8fc830') - version('2_7', 'faaea2d6e1958c1105cfc9147824e03c') - version('2_6', '784210976f259f9d19c0798c19778d34') + version('2_8', sha256='8a397d6ef02bb714bb0cbdb259819fc2311f5d36231783cd520d606c97759c2a') + version('2_7', sha256='29a111a86fa70dbbc529a5d3e5a6befc1681e64e32dc019a1a6a98cd43ffb204') + version('2_6', sha256='2823a564801fb71d06fe6fbc3a37f11962af75b33c53bf698f26776ec972fe68') depends_on('globus-toolkit') diff --git a/var/spack/repos/builtin/packages/ucx/package.py b/var/spack/repos/builtin/packages/ucx/package.py index 9897f3a2311..b5fd8a0590b 100644 --- a/var/spack/repos/builtin/packages/ucx/package.py +++ b/var/spack/repos/builtin/packages/ucx/package.py @@ -21,10 +21,10 @@ class Ucx(AutotoolsPackage): version('1.4.0', sha256='99891a98476bcadc6ac4ef9c9f083bc6ffb188a96b3c3bc89c8bbca64de2c76e') # Still supported - version('1.3.1', '443ffdd64dc0e912b672a0ccb37ff666') - version('1.3.0', '2fdc3028eac3ef3ee1b1b523d170c071') - version('1.2.2', 'ff3fe65e4ebe78408fc3151a9ce5d286') - version('1.2.1', '697c2fd7912614fb5a1dadff3bfa485c') + version('1.3.1', sha256='e058c8ec830d2f50d9db1e3aaaee105cd2ad6c1e6df20ae58b9b4179de7a8992') + version('1.3.0', sha256='71e69e6d78a4950cc5a1edcbe59bf7a8f8e38d59c9f823109853927c4d442952') + version('1.2.2', sha256='914d10fee8f970d4fb286079dd656cf8a260ec7d724d5f751b3109ed32a6da63') + version('1.2.1', sha256='fc63760601c03ff60a2531ec3c6637e98f5b743576eb410f245839c84a0ad617') depends_on('numactl') depends_on('rdma-core') diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py index b0f81baacc7..c5704d6a5e1 100644 --- a/var/spack/repos/builtin/packages/udunits2/package.py +++ b/var/spack/repos/builtin/packages/udunits2/package.py @@ -12,8 +12,8 @@ class Udunits2(AutotoolsPackage): homepage = "http://www.unidata.ucar.edu/software/udunits" url = "https://www.gfd-dennou.org/arch/ucar/unidata/pub/udunits/udunits-2.2.24.tar.gz" - version('2.2.24', '898b90dc1890f172c493406d0f26f531') - version('2.2.23', '9f66006accecd621a4c3eda4ba9fa7c9') - version('2.2.21', '1585a5efb2c40c00601abab036a81299') + version('2.2.24', sha256='20bac512f2656f056385429a0e44902fdf02fc7fe01c14d56f3c724336177f95') + version('2.2.23', sha256='b745ae10753fe82cdc7cc834e6ce471ca7c25ba2662e6ff93be147cb3d4fd380') + version('2.2.21', sha256='a154d1f8428c24e92723f9e50bdb5cc00827e3f5ff9cba64d33e5409f5c03455') depends_on('expat') diff --git a/var/spack/repos/builtin/packages/ufo-core/package.py b/var/spack/repos/builtin/packages/ufo-core/package.py index 50811d82097..3dee84e57ab 100644 --- a/var/spack/repos/builtin/packages/ufo-core/package.py +++ b/var/spack/repos/builtin/packages/ufo-core/package.py @@ -15,7 +15,7 @@ class UfoCore(CMakePackage): homepage = "https://ufo.kit.edu" url = "https://github.com/ufo-kit/ufo-core/archive/v0.14.0.tar.gz" - version('0.14.0', '3bd94d10d0f589953aba11821a8295f3') + version('0.14.0', sha256='3bf0d1924d6ae3f51673cc8b0b31b17873e79f1a0129a9af54b4062b1b2b3ad7') depends_on('glib') depends_on('json-glib') diff --git a/var/spack/repos/builtin/packages/ufo-filters/package.py b/var/spack/repos/builtin/packages/ufo-filters/package.py index 54562f8c091..cd199e59451 100644 --- a/var/spack/repos/builtin/packages/ufo-filters/package.py +++ b/var/spack/repos/builtin/packages/ufo-filters/package.py @@ -14,6 +14,6 @@ class UfoFilters(CMakePackage): homepage = "https://ufo.kit.edu" url = "https://github.com/ufo-kit/ufo-filters/archive/v0.14.1.tar.gz" - version('0.14.1', 'f2a81f5d38cfa71de58cbb5279782297') + version('0.14.1', sha256='084d7cdef59205e1a048e5c142be1ffeaacedc42965824b642e8302ef30ebb13') depends_on('ufo-core') diff --git a/var/spack/repos/builtin/packages/unblur/package.py b/var/spack/repos/builtin/packages/unblur/package.py index 61336c8a0ff..a7c60e24fa1 100644 --- a/var/spack/repos/builtin/packages/unblur/package.py +++ b/var/spack/repos/builtin/packages/unblur/package.py @@ -13,7 +13,7 @@ class Unblur(AutotoolsPackage): homepage = "http://grigoriefflab.janelia.org/unblur" url = "http://grigoriefflab.janelia.org/sites/default/files/unblur_1.0.2.tar.gz" - version('1.0.2', 'b6e367061cd0cef1b62a391a6289f681') + version('1.0.2', sha256='1aa72b1f944114987ede644e1866eaebc08e191ecc566b3461409449360931e2') variant('openmp', default=True, description='Enable OpenMP support') variant('shared', default=True, description='Dynamic linking') diff --git a/var/spack/repos/builtin/packages/uncrustify/package.py b/var/spack/repos/builtin/packages/uncrustify/package.py index a1e050b65bb..c584c4b7b6b 100644 --- a/var/spack/repos/builtin/packages/uncrustify/package.py +++ b/var/spack/repos/builtin/packages/uncrustify/package.py @@ -12,8 +12,8 @@ class Uncrustify(Package): homepage = "http://uncrustify.sourceforge.net/" url = "http://downloads.sourceforge.net/project/uncrustify/uncrustify/uncrustify-0.61/uncrustify-0.61.tar.gz" - version('0.67', '0c9a08366e5c97cd02ae766064e957de41827611') - version('0.61', 'b6140106e74c64e831d0b1c4b6cf7727') + version('0.67', sha256='54f15c8ebddef120522db21f38fac1dd3b0a285fbf60a8b71f9e333e96cf6ddc') + version('0.61', sha256='1df0e5a2716e256f0a4993db12f23d10195b3030326fdf2e07f8e6421e172df9') depends_on('cmake', type='build', when='@0.64:') diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py index 2a0a5596a28..a51bb125949 100644 --- a/var/spack/repos/builtin/packages/unibilium/package.py +++ b/var/spack/repos/builtin/packages/unibilium/package.py @@ -11,7 +11,7 @@ class Unibilium(Package): homepage = "https://github.com/mauke/unibilium" url = "https://github.com/mauke/unibilium/archive/v1.2.0.tar.gz" - version('1.2.0', '9b1c97839a880a373da6c097443b43c4') + version('1.2.0', sha256='623af1099515e673abfd3cae5f2fa808a09ca55dda1c65a7b5c9424eb304ead8') depends_on('libtool', type='build') diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py index 2b654e9e3c6..3f5744d96fa 100644 --- a/var/spack/repos/builtin/packages/unison/package.py +++ b/var/spack/repos/builtin/packages/unison/package.py @@ -17,7 +17,7 @@ class Unison(Package): homepage = "https://www.cis.upenn.edu/~bcpierce/unison/" url = "https://www.seas.upenn.edu/~bcpierce/unison//download/releases/stable/unison-2.48.4.tar.gz" - version('2.48.4', '5334b78c7e68169df7de95f4c6c4b60f') + version('2.48.4', sha256='30aa53cd671d673580104f04be3cf81ac1e20a2e8baaf7274498739d59e99de8') depends_on('ocaml', type='build') diff --git a/var/spack/repos/builtin/packages/units/package.py b/var/spack/repos/builtin/packages/units/package.py index 000f470bebe..354489d54a6 100644 --- a/var/spack/repos/builtin/packages/units/package.py +++ b/var/spack/repos/builtin/packages/units/package.py @@ -12,6 +12,6 @@ class Units(AutotoolsPackage): homepage = "https://www.gnu.org/software/units/" url = "https://ftpmirror.gnu.org/units/units-2.13.tar.gz" - version('2.13', '5cbf2a6af76e94ba0ac55fc8d99d5a3e') + version('2.13', sha256='0ba5403111f8e5ea22be7d51ab74c8ccb576dc30ddfbf18a46cb51f9139790ab') depends_on('python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/unittest-cpp/package.py b/var/spack/repos/builtin/packages/unittest-cpp/package.py index a931ec389ec..b0b68f2f1ef 100644 --- a/var/spack/repos/builtin/packages/unittest-cpp/package.py +++ b/var/spack/repos/builtin/packages/unittest-cpp/package.py @@ -17,5 +17,5 @@ class UnittestCpp(CMakePackage): homepage = "https://github.com/unittest-cpp/unittest-cpp/wiki" url = "https://github.com/unittest-cpp/unittest-cpp/archive/v1.6.0.tar.gz" - version('2.0.0', 'edaccca3e61d977881bdf1e0cf372243') - version('1.6.0', '50f2500f76efd5b9312f19186b66b329') + version('2.0.0', sha256='74852198877dc2fdebdc4e5e9bd074018bf8ee03a13de139bfe41f4585b2f5b9') + version('1.6.0', sha256='9fa7e797816e16669d68171418b0dc41ec6b7eaf8483f782441f5f159598c3c0') diff --git a/var/spack/repos/builtin/packages/unixodbc/package.py b/var/spack/repos/builtin/packages/unixodbc/package.py index 98e4e713c3f..2a9fac6f33f 100644 --- a/var/spack/repos/builtin/packages/unixodbc/package.py +++ b/var/spack/repos/builtin/packages/unixodbc/package.py @@ -14,7 +14,7 @@ class Unixodbc(AutotoolsPackage): homepage = "http://www.unixodbc.org/" url = "http://www.unixodbc.org/unixODBC-2.3.4.tar.gz" - version('2.3.4', 'bd25d261ca1808c947cb687e2034be81') + version('2.3.4', sha256='2e1509a96bb18d248bf08ead0d74804957304ff7c6f8b2e5965309c632421e39') depends_on('libiconv') depends_on('libtool') diff --git a/var/spack/repos/builtin/packages/unuran/package.py b/var/spack/repos/builtin/packages/unuran/package.py index d1c126d7a58..71f4cc99837 100644 --- a/var/spack/repos/builtin/packages/unuran/package.py +++ b/var/spack/repos/builtin/packages/unuran/package.py @@ -12,7 +12,7 @@ class Unuran(AutotoolsPackage): homepage = "http://statmath.wu.ac.at/unuran" url = "http://statmath.wu.ac.at/unuran/unuran-1.8.1.tar.gz" - version('1.8.1', 'a5885baab53a2608c1d85517bf5d06a5') + version('1.8.1', sha256='c270ae96857857dbac6450043df865e0517f52856ddbe5202fd35583b13c5193') variant('shared', default=True, description="Enable the build of shared libraries") diff --git a/var/spack/repos/builtin/packages/unzip/package.py b/var/spack/repos/builtin/packages/unzip/package.py index 6abcd42248d..e565b64defb 100644 --- a/var/spack/repos/builtin/packages/unzip/package.py +++ b/var/spack/repos/builtin/packages/unzip/package.py @@ -12,7 +12,7 @@ class Unzip(MakefilePackage): homepage = 'http://www.info-zip.org/Zip.html' url = 'http://downloads.sourceforge.net/infozip/unzip60.tar.gz' - version('6.0', '62b490407489521db863b523a7f86375') + version('6.0', sha256='036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37') # The Cray cc wrapper doesn't handle the '-s' flag (strip) cleanly. @when('platform=cray') diff --git a/var/spack/repos/builtin/packages/upcxx/package.py b/var/spack/repos/builtin/packages/upcxx/package.py index bf78c3d27b7..8afd7286e2d 100644 --- a/var/spack/repos/builtin/packages/upcxx/package.py +++ b/var/spack/repos/builtin/packages/upcxx/package.py @@ -24,8 +24,8 @@ class Upcxx(Package): homepage = "https://upcxx.lbl.gov" - version('2019.9.0', '7642877e05300e38f6fa0afbc6062788') - version('2019.3.2', '844722cb0e8c0bc649017fce86469457') + version('2019.9.0', sha256='7d67ccbeeefb59de9f403acc719f52127a30801a2c2b9774a1df03f850f8f1d4') + version('2019.3.2', sha256='dcb0b337c05a0feb2ed5386f5da6c60342412b49cab10f282f461e74411018ad') variant('cuda', default=False, description='Builds a CUDA-enabled version of UPC++') diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py index 60319d9364d..e9411517bc6 100644 --- a/var/spack/repos/builtin/packages/util-linux/package.py +++ b/var/spack/repos/builtin/packages/util-linux/package.py @@ -14,9 +14,9 @@ class UtilLinux(AutotoolsPackage): list_url = "https://www.kernel.org/pub/linux/utils/util-linux" list_depth = 1 - version('2.29.2', '24e0c67aac6f5c2535208866a42aeea2') - version('2.29.1', 'c7d5c111ef6bc5df65659e0b523ac9d9') - version('2.25', 'f6d7fc6952ec69c4dc62c8d7c59c1d57') + version('2.29.2', sha256='29ccdf91d2c3245dc705f0ad3bf729ac41d8adcdbeff914e797c552ecb04a4c7') + version('2.29.1', sha256='a6a7adba65a368e6dad9582d9fbedee43126d990df51266eaee089a73c893653') + version('2.25', sha256='7e43273a9e2ab99b5a54ac914fddf5d08ba7ab9b114c550e9f03474672bd23a1') depends_on('python@2.7:') depends_on('pkgconfig') diff --git a/var/spack/repos/builtin/packages/util-macros/package.py b/var/spack/repos/builtin/packages/util-macros/package.py index b10a6ce121b..26de9b3efd4 100644 --- a/var/spack/repos/builtin/packages/util-macros/package.py +++ b/var/spack/repos/builtin/packages/util-macros/package.py @@ -14,8 +14,8 @@ class UtilMacros(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/util/macros/" url = "https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2" - version('1.19.1', '6e76e546a4e580f15cebaf8019ef1625') - version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1') + version('1.19.1', sha256='18d459400558f4ea99527bc9786c033965a3db45bf4c6a32eefdc07aa9e306a6') + version('1.19.0', sha256='2835b11829ee634e19fa56517b4cfc52ef39acea0cd82e15f68096e27cbed0ba') def setup_dependent_environment(self, spack_env, run_env, dependent_spec): """Adds the ACLOCAL path for autotools.""" diff --git a/var/spack/repos/builtin/packages/uuid/package.py b/var/spack/repos/builtin/packages/uuid/package.py index 2a5c8858095..76219943e1d 100644 --- a/var/spack/repos/builtin/packages/uuid/package.py +++ b/var/spack/repos/builtin/packages/uuid/package.py @@ -15,4 +15,4 @@ class Uuid(AutotoolsPackage): homepage = "http://www.ossp.org/pkg/lib/uuid" url = "http://www.mirrorservice.org/sites/ftp.ossp.org/pkg/lib/uuid/uuid-1.6.2.tar.gz" - version('1.6.2', '5db0d43a9022a6ebbbc25337ae28942f') + version('1.6.2', sha256='11a615225baa5f8bb686824423f50e4427acd3f70d394765bdff32801f0fd5b0') diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py index 1ab999c4220..a32760aed70 100644 --- a/var/spack/repos/builtin/packages/valgrind/package.py +++ b/var/spack/repos/builtin/packages/valgrind/package.py @@ -23,12 +23,12 @@ class Valgrind(AutotoolsPackage): version('develop', branch='master') version('3.15.0', sha256='417c7a9da8f60dd05698b3a7bc6002e4ef996f14c13f0ff96679a16873e78ab1') - version('3.14.0', '74175426afa280184b62591b58c671b3') - version('3.13.0', '817dd08f1e8a66336b9ff206400a5369') - version('3.12.0', '6eb03c0c10ea917013a7622e483d61bb') - version('3.11.0', '4ea62074da73ae82e0162d6550d3f129') - version('3.10.1', '60ddae962bc79e7c95cfc4667245707f') - version('3.10.0', '7c311a72a20388aceced1aa5573ce970') + version('3.14.0', sha256='037c11bfefd477cc6e9ebe8f193bb237fe397f7ce791b4a4ce3fa1c6a520baa5') + version('3.13.0', sha256='d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b') + version('3.12.0', sha256='67ca4395b2527247780f36148b084f5743a68ab0c850cb43e4a5b4b012cf76a1') + version('3.11.0', sha256='6c396271a8c1ddd5a6fb9abe714ea1e8a86fce85b30ab26b4266aeb4c2413b42') + version('3.10.1', sha256='fa253dc26ddb661b6269df58144eff607ea3f76a9bcfe574b0c7726e1dfcb997') + version('3.10.0', sha256='03047f82dfc6985a4c7d9d2700e17bc05f5e1a0ca6ad902e5d6c81aeb720edc9') variant('mpi', default=True, description='Activates MPI support for valgrind') diff --git a/var/spack/repos/builtin/packages/vampirtrace/package.py b/var/spack/repos/builtin/packages/vampirtrace/package.py index 4b142f8a514..8f5c23ea7dd 100644 --- a/var/spack/repos/builtin/packages/vampirtrace/package.py +++ b/var/spack/repos/builtin/packages/vampirtrace/package.py @@ -14,7 +14,7 @@ class Vampirtrace(AutotoolsPackage): homepage = "https://tu-dresden.de/zih/forschung/projekte/vampirtrace" url = "http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz" - version('5.14.4', '1c92b23169df9bcc860e5fc737dbc9c9') + version('5.14.4', sha256='1719a1666dd274c221b781631958cae56aa8bcb3f22861fb4ba6526c1b465a30') variant('mpi', default=True, description='Enable MPI support') diff --git a/var/spack/repos/builtin/packages/vardictjava/package.py b/var/spack/repos/builtin/packages/vardictjava/package.py index 785d43df85e..3806174edb0 100644 --- a/var/spack/repos/builtin/packages/vardictjava/package.py +++ b/var/spack/repos/builtin/packages/vardictjava/package.py @@ -14,8 +14,8 @@ class Vardictjava(Package): homepage = "https://github.com/AstraZeneca-NGS/VarDictJava" url = "https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.5.1/VarDict-1.5.1.tar" - version('1.5.1', '8c0387bcc1f7dc696b04e926c48b27e6') - version('1.4.4', '6b2d7e1e5502b875760fc9938a0fe5e0') + version('1.5.1', sha256='f1d710d238e8ab41b02a99fa8698baeee8c8668635a847b826913dd03a9176b9') + version('1.4.4', md5='6b2d7e1e5502b875760fc9938a0fe5e0') depends_on('java@8:', type='run') diff --git a/var/spack/repos/builtin/packages/varscan/package.py b/var/spack/repos/builtin/packages/varscan/package.py index fc9f506422b..9b6dc2e36ca 100644 --- a/var/spack/repos/builtin/packages/varscan/package.py +++ b/var/spack/repos/builtin/packages/varscan/package.py @@ -14,7 +14,7 @@ class Varscan(Package): homepage = "http://dkoboldt.github.io/varscan/" url = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar" - version('2.4.2', '4b810741505a8145a7f8f9f6791bbacf', expand=False) + version('2.4.2', sha256='34ff6462f91fb6ed3f11e867ab4a179efae5dd8214b97fa261fc616f23d4d031', expand=False) depends_on('java', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/vc/package.py b/var/spack/repos/builtin/packages/vc/package.py index 633fc49ffee..78f084b7563 100644 --- a/var/spack/repos/builtin/packages/vc/package.py +++ b/var/spack/repos/builtin/packages/vc/package.py @@ -12,9 +12,9 @@ class Vc(CMakePackage): homepage = "https://github.com/VcDevel/Vc" url = "https://github.com/VcDevel/Vc/archive/1.3.0.tar.gz" - version('1.3.0', '77efc1c16691c7925d4b58f9b30cf03b') - version('1.2.0', 'a5236df286b845d2fee5ef1e4d27549f') - version('1.1.0', 'e354c1e3ea1d674b6f2af9c6fd230d81') + version('1.3.0', sha256='2309a19eea136e1f9d5629305b2686e226093e23fe5b27de3d6e3d6084991c3a') + version('1.2.0', sha256='9cd7b6363bf40a89e8b1d2b39044b44a4ce3f1fd6672ef3fc45004198ba28a2b') + version('1.1.0', sha256='281b4c6152fbda11a4b313a0a0ca18565ee049a86f35f672f1383967fef8f501') variant('build_type', default='RelWithDebInfo', description='The build type to build', diff --git a/var/spack/repos/builtin/packages/vcftools/package.py b/var/spack/repos/builtin/packages/vcftools/package.py index 17a51db0eb3..b32ee81ee1c 100644 --- a/var/spack/repos/builtin/packages/vcftools/package.py +++ b/var/spack/repos/builtin/packages/vcftools/package.py @@ -17,8 +17,8 @@ class Vcftools(AutotoolsPackage): url = "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz" # this is "a pre-release" - # version('0.1.15', '61045197848dea20a0158d2faf02e5be') - version('0.1.14', 'a110662535651caa6cc8c876216a9f77') + # version('0.1.15', md5='61045197848dea20a0158d2faf02e5be') + version('0.1.14', sha256='76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582') depends_on('perl', type=('build', 'run')) depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/vcsh/package.py b/var/spack/repos/builtin/packages/vcsh/package.py index 3d9d53d392f..8ac126db613 100644 --- a/var/spack/repos/builtin/packages/vcsh/package.py +++ b/var/spack/repos/builtin/packages/vcsh/package.py @@ -12,11 +12,11 @@ class Vcsh(Package): homepage = "https://github.com/RichiH/vcsh" url = "https://github.com/RichiH/vcsh/archive/v1.20151229.tar.gz" - version('1.20151229-1', '85c18fb15e5837d417b22980683e69ed') - version('1.20151229', '61edf032807bba98c41c62bb2bd3d497') - version('1.20150502', 'a6c75b5754e04bd74ae701967bb38e19') - version('1.20141026', 'e8f42a9dbb7460f641545bea5ca1cbc4') - version('1.20141025', '93c7fad67ab4300d76d753a32c300831') + version('1.20151229-1', sha256='7682a517eaf88a86ea5e38ad81707800e965375eaff8b5cfd882e210fe2fef71') + version('1.20151229', sha256='ae069506b0490287aefa582ab4e6af1c7ebc4dca743b17d91e0c8d0327d7a3fa') + version('1.20150502', sha256='127c7f35e9b097b722917d42f9652375033b12f14b6702a08621cb16205d253f') + version('1.20141026', sha256='63e65df01f35611b3dfca97317298fc2da6c33bfad6edb778ea44b23857e7c54') + version('1.20141025', sha256='2a9009b19289f60d5919d9e19d2a3f53dbe373dbc84e6d50ec0ee1b5ffb2f282') depends_on('git', type='run') diff --git a/var/spack/repos/builtin/packages/vdt/package.py b/var/spack/repos/builtin/packages/vdt/package.py index 7341ec92d78..d03dc7dba55 100644 --- a/var/spack/repos/builtin/packages/vdt/package.py +++ b/var/spack/repos/builtin/packages/vdt/package.py @@ -13,10 +13,10 @@ class Vdt(CMakePackage): url = "https://github.com/dpiparo/vdt/archive/v0.3.9.tar.gz" version('0.4.3', sha256='705674612ebb5c182b65a8f61f4d173eb7fe7cdeee2235b402541a492e08ace1') - version('0.3.9', '80a2d73a82f7ef8257a8206ca22dd145') - version('0.3.8', '25b07c72510aaa95fffc11e33579061c') - version('0.3.7', 'd2621d4c489894fd1fe8e056d9a0a67c') - version('0.3.6', '6eaff3bbbd5175332ccbd66cd71a741d') + version('0.3.9', sha256='1662d21037a29cae717ee50b73bd177bea79582f4138b7ad11404fc4be4e542e') + version('0.3.8', sha256='e6d8485c3c8923993cb1b1a5bb85068a86746285058bf77faeb177363647be62') + version('0.3.7', sha256='713a7e6d76d98f3b2b56b5216e7d5906e30f17865a5c7c889968e9a0b0664949') + version('0.3.6', sha256='fb8f6386f2cd1eeb03db43f2b5c83a172107949bb5e5e8d4dfa603660a9757b0') @property def build_directory(self): diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py index 1bf0bbbdd23..599c250ee6f 100644 --- a/var/spack/repos/builtin/packages/vecgeom/package.py +++ b/var/spack/repos/builtin/packages/vecgeom/package.py @@ -17,7 +17,7 @@ class Vecgeom(CMakePackage): version('01.00.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v01.00.00') version('00.05.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v00.05.00', preferred=True) - version('0.3.rc', 'c1f5d620f655f3c0610a44e7735203b5') + version('0.3.rc', sha256='a87a9ea4ab126b59ff9c79182bc0911ead3d76dd197194742e2a35ccd341299d') variant('cxxstd', default='17', diff --git a/var/spack/repos/builtin/packages/veclibfort/package.py b/var/spack/repos/builtin/packages/veclibfort/package.py index ad05471daeb..2a114289995 100644 --- a/var/spack/repos/builtin/packages/veclibfort/package.py +++ b/var/spack/repos/builtin/packages/veclibfort/package.py @@ -17,7 +17,7 @@ class Veclibfort(Package): git = "https://github.com/mcg1969/vecLibFort.git" version('develop', branch='master') - version('0.4.2', '83395ffcbe8a2122c3f726a5c3a7cf93') + version('0.4.2', sha256='c61316632bffa1c76e3c7f92b11c9def4b6f41973ecf9e124d68de6ae37fbc85') variant('shared', default=True, description="Build shared libraries as well as static libs.") diff --git a/var/spack/repos/builtin/packages/vegas2/package.py b/var/spack/repos/builtin/packages/vegas2/package.py index e85e12ce25f..b61b63a0db6 100644 --- a/var/spack/repos/builtin/packages/vegas2/package.py +++ b/var/spack/repos/builtin/packages/vegas2/package.py @@ -13,7 +13,7 @@ class Vegas2(Package): homepage = "https://vegas2.qimrberghofer.edu.au/" url = "https://vegas2.qimrberghofer.edu.au/vegas2v2" - version('2', '815d80b86e9e294f99332bb5181e897a', expand=False) + version('2', sha256='dc85834219141a4e9a246391b48185a739223a5e00b1b1c4d2517822388278ba', expand=False) depends_on('perl', type='run') depends_on('r', type='run') diff --git a/var/spack/repos/builtin/packages/veloc/package.py b/var/spack/repos/builtin/packages/veloc/package.py index f36324705ac..29c488fbcb3 100644 --- a/var/spack/repos/builtin/packages/veloc/package.py +++ b/var/spack/repos/builtin/packages/veloc/package.py @@ -17,9 +17,9 @@ class Veloc(CMakePackage): tags = ['ecp'] version('master', branch='master') - version('1.1', '6af8f1706c853f924c6ae2ce934de668', preferred=True) - version('1.0', '98fe2d9abd2a1b53d7a52267dab91fae') - version('1.0rc1', 'c6db0de56b5b865183b1fa719ac74c1d') + version('1.1', sha256='2bbdacf3e0ce4e7c9e360874d8d85b405525bdc7bd992bdb1f1ba49218072160', preferred=True) + version('1.0', sha256='d594b73d6549a61fce8e67b8984a17cebc3e766fc520ed1636ae3683cdde77cb') + version('1.0rc1', sha256='81686ca0994a22475911d38d21c7c74b64ffef4ca872fd01f76d155c5124b0bc') depends_on('boost~atomic~chrono~clanglibcpp~date_time~debug~exception' '~filesystem~graph~icu~iostreams~locale~log~math~mpi' diff --git a/var/spack/repos/builtin/packages/velvet/package.py b/var/spack/repos/builtin/packages/velvet/package.py index 620441a8cea..010be8238a9 100644 --- a/var/spack/repos/builtin/packages/velvet/package.py +++ b/var/spack/repos/builtin/packages/velvet/package.py @@ -13,7 +13,7 @@ class Velvet(MakefilePackage): homepage = "http://www.ebi.ac.uk/~zerbino/velvet/" url = "http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz" - version('1.2.10', '6e28c4b9bedc5f7ab2b947e7266a02f6') + version('1.2.10', sha256='884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/verilator/package.py b/var/spack/repos/builtin/packages/verilator/package.py index 64b19561294..89da6e14091 100644 --- a/var/spack/repos/builtin/packages/verilator/package.py +++ b/var/spack/repos/builtin/packages/verilator/package.py @@ -35,8 +35,8 @@ class Verilator(AutotoolsPackage): homepage = "https://www.veripool.org/projects/verilator" url = "https://www.veripool.org/ftp/verilator-3.920.tgz" - version('3.920', '71de7b9ddb27a72e96ed2a04e5ccf933') - version('3.904', '7d4dc8e61d5e0e564c3016a06f0b9d07') + version('3.920', sha256='2b5c38aa432d0766a38475219f9548d64d18104ce8bdcb5d29e42f5da06943ff') + version('3.904', sha256='ea95e08b2d70682ad42e6c2f5ba99f59b2e7b220791214076099cdf6b7a8c1cb') depends_on('bison', type='build') depends_on('flex') diff --git a/var/spack/repos/builtin/packages/verrou/package.py b/var/spack/repos/builtin/packages/verrou/package.py index 56f3cac6222..79cfd37bc23 100644 --- a/var/spack/repos/builtin/packages/verrou/package.py +++ b/var/spack/repos/builtin/packages/verrou/package.py @@ -25,9 +25,9 @@ class Verrou(AutotoolsPackage): git = "https://github.com/edf-hpc/verrou.git" version('develop', branch='master') - version('2.1.0', 'b1ba49f84aebab15b8ab5649946c9c31b53ad1499f6ffb681c98db41ed28566d') - version('2.0.0', '388d493df3f253c9b049ce0ceae55fd6') - version('1.1.0', '9752d776fb534890e5e29f9721ee6125') + version('2.1.0', sha256='b1ba49f84aebab15b8ab5649946c9c31b53ad1499f6ffb681c98db41ed28566d') + version('2.0.0', sha256='798df6e426ec57646a2a626d756b72f0171647ae5b07c982952dae2d71e26045') + version('1.1.0', sha256='b5105f61c65680f31551199cd143b2e15f412c34c821537998a7165e315dde2d') resource(name='valgrind-3.14.0', url='https://sourceware.org/pub/valgrind/valgrind-3.14.0.tar.bz2', diff --git a/var/spack/repos/builtin/packages/vesta/package.py b/var/spack/repos/builtin/packages/vesta/package.py index e9e0c2c5596..918c44b7fb9 100644 --- a/var/spack/repos/builtin/packages/vesta/package.py +++ b/var/spack/repos/builtin/packages/vesta/package.py @@ -13,7 +13,7 @@ class Vesta(Package): homepage = "http://jp-minerals.org/vesta" url = "https://jp-minerals.org/vesta/archives/3.4.6/VESTA-x86_64.tar.bz2" - version('3.4.6', '1d4651e86193f305831aa5db3dcfe789') + version('3.4.6', sha256='fb00ac9a7bf46a3d9a1d745859c5e8757ba30f017a46470eb2c123b9afcf66ee') depends_on('gtkplus@2.1.0:') depends_on('mesa') diff --git a/var/spack/repos/builtin/packages/videoproto/package.py b/var/spack/repos/builtin/packages/videoproto/package.py index 0e5efff1681..e50f00e27d9 100644 --- a/var/spack/repos/builtin/packages/videoproto/package.py +++ b/var/spack/repos/builtin/packages/videoproto/package.py @@ -15,7 +15,7 @@ class Videoproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/videoproto" url = "https://www.x.org/archive/individual/proto/videoproto-2.3.3.tar.gz" - version('2.3.3', 'd984100603ee2420072f27bb491f4b7d') + version('2.3.3', sha256='df8dfeb158767f843054248d020e291a2c40f7f5e0ac6d8706966686fee7c5c0') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/viennarna/package.py b/var/spack/repos/builtin/packages/viennarna/package.py index d997600dc0b..7809750efd9 100644 --- a/var/spack/repos/builtin/packages/viennarna/package.py +++ b/var/spack/repos/builtin/packages/viennarna/package.py @@ -15,8 +15,8 @@ class Viennarna(AutotoolsPackage): homepage = "https://www.tbi.univie.ac.at/RNA/" url = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.3.tar.gz" - version('2.4.3', '41be2fd36a5323a35ed50debfc7bd118') - version('2.3.5', '4542120adae9b7abb605e2304c2a1326') + version('2.4.3', sha256='4cda6e22029b34bb9f5375181562f69e4a780a89ead50fe952891835e9933ac0') + version('2.3.5', sha256='26b62a00da21bc5597b580ab8fef4e624234ec446d7d3cb0ce22803a5d7074ca') variant('sse', default=True, description='Enable SSE in order to substantially speed up execution') variant('perl', default=True, description='Build ViennaRNA with Perl interface') diff --git a/var/spack/repos/builtin/packages/viewres/package.py b/var/spack/repos/builtin/packages/viewres/package.py index 1d5c65d9b6e..54389960fe8 100644 --- a/var/spack/repos/builtin/packages/viewres/package.py +++ b/var/spack/repos/builtin/packages/viewres/package.py @@ -13,7 +13,7 @@ class Viewres(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/viewres" url = "https://www.x.org/archive/individual/app/viewres-1.0.4.tar.gz" - version('1.0.4', 'a3c7fe561945951f848e319680753760') + version('1.0.4', sha256='fd2aaec85c952fd6984fe14d0fcbda4d2ab9849a9183e4787b0ef552a10a87a1') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py index a4681a0bfba..d59f8372db3 100644 --- a/var/spack/repos/builtin/packages/vim/package.py +++ b/var/spack/repos/builtin/packages/vim/package.py @@ -18,13 +18,13 @@ class Vim(AutotoolsPackage): homepage = "http://www.vim.org" url = "https://github.com/vim/vim/archive/v8.1.0338.tar.gz" - version('8.1.0338', '94191b4141245a5deb4955c4a80359bb') - version('8.1.0001', 'edb6f5c67cb3100ea9e3966a43b9c9da') - version('8.0.1376', '62855881a2d96d48956859d74cfb8a3b') - version('8.0.0503', '82b77bd5cb38b70514bed47cfe033b8c') - version('8.0.0454', '4030bf677bdfbd14efb588e4d9a24128') - version('8.0.0134', 'c74668d25c2acc85d655430dd60886cd') - version('7.4.2367', 'a0a7bc394f7ab1d95571fe6ab05da3ea') + version('8.1.0338', sha256='3febcc4e49eaca458be1a1e8055a3a52887aa2054b03e24d5f38d192c3de51a0') + version('8.1.0001', sha256='c342acaa26589f371fa34a5ca213b95811f26185c12443f8f48ad2868dee2935') + version('8.0.1376', sha256='1ad8b5a0b9b63df5abc3f8050e31e1cb49379ffcfd2662a56daeff8bd3d780b9') + version('8.0.0503', sha256='f2a316a7ae83eccfecf4a700e631094fce9df873358e3d5f112134faa74082ac') + version('8.0.0454', sha256='e1f683c4a0e3fa56fa02769bbca576e4960850b0ca8640514a7b114b88c27b89') + version('8.0.0134', sha256='1b3e3e7d187eed55cbdb0a1dae6b8f3b885005fbae84222420877d7afa3b2310') + version('7.4.2367', sha256='a9ae4031ccd73cc60e771e8bf9b3c8b7f10f63a67efce7f61cd694cd8d7cda5c') feature_sets = ('huge', 'big', 'normal', 'small', 'tiny') for fs in feature_sets: diff --git a/var/spack/repos/builtin/packages/virtualgl/package.py b/var/spack/repos/builtin/packages/virtualgl/package.py index b279c7bcf91..aceae5e7e7c 100644 --- a/var/spack/repos/builtin/packages/virtualgl/package.py +++ b/var/spack/repos/builtin/packages/virtualgl/package.py @@ -16,7 +16,7 @@ class Virtualgl(CMakePackage): homepage = "http://www.virtualgl.org/Main/HomePage" url = "http://downloads.sourceforge.net/project/virtualgl/2.5.2/VirtualGL-2.5.2.tar.gz" - version('2.5.2', '1a9f404f4a35afa9f56381cb33ed210c') + version('2.5.2', sha256='4f43387678b289a24139c5b7c3699740ca555a9f10011c979e51aa4df2b93238') depends_on("jpeg") depends_on("glu") diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py index 4c7e25e6935..e9bea6592f5 100644 --- a/var/spack/repos/builtin/packages/visit/package.py +++ b/var/spack/repos/builtin/packages/visit/package.py @@ -12,14 +12,14 @@ class Visit(CMakePackage): homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/" url = "https://portal.nersc.gov/project/visit/releases/3.0.1/visit3.0.1.tar.gz" - version('3.0.1', 'a506d4d83b8973829e68787d8d721199523ce7ec73e7594e93333c214c2c12bd') - version('2.13.3', 'cf0b3d2e39e1cd102dd886d3ef6da892733445e362fc28f24d9682012cccf2e5') - version('2.13.0', '716644b8e78a00ff82691619d4d1e7a914965b6535884890b667b97ba08d6a0f') - version('2.12.3', '2dd351a291ee3e79926bc00391ca89b202cfa4751331b0fdee1b960c7922161f') - version('2.12.2', '355779b1dbf440cdd548526eecd77b60') - version('2.10.3', 'a1082a6f6dab3e2dcb58993603456c2b') - version('2.10.2', '253de0837a9d69fb689befc98ea4d068') - version('2.10.1', '3cbca162fdb0249f17c4456605c4211e') + version('3.0.1', sha256='a506d4d83b8973829e68787d8d721199523ce7ec73e7594e93333c214c2c12bd') + version('2.13.3', sha256='cf0b3d2e39e1cd102dd886d3ef6da892733445e362fc28f24d9682012cccf2e5') + version('2.13.0', sha256='716644b8e78a00ff82691619d4d1e7a914965b6535884890b667b97ba08d6a0f') + version('2.12.3', sha256='2dd351a291ee3e79926bc00391ca89b202cfa4751331b0fdee1b960c7922161f') + version('2.12.2', sha256='55897d656ac2ea4eb87a30118b2e3963d6c8a391dda0790268426a73e4b06943') + version('2.10.3', sha256='05018215c4727eb42d47bb5cc4ff937b2a2ccaca90d141bc7fa426a0843a5dbc') + version('2.10.2', sha256='89ecdfaf197ef431685e31b75628774deb6cd75d3e332ef26505774403e8beff') + version('2.10.1', sha256='6b53dea89a241fd03300a7a3a50c0f773e2fb8458cd3ad06816e9bd2f0337cd8') variant('gui', default=True, description='Enable VisIt\'s GUI') variant('adios2', default=False, description='Enable ADIOS2 file format') diff --git a/var/spack/repos/builtin/packages/vmatch/package.py b/var/spack/repos/builtin/packages/vmatch/package.py index 987af7f8751..3cedce4ede6 100644 --- a/var/spack/repos/builtin/packages/vmatch/package.py +++ b/var/spack/repos/builtin/packages/vmatch/package.py @@ -13,7 +13,7 @@ class Vmatch(Package): homepage = "http://www.vmatch.de/" url = "http://www.vmatch.de/distributions/vmatch-2.3.0-Linux_x86_64-64bit.tar.gz" - version('2.3.0', '592a4f941239494d892f3c6ff21a1423') + version('2.3.0', sha256='5e18d0dddf04e86dad193fcdde6e48f3901365932634125602d8808f35acf979') def url_for_version(self, version): url = 'http://www.vmatch.de/distributions/vmatch-{0}-Linux_x86_64-64bit.tar.gz' diff --git a/var/spack/repos/builtin/packages/voropp/package.py b/var/spack/repos/builtin/packages/voropp/package.py index 393edee873b..a755e4d7042 100644 --- a/var/spack/repos/builtin/packages/voropp/package.py +++ b/var/spack/repos/builtin/packages/voropp/package.py @@ -17,7 +17,7 @@ class Voropp(MakefilePackage): variant('pic', default=True, description='Position independent code') - version('0.4.6', '2338b824c3b7b25590e18e8df5d68af9') + version('0.4.6', sha256='ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e') def edit(self, spec, prefix): filter_file(r'CC=g\+\+', diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py index 750e1d083fa..bf48ceaf21c 100644 --- a/var/spack/repos/builtin/packages/votca-csg/package.py +++ b/var/spack/repos/builtin/packages/votca-csg/package.py @@ -21,8 +21,8 @@ class VotcaCsg(CMakePackage): version('develop', branch='master') version('1.5', sha256='160387cdc51f87dd20ff2e2eed97086beee415d48f3c92f4199f6109068c8ff4') - version('1.4.1', 'e4195d69db2036e9d76f22115ae31f81') - version('1.4', 'd009e761e5e3afd51eed89c420610a67') + version('1.4.1', sha256='41dccaecadd0165c011bec36a113629e27745a5a133d1a042efe4356acdb5450') + version('1.4', sha256='c13e7febd792de8c3d426203f089bd4d33b8067f9db5e8840e4579c88b61146e') depends_on("cmake@2.8:", type='build') for v in ["1.4", "1.4.1", "1.5", "develop"]: diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py index 04e6cff8533..84f90ea9f02 100644 --- a/var/spack/repos/builtin/packages/votca-tools/package.py +++ b/var/spack/repos/builtin/packages/votca-tools/package.py @@ -21,8 +21,8 @@ class VotcaTools(CMakePackage): version('develop', branch='master') version('1.5', sha256='a82a6596c24ff06e79eab17ca02f4405745ceeeb66369693a59023ad0b62cf22') - version('1.4.1', '3176b72f8a41ec053cc740a5398e7dc4') - version('1.4', 'cd47868e9f28e2c7b9d01f95aa0185ca') + version('1.4.1', sha256='b6b87f6bec8db641a1d8660422ca44919252a69494b32ba6c8c9ac986bae9a65') + version('1.4', sha256='41638122e7e59852af61d391b4ab8c308fd2e16652f768077e13a99d206ec5d3') depends_on("cmake@2.8:", type='build') depends_on("expat") diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py index a3a8e84cb22..dd4b4233e0b 100644 --- a/var/spack/repos/builtin/packages/votca-xtp/package.py +++ b/var/spack/repos/builtin/packages/votca-xtp/package.py @@ -21,7 +21,7 @@ class VotcaXtp(CMakePackage): version('develop', branch='master') version('1.5', sha256='b40b6d19e13f0650e84b8beebe86ce5c09071624f18d66df826f9d8584b4d3c8') - version('1.4.1', '31a2dbd8bd48bf337bc88b20ab312050') + version('1.4.1', sha256='4b53d371d6cf648c9e9e9bd1f104d349cafeaf10a02866e3f1d05c574b595a21') depends_on("cmake@2.8:", type='build') for v in ["1.4.1", "1.5", "develop"]: diff --git a/var/spack/repos/builtin/packages/vsearch/package.py b/var/spack/repos/builtin/packages/vsearch/package.py index 8a0f4039609..4598dc4ee48 100644 --- a/var/spack/repos/builtin/packages/vsearch/package.py +++ b/var/spack/repos/builtin/packages/vsearch/package.py @@ -12,7 +12,7 @@ class Vsearch(AutotoolsPackage): homepage = "https://github.com/torognes/vsearch" url = "https://github.com/torognes/vsearch/archive/v2.4.3.tar.gz" - version('2.4.3', '8f57210fe447a781078fde06e6402650') + version('2.4.3', sha256='f7ffc2aec5d76bdaf1ffe7fb733102138214cec3e3846eb225455dcc3c088141') depends_on('m4', type='build') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/vt/package.py b/var/spack/repos/builtin/packages/vt/package.py index 1687b6d7cc0..99d36b987b3 100644 --- a/var/spack/repos/builtin/packages/vt/package.py +++ b/var/spack/repos/builtin/packages/vt/package.py @@ -12,7 +12,7 @@ class Vt(MakefilePackage): homepage = "http://genome.sph.umich.edu/wiki/vt" url = "https://github.com/atks/vt/archive/0.577.tar.gz" - version('0.577', '59807456022bcecf978314c93254fe15') + version('0.577', sha256='009e2592e787ab37e471b4e8a66520141bb2791ca78142ca1767d27036f460d0') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 1be771e9f44..3d9d108ae44 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -23,11 +23,11 @@ class Vtk(CMakePackage): version('8.1.2', sha256='0995fb36857dd76ccfb8bb07350c214d9f9099e80b1e66b4a8909311f24ff0db') version('8.1.1', sha256='71a09b4340f0a9c58559fe946dc745ab68a866cf20636a41d97b6046cb736324') version('8.1.0', sha256='6e269f07b64fb13774f5925161fb4e1f379f4e6a0131c8408c555f6b58ef3cb7') - version('8.0.1', '692d09ae8fadc97b59d35cab429b261a') - version('7.1.0', 'a7e814c1db503d896af72458c2d0228f') - version('7.0.0', '5fe35312db5fb2341139b8e4955c367d') - version('6.3.0', '0231ca4840408e9dd60af48b314c5b6d') - version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') + version('8.0.1', sha256='49107352923dea6de05a7b4c3906aaf98ef39c91ad81c383136e768dcf304069') + version('7.1.0', sha256='5f3ea001204d4f714be972a810a62c0f2277fbb9d8d2f8df39562988ca37497a') + version('7.0.0', sha256='78a990a15ead79cdc752e86b83cfab7dbf5b7ef51ba409db02570dbdd9ec32c3') + version('6.3.0', sha256='92a493354c5fa66bea73b5fc014154af5d9f3f6cee8d20a826f4cd5d4b0e8a5e') + version('6.1.0', sha256='bd7df10a479606d529a8b71f466c44a2bdd11fd534c62ce0aa44fad91883fa34') # VTK7 defaults to OpenGL2 rendering backend variant('opengl2', default=True, description='Enable OpenGL2 backend') diff --git a/var/spack/repos/builtin/packages/vtkm/package.py b/var/spack/repos/builtin/packages/vtkm/package.py index 19f0c74afe4..eee37bf9af1 100644 --- a/var/spack/repos/builtin/packages/vtkm/package.py +++ b/var/spack/repos/builtin/packages/vtkm/package.py @@ -22,10 +22,10 @@ class Vtkm(CMakePackage, CudaPackage): git = "https://gitlab.kitware.com/vtk/vtk-m.git" version('master', branch='master') - version('1.4.0', "b0d76bbf5a69c18ec6f1fca4f7858047b65330bd") - version('1.3.0', "d9f6e274dec2ea01273cccaba356d23ca88c5a25") - version('1.2.0', "3295fed86012226c107e1f2605ca7cc583586b63") - version('1.1.0', "6aab1c0885f6ffaaffcf07930873d0df") + version('1.4.0', sha256="60e1ce73a8c6beda8aed5f2d3ae670b6b0c78c068c6eff4ece769e6d719d5065") + version('1.3.0', sha256="72c2c8525a77a456fe0b6a1af0328dad6b9a688f402a3d3ebfa8942e0b5dba1a") + version('1.2.0', sha256="9103d954284661f6f03e5b18be6d7bc94254603e6abc8fce67f617f4ad325a0e") + version('1.1.0', sha256="a1746b1547d6fb901ea7d7ed50834e8832d6d41ddd497c84d02e1481100d43bc") # use release, instead of release with debug symbols b/c vtkm libs # can overwhelm compilers with too many symbols diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py index 0db3762a6f7..a8e47c96a84 100644 --- a/var/spack/repos/builtin/packages/wannier90/package.py +++ b/var/spack/repos/builtin/packages/wannier90/package.py @@ -17,8 +17,8 @@ class Wannier90(MakefilePackage): homepage = 'http://wannier.org' url = 'http://wannier.org/code/wannier90-2.0.1.tar.gz' - version('2.1.0', '07a81c002b41d6d0f97857e55c57d769') - version('2.0.1', '4edd742506eaba93317249d33261fb22') + version('2.1.0', sha256='ee90108d4bc4aa6a1cf16d72abebcb3087cf6c1007d22dda269eb7e7076bddca') + version('2.0.1', sha256='05ea7cd421a219ce19d379ad6ae3d9b1a84be4ffb367506ffdfab1e729309e94') depends_on('mpi') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/wcslib/package.py b/var/spack/repos/builtin/packages/wcslib/package.py index 60fc76672a2..834ab583955 100644 --- a/var/spack/repos/builtin/packages/wcslib/package.py +++ b/var/spack/repos/builtin/packages/wcslib/package.py @@ -14,7 +14,7 @@ class Wcslib(AutotoolsPackage): url = "ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib-6.4.tar.bz2" version('6.4', sha256='13c11ff70a7725563ec5fa52707a9965fce186a1766db193d08c9766ea107000') - version('5.18', '67a78354be74eca4f17d3e0853d5685f') + version('5.18', md5='67a78354be74eca4f17d3e0853d5685f') variant('cfitsio', default=False, description='Include CFITSIO support') variant('x', default=False, description='Use the X Window System') diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py index bc27526ac46..1eaf254bbef 100644 --- a/var/spack/repos/builtin/packages/wget/package.py +++ b/var/spack/repos/builtin/packages/wget/package.py @@ -16,9 +16,9 @@ class Wget(AutotoolsPackage): url = "https://ftpmirror.gnu.org/wget/wget-1.19.1.tar.gz" version('1.20.3', sha256='31cccfc6630528db1c8e3a06f6decf2a370060b982841cfab2b8677400a5092e') - version('1.19.1', '87cea36b7161fd43e3fd51a4e8b89689') - version('1.17', 'c4c4727766f24ac716936275014a0536') - version('1.16', '293a37977c41b5522f781d3a3a078426') + version('1.19.1', sha256='9e4f12da38cc6167d0752d934abe27c7b1599a9af294e73829be7ac7b5b4da40') + version('1.17', sha256='3e04ad027c5b6ebd67c616eec13e66fbedb3d4d8cbe19cc29dadde44b92bda55') + version('1.16', sha256='b977fc10ac7a72d987d48136251aeb332f2dced1aabd50d6d56bdf72e2b79101') variant('ssl', default='openssl', values=('gnutls', 'openssl'), description='Specify SSL backend') diff --git a/var/spack/repos/builtin/packages/windowswmproto/package.py b/var/spack/repos/builtin/packages/windowswmproto/package.py index 571950f42e3..9213d245578 100644 --- a/var/spack/repos/builtin/packages/windowswmproto/package.py +++ b/var/spack/repos/builtin/packages/windowswmproto/package.py @@ -17,4 +17,4 @@ class Windowswmproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/windowswmproto" url = "https://www.x.org/archive/individual/proto/windowswmproto-1.0.4.tar.gz" - version('1.0.4', '558db92a8e4e1b07e9c62eca3f04dd8d') + version('1.0.4', sha256='2dccf510cf18a1b5cfd3a277c678d88303efc85478b479fec46228a861956eb7') diff --git a/var/spack/repos/builtin/packages/wireshark/package.py b/var/spack/repos/builtin/packages/wireshark/package.py index 8cecae2a86a..5df47d773b0 100644 --- a/var/spack/repos/builtin/packages/wireshark/package.py +++ b/var/spack/repos/builtin/packages/wireshark/package.py @@ -13,7 +13,7 @@ class Wireshark(CMakePackage): homepage = "https://www.wireshark.org" url = "https://www.wireshark.org/download/src/all-versions/wireshark-2.6.0.tar.xz" - version('2.6.0', 'd9f9e206977da14427bfd66b582601ae') + version('2.6.0', sha256='711c7f01d27a8817d58277a5487cef3e3c7bab1c8caaf8f4c92aa21015b9117f') variant('smi', default=False, description='Build with libsmi') variant('libssh', default=False, description='Build with libssh') diff --git a/var/spack/repos/builtin/packages/workrave/package.py b/var/spack/repos/builtin/packages/workrave/package.py index 6aacff16666..fa5a597484a 100644 --- a/var/spack/repos/builtin/packages/workrave/package.py +++ b/var/spack/repos/builtin/packages/workrave/package.py @@ -16,16 +16,16 @@ class Workrave(AutotoolsPackage): homepage = "http://www.workrave.org/" url = "https://github.com/rcaelers/workrave/archive/v1_10_20.tar.gz" - version('1_10_20', '095567c10311bd2c1a52f98035cc8590') - version('1_10_19', 'a87ed53d5b321133e8b6b98fd715507b') - version('1_10_18', 'd36c2aba0485116b831d5b36a862f343') - version('1_10_17', 'ba829bb2c0ec999b3194b4d845549c39') - version('1_10_16', 'b9bf77bfe0c909fff56759e7dda40f9d') - version('1_10_15', '4a70c2e325503249d1a40fcc236d6802') - version('1_10_14', '67108d993719d9438a1b69f0cb8fc9b8') - version('1_10_13', 'd5e7110dfb0b0a31c909405913ac2a75') - version('1_10_12', '0bfbaa1dc35901ffa8f1a3676421a992') - version('1_10_10', 'cf827672c8a1ece074f8ddfcf73d0fe2') + version('1_10_20', sha256='a89c6e82d5bbbaae5e171100b87c4efd8316ab8a18d82b83714035e1116983ec') + version('1_10_19', sha256='3a24d87e22fc9f463b6a9319843751038cbf6acfab9cd67893221a0071cf5405') + version('1_10_18', sha256='f0de5abd2c3a29106b915f1c051808f6083e1052b46c5143ff96e2334757e91b') + version('1_10_17', sha256='d911fd4738b6b4737cc2fc54c1683eb5d290f2764398c432fcc3b61bb326e71a') + version('1_10_16', sha256='4368306db0d06e76a3a90fc8e81b3648c1218259833b01cdc6899b1e98e5895c') + version('1_10_15', sha256='fa05bedbb32baae9d22ef2b1ac25e90bc9f1363ce588b396190b0240559f471c') + version('1_10_14', sha256='de342be4ff131645ff29fe003b476816965a65a44f4ddc85109960502d9e7310') + version('1_10_13', sha256='cbb5dab1073d2715e5b9cb8ccf8b3362ab6fa8ab05aa44629ecc78d6b93769e3') + version('1_10_12', sha256='eb7a4b7ba137e6997d7b44ed38b705daf391e9c646a5a068c9b002830f35be47') + version('1_10_10', sha256='84f9dca7634e291631017053a63ac20cd23c4da8c8f09ca4beef6f1419d904e3') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/wt/package.py b/var/spack/repos/builtin/packages/wt/package.py index a5d05c0a329..506e4450713 100644 --- a/var/spack/repos/builtin/packages/wt/package.py +++ b/var/spack/repos/builtin/packages/wt/package.py @@ -16,7 +16,7 @@ class Wt(CMakePackage): git = "https://github.com/emweb/wt.git" version('master', branch='master') - version('3.3.7', '09858901f2dcf5c3d36a9237daba3e3f') + version('3.3.7', sha256='054af8d62a7c158df62adc174a6a57610868470a07e7192ee7ce60a18552851d') # wt builds in parallel, but requires more than 5 GByte RAM per -j # which most machines do not provide and crash the build diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py index ed79bc50ba1..8e2d0206e45 100644 --- a/var/spack/repos/builtin/packages/wxpropgrid/package.py +++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py @@ -14,7 +14,7 @@ class Wxpropgrid(Package): homepage = "http://wxpropgrid.sourceforge.net/" url = "http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz" - version('1.4.15', 'f44b5cd6fd60718bacfabbf7994f1e93') + version('1.4.15', sha256='f0c9a86656828f592c8e57d2c89401f07f0af6a45b17bbca3990e8d29121c2b8') depends_on("wxwidgets") diff --git a/var/spack/repos/builtin/packages/wxwidgets/package.py b/var/spack/repos/builtin/packages/wxwidgets/package.py index 39e235f1f3a..c1735f6774c 100644 --- a/var/spack/repos/builtin/packages/wxwidgets/package.py +++ b/var/spack/repos/builtin/packages/wxwidgets/package.py @@ -22,9 +22,9 @@ class Wxwidgets(AutotoolsPackage): git = "https://github.com/wxWidgets/wxWidgets.git" version('develop', branch='master') - version('3.1.0', '2170839cfa9d9322e8ee8368b21a15a2497b4f11') - version('3.0.2', '6461eab4428c0a8b9e41781b8787510484dea800') - version('3.0.1', '73e58521d6871c9f4d1e7974c6e3a81629fddcf8') + version('3.1.0', sha256='e082460fb6bf14b7dd6e8ac142598d1d3d0b08a7b5ba402fdbf8711da7e66da8') + version('3.0.2', sha256='346879dc554f3ab8d6da2704f651ecb504a22e9d31c17ef5449b129ed711585d') + version('3.0.1', sha256='bd671b79ec56af8fb3844e11cafceac1a4276fb02c79404d06b91b6c19d2c5f5') patch('math_include.patch', when='@3.0.1:3.0.2') diff --git a/var/spack/repos/builtin/packages/x11perf/package.py b/var/spack/repos/builtin/packages/x11perf/package.py index 38aae1d31e1..c01f894f530 100644 --- a/var/spack/repos/builtin/packages/x11perf/package.py +++ b/var/spack/repos/builtin/packages/x11perf/package.py @@ -12,7 +12,7 @@ class X11perf(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/x11perf" url = "https://www.x.org/archive/individual/app/x11perf-1.6.0.tar.gz" - version('1.6.0', '8dcdb74db8c70dca4b4eab11dc33dd31') + version('1.6.0', sha256='d33051c4e93100ab60609aee14ff889bb2460f28945063d793e21eda19381abb') depends_on('libx11') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xapian-core/package.py b/var/spack/repos/builtin/packages/xapian-core/package.py index 5590f496834..1ad6471fce3 100644 --- a/var/spack/repos/builtin/packages/xapian-core/package.py +++ b/var/spack/repos/builtin/packages/xapian-core/package.py @@ -15,6 +15,6 @@ class XapianCore(AutotoolsPackage): homepage = "https://xapian.org" url = "http://oligarchy.co.uk/xapian/1.4.3/xapian-core-1.4.3.tar.xz" - version('1.4.3', '143f72693219f7fc5913815ed858f295') + version('1.4.3', sha256='7d5295511ca2de70463a29e75f6a2393df5dc1485bf33074b778c66e1721e475') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/xauth/package.py b/var/spack/repos/builtin/packages/xauth/package.py index 89156f80a2a..d178fbd9f63 100644 --- a/var/spack/repos/builtin/packages/xauth/package.py +++ b/var/spack/repos/builtin/packages/xauth/package.py @@ -13,7 +13,7 @@ class Xauth(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xauth" url = "https://www.x.org/archive/individual/app/xauth-1.0.9.tar.gz" - version('1.0.9', 'def3b4588504ee3d8ec7be607826df02') + version('1.0.9', sha256='0709070caf23ba2fb99536907b75be1fe31853999c62d3e87a6a8d26ba8a8cdb') depends_on('libx11') depends_on('libxau') diff --git a/var/spack/repos/builtin/packages/xbacklight/package.py b/var/spack/repos/builtin/packages/xbacklight/package.py index 7d0a28c08a2..0fbfe555536 100644 --- a/var/spack/repos/builtin/packages/xbacklight/package.py +++ b/var/spack/repos/builtin/packages/xbacklight/package.py @@ -15,7 +15,7 @@ class Xbacklight(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xbacklight" url = "https://www.x.org/archive/individual/app/xbacklight-1.2.1.tar.gz" - version('1.2.1', 'e8e4c86b0f867e23aa3532618a697609') + version('1.2.1', sha256='82c80cd851e3eb6d7a216d92465fcf6d5e456c2d5ac12c63cd2757b39fb65b10') depends_on('libxcb') depends_on('xcb-util') diff --git a/var/spack/repos/builtin/packages/xbiff/package.py b/var/spack/repos/builtin/packages/xbiff/package.py index 9891e964503..1f625dad7c0 100644 --- a/var/spack/repos/builtin/packages/xbiff/package.py +++ b/var/spack/repos/builtin/packages/xbiff/package.py @@ -14,7 +14,7 @@ class Xbiff(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xbiff" url = "https://www.x.org/archive/individual/app/xbiff-1.0.3.tar.gz" - version('1.0.3', '779c888cb45da82a612e7f47971df9ab') + version('1.0.3', sha256='b4b702348674985741685e3ec7fcb5640ffb7bf20e753fc2d708f70f2e4c304d') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xbitmaps/package.py b/var/spack/repos/builtin/packages/xbitmaps/package.py index e40cacbf6ff..c0505646e2a 100644 --- a/var/spack/repos/builtin/packages/xbitmaps/package.py +++ b/var/spack/repos/builtin/packages/xbitmaps/package.py @@ -13,7 +13,7 @@ class Xbitmaps(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/data/bitmaps/" url = "https://www.x.org/archive/individual/data/xbitmaps-1.1.1.tar.gz" - version('1.1.1', '288bbe310db67280a9e2e5ebc5602595') + version('1.1.1', sha256='3bc89e05be4179ce4d3dbba1ae554da4591d41f7a489d9e2735a18cfd8378188') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xbraid/package.py b/var/spack/repos/builtin/packages/xbraid/package.py index 22cf22e4010..29ccda623aa 100644 --- a/var/spack/repos/builtin/packages/xbraid/package.py +++ b/var/spack/repos/builtin/packages/xbraid/package.py @@ -14,7 +14,7 @@ class Xbraid(MakefilePackage): homepage = "https://computing.llnl.gov/projects/parallel-time-integration-multigrid/software" url = "https://computing.llnl.gov/projects/parallel-time-integration-multigrid/download/braid_2.2.0.tar.gz" - version('2.2.0', '0a9c2fc3eb8f605f73cce78ab0d8a7d9') + version('2.2.0', sha256='082623b2ddcd2150b3ace65b96c1e00be637876ec6c94dc8fefda88743b35ba3') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/xcalc/package.py b/var/spack/repos/builtin/packages/xcalc/package.py index 618d9644aa2..4aadefe775f 100644 --- a/var/spack/repos/builtin/packages/xcalc/package.py +++ b/var/spack/repos/builtin/packages/xcalc/package.py @@ -13,7 +13,7 @@ class Xcalc(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xcalc" url = "https://www.x.org/archive/individual/app/xcalc-1.0.6.tar.gz" - version('1.0.6', 'a192ebb5e5f33925c71713501173d8e0') + version('1.0.6', sha256='7fd5cd9a35160925c41cbadfb1ea23599fa20fd26cd873dab20a650b24efe8d1') depends_on('libxaw') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xcb-demo/package.py b/var/spack/repos/builtin/packages/xcb-demo/package.py index 0554b4e8498..a4d43257e8c 100644 --- a/var/spack/repos/builtin/packages/xcb-demo/package.py +++ b/var/spack/repos/builtin/packages/xcb-demo/package.py @@ -12,7 +12,7 @@ class XcbDemo(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-demo-0.1.tar.gz" - version('0.1', '803c5c91d54e734e6f6fa3f04f2463ff') + version('0.1', sha256='19ace2812a05313747356dc5e2331a9a6f5eb46631a26819cf30eeeaa38077f9') depends_on('libxcb') depends_on('xcb-util') diff --git a/var/spack/repos/builtin/packages/xcb-proto/package.py b/var/spack/repos/builtin/packages/xcb-proto/package.py index 9d100a9e4ec..a9175a950a6 100644 --- a/var/spack/repos/builtin/packages/xcb-proto/package.py +++ b/var/spack/repos/builtin/packages/xcb-proto/package.py @@ -13,9 +13,9 @@ class XcbProto(AutotoolsPackage): homepage = "http://xcb.freedesktop.org/" url = "http://xcb.freedesktop.org/dist/xcb-proto-1.13.tar.gz" - version('1.13', '0cc0294eb97e4af3a743e470e6a9d910') - version('1.12', '5ee1ec124ea8d56bd9e83b8e9e0b84c4') - version('1.11', 'c8c6cb72c84f58270f4db1f39607f66a') + version('1.13', sha256='0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7') + version('1.12', sha256='cfa49e65dd390233d560ce4476575e4b76e505a0e0bacdfb5ba6f8d0af53fd59') + version('1.11', sha256='d12152193bd71aabbdbb97b029717ae6d5d0477ab239614e3d6193cc0385d906') # TODO: uncomment once build deps can be resolved separately # See #7646, #4145, #4063, and #2548 for details diff --git a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py index 4c9dd17597b..041935cadfd 100644 --- a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py @@ -17,7 +17,7 @@ class XcbUtilCursor(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-util-cursor-0.1.3.tar.gz" - version('0.1.3', '4b0768fa497127131a47f07e5c8cf745') + version('0.1.3', sha256='a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8') depends_on('libxcb@1.4:') depends_on('xcb-util-renderutil') diff --git a/var/spack/repos/builtin/packages/xcb-util-errors/package.py b/var/spack/repos/builtin/packages/xcb-util-errors/package.py index 6bd23eae936..5db6d332f30 100644 --- a/var/spack/repos/builtin/packages/xcb-util-errors/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-errors/package.py @@ -17,7 +17,7 @@ class XcbUtilErrors(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-util-errors-1.0.tar.gz" - version('1.0', 'dc4a6ce073a81a0b7e614a2988f275cc') + version('1.0', sha256='7752a722e580efdbada30632cb23aed35c18757399ac3b547b59fd7257cf5e33') depends_on('libxcb@1.4:') diff --git a/var/spack/repos/builtin/packages/xcb-util-image/package.py b/var/spack/repos/builtin/packages/xcb-util-image/package.py index 4fd8c046488..5960cd1ae8e 100644 --- a/var/spack/repos/builtin/packages/xcb-util-image/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-image/package.py @@ -17,7 +17,7 @@ class XcbUtilImage(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-util-image-0.4.0.tar.gz" - version('0.4.0', '32c9c2f72ebd58a2b2e210f27fee86f7') + version('0.4.0', sha256='cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42') depends_on('libxcb@1.4:') depends_on('xcb-util') diff --git a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py index c02e2fb8404..436b3ee2f55 100644 --- a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py @@ -17,7 +17,7 @@ class XcbUtilKeysyms(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-util-keysyms-0.4.0.tar.gz" - version('0.4.0', '2decde7b02b4b3bde99a02c17b64d5dc') + version('0.4.0', sha256='0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96') depends_on('libxcb@1.4:') diff --git a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py index ed7bcfef301..28b11d1443c 100644 --- a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py @@ -17,7 +17,7 @@ class XcbUtilRenderutil(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-util-renderutil-0.3.9.tar.gz" - version('0.3.9', 'ac18c1b70ae69845e112f1d987926436') + version('0.3.9', sha256='55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5') depends_on('libxcb@1.4:') diff --git a/var/spack/repos/builtin/packages/xcb-util-wm/package.py b/var/spack/repos/builtin/packages/xcb-util-wm/package.py index ee3f30c3aa2..5decbfbdbd7 100644 --- a/var/spack/repos/builtin/packages/xcb-util-wm/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-wm/package.py @@ -17,7 +17,7 @@ class XcbUtilWm(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-util-wm-0.4.1.tar.gz" - version('0.4.1', '0831399918359bf82930124fa9fd6a9b') + version('0.4.1', sha256='038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334') depends_on('m4', type='build') diff --git a/var/spack/repos/builtin/packages/xcb-util/package.py b/var/spack/repos/builtin/packages/xcb-util/package.py index f89440fff8f..a2549d174b6 100644 --- a/var/spack/repos/builtin/packages/xcb-util/package.py +++ b/var/spack/repos/builtin/packages/xcb-util/package.py @@ -17,7 +17,7 @@ class XcbUtil(AutotoolsPackage): homepage = "https://xcb.freedesktop.org/" url = "https://xcb.freedesktop.org/dist/xcb-util-0.4.0.tar.gz" - version('0.4.0', '157d82738aa89934b6adaf3ca508a0f5') + version('0.4.0', sha256='0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7') depends_on('libxcb@1.4:') diff --git a/var/spack/repos/builtin/packages/xclipboard/package.py b/var/spack/repos/builtin/packages/xclipboard/package.py index 8c08900e72a..7400fac97a4 100644 --- a/var/spack/repos/builtin/packages/xclipboard/package.py +++ b/var/spack/repos/builtin/packages/xclipboard/package.py @@ -15,7 +15,7 @@ class Xclipboard(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xclipboard" url = "https://www.x.org/archive/individual/app/xclipboard-1.1.3.tar.gz" - version('1.1.3', 'cee91df9df1b5d63034681546fd78c0b') + version('1.1.3', sha256='a8c335cf166cbb27ff86569503db7e639f85741ad199bfb3ba45dd0cfda3da7f') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xclock/package.py b/var/spack/repos/builtin/packages/xclock/package.py index 4d4c610d743..582b3eba849 100644 --- a/var/spack/repos/builtin/packages/xclock/package.py +++ b/var/spack/repos/builtin/packages/xclock/package.py @@ -14,7 +14,7 @@ class Xclock(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xclock" url = "https://www.x.org/archive/individual/app/xclock-1.0.7.tar.gz" - version('1.0.7', 'bbade10e6234d8db276212014e8c77fa') + version('1.0.7', sha256='e730bd575938d5628ef47003a9d4d41b882621798227f5d0c12f4a26365ed1b5') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xcmiscproto/package.py b/var/spack/repos/builtin/packages/xcmiscproto/package.py index 6b090ad188d..37e9501d2e6 100644 --- a/var/spack/repos/builtin/packages/xcmiscproto/package.py +++ b/var/spack/repos/builtin/packages/xcmiscproto/package.py @@ -15,7 +15,7 @@ class Xcmiscproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/xcmiscproto" url = "https://www.x.org/archive/individual/proto/xcmiscproto-1.2.2.tar.gz" - version('1.2.2', 'ded6cd23fb2800df93ebf2b3f3b01119') + version('1.2.2', sha256='48013cfbe4bd5580925a854a43e2bccbb4c7a5a31128070644617b6dc7f8ef85') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xcmsdb/package.py b/var/spack/repos/builtin/packages/xcmsdb/package.py index 5b43636f147..a86e15b7587 100644 --- a/var/spack/repos/builtin/packages/xcmsdb/package.py +++ b/var/spack/repos/builtin/packages/xcmsdb/package.py @@ -15,7 +15,7 @@ class Xcmsdb(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xcmsdb" url = "https://www.x.org/archive/individual/app/xcmsdb-1.0.5.tar.gz" - version('1.0.5', 'e7b1699c831b44d7005bff45977ed56a') + version('1.0.5', sha256='8442352ee5eb3ea0d3a489c26d734e784ef6964150c2a173401d0dc6638ca236') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xcompmgr/package.py b/var/spack/repos/builtin/packages/xcompmgr/package.py index 3e1fcd4276f..aaf8dd39be7 100644 --- a/var/spack/repos/builtin/packages/xcompmgr/package.py +++ b/var/spack/repos/builtin/packages/xcompmgr/package.py @@ -14,7 +14,7 @@ class Xcompmgr(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xcompmgr" url = "https://www.x.org/archive/individual/app/xcompmgr-1.1.7.tar.gz" - version('1.1.7', '4992895c8934bbc99bb2447dfe5081f2') + version('1.1.7', sha256='ef4b23c370f99403bbd9b6227f8aa4edc3bc83fc6d57ee71f6f442397cef505a') depends_on('libxcomposite') depends_on('libxfixes') diff --git a/var/spack/repos/builtin/packages/xconsole/package.py b/var/spack/repos/builtin/packages/xconsole/package.py index 428c448503d..aa8ba6d5520 100644 --- a/var/spack/repos/builtin/packages/xconsole/package.py +++ b/var/spack/repos/builtin/packages/xconsole/package.py @@ -13,7 +13,7 @@ class Xconsole(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xconsole" url = "https://www.x.org/archive/individual/app/xconsole-1.0.6.tar.gz" - version('1.0.6', '46cb988e31a0cf9a02c2bbc4a82bd572') + version('1.0.6', sha256='28151453a0a687462516de133bac0287b488a2ff56da78331fee34bc1bf3e7d5') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xcursor-themes/package.py b/var/spack/repos/builtin/packages/xcursor-themes/package.py index 7b0df1ec7d2..98c19d7c776 100644 --- a/var/spack/repos/builtin/packages/xcursor-themes/package.py +++ b/var/spack/repos/builtin/packages/xcursor-themes/package.py @@ -14,7 +14,7 @@ class XcursorThemes(Package): homepage = "http://cgit.freedesktop.org/xorg/data/cursors" url = "https://www.x.org/archive/individual/data/xcursor-themes-1.0.4.tar.gz" - version('1.0.4', 'c82628f35e9950ba225050ad5803b92a') + version('1.0.4', sha256='8ed23bab13a4010fe4e95b37eefb634e31ac7cb8240b8b3b7d919c3a2db09503') depends_on('libxcursor') diff --git a/var/spack/repos/builtin/packages/xcursorgen/package.py b/var/spack/repos/builtin/packages/xcursorgen/package.py index 5722dc549c6..7344a4b0e3a 100644 --- a/var/spack/repos/builtin/packages/xcursorgen/package.py +++ b/var/spack/repos/builtin/packages/xcursorgen/package.py @@ -12,7 +12,7 @@ class Xcursorgen(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xcursorgen" url = "https://www.x.org/archive/individual/app/xcursorgen-1.0.6.tar.gz" - version('1.0.6', '669df84fc30d89c12ce64b95aba26677') + version('1.0.6', sha256='4559f2b6eaa93de4cb6968679cf40e39bcbe969b62ebf3ff84f6780f8048ef8c') depends_on('libx11') depends_on('libxcursor') diff --git a/var/spack/repos/builtin/packages/xdbedizzy/package.py b/var/spack/repos/builtin/packages/xdbedizzy/package.py index 4f727e36bf9..e19ed501691 100644 --- a/var/spack/repos/builtin/packages/xdbedizzy/package.py +++ b/var/spack/repos/builtin/packages/xdbedizzy/package.py @@ -13,7 +13,7 @@ class Xdbedizzy(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xdbedizzy" url = "https://www.x.org/archive/individual/app/xdbedizzy-1.1.0.tar.gz" - version('1.1.0', '969be2f6bc62455431ab027f99720dc3') + version('1.1.0', sha256='810e88b087b76f8b5993db4fc5165de3e5d29b0d4bf0e893750ee408fc7a5c0a') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/xditview/package.py b/var/spack/repos/builtin/packages/xditview/package.py index 2f4113aa692..d51ef31fc8b 100644 --- a/var/spack/repos/builtin/packages/xditview/package.py +++ b/var/spack/repos/builtin/packages/xditview/package.py @@ -12,7 +12,7 @@ class Xditview(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xditview" url = "https://www.x.org/archive/individual/app/xditview-1.0.4.tar.gz" - version('1.0.4', '46dffbbc4de3039fdecabb73d10d6a4f') + version('1.0.4', sha256='73ad88cfc879edcc6ede65999c11d670da27575388126795d71f3ad60286d379') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xdm/package.py b/var/spack/repos/builtin/packages/xdm/package.py index 606ef0dec36..a719d627c03 100644 --- a/var/spack/repos/builtin/packages/xdm/package.py +++ b/var/spack/repos/builtin/packages/xdm/package.py @@ -12,7 +12,7 @@ class Xdm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xdm" url = "https://www.x.org/archive/individual/app/xdm-1.1.11.tar.gz" - version('1.1.11', 'aaf8c3d05d4a1e689d2d789c99a6023c') + version('1.1.11', sha256='38c544a986143b1f24566c1a0111486b339b92224b927be78714eeeedca12a14') depends_on('libxmu') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xdpyinfo/package.py b/var/spack/repos/builtin/packages/xdpyinfo/package.py index 355540ac78e..38d6b5ba860 100644 --- a/var/spack/repos/builtin/packages/xdpyinfo/package.py +++ b/var/spack/repos/builtin/packages/xdpyinfo/package.py @@ -17,7 +17,7 @@ class Xdpyinfo(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xdpyinfo" url = "https://www.x.org/archive/individual/app/xdpyinfo-1.3.2.tar.gz" - version('1.3.2', 'dab410719d36c9df690cf3a8cd7d117e') + version('1.3.2', sha256='ef39935e8e9b328e54a85d6218d410d6939482da6058db1ee1b39749d98cbcf2') depends_on('libxext') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xdriinfo/package.py b/var/spack/repos/builtin/packages/xdriinfo/package.py index 3df483e6afb..a1a3c38065c 100644 --- a/var/spack/repos/builtin/packages/xdriinfo/package.py +++ b/var/spack/repos/builtin/packages/xdriinfo/package.py @@ -12,7 +12,7 @@ class Xdriinfo(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xdriinfo" url = "https://www.x.org/archive/individual/app/xdriinfo-1.0.5.tar.gz" - version('1.0.5', '34a4a9ae69c60f4c2566bf9ea4bcf311') + version('1.0.5', sha256='e4e6abaa4591c540ab63133927a6cebf0a5f4d27dcd978878ab4a422d62a838e') depends_on('libx11') depends_on('expat') diff --git a/var/spack/repos/builtin/packages/xedit/package.py b/var/spack/repos/builtin/packages/xedit/package.py index c6dd2761a87..92e8c5d4555 100644 --- a/var/spack/repos/builtin/packages/xedit/package.py +++ b/var/spack/repos/builtin/packages/xedit/package.py @@ -12,7 +12,7 @@ class Xedit(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/app/xedit" url = "https://www.x.org/archive/individual/app/xedit-1.2.2.tar.gz" - version('1.2.2', '9fb9d6f63b574e5a4937384fbe6579c1') + version('1.2.2', sha256='7e2dacbc2caed81d462ee028e108866893217d55e35e4b860b09be2b409ee18f') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py index 1e2d6f3858d..f2448ed4785 100644 --- a/var/spack/repos/builtin/packages/xerces-c/package.py +++ b/var/spack/repos/builtin/packages/xerces-c/package.py @@ -17,9 +17,9 @@ class XercesC(AutotoolsPackage): homepage = "https://xerces.apache.org/xerces-c" url = "https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.2.1.tar.bz2" - version('3.2.2', '4c395216ecbef3c88a756ff4090e6f7e') - version('3.2.1', '8f98a81a3589bbc2dad9837452f7d319') - version('3.1.4', 'd04ae9d8b2dee2157c6db95fa908abfd') + version('3.2.2', sha256='1f2a4d1dbd0086ce0f52b718ac0fa4af3dc1ce7a7ff73a581a05fbe78a82bce0') + version('3.2.1', sha256='a36b6e162913ec218cfb84772d2535d43c3365355a601d45d4b8ce11f0ece0da') + version('3.1.4', sha256='9408f12c1628ecf80730bedbe8b2caad810edd01bb4c66f77b60c873e8cc6891') # Whilst still using Autotools, can use full cxxstd with 'default' # If build is moved to CMake, then will also need a patch to Xerces-C's diff --git a/var/spack/repos/builtin/packages/xev/package.py b/var/spack/repos/builtin/packages/xev/package.py index 596c69329c5..968e47a3a8c 100644 --- a/var/spack/repos/builtin/packages/xev/package.py +++ b/var/spack/repos/builtin/packages/xev/package.py @@ -18,7 +18,7 @@ class Xev(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xev" url = "https://www.x.org/archive/individual/app/xev-1.2.2.tar.gz" - version('1.2.2', 'fdb374f77cdad8e104b989a0148c4c1f') + version('1.2.2', sha256='e4c0c7b6f411e8b9731f2bb10d729d167bd00480d172c28b62607a6ea9e45c57') depends_on('libxrandr@1.2:') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xextproto/package.py b/var/spack/repos/builtin/packages/xextproto/package.py index d608f36cf0a..88a755eeb9b 100644 --- a/var/spack/repos/builtin/packages/xextproto/package.py +++ b/var/spack/repos/builtin/packages/xextproto/package.py @@ -12,7 +12,7 @@ class Xextproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/xextproto" url = "https://www.x.org/archive/individual/proto/xextproto-7.3.0.tar.gz" - version('7.3.0', '37b700baa8c8ea7964702d948dd13821') + version('7.3.0', sha256='1b1bcdf91221e78c6c33738667a57bd9aaa63d5953174ad8ed9929296741c9f5') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xeyes/package.py b/var/spack/repos/builtin/packages/xeyes/package.py index 7bfed2151aa..0aa1340cbbf 100644 --- a/var/spack/repos/builtin/packages/xeyes/package.py +++ b/var/spack/repos/builtin/packages/xeyes/package.py @@ -12,7 +12,7 @@ class Xeyes(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xeyes" url = "https://www.x.org/archive/individual/app/xeyes-1.1.1.tar.gz" - version('1.1.1', '2c0522bce5c61bbe784d2b3491998d31') + version('1.1.1', sha256='3a1871a560ab87c72a2e2ecb7fd582474448faec3e254c9bd8bead428ab1bca3') depends_on('libx11') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py index 3d178e5758a..d2d97a3c232 100644 --- a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py +++ b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py @@ -12,4 +12,4 @@ class Xf86bigfontproto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/xf86bigfontproto" url = "https://www.x.org/archive/individual/proto/xf86bigfontproto-1.2.0.tar.gz" - version('1.2.0', '91b0733ff4cbe55808d96073258aa3d1') + version('1.2.0', sha256='d190e6462b2bbbac6ee9a007fb8eccb9ad9f5f70544154f388266f031d4bbb23') diff --git a/var/spack/repos/builtin/packages/xf86dga/package.py b/var/spack/repos/builtin/packages/xf86dga/package.py index c338f02e67f..16c3c01cabf 100644 --- a/var/spack/repos/builtin/packages/xf86dga/package.py +++ b/var/spack/repos/builtin/packages/xf86dga/package.py @@ -12,7 +12,7 @@ class Xf86dga(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xf86dga" url = "https://www.x.org/archive/individual/app/xf86dga-1.0.3.tar.gz" - version('1.0.3', '3b87bb916c9df68cf5e4e969307b25b5') + version('1.0.3', sha256='acbf89f60a99b18c161d2beb0e4145a0fdf6c516f7f45fa52e547d88491f75c9') depends_on('libx11') depends_on('libxxf86dga@1.1:') diff --git a/var/spack/repos/builtin/packages/xf86dgaproto/package.py b/var/spack/repos/builtin/packages/xf86dgaproto/package.py index a5f3b8d6eee..25f29f1b66a 100644 --- a/var/spack/repos/builtin/packages/xf86dgaproto/package.py +++ b/var/spack/repos/builtin/packages/xf86dgaproto/package.py @@ -12,4 +12,4 @@ class Xf86dgaproto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/xf86dgaproto" url = "https://www.x.org/archive/individual/proto/xf86dgaproto-2.1.tar.gz" - version('2.1', '1fe79dc07857ad3e1fb8b8f2bdd70d1b') + version('2.1', sha256='73bc6fc830cce5a0ec9c750d4702601fc0fca12d6353ede8b4c0092c9c4ca2af') diff --git a/var/spack/repos/builtin/packages/xf86driproto/package.py b/var/spack/repos/builtin/packages/xf86driproto/package.py index 05ff9f11888..f299d4c3c6f 100644 --- a/var/spack/repos/builtin/packages/xf86driproto/package.py +++ b/var/spack/repos/builtin/packages/xf86driproto/package.py @@ -16,7 +16,7 @@ class Xf86driproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/xf86driproto" url = "https://www.x.org/archive/individual/proto/xf86driproto-2.1.1.tar.gz" - version('2.1.1', '3ba16a48d8d9f9f746f9bd281ba8fb3f') + version('2.1.1', sha256='18ff8de129b89fa24a412a1ec1799f8687f96c186c655b44b1a714a3a5d15d6c') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xf86miscproto/package.py b/var/spack/repos/builtin/packages/xf86miscproto/package.py index 91cf766650c..f0e189899ae 100644 --- a/var/spack/repos/builtin/packages/xf86miscproto/package.py +++ b/var/spack/repos/builtin/packages/xf86miscproto/package.py @@ -15,4 +15,4 @@ class Xf86miscproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/xf86miscproto" url = "https://www.x.org/archive/individual/proto/xf86miscproto-0.9.3.tar.gz" - version('0.9.3', 'c6432f04f84929c94fa05b3a466c489d') + version('0.9.3', sha256='1b05cb76ac165c703b82bdd270b86ebbc4d42a7d04d299050b07ba2099c31352') diff --git a/var/spack/repos/builtin/packages/xf86rushproto/package.py b/var/spack/repos/builtin/packages/xf86rushproto/package.py index 8f917e2e8c5..3ee53542fdd 100644 --- a/var/spack/repos/builtin/packages/xf86rushproto/package.py +++ b/var/spack/repos/builtin/packages/xf86rushproto/package.py @@ -12,4 +12,4 @@ class Xf86rushproto(AutotoolsPackage): homepage = "https://cgit.freedesktop.org/xorg/proto/xf86rushproto" url = "https://www.x.org/archive/individual/proto/xf86rushproto-1.1.2.tar.gz" - version('1.1.2', '6a6389473332ace01146cccfef228576') + version('1.1.2', sha256='7d420ae7e5f0dd94c6010c764c66acc93eed7df7f81bcf93d2a57739970ec841') diff --git a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py index 1caae06dc73..1ba37dad8e4 100644 --- a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py +++ b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py @@ -15,7 +15,7 @@ class Xf86vidmodeproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/xf86vidmodeproto" url = "https://www.x.org/archive/individual/proto/xf86vidmodeproto-2.3.1.tar.gz" - version('2.3.1', '99016d0fe355bae0bb23ce00fb4d4a2c') + version('2.3.1', sha256='c3512b11cefa7558576551f8582c6e7071c8a24d78176059d94b84b48b262979') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xfd/package.py b/var/spack/repos/builtin/packages/xfd/package.py index 1e63d6e2c4a..dab0cb18e8d 100644 --- a/var/spack/repos/builtin/packages/xfd/package.py +++ b/var/spack/repos/builtin/packages/xfd/package.py @@ -13,8 +13,8 @@ class Xfd(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xfd" url = "https://www.x.org/archive/individual/app/xfd-1.1.2.tar.gz" - version('1.1.3', '4a1bd18f324c239b1a807ed4ccaeb172ba771d65a7307fb492d8dd8d27f01527') - version('1.1.2', '12fe8f7c3e71352bf22124ad56d4ceaf') + version('1.1.3', sha256='4a1bd18f324c239b1a807ed4ccaeb172ba771d65a7307fb492d8dd8d27f01527') + version('1.1.2', sha256='4eff3e15b2526ceb48d0236d7ca126face399289eabc0ef67e6ed3b3fdcb60ad') depends_on('fontconfig') depends_on('gettext') diff --git a/var/spack/repos/builtin/packages/xfindproxy/package.py b/var/spack/repos/builtin/packages/xfindproxy/package.py index 21e7635a26e..04c817f0947 100644 --- a/var/spack/repos/builtin/packages/xfindproxy/package.py +++ b/var/spack/repos/builtin/packages/xfindproxy/package.py @@ -17,7 +17,7 @@ class Xfindproxy(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xfindproxy" url = "https://www.x.org/archive/individual/app/xfindproxy-1.0.4.tar.gz" - version('1.0.4', 'd0a7b53ae5827b342bccd3ebc7ec672f') + version('1.0.4', sha256='fa6152fcf9c16fbb2ef52259731df5df899a39a86894b0508456613f26ff924a') depends_on('libice') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xfontsel/package.py b/var/spack/repos/builtin/packages/xfontsel/package.py index a717a333a86..7eacb5a2091 100644 --- a/var/spack/repos/builtin/packages/xfontsel/package.py +++ b/var/spack/repos/builtin/packages/xfontsel/package.py @@ -14,7 +14,7 @@ class Xfontsel(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xfontsel" url = "https://www.x.org/archive/individual/app/xfontsel-1.0.5.tar.gz" - version('1.0.5', '72a35e7fa786eb2b0194d75eeb4a02e3') + version('1.0.5', sha256='9b3ad0cc274398d22be9fa7efe930f4e3749fd4b1b61d9c31a7fb6c1f1ff766e') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xfs/package.py b/var/spack/repos/builtin/packages/xfs/package.py index d59d65746c7..0821ec4a7f2 100644 --- a/var/spack/repos/builtin/packages/xfs/package.py +++ b/var/spack/repos/builtin/packages/xfs/package.py @@ -12,7 +12,7 @@ class Xfs(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xfs" url = "https://www.x.org/archive/individual/app/xfs-1.1.4.tar.gz" - version('1.1.4', '0818a2e0317e0f0a1e8a15ca811827e2') + version('1.1.4', sha256='28f89b854d1ff14fa1efa5b408e5e1c4f6a145420310073c4e44705feeb6d23b') depends_on('libxfont@1.4.5:') depends_on('font-util') diff --git a/var/spack/repos/builtin/packages/xfsinfo/package.py b/var/spack/repos/builtin/packages/xfsinfo/package.py index 3a8801b6845..20a3c19da84 100644 --- a/var/spack/repos/builtin/packages/xfsinfo/package.py +++ b/var/spack/repos/builtin/packages/xfsinfo/package.py @@ -16,7 +16,7 @@ class Xfsinfo(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xfsinfo" url = "https://www.x.org/archive/individual/app/xfsinfo-1.0.5.tar.gz" - version('1.0.5', '36b64a3f37b87c759c5d17634e129fb9') + version('1.0.5', sha256='56a0492ed2cde272dc8f4cff4ba0970ccb900e51c10bb8ec62747483d095fd69') depends_on('libfs') diff --git a/var/spack/repos/builtin/packages/xfwp/package.py b/var/spack/repos/builtin/packages/xfwp/package.py index d678b334434..8a8bf4d36ec 100644 --- a/var/spack/repos/builtin/packages/xfwp/package.py +++ b/var/spack/repos/builtin/packages/xfwp/package.py @@ -12,7 +12,7 @@ class Xfwp(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xfwp" url = "https://www.x.org/archive/individual/app/xfwp-1.0.3.tar.gz" - version('1.0.3', 'e23cc01894ae57e5959ca6a56d0f4f94') + version('1.0.3', sha256='6fe243bde0374637e271a3f038b5d6d79a04621fc18162727782392069c5c04d') depends_on('libice') diff --git a/var/spack/repos/builtin/packages/xgamma/package.py b/var/spack/repos/builtin/packages/xgamma/package.py index c0ffc1495ae..7cdc53f1acb 100644 --- a/var/spack/repos/builtin/packages/xgamma/package.py +++ b/var/spack/repos/builtin/packages/xgamma/package.py @@ -13,7 +13,7 @@ class Xgamma(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xgamma" url = "https://www.x.org/archive/individual/app/xgamma-1.0.6.tar.gz" - version('1.0.6', 'ac4f91bf1d9aa0433152ba6196288cc6') + version('1.0.6', sha256='66da1d67e84146518b69481c6283c5d8f1027ace9ff7e214d3f81954842e796a') depends_on('libx11') depends_on('libxxf86vm') diff --git a/var/spack/repos/builtin/packages/xgc/package.py b/var/spack/repos/builtin/packages/xgc/package.py index 0536ff7c10c..708fff1da79 100644 --- a/var/spack/repos/builtin/packages/xgc/package.py +++ b/var/spack/repos/builtin/packages/xgc/package.py @@ -13,7 +13,7 @@ class Xgc(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xgc" url = "https://www.x.org/archive/individual/app/xgc-1.0.5.tar.gz" - version('1.0.5', '605557a9c138f6dc848c87a21bc7c7fc') + version('1.0.5', sha256='16645fb437699bad2360f36f54f42320e33fce5a0ab9a086f6e0965963205b02') depends_on('libxaw') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xhost/package.py b/var/spack/repos/builtin/packages/xhost/package.py index ae1439d3b7f..b0446d474ff 100644 --- a/var/spack/repos/builtin/packages/xhost/package.py +++ b/var/spack/repos/builtin/packages/xhost/package.py @@ -13,7 +13,7 @@ class Xhost(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xhost" url = "https://www.x.org/archive/individual/app/xhost-1.0.7.tar.gz" - version('1.0.7', 'de34b4ba5194634dbeb29a1f008f495a') + version('1.0.7', sha256='8dd1b6245dfbdef45a64a18ea618f233f77432c2f30881b1db9dc40d510d9490') depends_on('libx11') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xineramaproto/package.py b/var/spack/repos/builtin/packages/xineramaproto/package.py index d54fa23bad4..6226a4ca4f6 100644 --- a/var/spack/repos/builtin/packages/xineramaproto/package.py +++ b/var/spack/repos/builtin/packages/xineramaproto/package.py @@ -15,7 +15,7 @@ class Xineramaproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/xineramaproto" url = "https://www.x.org/archive/individual/proto/xineramaproto-1.2.1.tar.gz" - version('1.2.1', 'e0e148b11739e144a546b8a051b17dde') + version('1.2.1', sha256='d99e121edf7b310008d7371ac5dbe3aa2810996d476b754dc78477cc26e5e7c1') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xinit/package.py b/var/spack/repos/builtin/packages/xinit/package.py index d31994d9244..997b226c092 100644 --- a/var/spack/repos/builtin/packages/xinit/package.py +++ b/var/spack/repos/builtin/packages/xinit/package.py @@ -14,7 +14,7 @@ class Xinit(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xinit" url = "https://www.x.org/archive/individual/app/xinit-1.3.4.tar.gz" - version('1.3.4', '91c5697345016ec7841f5e5fccbe7a4c') + version('1.3.4', sha256='754c284875defa588951c1d3d2b20897d3b84918d0a97cb5a4724b00c0da0746') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xinput/package.py b/var/spack/repos/builtin/packages/xinput/package.py index 5610c98bc60..5856dd9dc3a 100644 --- a/var/spack/repos/builtin/packages/xinput/package.py +++ b/var/spack/repos/builtin/packages/xinput/package.py @@ -12,7 +12,7 @@ class Xinput(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xinput" url = "https://www.x.org/archive/individual/app/xinput-1.6.2.tar.gz" - version('1.6.2', '6684f6015298d22936438173be3b7ef5') + version('1.6.2', sha256='2c8ca5ff2a8703cb7d898629a4311db720dbd30d0c162bfe37f18849a727bd42') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/xkbcomp/package.py b/var/spack/repos/builtin/packages/xkbcomp/package.py index 47ab6c11364..63c0dee249b 100644 --- a/var/spack/repos/builtin/packages/xkbcomp/package.py +++ b/var/spack/repos/builtin/packages/xkbcomp/package.py @@ -17,7 +17,7 @@ class Xkbcomp(AutotoolsPackage): homepage = "https://www.x.org/wiki/XKB/" url = "https://www.x.org/archive/individual/app/xkbcomp-1.3.1.tar.gz" - version('1.3.1', '9e8ca110ed40d4703f8f73d99bc81576') + version('1.3.1', sha256='018e83a922430652d4bc3f3db610d2296e618c76c9b3fbcdccde975aeb655749') depends_on('libx11') depends_on('libxkbfile') diff --git a/var/spack/repos/builtin/packages/xkbdata/package.py b/var/spack/repos/builtin/packages/xkbdata/package.py index 2ee0570a13a..ca1d18599f5 100644 --- a/var/spack/repos/builtin/packages/xkbdata/package.py +++ b/var/spack/repos/builtin/packages/xkbdata/package.py @@ -13,6 +13,6 @@ class Xkbdata(AutotoolsPackage): homepage = "https://www.x.org/wiki/XKB/" url = "https://www.x.org/archive/individual/data/xkbdata-1.0.1.tar.gz" - version('1.0.1', 'a7e0fbc9cc84c621243c777694388064') + version('1.0.1', sha256='5b43ca5219cd4022a158a8d4bfa30308ea5e16c9b5270a64589ebfe7f875f430') depends_on('xkbcomp', type='build') diff --git a/var/spack/repos/builtin/packages/xkbevd/package.py b/var/spack/repos/builtin/packages/xkbevd/package.py index 5e2fca8c3a8..6bc8da7947f 100644 --- a/var/spack/repos/builtin/packages/xkbevd/package.py +++ b/var/spack/repos/builtin/packages/xkbevd/package.py @@ -12,7 +12,7 @@ class Xkbevd(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xkbevd" url = "https://www.x.org/archive/individual/app/xkbevd-1.1.4.tar.gz" - version('1.1.4', '0e9e05761551b1e58bd541231f90ae87') + version('1.1.4', sha256='97dc2c19617da115c3d1183807338fa78c3fd074d8355d10a484f7b1c5b18459') depends_on('libxkbfile') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xkbprint/package.py b/var/spack/repos/builtin/packages/xkbprint/package.py index 63c372c5a7c..7b317ea7ade 100644 --- a/var/spack/repos/builtin/packages/xkbprint/package.py +++ b/var/spack/repos/builtin/packages/xkbprint/package.py @@ -13,7 +13,7 @@ class Xkbprint(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xkbprint" url = "https://www.x.org/archive/individual/app/xkbprint-1.0.4.tar.gz" - version('1.0.4', '4dd9d4fdbdc08f70dc402da149e4d5d8') + version('1.0.4', sha256='169ebbf57fc8b7685c577c73a435998a38c27e0d135ce0a55fccc64cbebec768') depends_on('libxkbfile') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xkbutils/package.py b/var/spack/repos/builtin/packages/xkbutils/package.py index 38239a54059..5bf7e33d7dc 100644 --- a/var/spack/repos/builtin/packages/xkbutils/package.py +++ b/var/spack/repos/builtin/packages/xkbutils/package.py @@ -13,7 +13,7 @@ class Xkbutils(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xkbutils" url = "https://www.x.org/archive/individual/app/xkbutils-1.0.4.tar.gz" - version('1.0.4', '6b898346b84e07c2f13b097193ca0413') + version('1.0.4', sha256='cf31303cbdd6a86c34cab46f4b6e0c7acd2e84578593b334a146142894529bca') depends_on('libxaw') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xkeyboard-config/package.py b/var/spack/repos/builtin/packages/xkeyboard-config/package.py index c26fd8c3199..a3356aaf09d 100644 --- a/var/spack/repos/builtin/packages/xkeyboard-config/package.py +++ b/var/spack/repos/builtin/packages/xkeyboard-config/package.py @@ -14,7 +14,7 @@ class XkeyboardConfig(AutotoolsPackage): homepage = "https://www.freedesktop.org/wiki/Software/XKeyboardConfig/" url = "https://www.x.org/archive/individual/data/xkeyboard-config/xkeyboard-config-2.18.tar.gz" - version('2.18', '96c43e04dbfbb1e6e6abd4678292062c') + version('2.18', sha256='d5c511319a3bd89dc40622a33b51ba41a2c2caad33ee2bfe502363fcc4c3817d') depends_on('libx11@1.4.3:') diff --git a/var/spack/repos/builtin/packages/xkill/package.py b/var/spack/repos/builtin/packages/xkill/package.py index be08eb47e24..355a7b6cc61 100644 --- a/var/spack/repos/builtin/packages/xkill/package.py +++ b/var/spack/repos/builtin/packages/xkill/package.py @@ -14,7 +14,7 @@ class Xkill(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xkill" url = "https://www.x.org/archive/individual/app/xkill-1.0.4.tar.gz" - version('1.0.4', 'b04c15bfd0b619f1e4ff3e44607e738d') + version('1.0.4', sha256='f80115f2dcca3d4b61f3c28188752c21ca7b2718b54b6e0274c0497a7f827da0') depends_on('libx11') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xload/package.py b/var/spack/repos/builtin/packages/xload/package.py index 54710d00505..018c3b9f781 100644 --- a/var/spack/repos/builtin/packages/xload/package.py +++ b/var/spack/repos/builtin/packages/xload/package.py @@ -13,7 +13,7 @@ class Xload(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xload" url = "https://www.x.org/archive/individual/app/xload-1.1.2.tar.gz" - version('1.1.2', '0af9a68193849b16f8168f096682efb4') + version('1.1.2', sha256='4863ad339d22c41a0ca030dc5886404f5ae8b8c47cd5e09f0e36407edbdbe769') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xlogo/package.py b/var/spack/repos/builtin/packages/xlogo/package.py index 0c0b49ba682..ce8fc1325c2 100644 --- a/var/spack/repos/builtin/packages/xlogo/package.py +++ b/var/spack/repos/builtin/packages/xlogo/package.py @@ -12,7 +12,7 @@ class Xlogo(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xlogo" url = "https://www.x.org/archive/individual/app/xlogo-1.0.4.tar.gz" - version('1.0.4', '4c4f82c196a55a90800a77906f4353fb') + version('1.0.4', sha256='0072eb3b41af77d5edfafb12998c7dd875f2795dc94735a998fd2ed8fc246e57') depends_on('libsm') depends_on('libxaw') diff --git a/var/spack/repos/builtin/packages/xlsatoms/package.py b/var/spack/repos/builtin/packages/xlsatoms/package.py index 0e28e463a31..dd8aff90a47 100644 --- a/var/spack/repos/builtin/packages/xlsatoms/package.py +++ b/var/spack/repos/builtin/packages/xlsatoms/package.py @@ -12,7 +12,7 @@ class Xlsatoms(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xlsatoms" url = "https://www.x.org/archive/individual/app/xlsatoms-1.1.2.tar.gz" - version('1.1.2', '1f32e2b8c2135b5867291517848cb396') + version('1.1.2', sha256='5400e22211795e40c4c4d28a048250f92bfb8c373004f0e654a2ad3138c2b36d') depends_on('libxcb', when='@1.1:') depends_on('libx11', when='@:1.0') diff --git a/var/spack/repos/builtin/packages/xlsclients/package.py b/var/spack/repos/builtin/packages/xlsclients/package.py index 9e4768bfd1a..cc5e80a889c 100644 --- a/var/spack/repos/builtin/packages/xlsclients/package.py +++ b/var/spack/repos/builtin/packages/xlsclients/package.py @@ -13,7 +13,7 @@ class Xlsclients(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xlsclients" url = "https://www.x.org/archive/individual/app/xlsclients-1.1.3.tar.gz" - version('1.1.3', '093c748d98b61dbddcaf3de1740fbd26') + version('1.1.3', sha256='4670a4003aae01e9172efb969246c3d8f33481f290aa8726ff50398c838e6994') depends_on('libxcb@1.6:', when='@1.1:') depends_on('libx11', when='@:1.0') diff --git a/var/spack/repos/builtin/packages/xlsfonts/package.py b/var/spack/repos/builtin/packages/xlsfonts/package.py index 83d0f1e4d1a..4211a5b36a8 100644 --- a/var/spack/repos/builtin/packages/xlsfonts/package.py +++ b/var/spack/repos/builtin/packages/xlsfonts/package.py @@ -13,7 +13,7 @@ class Xlsfonts(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xlsfonts" url = "https://www.x.org/archive/individual/app/xlsfonts-1.0.5.tar.gz" - version('1.0.5', '074cc44e5238c6a501523ef06caba517') + version('1.0.5', sha256='2a7aeca1023a3918ad2a1af2258ed63d8f8b6c48e53841b3a3f15fb9a0c008ce') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xmag/package.py b/var/spack/repos/builtin/packages/xmag/package.py index 66c1969598d..9c0183e2440 100644 --- a/var/spack/repos/builtin/packages/xmag/package.py +++ b/var/spack/repos/builtin/packages/xmag/package.py @@ -12,7 +12,7 @@ class Xmag(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xmag" url = "https://www.x.org/archive/individual/app/xmag-1.0.6.tar.gz" - version('1.0.6', '2827ae4b293535623b9f7b659c506dcd') + version('1.0.6', sha256='07c5ec9114376dcd9a3303a38779e79b949d486f3b832d4a438550357d797aa5') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xman/package.py b/var/spack/repos/builtin/packages/xman/package.py index 022eedace77..813b0cdf857 100644 --- a/var/spack/repos/builtin/packages/xman/package.py +++ b/var/spack/repos/builtin/packages/xman/package.py @@ -13,7 +13,7 @@ class Xman(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xman" url = "https://www.x.org/archive/individual/app/xman-1.1.4.tar.gz" - version('1.1.4', 'f4238c79ee7227ea193898fc159f31e5') + version('1.1.4', sha256='72fd0d479624a31d9a7330e5fdd220b7aa144744781f8e78aa12deece86e05c7') depends_on('libxaw') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xmessage/package.py b/var/spack/repos/builtin/packages/xmessage/package.py index 8a717a24ff9..d852f54ea46 100644 --- a/var/spack/repos/builtin/packages/xmessage/package.py +++ b/var/spack/repos/builtin/packages/xmessage/package.py @@ -14,7 +14,7 @@ class Xmessage(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xmessage" url = "https://www.x.org/archive/individual/app/xmessage-1.0.4.tar.gz" - version('1.0.4', '69df5761fbec14c782948065a6f36028') + version('1.0.4', sha256='883099c3952c8cace5bd11d3df2e9ca143fc07375997435d5ff4f2d50353acca') depends_on('libxaw') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xmh/package.py b/var/spack/repos/builtin/packages/xmh/package.py index 1ddc569436a..ae11336b10a 100644 --- a/var/spack/repos/builtin/packages/xmh/package.py +++ b/var/spack/repos/builtin/packages/xmh/package.py @@ -14,7 +14,7 @@ class Xmh(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xmh" url = "https://www.x.org/archive/individual/app/xmh-1.0.3.tar.gz" - version('1.0.3', '7547c5a5ab7309a1b10e8ecf48e60105') + version('1.0.3', sha256='f90baf2615a4e1e01232c50cfd36ee4d50ad2fb2f76b8b5831fb796661f194d2') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/xmlf90/package.py b/var/spack/repos/builtin/packages/xmlf90/package.py index e45abb7a7d0..d9e51332d97 100644 --- a/var/spack/repos/builtin/packages/xmlf90/package.py +++ b/var/spack/repos/builtin/packages/xmlf90/package.py @@ -13,7 +13,7 @@ class Xmlf90(AutotoolsPackage): homepage = "https://launchpad.net/xmlf90" url = "https://launchpad.net/xmlf90/trunk/1.5/+download/xmlf90-1.5.2.tgz" - version('1.5.2', '324fdcba7dafce83db26e72aab9f6656') + version('1.5.2', sha256='666694db793828d1d1e9aea665f75c75ee21772693465a88b43e6370862abfa6') depends_on('autoconf@2.69:', type='build') depends_on('automake@1.14:', type='build') diff --git a/var/spack/repos/builtin/packages/xmlto/package.py b/var/spack/repos/builtin/packages/xmlto/package.py index 48c3cc380c4..e50a038f992 100644 --- a/var/spack/repos/builtin/packages/xmlto/package.py +++ b/var/spack/repos/builtin/packages/xmlto/package.py @@ -15,7 +15,7 @@ class Xmlto(AutotoolsPackage): homepage = "https://pagure.io/xmlto" url = "https://releases.pagure.org/xmlto/xmlto-0.0.28.tar.gz" - version('0.0.28', 'a1fefad9d83499a15576768f60f847c6') + version('0.0.28', sha256='2f986b7c9a0e9ac6728147668e776d405465284e13c74d4146c9cbc51fd8aad3') # FIXME: missing a lot of dependencies depends_on('libxslt') diff --git a/var/spack/repos/builtin/packages/xmodmap/package.py b/var/spack/repos/builtin/packages/xmodmap/package.py index 198442df1b8..3c312975957 100644 --- a/var/spack/repos/builtin/packages/xmodmap/package.py +++ b/var/spack/repos/builtin/packages/xmodmap/package.py @@ -16,7 +16,7 @@ class Xmodmap(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xmodmap" url = "https://www.x.org/archive/individual/app/xmodmap-1.0.9.tar.gz" - version('1.0.9', '771cf86bcdc3589e7add2e761f675099') + version('1.0.9', sha256='73427a996f0fcda2a2c7ac96cfc4edd5985aeb13b48053f55ae7f63a668fadef') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xmore/package.py b/var/spack/repos/builtin/packages/xmore/package.py index 0b3be5f4187..b8b4e68cdcc 100644 --- a/var/spack/repos/builtin/packages/xmore/package.py +++ b/var/spack/repos/builtin/packages/xmore/package.py @@ -12,7 +12,7 @@ class Xmore(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xmore" url = "https://www.x.org/archive/individual/app/xmore-1.0.2.tar.gz" - version('1.0.2', '40b1850494f8af0939a1989c399efa11') + version('1.0.2', sha256='7371631d05986f1111f2026a77e43e048519738cfcc493c6222b66e7b0f309c0') depends_on('libxaw') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xorg-cf-files/package.py b/var/spack/repos/builtin/packages/xorg-cf-files/package.py index feff0f16a28..36c940682d0 100644 --- a/var/spack/repos/builtin/packages/xorg-cf-files/package.py +++ b/var/spack/repos/builtin/packages/xorg-cf-files/package.py @@ -15,6 +15,6 @@ class XorgCfFiles(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/util/cf" url = "https://www.x.org/archive/individual/util/xorg-cf-files-1.0.6.tar.gz" - version('1.0.6', 'c0ce98377c70d95fb48e1bd856109bf8') + version('1.0.6', sha256='6d56094e5d1a6c7d7a9576ac3a0fc2c042344509ea900d59f4b23df668b96c7a') depends_on('pkgconfig', type='build') diff --git a/var/spack/repos/builtin/packages/xorg-docs/package.py b/var/spack/repos/builtin/packages/xorg-docs/package.py index c0331e2a584..115186e777a 100644 --- a/var/spack/repos/builtin/packages/xorg-docs/package.py +++ b/var/spack/repos/builtin/packages/xorg-docs/package.py @@ -15,7 +15,7 @@ class XorgDocs(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/doc/xorg-docs" url = "https://www.x.org/archive/individual/doc/xorg-docs-1.7.1.tar.gz" - version('1.7.1', 'ca689ccbf8ebc362afbe5cc5792a4abd') + version('1.7.1', sha256='360707db2ba48f6deeb53d570deca9fa98218af48ead4a726a67f63e3ef63816') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xorg-gtest/package.py b/var/spack/repos/builtin/packages/xorg-gtest/package.py index 0c10cfaa68e..577d4bdb31b 100644 --- a/var/spack/repos/builtin/packages/xorg-gtest/package.py +++ b/var/spack/repos/builtin/packages/xorg-gtest/package.py @@ -13,7 +13,7 @@ class XorgGtest(AutotoolsPackage): homepage = "https://people.freedesktop.org/~cndougla/xorg-gtest/" url = "https://www.x.org/archive/individual/test/xorg-gtest-0.7.1.tar.bz2" - version('0.7.1', '31beb4d7d2b4eba7f9265fa0cb4c6428') + version('0.7.1', sha256='6cedc7904c698472783203bd686e777db120b808bb4052e451a822e437b72682') depends_on('libx11') depends_on('libxi') diff --git a/var/spack/repos/builtin/packages/xorg-server/package.py b/var/spack/repos/builtin/packages/xorg-server/package.py index 91b81c5845b..53260ad16dc 100644 --- a/var/spack/repos/builtin/packages/xorg-server/package.py +++ b/var/spack/repos/builtin/packages/xorg-server/package.py @@ -13,7 +13,7 @@ class XorgServer(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/xserver" url = "https://www.x.org/archive/individual/xserver/xorg-server-1.18.99.901.tar.gz" - version('1.18.99.901', 'd0242b95991c221c4fcc0d283aba7a42') + version('1.18.99.901', sha256='c8425163b588de2ee7e5c8e65b0749f2710f55a7e02a8d1dc83b3630868ceb21') depends_on('pixman@0.27.2:') depends_on('font-util') diff --git a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py index f9a9bf4c65e..8bf7209c328 100644 --- a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py +++ b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py @@ -14,7 +14,7 @@ class XorgSgmlDoctools(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/doc/xorg-sgml-doctools" url = "https://www.x.org/archive/individual/doc/xorg-sgml-doctools-1.11.tar.gz" - version('1.11', '51cf4c6b476e2b98a068fea6975b9b21') + version('1.11', sha256='986326d7b4dd2ad298f61d8d41fe3929ac6191c6000d6d7e47a8ffc0c34e7426') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xphelloworld/package.py b/var/spack/repos/builtin/packages/xphelloworld/package.py index 361a2f5008f..31c5f00a922 100644 --- a/var/spack/repos/builtin/packages/xphelloworld/package.py +++ b/var/spack/repos/builtin/packages/xphelloworld/package.py @@ -12,7 +12,7 @@ class Xphelloworld(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xphelloworld" url = "https://www.x.org/archive/individual/app/xphelloworld-1.0.1.tar.gz" - version('1.0.1', 'b1851337a8e850d5c8e5a5ca5e3033da') + version('1.0.1', sha256='ead6437c4dc9540698a41e174c9d1ac792de07baeead81935d72cb123196f866') depends_on('libx11') depends_on('libxaw') diff --git a/var/spack/repos/builtin/packages/xplsprinters/package.py b/var/spack/repos/builtin/packages/xplsprinters/package.py index a8e0b80d42d..9214cc6f390 100644 --- a/var/spack/repos/builtin/packages/xplsprinters/package.py +++ b/var/spack/repos/builtin/packages/xplsprinters/package.py @@ -12,7 +12,7 @@ class Xplsprinters(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xplsprinters" url = "https://www.x.org/archive/individual/app/xplsprinters-1.0.1.tar.gz" - version('1.0.1', '8e5698b5a2a2a0fc78caeb23909dd284') + version('1.0.1', sha256='33377e499429ce3e100fbd7b59153c87ad79bf55872561db08419f69cac4fbfd') depends_on('libxp') depends_on('libxprintutil') diff --git a/var/spack/repos/builtin/packages/xpr/package.py b/var/spack/repos/builtin/packages/xpr/package.py index 34a84947cdc..914be1ec8f6 100644 --- a/var/spack/repos/builtin/packages/xpr/package.py +++ b/var/spack/repos/builtin/packages/xpr/package.py @@ -13,7 +13,7 @@ class Xpr(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xpr" url = "https://www.x.org/archive/individual/app/xpr-1.0.4.tar.gz" - version('1.0.4', '6adfa60f458474c0c226454c233fc32f') + version('1.0.4', sha256='9ec355388ae363fd40239a3fa56908bb2f3e53b5bfc872cf0182d14d730c6207') depends_on('libxmu') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py index 69f1404f043..f084e0dbf75 100644 --- a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py +++ b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py @@ -12,7 +12,7 @@ class Xprehashprinterlist(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xprehashprinterlist" url = "https://www.x.org/archive/individual/app/xprehashprinterlist-1.0.1.tar.gz" - version('1.0.1', '395578955634e4b2daa5b78f6fa9222c') + version('1.0.1', sha256='396986da064b584138cfcff79a8aed12590a9dab24f1cd2d80b08bc1cb896a43') depends_on('libxp') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xprop/package.py b/var/spack/repos/builtin/packages/xprop/package.py index aa00b8c25f1..b3c4e79dc46 100644 --- a/var/spack/repos/builtin/packages/xprop/package.py +++ b/var/spack/repos/builtin/packages/xprop/package.py @@ -13,7 +13,7 @@ class Xprop(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xprop" url = "https://www.x.org/archive/individual/app/xprop-1.2.2.tar.gz" - version('1.2.2', 'db03a6bcf7b0d0c2e691ea3083277cbc') + version('1.2.2', sha256='3db78771ce8fb8954fb242ed9d4030372523649c5e9c1a9420340020dd0afbc2') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py index f19b560d432..915fe003473 100644 --- a/var/spack/repos/builtin/packages/xproto/package.py +++ b/var/spack/repos/builtin/packages/xproto/package.py @@ -19,8 +19,8 @@ class Xproto(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/x11proto" url = "https://www.x.org/archive/individual/proto/xproto-7.0.31.tar.gz" - version('7.0.31', '04b925bf9e472c80f9212615cd684f1e') - version('7.0.29', '16a78dd2c5ad73011105c96235f6a0af') + version('7.0.31', sha256='6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7') + version('7.0.29', sha256='628243b3a0fa9b65eda804810ab7238cb88af92fe89efdbc858f25ee5e93a324') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py index 7ca9de41233..6a2198e2460 100644 --- a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py +++ b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py @@ -14,4 +14,4 @@ class Xproxymanagementprotocol(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/proto/pmproto" url = "https://www.x.org/archive/individual/proto/xproxymanagementprotocol-1.0.3.tar.gz" - version('1.0.3', 'c4ab05a6174b4e9b6ae5b7cfbb6d718e') + version('1.0.3', sha256='c1501045ec781f36b6f867611ab2b4e81be542f5c669b2fd0cc4ec1340c42bcf') diff --git a/var/spack/repos/builtin/packages/xqilla/package.py b/var/spack/repos/builtin/packages/xqilla/package.py index 6f6da488de2..b1ec632a7d6 100644 --- a/var/spack/repos/builtin/packages/xqilla/package.py +++ b/var/spack/repos/builtin/packages/xqilla/package.py @@ -13,7 +13,7 @@ class Xqilla(AutotoolsPackage): homepage = "http://xqilla.sourceforge.net/HomePage" url = "https://downloads.sourceforge.net/project/xqilla/XQilla-2.3.3.tar.gz" - version('2.3.3', '8ece20348687b6529bb934c17067803c') + version('2.3.3', sha256='8f76b9b4f966f315acc2a8e104e426d8a76ba4ea3441b0ecfdd1e39195674fd6') variant('debug', default=False, description='Build a debugging version.') variant('shared', default=True, description='Build shared libraries.') diff --git a/var/spack/repos/builtin/packages/xrandr/package.py b/var/spack/repos/builtin/packages/xrandr/package.py index f75dffbfbe6..7a246c809ef 100644 --- a/var/spack/repos/builtin/packages/xrandr/package.py +++ b/var/spack/repos/builtin/packages/xrandr/package.py @@ -13,7 +13,7 @@ class Xrandr(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xrandr" url = "https://www.x.org/archive/individual/app/xrandr-1.5.0.tar.gz" - version('1.5.0', 'fe9cf76033fe5d973131eac67b6a3118') + version('1.5.0', sha256='ddfe8e7866149c24ccce8e6aaa0623218ae19130c2859cadcaa4228d8bb4a46d') depends_on('libxrandr@1.5:') depends_on('libxrender') diff --git a/var/spack/repos/builtin/packages/xrdb/package.py b/var/spack/repos/builtin/packages/xrdb/package.py index ec18884f3a1..384ea1fd466 100644 --- a/var/spack/repos/builtin/packages/xrdb/package.py +++ b/var/spack/repos/builtin/packages/xrdb/package.py @@ -12,7 +12,7 @@ class Xrdb(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xrdb" url = "https://www.x.org/archive/individual/app/xrdb-1.1.0.tar.gz" - version('1.1.0', 'd48983e561ef8b4b2e245feb584c11ce') + version('1.1.0', sha256='44b0b6b7b7eb80b83486dfea67c880f6b0059052386c7ddec4d58fd2ad9ae8e9') depends_on('libxmu') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xrefresh/package.py b/var/spack/repos/builtin/packages/xrefresh/package.py index a8e2dbb840f..e00067cf6af 100644 --- a/var/spack/repos/builtin/packages/xrefresh/package.py +++ b/var/spack/repos/builtin/packages/xrefresh/package.py @@ -12,7 +12,7 @@ class Xrefresh(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xrefresh" url = "https://www.x.org/archive/individual/app/xrefresh-1.0.5.tar.gz" - version('1.0.5', 'e41c5148d894406484af59887257c465') + version('1.0.5', sha256='b373cc1ecd37c3d787e7074ce89a8a06ea173d7ba9e73fa48de973c759fbcf38') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py index ea9ff1d710f..b5e67e31313 100644 --- a/var/spack/repos/builtin/packages/xrootd/package.py +++ b/var/spack/repos/builtin/packages/xrootd/package.py @@ -17,18 +17,18 @@ class Xrootd(CMakePackage): sha256='42e4d2cc6f8b442135f09bcc12c7be38b1a0c623a005cb5e69ff3d27997bdf73') version('4.8.4', sha256='f148d55b16525567c0f893edf9bb2975f7c09f87f0599463e19e1b456a9d95ba') - version('4.8.3', 'bb6302703ffc123f7f9141ddb589435e') - version('4.8.2', '531b632191b59c2cf76ab8d31af4a866') - version('4.8.1', 'a307973f7f43b0cc2688dfe502e17709') - version('4.8.0', '4349e7f664e686b72855e894b49063ad') - version('4.7.1', '4006422bcf99e0a19996ace4ebb99175') - version('4.7.0', '2a92ba483f574c6ba6a9ff061878af22') - version('4.6.1', '70c6f6e1f5f2b4eeb3c7d2c41a36bb2c') - version('4.6.0', '5d60aade2d995b68fe0c46896bc4a5d1') - version('4.5.0', 'd485df3d4a991e1c35efa4bf9ef663d7') - version('4.4.1', '72b0842f802ccc94dede4ac5ab2a589e') - version('4.4.0', '58f55e56801d3661d753ff5fd33dbcc9') - version('4.3.0', '39c2fab9f632f35e12ff607ccaf9e16c') + version('4.8.3', sha256='9cd30a343758b8f50aea4916fa7bd37de3c37c5b670fe059ae77a8b2bbabf299') + version('4.8.2', sha256='8f28ec53e799d4aa55bd0cc4ab278d9762e0e57ac40a4b02af7fc53dcd1bef39') + version('4.8.1', sha256='edee2673d941daf7a6e5c963d339d4a69b4db5c4b6f77b4548b3129b42198029') + version('4.8.0', sha256='0b59ada295341902ca01e9d23e29780fb8df99a6d2bd1c2d654e9bb70c877ad8') + version('4.7.1', sha256='90ddc7042f05667045b06e02c8d9c2064c55d9a26c02c50886254b8df85fc577') + version('4.7.0', sha256='6cc69d9a3694e8dcf2392e9c3b518bd2497a89b3a9f25ffaec62efa52170349b') + version('4.6.1', sha256='0261ce760e8788f85d68918d7702ae30ec677a8f331dae14adc979b4cc7badf5') + version('4.6.0', sha256='b50f7c64ed2a4aead987de3fdf6fce7ee082407ba9297b6851cd917db72edd1d') + version('4.5.0', sha256='27a8e4ef1e6bb6bfe076fef50afe474870edd198699d43359ef01de2f446c670') + version('4.4.1', sha256='3c295dbf750de086c04befc0d3c7045fd3976611c2e75987c1477baca37eb549') + version('4.4.0', sha256='f066e7488390c0bc50938d23f6582fb154466204209ca92681f0aa06340e77c8') + version('4.3.0', sha256='d34865772d975b5d58ad80bb05312bf49aaf124d5431e54dc8618c05a0870e3c') variant('http', default=True, description='Build with HTTP support') diff --git a/var/spack/repos/builtin/packages/xrx/package.py b/var/spack/repos/builtin/packages/xrx/package.py index 394b804dd15..3970997b131 100644 --- a/var/spack/repos/builtin/packages/xrx/package.py +++ b/var/spack/repos/builtin/packages/xrx/package.py @@ -17,7 +17,7 @@ class Xrx(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xrx" url = "https://www.x.org/archive/individual/app/xrx-1.0.4.tar.gz" - version('1.0.4', 'dd4b8bf6eca5fc5be5df30c14050074c') + version('1.0.4', sha256='1ffa1c2af28587c6ed7ded3af2e62e93bad8f9900423d09c45b1d59449d15134') depends_on('libx11') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xsbench/package.py b/var/spack/repos/builtin/packages/xsbench/package.py index 8fb3ee3568a..a8b7b429245 100644 --- a/var/spack/repos/builtin/packages/xsbench/package.py +++ b/var/spack/repos/builtin/packages/xsbench/package.py @@ -19,8 +19,8 @@ class Xsbench(MakefilePackage): tags = ['proxy-app', 'ecp-proxy-app'] version('18', sha256='a9a544eeacd1be8d687080d2df4eeb701c04eda31d3806e7c3ea1ff36c26f4b0') - version('14', '94d5d28eb031fd4ef35507c9c1862169') - version('13', '72a92232d2f5777fb52f5ea4082aff37') + version('14', sha256='595afbcba8c1079067d5d17eedcb4ab0c1d115f83fd6f8c3de01d74b23015e2d') + version('13', sha256='b503ea468d3720a0369304924477b758b3d128c8074776233fa5d567b7ffcaa2') variant('mpi', default=True, description='Build with MPI support') variant('openmp', default=True, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/xscope/package.py b/var/spack/repos/builtin/packages/xscope/package.py index dc3c5378ab1..27e4901e85d 100644 --- a/var/spack/repos/builtin/packages/xscope/package.py +++ b/var/spack/repos/builtin/packages/xscope/package.py @@ -12,7 +12,7 @@ class Xscope(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xscope" url = "https://www.x.org/archive/individual/app/xscope-1.4.1.tar.gz" - version('1.4.1', 'c476fb73b354f4a5c388f3814052ce0d') + version('1.4.1', sha256='f99558a64e828cd2c352091ed362ad2ef42b1c55ef5c01cbf782be9735bb6de3') depends_on('xproto@7.0.17:', type='build') depends_on('xtrans', type='build') diff --git a/var/spack/repos/builtin/packages/xsd/package.py b/var/spack/repos/builtin/packages/xsd/package.py index 956ddbf4ee5..5e9fe140876 100644 --- a/var/spack/repos/builtin/packages/xsd/package.py +++ b/var/spack/repos/builtin/packages/xsd/package.py @@ -16,7 +16,7 @@ class Xsd(MakefilePackage): homepage = "https://www.codesynthesis.com" url = "https://www.codesynthesis.com/download/xsd/4.0/xsd-4.0.0+dep.tar.bz2" - version('4.0.0', 'ad3de699eb140e747a0a214462d95fc81a21b494') + version('4.0.0', sha256='eca52a9c8f52cdbe2ae4e364e4a909503493a0d51ea388fc6c9734565a859817') depends_on('xerces-c') depends_on('libtool', type='build') diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py index 267433f33ef..d0bb98832d6 100644 --- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py +++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py @@ -18,8 +18,8 @@ class Xsdktrilinos(CMakePackage): version('develop', tag='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') - version('12.8.1', '9cc338ded17d1e10ea6c0dc18b22dcd4') - version('12.6.4', '44c4c54ccbac73bb8939f68797b9454a') + version('12.8.1', sha256='f545c0821743f23af3b48f242c66bbc4593e3804436336db4eb3bb08622ad794') + version('12.6.4', md5='44c4c54ccbac73bb8939f68797b9454a') variant('hypre', default=True, description='Compile with Hypre preconditioner') diff --git a/var/spack/repos/builtin/packages/xset/package.py b/var/spack/repos/builtin/packages/xset/package.py index 89d94e42303..128dfa14352 100644 --- a/var/spack/repos/builtin/packages/xset/package.py +++ b/var/spack/repos/builtin/packages/xset/package.py @@ -12,7 +12,7 @@ class Xset(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xset" url = "https://www.x.org/archive/individual/app/xset-1.2.3.tar.gz" - version('1.2.3', '1a76965ed0e8cb51d3fa04d458cb3d8f') + version('1.2.3', sha256='5ecb2bb2cbf3c9349b735080b155a08c97b314dacedfc558c7f5a611ee1297f7') depends_on('libxmu') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xsetmode/package.py b/var/spack/repos/builtin/packages/xsetmode/package.py index 501789feb35..39c27710751 100644 --- a/var/spack/repos/builtin/packages/xsetmode/package.py +++ b/var/spack/repos/builtin/packages/xsetmode/package.py @@ -12,7 +12,7 @@ class Xsetmode(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xsetmode" url = "https://www.x.org/archive/individual/app/xsetmode-1.0.0.tar.gz" - version('1.0.0', '0dc2a917138d0345c00e016ac720e085') + version('1.0.0', sha256='9ee0d6cf72dfaacb997f9570779dcbc42f5395ae102180cb19382860b4b02ef3') depends_on('libxi') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xsetpointer/package.py b/var/spack/repos/builtin/packages/xsetpointer/package.py index 56c8f57ce58..80ae9d996c4 100644 --- a/var/spack/repos/builtin/packages/xsetpointer/package.py +++ b/var/spack/repos/builtin/packages/xsetpointer/package.py @@ -12,7 +12,7 @@ class Xsetpointer(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xsetpointer" url = "https://www.x.org/archive/individual/app/xsetpointer-1.0.1.tar.gz" - version('1.0.1', 'bb206b6875f2428c2281e1165b6c7f88') + version('1.0.1', sha256='54be93b20fd6f1deac67246d6e214a60b02dcfbf05295e43751f7a04edb986ac') depends_on('libxi') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xsetroot/package.py b/var/spack/repos/builtin/packages/xsetroot/package.py index bd94848841d..d885514a520 100644 --- a/var/spack/repos/builtin/packages/xsetroot/package.py +++ b/var/spack/repos/builtin/packages/xsetroot/package.py @@ -12,7 +12,7 @@ class Xsetroot(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xsetroot" url = "https://www.x.org/archive/individual/app/xsetroot-1.1.1.tar.gz" - version('1.1.1', '8c794914a2d0456317288c41451dbee3') + version('1.1.1', sha256='6cdd48757d18835251124138b4a8e4008c3bbc51cf92533aa39c6ed03277168b') depends_on('libxmu') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xsimd/package.py b/var/spack/repos/builtin/packages/xsimd/package.py index 7dbff47b0f7..b4f82067618 100644 --- a/var/spack/repos/builtin/packages/xsimd/package.py +++ b/var/spack/repos/builtin/packages/xsimd/package.py @@ -17,8 +17,8 @@ class Xsimd(CMakePackage): version('develop', branch='master') version('7.2.3', sha256='bbc673ad3e9d4523503a4222da05886e086b0e0bd6bd93d03ea3b663c74297b9') - version('4.0.0', '4186ec94985daa3fc284d9d0d4aa03e8') - version('3.1.0', '29c1c525116cbda28f610e2bf24a827e') + version('4.0.0', sha256='67b818601c15ef15ea4d611a8cd7382588c340ebd9146c799a0210d212540455') + version('3.1.0', sha256='d56288826f6b82fd9583f83ace6aa2306ba2ae82cec003de1d04ce17fbb1e91f') depends_on('googletest', type='test') diff --git a/var/spack/repos/builtin/packages/xsm/package.py b/var/spack/repos/builtin/packages/xsm/package.py index b680aaeab4f..6d54a353dd7 100644 --- a/var/spack/repos/builtin/packages/xsm/package.py +++ b/var/spack/repos/builtin/packages/xsm/package.py @@ -12,7 +12,7 @@ class Xsm(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xsm" url = "https://www.x.org/archive/individual/app/xsm-1.0.3.tar.gz" - version('1.0.3', '60a2e5987d8e49a568599ba8fe59c8db') + version('1.0.3', sha256='f70815139d62416dbec5915ec37db66f325932a69f6350bb1a74c0940cdc796a') depends_on('libx11') depends_on('libxt@1.1.0:') diff --git a/var/spack/repos/builtin/packages/xssp/package.py b/var/spack/repos/builtin/packages/xssp/package.py index 6c3f1eae930..6d65369901d 100644 --- a/var/spack/repos/builtin/packages/xssp/package.py +++ b/var/spack/repos/builtin/packages/xssp/package.py @@ -13,16 +13,16 @@ class Xssp(AutotoolsPackage): homepage = "https://github.com/cmbi/xssp" url = "https://github.com/cmbi/xssp/archive/3.0.10.tar.gz" - version('3.0.10', '01df63c3672eec95662651da45f8c29e') - version('3.0.9', '5e47e531095c874f665b83a0a05e8e87') - version('3.0.8', '2f95aa39977a4675c7a2810c8d55a2e0') - version('3.0.7', '1fe4357628a493664cd67d6b87f701c1') - version('3.0.6', '80e3bb3ffb0e6e675e6ecc2a4226b03b') - version('3.0.5', '1da38d5a8119c50d49045dab211ee391') - version('3.0.4', '92d7fe70a1086d33220959e846ff7052') - version('3.0.3', '96632417270259b0549348dfead1fd0d') - version('3.0.2', '5a06fb81d7c1ed3d64b79f2cc0f78bb9') - version('3.0.1', '2a347ea8ed91583d01026e44035950de') + version('3.0.10', sha256='b475d6fa62098df0e54c8dbdaa0b32de93bf5a393335f73f9b5a7e95f3090d2a') + version('3.0.9', sha256='42a9a93c48d22478212dcaf6ceb3feb64443e4cb2e8cccdd402b47a595d16658') + version('3.0.8', sha256='45e316ff2c700f09971027f9e813cf3139d36ab5951d337948fafab53e00d821') + version('3.0.7', sha256='eb6c3276eeb1261c55568ebfae301033904fe619d84b380313dbf137a2b06cd1') + version('3.0.6', sha256='b868e0077270361276c1c256e2f137ad95f7e84deeb61ae267f7559ebaab7d59') + version('3.0.5', sha256='fded09f08cfb12e578e4823295dc0d0aaeff6559d5e099df23c5bcc911597ccd') + version('3.0.4', sha256='fe786c3a75dafe93bb6a97c2840c3edb0d0e81446874082dc053e136dd3b7f68') + version('3.0.3', sha256='c4826ed74a74e3238f45104cb21ca4ad9e5b49498891e991a3a3a7a3b9bdbe1d') + version('3.0.2', sha256='edb43dc7407a5e91d68d27b732887c6e70a1988e8ddbba03d430713c40c40139') + version('3.0.1', sha256='8f56bc51d7b5f035442c189dd7096f0dd25528303722507365f5e746d5ad9a73') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/xstdcmap/package.py b/var/spack/repos/builtin/packages/xstdcmap/package.py index 2ed01988c58..fc4a0621ae5 100644 --- a/var/spack/repos/builtin/packages/xstdcmap/package.py +++ b/var/spack/repos/builtin/packages/xstdcmap/package.py @@ -15,7 +15,7 @@ class Xstdcmap(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xstdcmap" url = "https://www.x.org/archive/individual/app/xstdcmap-1.0.3.tar.gz" - version('1.0.3', '70c1fd18b79c3ea1dae136e2eabe1c82') + version('1.0.3', sha256='b97aaa883a9eedf9c3056ea1a7e818e3d93b63aa1f54193ef481d392bdef5711') depends_on('libxmu') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xtensor-python/package.py b/var/spack/repos/builtin/packages/xtensor-python/package.py index 1b2183fa7db..50ce72ed7b5 100644 --- a/var/spack/repos/builtin/packages/xtensor-python/package.py +++ b/var/spack/repos/builtin/packages/xtensor-python/package.py @@ -17,7 +17,7 @@ class XtensorPython(CMakePackage): version('develop', branch='master') version('0.23.1', sha256='450b25f5c739df174b2a50774b89e68b23535fdc37cb55bd542ffdb7c78991ab') - version('0.17.0', '51d22e42909a81201c3421d9e119eed0') + version('0.17.0', sha256='30f2e8c99376e38f942d62c0d2959bc1e52a562a4f8cc5e27ddc4d572a25e34c') depends_on('xtensor', when='@develop') depends_on('xtensor@0.20.6:0.20.99', when='@0.23.1') diff --git a/var/spack/repos/builtin/packages/xtensor/package.py b/var/spack/repos/builtin/packages/xtensor/package.py index e1fd45a9431..ff1ef0c0186 100644 --- a/var/spack/repos/builtin/packages/xtensor/package.py +++ b/var/spack/repos/builtin/packages/xtensor/package.py @@ -17,8 +17,8 @@ class Xtensor(CMakePackage): version('develop', branch='master') version('0.20.7', sha256='b45290d1bb0d6cef44771e7482f1553b2aa54dbf99ef9406fec3eb1e4d01d52b') - version('0.15.1', 'c24ecc406003bd1ac22291f1f7cac29a') - version('0.13.1', '80e7e33f05066d17552bf0f8b582dcc5') + version('0.15.1', sha256='2f4ac632f7aa8c8e9da99ebbfc949d9129b4d644f715ef16c27658bf4fddcdd3') + version('0.13.1', sha256='f9ce4cd2110386d49e3f36bbab62da731c557b6289be19bc172bd7209b92a6bc') variant('xsimd', default=True, description='Enable SIMD intrinsics') diff --git a/var/spack/repos/builtin/packages/xterm/package.py b/var/spack/repos/builtin/packages/xterm/package.py index 0c13fd4ed9e..14ad9d207ad 100644 --- a/var/spack/repos/builtin/packages/xterm/package.py +++ b/var/spack/repos/builtin/packages/xterm/package.py @@ -14,7 +14,7 @@ class Xterm(AutotoolsPackage): homepage = "http://invisible-island.net/xterm/" url = "ftp://ftp.invisible-island.net/xterm/xterm-327.tgz" - version('327', '3c32e931adcad44e64e57892e75d9e02') + version('327', sha256='66fb2f6c35b342148f549c276b12a3aa3fb408e27ab6360ddec513e14376150b') depends_on('libxft') depends_on('fontconfig') diff --git a/var/spack/repos/builtin/packages/xtl/package.py b/var/spack/repos/builtin/packages/xtl/package.py index 54b9902774d..e15f517655a 100644 --- a/var/spack/repos/builtin/packages/xtl/package.py +++ b/var/spack/repos/builtin/packages/xtl/package.py @@ -17,9 +17,9 @@ class Xtl(CMakePackage): version('develop', branch='master') version('0.6.4', sha256='5db5087c37daab3e1d35337782f79972aaaf19218a0de786a0515f247244e390') - version('0.4.0', '48c76b63ab12e497a53fb147c41ae747') - version('0.3.4', 'b76548a55f1e171a9c849e5ed543e8b3') - version('0.3.3', '09b6d9611e460d9280bf1156bcca20f5') + version('0.4.0', sha256='2cfe9acbcc4e484f3aa33a98892a09ffe79bb9c0dfd3ffc57b3561f44c591e7c') + version('0.3.4', sha256='618536c3998091b0bdd7f8202e8bec9c34e82409c8ee0ea179a2759bdea426e2') + version('0.3.3', sha256='1110364c2ea0a2536ec6673e46afcb8fa7e92a66593211270bbeb26b85342600') # C++14 support conflicts('%gcc@:4.8') diff --git a/var/spack/repos/builtin/packages/xtrans/package.py b/var/spack/repos/builtin/packages/xtrans/package.py index 1f53c1d377e..60656232a93 100644 --- a/var/spack/repos/builtin/packages/xtrans/package.py +++ b/var/spack/repos/builtin/packages/xtrans/package.py @@ -15,7 +15,7 @@ class Xtrans(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/lib/libxtrans" url = "https://www.x.org/archive//individual/lib/xtrans-1.3.5.tar.gz" - version('1.3.5', '6e4eac1b7c6591da0753052e1eccfb58') + version('1.3.5', sha256='b7a577c1b6c75030145e53b4793db9c88f9359ac49e7d771d4385d21b3e5945d') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') diff --git a/var/spack/repos/builtin/packages/xtrap/package.py b/var/spack/repos/builtin/packages/xtrap/package.py index 5b0e798fa5f..052c3624e19 100644 --- a/var/spack/repos/builtin/packages/xtrap/package.py +++ b/var/spack/repos/builtin/packages/xtrap/package.py @@ -12,7 +12,7 @@ class Xtrap(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xtrap" url = "https://www.x.org/archive/individual/app/xtrap-1.0.2.tar.gz" - version('1.0.2', '601e4945535d2d25eb1bc640332e2363') + version('1.0.2', sha256='e8916e05bfb0d72a088aaaac0feaf4ad7671d0f509d1037fb3c0c9ea131b93d2') depends_on('libx11') depends_on('libxtrap') diff --git a/var/spack/repos/builtin/packages/xts/package.py b/var/spack/repos/builtin/packages/xts/package.py index 23f07e7bb77..51507086f66 100644 --- a/var/spack/repos/builtin/packages/xts/package.py +++ b/var/spack/repos/builtin/packages/xts/package.py @@ -13,7 +13,7 @@ class Xts(AutotoolsPackage): homepage = "https://www.x.org/wiki/XorgTesting/" url = "https://www.x.org/archive/individual/test/xts-0.99.1.tar.gz" - version('0.99.1', '1e5443fede389be606f3745a71483bac') + version('0.99.1', sha256='d04d987b9a9f8b3921dfe8de8577d0c2a0f21d2c4c3196948fc9805838a352e6') depends_on('libx11') depends_on('libxext') diff --git a/var/spack/repos/builtin/packages/xvidtune/package.py b/var/spack/repos/builtin/packages/xvidtune/package.py index fd1a39f5db3..0ccf0330694 100644 --- a/var/spack/repos/builtin/packages/xvidtune/package.py +++ b/var/spack/repos/builtin/packages/xvidtune/package.py @@ -13,7 +13,7 @@ class Xvidtune(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xvidtune" url = "https://www.x.org/archive/individual/app/xvidtune-1.0.3.tar.gz" - version('1.0.3', 'e0c31d78741ae4aab2f4bfcc2abd4a3d') + version('1.0.3', sha256='c0e158388d60e1ce054ce462958a46894604bd95e13093f3476ec6d9bbd786d4') depends_on('libxxf86vm') depends_on('libxt') diff --git a/var/spack/repos/builtin/packages/xvinfo/package.py b/var/spack/repos/builtin/packages/xvinfo/package.py index 517a7eeadbe..2ceb837c8d6 100644 --- a/var/spack/repos/builtin/packages/xvinfo/package.py +++ b/var/spack/repos/builtin/packages/xvinfo/package.py @@ -13,7 +13,7 @@ class Xvinfo(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xvinfo" url = "https://www.x.org/archive/individual/app/xvinfo-1.1.3.tar.gz" - version('1.1.3', '6890a19226c07344ae12e7a2ef12f2c6') + version('1.1.3', sha256='1c1c2f97abfe114389e94399cc7bf3dfd802ed30ad41ba23921d005bd8a6c39f') depends_on('libxv') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xwd/package.py b/var/spack/repos/builtin/packages/xwd/package.py index a585a35c251..1978d6ec279 100644 --- a/var/spack/repos/builtin/packages/xwd/package.py +++ b/var/spack/repos/builtin/packages/xwd/package.py @@ -12,7 +12,7 @@ class Xwd(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xwd" url = "https://www.x.org/archive/individual/app/xwd-1.0.6.tar.gz" - version('1.0.6', 'd6c132f5f00188ce2a1393f12bd34ad4') + version('1.0.6', sha256='ff01f0a4b736f955aaf7c8c3942211bc52f9fb75d96f2b19777f33fff5dc5b83') depends_on('libx11') depends_on('libxkbfile') diff --git a/var/spack/repos/builtin/packages/xwininfo/package.py b/var/spack/repos/builtin/packages/xwininfo/package.py index e9dcd7753f2..f946eef5e64 100644 --- a/var/spack/repos/builtin/packages/xwininfo/package.py +++ b/var/spack/repos/builtin/packages/xwininfo/package.py @@ -13,7 +13,7 @@ class Xwininfo(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xwininfo" url = "https://www.x.org/archive/individual/app/xwininfo-1.1.3.tar.gz" - version('1.1.3', 'd26623fe240659a320367bc453f1d301') + version('1.1.3', sha256='784f8b9c9ddab24ce4faa65fde6430a8d7cf3c0564573582452cc99c599bd941') depends_on('libxcb@1.6:') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xwud/package.py b/var/spack/repos/builtin/packages/xwud/package.py index f44eeb132c6..13ebeebf0ac 100644 --- a/var/spack/repos/builtin/packages/xwud/package.py +++ b/var/spack/repos/builtin/packages/xwud/package.py @@ -13,7 +13,7 @@ class Xwud(AutotoolsPackage): homepage = "http://cgit.freedesktop.org/xorg/app/xwud" url = "https://www.x.org/archive/individual/app/xwud-1.0.4.tar.gz" - version('1.0.4', 'bb44485a37496f0121e5843bcf5bb01b') + version('1.0.4', sha256='b7c124ccd87f529daedb7ef01c670ce6049fe141fd9ba7f444361de34510cd6c') depends_on('libx11') diff --git a/var/spack/repos/builtin/packages/xxhash/package.py b/var/spack/repos/builtin/packages/xxhash/package.py index cb8e37bfaa5..8222262394f 100644 --- a/var/spack/repos/builtin/packages/xxhash/package.py +++ b/var/spack/repos/builtin/packages/xxhash/package.py @@ -17,14 +17,14 @@ class Xxhash(MakefilePackage): homepage = "https://github.com/Cyan4973/xxHash" url = "https://github.com/Cyan4973/xxHash/archive/v0.6.5.tar.gz" - version('0.6.5', '6af3a964f3c2accebce66e54b44b6446') - version('0.6.4', '3c071c95e31bd601cca149cc354e6f19') - version('0.6.3', 'f2ec1497317c0eb89addd7f333c83228') - version('0.6.2', 'b2d12d99094b824e0a5f3ab63abc6c58') - version('0.6.1', 'f4ced3767aad8384b1ecb73bd5f992ca') - version('0.6.0', 'e0fd163b07ab0038f389a180dc263cf2') - version('0.5.1', '9417fd8a4d88204b680e21a60f0ccada') - version('0.5.0', '42e9a31a2cfc2f626fde17e84a0b6bb7') + version('0.6.5', sha256='19030315f4fc1b4b2cdb9d7a317069a109f90e39d1fe4c9159b7aaa39030eb95') + version('0.6.4', sha256='4570ccd111df6b6386502791397906bf69b7371eb209af7d41debc2f074cdb22') + version('0.6.3', sha256='d8c739ec666ac2af983a61dc932aaa2a8873df974d333a9922d472a121f2106e') + version('0.6.2', sha256='e4da793acbe411e7572124f958fa53b280e5f1821a8bf78d79ace972950b8f82') + version('0.6.1', sha256='a940123baa6c71b75b6c02836bae2155cd2f74f7682e1a1d6f7b889f7bc9e7f8') + version('0.6.0', sha256='2adee77416e1bd53d1bf689d78947ff4e9a603aa319c84c9111ccf53f1a646e8') + version('0.5.1', sha256='0171af39eefa06be1e616bc43b250d13bba417e4741135ec85c1fe8dc391997d') + version('0.5.0', sha256='9605cd18d40d798eb1262bc0c2a154e1a3c138a6a9a0c4c792e855d0c08c23e1') def edit(self, spec, prefix): makefile = FileFilter("Makefile") diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py index c7f53e840b4..e6579ee6dc5 100644 --- a/var/spack/repos/builtin/packages/xz/package.py +++ b/var/spack/repos/builtin/packages/xz/package.py @@ -16,10 +16,10 @@ class Xz(AutotoolsPackage): url = "http://tukaani.org/xz/xz-5.2.4.tar.bz2" list_url = "http://tukaani.org/xz/old.html" - version('5.2.4', 'b3264b15ab1db04c8c428dc81838d4eb') - version('5.2.3', '1592e7ca3eece099b03b35f4d9179e7c') - version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af') - version('5.2.0', '867cc8611760240ebf3440bd6e170bb9') + version('5.2.4', sha256='3313fd2a95f43d88e44264e6b015e7d03053e681860b0d5d3f9baca79c57b7bf') + version('5.2.3', sha256='fd9ca16de1052aac899ad3495ad20dfa906c27b4a5070102a2ec35ca3a4740c1') + version('5.2.2', sha256='6ff5f57a4b9167155e35e6da8b529de69270efb2b4cf3fbabf41a4ee793840b5') + version('5.2.0', sha256='f7357d7455a1670229b3cca021da71dd5d13b789db62743c20624bdffc9cc4a5') @property def libs(self): diff --git a/var/spack/repos/builtin/packages/yajl/package.py b/var/spack/repos/builtin/packages/yajl/package.py index 0d9e8598602..4ad9af1364f 100644 --- a/var/spack/repos/builtin/packages/yajl/package.py +++ b/var/spack/repos/builtin/packages/yajl/package.py @@ -14,4 +14,4 @@ class Yajl(CMakePackage): git = "https://github.com/lloyd/yajl.git" version('develop', branch='master') - version('2.1.0', '5eb9c16539bf354b937fcb20e263d1eb') + version('2.1.0', sha256='7458c4ed10ebe52c54f57e741bbfde69c73495e76e0f6a45d6d1986cf24794bc') diff --git a/var/spack/repos/builtin/packages/yambo/package.py b/var/spack/repos/builtin/packages/yambo/package.py index 5e70c358eac..29d84a20b79 100644 --- a/var/spack/repos/builtin/packages/yambo/package.py +++ b/var/spack/repos/builtin/packages/yambo/package.py @@ -20,9 +20,9 @@ class Yambo(AutotoolsPackage): homepage = "http://www.yambo-code.org/index.php" url = "https://github.com/yambo-code/yambo/archive/4.2.2.tar.gz" - version('4.2.2', '97f3513bd726141be5e18072118b6fb5') - version('4.2.1', '99027014192c0f0f4b5d9b48414ad85d') - version('4.2.0', '0cbb4d7c9790596d163ebe872d95bd30') + version('4.2.2', sha256='86b4ebe679387233266aba49948246c85a32b1e6840d024f162962bd0112448c') + version('4.2.1', sha256='8ccd0ca75cc32d9266d4a37edd2a7396cf5038f3a68be07c0f0f77d1afc72bdc') + version('4.2.0', sha256='9f78c4237ff363ff4e9ea5eeea671b6fff783d9a6078cc31b0b1abeb1f040f4d') variant('dp', default=False, description='Enable double precision') variant( diff --git a/var/spack/repos/builtin/packages/yaml-cpp/package.py b/var/spack/repos/builtin/packages/yaml-cpp/package.py index 5f47eab9c5a..49891b2a072 100644 --- a/var/spack/repos/builtin/packages/yaml-cpp/package.py +++ b/var/spack/repos/builtin/packages/yaml-cpp/package.py @@ -17,8 +17,8 @@ class YamlCpp(CMakePackage): git = "https://github.com/jbeder/yaml-cpp.git" version('develop', branch='master') - version('0.6.2', '5b943e9af0060d0811148b037449ef82') - version('0.5.3', '2bba14e6a7f12c7272f87d044e4a7211') + version('0.6.2', sha256='e4d8560e163c3d875fd5d9e5542b5fd5bec810febdcba61481fe5fc4e6b1fd05') + version('0.5.3', sha256='decc5beabb86e8ed9ebeb04358d5363a5c4f72d458b2c788cb2f3ac9c19467b2') variant('shared', default=True, description='Enable build of shared libraries') diff --git a/var/spack/repos/builtin/packages/yasm/package.py b/var/spack/repos/builtin/packages/yasm/package.py index e3eebfdb3b2..345f939b344 100644 --- a/var/spack/repos/builtin/packages/yasm/package.py +++ b/var/spack/repos/builtin/packages/yasm/package.py @@ -17,7 +17,7 @@ class Yasm(AutotoolsPackage): git = "https://github.com/yasm/yasm.git" version('develop', branch='master') - version('1.3.0', 'fc9e586751ff789b34b1f21d572d96af') + version('1.3.0', sha256='3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f') depends_on('autoconf', when='@develop') depends_on('automake', when='@develop') diff --git a/var/spack/repos/builtin/packages/z3/package.py b/var/spack/repos/builtin/packages/z3/package.py index 1210098dd53..b558fa010f3 100644 --- a/var/spack/repos/builtin/packages/z3/package.py +++ b/var/spack/repos/builtin/packages/z3/package.py @@ -14,9 +14,9 @@ class Z3(MakefilePackage): homepage = "https://github.com/Z3Prover/z3/wiki" url = "https://github.com/Z3Prover/z3/archive/z3-4.5.0.tar.gz" - version('4.5.0', 'f332befa0d66d81818a06279a0973e25') - version('4.4.1', '4336a9df24f090e711c6d42fd4e2b1fc') - version('4.4.0', '2bcbb0381cc1572cace99aac8af08990') + version('4.5.0', sha256='aeae1d239c5e06ac183be7dd853775b84698db1265cb2258e5918a28372d4a0c') + version('4.4.1', sha256='50967cca12c5c6e1612d0ccf8b6ebf5f99840a783d6cf5216336a2b59c37c0ce') + version('4.4.0', sha256='65b72f9eb0af50949e504b47080fb3fc95f11c435633041d9a534473f3142cba') phases = ['bootstrap', 'build', 'install'] diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/zeromq/package.py index 72c5d674997..7612bf5695d 100644 --- a/var/spack/repos/builtin/packages/zeromq/package.py +++ b/var/spack/repos/builtin/packages/zeromq/package.py @@ -17,14 +17,14 @@ class Zeromq(AutotoolsPackage): version('4.3.2', sha256='ebd7b5c830d6428956b67a0454a7f8cbed1de74b3b01e5c33c5378e22740f763') version('4.3.1', sha256='bcbabe1e2c7d0eec4ed612e10b94b112dd5f06fcefa994a0c79a45d835cd21eb') version('4.3.0', sha256='8e9c3af6dc5a8540b356697081303be392ade3f014615028b3c896d0148397fd') - version('4.2.5', 'a1c95b34384257e986842f4d006957b8') - version('4.2.2', '52499909b29604c1e47a86f1cb6a9115') - version('4.1.4', 'a611ecc93fffeb6d058c0e6edf4ad4fb') - version('4.1.2', '159c0c56a895472f02668e692d122685') - version('4.1.1', '0a4b44aa085644f25c177f79dc13f253') - version('4.0.7', '9b46f7e7b0704b83638ef0d461fd59ab') - version('4.0.6', 'd47dd09ed7ae6e7fd6f9a816d7f5fdf6') - version('4.0.5', '73c39f5eb01b9d7eaf74a5d899f1d03d') + version('4.2.5', sha256='cc9090ba35713d59bb2f7d7965f877036c49c5558ea0c290b0dcc6f2a17e489f') + version('4.2.2', sha256='5b23f4ca9ef545d5bd3af55d305765e3ee06b986263b31967435d285a3e6df6b') + version('4.1.4', sha256='e99f44fde25c2e4cb84ce440f87ca7d3fe3271c2b8cfbc67d55e4de25e6fe378') + version('4.1.2', sha256='f9162ead6d68521e5154d871bac304f88857308bb02366b81bb588497a345927') + version('4.1.1', sha256='43d61e5706b43946aad4a661400627bcde9c63cc25816d4749c67b64c3dab8db') + version('4.0.7', sha256='e00b2967e074990d0538361cc79084a0a92892df2c6e7585da34e4c61ee47b03') + version('4.0.6', sha256='28a2a9c9b77014c39087a498942449df18bb9885cdb63334833525a1d19f2894') + version('4.0.5', sha256='3bc93c5f67370341428364ce007d448f4bb58a0eaabd0a60697d8086bc43342b') variant("libsodium", default=True, description="Build with message encryption support via libsodium") diff --git a/var/spack/repos/builtin/packages/zip/package.py b/var/spack/repos/builtin/packages/zip/package.py index 94136261cd2..6a9446a9056 100644 --- a/var/spack/repos/builtin/packages/zip/package.py +++ b/var/spack/repos/builtin/packages/zip/package.py @@ -12,7 +12,7 @@ class Zip(MakefilePackage): homepage = 'http://www.info-zip.org/Zip.html' url = 'http://downloads.sourceforge.net/infozip/zip30.tar.gz' - version('3.0', '7b74551e63f8ee6aab6fbc86676c0d37') + version('3.0', sha256='f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369') depends_on('bzip2') diff --git a/var/spack/repos/builtin/packages/zlib/package.py b/var/spack/repos/builtin/packages/zlib/package.py index c433f8f1f13..034fad745a5 100644 --- a/var/spack/repos/builtin/packages/zlib/package.py +++ b/var/spack/repos/builtin/packages/zlib/package.py @@ -16,11 +16,11 @@ class Zlib(Package): # URL must remain http:// so Spack can bootstrap curl url = "http://zlib.net/fossils/zlib-1.2.11.tar.gz" - version('1.2.11', '1c9f62f0778697a09d36121ead88e08e') + version('1.2.11', sha256='c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1') # Due to the bug fixes, any installations of 1.2.9 or 1.2.10 should be # immediately replaced with 1.2.11. - version('1.2.8', '44d667c142d7cda120332623eab69f40') - version('1.2.3', 'debc62758716a169df9f62e6ab2bc634') + version('1.2.8', sha256='36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d') + version('1.2.3', sha256='1795c7d067a43174113fdf03447532f373e1c6c57c08d61d9e4e9be5e244b05e') variant('pic', default=True, description='Produce position-independent code (for shared libs)') diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py index 3d7893aca19..9f701699703 100644 --- a/var/spack/repos/builtin/packages/zoltan/package.py +++ b/var/spack/repos/builtin/packages/zoltan/package.py @@ -22,10 +22,10 @@ class Zoltan(AutotoolsPackage): homepage = "http://www.cs.sandia.gov/zoltan" url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.83.tar.gz" - version('3.83', '1ff1bc93f91e12f2c533ddb01f2c095f') - version('3.8', '9d8fba8a990896881b85351d4327c4a9') - version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9') - version('3.3', '5eb8f00bda634b25ceefa0122bd18d65') + version('3.83', sha256='d0d78fdeab7a385c87d3666b8a8dc748994ff04d3fd846872a4845e12d79c1bb') + version('3.8', sha256='5bdd46548fb9c73b225bbcf3d206c558c318cb292f0b19645e536315d14aafb7') + version('3.6', sha256='d2cb41e5fb72ca564b24bc5f21d82d9f7992f2c977bc82b243a01a8a8ee4eb9c') + version('3.3', sha256='8a90585674ab1bbd011dab29f778b9816519712c78d0aab4cdde9c68f02b30dc') patch('notparallel.patch', when='@3.8') diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py index d709d655685..03e43c5400f 100644 --- a/var/spack/repos/builtin/packages/zstd/package.py +++ b/var/spack/repos/builtin/packages/zstd/package.py @@ -17,8 +17,8 @@ class Zstd(MakefilePackage): version('1.4.2', sha256='7a6e1dad34054b35e2e847eb3289be8820a5d378228802239852f913c6dcf6a7') version('1.4.0', sha256='63be339137d2b683c6d19a9e34f4fb684790e864fee13c7dd40e197a64c705c1') version('1.3.8', sha256='90d902a1282cc4e197a8023b6d6e8d331c1fd1dfe60f7f8e4ee9da40da886dc3') - version('1.3.0', '888660a850e33c2dcc7c4f9d0b04d347') - version('1.1.2', '4c57a080d194bdaac83f2d3251fc7ffc') + version('1.3.0', sha256='0fdba643b438b7cbce700dcc0e7b3e3da6d829088c63757a5984930e2f70b348') + version('1.1.2', sha256='980b8febb0118e22f6ed70d23b5b3e600995dbf7489c1f6d6122c1411cdda8d8') variant('pic', default=True, description='Build position independent code') From 00f91ab22bb260427302ef5662f0b3f4be4e3899 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 11 Oct 2019 22:04:41 -0700 Subject: [PATCH 191/499] checksums: Remove or fix up unfetchable or unverifiable md5 versions This commit either removes remaining md5 checksums, or it replaces them with sha256 checksums verified by fetching over https. --- .../repos/builtin/packages/adlbx/package.py | 1 - .../builtin/packages/armadillo/package.py | 5 ---- .../repos/builtin/packages/bazel/package.py | 5 ---- .../builtin/packages/bcl2fastq2/package.py | 5 ---- .../repos/builtin/packages/beast1/package.py | 1 - .../repos/builtin/packages/braker/package.py | 1 - .../repos/builtin/packages/branson/package.py | 5 +--- .../repos/builtin/packages/busco/package.py | 2 +- .../repos/builtin/packages/bwa/package.py | 1 - .../packages/candle-benchmarks/package.py | 1 - .../repos/builtin/packages/cmocka/package.py | 1 - .../repos/builtin/packages/cub/package.py | 2 -- .../repos/builtin/packages/esmf/package.py | 1 - .../repos/builtin/packages/flit/package.py | 4 ---- .../builtin/packages/font-util/package.py | 4 ++-- .../repos/builtin/packages/funhpc/package.py | 6 ----- .../builtin/packages/genemark-et/package.py | 1 - .../repos/builtin/packages/gmp/package.py | 1 - .../repos/builtin/packages/hpx/package.py | 2 -- .../repos/builtin/packages/hub/package.py | 1 - .../builtin/packages/hydrogen/package.py | 1 - .../repos/builtin/packages/ilmbase/package.py | 2 -- .../builtin/packages/intel-ipp/package.py | 2 -- .../repos/builtin/packages/jdk/package.py | 8 ------- .../repos/builtin/packages/julia/package.py | 2 +- .../repos/builtin/packages/latte/package.py | 3 --- .../builtin/packages/libconfig/package.py | 8 ++----- .../repos/builtin/packages/libelf/package.py | 1 - .../builtin/packages/libepoxy/package.py | 1 - .../repos/builtin/packages/libffi/package.py | 3 --- .../repos/builtin/packages/libgd/package.py | 2 -- .../repos/builtin/packages/libgit2/package.py | 1 - .../builtin/packages/libgpuarray/package.py | 2 -- .../repos/builtin/packages/libnl/package.py | 1 - .../builtin/packages/libsodium/package.py | 3 --- .../repos/builtin/packages/libtiff/package.py | 1 - .../repos/builtin/packages/lmod/package.py | 7 +++--- .../builtin/packages/log4cplus/package.py | 1 - .../repos/builtin/packages/macsio/package.py | 1 - .../builtin/packages/mpifileutils/package.py | 4 ---- .../builtin/packages/muparser/package.py | 2 -- .../builtin/packages/mvapich2/package.py | 1 - .../repos/builtin/packages/mxml/package.py | 3 --- .../repos/builtin/packages/mxnet/package.py | 6 ----- .../repos/builtin/packages/nag/package.py | 6 ++--- .../builtin/packages/netcdf-cxx4/package.py | 4 +--- .../repos/builtin/packages/nwchem/package.py | 2 -- .../builtin/packages/ont-albacore/package.py | 4 +--- .../repos/builtin/packages/pexsi/package.py | 2 +- .../repos/builtin/packages/phylip/package.py | 1 - .../repos/builtin/packages/pism/package.py | 1 - .../packages/planck-likelihood/package.py | 2 +- .../repos/builtin/packages/prank/package.py | 1 - .../builtin/packages/protobuf/package.py | 2 -- .../builtin/packages/py-astroid/package.py | 2 +- .../builtin/packages/py-certifi/package.py | 3 +-- .../builtin/packages/py-cython/package.py | 1 - .../builtin/packages/py-espressopp/package.py | 4 +--- .../builtin/packages/py-git-review/package.py | 4 ---- .../builtin/packages/py-maestrowf/package.py | 1 - .../builtin/packages/py-openpyxl/package.py | 1 - .../builtin/packages/py-pygpu/package.py | 2 -- .../builtin/packages/py-pylint/package.py | 2 +- .../builtin/packages/py-pysam/package.py | 7 ++---- .../builtin/packages/py-pyside/package.py | 3 --- .../repos/builtin/packages/py-pytz/package.py | 1 - .../builtin/packages/py-setuptools/package.py | 1 - .../repos/builtin/packages/py-sip/package.py | 2 -- .../builtin/packages/py-spyder/package.py | 1 - .../builtin/packages/py-traitlets/package.py | 1 - .../builtin/packages/qt-creator/package.py | 3 --- .../builtin/packages/r-checkpoint/package.py | 1 - .../repos/builtin/packages/r-hmisc/package.py | 1 - .../repos/builtin/packages/r-knitr/package.py | 1 - .../repos/builtin/packages/r-mass/package.py | 3 +-- .../builtin/packages/r-matrix/package.py | 5 ++-- .../repos/builtin/packages/r-nlme/package.py | 1 - .../repos/builtin/packages/r-nmf/package.py | 1 - .../builtin/packages/r-pkgmaker/package.py | 1 - .../packages/r-randomfieldsutils/package.py | 1 - .../builtin/packages/r-rngtools/package.py | 1 - .../repos/builtin/packages/r-xlsx/package.py | 1 - .../repos/builtin/packages/re2c/package.py | 1 - .../builtin/packages/revbayes/package.py | 2 -- .../repos/builtin/packages/rose/package.py | 23 +++++-------------- .../repos/builtin/packages/rtags/package.py | 1 - .../repos/builtin/packages/scr/package.py | 5 ---- .../builtin/packages/simulationio/package.py | 2 -- .../repos/builtin/packages/thrift/package.py | 1 - .../repos/builtin/packages/turbine/package.py | 1 - .../builtin/packages/vardictjava/package.py | 1 - .../builtin/packages/vcftools/package.py | 2 +- .../repos/builtin/packages/wcslib/package.py | 1 - .../builtin/packages/xsdktrilinos/package.py | 11 ++++----- 94 files changed, 37 insertions(+), 211 deletions(-) diff --git a/var/spack/repos/builtin/packages/adlbx/package.py b/var/spack/repos/builtin/packages/adlbx/package.py index 6abab59d801..e4e7c178f9c 100644 --- a/var/spack/repos/builtin/packages/adlbx/package.py +++ b/var/spack/repos/builtin/packages/adlbx/package.py @@ -17,7 +17,6 @@ class Adlbx(AutotoolsPackage): version('master', branch='master') version('0.9.2', sha256='524902d648001b689a98492402d754a607b8c1d0734699154063c1a4f3410d4a') version('0.9.1', sha256='8913493fe0c097ff13c721ab057514e5bdb55f6318d4e3512692ab739c3190b3') - version('0.8.0', md5='34ade59ce3be5bc296955231d47a27dd') depends_on('exmcutils@master', when='@master') depends_on('exmcutils@:0.5.3', when='@:0.8.0') diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index 7709bcd3201..de4c92c3852 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -16,11 +16,6 @@ class Armadillo(CMakePackage): version('8.100.1', sha256='54773f7d828bd3885c598f90122b530ded65d9b195c9034e082baea737cd138d') version('7.950.1', sha256='a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b') - # NOTE: v7.900.1 download url seems broken is no v7.950.1? - version('7.900.1', md5='5ef71763bd429a3d481499878351f3be') - version('7.500.0', md5='7d316fdf3c3c7ea92b64704180ae315d') - version('7.200.2', md5='b21585372d67a8876117fd515d8cf0a2') - version('7.200.1', md5='ed86d6df0058979e107502e1fe3e469e') variant('hdf5', default=False, description='Include HDF5 support') diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py index b976301f3aa..ef5e26edded 100644 --- a/var/spack/repos/builtin/packages/bazel/package.py +++ b/var/spack/repos/builtin/packages/bazel/package.py @@ -30,11 +30,6 @@ class Bazel(Package): version('0.9.0', sha256='efb28fed4ffcfaee653e0657f6500fc4cbac61e32104f4208da385676e76312a') version('0.4.5', sha256='2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b') version('0.4.4', sha256='d52a21dda271ae645711ce99c70cf44c5d3a809138e656bbff00998827548ebb') - version('0.3.1', md5='5c959467484a7fc7dd2e5e4a1e8e866b') - version('0.3.0', md5='33a2cb457d28e1bee9282134769b9283') - version('0.2.3', md5='393a491d690e43caaba88005efe6da91') - version('0.2.2b', md5='75081804f073cbd194da1a07b16cba5f') - version('0.2.2', md5='644bc4ea7f429d835e74f255dc1054e6') depends_on('java@8:', type=('build', 'link', 'run')) depends_on('zip') diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py index d884fbd965a..009386b85a7 100644 --- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py +++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py @@ -21,11 +21,6 @@ class Bcl2fastq2(Package): version('2.20.0.422', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3') version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806') - version('2.18.0.12', md5='fbe06492117f65609c41be0c27e3215c') - # 2.17.1.14 is no longer distributed. If you have a copy of the - # source tarball, you can drop it into a local mirror w/ the name - # mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there. - version('2.17.1.14', md5='7426226c6db095862e636b95c38608d3') conflicts('platform=darwin', msg='malloc.h/etc requirements break build on macs') diff --git a/var/spack/repos/builtin/packages/beast1/package.py b/var/spack/repos/builtin/packages/beast1/package.py index 4d895e814cc..2361dd95c09 100644 --- a/var/spack/repos/builtin/packages/beast1/package.py +++ b/var/spack/repos/builtin/packages/beast1/package.py @@ -13,7 +13,6 @@ class Beast1(Package): homepage = "http://beast.community/" version('1.10.4', sha256='be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8') - version('1.10.0', md5='bcf2f2c074319360ec8a2ebad57d2e57') version('1.8.4', sha256='c14e93976008463108aefa34ecc23287ab70703caccf4962e36e295207120d78') variant('beagle', default=True, description='Build with libbeagle support') diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py index 973268a4b66..f9db018c1d6 100644 --- a/var/spack/repos/builtin/packages/braker/package.py +++ b/var/spack/repos/builtin/packages/braker/package.py @@ -17,7 +17,6 @@ class Braker(Package): list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old" version('2.1.4', sha256='d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52') - version('2.1.0', md5='5f974abcceb9f96a11668fa20a6f6a56') version('1.11', sha256='cb2d9abe1720ed58753d362eee4af3791007efc617754804882d31f9fe2eab00', url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz') diff --git a/var/spack/repos/builtin/packages/branson/package.py b/var/spack/repos/builtin/packages/branson/package.py index 38d76499d83..8104ad40859 100644 --- a/var/spack/repos/builtin/packages/branson/package.py +++ b/var/spack/repos/builtin/packages/branson/package.py @@ -18,10 +18,7 @@ class Branson(CMakePackage): tags = ['proxy-app'] version('develop', branch='develop') - # Version 1.01 is actually deprecated and older than any of the 0.8 series. - # However, its entry is left here to reflect older versions of this - # spackage. - version('1.01', md5='cf7095a887a8dd7d417267615bd0452a') + version('0.82', sha256='7d83d41d0c7ab9c1c906a902165af31182da4604dd0b69aec28d709fe4d7a6ec', preferred=True) version('0.81', sha256='493f720904791f06b49ff48c17a681532c6a4d9fa59636522cf3f9700e77efe4') diff --git a/var/spack/repos/builtin/packages/busco/package.py b/var/spack/repos/builtin/packages/busco/package.py index fe3a8fbf0ae..c23ad62fb3a 100644 --- a/var/spack/repos/builtin/packages/busco/package.py +++ b/var/spack/repos/builtin/packages/busco/package.py @@ -16,7 +16,7 @@ class Busco(PythonPackage): # TODO: check the installation procedure for version 3.0.2 # and uncomment the following line - # version('3.0.2', md5='31d80042bb7e96422843fa43d0acbd21') + # version('3.0.2', sha256='dbea093315b766b0f7c4fe3cafbbdf51ade79ec84bde04f1f437b48333200f34') # There is no tag for version 3.0.1 version('3.0.1', commit='078252e00399550d7b0e8941cd4d986c8e868a83') diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py index dc4c65a62bd..6e0864f2b6b 100644 --- a/var/spack/repos/builtin/packages/bwa/package.py +++ b/var/spack/repos/builtin/packages/bwa/package.py @@ -13,7 +13,6 @@ class Bwa(Package): url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2" version('0.7.17', sha256='de1b4d4e745c0b7fc3e107b5155a51ac063011d33a5d82696331ecf4bed8d0fd') - version('0.7.16a', md5='c5115c9a5ea0406848500e4b23a7708c') version('0.7.15', sha256='2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515') version('0.7.13', sha256='559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc') version('0.7.12', sha256='285f55b7fa1f9e873eda9a9b06752378a799ecdecbc886bbd9ba238045bf62e0', diff --git a/var/spack/repos/builtin/packages/candle-benchmarks/package.py b/var/spack/repos/builtin/packages/candle-benchmarks/package.py index af517463b09..fb8401108d1 100644 --- a/var/spack/repos/builtin/packages/candle-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/candle-benchmarks/package.py @@ -15,7 +15,6 @@ class CandleBenchmarks(Package): tags = ['proxy-app', 'ecp-proxy-app'] version('0.1', sha256='767f74f43ee3a5d4e0f26750f2a96b8433e25a9cd4f2d29938ac8acf263ab58d') - version('0.0', md5='6eced30dc15374bc9f90a86d0396e470') variant('mpi', default=True, description='Build with MPI support') diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py index 89cf3b3b235..eedc77f312e 100644 --- a/var/spack/repos/builtin/packages/cmocka/package.py +++ b/var/spack/repos/builtin/packages/cmocka/package.py @@ -13,7 +13,6 @@ class Cmocka(CMakePackage): version('1.1.1', sha256='f02ef48a7039aa77191d525c5b1aee3f13286b77a13615d11bc1148753fc0389') version('1.1.0', sha256='e960d3bf1be618634a4b924f18bb4d6f20a825c109a8ad6d1af03913ba421330') - version('1.0.1', md5='ed861e501a21a92b2af63e466df2015e') depends_on('cmake@2.6.0:', type='build') diff --git a/var/spack/repos/builtin/packages/cub/package.py b/var/spack/repos/builtin/packages/cub/package.py index 81e71ff6c27..9076ac78b11 100644 --- a/var/spack/repos/builtin/packages/cub/package.py +++ b/var/spack/repos/builtin/packages/cub/package.py @@ -14,8 +14,6 @@ class Cub(Package): url = "https://github.com/NVlabs/cub/archive/1.6.4.zip" version('1.7.1', sha256='50b8777b83093fdfdab429a61fccdbfbbb991b3bbc08385118e5ad58e8f62e1d') - version('1.6.4', md5='924fc12c0efb17264c3ad2d611ed1c51') - version('1.4.1', md5='74a36eb84e5b5f0bf54aa3df39f660b2') def install(self, spec, prefix): mkdirp(prefix.include) diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py index 007c13b8536..bfe35d9f198 100644 --- a/var/spack/repos/builtin/packages/esmf/package.py +++ b/var/spack/repos/builtin/packages/esmf/package.py @@ -18,7 +18,6 @@ class Esmf(MakefilePackage): url = "http://www.earthsystemmodeling.org/esmf_releases/public/ESMF_7_1_0r/esmf_7_1_0r_src.tar.gz" version('7.1.0r', sha256='ae9a5edb8d40ae97a35cbd4bd00b77061f995c77c43d36334dbb95c18b00a889') - version('7.0.1', md5='d3316ea79b032b8fb0cd40e5868a0261') variant('mpi', default=True, description='Build with MPI support') variant('lapack', default=True, description='Build with LAPACK support') diff --git a/var/spack/repos/builtin/packages/flit/package.py b/var/spack/repos/builtin/packages/flit/package.py index caf97fc474c..7b3364ef130 100644 --- a/var/spack/repos/builtin/packages/flit/package.py +++ b/var/spack/repos/builtin/packages/flit/package.py @@ -17,10 +17,6 @@ class Flit(MakefilePackage): url = "https://github.com/PRUNERS/FLiT/archive/v2.0-alpha.1.tar.gz" version('2.0-alpha.1', sha256='8de2bd400acf0f513d69f3dbf588e8984dfb18b8ccaaf684391811a0582f694b') - # FIXME: fix install and build to handle the old version, which is not - # installable - # version('1.0.0', md5='27763c89b044c5e3cfe62dd319a36a2b') - conflicts("@:1.999", msg="Only can build version 2.0 and up") # Add dependencies depends_on('python@3:', type='run') diff --git a/var/spack/repos/builtin/packages/font-util/package.py b/var/spack/repos/builtin/packages/font-util/package.py index 081e3be2539..11635276fa8 100644 --- a/var/spack/repos/builtin/packages/font-util/package.py +++ b/var/spack/repos/builtin/packages/font-util/package.py @@ -26,7 +26,7 @@ class FontUtil(AutotoolsPackage): font_baseurl = 'https://www.x.org/archive/individual/font/' fonts = [] - # name, version, md5 + # name, version, sha256 fonts_resource = [ ['encodings', '1.0.4', '55861d9cf456bd717a3d30a3193402c02174ed3c0dcee828798165fe307ee324'], ['font-alias', '1.0.3', '63087cb61d17bfc9cd6f4f9359f63a3b1dd83300a31a42fd93dca084724c6afb'], @@ -68,7 +68,7 @@ class FontUtil(AutotoolsPackage): for f_r in fonts_resource: f = f_r[0] resource(name=f, url=font_baseurl + f + '-' + f_r[1] + '.tar.gz', - md5=f_r[2], destination=f, when='fonts=' + f) + sha256=f_r[2], destination=f, when='fonts=' + f) fonts.append(f) variant('fonts', diff --git a/var/spack/repos/builtin/packages/funhpc/package.py b/var/spack/repos/builtin/packages/funhpc/package.py index 4fce8b68d54..ed69e4f88ee 100644 --- a/var/spack/repos/builtin/packages/funhpc/package.py +++ b/var/spack/repos/builtin/packages/funhpc/package.py @@ -16,12 +16,6 @@ class Funhpc(CMakePackage): version('develop', branch='master') version('1.3.0', sha256='140e60f55a307f21117bd43fa16db35d60c0df5ef37e17a4da1cb3f5da5e29c1') - version('1.2.0', md5='ba2bbeea3091e999b6b85eaeb1b67a83') - version('1.1.1', md5='7b9ef638b02fffe35b75517e8eeff580') - version('1.1.0', md5='897bd968c42cd4f14f86fcf67da70444') - version('1.0.0', md5='f34e71ccd5548b42672e692c913ba5ee') - version('0.1.1', md5='f0248710f2de88ed2a595ad40d99997c') - version('0.1.0', md5='00f7dabc08ed1ab77858785ce0809f50') variant('pic', default=True, description="Produce position-independent code") diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py index a25a9424178..a66cfa87a0a 100644 --- a/var/spack/repos/builtin/packages/genemark-et/package.py +++ b/var/spack/repos/builtin/packages/genemark-et/package.py @@ -21,7 +21,6 @@ class GenemarkEt(Package): version('4.46', sha256='856b0b6c7cbd12835e140ff04ecd9124376348efd65f76bfd8b8e08c1834eac0') version('4.38', sha256='cee3bd73d331be44159eac15469560d0b07ffa2c98ac764c37219e1f3b7d3146') - version('4.33', '4ab7d7d3277a685dfb49e11bc5b493c3') depends_on('perl', type=('build', 'run')) depends_on('perl-yaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index b9c034008b5..8d829e5d309 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -17,7 +17,6 @@ class Gmp(AutotoolsPackage): version('6.1.1', sha256='a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6') version('6.1.0', sha256='498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8') version('6.0.0a', sha256='7f8e9a804b9c6d07164cf754207be838ece1219425d64e28cfa3e70d5c759aaf') - version('6.0.0', md5='6ef5869ae735db9995619135bd856b84') version('5.1.3', sha256='752079520b4690531171d0f4532e40f08600215feefede70b24fabdc6f1ab160') # Old version needed for a binary package in ghc-bootstrap version('4.3.2', sha256='936162c0312886c21581002b79932829aa048cfaf9937c6265aeaa14f1cd1775') diff --git a/var/spack/repos/builtin/packages/hpx/package.py b/var/spack/repos/builtin/packages/hpx/package.py index d3c6971cb70..e5f6cf75cf4 100644 --- a/var/spack/repos/builtin/packages/hpx/package.py +++ b/var/spack/repos/builtin/packages/hpx/package.py @@ -18,8 +18,6 @@ class Hpx(CMakePackage, CudaPackage): version('1.2.0', sha256='20942314bd90064d9775f63b0e58a8ea146af5260a4c84d0854f9f968077c170') version('1.1.0', sha256='1f28bbe58d8f0da600d60c3a74a644d75ac777b20a018a5c1c6030a470e8a1c9') - version('1.0.0', md5='4983e7c6402417ec794d40343e36e417', url='http://stellar.cct.lsu.edu/files/hpx_1.0.0') - variant('cxxstd', default='17', values=('98', '11', '14', '17'), diff --git a/var/spack/repos/builtin/packages/hub/package.py b/var/spack/repos/builtin/packages/hub/package.py index aea764b448b..068e7b4a35a 100644 --- a/var/spack/repos/builtin/packages/hub/package.py +++ b/var/spack/repos/builtin/packages/hub/package.py @@ -15,7 +15,6 @@ class Hub(Package): git = "https://github.com/github/hub.git" version('head', branch='master') - version('2.2.3', md5='6675992ddd16d186eac7ba4484d57f5b') version('2.2.2', sha256='610572ee903aea1fa8622c16ab7ddef2bd1bfec9f4854447ab8e0fbdbe6a0cae') version('2.2.1', sha256='9350aba6a8e3da9d26b7258a4020bf84491af69595f7484f922d75fc8b86dc10') version('2.2.0', sha256='2da1351197eb5696c207f22c69a5422af052d74277b73d0b8661efb9ec1d0eb1') diff --git a/var/spack/repos/builtin/packages/hydrogen/package.py b/var/spack/repos/builtin/packages/hydrogen/package.py index c77bae4ed10..7dce9c06960 100644 --- a/var/spack/repos/builtin/packages/hydrogen/package.py +++ b/var/spack/repos/builtin/packages/hydrogen/package.py @@ -20,7 +20,6 @@ class Hydrogen(CMakePackage): version('1.1.0', sha256='b4c12913acd01c72d31f4522266bfeb8df1d4d3b4aef02e07ccbc9a477894e71') version('1.0.1', sha256='27cf76e1ef1d58bd8f9b1e34081a14a682b7ff082fb5d1da56713e5e0040e528') version('1.0', sha256='d8a97de3133f2c6b6bb4b80d32b4a4cc25eb25e0df4f0cec0f8cb19bf34ece98') - version('0.99', md5='b678433ab1d498da47acf3dc5e056c23') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/ilmbase/package.py b/var/spack/repos/builtin/packages/ilmbase/package.py index 3f16959e214..129c02f8d71 100644 --- a/var/spack/repos/builtin/packages/ilmbase/package.py +++ b/var/spack/repos/builtin/packages/ilmbase/package.py @@ -16,8 +16,6 @@ class Ilmbase(AutotoolsPackage): version('2.2.0', sha256='ecf815b60695555c1fbc73679e84c7c9902f4e8faa6e8000d2f905b8b86cedc7', url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.2.0.tar.gz') - version('2.1.0', md5='af1115f4d759c574ce84efcde9845d29', - url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.1.0.tar.gz') version('2.0.1', sha256='19b03975fea4461f2eff91f5df138b301b3ea9709eccbda98447f372bf09735f', url='http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.0.1.tar.gz') version('1.0.2', sha256='2e5cda799ffdfca9b1a16bb120d49c74a39af1457ef22f968918c6200ba62e44', diff --git a/var/spack/repos/builtin/packages/intel-ipp/package.py b/var/spack/repos/builtin/packages/intel-ipp/package.py index 7055268bf9a..cb9c0ccdb51 100644 --- a/var/spack/repos/builtin/packages/intel-ipp/package.py +++ b/var/spack/repos/builtin/packages/intel-ipp/package.py @@ -23,8 +23,6 @@ class IntelIpp(IntelPackage): url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13006/l_ipp_2018.3.222.tgz') version('2018.2.199', sha256='55cb5c910b2c1e2bd798163fb5019b992b1259a0692e328bb9054778cf01562b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12726/l_ipp_2018.2.199.tgz') - version('2018.1.163', md5='183d4888f3d91f632b617fdd401f04ed', - url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_ipp_2018.1.163.tgz') version('2018.0.128', sha256='da568ceec1b7acbcc8f666b73d4092788b037b1b03c0436974b82155056ed166', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12071/l_ipp_2018.0.128.tgz') version('2017.3.196', sha256='50d49a1000a88a8a58bd610466e90ae28d07a70993a78cbbf85d44d27c4232b6', diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index 461b0e6aa23..d4b3371ff0d 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -50,18 +50,10 @@ class Jdk(Package): url='http://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz') version('1.8.0_202', sha256='9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0', curl_options=curl_options, url='https://download.oracle.com/otn-pub/java/jdk/8u202-b08/1961070e4c9b4e26a04e7f5a083f551e/jdk-8u202-linux-x64.tar.gz') - version('1.8.0_181-b13', md5='ef599e322eee42f6769991dd3e3b1a31', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/8u181-b13/96a7b8442fe848ef90c96a2fad6ed6d1/jdk-8u181-linux-x64.tar.gz') - version('1.8.0_172-b11', md5='eda2945e8c02b84adbf78f46c37b71c1', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/8u172-b11/a58eab1ec242421181065cdc37240b08/jdk-8u172-linux-x64.tar.gz') version('1.8.0_141-b15', sha256='041d5218fbea6cd7e81c8c15e51d0d32911573af2ed69e066787a8dc8a39ba4f', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz') version('1.8.0_131-b11', sha256='62b215bdfb48bace523723cdbb2157c665e6a25429c73828a32f00e587301236', curl_options=curl_options, url='http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz') - version('1.8.0_92-b14', md5='65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options) - version('1.8.0_73-b02', md5='1b0120970aa8bc182606a16bf848a686', curl_options=curl_options) - version('1.8.0_66-b17', md5='88f31f3d642c3287134297b8c10e61bf', curl_options=curl_options) - version('1.7.0_80-b0', md5='6152f8a7561acf795ca4701daa10a965', curl_options=curl_options) provides('java') provides('java@12', when='@12.0:12.999') diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 4a0e138c2cf..7191faf2345 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -25,7 +25,7 @@ class Julia(Package): version('0.5.1', sha256='533b6427a1b01bd38ea0601f58a32d15bf403f491b8415e9ce4305b8bc83bb21') version('0.5.0', sha256='732478536b6dccecbf56e541eef0aed04de0e6d63ae631b136e033dda2e418a9') version('release-0.4', branch='release-0.4') - version('0.4.7', md5='75a7a7dd882b7840829d8f165e9b9078') + version('0.4.7', sha256='d658d5bd5fb79b19f3c01cadb9aba8622ca8a12a4b687acc7d99c21413623570') version('0.4.6', sha256='4c23c9fc72398014bd39327c2f7efd3a301884567d4cb2a89105c984d4d633ba') version('0.4.5', sha256='cbf361c23a77e7647040e8070371691083e92aa93c8a318afcc495ad1c3a71d9') version('0.4.3', sha256='2b9df25a8f58df8e43038ec30bae195dfb160abdf925f3fa193b59d40e4113c5') diff --git a/var/spack/repos/builtin/packages/latte/package.py b/var/spack/repos/builtin/packages/latte/package.py index 9a0898b220a..0656e6cc307 100644 --- a/var/spack/repos/builtin/packages/latte/package.py +++ b/var/spack/repos/builtin/packages/latte/package.py @@ -18,9 +18,6 @@ class Latte(CMakePackage): version('develop', branch='master') version('1.2.1', sha256='a21dda5ebdcefa56e9ff7296d74ef03f89c200d2e110a02af7a84612668bf702') - version('1.2.0', md5='b9bf8f84a0e0cf7b0e278a1bc7751b3d') - version('1.1.1', md5='ab11867ba6235189681cf6e50a50cc50') - version('1.0.1', md5='d0b99edbcf7a19abe0a68a192d6f6234') variant('mpi', default=True, description='Build with mpi') diff --git a/var/spack/repos/builtin/packages/libconfig/package.py b/var/spack/repos/builtin/packages/libconfig/package.py index 0a6caccf9ce..c3b046b9a00 100644 --- a/var/spack/repos/builtin/packages/libconfig/package.py +++ b/var/spack/repos/builtin/packages/libconfig/package.py @@ -14,12 +14,8 @@ class Libconfig(AutotoolsPackage): force_autoreconf = True - version('1.7.1', - sha256='d288e6ae817f4ef78df43cdb2647f768dc97899ee82fcc41f857e8eb9fd7fbdb') - # there is currently a build error with version 1.6, see: - # https://github.com/hyperrealm/libconfig/issues/47 - # version('1.6', md5='2ccd24b6a2ee39f7ff8a3badfafb6539') - version('1.5', sha256='cae5c02361d8a9b2bb26946c64f089d2e5e599972f386203fbc48975c0d885c8') + version('1.7.1', sha256='d288e6ae817f4ef78df43cdb2647f768dc97899ee82fcc41f857e8eb9fd7fbdb') + version('1.5', sha256='cae5c02361d8a9b2bb26946c64f089d2e5e599972f386203fbc48975c0d885c8') depends_on('m4', type=('build')) depends_on('autoconf', type=('build')) diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index b6395b0b275..cd3a659aacc 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -22,7 +22,6 @@ class Libelf(AutotoolsPackage): url = "https://fossies.org/linux/misc/old/libelf-0.8.13.tar.gz" version('0.8.13', sha256='591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d') - # version('0.8.12', md5='e21f8273d9f5f6d43a59878dc274fec7') provides('elf@0') diff --git a/var/spack/repos/builtin/packages/libepoxy/package.py b/var/spack/repos/builtin/packages/libepoxy/package.py index 56fdb9887b4..d3bc68d4528 100644 --- a/var/spack/repos/builtin/packages/libepoxy/package.py +++ b/var/spack/repos/builtin/packages/libepoxy/package.py @@ -14,7 +14,6 @@ class Libepoxy(AutotoolsPackage): list_url = "https://github.com/anholt/libepoxy/releases" version('1.4.3', sha256='0b808a06c9685a62fca34b680abb8bc7fb2fda074478e329b063c1f872b826f6') - version('1.3.1', md5='96f6620a9b005a503e7b44b0b528287d') depends_on('pkgconfig', type='build') depends_on('meson') diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py index 9d0377e28da..825d52b7e25 100644 --- a/var/spack/repos/builtin/packages/libffi/package.py +++ b/var/spack/repos/builtin/packages/libffi/package.py @@ -15,9 +15,6 @@ class Libffi(AutotoolsPackage): version('3.2.1', sha256='d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37', url="https://www.mirrorservice.org/sites/sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") - # version('3.1', md5='f5898b29bbfd70502831a212d9249d10',url = - # "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug - # $(lib64) instead of ${lib64} in libffi.pc @property def headers(self): diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index eb6d6800742..8c77d01e4a1 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -22,8 +22,6 @@ class Libgd(AutotoolsPackage): url = 'https://github.com/libgd/libgd/releases/download/gd-2.2.4/libgd-2.2.4.tar.gz' version('2.2.4', sha256='487a650aa614217ed08ab1bd1aa5d282f9d379cfd95c756aed0b43406381be65') - version('2.2.3', md5='a67bd15fa33d4aac0a1c7904aed19f49') - version('2.1.1', md5='e91a1a99903e460e7ba00a794e72cc1e') # Build dependencies depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py index d788b09a04e..5ada427806b 100644 --- a/var/spack/repos/builtin/packages/libgit2/package.py +++ b/var/spack/repos/builtin/packages/libgit2/package.py @@ -17,7 +17,6 @@ class Libgit2(CMakePackage): url = "https://github.com/libgit2/libgit2/archive/v0.24.2.tar.gz" version('0.26.0', sha256='6a62393e0ceb37d02fe0d5707713f504e7acac9006ef33da1e88960bd78b6eac') - version('0.24.2', md5='735661b5b73e3c120d13e2bae21e49b3') depends_on('cmake@2.8:', type='build') depends_on('libssh2') diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py index 017d20048df..1f26b756280 100644 --- a/var/spack/repos/builtin/packages/libgpuarray/package.py +++ b/var/spack/repos/builtin/packages/libgpuarray/package.py @@ -15,8 +15,6 @@ class Libgpuarray(CMakePackage): url = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz" version('0.7.5', sha256='39c4d2e743848be43c8819c736e089ae51b11aa446cc6ee05af945c2dfd63420') - version('0.7.4', md5='19f57cd381175162048c8154f5251546') - version('0.7.3', md5='cb44aeb8482330974abdb36b0a477e5d') version('0.7.2', sha256='ef11ee6f8d62d53831277fd3dcab662aa770a5b5de2d30fe3018c4af959204da') version('0.7.1', sha256='4d0f9dd63b0595a8c04d8cee91b2619847c033b011c71d776caa784322382ed6') version('0.7.0', sha256='afe7907435dcbf78b3ea9b9f6c97e5a0d4a219a7170f5025ca0db1c289bb88df') diff --git a/var/spack/repos/builtin/packages/libnl/package.py b/var/spack/repos/builtin/packages/libnl/package.py index d976a504ecc..bd4a9e4cdf6 100644 --- a/var/spack/repos/builtin/packages/libnl/package.py +++ b/var/spack/repos/builtin/packages/libnl/package.py @@ -14,7 +14,6 @@ class Libnl(AutotoolsPackage): url = "https://github.com/thom311/libnl/releases/download/libnl3_3_0/libnl-3.3.0.tar.gz" version('3.3.0', sha256='705468b5ae4cd1eb099d2d1c476d6a3abe519bc2810becf12fb1e32de1e074e4') - version('3.2.25', md5='03f74d0cd5037cadc8cdfa313bbd195c') depends_on('bison', type='build') depends_on('flex', type='build') diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py index 00371cfc3e7..5f5d2832233 100644 --- a/var/spack/repos/builtin/packages/libsodium/package.py +++ b/var/spack/repos/builtin/packages/libsodium/package.py @@ -17,9 +17,6 @@ class Libsodium(AutotoolsPackage): version('1.0.16', sha256='eeadc7e1e1bcef09680fb4837d448fbdf57224978f865ac1c16745868fbd0533') version('1.0.15', sha256='fb6a9e879a2f674592e4328c5d9f79f082405ee4bb05cb6e679b90afe9e178f4') version('1.0.13', sha256='9c13accb1a9e59ab3affde0e60ef9a2149ed4d6e8f99c93c7a5b97499ee323fd') - version('1.0.12', md5='c308e3faa724b630b86cc0aaf887a5d4') - version('1.0.11', md5='b58928d035064b2a46fb564937b83540') - version('1.0.10', md5='ea89dcbbda0b2b6ff6a1c476231870dd') version('1.0.3', sha256='cbcfc63cc90c05d18a20f229a62c7e7054a73731d0aa858c0517152c549b1288') version('1.0.2', sha256='961d8f10047f545ae658bcc73b8ab0bf2c312ac945968dd579d87c768e5baa19') version('1.0.1', sha256='c3090887a4ef9e2d63af1c1e77f5d5a0656fadb5105ebb9fb66a302210cb3af5') diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py index 9694e9269a3..3d23210b563 100644 --- a/var/spack/repos/builtin/packages/libtiff/package.py +++ b/var/spack/repos/builtin/packages/libtiff/package.py @@ -17,7 +17,6 @@ class Libtiff(AutotoolsPackage): version('4.0.8', sha256='59d7a5a8ccd92059913f246877db95a2918e6c04fb9d43fd74e5c3390dac2910') version('4.0.7', sha256='9f43a2cfb9589e5cecaa66e16bf87f814c945f22df7ba600d63aac4632c4f019') version('4.0.6', sha256='4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c') - version('4.0.3', md5='051c1068e6a0627f461948c365290410') version('3.9.7', sha256='f5d64dd4ce61c55f5e9f6dc3920fbe5a41e02c2e607da7117a35eb5c320cef6a') depends_on('jpeg') diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index 3596ae4362c..697eb9c1bcd 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -19,10 +19,10 @@ class Lmod(AutotoolsPackage): homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod' url = 'https://github.com/TACC/Lmod/archive/7.4.11.tar.gz' - version('8.1.5', sha256='3e5846d3d8e593cbcdfa0aed1474569bf5b5cfd19fd288de22051823d449d344') - version('8.0.9', sha256='9813c22ae4dd21eb3dc480f6ce307156512092b4bca954bf8aacc15944f23673') + version('8.1.5', sha256='3e5846d3d8e593cbcdfa0aed1474569bf5b5cfd19fd288de22051823d449d344') + version('8.0.9', sha256='9813c22ae4dd21eb3dc480f6ce307156512092b4bca954bf8aacc15944f23673') version('7.8.15', sha256='00a257f5073d656adc73045997c28f323b7a4f6d901f1c57b7db2b0cd6bee6e6') - version('7.8', sha256='40388380a36a00c3ce929a9f88c8fffc93deeabf87a7c3f8864a82acad38c3ba') + version('7.8', sha256='40388380a36a00c3ce929a9f88c8fffc93deeabf87a7c3f8864a82acad38c3ba') version('7.7.29', sha256='269235d07d8ea387a2578f90bb64cf8ad16b4f28dcce196b293eb48cf1f71fb4') version('7.7.13', sha256='6145f075e5d49e12fcf0e75bb38afb27f205d23ba3496c1ff6c8b2cbaa9908be') version('7.7', sha256='090118fcecedbce5515cca8b77297f082686583aa06ca811b9703cd828f10e0a') @@ -37,7 +37,6 @@ class Lmod(AutotoolsPackage): version('6.4.5', sha256='741744a2837c9d92fceeccfebdc8e07ce4f4b7e56f67b214d317955bbd8786b7') version('6.4.1', sha256='a260b4e42269a80b517c066ba8484658362ea095e80767a2376bbe33d9b070a5') version('6.3.7', sha256='55ddb52cbdc0e2e389b3405229336df9aabfa582c874f5df2559ea264e2ee4ae') - version('6.0.1', md5='91abf52fe5033bd419ffe2842ebe7af9') depends_on('lua@5.1:') depends_on('lua-luaposix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/log4cplus/package.py b/var/spack/repos/builtin/packages/log4cplus/package.py index 3313570d81c..5ea94a877e0 100644 --- a/var/spack/repos/builtin/packages/log4cplus/package.py +++ b/var/spack/repos/builtin/packages/log4cplus/package.py @@ -16,4 +16,3 @@ class Log4cplus(CMakePackage): version('2.0.1', sha256='43baa7dec3db1ecc97dd9ecf3b50220439d2c7041d15860c36aa1d48dcf480b5') version('1.2.1', sha256='ada80be050033d7636beb894eb54de5575ceca95a5572e9437b0fc4ed7d877c4') - version('1.2.0', md5='e250f0f431c0723f8b625323e7b6465d') diff --git a/var/spack/repos/builtin/packages/macsio/package.py b/var/spack/repos/builtin/packages/macsio/package.py index c343e75cba3..d90aad340dd 100644 --- a/var/spack/repos/builtin/packages/macsio/package.py +++ b/var/spack/repos/builtin/packages/macsio/package.py @@ -18,7 +18,6 @@ class Macsio(CMakePackage): version('develop', branch='master') version('1.1', sha256='a86249b0f10647c0b631773db69568388094605ec1a0af149d9e61e95e6961ec') - version('1.0', md5='90e8e00ea84af2a47bee387ad331dbde') variant('mpi', default=True, description="Build MPI plugin") variant('silo', default=True, description="Build with SILO plugin") diff --git a/var/spack/repos/builtin/packages/mpifileutils/package.py b/var/spack/repos/builtin/packages/mpifileutils/package.py index e547a38a7a6..6bcdd02ce2a 100644 --- a/var/spack/repos/builtin/packages/mpifileutils/package.py +++ b/var/spack/repos/builtin/packages/mpifileutils/package.py @@ -23,10 +23,6 @@ class Mpifileutils(Package): version('develop', branch='master') version('0.9.1', sha256='15a22450f86b15e7dc4730950b880fda3ef6f59ac82af0b268674d272aa61c69') version('0.9', sha256='1b8250af01aae91c985ca5d61521bfaa4564e46efa15cee65cd0f82cf5a2bcfb') - version('0.8.1', md5='acbd5b5c15919a67392509614bb7871e') - version('0.8', md5='1082600e7ac4e6b2c13d91bbec40cffb') - version('0.7', md5='c081f7f72c4521dddccdcf9e087c5a2b') - version('0.6', md5='620bcc4966907481f1b1a965b28fc9bf') conflicts('platform=darwin') diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py index 46a066d393e..33800c9afab 100644 --- a/var/spack/repos/builtin/packages/muparser/package.py +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -12,8 +12,6 @@ class Muparser(Package): url = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz" version('2.2.6.1', sha256='d2562853d972b6ddb07af47ce8a1cdeeb8bb3fa9e8da308746de391db67897b3') - # 2.2.6 presents itself as 2.2.5, don't add it to Spack - # version('2.2.6', md5='f197b2815ca0422b2091788a78f2dc8a') version('2.2.5', sha256='0666ef55da72c3e356ca85b6a0084d56b05dd740c3c21d26d372085aa2c6e708') # Replace std::auto_ptr by std::unique_ptr diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index e0d4aff45ff..1673316bb7d 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -22,7 +22,6 @@ class Mvapich2(AutotoolsPackage): version('2.3a', sha256='7f0bc94265de9f66af567a263b1be6ef01755f7f6aedd25303d640cc4d8b1cff') version('2.2', sha256='791a6fc2b23de63b430b3e598bf05b1b25b82ba8bf7e0622fc81ba593b3bb131') version('2.1', sha256='49f3225ad17d2f3b6b127236a0abdc979ca8a3efb8d47ab4b6cd4f5252d05d29') - version('2.0', md5='9fbb68a4111a8b6338e476dc657388b4') provides('mpi') provides('mpi@:3.0') diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py index 718284c0fc1..17c5344031e 100644 --- a/var/spack/repos/builtin/packages/mxml/package.py +++ b/var/spack/repos/builtin/packages/mxml/package.py @@ -18,9 +18,6 @@ class Mxml(AutotoolsPackage): version('2.10', sha256='267ff58b64ddc767170d71dab0c729c06f45e1df9a9b6f75180b564f09767891') version('2.9', sha256='cded54653c584b24c4a78a7fa1b3b4377d49ac4f451ddf170ebbc8161d85ff92') version('2.8', sha256='0c9369f91a718d82e32cb007c0bd41b6642822c9a0ffe1d10eccbdea9a3011d5') - version('2.7', md5='76f2ae49bf0f5745d5cb5d9507774dc9') - version('2.6', md5='68977789ae64985dddbd1a1a1652642e') - version('2.5', md5='f706377fba630b39fa02fd63642b17e5') def url_for_version(self, version): if version <= Version('2.7'): diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py index db5946e59ce..43796ab7d8f 100644 --- a/var/spack/repos/builtin/packages/mxnet/package.py +++ b/var/spack/repos/builtin/packages/mxnet/package.py @@ -15,12 +15,6 @@ class Mxnet(MakefilePackage): version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2', url='https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz') - version('0.10.0.post2', md5='7819d511cf4a6efad681e6662fa966e4', - url="https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz") - version('0.10.0.post1', md5='16d540f407cd22285555b3ab22040032', - url="https://github.com/apache/incubator-mxnet/archive/v0.10.0.post1.tar.gz") - version('0.10.0', md5='2d0c83c33eda729932d620cca3078826', - url="https://github.com/apache/incubator-mxnet/archive/v0.10.0.tar.gz") variant('cuda', default=False, description='Enable CUDA support') variant('opencv', default=True, description='Enable OpenCV support') diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py index 267f7062d0d..06e51c1cab8 100644 --- a/var/spack/repos/builtin/packages/nag/package.py +++ b/var/spack/repos/builtin/packages/nag/package.py @@ -11,9 +11,9 @@ class Nag(Package): """The NAG Fortran Compiler.""" homepage = "http://www.nag.com/nagware/np.asp" - version('6.2', md5='8b119cc3296969bbd68b781f625de272') + version('6.2', sha256='e22f70f52949c4eb5526229c13920c924af5254d07a584cf54fefecd130fd29c') version('6.1', sha256='32580e0004e6798abf1fa52f0070281b28abeb0da2387530a4cc41218e813c7c') - version('6.0', md5='3fa1e7f7b51ef8a23e6c687cdcad9f96') + version('6.0', sha256='d5a326777a20303626b121da58522a122fcb1e3b4f2fcd657d9848e7b39fe7f8') # Licensing license_required = True @@ -25,7 +25,7 @@ class Nag(Package): def url_for_version(self, version): # TODO: url and checksum are architecture dependent # TODO: We currently only support x86_64 - url = 'http://www.nag.com/downloads/impl/npl6a{0}na_amd64.tgz' + url = 'https://www.nag.com/downloads/impl/npl6a{0}na_amd64.tgz' return url.format(version.joined) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index 1eb3508b30e..6788f7dae1d 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -13,12 +13,10 @@ class NetcdfCxx4(AutotoolsPackage): url = "https://www.github.com/unidata/netcdf-cxx4/tarball/v4.3.0" version('4.3.0', sha256='f4766d5a19c91093be80ddd2eaf1fbbd8d203854cc69fc73d2ad293b099ac799') - version('4.2.1', md5='d019853802092cf686254aaba165fc81') # Usually the configure automatically inserts the pic flags, but we can # force its usage with this variant. - variant('pic', default=True, - description='Produce position-independent code (for shared libs)') + variant('pic', default=True, description='Produce position-independent code (for shared libs)') depends_on('netcdf') diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py index 3c5b7556efa..6a18e54c5c1 100644 --- a/var/spack/repos/builtin/packages/nwchem/package.py +++ b/var/spack/repos/builtin/packages/nwchem/package.py @@ -20,8 +20,6 @@ class Nwchem(Package): url='https://github.com/nwchemgit/nwchem/releases/download/6.8.1-release/nwchem-6.8.1-release.revision-v6.8-133-ge032219-srconly.2018-06-14.tar.bz2') version('6.8', sha256='8401d9f4cce2f653a38639df61260b06be580ff0e1b8d77ed3262da159b372a6', url='https://github.com/nwchemgit/nwchem/archive/v6.8-release.tar.gz') - version('6.6', md5='c581001c004ea5e5dfacb783385825e3', - url='http://www.nwchem-sw.org/images/Nwchem-6.6.revision27746-src.2015-10-20.tar.gz') depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/ont-albacore/package.py b/var/spack/repos/builtin/packages/ont-albacore/package.py index be11466ad28..b9e070dcaf2 100644 --- a/var/spack/repos/builtin/packages/ont-albacore/package.py +++ b/var/spack/repos/builtin/packages/ont-albacore/package.py @@ -17,9 +17,7 @@ class OntAlbacore(Package): url = "https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.3.1-cp35-cp35m-manylinux1_x86_64.whl" version('2.3.1', sha256='dc1af11b0f38b26d071e5389c2b4595c496319c987401754e1853de42467a7d1', expand=False) - version('2.1.2', md5='1e60cfb95628829f2a61a85247f1b6af', expand=False) - version('1.2.4', md5='559640bec4693af12e4d923e8d77adf6', expand=False) - version('1.1.0', md5='fab4502ea1bad99d813aa2629e03e83d', expand=False) + extends('python') depends_on('python@3.5.0:3.5.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py index 632e6818272..12cbbcdb61d 100644 --- a/var/spack/repos/builtin/packages/pexsi/package.py +++ b/var/spack/repos/builtin/packages/pexsi/package.py @@ -26,7 +26,7 @@ class Pexsi(MakefilePackage): homepage = 'https://math.berkeley.edu/~linlin/pexsi/index.html' url = 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz' - # version('1.0', md5='4600b03e235935fe623acf500df0edfa') + # version('1.0', sha256='1574c66fd69ff2a37c6250d65c4df43b57c79822b49bd65662582a0cd5d82f54') version('0.10.2', sha256='8714c71b76542e096211b537a9cb1ffb2c28f53eea4f5a92f94cc1ca1e7b499f') version('0.9.2', sha256='9dc0fb66fc52c2b68e8fe485bbf4354ab0d9a548a4eaf7211eb4174c51bcf1de') version('0.9.0', sha256='e5efe0c129013392cdac3234e37f1f4fea641c139b1fbea47618b4b839d05029') diff --git a/var/spack/repos/builtin/packages/phylip/package.py b/var/spack/repos/builtin/packages/phylip/package.py index 53454ab8967..9233b98b7a8 100644 --- a/var/spack/repos/builtin/packages/phylip/package.py +++ b/var/spack/repos/builtin/packages/phylip/package.py @@ -14,7 +14,6 @@ class Phylip(Package): url = "http://evolution.gs.washington.edu/phylip/download/phylip-3.697.tar.gz" version('3.697', sha256='9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1') - version('3.696', md5='dbe5abc26f6089ead3dba41c2db526ee') def install(self, spec, prefix): with working_dir('src'): diff --git a/var/spack/repos/builtin/packages/pism/package.py b/var/spack/repos/builtin/packages/pism/package.py index 11dac2f4474..10bc658dff6 100644 --- a/var/spack/repos/builtin/packages/pism/package.py +++ b/var/spack/repos/builtin/packages/pism/package.py @@ -17,7 +17,6 @@ class Pism(CMakePackage): version('develop', branch='dev') version('1.1.4', sha256='8ccb867af3b37e8d103351dadc1d7e77512e64379519fe8a2592668deb27bc44') - version('0.7.3', md5='7cfb034100d99d5c313c4ac06b7f17b6') version('0.7.x', branch='stable0.7') version('icebin', branch='efischer/dev') diff --git a/var/spack/repos/builtin/packages/planck-likelihood/package.py b/var/spack/repos/builtin/packages/planck-likelihood/package.py index fc6e23cf782..70ab82de2eb 100644 --- a/var/spack/repos/builtin/packages/planck-likelihood/package.py +++ b/var/spack/repos/builtin/packages/planck-likelihood/package.py @@ -55,7 +55,7 @@ class PlanckLikelihood(Package): resource( name='plik-unbinned', url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-plik-unbinned.R2.00.tar.gz", - md5='c5869aa6b6581b6863d2a6e0ffd3826c', + sha256='69cdfee40d63a8b60b1f715d4e276d76693ec1a6f1b2658abac2b8d7dff4fa44', destination='.', when='+plik-unbinned') diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py index 7666b705621..0eb0050d341 100644 --- a/var/spack/repos/builtin/packages/prank/package.py +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -13,7 +13,6 @@ class Prank(Package): url = "http://wasabiapp.org/download/prank/prank.source.150803.tgz" version('170427', sha256='623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859') - version('150803', md5='71ac2659e91c385c96473712c0a23e8a') depends_on('mafft') depends_on('exonerate') diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py index 512fcb3d535..de252690d05 100644 --- a/var/spack/repos/builtin/packages/protobuf/package.py +++ b/var/spack/repos/builtin/packages/protobuf/package.py @@ -29,8 +29,6 @@ class Protobuf(CMakePackage): version('3.2.0', sha256='a839d3f1519ff9d68ab908de5a0f269650ef1fc501c10f6eefd4cae51d29b86f') version('3.1.0', sha256='fb2a314f4be897491bb2446697be693d489af645cb0e165a85e7e64e07eb134d') version('3.0.2', sha256='a0a265bcc9d4e98c87416e59c33afc37cede9fb277292523739417e449b18c1e') - # does not build with CMake: - # version('2.5.0', md5='9c21577a03adc1879aba5b52d06e25cf') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py index 2dcc335375c..fe4c4410e48 100644 --- a/var/spack/repos/builtin/packages/py-astroid/package.py +++ b/var/spack/repos/builtin/packages/py-astroid/package.py @@ -14,7 +14,7 @@ class PyAstroid(PythonPackage): url = "https://github.com/PyCQA/astroid/archive/astroid-1.4.5.tar.gz" version('2.2.0', sha256='7e289d0aa4a537b4aa798bd609fdf745de0f3c37e6b67642ed328e1482421a6d') - # version('1.5.3', md5='6f65e4ea8290ec032320460905afb828') # has broken unit tests + # version('1.5.3', sha256='6f65e4ea8290ec032320460905afb828') # has broken unit tests version('1.4.5', sha256='28d8f5b898087ecf86fd66ca0934e5c0e51fc0beb5972cfc4e0c11080e0cb6ab') version('1.4.4', sha256='a521dfdbb728ec36c4cc7a9287285e2c30233fb19faffcec8d080d1b2b2e7d1e') version('1.4.3', sha256='381a8b1a7e3861b0e7f5f25fb8d70fccf5d6b19ed81fcf76f569a5c5affe1bcc') diff --git a/var/spack/repos/builtin/packages/py-certifi/package.py b/var/spack/repos/builtin/packages/py-certifi/package.py index e4fe465ba7e..770877e3af6 100644 --- a/var/spack/repos/builtin/packages/py-certifi/package.py +++ b/var/spack/repos/builtin/packages/py-certifi/package.py @@ -18,7 +18,6 @@ class PyCertifi(PythonPackage): version('2019.6.16', sha256='945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695') version('2017.4.17', sha256='f7527ebf7461582ce95f7a9e03dd141ce810d40590834f4ec20cddd54234c10a') - version('2017.1.23', sha256='81877fb7ac126e9215dfb15bfef7115fdc30e798e0013065158eed0707fd99ce') - version('2016.02.28', sha1='5ccfc23bd5e931863f0b01ef3e9d2dbd3bef0e1b') + version('2017.1.23', sha256='81877fb7ac126e9215dfb15bfef7115fdc30e798e0013065158eed0707fd99ce') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index 35c1bb45499..603b3782fa2 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -29,7 +29,6 @@ class PyCython(PythonPackage): version('0.25.2', sha256='f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306') version('0.23.5', sha256='0ae5a5451a190e03ee36922c4189ca2c88d1df40a89b4f224bc842d388a0d1b6') version('0.23.4', sha256='fec42fecee35d6cc02887f1eef4e4952c97402ed2800bfe41bbd9ed1a0730d8e') - version('0.22', md5='1ae25add4ef7b63ee9b4af697300d6b6') version('0.21.2', sha256='b01af23102143515e6138a4d5e185c2cfa588e0df61c0827de4257bac3393679') depends_on('python@:2', type=('build', 'run'), when='@:0.22') diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py index 6b528439b03..95bf54a8e98 100644 --- a/var/spack/repos/builtin/packages/py-espressopp/package.py +++ b/var/spack/repos/builtin/packages/py-espressopp/package.py @@ -18,10 +18,8 @@ class PyEspressopp(CMakePackage): git = "https://github.com/espressopp/espressopp.git" version('develop', branch='master') - version('2.0.2', sha256='8cf4525bca06426379f5b9fbb8cc2603f559d28a2e74d1d7694df963b8f3dc6c') + version('2.0.2', sha256='8cf4525bca06426379f5b9fbb8cc2603f559d28a2e74d1d7694df963b8f3dc6c') version('1.9.5', sha256='8093f1a226f9fee8fb37c401767439a29ff3656dede3a44b4160169fc90d4d91') - version('1.9.4.1', md5='0da74a6d4e1bfa6a2a24fca354245a4f') - version('1.9.4', md5='f2a27993a83547ad014335006eea74ea') variant('ug', default=False, description='Build user guide') variant('pdf', default=False, description='Build user guide in pdf format') diff --git a/var/spack/repos/builtin/packages/py-git-review/package.py b/var/spack/repos/builtin/packages/py-git-review/package.py index d42a20e6511..38d860e86fa 100644 --- a/var/spack/repos/builtin/packages/py-git-review/package.py +++ b/var/spack/repos/builtin/packages/py-git-review/package.py @@ -14,10 +14,6 @@ class PyGitReview(PythonPackage): version('1.26.0', sha256='487c3c1d7cc81d02b303a1245e432579f683695c827ad454685b3953f70f0b94') version('1.25.0', sha256='087e0a7dc2415796a9f21c484a6f652c5410e6ba4562c36291c5399f9395a11d') - version('1.24', md5='145116fe58a3487c3ad1bf55538fd741') - version('1.23', md5='b0023ad8c037ab710da81412194c6a3a') - version('1.22', md5='e889df5838c059362e5e0d411bde9c48') - version('1.21', md5='eee88bdef1aa37a55cc8becd48c6aba9') extends('python') diff --git a/var/spack/repos/builtin/packages/py-maestrowf/package.py b/var/spack/repos/builtin/packages/py-maestrowf/package.py index e090b847016..66e766536f0 100644 --- a/var/spack/repos/builtin/packages/py-maestrowf/package.py +++ b/var/spack/repos/builtin/packages/py-maestrowf/package.py @@ -16,7 +16,6 @@ class PyMaestrowf(PythonPackage): maintainers = ['FrankD412'] version('1.1.4', sha256='2cb0fa6f6281d8618ac79217ea5f4fd8cb24955c4315e873657f96b815f171d5') - version('1.1.3', md5='0299e4ae3ec8b8c0296df0efaa8b517f') version('1.1.2', sha256='ebb45bff54625435bc9f2462e1bdc3b5bdc4d943378c53e7810c11836794c5e0') version('1.1.1', sha256='a476ad4b40846d7b7f9540d6413df1b42eb655735e8d3c6c07e0baa68e20a8bb') version('1.1.0', sha256='14e701d6a10ab758215aab6b6809817d9a39416a4f477cd2f2551883fc68477b') diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py index 3b75d17a6d4..75411cd5ff0 100644 --- a/var/spack/repos/builtin/packages/py-openpyxl/package.py +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -13,7 +13,6 @@ class PyOpenpyxl(PythonPackage): url = "https://pypi.io/packages/source/o/openpyxl/openpyxl-2.4.5.tar.gz" version('2.4.5', sha256='78c331e819fb0a63a1339d452ba0b575d1a31f09fdcce793a31bec7e9ef4ef21') - version('2.2.0-b1', md5='eeefabe384f6e53166c8c2e6abe5d11b') depends_on('python@2.6:2.8,3.0:3.1,3.3:') diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py index dfa0fe4790f..3675482b086 100644 --- a/var/spack/repos/builtin/packages/py-pygpu/package.py +++ b/var/spack/repos/builtin/packages/py-pygpu/package.py @@ -13,8 +13,6 @@ class PyPygpu(PythonPackage): url = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz" version('0.7.5', sha256='39c4d2e743848be43c8819c736e089ae51b11aa446cc6ee05af945c2dfd63420') - version('0.7.4', md5='19f57cd381175162048c8154f5251546') - version('0.7.3', md5='cb44aeb8482330974abdb36b0a477e5d') version('0.7.2', sha256='ef11ee6f8d62d53831277fd3dcab662aa770a5b5de2d30fe3018c4af959204da') version('0.7.1', sha256='4d0f9dd63b0595a8c04d8cee91b2619847c033b011c71d776caa784322382ed6') version('0.7.0', sha256='afe7907435dcbf78b3ea9b9f6c97e5a0d4a219a7170f5025ca0db1c289bb88df') diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py index 5ee8763e8c5..01e14ba11e4 100644 --- a/var/spack/repos/builtin/packages/py-pylint/package.py +++ b/var/spack/repos/builtin/packages/py-pylint/package.py @@ -13,7 +13,7 @@ class PyPylint(PythonPackage): url = "https://pypi.io/packages/source/p/pylint/pylint-1.6.5.tar.gz" version('2.3.0', sha256='ee80c7af4f127b2a480d83010c9f0e97beb8eaa652b78c2837d3ed30b12e1182') - # version('1.7.2', md5='27ee752cdcfacb05bf4940947e6b35c6') # see dependencies + # version('1.7.2', sha256='ea6afb93a9ed810cf52ff3838eb3a15e2bf6a81b80de0eaede1ce442caa5ca69') # see dependencies version('1.6.5', sha256='a673984a8dd78e4a8b8cfdee5359a1309d833cf38405008f4a249994a8456719') version('1.4.3', sha256='1dce8c143a5aa15e0638887c2b395e2e823223c63ebaf8d5f432a99e44b29f60') version('1.4.1', sha256='3e383060edd432cbbd0e8bd686f5facfe918047ffe1bb401ab5897cb6ee0f030') diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py index f95031cd3b9..1cac32702a4 100644 --- a/var/spack/repos/builtin/packages/py-pysam/package.py +++ b/var/spack/repos/builtin/packages/py-pysam/package.py @@ -13,12 +13,9 @@ class PyPysam(PythonPackage): homepage = "https://pypi.python.org/pypi/pysam" url = "https://github.com/pysam-developers/pysam/archive/v0.14.1.tar.gz" - version('0.15.2', sha256='8cb3dd70f0d825086ac059ec2445ebd2ec5f14af73e7f1f4bd358966aaee5ed3') - version('0.15.1', sha256='12221285af17e32b8f3fed033f90c6177a798afe41420eb5c3352d4e18ee12ed') + version('0.15.2', sha256='8cb3dd70f0d825086ac059ec2445ebd2ec5f14af73e7f1f4bd358966aaee5ed3') + version('0.15.1', sha256='12221285af17e32b8f3fed033f90c6177a798afe41420eb5c3352d4e18ee12ed') version('0.14.1', sha256='d2bb40cd083c1357768e4683377f03471d160cfe8421136630bfa47f5adb3219') - version('0.13', md5='a9b502dd1a7e6403e35e6972211688a2') - version('0.11.2.2', md5='56230cd5f55b503845915b76c22d620a') - version('0.7.7', md5='eaf9f37cbccc5e2708754d045909c1a0') depends_on('py-setuptools', type='build') depends_on('py-cython@0.21:', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py index 17f3277fa4a..bd4f622d9b4 100644 --- a/var/spack/repos/builtin/packages/py-pyside/package.py +++ b/var/spack/repos/builtin/packages/py-pyside/package.py @@ -23,9 +23,6 @@ class PyPyside(PythonPackage): # and show little interest in certifying PySide 1.2.4 for Python. version('1.2.4', sha256='1421bc1bf612c396070de9e1ffe227c07c1f3129278bc7d30c754b5146be2433') # rpath problems - # This is not available from pypi - # version('1.2.3', md5='fa5d5438b045ede36104bba25a6ccc10') - # v1.2.2 does not work with Python3 version('1.2.2', sha256='53129fd85e133ef630144c0598d25c451eab72019cdcb1012f2aec773a3f25be', preferred=True) diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index e46202e584f..ca4bc083cac 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -15,7 +15,6 @@ class PyPytz(PythonPackage): import_modules = ['pytz'] version('2018.4', sha256='c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749') - version('2017.2', md5='f89bde8a811c8a1a5bac17eaaa94383c') version('2016.10', sha256='9a43e20aa537cfad8fe7a1715165c91cb4a6935d40947f2d070e4c80f2dcd22b') version('2016.6.1', sha256='6f57732f0f8849817e9853eb9d50d85d1ebb1404f702dbc44ee627c642a486ca') version('2014.10', sha256='a94138b638907491f473c875e8c95203a6a02efef52b6562be302e435016f4f3') diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 0c7afe3c67d..3e61d514620 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -33,7 +33,6 @@ class PySetuptools(PythonPackage): version('25.2.0', sha256='b2757ddac2c41173140b111e246d200768f6dd314110e1e40661d0ecf9b4d6a6') version('20.7.0', sha256='505cdf282c5f6e3a056e79f0244b8945f3632257bba8469386c6b9b396400233') version('20.6.7', sha256='d20152ee6337323d3b6d95cd733fb719d6b4f3fbc40f61f7a48e5a1bb96478b2') - version('20.5', md5='fadc1e1123ddbe31006e5e43e927362b') version('19.2', sha256='f90ed8eb70b14b0594ba74e9de4ffca040c0ec8ee505cbf3570499467859f71a') version('18.1', sha256='ad52a9d5b3a6f39c2a1c2deb96cc4f6aff29d6511bdea2994322c40b60c9c36a') version('16.0', sha256='aa86255dee2c4a0056509750008007667c29306b7a6c13801468515b2c672845') diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py index dc09ad6902d..997b4f9c01a 100644 --- a/var/spack/repos/builtin/packages/py-sip/package.py +++ b/var/spack/repos/builtin/packages/py-sip/package.py @@ -18,8 +18,6 @@ class PySip(Package): version('develop', hg=hg) # wasn't actually able to clone this version('4.19.18', sha256='c0bd863800ed9b15dcad477c4017cdb73fa805c25908b0240564add74d697e1e') version('4.19.13', sha256='e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e') - version('4.16.7', md5='32abc003980599d33ffd789734de4c36') - version('4.16.5', md5='6d01ea966a53e4c7ae5c5e48c40e49e5') variant('module', default='sip', description='Name of private SIP module', values=str, multi=False) diff --git a/var/spack/repos/builtin/packages/py-spyder/package.py b/var/spack/repos/builtin/packages/py-spyder/package.py index 5566a4a44e5..607a52393bf 100644 --- a/var/spack/repos/builtin/packages/py-spyder/package.py +++ b/var/spack/repos/builtin/packages/py-spyder/package.py @@ -13,7 +13,6 @@ class PySpyder(PythonPackage): url = "https://pypi.io/packages/source/s/spyder/spyder-3.1.3.tar.gz" version('3.1.3', sha256='4978872cc5a006803bc8742d0a8fb43c49aef9524f0a9fcb8bd6dfcfdc2d2d6a') - version('2.3.9', md5='dd01e07a77123c128ff79ba57b97c1d7') depends_on('python@2.7.0:2.8.0,3.3.0:', type=('build', 'run')) depends_on('py-rope@0.9.4:', type=('build', 'run'), when='^python@:3') diff --git a/var/spack/repos/builtin/packages/py-traitlets/package.py b/var/spack/repos/builtin/packages/py-traitlets/package.py index 6c886e21220..945e469bf21 100644 --- a/var/spack/repos/builtin/packages/py-traitlets/package.py +++ b/var/spack/repos/builtin/packages/py-traitlets/package.py @@ -21,7 +21,6 @@ class PyTraitlets(PythonPackage): version('4.2.0', sha256='923cbe84bef30c27d2083f014f23a5da0ebe7da2e67a683d97acb07002e2ce0d') version('4.1.0', sha256='93ead8dbf7e9617c88b79620072bfc499e7f25613f3df2234e5fdf08348c0a83') version('4.0.0', sha256='03f380cb2e47689ae55dbe9a5dccbdde5cad8c4637312d720f4c3a991fb15cd2') - version('4.0', md5='14544e25ccf8e920ed1cbf833852481f') depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/qt-creator/package.py b/var/spack/repos/builtin/packages/qt-creator/package.py index 4d8bd4808a0..9b23300a655 100644 --- a/var/spack/repos/builtin/packages/qt-creator/package.py +++ b/var/spack/repos/builtin/packages/qt-creator/package.py @@ -15,9 +15,6 @@ class QtCreator(QMakePackage): list_depth = 2 version('4.8.0', sha256='4c4813454637141a45aa8f18be5733e4ba993335d95940aadf12fda66cf6f849') - version('4.4.0', md5='bae2e08bb5087aba65d41eb3f9328d9a') - version('4.3.1', md5='6769ea47f287e2d9e30ff92acb899eef') - version('4.1.0', md5='657727e4209befa4bf5889dff62d9e0a') depends_on('qt@5.6.0:+opengl') # Qt Creator comes bundled with its own copy of sqlite. Qt has a build diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index 6079866f31b..c212794956b 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -18,7 +18,6 @@ class RCheckpoint(RPackage): version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') version('0.4.3', sha256='c3e862f89f8838183d6028f7ed13683aec562e6dab77ad4b6a5e24ec653cfb64') - version('0.3.18', md5='021d7faeb72c36167951e103b2b065ea') version('0.3.15', sha256='09f1feeb2b5b8b409a2e16a9185827b8da5e555f1aa84442a287f15e452beed7') depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py index 8d041a28c01..eae2b5be522 100644 --- a/var/spack/repos/builtin/packages/r-hmisc/package.py +++ b/var/spack/repos/builtin/packages/r-hmisc/package.py @@ -20,7 +20,6 @@ class RHmisc(RPackage): version('4.2-0', sha256='9e9614673288dd00295f250fa0bf96fc9e9fed692c69bf97691081c1a01411d9') version('4.1-1', sha256='991db21cdf73ffbf5b0239a4876b2e76fd243ea33528afd88dc968792f281498') - version('4.0-3', md5='7091924db1e473419d8116c3335f82da') depends_on('r-lattice', type=('build', 'run')) depends_on('r-survival@2.40-1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index 812478b0ccf..af0cc893d8c 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -19,7 +19,6 @@ class RKnitr(RPackage): version('1.23', sha256='063bfb3300fc9f3e7d223c346e19b93beced0e6784470b9bef2524868a206a99') version('1.17', sha256='9484a2b2c7b0c2aae24ab7f4eec6db48affbceb0e42bd3d69e34d953fe92f401') version('1.14', sha256='ba6d301482d020a911390d5eff181e1771f0e02ac3f3d9853a9724b1ec041aec') - version('0.6', md5='c67d6db84cd55594a9e870c90651a3db') depends_on('r@2.14.1:', when='@:1.9', type=('build', 'run')) depends_on('r@3.0.2:', when='@1.10:1.14', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index 33516c27cd9..fd3995f9e54 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -16,7 +16,6 @@ class RMass(RPackage): version('7.3-51.4', sha256='9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74') version('7.3-51.3', sha256='5b0e0e7704d43a94b08dcc4b3fe600b9723d1b3e446dd393e82d39ddf66608b6') - version('7.3-47', sha256='ed44cdabe84fff3553122267ade61d5cc68071c435f7645d36c8f2e4e9f9c6bf') - version('7.3-45', md5='aba3d12fab30f1793bee168a1efea88b') + version('7.3-47', sha256='ed44cdabe84fff3553122267ade61d5cc68071c435f7645d36c8f2e4e9f9c6bf') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index 558d02308b5..b80ec008bad 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -16,10 +16,9 @@ class RMatrix(RPackage): version('1.2-17', sha256='db43e6f0196fd5dfd05a7e88cac193877352c60d771d4ec8772763e645723fcc') version('1.2-14', sha256='49a6403547b66675cb44c1afb04bb87130c054510cb2b94971435a826ab41396') - version('1.2-12', md5='0ade6e374716f08650cc8b8da99a313c') version('1.2-11', sha256='ba8cd6565612552fe397e909721817b6cc0604a91299d56d118208006888dc0b') - version('1.2-8', sha256='3cd2a187c45fc18a0766dc148b7f83dbf6f2163c256e887c41cbaa7c9a20dbb7') - version('1.2-6', sha256='4b49b639b7bf612fa3d1c1b1c68125ec7859c8cdadae0c13f499f24099fd5f20') + version('1.2-8', sha256='3cd2a187c45fc18a0766dc148b7f83dbf6f2163c256e887c41cbaa7c9a20dbb7') + version('1.2-6', sha256='4b49b639b7bf612fa3d1c1b1c68125ec7859c8cdadae0c13f499f24099fd5f20') depends_on('r@3.0.1:', when='@:1.2-12', type=('build', 'run')) depends_on('r@3.2.0:', when='@1.2.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index d03e9a3e8ea..59fc2342a90 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -17,7 +17,6 @@ class RNlme(RPackage): version('3.1-139', sha256='0460fc69d85122177e7ef01bad665d56bcaf63d31bdbfdbdfdcba2c082085739') version('3.1-131', sha256='79daa167eb9bc7d8dba506da4b24b5250665b051d4e0a51dfccbb0087fdb564c') version('3.1-130', sha256='ec576bd906ef2e1c79b6a4382743d425846f63be2a43de1cce6aa397b40e290e') - version('3.1-128', md5='3d75ae7380bf123761b95a073eb55008') depends_on('r@3.0.2:', when='@:3.1-131', type=('build', 'run')) depends_on('r@3.3.0:', when='@3.1-131.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index a96023e11be..95346b8290d 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -19,7 +19,6 @@ class RNmf(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') - version('0.20.6', md5='81df07b3bf710a611db5af24730ff3d0') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-pkgmaker@0.20:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index c6a312f2c09..e400f1228fb 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -20,7 +20,6 @@ class RPkgmaker(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') - version('0.22', md5='73a0c6d3e84c6dadf3de7582ef7e88a4') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-registry', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index 587b0e356fc..f8420eebb0a 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -18,6 +18,5 @@ class RRandomfieldsutils(RPackage): version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') version('0.5.1', sha256='a95aab4e2025c4247503ff513570a65aa3c8e63cb7ce2979c9317a2798dfaca2') - version('0.3.25', md5='026c15a23296c9726012135891f016d5') depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index 9269273cf87..c4b52c34371 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -20,7 +20,6 @@ class RRngtools(RPackage): version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') version('1.3.1.1', sha256='99e1a8fde6b81128d0946746c1ef84ec5b6c2973ad843a080098baf73aa3364c') version('1.3.1', sha256='763fc493cb821a4d3e514c0dc876d602a692c528e1d67f295dde70c77009e224') - version('1.2.4', md5='715967f8b3af2848a76593a7c718c1cd') depends_on('r@3.0.0:', when='@:1.3.1', type=('build', 'run')) depends_on('r@3.6.0:', when='@1.3.1.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index cdc2f237a5e..ee0f934447b 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -15,7 +15,6 @@ class RXlsx(RPackage): listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') - version('0.5.7', md5='36b1b16f29c54b6089b1dae923180dd5') depends_on('r-rjava', type=('build', 'run')) depends_on('r-xlsxjars', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/re2c/package.py b/var/spack/repos/builtin/packages/re2c/package.py index 580e2704ac9..5b64b2ec66c 100644 --- a/var/spack/repos/builtin/packages/re2c/package.py +++ b/var/spack/repos/builtin/packages/re2c/package.py @@ -14,7 +14,6 @@ class Re2c(AutotoolsPackage): url = "https://github.com/skvadrik/re2c/releases/download/1.2.1/re2c-1.2.1.tar.xz" version('1.2.1', sha256='1a4cd706b5b966aeffd78e3cf8b24239470ded30551e813610f9cd1a4e01b817') - version('1.0.3', md5='8f575e2bf2efd3c685c87042f279ae4f') def configure_args(self): args = ['--disable-dependency-tracking'] diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py index 43ac1e72161..50176857bf3 100644 --- a/var/spack/repos/builtin/packages/revbayes/package.py +++ b/var/spack/repos/builtin/packages/revbayes/package.py @@ -15,8 +15,6 @@ class Revbayes(CMakePackage): version('1.0.11', sha256='7e81b1952e3a63cb84617fa632f4ccdf246b4d79e7d537a423540de047dadf50') version('1.0.10', sha256='95e9affe8ca8d62880cf46778b6ec9dd8726e62a185670ebcbadf2eb2bb79f93') - version('1.0.4', md5='5d6de96bcb3b2686b270856de3555a58', - url='https://github.com/revbayes/revbayes/archive/v1.0.4-release.tar.gz') variant('mpi', default=True, description='Enable MPI parallel support') diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index e462fd70bd8..23b497a2e74 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -18,27 +18,16 @@ class Rose(AutotoolsPackage): homepage = "http://rosecompiler.org/" # url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.7.0.tar.gz" url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.9.104.zip" + git = "https://github.com/rose-compiler/rose-develop.git" # -------------------------------------------------------------------------- # ROSE Versions # -------------------------------------------------------------------------- - version( - "0.9.10.0", - sha256="7b53b6913fd6ca0c5050b630dae380f3e6b0897cde6148172ba01095f71cbaca", - ) - version("0.9.9.104", md5="b01cf9d2fd440fc0fe77a713c5f7831e") - version("0.9.9.0", md5="8f47fb8aa803d019657bd42c8b892cce") - version("0.9.7.0", md5="be0d0941ba4c0349a20d6394c20d16d7") - version( - "0.9.9.52", - commit="bd4fc0cc332ce62d9fa54db19879507d9e4f239b", - git="https://github.com/rose-compiler/rose-develop.git", - ) - version( - "develop", - branch="master", - git="https://github.com/rose-compiler/rose-develop.git", - ) + version("0.9.10.0", sha256="7b53b6913fd6ca0c5050b630dae380f3e6b0897cde6148172ba01095f71cbaca") + + # git versions + version("0.9.9.52", commit="bd4fc0cc332ce62d9fa54db19879507d9e4f239b") + version("develop", branch="master") # -------------------------------------------------------------------------- # Dependencies diff --git a/var/spack/repos/builtin/packages/rtags/package.py b/var/spack/repos/builtin/packages/rtags/package.py index 54f55884a47..4ee2464b4eb 100644 --- a/var/spack/repos/builtin/packages/rtags/package.py +++ b/var/spack/repos/builtin/packages/rtags/package.py @@ -13,7 +13,6 @@ class Rtags(CMakePackage): url = "https://andersbakken.github.io/rtags-releases/rtags-2.17.tar.gz" version('2.17', sha256='cde8882aceb09d65690007e214cc1979e0105842beb7747d49f79e33ed37d383') - # version('2.12', md5='84988aaff27915a79d4b4b57299f9a51') # no available depends_on("llvm@3.3: +clang") depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py index e038def9f36..133c89eff34 100644 --- a/var/spack/repos/builtin/packages/scr/package.py +++ b/var/spack/repos/builtin/packages/scr/package.py @@ -17,11 +17,6 @@ class Scr(CMakePackage): url = "https://github.com/LLNL/scr/archive/v1.2.0.tar.gz" git = "https://github.com/llnl/scr.git" - # NOTE: scr-v1.1.8 is built with autotools and is not properly build here. - # scr-v1.1.8 will be deprecated with the upcoming release of v1.2.0 - # url = "https://github.com/LLNL/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz" - # version('1.1.8', md5='6a0f11ad18e27fcfc00a271ff587b06e') - version('master', branch='master') version('1.2.2', sha256='764a85638a9e8762667ec1f39fa5f7da7496fca78de379a22198607b3e027847') version('1.2.1', sha256='23acab2dc7203e9514455a5168f2fd57bc590affb7a1876912b58201513628fe') diff --git a/var/spack/repos/builtin/packages/simulationio/package.py b/var/spack/repos/builtin/packages/simulationio/package.py index 400eb7d2ba9..51b43719d89 100644 --- a/var/spack/repos/builtin/packages/simulationio/package.py +++ b/var/spack/repos/builtin/packages/simulationio/package.py @@ -16,8 +16,6 @@ class Simulationio(CMakePackage): version('develop', branch='master') version('9.0.1', sha256='c2f6c99417165f6eb8cbb9c44822d119586675abb34eabd553eb80f44b53e0c8') - version('1.0.0', md5='5cbf1d0084eb436d861ffcdd297eaa08') - version('0.1.0', md5='00f7dabc08ed1ab77858785ce0809f50') variant('julia', default=False) variant('python', default=True) diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 5c56f651d04..0644ed1feaa 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -22,7 +22,6 @@ class Thrift(Package): version('0.11.0', sha256='c4ad38b6cb4a3498310d405a91fef37b9a8e79a50cd0968148ee2524d2fa60c2') version('0.10.0', sha256='2289d02de6e8db04cbbabb921aeb62bfe3098c4c83f36eec6c31194301efa10b') version('0.9.3', sha256='b0740a070ac09adde04d43e852ce4c320564a292f26521c46b78e0641564969e') - version('0.9.2', md5='89f63cc4d0100912f4a1f8a9dee63678') # Currently only support for c-family and python variant('c', default=True, diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py index 8ec3b9de39f..4788efd070f 100644 --- a/var/spack/repos/builtin/packages/turbine/package.py +++ b/var/spack/repos/builtin/packages/turbine/package.py @@ -19,7 +19,6 @@ class Turbine(AutotoolsPackage): version('master', branch='master') version('1.2.3', sha256='a3156c7e0b39e166da3de8892f55fa5d535b0c99c87a9add067c801098fe51ba') - version('1.2.1', md5='c8976b22849aafe02a8fb4259dfed434') version('1.1.0', sha256='98fad47597935a04d15072e42bf85411d55ef00cb6f953e9f14d6de902e33209') variant('python', default=False, diff --git a/var/spack/repos/builtin/packages/vardictjava/package.py b/var/spack/repos/builtin/packages/vardictjava/package.py index 3806174edb0..a9f0f1b976a 100644 --- a/var/spack/repos/builtin/packages/vardictjava/package.py +++ b/var/spack/repos/builtin/packages/vardictjava/package.py @@ -15,7 +15,6 @@ class Vardictjava(Package): url = "https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.5.1/VarDict-1.5.1.tar" version('1.5.1', sha256='f1d710d238e8ab41b02a99fa8698baeee8c8668635a847b826913dd03a9176b9') - version('1.4.4', md5='6b2d7e1e5502b875760fc9938a0fe5e0') depends_on('java@8:', type='run') diff --git a/var/spack/repos/builtin/packages/vcftools/package.py b/var/spack/repos/builtin/packages/vcftools/package.py index b32ee81ee1c..5368ddd931c 100644 --- a/var/spack/repos/builtin/packages/vcftools/package.py +++ b/var/spack/repos/builtin/packages/vcftools/package.py @@ -17,7 +17,7 @@ class Vcftools(AutotoolsPackage): url = "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz" # this is "a pre-release" - # version('0.1.15', md5='61045197848dea20a0158d2faf02e5be') + # version('0.1.15', sha256='31e47afd5be679d89ece811a227525925b6907cce4af2c86f10f465e080383e3') version('0.1.14', sha256='76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582') depends_on('perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/wcslib/package.py b/var/spack/repos/builtin/packages/wcslib/package.py index 834ab583955..551306fe8c3 100644 --- a/var/spack/repos/builtin/packages/wcslib/package.py +++ b/var/spack/repos/builtin/packages/wcslib/package.py @@ -14,7 +14,6 @@ class Wcslib(AutotoolsPackage): url = "ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib-6.4.tar.bz2" version('6.4', sha256='13c11ff70a7725563ec5fa52707a9965fce186a1766db193d08c9766ea107000') - version('5.18', md5='67a78354be74eca4f17d3e0853d5685f') variant('cfitsio', default=False, description='Include CFITSIO support') variant('x', default=False, description='Use the X Window System') diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py index d0bb98832d6..c896e91134b 100644 --- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py +++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py @@ -19,14 +19,11 @@ class Xsdktrilinos(CMakePackage): version('develop', tag='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') version('12.8.1', sha256='f545c0821743f23af3b48f242c66bbc4593e3804436336db4eb3bb08622ad794') - version('12.6.4', md5='44c4c54ccbac73bb8939f68797b9454a') + version('12.6.4', sha256='a7664afeab37ccfcbb5aae0bb03cb73ca8e511e0fecc365b9ccd32ba208318e3') - variant('hypre', default=True, - description='Compile with Hypre preconditioner') - variant('petsc', default=True, - description='Compile with PETSc solvers') - variant('shared', default=True, - description='Enables the build of shared libraries') + variant('hypre', default=True, description='Compile with Hypre preconditioner') + variant('petsc', default=True, description='Compile with PETSc solvers') + variant('shared', default=True, description='Enables the build of shared libraries') # MPI related dependencies depends_on('mpi') From 45a9cfcdd72188350d47ed2d8be2e5698d6ecd15 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 12 Oct 2019 01:43:31 -0700 Subject: [PATCH 192/499] packages: remove packages that are no longer fetchable These packages have either been retired or are no longer retrievable from any site we can find. They also aren't needed by other packages, so we're removing them from Spack. - allinea-reports: is now arm performance reports - globus-toolkit: retired, globus is now a paid service. - uberftp: used globus-toolkit, github site is retired. - mpiblast: site is dead; no longer fetchable. - py-mxnet: site and github are gone - soap2, soapindel, soapsnp: site is gone, unfetchable - arlecore: could not verify md5 securely --- .../packages/allinea-reports/package.py | 33 ---- .../builtin/packages/arlecore/package.py | 20 -- .../packages/globus-toolkit/package.py | 20 -- .../mpiblast/mpiBLAST-1.6.0-patch-110806 | 182 ------------------ .../builtin/packages/mpiblast/package.py | 32 --- .../builtin/packages/py-mxnet/package.py | 39 ---- .../repos/builtin/packages/soap2/package.py | 23 --- .../builtin/packages/soapindel/package.py | 34 ---- .../repos/builtin/packages/soapsnp/package.py | 23 --- .../repos/builtin/packages/uberftp/package.py | 19 -- 10 files changed, 425 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/allinea-reports/package.py delete mode 100644 var/spack/repos/builtin/packages/arlecore/package.py delete mode 100644 var/spack/repos/builtin/packages/globus-toolkit/package.py delete mode 100644 var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806 delete mode 100644 var/spack/repos/builtin/packages/mpiblast/package.py delete mode 100644 var/spack/repos/builtin/packages/py-mxnet/package.py delete mode 100644 var/spack/repos/builtin/packages/soap2/package.py delete mode 100644 var/spack/repos/builtin/packages/soapindel/package.py delete mode 100644 var/spack/repos/builtin/packages/soapsnp/package.py delete mode 100644 var/spack/repos/builtin/packages/uberftp/package.py diff --git a/var/spack/repos/builtin/packages/allinea-reports/package.py b/var/spack/repos/builtin/packages/allinea-reports/package.py deleted file mode 100644 index 49496d43c93..00000000000 --- a/var/spack/repos/builtin/packages/allinea-reports/package.py +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class AllineaReports(Package): - """Allinea Performance Reports are the most effective way to characterize - and understand the performance of HPC application runs. One single-page - HTML report elegantly answers a range of vital questions for any HPC site - """ - - homepage = "http://www.allinea.com/products/allinea-performance-reports" - - version('6.0.4', '3f13b08a32682737bc05246fbb2fcc77') - - # Licensing - license_required = True - license_comment = '#' - license_files = ['licences/Licence'] - license_vars = ['ALLINEA_LICENCE_FILE', 'ALLINEA_LICENSE_FILE'] - license_url = 'http://www.allinea.com/user-guide/reports/Installation.html' - - def url_for_version(self, version): - # TODO: add support for other architectures/distributions - url = "http://content.allinea.com/downloads/" - return url + "allinea-reports-%s-Redhat-6.0-x86_64.tar" % version - - def install(self, spec, prefix): - textinstall = Executable('./textinstall.sh') - textinstall('--accept-licence', prefix) diff --git a/var/spack/repos/builtin/packages/arlecore/package.py b/var/spack/repos/builtin/packages/arlecore/package.py deleted file mode 100644 index 5c63056bd2a..00000000000 --- a/var/spack/repos/builtin/packages/arlecore/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Arlecore(Package): - """An Integrated Software for Population Genetics Data Analysis""" - - homepage = "http://cmpg.unibe.ch/software/arlequin35/" - url = "http://cmpg.unibe.ch/software/arlequin35/linux/arlecore_linux.zip" - - version('3.5.2.2', '347a589fc609f359eb61557a2e8ceb2f') - - depends_on('r', type=('build', 'run')) - - def install(self, spec, prefix): - install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/globus-toolkit/package.py b/var/spack/repos/builtin/packages/globus-toolkit/package.py deleted file mode 100644 index 7a434126081..00000000000 --- a/var/spack/repos/builtin/packages/globus-toolkit/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class GlobusToolkit(AutotoolsPackage): - """The Globus Toolkit is an open source software toolkit used for building - grids""" - - homepage = "http://toolkit.globus.org" - url = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1506371041.tar.gz" - - version('6.0.1506371041', 'e17146f68e03b3482aaea3874d4087a5') - version('6.0.1493989444', '9e9298b61d045e65732e12c9727ceaa8') - - depends_on('pkgconfig', type='build') - depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806 b/var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806 deleted file mode 100644 index 05de8ed074f..00000000000 --- a/var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806 +++ /dev/null @@ -1,182 +0,0 @@ -diff -rwu mpiblast-1.6.0/ncbi/corelib/ncbienv.c mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c ---- mpiblast-1.6.0/ncbi/corelib/ncbienv.c 2009-11-22 01:17:48.000000000 -0500 -+++ mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c 2011-08-06 17:10:08.000000000 -0400 -@@ -1932,7 +1932,7 @@ - static char **targv = NULL; - - --#if defined(WIN_MAC) -+#if defined(WIN_MAC) || defined(OS_UNIX_DARWIN) - static FSSpec apFileSpec; - static Str255 apName; - static Handle apParam; -@@ -2047,7 +2047,7 @@ - } - } - #endif /* defined(OS_UNIX_DARWIN) */ --#endif /* defined(WIN_MAC) */ -+#endif /* defined(WIN_MAC) || defined(OS_UNIX_DARWIN) */ - - - #if defined(OS_MSWIN) || defined(OS_VMS) -diff -rwu mpiblast-1.6.0/ncbi/make/makedis.csh mpiblast-1.6.0-patched/ncbi/make/makedis.csh ---- mpiblast-1.6.0/ncbi/make/makedis.csh 2010-06-28 21:04:36.000000000 -0400 -+++ mpiblast-1.6.0-patched/ncbi/make/makedis.csh 2011-08-06 17:06:42.000000000 -0400 -@@ -1,6 +1,6 @@ - #!/bin/csh -f - # --# $Id: makedis.csh 148594 2008-12-30 15:11:36Z ucko $ -+# $Id: makedis.csh 179886 2010-01-04 17:28:02Z ucko $ - # - ## PUBLIC DOMAIN NOTICE - # National Center for Biotechnology Information -@@ -54,7 +54,7 @@ - endif - - ls -l $tar_file -- tar xvf $tar_file -+ tar xf $tar_file - else - # make sure that ncbi/build directory exists - if ( ! -d "ncbi/build" ) then -@@ -74,6 +74,7 @@ - set HAVE_MAC=0 - #we will try to build OpenGL version of vibrant - set HAVE_OGL=1 -+set MPBL_HAVE_MAC=0 - - switch ($os) - case SunOS: -@@ -164,7 +165,7 @@ - gcc -v - switch (`uname -m`) - case "ia64": -- if (-e `which ecc`) then -+ if (-e `which icc`) then - set platform=linux_ecc - else - set platform=linux -@@ -253,7 +254,11 @@ - endif - endif - set HAVE_MOTIF=0 -- set HAVE_MAC=1 -+#MPIBLAST <<< -+# set HAVE_MAC=1 -+ set MPBL_HAVE_MAC=1 -+ set HAVE_MAC=0 -+#MPIBLAST - breaksw - case NetBSD: - set platform=netbsd -@@ -319,6 +324,7 @@ - goto BADPLATFORM - endif - -+ - set noglob - # take the file $NCBI_DOT_MK and convert it to be suitable for csh eval: - # (1) remove comments at the beginning of the lines -@@ -328,6 +334,7 @@ - eval `sed -e 's/^ *#.*//g' -e 's/\$(\([a-zA-Z_]*\))/\${\1}/g' -e 's/ *= */=/g' -e 's/^\([^=]*\)=\(.*\)$/setenv \1 "\2";/' < $NCBI_DOT_MK` - unset noglob - -+ - # disable assert() unless ENABLE_ASSERT is set - if ("$?ENABLE_ASSERT" == 0) then - set NCBI_OPTFLAG="-DNDEBUG $NCBI_OPTFLAG" -@@ -441,13 +448,23 @@ - set NET_VIB=(VIB=\"blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn gene2xml $NONVIBWWWBLAST \") - endif - -+# MPIBLAST <<<<< -+if ("$MPBL_HAVE_MAC" == 1) then -+set CMD='make $MFLG \ -+ CFLAGS1=\"-I/Developer/Headers/FlatCarbon $NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ -+ SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \ -+ RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all' -+else - set CMD='make $MFLG \ - CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \ - LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ - SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \ - RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all' -+endif - eval echo $CMD - eval echo $CMD | sh -+# MPIBLAST >>>>> - - set make_stat = $status - -@@ -463,12 +480,18 @@ - endif - - # MPIBLAST <<<<< -- -+if ("$MPBL_HAVE_MAC" == 1) then - set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ - LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ - LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"' -+else -+set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"' -+endif - eval echo $CMD - eval echo $CMD | sh -+if ($status != 0) exit $status - - if( "$platform" == "bluegenel" || "$platform" == "bluegenep" ) then - exit 0 -@@ -476,7 +499,7 @@ - # MPIBLAST >>>>> - - set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ -- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ - LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $DEMO_VIB' - eval echo $CMD - eval echo $CMD | sh -@@ -495,7 +518,7 @@ - - - set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ -- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ - LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" \ - THREAD_OBJ=$NCBI_THREAD_OBJ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ - $DEMO_VIB $mtapps' -diff -rwu mpiblast-1.6.0/src/Makefile.am mpiblast-1.6.0-patched/src/Makefile.am ---- mpiblast-1.6.0/src/Makefile.am 2009-11-22 01:17:48.000000000 -0500 -+++ mpiblast-1.6.0-patched/src/Makefile.am 2011-08-06 17:06:42.000000000 -0400 -@@ -2,7 +2,7 @@ - -D_LARGEFILE64_SOURCE -DMPIBLAST_PIO \ - -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \ - -I@CONFIG_NCBIDIR@/corelib/ --AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DINSTALL_PREFIX="\"@prefix@\"" \ -+AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX -DINSTALL_PREFIX="\"@prefix@\"" \ - @COMPILE_FLAGS@ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE \ - -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \ - -I@CONFIG_NCBIDIR@/corelib/ -@@ -31,7 +31,7 @@ - @CONFIG_NCBIDIR@/build/blast_hooks.o -lmyncbitool -lblastcompadj -lmyncbiobj \ - -lmyncbi -L. -L@CONFIG_NCBIDIR@/lib/ $(MPE_LIBS) -lm @LINK_FLAGS@ - mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ --mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK -+mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX - - mpiformatdb_SOURCES = mpiformatdb.cpp mpiblast_config.cpp mpiblast_config.hpp \ - file_util.cpp file_util.hpp mpiblast_util.cpp mpiblast_util.hpp \ -diff -rwu mpiblast-1.6.0/src/pio_intercept.h mpiblast-1.6.0-patched/src/pio_intercept.h ---- mpiblast-1.6.0/src/pio_intercept.h 2009-11-22 01:17:48.000000000 -0500 -+++ mpiblast-1.6.0-patched/src/pio_intercept.h 2011-08-06 17:06:42.000000000 -0400 -@@ -60,7 +60,7 @@ - #include - - /* marcros are duplicated in ncbi files to avoid header file conflict */ --#define CHECK_NULPTR(x) if(x==NULL) fprintf(stderr, "%s, line%d: cannot allocate enough memory\n", __FILE__, __LINE__); -+#define CHECK_NULPTR(x) if(x==NULL) { perror("Cannot allocate enough memory:"); exit(-1); } - - #ifndef NO_MPI - typedef struct _output_record { diff --git a/var/spack/repos/builtin/packages/mpiblast/package.py b/var/spack/repos/builtin/packages/mpiblast/package.py deleted file mode 100644 index d35bdecec79..00000000000 --- a/var/spack/repos/builtin/packages/mpiblast/package.py +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpiblast(AutotoolsPackage): - """mpiBLAST is a freely available, open-source, parallel implementation of - NCBI BLAST""" - - homepage = "http://www.mpiblast.org/" - url = "http://www.mpiblast.org/downloads/files/mpiBLAST-1.6.0.tgz" - - version('1.6.0', '707105ccd56825db776b50bfd81cecd5') - - patch('mpiBLAST-1.6.0-patch-110806') - - depends_on('mpi') - - def configure_args(self): - args = ['--with-mpi=%s' % self.spec['mpi'].prefix] - return args - - def build(self, spec, prefix): - make('ncbi') - make() - - def setup_environment(self, spack_env, run_env): - spack_env.set('ac_cv_path_CC', self.spec['mpi'].mpicc) - spack_env.set('ac_cv_path_CXX', self.spec['mpi'].mpicxx) diff --git a/var/spack/repos/builtin/packages/py-mxnet/package.py b/var/spack/repos/builtin/packages/py-mxnet/package.py deleted file mode 100644 index 8d789224726..00000000000 --- a/var/spack/repos/builtin/packages/py-mxnet/package.py +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PyMxnet(PythonPackage): - """Python binding for DMLC/MXNet.""" - - homepage = "http://mxnet.io" - url = "https://github.com/sjtuhpcc/python-mxnet/archive/0.10.0.post2.tar.gz" - - version('0.10.0.post2', '64a646fbf5d1b53ce1008da1bf94d77c', - url='https://github.com/sjtuhpcc/python-mxnet/archive/0.10.0.post2.tar.gz') - - # TODO - # install_time_test_callbacks = ['install_test', 'import_module_test'] - - # import_modules = ['mxnet', 'mxnet.module', 'mxnet._ctypes', 'mxnet.rnn', - # 'mxnet._cy2', 'mxnet._cy3', 'mxnet.notebook', 'mxnet.contrib'] - - variant('cuda', default=False, description='Enable CUDA support') - - depends_on('python@2.6:2.8,3.3:') - - depends_on('py-setuptools', type=('build', 'run')) - depends_on('py-numpy@1.7.1:', type=('build', 'run')) - # depends_on('py-pip', type='build') - - depends_on('mxnet', type=('build', 'run')) - depends_on('mxnet+cuda', when='+cuda', type=('build', 'run')) - - def patch(self): - spec = self.spec - filter_file('../../../', - spec['mxnet'].prefix.lib, - 'mxnet/libinfo.py', string=True) diff --git a/var/spack/repos/builtin/packages/soap2/package.py b/var/spack/repos/builtin/packages/soap2/package.py deleted file mode 100644 index 4c1368a49ee..00000000000 --- a/var/spack/repos/builtin/packages/soap2/package.py +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Soap2(Package): - """Software for short oligonucleotide alignment.""" - - homepage = "http://soap.genomics.org.cn/soapaligner.html" - url = "http://soap.genomics.org.cn/down/soap2.21release.tar.gz" - - version('2.21', '563b8b7235463b68413f9e841aa40779') - - def install(self, spec, prefix): - mkdirp(prefix.bin) - mkdirp(prefix.share.man) - install('soap', prefix.bin) - install('2bwt-builder', prefix.bin) - install('soap.1', prefix.share.man) - install('soap.man', prefix.share.man) diff --git a/var/spack/repos/builtin/packages/soapindel/package.py b/var/spack/repos/builtin/packages/soapindel/package.py deleted file mode 100644 index 7c4e8065fd2..00000000000 --- a/var/spack/repos/builtin/packages/soapindel/package.py +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Soapindel(MakefilePackage): - """SOAPindel is focusing on calling indels from the next-generation - paired-end sequencing data.""" - - homepage = "http://soap.genomics.org.cn/soapindel.html" - - version('2.1.7.17', '317ef494173969cdc6a8244dd87d06bd', - url='http://soap.genomics.org.cn/down/SOAPindel_20130918_2.1.7.17.zip') - - depends_on('perl', type=('build', 'run')) - - build_directory = 'indel_detection.release' - - def install(self, spec, prefix): - with working_dir('indel_detection.release'): - install_tree('tools', prefix.tools) - mkdirp(prefix.lib) - install('affine_align.pm', prefix.lib) - install('indel_lib.pm', prefix.lib) - mkdirp(prefix.bin) - install('assemble_align', prefix.bin) - install('cluster_reads', prefix.bin) - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PERL5LIB', self.prefix.lib) - run_env.prepend_path('PATH', self.prefix.tools) diff --git a/var/spack/repos/builtin/packages/soapsnp/package.py b/var/spack/repos/builtin/packages/soapsnp/package.py deleted file mode 100644 index 53d6a2b7775..00000000000 --- a/var/spack/repos/builtin/packages/soapsnp/package.py +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Soapsnp(MakefilePackage): - """SOAPsnp uses a method based on Bayes' theorem (the reverse probability - model) to call consensus genotype by carefully considering the data - quality, alignment, and recurring experimental errors.""" - - homepage = "http://soap.genomics.org.cn/soapsnp.html" - url = "http://soap.genomics.org.cn/down/SOAPsnp-v1.03.tar.gz" - - version('1.03', '8d69e196013657357ff840b611762ebc') - - depends_on('boost') - - def install(self, spec, prefix): - mkdirp(prefix.bin) - install('soapsnp', prefix.bin) diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py deleted file mode 100644 index c3b5729f1cb..00000000000 --- a/var/spack/repos/builtin/packages/uberftp/package.py +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Uberftp(AutotoolsPackage): - """UberFTP is an interactive (text-based) client for GridFTP""" - - homepage = "http://toolkit.globus.org/grid_software/data/uberftp.php" - url = "https://github.com/JasonAlt/UberFTP/archive/Version_2_8.tar.gz" - - version('2_8', sha256='8a397d6ef02bb714bb0cbdb259819fc2311f5d36231783cd520d606c97759c2a') - version('2_7', sha256='29a111a86fa70dbbc529a5d3e5a6befc1681e64e32dc019a1a6a98cd43ffb204') - version('2_6', sha256='2823a564801fb71d06fe6fbc3a37f11962af75b33c53bf698f26776ec972fe68') - - depends_on('globus-toolkit') From 8cbd349cb4c2420e64de138e848cbeaad232ec1d Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 12 Oct 2019 01:49:54 -0700 Subject: [PATCH 193/499] checksums: fix packages that needed new download locations Some packages had incorrect checksums because they needed to be downloaded from a new place or the package needed tweaking somehow. These packages to sha256 and the new checksums have been verified by fetching over https. --- var/spack/repos/builtin/packages/ape/package.py | 2 +- .../repos/builtin/packages/archer/package.py | 2 +- .../repos/builtin/packages/astra/package.py | 2 +- .../repos/builtin/packages/converge/package.py | 10 +++++----- .../repos/builtin/packages/cppad/package.py | 2 +- .../builtin/packages/cpprestsdk/package.py | 2 +- .../repos/builtin/packages/dislin/package.py | 3 +-- .../repos/builtin/packages/fenics/package.py | 10 ---------- .../repos/builtin/packages/fimpute/package.py | 2 +- .../repos/builtin/packages/fseq/package.py | 4 ++-- .../builtin/packages/gnu-prolog/package.py | 4 ++-- .../repos/builtin/packages/h5hut/package.py | 4 ++-- .../repos/builtin/packages/hadoop/package.py | 5 ++--- .../repos/builtin/packages/harminv/package.py | 2 +- .../repos/builtin/packages/hpx5/package.py | 17 ++++++++--------- .../repos/builtin/packages/hstr/package.py | 2 +- .../repos/builtin/packages/libbeato/package.py | 4 ++-- .../repos/builtin/packages/lsof/package.py | 2 +- .../repos/builtin/packages/nektar/package.py | 2 +- .../repos/builtin/packages/ocaml/package.py | 6 +++--- .../repos/builtin/packages/octopus/package.py | 10 +++++----- .../repos/builtin/packages/openmc/package.py | 2 +- .../builtin/packages/parmgridgen/package.py | 4 ++-- var/spack/repos/builtin/packages/pgi/package.py | 15 +++++---------- .../repos/builtin/packages/porta/package.py | 4 ++-- .../repos/builtin/packages/psi4/package.py | 4 ++-- .../repos/builtin/packages/pslib/package.py | 4 ++-- .../repos/builtin/packages/pstreams/package.py | 4 ++-- .../repos/builtin/packages/py-opppy/package.py | 2 +- .../repos/builtin/packages/py-perf/package.py | 6 +++--- .../builtin/packages/py-performance/package.py | 4 ++-- .../repos/builtin/packages/py-tomopy/package.py | 2 +- .../builtin/packages/py-udunits/package.py | 2 +- .../repos/builtin/packages/r-abadata/package.py | 4 ++-- .../repos/builtin/packages/r-acde/package.py | 4 ++-- .../builtin/packages/r-affydata/package.py | 4 ++-- .../repos/builtin/packages/raft/package.py | 2 +- .../repos/builtin/packages/snpeff/package.py | 4 ++-- .../repos/builtin/packages/stress/package.py | 8 +++++--- .../repos/builtin/packages/xdmf3/package.py | 2 +- .../repos/builtin/packages/yorick/package.py | 2 +- 41 files changed, 82 insertions(+), 98 deletions(-) diff --git a/var/spack/repos/builtin/packages/ape/package.py b/var/spack/repos/builtin/packages/ape/package.py index 52c0198802f..76633a14980 100644 --- a/var/spack/repos/builtin/packages/ape/package.py +++ b/var/spack/repos/builtin/packages/ape/package.py @@ -13,7 +13,7 @@ class Ape(Package): homepage = "http://www.tddft.org/programs/APE/" url = "http://www.tddft.org/programs/APE/sites/default/files/ape-2.2.1.tar.gz" - version('2.2.1', 'ab81da85bd749c0c136af088c7f9ad58') + version('2.2.1', sha256='1bdb7f987fde81f8a5f335da6b59fa884e6d185d4a0995c90fde7c04376ce9e3') depends_on('gsl') depends_on('libxc@:2.2.2') diff --git a/var/spack/repos/builtin/packages/archer/package.py b/var/spack/repos/builtin/packages/archer/package.py index 78ff54e8741..7437a3890d7 100644 --- a/var/spack/repos/builtin/packages/archer/package.py +++ b/var/spack/repos/builtin/packages/archer/package.py @@ -13,7 +13,7 @@ class Archer(CMakePackage): homepage = "https://github.com/PRUNERS/ARCHER" url = "https://github.com/PRUNERS/archer/archive/v1.0.0.tar.gz" - version('1.0.0', '790bfaf00b9f57490eb609ecabfe954a') + version('1.0.0', sha256='df814a475606b83c659932caa30a68bed1c62e713386b375c1b78eb8d60e0d15') depends_on('cmake@3.4.3:', type='build') depends_on('llvm') diff --git a/var/spack/repos/builtin/packages/astra/package.py b/var/spack/repos/builtin/packages/astra/package.py index 13a912dcbbb..c51d0694559 100644 --- a/var/spack/repos/builtin/packages/astra/package.py +++ b/var/spack/repos/builtin/packages/astra/package.py @@ -11,7 +11,7 @@ class Astra(Package): homepage = "http://www.desy.de/~mpyflo/" - version('2016-11-30', '17135b7a4adbacc1843a50a6a2ae2c25', expand=False, + version('2016-11-30', sha256='50738bf924724e2dd15f1d924b290ffb0f7c703e5d5ae02ffee2db554338801e', expand=False, url='http://www.desy.de/~mpyflo/Astra_for_64_Bit_Linux/Astra') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/converge/package.py b/var/spack/repos/builtin/packages/converge/package.py index 792bbedeb80..3b990ebd6af 100644 --- a/var/spack/repos/builtin/packages/converge/package.py +++ b/var/spack/repos/builtin/packages/converge/package.py @@ -27,13 +27,13 @@ class Converge(Package): # In order to view available versions, you need to register for an account: # https://download.convergecfd.com/wp-login.php?action=register - version('2.4.10', '53f5bd4bfb39005bebae46b8d6ee3ce6') - version('2.3.23', '2913c3e440f82db069051f8822115e5e') - version('2.2.0', 'd949cfe338c83ee736ca0be8f77df6bf', + version('2.4.10', sha256='5d3c39894598d2395149cfcc653af13b8b1091177290edd62fcf22c7e830d410') + version('2.3.23', sha256='1217d16eaf9d263f917ee468778508bad9dacb7e4397a293cfa6467f39fb4c52') + version('2.2.0', sha256='3885acbaf352c718ea69f0206c858a01be02f0928ffee738e4aceb1dd939a77a', url="https://download.convergecfd.com/download/CONVERGE_2.2/Full_Solver_Packages/converge_install_2.2.0_042916.tar.gz") - version('2.1.0', '327a917d46aa3bc8dee9511375ce112c', + version('2.1.0', sha256='6b8896d42cf7b9013cae5456f4dc118306a5bd271d4a15945ceb7dae913e825a', url="https://download.convergecfd.com/download/CONVERGE_2.1/Full_Solver_Packages/converge_install_2.1.0_111615.tar.gz") - version('2.0.0', '06f017521c3abc1a922b136e83d606dd', + version('2.0.0', sha256='f32c4824eb33724d85e283481d67ebd0630b1406011c528d775028bb2546f34e', url="https://download.convergecfd.com/download/CONVERGE_2.0/Full_Solver_Packages/converge_install_2.0.0_090214.tar.gz") variant('mpi', default=True, description='Build with MPI support') diff --git a/var/spack/repos/builtin/packages/cppad/package.py b/var/spack/repos/builtin/packages/cppad/package.py index 51ae4c01543..de6b4a5c238 100644 --- a/var/spack/repos/builtin/packages/cppad/package.py +++ b/var/spack/repos/builtin/packages/cppad/package.py @@ -14,7 +14,7 @@ class Cppad(CMakePackage): git = "https://github.com/coin-or/CppAD.git" version('develop', branch='master') - version('20170114', '565a534dc813fa1289764222cd8c11ea') + version('20170114', sha256='fa3980a882be2a668a7522146273a1b4f1d8dabe66ad4aafa8964c8c1fd6f957') def cmake_args(self): # This package does not obey CMAKE_INSTALL_PREFIX diff --git a/var/spack/repos/builtin/packages/cpprestsdk/package.py b/var/spack/repos/builtin/packages/cpprestsdk/package.py index 86b24761a19..a4f4a738178 100644 --- a/var/spack/repos/builtin/packages/cpprestsdk/package.py +++ b/var/spack/repos/builtin/packages/cpprestsdk/package.py @@ -15,7 +15,7 @@ class Cpprestsdk(CMakePackage): homepage = "https://github.com/Microsoft/cpprestsdk" url = "https://github.com/Microsoft/cpprestsdk/archive/v2.9.1.tar.gz" - version('2.9.1', 'c3dd67d8cde8a65c2e994e2ede4439a2') + version('2.9.1', sha256='537358760acd782f4d2ed3a85d92247b4fc423aff9c85347dc31dbb0ab9bab16') depends_on('boost') diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py index 53d0e901b29..cfdffeb9ba2 100644 --- a/var/spack/repos/builtin/packages/dislin/package.py +++ b/var/spack/repos/builtin/packages/dislin/package.py @@ -14,8 +14,7 @@ class Dislin(Package): homepage = "http://www.mps.mpg.de/dislin" url = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz" - version('11.1.linux.i586_64', '34218c257efedaf706f058bdf111ce9d') - version('11.0.linux.i586_64', '6fb099b54f41db009cafc702eebb5bc6') + version('11.2.linux.i586_64', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10') depends_on('motif') depends_on('gl') diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py index 97020e857f5..896edb583b6 100644 --- a/var/spack/repos/builtin/packages/fenics/package.py +++ b/var/spack/repos/builtin/packages/fenics/package.py @@ -102,16 +102,6 @@ class Fenics(CMakePackage): 'ufl': 'c75c4781e5104504f158cb42cd87aceffa9052e8e9db6e9764e6a5b6115d7f73', } }, - { - 'version': '1.5.0', - 'sha256': '9b589a3534299a5e6d22c13c5eb30bb8', - 'resources': { - 'ffc': '755be60597d66f13c1e113739e7b9b620ee4271e0f7cc1053553a568bc08e7f4', - 'fiat': '2b053fa9f70399f8903b987f98a4fa2b06df9559c07c1d5f0b2b5e43c51de670', - 'instant': '36e042de26d97f5e3d43f2f52544d91ba0f14e1c73c7d07ed7804030b43d935d', - 'ufl': '2879a5b0937502676fa55765bcb8237ff78e8b70995a118ffe1de042b20e491b', - } - }, ] for release in releases: diff --git a/var/spack/repos/builtin/packages/fimpute/package.py b/var/spack/repos/builtin/packages/fimpute/package.py index 6d79f220799..7ee5f361f60 100644 --- a/var/spack/repos/builtin/packages/fimpute/package.py +++ b/var/spack/repos/builtin/packages/fimpute/package.py @@ -14,7 +14,7 @@ class Fimpute(Package): homepage = "http://www.aps.uoguelph.ca/~msargol/fimpute/" url = "http://www.aps.uoguelph.ca/~msargol/fimpute/FImpute_Linux.zip" - version('2014-01', 'df934a25c76dabef7d7afcb5b8058d98') + version('2014-01', sha256='aecda2dfdd4e3ef6f2331cc1d479e6f297f722fcdca455ca05bb047405534461') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/fseq/package.py b/var/spack/repos/builtin/packages/fseq/package.py index e3fd92d946b..4858114ef00 100644 --- a/var/spack/repos/builtin/packages/fseq/package.py +++ b/var/spack/repos/builtin/packages/fseq/package.py @@ -10,9 +10,9 @@ class Fseq(Package): """F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags""" homepage = "http://fureylab.web.unc.edu/software/fseq/" - url = "http://fureylab.med.unc.edu/fseq/fseq_1.84.tgz" + url = "http://html-large-files-dept-fureylab.cloudapps.unc.edu/fureylabfiles/fseq/fseq_1.84.tgz" - version('1.84', 'f9124ad0f45c60f3a7eb74dde8c945b9') + version('1.84', sha256='22d603a51f127cb86cdecde9aeae14d273bb98bcd2b47724763ab3b3241a6e68') depends_on('java', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py index b0ea5ed293e..d3327110777 100644 --- a/var/spack/repos/builtin/packages/gnu-prolog/package.py +++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py @@ -9,9 +9,9 @@ class GnuProlog(Package): """A free Prolog compiler with constraint solving over finite domains.""" homepage = "http://www.gprolog.org/" - url = "http://www.gprolog.org/gprolog-1.4.4.tar.gz" + url = "http://www.gprolog.org/gprolog-1.4.5.tar.gz" - version('1.4.4', '37009da471e5217ff637ad1c516448c8') + version('1.4.5', sha256='bfdcf00e051e0628b4f9af9d6638d4fde6ad793401e58a5619d1cc6105618c7c') parallel = False diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py index ec7b441b8fe..48c5fa20203 100644 --- a/var/spack/repos/builtin/packages/h5hut/package.py +++ b/var/spack/repos/builtin/packages/h5hut/package.py @@ -12,9 +12,9 @@ class H5hut(AutotoolsPackage): High-Performance I/O Library for Particle-based Simulations.""" homepage = "https://amas.psi.ch/H5hut/" - url = "https://amas.psi.ch/H5hut/raw-attachment/wiki/DownloadSources/H5hut-1.99.13.tar.gz" + url = "http://amas.web.psi.ch/Downloads/H5hut/H5hut-2.0.0rc3.tar.gz" - version('1.99.13', '2a07a449afe50534de006ac6954a421a') + version('2.0.0rc3', sha256='1ca9a9478a99e1811ecbca3c02cc49258050d339ffb1a170006eab4ab2a01790') variant('fortran', default=True, description='Enable Fortran support') variant('mpi', default=True, description='Enable MPI support') diff --git a/var/spack/repos/builtin/packages/hadoop/package.py b/var/spack/repos/builtin/packages/hadoop/package.py index 8c51c228a6b..04b00e0a85b 100644 --- a/var/spack/repos/builtin/packages/hadoop/package.py +++ b/var/spack/repos/builtin/packages/hadoop/package.py @@ -13,10 +13,9 @@ class Hadoop(Package): """ homepage = "http://hadoop.apache.org/" - url = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-3.1.1/hadoop-3.1.1.tar.gz" + url = "http://apache-mirror.8birdsvideo.com/hadoop/common/hadoop-3.1.2/hadoop-3.1.2-src.tar.gz" - version('3.1.1', '0b6ab06b59ae75f433de387783f19011') - version('2.9.0', 'b443ead81aa2bd5086f99e62e66a8f64') + version('3.1.2', sha256='02f277c9fc75d4b13c7697ed6be30dba41667841ab5e37442855267c39bec6b6') depends_on('java', type='run') diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py index 1776f4de2d0..3570f87fe13 100644 --- a/var/spack/repos/builtin/packages/harminv/package.py +++ b/var/spack/repos/builtin/packages/harminv/package.py @@ -17,7 +17,7 @@ class Harminv(AutotoolsPackage): url = "http://ab-initio.mit.edu/harminv/harminv-1.4.tar.gz" list_url = "http://ab-initio.mit.edu/harminv/old" - version('1.4', 'b95e24a9bc7e07d3d2202d1605e9e86f') + version('1.4', sha256='e1b923c508a565f230aac04e3feea23b888b47d8e19b08816a97ee4444233670') depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py index 762d4d469df..5ea3937c462 100644 --- a/var/spack/repos/builtin/packages/hpx5/package.py +++ b/var/spack/repos/builtin/packages/hpx5/package.py @@ -18,16 +18,15 @@ class Hpx5(AutotoolsPackage): applications enabling scientists to write code that performs and scales better than contemporary runtimes.""" homepage = "http://hpx.crest.iu.edu" - url = "http://hpx.crest.iu.edu/release/hpx-3.1.0.tar.gz" + url = "https://github.com/adk9/hpx5/archive/v3.1.0.tar.gz" - version('4.1.0', '43cb78758506f77416b95276a472f84f') - version('4.0.0', 'b40dc03449ae1039cbb48ee149952b22') - version('3.1.0', '9e90b8ac46788c009079632828c77628') - version('2.0.0', '3d2ff3aab6c46481f9ec65c5b2bfe7a6') - version('1.3.0', '2260ecc7f850e71a4d365a43017d8cee') - version('1.2.0', '4972005f85566af4afe8b71afbf1480f') - version('1.1.0', '646afb460ecb7e0eea713a634933ce4f') - version('1.0.0', '8020822adf6090bd59ed7fe465f6c6cb') + version('4.1.0', sha256='3f01009f5e517c8dfca266dabb49894d688db5adce09608fb1c877263605a9f8') + version('4.0.0', sha256='e35b1161566a65ffbd875c1413ea97a84be0c7b528a3dee99f5e250b2aecbd19') + version('3.1.0', sha256='359d457a26b87abb415605911d791ce0ff6edbb064bc40b0f830960f8f612b84') + version('3.0.0', sha256='10f14ba198a32787cee05962e346bafb922f74a5135fb09a1ba8c32a1e942800') + version('2.2.0', sha256='e34c7513a287d517e67cce5aa3011474c48718e7860c3860ba1290c702be28a8') + version('2.1.0', sha256='675826f669eeb3eab40947715af8c8495e2b3d299223372431dc01c1f7d5d616') + version('2.0.0', sha256='0278728557b6684aeb86228f44d548ac809302f05a0b9c8b433cdd157629e384') # Don't second-guess what compiler we are using on Cray patch("configure.patch", when='@4.0.0') diff --git a/var/spack/repos/builtin/packages/hstr/package.py b/var/spack/repos/builtin/packages/hstr/package.py index b3669e09219..1a933f22fb7 100644 --- a/var/spack/repos/builtin/packages/hstr/package.py +++ b/var/spack/repos/builtin/packages/hstr/package.py @@ -14,7 +14,7 @@ class Hstr(AutotoolsPackage): homepage = "https://github.com/dvorka/hstr" url = "https://github.com/dvorka/hstr/archive/1.22.tar.gz" - version('1.22', '620dab922fadf2858938fbe36d9f99fd') + version('1.22', sha256='384fee04e4c80a1964dcf443131c1da4a20dd474fb48132a51d3de0a946ba996') depends_on('autoconf', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/libbeato/package.py b/var/spack/repos/builtin/packages/libbeato/package.py index 8c6db5eb774..58fde449eab 100644 --- a/var/spack/repos/builtin/packages/libbeato/package.py +++ b/var/spack/repos/builtin/packages/libbeato/package.py @@ -12,6 +12,6 @@ class Libbeato(AutotoolsPackage): from UCSC's Genome Browser Group.""" homepage = "https://github.com/CRG-Barcelona/libbeato" - url = "https://github.com/CRG-Barcelona/libbeato/archive/master.tar.gz" + git = "https://github.com/CRG-Barcelona/libbeato.git" - version('master', 'ee6f0f0f3f09c4f601fcfed3b13e7395') + version('master', brancch='master') diff --git a/var/spack/repos/builtin/packages/lsof/package.py b/var/spack/repos/builtin/packages/lsof/package.py index a65c0503f69..8bc2c8897a6 100644 --- a/var/spack/repos/builtin/packages/lsof/package.py +++ b/var/spack/repos/builtin/packages/lsof/package.py @@ -12,7 +12,7 @@ class Lsof(Package): homepage = "https://people.freebsd.org/~abe/" url = "https://www.mirrorservice.org/sites/lsof.itap.purdue.edu/pub/tools/unix/lsof/lsof_4.89.tar.gz" - version('4.89', '8afbaff3ee308edc130bdc5df0801c8f') + version('4.89', sha256='ff4ac555966b587f06338475c8fcc0f41402b4c8e970e730f6f83b62be8b5c0d') def install(self, spec, prefix): tar = which('tar') diff --git a/var/spack/repos/builtin/packages/nektar/package.py b/var/spack/repos/builtin/packages/nektar/package.py index 86e929ead59..d2cc96d92bb 100644 --- a/var/spack/repos/builtin/packages/nektar/package.py +++ b/var/spack/repos/builtin/packages/nektar/package.py @@ -12,7 +12,7 @@ class Nektar(CMakePackage): homepage = "https://www.nektar.info/" url = "https://gitlab.nektar.info/nektar/nektar/-/archive/v4.4.1/nektar-v4.4.1.tar.bz2" - version('4.4.1', '1be7d061c3cafd9a0f1eb8d281d99b89') + version('4.4.1', sha256='71cfd93d848a751ae9ae5e5ba336cee4b4827d4abcd56f6b8dc5c460ed6b738c') variant('mpi', default=True, description='Builds with mpi support') variant('fftw', default=True, description='Builds with fftw support') diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py index 73a64f861c0..e3d3cb9c83f 100644 --- a/var/spack/repos/builtin/packages/ocaml/package.py +++ b/var/spack/repos/builtin/packages/ocaml/package.py @@ -11,10 +11,10 @@ class Ocaml(Package): functional, imperative and object-oriented styles""" homepage = "http://ocaml.org/" - url = "http://caml.inria.fr/pub/distrib/ocaml-4.03/ocaml-4.03.0.tar.gz" + url = "https://caml.inria.fr/pub/distrib/ocaml-4.06/ocaml-4.06.0.tar.gz" - version('4.06.0', '66e5439eb63dbb8b8224cba5d1b20947') - version('4.03.0', '43812739ea1b4641cf480f57f977c149') + version('4.06.0', sha256='c17578e243c4b889fe53a104d8927eb8749c7be2e6b622db8b3c7b386723bf50') + version('4.03.0', sha256='7fdf280cc6c0a2de4fc9891d0bf4633ea417046ece619f011fd44540fcfc8da2') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py index d6dc0a2402d..4e7aa3322e4 100644 --- a/var/spack/repos/builtin/packages/octopus/package.py +++ b/var/spack/repos/builtin/packages/octopus/package.py @@ -10,12 +10,12 @@ class Octopus(Package): """A real-space finite-difference (time-dependent) density-functional theory code.""" - homepage = "http://www.tddft.org/programs/octopus/" - url = "http://www.tddft.org/programs/octopus/down.php?file=6.0/octopus-6.0.tar.gz" + homepage = "https://octopus-code.org/" + url = "http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz" - version('7.3', '87e51fa4a3a999706ea4ea5e9136996f') - version('6.0', '5d1168c2a8d7fd9cb9492eaebaa7182e') - version('5.0.1', '2b6392ab67b843f9d4ca7413fc07e822') + version('7.3', sha256='ad843d49d4beeed63e8b9a2ca6bfb2f4c5a421f13a4f66dc7b02f6d6a5c4d742') + version('6.0', sha256='4a802ee86c1e06846aa7fa317bd2216c6170871632c9e03d020d7970a08a8198') + version('5.0.1', sha256='3423049729e03f25512b1b315d9d62691cd0a6bd2722c7373a61d51bfbee14e0') variant('scalapack', default=False, description='Compile with Scalapack') diff --git a/var/spack/repos/builtin/packages/openmc/package.py b/var/spack/repos/builtin/packages/openmc/package.py index 247e6fe86dd..5627ac0dc66 100644 --- a/var/spack/repos/builtin/packages/openmc/package.py +++ b/var/spack/repos/builtin/packages/openmc/package.py @@ -18,7 +18,7 @@ class Openmc(CMakePackage): url = "https://github.com/openmc-dev/openmc/tarball/v0.10.0" git = "https://github.com/openmc-dev/openmc.git" - version('0.10.0', 'abb57bd1b226eb96909dafeec31369b0') + version('0.10.0', sha256='47650cb45e2c326ae439208d6f137d75ad3e5c657055912d989592c6e216178f') version('develop') depends_on("hdf5+hl") diff --git a/var/spack/repos/builtin/packages/parmgridgen/package.py b/var/spack/repos/builtin/packages/parmgridgen/package.py index 457770edb25..74305fc907d 100644 --- a/var/spack/repos/builtin/packages/parmgridgen/package.py +++ b/var/spack/repos/builtin/packages/parmgridgen/package.py @@ -16,9 +16,9 @@ class Parmgridgen(Package): """ homepage = "http://www-users.cs.umn.edu/~moulitsa/software.html" - url = "http://www-users.cs.umn.edu/~moulitsa/download/ParMGridGen-1.0.tar.gz" + url = "http://www.stasyan.com/devel/distfiles/ParMGridGen-1.0.tar.gz" - version('1.0', '2872fa95b7fb91d6bd525490eed62038') + version('1.0', sha256='62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395') variant('mpi', default=True, description='Activate the compilation of parallel libraries') diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py index b3c7bcbb238..c61611e22f0 100644 --- a/var/spack/repos/builtin/packages/pgi/package.py +++ b/var/spack/repos/builtin/packages/pgi/package.py @@ -20,17 +20,12 @@ class Pgi(Package): homepage = "http://www.pgroup.com/" - version('19.4', sha256='23eee0d4da751dd6f247d624b68b03538ebd172e63a053c41bb67013f07cf68e') - version('19.1', sha256='3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f') + version('19.4', sha256='23eee0d4da751dd6f247d624b68b03538ebd172e63a053c41bb67013f07cf68e') + version('19.1', sha256='3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f') version('18.10', sha256='4b3ff83d2a13de6001bed599246eff8e63ef711b8952d4a9ee12efd666b3e326') - version('18.4', 'b55461f9f0986acbd51902c51c2074b9') - version('17.10', '85ad6506e7ada610ab11ddb35d697efa') - version('17.4', 'a311d2756ddda657860bad8e5725597b') - version('17.3', '6eefc42f85e756cbaba76467ed640902') - version('16.10', '9bb6bfb7b1052f9e6a45829ba7a24e47') - version('16.5', 'a40e8852071b5d600cb42f31631b3de1') - version('16.3', '618cb7ddbc57d4e4ed1f21a0ab25f427') - version('15.7', '84a689217b17cdaf78c39270c70bea5d') + version('18.4', sha256='81e0dcf6000b026093ece180d42d77854c23269fb8409cedcf51c674ca580a0f') + version('17.10', sha256='9da8f869fb9b70c0c4423c903d40a9e22d54b997af359a43573c0841165cd1b6') + version('17.4', sha256='115c212d526695fc116fe44f1e722793e60b6f7d1b341cd7e77a95da8e7f6c34') variant('network', default=True, description="Perform a network install") diff --git a/var/spack/repos/builtin/packages/porta/package.py b/var/spack/repos/builtin/packages/porta/package.py index fac5198ce82..d3bc8a466bc 100644 --- a/var/spack/repos/builtin/packages/porta/package.py +++ b/var/spack/repos/builtin/packages/porta/package.py @@ -11,9 +11,9 @@ class Porta(Package): """PORTA is a collection of routines for analyzing polytopes and polyhedra""" homepage = "http://porta.zib.de" - url = "http://porta.zib.de/porta-1.4.1.tgz" + url = "http://porta.zib.de/porta-1.4.1.zip" - version('1.4.1', '585179bf19d214ed364663a5d17bd5fc') + version('1.4.1', sha256='21e3784f46f4f2154100a0c39cbd9211a26e513ffe0c9f70ab75a3bb2810b059') depends_on("libtool", type="build") diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py index f9c422baab9..be9d5046ebc 100644 --- a/var/spack/repos/builtin/packages/psi4/package.py +++ b/var/spack/repos/builtin/packages/psi4/package.py @@ -13,9 +13,9 @@ class Psi4(CMakePackage): a variety of molecular properties.""" homepage = "http://www.psicode.org/" - url = "https://github.com/psi4/psi4/archive/0.5.tar.gz" + url = "https://github.com/psi4/psi4/archive/v1.3.2.tar.gz" - version('0.5', '53041b8a9be3958384171d0d22f9fdd0') + version('1.3.2', sha256='ed76c67803b6420f35f57a6dd31c47108b9145b8c9fced5c94cdc179f6b5fbf3') variant('build_type', default='Release', description='The build type to build', diff --git a/var/spack/repos/builtin/packages/pslib/package.py b/var/spack/repos/builtin/packages/pslib/package.py index 1be61a940ba..7cb6601b2c7 100644 --- a/var/spack/repos/builtin/packages/pslib/package.py +++ b/var/spack/repos/builtin/packages/pslib/package.py @@ -10,9 +10,9 @@ class Pslib(AutotoolsPackage): """C-library to create PostScript files on the fly.""" homepage = "http://pslib.sourceforge.net/" - url = "https://kent.dl.sourceforge.net/project/pslib/pslib/0.4.5/pslib-0.4.5.tar.gz" + url = "https://sourceforge.net/projects/pslib/files/pslib/0.4.5/pslib-0.4.5.tar.gz" - version('0.4.5', '03f39393628a6d758799b9f845047e27') + version('0.4.5', sha256='7a33928982b281660206bb3749a4a563e3ac987eea64f41696f212df345212be') depends_on('jpeg') depends_on('libpng') diff --git a/var/spack/repos/builtin/packages/pstreams/package.py b/var/spack/repos/builtin/packages/pstreams/package.py index 48ae5819964..fc4bbff2d72 100644 --- a/var/spack/repos/builtin/packages/pstreams/package.py +++ b/var/spack/repos/builtin/packages/pstreams/package.py @@ -11,9 +11,9 @@ class Pstreams(Package): """C++ wrapper for the POSIX.2 functions popen(3) and pclose(3)""" homepage = "http://pstreams.sourceforge.net/" - url = "https://superb-sea2.dl.sourceforge.net/project/pstreams/pstreams/Release%201.0/pstreams-1.0.1.tar.gz" + url = "https://sourceforge.net/projects/pstreams/files/pstreams/Release%201.0/pstreams-1.0.1.tar.gz" - version('1.0.1', '23199e3d12a644a2a0c66ec889d4c064') + version('1.0.1', sha256='a5f1f2e014392cd0e2cdb508a429e11afe64140db05b7f0a83d7534faa1a9226') def install(self, spec, prefix): mkdirp(prefix.include) diff --git a/var/spack/repos/builtin/packages/py-opppy/package.py b/var/spack/repos/builtin/packages/py-opppy/package.py index a005332ab03..b6edea82268 100644 --- a/var/spack/repos/builtin/packages/py-opppy/package.py +++ b/var/spack/repos/builtin/packages/py-opppy/package.py @@ -16,7 +16,7 @@ class PyOpppy(PythonPackage): git = "https://github.com/lanl/opppy.git" version('master', branch='master') - version('0.1.1', '852a1329ce68d678623beed3fd01ea98') + version('0_1_1', sha256='505c023853e75552abc65de9777a125ecb6a99a1cb4e605a4f702af837e3168b') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-numpy@1.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-perf/package.py b/var/spack/repos/builtin/packages/py-perf/package.py index 211479fb94f..2d2c025691b 100644 --- a/var/spack/repos/builtin/packages/py-perf/package.py +++ b/var/spack/repos/builtin/packages/py-perf/package.py @@ -11,10 +11,10 @@ class PyPerf(PythonPackage): analyze benchmarks. """ - homepage = "https://pypi.python.org/pypi/perf" - url = "https://github.com/vstinner/perf/archive/1.5.1.tar.gz" + homepage = "https://pypi.python.org/pypi/pyperf" + url = "https://github.com/vstinner/pyperf/archive/1.5.1.tar.gz" - version('1.5.1', 'e3dc532fdbaf44f2d921556164bd74e5') + version('1.5.1', sha256='9c271862bc2911be8eb01031a4a86cbc3f5bb615971514383802d3dcf46f18ed') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-performance/package.py b/var/spack/repos/builtin/packages/py-performance/package.py index 3d07e1562b8..9abc3c4d482 100644 --- a/var/spack/repos/builtin/packages/py-performance/package.py +++ b/var/spack/repos/builtin/packages/py-performance/package.py @@ -17,8 +17,8 @@ class PyPerformance(PythonPackage): homepage = 'http://pyperformance.readthedocs.io/' url = 'https://github.com/python/performance/archive/0.6.1.tar.gz' - version('0.6.1', '95477b584a284582b66c922a5335b427') - version('0.6.0', 'b93661e07668fa0b461236dca164eedf') + version('0.6.1', sha256='cc48dd7579da2f4b0e4cff0c8220811f5ba7019493bb408819c1532acf53d13a') + version('0.6.0', sha256='4636e276445e96563f628e071cacd5df31dc587d83899e7d03fa8b31760f2cd2') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-tomopy/package.py b/var/spack/repos/builtin/packages/py-tomopy/package.py index 93a82bf0e90..b838561efd5 100644 --- a/var/spack/repos/builtin/packages/py-tomopy/package.py +++ b/var/spack/repos/builtin/packages/py-tomopy/package.py @@ -19,7 +19,7 @@ class PyTomopy(PythonPackage): 'tomopy.prep', 'tomopy.misc', 'tomopy.io', 'doc.demo' ] - version('1.0.0', '986ac2c85a4af9ada0403b4c746d2cd4') + version('1.0.0', sha256='ee45f7a062e5a66d6f18a904d2e204e48d85a1ce1464156f9e2f6353057dfe4c') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-udunits/package.py b/var/spack/repos/builtin/packages/py-udunits/package.py index f0f37ff0510..b7fb343439e 100644 --- a/var/spack/repos/builtin/packages/py-udunits/package.py +++ b/var/spack/repos/builtin/packages/py-udunits/package.py @@ -12,7 +12,7 @@ class PyUdunits(PythonPackage): homepage = "https://github.com/SciTools/cf_units" url = "https://github.com/SciTools/cf_units/archive/v1.1.3.tar.gz" - version('1.1.3', '61ea2239c87b4c1d5d30147800a9e750') + version('1.1.3', sha256='cc27f4f06c99d242c36beb8dc5c517e1b1124a8c65ca3f76f372b9674aa320ba') maintainers = ['citibeth'] diff --git a/var/spack/repos/builtin/packages/r-abadata/package.py b/var/spack/repos/builtin/packages/r-abadata/package.py index 8c79dce6c5b..2f4f6f1ebc9 100644 --- a/var/spack/repos/builtin/packages/r-abadata/package.py +++ b/var/spack/repos/builtin/packages/r-abadata/package.py @@ -17,6 +17,6 @@ class RAbadata(RPackage): All datasets are restricted to protein coding genes.""" homepage = "https://bioconductor.org/packages/ABAData/" - url = "https://bioconductor.org/packages/release/data/experiment/src/contrib/ABAData_1.6.0.tar.gz" + url = "https://bioconductor.org/packages/release/data/experiment/src/contrib/ABAData_1.14.0.tar.gz" - version('1.6.0', '9adfb9fbb39ad05cf72852a229476fb7') + version('1.14.0', sha256='d203d968044c292cdfab57a4d6bf52dfb60470bd78b4c9bd88892577ac42b2b7') diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py index 107c7937bcd..4b491048975 100644 --- a/var/spack/repos/builtin/packages/r-acde/package.py +++ b/var/spack/repos/builtin/packages/r-acde/package.py @@ -20,8 +20,8 @@ class RAcde(RPackage): (2015, pending publication).""" homepage = "https://www.bioconductor.org/packages/acde/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/acde_1.6.0.tar.gz" + url = "https://bioconductor.org/packages/release/bioc/src/contrib/acde_1.14.0.tar.gz" - version('1.6.0', 'e92ce91f75bab3bb1d79995bec1b42cc') + version('1.14.0', sha256='e8d9ad688610d4b72cab729141dc46fce580c97128d929885336bb138345b788') depends_on('r-boot', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py index a310286ef71..c5bcc2c329d 100644 --- a/var/spack/repos/builtin/packages/r-affydata/package.py +++ b/var/spack/repos/builtin/packages/r-affydata/package.py @@ -12,9 +12,9 @@ class RAffydata(RPackage): package affy.""" homepage = "https://www.bioconductor.org/packages/affydata/" - url = "https://www.bioconductor.org/packages/release/data/experiment/src/contrib/affydata_1.24.0.tar.gz" + url = "https://www.bioconductor.org/packages/release/data/experiment/src/contrib/affydata_1.32.0.tar.gz" - version('1.24.0', '0b6938685c450a56d65dd5628ebed42d') + version('1.32.0', sha256='059e05a2b8908720801d684d5617d5d5e45db7a5999c5659a22daf87658538d1') depends_on('r@3.4.0:3.4.9', when=('@1.24.0')) depends_on('r-affy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/raft/package.py b/var/spack/repos/builtin/packages/raft/package.py index f8426c663a5..fda2e02a50a 100644 --- a/var/spack/repos/builtin/packages/raft/package.py +++ b/var/spack/repos/builtin/packages/raft/package.py @@ -16,7 +16,7 @@ class Raft(CMakePackage): git = "https://bitbucket.org/gill_martinez/raft_aps.git" version('develop', branch='master') - version('1.2.3', '4d1b106d9b3493e63dde96f7dd44b834') + version('1.2.3', sha256='c41630e74491c8db272dcf4707e9b11cdcb226c0b7e978ca6eba8006f47bdae6') depends_on('mpi') depends_on('cmake', type='build') diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py index c9e8e1dcd56..d0c60c586e2 100644 --- a/var/spack/repos/builtin/packages/snpeff/package.py +++ b/var/spack/repos/builtin/packages/snpeff/package.py @@ -13,9 +13,9 @@ class Snpeff(Package): amino acid changes).""" homepage = "http://snpeff.sourceforge.net/" - url = "https://kent.dl.sourceforge.net/project/snpeff/snpEff_latest_core.zip" + url = "https://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip" - version('2017-11-24', '1fa84a703580a423e27f1e14a945901c') + version('2017-11-24', sha256='d55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244') depends_on('jdk', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/stress/package.py b/var/spack/repos/builtin/packages/stress/package.py index 65319620115..93cb3402205 100644 --- a/var/spack/repos/builtin/packages/stress/package.py +++ b/var/spack/repos/builtin/packages/stress/package.py @@ -12,7 +12,9 @@ class Stress(AutotoolsPackage): the system. It is written in C, and is free software licensed under the GPLv2.""" - homepage = "https://people.seas.harvard.edu/~apw/stress/" - url = "https://people.seas.harvard.edu/~apw/stress/stress-1.0.4.tar.gz" + # Moved from original homepage + # homepage = "https://people.seas.harvard.edu/~apw/stress/" + homepage = "https://github.com/javiroman/system-stress" + url = "https://github.com/javiroman/system-stress/archive/v1.0.4.tar.gz" - version('1.0.4', '890a4236dd1656792f3ef9a190cf99ef') + version('1.0.4', sha256='b03dbb9664d7f8dcb3eadc918c2e8eb822f5a3ba47d9bd51246540bac281bd75') diff --git a/var/spack/repos/builtin/packages/xdmf3/package.py b/var/spack/repos/builtin/packages/xdmf3/package.py index c14560816f5..772135846c4 100644 --- a/var/spack/repos/builtin/packages/xdmf3/package.py +++ b/var/spack/repos/builtin/packages/xdmf3/package.py @@ -18,7 +18,7 @@ class Xdmf3(CMakePackage): # There is no official release of XDMF and development has largely ceased, # but the current version, 3.x, is maintained on the master branch. - version('2019-01-14', '8d9c98081d89ac77a132d56bc8bef53581db4078') + version('2019-01-14', commit='8d9c98081d89ac77a132d56bc8bef53581db4078') variant('shared', default=True, description='Enable shared libraries') variant('mpi', default=True, description='Enable MPI') diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py index 59cc2751cf9..caffcfa11d4 100644 --- a/var/spack/repos/builtin/packages/yorick/package.py +++ b/var/spack/repos/builtin/packages/yorick/package.py @@ -22,7 +22,7 @@ class Yorick(Package): git = "https://github.com/dhmunro/yorick.git" version('master', branch='master') - version('2.2.04', '1b5b0da6ad81b2d9dba64d991ec17939') + version('2.2.04', sha256='4a4f3a18aed533cc5fadbb3d4bafb48f04834a22cbff6ad5c19d9dba74facbda') version('f90-plugin', branch='f90-plugin') variant('X', default=False, description='Enable X11 support') From 64bdc3251f86667cfe1df533ee8638e73514c540 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 12 Oct 2019 02:04:05 -0700 Subject: [PATCH 194/499] checksums: enforce that all mainline packages use sha256 checksums - Add a test that verifies checksums on all packages - Also add an attribute to packages that indicates whether they need a manual download or not, and add an exception in the tests for these packages until we can verify them. --- lib/spack/spack/package.py | 5 ++- lib/spack/spack/test/package_sanity.py | 42 ++++++++++++++++++- .../repos/builtin/packages/fsl/package.py | 1 + .../repos/builtin/packages/gams/package.py | 2 + .../builtin/packages/gapfiller/package.py | 1 + .../builtin/packages/gaussian/package.py | 1 + .../repos/builtin/packages/gurobi/package.py | 1 + .../repos/builtin/packages/matlab/package.py | 2 + .../repos/builtin/packages/molcas/package.py | 1 + .../repos/builtin/packages/namd/package.py | 1 + .../repos/builtin/packages/qbank/package.py | 1 + .../repos/builtin/packages/signalp/package.py | 1 + .../packages/sspace-longread/package.py | 1 + .../packages/sspace-standard/package.py | 1 + .../builtin/packages/star-ccm-plus/package.py | 1 + .../builtin/packages/supernova/package.py | 2 + .../repos/builtin/packages/targetp/package.py | 1 + .../repos/builtin/packages/tecplot/package.py | 2 + .../repos/builtin/packages/tmhmm/package.py | 1 + .../repos/builtin/packages/trf/package.py | 1 + .../builtin/packages/turbomole/package.py | 1 + .../repos/builtin/packages/usearch/package.py | 1 + .../repos/builtin/packages/vizglow/package.py | 1 + .../builtin/packages/xplor-nih/package.py | 1 + 24 files changed, 71 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 23763edf109..e8d78a6ac74 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -465,10 +465,13 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): #: _spack_build_envfile. archive_files = [] + #: Boolean. Set to ``True`` for packages that require a manual download. + #: This is currently only used by package sanity tests. + manual_download = False + # # Set default licensing information # - #: Boolean. If set to ``True``, this software requires a license. #: If set to ``False``, all of the ``license_*`` attributes will #: be ignored. Defaults to ``False``. diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py index e1a16e80af2..1dd96dccecd 100644 --- a/lib/spack/spack/test/package_sanity.py +++ b/lib/spack/spack/test/package_sanity.py @@ -8,9 +8,10 @@ import pytest +import spack.fetch_strategy import spack.paths import spack.repo -import spack.fetch_strategy +import spack.util.crypto as crypto def check_repo(): @@ -94,3 +95,42 @@ def test_docstring(): for name in spack.repo.all_package_names(): pkg = spack.repo.get(name) assert pkg.__doc__ + + +def test_all_packages_use_sha256_checksums(): + """Make sure that no packages use md5 checksums.""" + + errors = [] + for name in spack.repo.all_package_names(): + pkg = spack.repo.path.get(name) + + # for now, don't enforce on packages that require manual downloads + # TODO: eventually fix these, too. + if pkg.manual_download: + continue + + def invalid_sha256_digest(fetcher): + if getattr(fetcher, "digest", None): + h = crypto.hash_algo_for_digest(fetcher.digest) + if h != "sha256": + return h + + for v, args in pkg.versions.items(): + fetcher = spack.fetch_strategy.for_package_version(pkg, v) + bad_digest = invalid_sha256_digest(fetcher) + if bad_digest: + errors.append( + "All packages must use sha256 checksums. %s@%s uses %s." % + (name, v, bad_digest) + ) + + for _, resources in pkg.resources.items(): + for resource in resources: + bad_digest = invalid_sha256_digest(resource.fetcher) + if bad_digest: + errors.append( + "All packages must use sha256 checksums." + "Resource in %s uses %s." % (name, v, bad_digest) + ) + + assert [] == errors diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py index 5b115dcbc0a..642f09644ab 100644 --- a/var/spack/repos/builtin/packages/fsl/package.py +++ b/var/spack/repos/builtin/packages/fsl/package.py @@ -20,6 +20,7 @@ class Fsl(Package): homepage = "https://fsl.fmrib.ox.ac.uk" url = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd()) + manual_download = True version('5.0.10', '64823172a08aad679833240ba64c8e30') diff --git a/var/spack/repos/builtin/packages/gams/package.py b/var/spack/repos/builtin/packages/gams/package.py index 41cfed22e36..c900c6aad8f 100644 --- a/var/spack/repos/builtin/packages/gams/package.py +++ b/var/spack/repos/builtin/packages/gams/package.py @@ -13,6 +13,8 @@ class Gams(Package): linear, nonlinear, and mixed-integer optimization problems.""" homepage = "https://www.gams.com/" + manual_download = True + version('27.2', '4f3f3484a4389661e0522a4cfe0289fd', expand=False) def url_for_version(self, version): diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py index 6605ec12b88..6e97434f872 100644 --- a/var/spack/repos/builtin/packages/gapfiller/package.py +++ b/var/spack/repos/builtin/packages/gapfiller/package.py @@ -19,6 +19,7 @@ class Gapfiller(Package): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller" + manual_download = True version('1.10', '54d5e2ada131a1305a66e41c0d380382') diff --git a/var/spack/repos/builtin/packages/gaussian/package.py b/var/spack/repos/builtin/packages/gaussian/package.py index 86f0ede7306..3acb95974d0 100644 --- a/var/spack/repos/builtin/packages/gaussian/package.py +++ b/var/spack/repos/builtin/packages/gaussian/package.py @@ -12,6 +12,7 @@ class Gaussian(Package): homepage = "http://www.gaussian.com/" url = "file://{0}/g09.tgz".format(os.getcwd()) + manual_download = True version('09', '7d4c95b535e68e48af183920df427e4e') diff --git a/var/spack/repos/builtin/packages/gurobi/package.py b/var/spack/repos/builtin/packages/gurobi/package.py index 3741fe8e157..b9c416e46b9 100644 --- a/var/spack/repos/builtin/packages/gurobi/package.py +++ b/var/spack/repos/builtin/packages/gurobi/package.py @@ -23,6 +23,7 @@ class Gurobi(Package): $GUROBI_HOME/docs/quickstart_linux.pdf for more details.""" homepage = "http://www.gurobi.com/index" + manual_download = True version('7.5.2', '01f6dbb8d165838cca1664a1a14e4a85') diff --git a/var/spack/repos/builtin/packages/matlab/package.py b/var/spack/repos/builtin/packages/matlab/package.py index 177dad13589..65d4792bb87 100644 --- a/var/spack/repos/builtin/packages/matlab/package.py +++ b/var/spack/repos/builtin/packages/matlab/package.py @@ -23,6 +23,8 @@ class Matlab(Package): mirror, see http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "https://www.mathworks.com/products/matlab.html" + manual_download = True + version('R2018b', sha256='8cfcddd3878d3a69371c4e838773bcabf12aaf0362cc2e1ae7e8820845635cac') version('R2016b', 'b0e0b688894282139fa787b5a86a5cf7') diff --git a/var/spack/repos/builtin/packages/molcas/package.py b/var/spack/repos/builtin/packages/molcas/package.py index 1dff7a29b15..9b0d4424d88 100644 --- a/var/spack/repos/builtin/packages/molcas/package.py +++ b/var/spack/repos/builtin/packages/molcas/package.py @@ -15,6 +15,7 @@ class Molcas(CMakePackage): homepage = "http://www.molcas.org/" url = "file://{0}/molcas8.2.tar.gz".format(os.getcwd()) + manual_download = True version('8.2', '25b5fb8e1338b458a3eaea0b3d3b5e58') diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py index 1a25c462e81..7dde176df1f 100644 --- a/var/spack/repos/builtin/packages/namd/package.py +++ b/var/spack/repos/builtin/packages/namd/package.py @@ -15,6 +15,7 @@ class Namd(MakefilePackage): homepage = "http://www.ks.uiuc.edu/Research/namd/" url = "file://{0}/NAMD_2.12_Source.tar.gz".format(os.getcwd()) + manual_download = True version('2.13', '9e3323ed856e36e34d5c17a7b0341e38') version('2.12', '2a1191909b1ab03bf0205971ad4d8ee9') diff --git a/var/spack/repos/builtin/packages/qbank/package.py b/var/spack/repos/builtin/packages/qbank/package.py index 4d58b1562a7..fa362d6b5a7 100644 --- a/var/spack/repos/builtin/packages/qbank/package.py +++ b/var/spack/repos/builtin/packages/qbank/package.py @@ -22,6 +22,7 @@ class Qbank(Package): # by Scott Jackson homepage = "http://www.pnnl.gov/" url = "file://{0}/qbank-2.10.4.tar.gz".format(os.getcwd()) + manual_download = True version('2.10.4', '0820587353e63d32ddb49689dd4289e7') diff --git a/var/spack/repos/builtin/packages/signalp/package.py b/var/spack/repos/builtin/packages/signalp/package.py index ac9677c7e4a..fbaaff574e4 100644 --- a/var/spack/repos/builtin/packages/signalp/package.py +++ b/var/spack/repos/builtin/packages/signalp/package.py @@ -19,6 +19,7 @@ class Signalp(Package): homepage = "http://www.cbs.dtu.dk/services/SignalP/" url = "file://{0}/signalp-4.1f.Linux.tar.gz".format(os.getcwd()) + manual_download = True version('4.1f', 'a9aeb66259202649c959846f3f4d9744') diff --git a/var/spack/repos/builtin/packages/sspace-longread/package.py b/var/spack/repos/builtin/packages/sspace-longread/package.py index d8882b63ba9..48f4df8e16f 100644 --- a/var/spack/repos/builtin/packages/sspace-longread/package.py +++ b/var/spack/repos/builtin/packages/sspace-longread/package.py @@ -18,6 +18,7 @@ class SspaceLongread(Package): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread" + manual_download = True version('1.1', '0bb5d8603d7ead4ff1596135a520cc26') diff --git a/var/spack/repos/builtin/packages/sspace-standard/package.py b/var/spack/repos/builtin/packages/sspace-standard/package.py index a5b1ada2554..768bd3afb12 100644 --- a/var/spack/repos/builtin/packages/sspace-standard/package.py +++ b/var/spack/repos/builtin/packages/sspace-standard/package.py @@ -20,6 +20,7 @@ class SspaceStandard(Package): homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE" url = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd()) + manual_download = True version('3.0', '7e171b4861b9d514e80aafc3d9cdf554') diff --git a/var/spack/repos/builtin/packages/star-ccm-plus/package.py b/var/spack/repos/builtin/packages/star-ccm-plus/package.py index be3d0ee4c44..c673623d985 100644 --- a/var/spack/repos/builtin/packages/star-ccm-plus/package.py +++ b/var/spack/repos/builtin/packages/star-ccm-plus/package.py @@ -13,6 +13,7 @@ class StarCcmPlus(Package): homepage = "http://mdx.plm.automation.siemens.com/star-ccm-plus" url = "file://{0}/STAR-CCM+11.06.010_02_linux-x86_64.tar.gz".format(os.getcwd()) + manual_download = True version('11.06.010_02', 'd349c6ac8293d8e6e7a53533d695588f') diff --git a/var/spack/repos/builtin/packages/supernova/package.py b/var/spack/repos/builtin/packages/supernova/package.py index b4ed3bc8d46..43ccbe50c62 100644 --- a/var/spack/repos/builtin/packages/supernova/package.py +++ b/var/spack/repos/builtin/packages/supernova/package.py @@ -26,6 +26,8 @@ class Supernova(Package): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome" + manual_download = True + version('2.1.1', sha256='2f58eb66951e257b89359134ab8e35ad638c4ed51cb3fb8121625dfcc7761938') version('2.0.1', '3697ce043c798fcb672fe0a66c56d6f0') diff --git a/var/spack/repos/builtin/packages/targetp/package.py b/var/spack/repos/builtin/packages/targetp/package.py index e76a8e3a1c3..98dd5601039 100644 --- a/var/spack/repos/builtin/packages/targetp/package.py +++ b/var/spack/repos/builtin/packages/targetp/package.py @@ -18,6 +18,7 @@ class Targetp(Package): homepage = "http://www.cbs.dtu.dk/services/TargetP/" url = "file://{0}/targetp-1.1b.Linux.tar.gz".format(os.getcwd()) + manual_download = True version('1.1b', '80233d0056e11abfd22a4ce73d1808c6') diff --git a/var/spack/repos/builtin/packages/tecplot/package.py b/var/spack/repos/builtin/packages/tecplot/package.py index 8d2ab796ef4..6501c78ce7d 100644 --- a/var/spack/repos/builtin/packages/tecplot/package.py +++ b/var/spack/repos/builtin/packages/tecplot/package.py @@ -14,6 +14,8 @@ class Tecplot(Package): by post-processing charge density data.""" homepage = "https://www.tecplot.com/" + manual_download = True + version('2017r1', '06a8057d33a519607720d4c621cd3f50', expand=False) version('2018r2', 'd3cf54a7555e0259b7ba0d82fef23bc3', expand=False) diff --git a/var/spack/repos/builtin/packages/tmhmm/package.py b/var/spack/repos/builtin/packages/tmhmm/package.py index c0d6cdd703c..50141fc897f 100644 --- a/var/spack/repos/builtin/packages/tmhmm/package.py +++ b/var/spack/repos/builtin/packages/tmhmm/package.py @@ -18,6 +18,7 @@ class Tmhmm(Package): homepage = "http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm" url = "file://{0}/tmhmm-2.0c.Linux.tar.gz".format(os.getcwd()) + manual_download = True version('2.0c', '359db0c4ecf84d1ade5786abe844d54e') diff --git a/var/spack/repos/builtin/packages/trf/package.py b/var/spack/repos/builtin/packages/trf/package.py index 131f21a384f..5ba92e6ae9f 100644 --- a/var/spack/repos/builtin/packages/trf/package.py +++ b/var/spack/repos/builtin/packages/trf/package.py @@ -18,6 +18,7 @@ class Trf(Package): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "https://tandem.bu.edu/trf/trf.html" + manual_download = True version('4.09', '0c594fe666e0332db1df9d160d7fabc8', expand=False, url='file://{0}/trf409.linux64'.format(os.getcwd())) diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py index ab4c64d0fe8..fc331a1429b 100644 --- a/var/spack/repos/builtin/packages/turbomole/package.py +++ b/var/spack/repos/builtin/packages/turbomole/package.py @@ -20,6 +20,7 @@ class Turbomole(Package): see http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "http://www.turbomole-gmbh.com/" + manual_download = True version('7.0.2', '92b97e1e52e8dcf02a4d9ac0147c09d6', url="file://%s/turbolinux702.tar.gz" % os.getcwd()) diff --git a/var/spack/repos/builtin/packages/usearch/package.py b/var/spack/repos/builtin/packages/usearch/package.py index 8bebbe7c4d7..f2bd0ac18ec 100644 --- a/var/spack/repos/builtin/packages/usearch/package.py +++ b/var/spack/repos/builtin/packages/usearch/package.py @@ -18,6 +18,7 @@ class Usearch(Package): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "http://www.drive5.com/usearch/" + manual_download = True version('10.0.240', '05192b6d5e291530c190a19a3cc82b53', expand=False) diff --git a/var/spack/repos/builtin/packages/vizglow/package.py b/var/spack/repos/builtin/packages/vizglow/package.py index 7ecc10c1f38..9dca69bd10d 100644 --- a/var/spack/repos/builtin/packages/vizglow/package.py +++ b/var/spack/repos/builtin/packages/vizglow/package.py @@ -19,6 +19,7 @@ class Vizglow(Package): set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "http://esgeetech.com/products/vizglow-plasma-modeling/" + manual_download = True version('2.2alpha20', '2bef890c66f3a44aaf96f7c96788c89e', expand=False, url="file://{0}/VizGlow_v2.2alpha20-Linux-x86_64-R09December2016-Install".format(os.getcwd())) diff --git a/var/spack/repos/builtin/packages/xplor-nih/package.py b/var/spack/repos/builtin/packages/xplor-nih/package.py index 5c949c03b2b..d190d66fd66 100644 --- a/var/spack/repos/builtin/packages/xplor-nih/package.py +++ b/var/spack/repos/builtin/packages/xplor-nih/package.py @@ -17,6 +17,7 @@ class XplorNih(Package): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "https://nmr.cit.nih.gov/xplor-nih/" + manual_download = True version('2.45', 'ab3e046604beb0effc89a1adb7bab438') From ebb5ce4b69683c7ff87e100ee651e82ded66cb3d Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Sat, 12 Oct 2019 12:30:43 -0500 Subject: [PATCH 195/499] F18 Oct2019 Minor Update (#13192) * Minor clean-up of package information. * Add variants, fix dependencies, and add conflicts for compilers that do not support C++17. * Correct dependency type for CMake. --- .../repos/builtin/packages/f18/package.py | 20 ++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/f18/package.py b/var/spack/repos/builtin/packages/f18/package.py index 3b0a4d8b4f9..fce4359cf01 100644 --- a/var/spack/repos/builtin/packages/f18/package.py +++ b/var/spack/repos/builtin/packages/f18/package.py @@ -10,10 +10,24 @@ class F18(CMakePackage): """F18 is a front-end for Fortran intended to replace the existing front-end in the Flang compiler""" + # Package information homepage = "https://github.com/flang-compiler/f18" - - git = "https://github.com/flang-compiler/f18" + git = "https://github.com/flang-compiler/f18.git" version('master', branch='master') - depends_on('llvm@6.0.0+clang', when='@master') + # Variants + variant('build_type', default='Release', + description='The build type to build', + values=('Debug', 'Release', 'RelWithDebInfo')) + + # Dependencies + depends_on('cmake@3.9.0:', type='build') + depends_on('llvm+clang@7:') + + # Conflicts + compiler_warning = 'F18 requires a compiler with support for C++17' + conflicts('%clang@:6', msg=compiler_warning) + conflicts('%gcc@:7.1', msg=compiler_warning) + conflicts('%intel', msg=compiler_warning) + conflicts('%pgi', msg=compiler_warning) From 1808ba3c68c8a063157328883788eef4439785a9 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Sat, 12 Oct 2019 11:43:37 -0700 Subject: [PATCH 196/499] install: add --cache-only option (#12729) * add `--cache-only` option to install * testing for `--cache-only` * remove extraneous stage creation at stage destroy time --- lib/spack/spack/cmd/bootstrap.py | 6 +++++- lib/spack/spack/cmd/install.py | 6 +++++- lib/spack/spack/package.py | 4 +++- lib/spack/spack/test/cmd/install.py | 9 +++++++++ 4 files changed, 22 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index 27ebb7320d4..71db75c788a 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -34,6 +34,9 @@ def setup_parser(subparser): cache_group.add_argument( '--no-cache', action='store_false', dest='use_cache', default=True, help="do not check for pre-built Spack packages in mirrors") + cache_group.add_argument( + '--cache-only', action='store_true', dest='cache_only', default=False, + help="only install package from binary mirrors") cd_group = subparser.add_mutually_exclusive_group() arguments.add_common_arguments(cd_group, ['clean', 'dirty']) @@ -46,7 +49,8 @@ def bootstrap(parser, args, **kwargs): 'install_deps': 'dependencies', 'verbose': args.verbose, 'dirty': args.dirty, - 'use_cache': args.use_cache + 'use_cache': args.use_cache, + 'cache_only': args.cache_only }) # Define requirement dictionary defining general specs which need diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py index b9923c7e1ba..b625078a0bf 100644 --- a/lib/spack/spack/cmd/install.py +++ b/lib/spack/spack/cmd/install.py @@ -38,7 +38,8 @@ def update_kwargs_from_args(args, kwargs): 'verbose': args.verbose, 'fake': args.fake, 'dirty': args.dirty, - 'use_cache': args.use_cache + 'use_cache': args.use_cache, + 'cache_only': args.cache_only }) if hasattr(args, 'setup'): setups = set() @@ -81,6 +82,9 @@ def setup_parser(subparser): cache_group.add_argument( '--no-cache', action='store_false', dest='use_cache', default=True, help="do not check for pre-built Spack packages in mirrors") + cache_group.add_argument( + '--cache-only', action='store_true', dest='cache_only', default=False, + help="only install package from binary mirrors") subparser.add_argument( '--show-log-on-error', action='store_true', diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index e8d78a6ac74..686bbc2e1e9 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1499,6 +1499,7 @@ def do_install(self, **kwargs): restage (bool): Force spack to restage the package source. force (bool): Install again, even if already installed. use_cache (bool): Install from binary package, if available. + cache_only (bool): Fail if binary package unavailable. stop_at (InstallPhase): last installation phase to be executed (or None) """ @@ -1577,6 +1578,8 @@ def do_install(self, **kwargs): print_pkg(self.prefix) spack.hooks.post_install(self.spec) return + elif kwargs.get('cache_only', False): + tty.die('No binary for %s found and cache-only specified') tty.msg('No binary for %s found: installing from source' % self.name) @@ -1792,7 +1795,6 @@ def check_for_unfinished_installation( if restage and self.stage.managed_by_spack: self.stage.destroy() - self.stage.create() return partial diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py index 5b5ee1bc49b..3892a1da7b3 100644 --- a/lib/spack/spack/test/cmd/install.py +++ b/lib/spack/spack/test/cmd/install.py @@ -591,3 +591,12 @@ def test_build_warning_output(tmpdir, mock_fetch, install_mockery, capfd): assert 'WARNING: ALL CAPITAL WARNING!' in msg assert 'foo.c:89: warning: some weird warning!' in msg + + +def test_cache_only_fails(tmpdir, mock_fetch, install_mockery, capfd): + with capfd.disabled(): + try: + install('--cache-only', 'libdwarf') + assert False + except spack.main.SpackCommandError: + pass From 18ab37596855451c45210a2a107b3ecf61d698a3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 19:40:05 -0500 Subject: [PATCH 197/499] Add utf8proc package (#13144) --- .../repos/builtin/packages/utf8proc/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/utf8proc/package.py diff --git a/var/spack/repos/builtin/packages/utf8proc/package.py b/var/spack/repos/builtin/packages/utf8proc/package.py new file mode 100644 index 00000000000..2a48842c446 --- /dev/null +++ b/var/spack/repos/builtin/packages/utf8proc/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Utf8proc(CMakePackage): + """A clean C library for processing UTF-8 Unicode data: + normalization, case-folding, graphemes, and more""" + + homepage = "https://juliastrings.github.io/utf8proc/" + url = "https://github.com/JuliaStrings/utf8proc/archive/v2.4.0.tar.gz" + + version('2.4.0', sha256='b2e5d547c1d94762a6d03a7e05cea46092aab68636460ff8648f1295e2cdfbd7') + + depends_on('cmake@2.8.12:', type='build') From 0a8be4e31132ffceaac3967f815e8b5f4f2f8d95 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 19:52:47 -0500 Subject: [PATCH 198/499] Add cmake 3.15.4 (#13148) --- var/spack/repos/builtin/packages/cmake/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index c94d6aff0ba..ac74bea71a1 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -10,9 +10,10 @@ class Cmake(Package): """A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" homepage = 'https://www.cmake.org' - url = 'https://github.com/Kitware/CMake/releases/download/v3.13.0/cmake-3.13.0.tar.gz' + url = 'https://github.com/Kitware/CMake/releases/download/v3.15.4/cmake-3.15.4.tar.gz' maintainers = ['chuckatkins'] + version('3.15.4', sha256='8a211589ea21374e49b25fc1fc170e2d5c7462b795f1b29c84dd0e984301ed7a') version('3.15.3', sha256='13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5') version('3.15.2', sha256='539088cb29a68e6d6a8fba5c00951e5e5b1a92c68fa38a83e1ed2f355933f768') version('3.15.1', sha256='18dec548d8f8b04d53c60f9cedcebaa6762f8425339d1e2c889c383d3ccdd7f7') From 681c5bcceb464c43afbd19f8aef70e7eabe82949 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 19:54:46 -0500 Subject: [PATCH 199/499] Add graphviz 2.42.2 (#13150) --- var/spack/repos/builtin/packages/graphviz/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 78cf3e6db47..8e7a12e3031 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -19,6 +19,8 @@ class Graphviz(AutotoolsPackage): homepage = 'http://www.graphviz.org' git = 'https://gitlab.com/graphviz/graphviz.git' + # This commit hash is tag='stable_release_2.42.2' + version('2.42.2', commit='da4c2ec6f24ca1b6d1752c6b5bc4389e55682147') # This commit hash is tag='stable_release_2.40.1' version('2.40.1', commit='67cd2e5121379a38e0801cc05cce5033f8a2a609') @@ -92,7 +94,7 @@ class Graphviz(AutotoolsPackage): depends_on('glib', when='+pangocairo') depends_on('libpng', when='+pangocairo') depends_on('pango', when='+pangocairo') - depends_on('zlib', when='+pangocairo') + depends_on('zlib') depends_on('qt@4', when='+qt') depends_on('libx11', when="+x") From 1e2754f0d2514ed773fb24af9b4226e38b1635eb Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 19:55:14 -0500 Subject: [PATCH 200/499] Add help2man 1.47.11 (#13151) --- var/spack/repos/builtin/packages/help2man/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/help2man/package.py b/var/spack/repos/builtin/packages/help2man/package.py index caafb79950b..d1365016b09 100644 --- a/var/spack/repos/builtin/packages/help2man/package.py +++ b/var/spack/repos/builtin/packages/help2man/package.py @@ -11,8 +11,9 @@ class Help2man(AutotoolsPackage): output of other commands.""" homepage = "https://www.gnu.org/software/help2man/" - url = "https://ftpmirror.gnu.org/help2man/help2man-1.47.4.tar.xz" + url = "https://ftpmirror.gnu.org/help2man/help2man-1.47.11.tar.xz" + version('1.47.11', sha256='5985b257f86304c8791842c0c807a37541d0d6807ee973000cf8a3fe6ad47b88') version('1.47.8', sha256='528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc') version('1.47.4', sha256='d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753') From 94d57446c7e74881816115954a1b8528421df2f1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 19:55:44 -0500 Subject: [PATCH 201/499] Add libjpeg-turbo 2.0.3 (#13152) --- .../builtin/packages/libjpeg-turbo/package.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py index f7e31f475b0..6c0f5443808 100644 --- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py +++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py @@ -13,8 +13,9 @@ class LibjpegTurbo(Package): transcoding.""" # https://github.com/libjpeg-turbo/libjpeg-turbo/blob/master/BUILDING.md homepage = "https://libjpeg-turbo.org/" - url = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/2.0.2.tar.gz" + url = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/2.0.3.tar.gz" + version('2.0.3', sha256='a69598bf079463b34d45ca7268462a18b6507fdaa62bb1dfd212f02041499b5d') version('2.0.2', sha256='b45255bd476c19c7c6b198c07c0487e8b8536373b82f2b38346b32b4fa7bb942') version('1.5.90', sha256='cb948ade92561d8626fd7866a4a7ba3b952f9759ea3dd642927bc687470f60b7') version('1.5.3', sha256='1a17020f859cb12711175a67eab5c71fc1904e04b587046218e36106e07eabde') @@ -27,16 +28,16 @@ class LibjpegTurbo(Package): # only nasm is used. In order to use yasm an environmental variable # NASM must be set. # TODO: Implement the selection between two supported assemblers. - # depends_on("yasm", type='build') - depends_on("nasm", type='build') - depends_on('autoconf', type='build', when="@1.3.1:1.5.3") - depends_on('automake', type='build', when="@1.3.1:1.5.3") - depends_on('libtool', type='build', when="@1.3.1:1.5.3") - depends_on('cmake', type='build', when="@1.5.90:") + # depends_on('yasm', type='build') + depends_on('nasm', type='build') + depends_on('autoconf', type='build', when='@1.3.1:1.5.3') + depends_on('automake', type='build', when='@1.3.1:1.5.3') + depends_on('libtool', type='build', when='@1.3.1:1.5.3') + depends_on('cmake', type='build', when='@1.5.90:') @property def libs(self): - return find_libraries("libjpeg*", root=self.prefix, recursive=True) + return find_libraries('libjpeg*', root=self.prefix, recursive=True) def flag_handler(self, name, flags): if self.spec.satisfies('@1.5.90:'): From 73b2b2a70f6fe84dc97bad3ddc8a7e3bbce8a7e4 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 19:57:36 -0500 Subject: [PATCH 202/499] Add LLVM OpenMP 9.0.0 (#13154) --- var/spack/repos/builtin/packages/llvm-openmp/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/llvm-openmp/package.py b/var/spack/repos/builtin/packages/llvm-openmp/package.py index a11162b38dc..356b0c93f5a 100644 --- a/var/spack/repos/builtin/packages/llvm-openmp/package.py +++ b/var/spack/repos/builtin/packages/llvm-openmp/package.py @@ -11,8 +11,9 @@ class LlvmOpenmp(CMakePackage): an executable OpenMP program that are outside the compiler itself.""" homepage = "https://openmp.llvm.org/" - url = "https://releases.llvm.org/8.0.0/openmp-8.0.0.src.tar.xz" + url = "https://releases.llvm.org/9.0.0/openmp-9.0.0.src.tar.xz" + version('9.0.0', sha256='9979eb1133066376cc0be29d1682bc0b0e7fb541075b391061679111ae4d3b5b') version('8.0.0', sha256='f7b1705d2f16c4fc23d6531f67d2dd6fb78a077dd346b02fed64f4b8df65c9d5') depends_on('cmake@2.8:', type='build') From 22e9aafe5f07b3d303dd4183ac4f09f5d706beae Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:00:28 -0500 Subject: [PATCH 203/499] Add SCons 3.1.1 (#13157) --- var/spack/repos/builtin/packages/scons/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py index 8a898f69665..3dead9eabba 100644 --- a/var/spack/repos/builtin/packages/scons/package.py +++ b/var/spack/repos/builtin/packages/scons/package.py @@ -10,8 +10,9 @@ class Scons(PythonPackage): """SCons is a software construction tool""" homepage = "http://scons.org" - url = "https://pypi.io/packages/source/s/scons/scons-3.0.1.tar.gz" + url = "https://pypi.io/packages/source/s/scons/scons-3.1.1.tar.gz" + version('3.1.1', sha256='fd44f8f2a4562e7e5bc8c63c82b01e469e8115805a3e9c2923ee54cdcd6678b3') version('3.1.0', sha256='94e0d0684772d3e6d9368785296716e0ed6ce757270b3ed814e5aa72d3163890') version('3.0.5', sha256='e95eaae17d9e490cf12cd37f091a6cbee8a628b5c8dbd3cab1f348f602f46462') version('3.0.4', sha256='72c0b56db84f40d3558f351918a0ab98cb4345e8696e879d3e271f4df4a5913c') From 6beb5da49791ef3ea599a0922e6a335701f3fb45 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:02:05 -0500 Subject: [PATCH 204/499] Fix valgrind concretization on macOS (#13159) --- var/spack/repos/builtin/packages/valgrind/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py index a32760aed70..5691af014cd 100644 --- a/var/spack/repos/builtin/packages/valgrind/package.py +++ b/var/spack/repos/builtin/packages/valgrind/package.py @@ -36,7 +36,7 @@ class Valgrind(AutotoolsPackage): description='Activates boost support for valgrind') variant('only64bit', default=True, description='Sets --enable-only64bit option for valgrind') - variant('ubsan', default=True, + variant('ubsan', default=sys.platform != 'darwin', description='Activates ubsan support for valgrind') conflicts('+ubsan', when='platform=darwin %clang', From 7a438172054055eea081653e88fe023d88e34cf7 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:02:24 -0500 Subject: [PATCH 205/499] Add missing gettext dependency to watch (#13160) --- var/spack/repos/builtin/packages/watch/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/watch/package.py b/var/spack/repos/builtin/packages/watch/package.py index 760bd8b187e..4e805a7bc94 100644 --- a/var/spack/repos/builtin/packages/watch/package.py +++ b/var/spack/repos/builtin/packages/watch/package.py @@ -24,6 +24,7 @@ class Watch(AutotoolsPackage): depends_on('libtool', type='build') depends_on('m4', type='build') depends_on('pkgconfig@0.9.0:', type='build') + depends_on('gettext', type='build') depends_on('ncurses') # https://github.com/Homebrew/homebrew-core/blob/master/Formula/watch.rb From b18e4ad14253148dd4d5f863de1300c4a7a48c1d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:02:41 -0500 Subject: [PATCH 206/499] Add missing libiconv dependency to wget (#13161) --- var/spack/repos/builtin/packages/wget/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py index 1eaf254bbef..aecb845f110 100644 --- a/var/spack/repos/builtin/packages/wget/package.py +++ b/var/spack/repos/builtin/packages/wget/package.py @@ -43,6 +43,7 @@ class Wget(AutotoolsPackage): depends_on('perl@5.12.0:', type='build') depends_on('pkgconfig', type='build') + depends_on('libiconv') depends_on('valgrind', type='test') From 1078dfb6ccad36b51c9e0f348c2e8eb723473eda Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:03:01 -0500 Subject: [PATCH 207/499] Add py-atomicwrites 1.3.0 (#13162) --- var/spack/repos/builtin/packages/py-atomicwrites/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-atomicwrites/package.py b/var/spack/repos/builtin/packages/py-atomicwrites/package.py index 96684c07527..d2a84065476 100644 --- a/var/spack/repos/builtin/packages/py-atomicwrites/package.py +++ b/var/spack/repos/builtin/packages/py-atomicwrites/package.py @@ -10,10 +10,12 @@ class PyAtomicwrites(PythonPackage): """Atomic file writes.""" homepage = "https://github.com/untitaker/python-atomicwrites" - url = "https://pypi.io/packages/source/a/atomicwrites/atomicwrites-1.1.5.tar.gz" + url = "https://pypi.io/packages/source/a/atomicwrites/atomicwrites-1.3.0.tar.gz" import_modules = ['atomicwrites'] + version('1.3.0', sha256='75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6') version('1.1.5', sha256='240831ea22da9ab882b551b31d4225591e5e447a68c5e188db5b89ca1d487585') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') From a59e77e374450956322292ec8d36a6f6ce7e8eaf Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:04:34 -0500 Subject: [PATCH 208/499] Add missing test dependency to py-bottleneck (#13164) --- var/spack/repos/builtin/packages/py-bottleneck/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index 3b426c4d71d..f1b246cb2fb 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -16,3 +16,4 @@ class PyBottleneck(PythonPackage): depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) + depends_on('py-nose', type='test') From 1d7eab10ac9464c1c00bd9d6b49515e6a52e4a11 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:05:00 -0500 Subject: [PATCH 209/499] Add py-certifi 2019.9.11 (#13165) --- var/spack/repos/builtin/packages/py-certifi/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-certifi/package.py b/var/spack/repos/builtin/packages/py-certifi/package.py index 770877e3af6..e93c0886314 100644 --- a/var/spack/repos/builtin/packages/py-certifi/package.py +++ b/var/spack/repos/builtin/packages/py-certifi/package.py @@ -16,6 +16,7 @@ class PyCertifi(PythonPackage): import_modules = ['certifi'] + version('2019.9.11', sha256='e4f3620cfea4f83eedc95b24abd9cd56f3c4b146dd0177e83a21b4eb49e21e50') version('2019.6.16', sha256='945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695') version('2017.4.17', sha256='f7527ebf7461582ce95f7a9e03dd141ce810d40590834f4ec20cddd54234c10a') version('2017.1.23', sha256='81877fb7ac126e9215dfb15bfef7115fdc30e798e0013065158eed0707fd99ce') From db4d06f953528737a90b3b1d6e80628bf7722193 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:08:33 -0500 Subject: [PATCH 210/499] Add py-importlib-metadata 0.23 (#13168) --- .../repos/builtin/packages/py-importlib-metadata/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-importlib-metadata/package.py b/var/spack/repos/builtin/packages/py-importlib-metadata/package.py index ccc268763a0..b456fe128f2 100644 --- a/var/spack/repos/builtin/packages/py-importlib-metadata/package.py +++ b/var/spack/repos/builtin/packages/py-importlib-metadata/package.py @@ -10,14 +10,16 @@ class PyImportlibMetadata(PythonPackage): """Read metadata from Python packages.""" homepage = "http://importlib-metadata.readthedocs.io/" - url = "https://pypi.io/packages/source/i/importlib_metadata/importlib_metadata-0.19.tar.gz" + url = "https://pypi.io/packages/source/i/importlib_metadata/importlib_metadata-0.23.tar.gz" + version('0.23', sha256='aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26') version('0.19', sha256='23d3d873e008a513952355379d93cbcab874c58f4f034ff657c7a87422fa64e8') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-setuptools-scm', type='build') depends_on('py-zipp@0.5:', type=('build', 'run')) - depends_on('py-pathlib2', when='^python@:3.3', type=('build', 'run')) + depends_on('py-pathlib2', when='^python@:3.4', type=('build', 'run')) depends_on('py-contextlib2', when='^python@:2.8', type=('build', 'run')) depends_on('py-configparser@3.5:', when='^python@:2.8', type=('build', 'run')) + depends_on('py-packaging', type='test') From 101c287e7b6b7e47256c283fb0095d55507f3e0a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:11:57 -0500 Subject: [PATCH 211/499] Add py-numexpr 2.7.0 (#13172) --- var/spack/repos/builtin/packages/py-numexpr/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index cee9f525d9a..062c7d6d4f2 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -9,8 +9,9 @@ class PyNumexpr(PythonPackage): """Fast numerical expression evaluator for NumPy""" homepage = "https://pypi.python.org/pypi/numexpr" - url = "https://github.com/pydata/numexpr/archive/v2.6.9.tar.gz" + url = "https://github.com/pydata/numexpr/archive/v2.7.0.tar.gz" + version('2.7.0', sha256='1923f038b90cc69635871968ed742be7775c879451c612f173c2547c823c9561') version('2.6.9', sha256='d57267bbdf10906f5ed7841b3484bec4af0494102b50e89ba316924cc7a7fd46') version('2.6.5', sha256='fe78a78e002806e87e012b6105f3b3d52d47fc7a72bafb56341fcec7ce02cfd7') version('2.6.1', sha256='e92c83d066fa8da63864d69b5f218287cc31437ae844db77390f2183123aab22') From 50e9dc5e2e344a6ea79e05e9d8175f78ff7d905b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:12:19 -0500 Subject: [PATCH 212/499] Add py-packaging 19.2 (#13173) --- var/spack/repos/builtin/packages/py-packaging/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-packaging/package.py b/var/spack/repos/builtin/packages/py-packaging/package.py index f6c51442a30..8137fb84ea9 100644 --- a/var/spack/repos/builtin/packages/py-packaging/package.py +++ b/var/spack/repos/builtin/packages/py-packaging/package.py @@ -10,16 +10,17 @@ class PyPackaging(PythonPackage): """Core utilities for Python packages.""" homepage = "https://github.com/pypa/packaging" - url = "https://pypi.io/packages/source/p/packaging/packaging-19.1.tar.gz" + url = "https://pypi.io/packages/source/p/packaging/packaging-19.2.tar.gz" import_modules = ['packaging'] + version('19.2', sha256='28b924174df7a2fa32c1953825ff29c61e2f5e082343165438812f00d3a7fc47') version('19.1', sha256='c491ca87294da7cc01902edbe30a5bc6c4c28172b5138ab4e4aa1b9d7bfaeafe') version('17.1', sha256='f019b770dd64e585a99714f1fd5e01c7a8f11b45635aa953fd41c689a657375b') version('16.8', sha256='5d50835fdf0a7edf0b55e311b7c887786504efea1177abd7e69329a8e5ea619e') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) - depends_on('py-attrs', type=('build', 'run')) + depends_on('py-attrs', when='@:19.1', type=('build', 'run')) depends_on('py-pyparsing@2.0.2:', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) From 2ced690efbaf895a3121a2fa2ddb0cd21573dfbd Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:12:41 -0500 Subject: [PATCH 213/499] Add py-pandas 0.25.1 (#13174) --- var/spack/repos/builtin/packages/py-pandas/package.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 80075772d66..8a604a339fb 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -17,7 +17,7 @@ class PyPandas(PythonPackage): """ homepage = "http://pandas.pydata.org/" - url = "https://pypi.io/packages/source/p/pandas/pandas-0.25.0.tar.gz" + url = "https://pypi.io/packages/source/p/pandas/pandas-0.25.1.tar.gz" maintainers = ['adamjstewart'] import_modules = [ @@ -34,6 +34,7 @@ class PyPandas(PythonPackage): 'pandas.api.extensions' ] + version('0.25.1', sha256='cb2e197b7b0687becb026b84d3c242482f20cbb29a9981e43604eb67576da9f6') version('0.25.0', sha256='914341ad2d5b1ea522798efa4016430b66107d05781dbfe7cf05eba8f37df995') version('0.24.2', sha256='4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2') version('0.24.1', sha256='435821cb2501eabbcee7e83614bd710940dc0cf28b5afbc4bdb816c31cec71af') @@ -46,7 +47,7 @@ class PyPandas(PythonPackage): version('0.16.1', sha256='570d243f8cb068bf780461b9225d2e7bef7c90aa10d43cf908fe541fc92df8b6') version('0.16.0', sha256='4013de6f8796ca9d2871218861823bd9878a8dfacd26e08ccf9afdd01bbad9f1') - # https://dev.pandas.io/install.html#dependencies + # https://pandas.pydata.org/pandas-docs/stable/install.html#dependencies # Required dependencies depends_on('python@3.5.3:', type=('build', 'run'), when='@0.25:') depends_on('py-setuptools@24.2.0:', type='build') @@ -63,9 +64,10 @@ class PyPandas(PythonPackage): depends_on('py-bottleneck@1.2.1:', type=('build', 'run'), when='@0.25:') # Optional dependencies - # https://dev.pandas.io/install.html#optional-dependencies + # https://pandas.pydata.org/pandas-docs/stable/install.html#optional-dependencies # Test dependencies - # https://dev.pandas.io/install.html#running-the-test-suite + # https://pandas.pydata.org/pandas-docs/stable/development/contributing.html#running-the-test-suite depends_on('py-pytest@4.0.2:', type='test') depends_on('py-hypothesis@3.58:', type='test') + depends_on('py-pyarrow@0.10.0:', type='test') From 328583decceda16b73d0c278a398a1cc632f3ce3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:14:12 -0500 Subject: [PATCH 214/499] Add py-pluggy 0.13.0 (#13176) --- var/spack/repos/builtin/packages/py-pluggy/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pluggy/package.py b/var/spack/repos/builtin/packages/py-pluggy/package.py index d1462389e08..8e9dd50cf36 100644 --- a/var/spack/repos/builtin/packages/py-pluggy/package.py +++ b/var/spack/repos/builtin/packages/py-pluggy/package.py @@ -10,10 +10,11 @@ class PyPluggy(PythonPackage): """Plugin and hook calling mechanisms for python.""" homepage = "https://github.com/pytest-dev/pluggy" - url = "https://pypi.io/packages/source/p/pluggy/pluggy-0.12.0.tar.gz" + url = "https://pypi.io/packages/source/p/pluggy/pluggy-0.13.0.tar.gz" import_modules = ['pluggy'] + version('0.13.0', sha256='fa5fa1622fa6dd5c030e9cad086fa19ef6a0cf6d7a2d12318e10cb49d6d68f34') version('0.12.0', sha256='0825a152ac059776623854c1543d65a4ad408eb3d33ee114dff91e57ec6ae6fc') version('0.7.1', sha256='95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1') version('0.6.0', sha256='7f8ae7f5bdf75671a718d2daf0a64b7885f74510bcd98b1a0bb420eb9a9d0cff') @@ -22,4 +23,4 @@ class PyPluggy(PythonPackage): depends_on('py-setuptools', type='build') depends_on('py-setuptools-scm', type='build') - depends_on('py-importlib-metadata@0.12:', type=('build', 'run')) + depends_on('py-importlib-metadata@0.12:', when='^python@:3.7', type=('build', 'run')) From ebfd06d24896877958637c0f89d926bf942701c4 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:18:31 -0500 Subject: [PATCH 215/499] Add py-pytest 5.2.1 (#13181) --- var/spack/repos/builtin/packages/py-pytest/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pytest/package.py b/var/spack/repos/builtin/packages/py-pytest/package.py index 88855880c03..23c18774003 100644 --- a/var/spack/repos/builtin/packages/py-pytest/package.py +++ b/var/spack/repos/builtin/packages/py-pytest/package.py @@ -10,10 +10,11 @@ class PyPytest(PythonPackage): """pytest: simple powerful testing with Python.""" homepage = "http://pytest.org/" - url = "https://pypi.io/packages/source/p/pytest/pytest-5.1.1.tar.gz" + url = "https://pypi.io/packages/source/p/pytest/pytest-5.2.1.tar.gz" import_modules = ['pytest'] + version('5.2.1', sha256='ca563435f4941d0cb34767301c27bc65c510cb82e90b9ecf9cb52dc2c63caaa0') version('5.1.1', sha256='c3d5020755f70c82eceda3feaf556af9a341334414a8eca521a18f463bcead88') version('4.6.5', sha256='8fc39199bdda3d9d025d3b1f4eb99a192c20828030ea7c9a0d2840721de7d347') version('4.3.0', sha256='067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c') @@ -35,7 +36,7 @@ class PyPytest(PythonPackage): depends_on('py-setuptools@30.3:', when='@3.9.0:3.9.1', type=('build', 'run')) depends_on('py-setuptools', type=('build', 'run')) depends_on('py-setuptools-scm', when='@3.1:', type='build') - depends_on('py-py@1.5.0:', type=('build', 'run')) + depends_on('py-py@1.5.0:', when='@3.3:', type=('build', 'run')) depends_on('py-py@1.4.33:', when='@3.1.2:3.2.3,3.2.5:3.2.999', type=('build', 'run')) depends_on('py-py@1.4.33:1.4.999', when='@3.2.4', type=('build', 'run')) depends_on('py-py@1.4.29:', when='@:3.1.1', type=('build', 'run')) From 3df6b05c04f85f3a00de57da0ba496c06ac786fc Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:20:41 -0500 Subject: [PATCH 216/499] Add py-setuptools 41.4.0 (#13184) --- var/spack/repos/builtin/packages/py-setuptools/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 3e61d514620..3ac2236f7a1 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -21,6 +21,7 @@ class PySetuptools(PythonPackage): 'easy_install' ] + version('41.4.0', sha256='7eae782ccf36b790c21bde7d86a4f303a441cd77036b25c559a602cf5186ce4d') version('41.0.1', sha256='a222d126f5471598053c9a77f4b5d4f26eaa1f150ad6e01dcf1a42e185d05613') version('40.8.0', sha256='6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d') version('40.4.3', sha256='acbc5740dd63f243f46c2b4b8e2c7fd92259c2ddb55a4115b16418a2ed371b15') From 41e0b069d78c6a3012dfb10e47fa9852752b36cc Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:21:03 -0500 Subject: [PATCH 217/499] Fix external numpy package support (#13197) --- var/spack/repos/builtin/packages/py-numpy/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index e1b19ee4d71..8dc9db262d6 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -203,7 +203,7 @@ def setup_environment(self, spack_env, run_env): spec = self.spec # https://numpy.org/devdocs/user/building.html#blas - if '~blas' in spec: + if 'blas' not in spec: blas = '' elif spec['blas'].name == 'intel-mkl' or \ spec['blas'].name == 'intel-parallel-studio': @@ -222,7 +222,7 @@ def setup_environment(self, spack_env, run_env): spack_env.set('NPY_BLAS_ORDER', blas) # https://numpy.org/devdocs/user/building.html#lapack - if '~lapack' in spec: + if 'lapack' not in spec: lapack = '' elif spec['lapack'].name == 'intel-mkl' or \ spec['lapack'].name == 'intel-parallel-studio': From 08d448bc54e92f587899fcb68f7ebeb975119797 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:21:23 -0500 Subject: [PATCH 218/499] mpfr: fix make check on catalina (#13200) --- var/spack/repos/builtin/packages/mpfr/package.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py index 97436ccaf18..97d0f090b2c 100644 --- a/var/spack/repos/builtin/packages/mpfr/package.py +++ b/var/spack/repos/builtin/packages/mpfr/package.py @@ -42,6 +42,13 @@ class Mpfr(AutotoolsPackage): patch('https://www.mpfr.org/mpfr-{0}/allpatches'.format(ver), when='@' + ver, sha256=checksum) + def flag_handler(self, name, flags): + # Work around macOS Catalina / Xcode 11 code generation bug + # (test failure t-toom53, due to wrong code in mpn/toom53_mul.o) + if self.spec.satisfies('os=catalina') and name == 'cflags': + flags.append('-fno-stack-check') + return (flags, None, None) + def configure_args(self): args = [ '--with-gmp=' + self.spec['gmp'].prefix, From ea4f9ebbde50ae3606a6d8955512bc1b54299c51 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 12 Oct 2019 20:21:45 -0500 Subject: [PATCH 219/499] gmp: fix make check on catalina (#13201) --- var/spack/repos/builtin/packages/gmp/package.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index 8d829e5d309..5e333f8b22f 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -30,10 +30,15 @@ class Gmp(AutotoolsPackage): # shared library support. Regenerating it fixes the issue. force_autoreconf = True - def configure_args(self): - args = ['--enable-cxx'] + def flag_handler(self, name, flags): + # Work around macOS Catalina / Xcode 11 code generation bug + # (test failure t-toom53, due to wrong code in mpn/toom53_mul.o) + if self.spec.satisfies('os=catalina') and name == 'cflags': + flags.append('-fno-stack-check') # This flag is necessary for the Intel build to pass `make check` - if self.spec.compiler.name == 'intel': - args.append('CXXFLAGS=-no-ftz') + elif self.spec.satisfies('%intel') and name == 'cxxflags': + flags.append('-no-ftz') + return (flags, None, None) - return args + def configure_args(self): + return ['--enable-cxx'] From 2835e9bf17d435c3d60e3a9c05ab65e3801c0e77 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:42:35 -0500 Subject: [PATCH 220/499] Add py-setuptools-scm 3.3.3 (#13183) --- var/spack/repos/builtin/packages/py-setuptools-scm/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py index 69f69a23859..45a8706a957 100644 --- a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py @@ -10,10 +10,11 @@ class PySetuptoolsScm(PythonPackage): """The blessed package to manage your versions by scm tags.""" homepage = "https://github.com/pypa/setuptools_scm" - url = "https://pypi.io/packages/source/s/setuptools_scm/setuptools_scm-3.1.0.tar.gz" + url = "https://pypi.io/packages/source/s/setuptools_scm/setuptools_scm-3.3.3.tar.gz" import_modules = ['setuptools_scm'] + version('3.3.3', sha256='bd25e1fb5e4d603dcf490f1fde40fb4c595b357795674c3e5cb7f6217ab39ea5') version('3.1.0', sha256='1191f2a136b5e86f7ca8ab00a97ef7aef997131f1f6d4971be69a1ef387d8b40') version('1.15.6', sha256='49ab4685589986a42da85706b3311a2f74f1af567d39fee6cb1e088d7a75fb5f') From d6f6c41d58eb7d3e683d227d7f79a032bc8d1918 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:42:55 -0500 Subject: [PATCH 221/499] Add py-pytz 2019.3 (#13182) --- var/spack/repos/builtin/packages/py-pytz/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index ca4bc083cac..7e42f9af9f6 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -10,10 +10,11 @@ class PyPytz(PythonPackage): """World timezone definitions, modern and historical.""" homepage = "http://pythonhosted.org/pytz" - url = "https://pypi.io/packages/source/p/pytz/pytz-2016.10.tar.gz" + url = "https://pypi.io/packages/source/p/pytz/pytz-2019.3.tar.gz" import_modules = ['pytz'] + version('2019.3', sha256='b02c06db6cf09c12dd25137e563b31700d3b80fcc4ad23abb7a315f2789819be') version('2018.4', sha256='c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749') version('2016.10', sha256='9a43e20aa537cfad8fe7a1715165c91cb4a6935d40947f2d070e4c80f2dcd22b') version('2016.6.1', sha256='6f57732f0f8849817e9853eb9d50d85d1ebb1404f702dbc44ee627c642a486ca') From 8c2096aac53e705cfbd41ad0d17794179566dd69 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:43:14 -0500 Subject: [PATCH 222/499] Add py-pyparsing 2.4.2 (#13180) --- var/spack/repos/builtin/packages/py-pyparsing/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pyparsing/package.py b/var/spack/repos/builtin/packages/py-pyparsing/package.py index a4aa1e7a9dd..cdf415e3b29 100644 --- a/var/spack/repos/builtin/packages/py-pyparsing/package.py +++ b/var/spack/repos/builtin/packages/py-pyparsing/package.py @@ -9,10 +9,11 @@ class PyPyparsing(PythonPackage): """A Python Parsing Module.""" homepage = "http://pyparsing.wikispaces.com/" - url = "https://pypi.io/packages/source/p/pyparsing/pyparsing-2.2.0.tar.gz" + url = "https://pypi.io/packages/source/p/pyparsing/pyparsing-2.4.2.tar.gz" import_modules = ['pyparsing'] + version('2.4.2', sha256='6f98a7b9397e206d78cc01df10131398f1c8b8510a2f4d97d9abd82e1aacdd80') version('2.3.1', sha256='66c9268862641abcac4a96ba74506e594c884e3f57690a696d21ad8210ed667a') version('2.2.0', sha256='0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04') version('2.1.10', sha256='811c3e7b0031021137fc83e051795025fcb98674d07eb8fe922ba4de53d39188') @@ -20,6 +21,7 @@ class PyPyparsing(PythonPackage): patch('setuptools-import.patch', when='@:2.1.10') + depends_on('python@2.6:2.8,3.3:', type=('build', 'run')) # Newer versions of setuptools require pyparsing. Although setuptools is an # optional dependency of pyparsing, if it is not found, setup.py will # fallback on distutils.core instead. Don't add a setuptools dependency From 1276a182b6811fc6b3cd83eb7348cc056bb4b40c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:43:34 -0500 Subject: [PATCH 223/499] Add py-pygments 2.4.2 (#13179) --- var/spack/repos/builtin/packages/py-pygments/package.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py index d3e3445e985..3391dbec81b 100644 --- a/var/spack/repos/builtin/packages/py-pygments/package.py +++ b/var/spack/repos/builtin/packages/py-pygments/package.py @@ -10,17 +10,23 @@ class PyPygments(PythonPackage): """Pygments is a syntax highlighting package written in Python.""" homepage = "http://pygments.org/" - url = "https://pypi.io/packages/source/P/Pygments/Pygments-2.2.0.tar.gz" + url = "https://pypi.io/packages/source/P/Pygments/Pygments-2.4.2.tar.gz" import_modules = [ 'pygments', 'pygments.filters', 'pygments.formatters', 'pygments.lexers', 'pygments.styles' ] + version('2.4.2', sha256='881c4c157e45f30af185c1ffe8d549d48ac9127433f2c380c24b84572ad66297') version('2.3.1', sha256='5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a') version('2.2.0', sha256='dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc') version('2.1.3', sha256='88e4c8a91b2af5962bfa5ea2447ec6dd357018e86e94c7d14bd8cacbc5b55d81') version('2.0.1', sha256='5e039e1d40d232981ed58914b6d1ac2e453a7e83ddea22ef9f3eeadd01de45cb') version('2.0.2', sha256='7320919084e6dac8f4540638a46447a3bd730fca172afc17d2c03eed22cf4f51') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') + + def test(self): + # Unit tests require sphinx, but that creates a circular dependency + pass From f7b3524765c00e36b57b651fa4f848e9b0c7cf29 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:43:50 -0500 Subject: [PATCH 224/499] Add py-pyflakes 2.1.1 (#13178) --- var/spack/repos/builtin/packages/py-pyflakes/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pyflakes/package.py b/var/spack/repos/builtin/packages/py-pyflakes/package.py index 898c8dc9f87..4176626812b 100644 --- a/var/spack/repos/builtin/packages/py-pyflakes/package.py +++ b/var/spack/repos/builtin/packages/py-pyflakes/package.py @@ -10,8 +10,9 @@ class PyPyflakes(PythonPackage): """A simple program which checks Python source files for errors.""" homepage = "https://github.com/PyCQA/pyflakes" - url = "https://github.com/PyCQA/pyflakes/archive/1.3.0.tar.gz" + url = "https://github.com/PyCQA/pyflakes/archive/2.1.1.tar.gz" + version('2.1.1', sha256='2c98f07a9dd57d9f33561f6b54a64a766cdf79a3c869bd8c07b7fe03094fb8c3') version('2.1.0', sha256='6cd8775b6430daad386c0de00dfbc27ce2c24468cdcc4d3da41e4aa39d8ce167') version('1.6.0', sha256='f9c72359e05bf8dc27eaaee8cdcae464497f2ccadae87ac6517605ba6040ec99') version('1.5.0', sha256='943ba426420a66b5adebdbe8007e676bba11bf4006e7964d9d9ae98478c57792') @@ -27,6 +28,7 @@ class PyPyflakes(PythonPackage): version('0.9.1', sha256='e22d2e24cc97a03db24aa8d96cb0fc66ca110adabc321215f5feca2f1068d29a') version('0.9.0', sha256='b1d395d1af3922edbfdbd05ac7082d855a2613aff2cd949ff0f29e25fb51f7f3') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) # Most Python packages only require py-setuptools as a build dependency. # However, py-pyflakes requires py-setuptools during runtime as well. depends_on('py-setuptools', type=('build', 'run')) From ec3b891714f7347f87d9986cf89365a4fa8ea825 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:44:08 -0500 Subject: [PATCH 225/499] Add py-py 1.8.0 (#13177) --- var/spack/repos/builtin/packages/py-py/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-py/package.py b/var/spack/repos/builtin/packages/py-py/package.py index 4ac93458a99..1d6bb4ec45f 100644 --- a/var/spack/repos/builtin/packages/py-py/package.py +++ b/var/spack/repos/builtin/packages/py-py/package.py @@ -10,13 +10,14 @@ class PyPy(PythonPackage): """Library with cross-python path, ini-parsing, io, code, log facilities""" homepage = "http://pylib.readthedocs.io/en/latest/" - url = "https://pypi.io/packages/source/p/py/py-1.5.4.tar.gz" + url = "https://pypi.io/packages/source/p/py/py-1.8.0.tar.gz" import_modules = [ 'py', 'py._process', 'py._vendored_packages', 'py._path', 'py._log', 'py._code', 'py._io' ] + version('1.8.0', sha256='dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53') version('1.5.4', sha256='3fd59af7435864e1a243790d322d763925431213b6b8529c6ca71081ace3bbf7') version('1.5.3', sha256='29c9fab495d7528e80ba1e343b958684f4ace687327e6f789a94bf3d1915f881') version('1.4.33', sha256='1f9a981438f2acc20470b301a07a496375641f902320f70e31916fe3377385a9') From d61743561bc311deb3b47c08d6b0e247c41c925c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:45:23 -0500 Subject: [PATCH 226/499] Add py-pillow 6.2.0 (#13175) * Add py-pillow 6.2.0 * Flake8 fix --- .../builtin/packages/py-pillow/package.py | 34 ++++++++----------- 1 file changed, 15 insertions(+), 19 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index 861dca8b41f..50c16e11758 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -14,8 +14,9 @@ class PyPillow(PythonPackage): capabilities.""" homepage = "https://python-pillow.org/" - url = "https://pypi.io/packages/source/P/Pillow/Pillow-5.1.0.tar.gz" + url = "https://pypi.io/packages/source/P/Pillow/Pillow-6.2.0.tar.gz" + version('6.2.0', sha256='4548236844327a718ce3bb182ab32a16fa2050c61e334e959f554cac052fb0df') version('5.4.1', sha256='5233664eadfa342c639b9b9977190d64ad7aca4edc51a966394d7e08e7f38a9f') version('5.1.0', sha256='cee9bc75bff455d317b6947081df0824a8f118de2786dc3d74a3503fd631f4ef') version('3.2.0', sha256='64b0a057210c480aea99406c9391180cd866fc0fd8f0b53367e3af21b195784a') @@ -24,11 +25,9 @@ class PyPillow(PythonPackage): provides('pil') # These defaults correspond to Pillow defaults - variant('jpeg', default=True, description='Provide JPEG functionality') - variant('zlib', default=True, description='Access to compressed PNGs') - variant('tiff', default=False, description='Access to TIFF files') + variant('tiff', default=False, description='Access to TIFF files') variant('freetype', default=False, description='Font related services') - variant('lcms', default=False, description='Color management') + variant('lcms', default=False, description='Color management') variant('jpeg2000', default=False, description='Provide JPEG 2000 functionality') # Spack does not (yet) support these modes of building @@ -40,11 +39,10 @@ class PyPillow(PythonPackage): # Required dependencies depends_on('binutils', type='build', when=sys.platform != 'darwin') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') - - # Recommended dependencies - depends_on('jpeg', when='+jpeg') - depends_on('zlib', when='+zlib') + depends_on('jpeg') + depends_on('zlib') # Optional dependencies depends_on('libtiff', when='+tiff') @@ -66,16 +64,14 @@ def patch(self): spec = self.spec setup = FileFilter('setup.py') - if '+jpeg' in spec: - setup.filter('JPEG_ROOT = None', - 'JPEG_ROOT=("{0}","{1}")'.format( - spec['jpeg'].libs.directories[0], - spec['jpeg'].prefix.include)) - if '+zlib' in spec: - setup.filter('ZLIB_ROOT = None', - 'ZLIB_ROOT = ("{0}", "{1}")'.format( - spec['zlib'].prefix.lib, - spec['zlib'].prefix.include)) + setup.filter('JPEG_ROOT = None', + 'JPEG_ROOT=("{0}","{1}")'.format( + spec['jpeg'].libs.directories[0], + spec['jpeg'].prefix.include)) + setup.filter('ZLIB_ROOT = None', + 'ZLIB_ROOT = ("{0}", "{1}")'.format( + spec['zlib'].prefix.lib, + spec['zlib'].prefix.include)) if '+tiff' in spec: setup.filter('TIFF_ROOT = None', 'TIFF_ROOT = ("{0}", "{1}")'.format( From e72c20bc473d4a83e46e8919b3d972732e42cbc1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:46:13 -0500 Subject: [PATCH 227/499] Add py-more-itertools 7.2.0 (#13171) --- .../repos/builtin/packages/py-more-itertools/package.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-more-itertools/package.py b/var/spack/repos/builtin/packages/py-more-itertools/package.py index 4a7e569dc25..2989bc38430 100644 --- a/var/spack/repos/builtin/packages/py-more-itertools/package.py +++ b/var/spack/repos/builtin/packages/py-more-itertools/package.py @@ -10,13 +10,18 @@ class PyMoreItertools(PythonPackage): """Additions to the standard Python itertools package.""" homepage = "https://github.com/erikrose/more-itertools" - url = "https://pypi.io/packages/source/m/more-itertools/more-itertools-4.3.0.tar.gz" + url = "https://pypi.io/packages/source/m/more-itertools/more-itertools-7.2.0.tar.gz" import_modules = ['more_itertools', 'more_itertools.tests'] + version('7.2.0', sha256='409cd48d4db7052af495b09dec721011634af3753ae1ef92d2b32f73a745f832') version('4.3.0', sha256='c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e') version('4.1.0', sha256='c9ce7eccdcb901a2c75d326ea134e0886abfbea5f93e91cc95de9507c0816c44') version('2.2', sha256='93e62e05c7ad3da1a233def6731e8285156701e3419a5fe279017c429ec67ce0') + depends_on('python@3.5:', when='@7.1:', type=('build', 'run')) + depends_on('python@3.4:', when='@6:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.2:', when='@2.3:', type=('build', 'run')) + depends_on('python@2.6:2.8,3.2:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-six@1.0.0:1.999', type=('build', 'run')) + depends_on('py-six@1.0.0:1.999', when='@:5', type=('build', 'run')) From 83a96755ef9fa0b09873cad728b6054cd013e00b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:47:07 -0500 Subject: [PATCH 228/499] Add py-joblib 0.14.0 (#13169) --- var/spack/repos/builtin/packages/py-joblib/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-joblib/package.py b/var/spack/repos/builtin/packages/py-joblib/package.py index 56e9e1b548e..bf77972969b 100644 --- a/var/spack/repos/builtin/packages/py-joblib/package.py +++ b/var/spack/repos/builtin/packages/py-joblib/package.py @@ -10,14 +10,17 @@ class PyJoblib(PythonPackage): """Python function as pipeline jobs""" homepage = "http://packages.python.org/joblib/" - url = "https://pypi.io/packages/source/j/joblib/joblib-0.13.2.tar.gz" + url = "https://pypi.io/packages/source/j/joblib/joblib-0.14.0.tar.gz" import_modules = [ 'joblib', 'joblib.externals', 'joblib.externals.cloudpickle', 'joblib.externals.loky', 'joblib.externals.loky.backend' ] + version('0.14.0', sha256='6fcc57aacb4e89451fd449e9412687c51817c3f48662c3d8f38ba3f8a0a193ff') version('0.13.2', sha256='315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524') version('0.10.3', sha256='29b2965a9efbc90a5fe66a389ae35ac5b5b0c1feabfc7cab7fd5d19f429a071d') version('0.10.2', sha256='3123553bdad83b143428033537c9e1939caf4a4d8813dade6a2246948c94494b') version('0.10.0', sha256='49b3a0ba956eaa2f077e1ebd230b3c8d7b98afc67520207ada20a4d8b8efd071') + + depends_on('py-setuptools', when='@0.14:', type='build') From 2884a862e8740c115d5ead040521ce364b690ed2 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:47:25 -0500 Subject: [PATCH 229/499] Add py-docutils 0.15.2 (#13167) --- .../repos/builtin/packages/py-docutils/package.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-docutils/package.py b/var/spack/repos/builtin/packages/py-docutils/package.py index a61bf54c23e..93d8a0bd7f3 100644 --- a/var/spack/repos/builtin/packages/py-docutils/package.py +++ b/var/spack/repos/builtin/packages/py-docutils/package.py @@ -14,7 +14,7 @@ class PyDocutils(PythonPackage): markup language.""" homepage = "http://docutils.sourceforge.net/" - url = "https://pypi.io/packages/source/d/docutils/docutils-0.13.1.tar.gz" + url = "https://pypi.io/packages/source/d/docutils/docutils-0.15.2.tar.gz" import_modules = [ 'docutils', 'docutils.languages', 'docutils.parsers', @@ -27,6 +27,15 @@ class PyDocutils(PythonPackage): 'docutils.writers.s5_html', 'docutils.writers.xetex' ] - version('0.14', sha256='51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274') + version('0.15.2', sha256='a2aeea129088da402665e92e0b25b04b073c04b2dce4ab65caaa38b7ce2e1a99') + version('0.14', sha256='51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274') version('0.13.1', sha256='718c0f5fb677be0f34b781e04241c4067cbd9327b66bdd8e763201130f5175be') version('0.12', sha256='c7db717810ab6965f66c8cf0398a98c9d8df982da39b4cd7f162911eb89596fa') + + depends_on('py-setuptools', when='@0.15:', type='build') + depends_on('python@2.7:2.8,3.5:', when='@0.16:', type=('build', 'run')) + depends_on('python@2.6:2.8,3.3:', when='@0.14:0.15', type=('build', 'run')) + depends_on('python@2.4:3', when='@0.10:0.13', type=('build', 'run')) + depends_on('python@2.2.1:3', when='@0.6:0.9', type=('build', 'run')) + depends_on('python@2.2.1:2.8', when='@0.5.0:0.5.999', type=('build', 'run')) + depends_on('python@2.1:2.8', when='@:0.4', type=('build', 'run')) From 4b2b54898146b229aa7c04fd7aac38433d220bab Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:49:07 -0500 Subject: [PATCH 230/499] Add py-cython 0.29.13 (#13166) --- .../builtin/packages/py-cython/package.py | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index 603b3782fa2..c65733652d2 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -10,7 +10,7 @@ class PyCython(PythonPackage): """The Cython compiler for writing C extensions for the Python language.""" homepage = "https://pypi.python.org/pypi/cython" - url = "https://pypi.io/packages/source/c/cython/Cython-0.29.7.tar.gz" + url = "https://pypi.io/packages/source/c/cython/Cython-0.29.13.tar.gz" import_modules = [ 'cython', 'Cython', 'Cython.Build', 'Cython.Compiler', @@ -20,18 +20,20 @@ class PyCython(PythonPackage): 'Cython.Tempita', 'pyximport', ] - version('0.29.7', sha256='55d081162191b7c11c7bfcb7c68e913827dfd5de6ecdbab1b99dab190586c1e8') - version('0.29.5', sha256='9d5290d749099a8e446422adfb0aa2142c711284800fb1eb70f595101e32cbf1') - version('0.29', sha256='94916d1ede67682638d3cc0feb10648ff14dc51fb7a7f147f4fedce78eaaea97') - version('0.28.6', sha256='68aa3c00ef1deccf4dd50f0201d47c268462978c12c42943bc33dc9dc816ac1b') - version('0.28.3', sha256='1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526') - version('0.28.1', sha256='152ee5f345012ca3bb7cc71da2d3736ee20f52cd8476e4d49e5e25c5a4102b12') - version('0.25.2', sha256='f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306') - version('0.23.5', sha256='0ae5a5451a190e03ee36922c4189ca2c88d1df40a89b4f224bc842d388a0d1b6') - version('0.23.4', sha256='fec42fecee35d6cc02887f1eef4e4952c97402ed2800bfe41bbd9ed1a0730d8e') - version('0.21.2', sha256='b01af23102143515e6138a4d5e185c2cfa588e0df61c0827de4257bac3393679') + version('0.29.13', sha256='c29d069a4a30f472482343c866f7486731ad638ef9af92bfe5fca9c7323d638e') + version('0.29.7', sha256='55d081162191b7c11c7bfcb7c68e913827dfd5de6ecdbab1b99dab190586c1e8') + version('0.29.5', sha256='9d5290d749099a8e446422adfb0aa2142c711284800fb1eb70f595101e32cbf1') + version('0.29', sha256='94916d1ede67682638d3cc0feb10648ff14dc51fb7a7f147f4fedce78eaaea97') + version('0.28.6', sha256='68aa3c00ef1deccf4dd50f0201d47c268462978c12c42943bc33dc9dc816ac1b') + version('0.28.3', sha256='1aae6d6e9858888144cea147eb5e677830f45faaff3d305d77378c3cba55f526') + version('0.28.1', sha256='152ee5f345012ca3bb7cc71da2d3736ee20f52cd8476e4d49e5e25c5a4102b12') + version('0.25.2', sha256='f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306') + version('0.23.5', sha256='0ae5a5451a190e03ee36922c4189ca2c88d1df40a89b4f224bc842d388a0d1b6') + version('0.23.4', sha256='fec42fecee35d6cc02887f1eef4e4952c97402ed2800bfe41bbd9ed1a0730d8e') + version('0.21.2', sha256='b01af23102143515e6138a4d5e185c2cfa588e0df61c0827de4257bac3393679') - depends_on('python@:2', type=('build', 'run'), when='@:0.22') + depends_on('python@2.6:2.8,3.3:', when='@0.23:', type=('build', 'run')) + depends_on('python@:2', when='@:0.22', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('gdb@7.2:', type='test') From 143afbd3a061367e6e173482e45238a4fa240a00 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:49:29 -0500 Subject: [PATCH 231/499] Add py-attrs 19.2.0 (#13163) --- var/spack/repos/builtin/packages/py-attrs/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-attrs/package.py b/var/spack/repos/builtin/packages/py-attrs/package.py index 66bb4df72de..11276842337 100644 --- a/var/spack/repos/builtin/packages/py-attrs/package.py +++ b/var/spack/repos/builtin/packages/py-attrs/package.py @@ -10,13 +10,15 @@ class PyAttrs(PythonPackage): """Classes Without Boilerplate""" homepage = "http://attrs.org/" - url = "https://pypi.io/packages/source/a/attrs/attrs-18.1.0.tar.gz" + url = "https://pypi.io/packages/source/a/attrs/attrs-19.2.0.tar.gz" import_modules = ['attr'] + version('19.2.0', sha256='f913492e1663d3c36f502e5e9ba6cd13cf19d7fab50aa13239e420fef95e1396') version('18.1.0', sha256='e0d0eb91441a3b53dab4d9b743eafc1ac44476296a2053b6ca3af0b139faf87b') version('16.3.0', sha256='80203177723e36f3bbe15aa8553da6e80d47bfe53647220ccaa9ad7a5e473ccc') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-coverage', type='test') From e5d1810bec36f4f6995775529c87897eadbdaac8 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:49:53 -0500 Subject: [PATCH 232/499] Add subversion 1.12.2 (#13158) --- .../builtin/packages/subversion/package.py | 124 ++++++++++-------- 1 file changed, 72 insertions(+), 52 deletions(-) diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index 29c897ecfb7..de26e0decea 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -6,82 +6,102 @@ from spack import * -class Subversion(Package): +class Subversion(AutotoolsPackage): """Apache Subversion - an open source version control system.""" + homepage = 'https://subversion.apache.org/' - url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz' + url = 'https://archive.apache.org/dist/subversion/subversion-1.12.2.tar.gz' - version('1.9.7', sha256='c72a209c883e20245f14c4e644803f50ae83ae24652e385ff5e82300a0d06c3c') - version('1.9.6', sha256='a400cbc46d05cb29f2d7806405bb539e9e045b24013b0f12f8f82688513321a7') - version('1.9.5', sha256='280ba586c5d51d7b976b65d22d5e8e42f3908ed1c968d71120dcf534ce857a83') - version('1.9.3', sha256='74cd21d2f8a2a54e4dbd2389fe1605a19dbda8ba88ffc4bb0edc9a66e143cc93') - version('1.8.17', sha256='1b2cb9a0ca454035e55b114ee91c6433b9ede6c2893f2fb140939094d33919e4') - version('1.8.13', sha256='17e8900a877ac9f0d5ef437c20df437fec4eb2c5cb9882609d2277e2312da52c') + version('1.12.2', sha256='f4927d6603d96c5ddabebbafe9a0f6833c18a891ff0ce1ea6ffd186ce9bc21f3') + version('1.9.7', sha256='c72a209c883e20245f14c4e644803f50ae83ae24652e385ff5e82300a0d06c3c') + version('1.9.6', sha256='a400cbc46d05cb29f2d7806405bb539e9e045b24013b0f12f8f82688513321a7') + version('1.9.5', sha256='280ba586c5d51d7b976b65d22d5e8e42f3908ed1c968d71120dcf534ce857a83') + version('1.9.3', sha256='74cd21d2f8a2a54e4dbd2389fe1605a19dbda8ba88ffc4bb0edc9a66e143cc93') + version('1.8.17', sha256='1b2cb9a0ca454035e55b114ee91c6433b9ede6c2893f2fb140939094d33919e4') + version('1.8.13', sha256='17e8900a877ac9f0d5ef437c20df437fec4eb2c5cb9882609d2277e2312da52c') + variant('serf', default=True, description='Serf HTTP client library') variant('perl', default=False, description='Build with Perl bindings') depends_on('apr') depends_on('apr-util') depends_on('zlib') - depends_on('sqlite') - depends_on('serf') + depends_on('sqlite@3.8.2:') + depends_on('expat') + depends_on('lz4', when='@1.10:') + depends_on('utf8proc', when='@1.10:') + depends_on('serf', when='+serf') extends('perl', when='+perl') depends_on('swig@1.3.24:3.0.0', when='+perl') depends_on('perl-term-readkey', when='+perl') - # Optional: We need swig if we want the Perl, Python or Ruby - # bindings. - # depends_on('swig') - # depends_on('python') - # depends_on('perl') - # depends_on('ruby') - # Installation has race cases. parallel = False - def install(self, spec, prefix): + # http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html + def configure_args(self): + spec = self.spec + args = [ + '--with-apr={0}'.format(spec['apr'].prefix), + '--with-apr-util={0}'.format(spec['apr-util'].prefix), + '--with-sqlite={0}'.format(spec['sqlite'].prefix), + '--with-expat={0}:{1}:{2}'.format( + spec['expat'].headers.directories[0], + spec['expat'].libs.directories[0], + spec['expat'].libs.names[0] + ), + '--with-zlib={0}'.format(spec['zlib'].prefix), + '--without-apxs', + '--without-trang', + '--without-doxygen', + '--without-berkeley-db', + '--without-sasl', + '--without-libmagic', + '--without-kwallet', + '--without-jdk', + '--without-boost', + ] - # configure, build, install: - # Ref: - # http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html - options = ['--prefix=%s' % prefix] - options.append('--with-apr=%s' % spec['apr'].prefix) - options.append('--with-apr-util=%s' % spec['apr-util'].prefix) - options.append('--with-zlib=%s' % spec['zlib'].prefix) - options.append('--with-sqlite=%s' % spec['sqlite'].prefix) - options.append('--with-serf=%s' % spec['serf'].prefix) + if spec.satisfies('@1.10:'): + args.extend([ + '--with-lz4={0}'.format(spec['lz4'].prefix), + '--with-utf8proc={0}'.format(spec['utf8proc'].prefix), + ]) + + if '+serf' in spec: + args.append('--with-serf={0}'.format(spec['serf'].prefix)) + else: + args.append('--without-serf') if 'swig' in spec: - options.append('--with-swig=%s' % spec['swig'].prefix) - if 'perl' in spec: - options.append('PERL=%s' % spec['perl'].command.path) + args.append('--with-swig={0}'.format(spec['swig'].prefix)) + else: + args.append('--without-swig') - configure(*options) + if '+perl' in spec: + args.append('PERL={0}'.format(spec['perl'].command.path)) + + return args + + def build(self, spec, prefix): make() - if self.run_tests: - make('check') - make('install') - - if spec.satisfies('+perl'): + if '+perl' in spec: make('swig-pl') - if self.run_tests: - make('check-swig-pl') + with working_dir(join_path( + 'subversion', 'bindings', 'swig', 'perl', 'native')): + perl = spec['perl'].command + perl('Makefile.PL', 'INSTALL_BASE={0}'.format(prefix)) + + def test(self): + make('check') + if '+perl' in self.spec: + make('check-swig-pl') + + def install(self, spec, prefix): + make('install') + if '+perl' in spec: make('install-swig-pl-lib') with working_dir(join_path( 'subversion', 'bindings', 'swig', 'perl', 'native')): - perl = which('perl') - perl('Makefile.PL', 'INSTALL_BASE=%s' % prefix) make('install') - - # python bindings - # make('swig-py', - # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', - # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') - # make('install-swig-py', - # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', - # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') - - # ruby bindings - # make('swig-rb') - # make('isntall-swig-rb') From 48cd455cc1ef2aa808e94aa9c2e31c864c859432 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:50:19 -0500 Subject: [PATCH 233/499] Add mercurial 5.1.2 (#13156) --- .../builtin/packages/mercurial/package.py | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py index 5b7ec7bdd31..f099bb17746 100644 --- a/var/spack/repos/builtin/packages/mercurial/package.py +++ b/var/spack/repos/builtin/packages/mercurial/package.py @@ -11,7 +11,7 @@ class Mercurial(PythonPackage): """Mercurial is a free, distributed source control management tool.""" homepage = "https://www.mercurial-scm.org" - url = "https://www.mercurial-scm.org/release/mercurial-5.1.1.tar.gz" + url = "https://www.mercurial-scm.org/release/mercurial-5.1.2.tar.gz" import_modules = [ 'hgext', 'hgext3rd', 'mercurial', 'hgext.convert', 'hgext.fsmonitor', @@ -20,8 +20,9 @@ class Mercurial(PythonPackage): 'mercurial.httpclient', 'mercurial.pure' ] - version('5.1.1', sha256='35fc8ba5e0379c1b3affa2757e83fb0509e8ac314cbd9f1fd133cf265d16e49f') - version('4.9.1', sha256='1bdd21bb87d1e05fb5cd395d488d0e0cc2f2f90ce0fd248e31a03595da5ccb47') + version('5.1.2', sha256='15af0b090b23649e0e53621a88dde97b55a734d7cb08b77d3df284db70d44e2e') + version('5.1.1', sha256='35fc8ba5e0379c1b3affa2757e83fb0509e8ac314cbd9f1fd133cf265d16e49f') + version('4.9.1', sha256='1bdd21bb87d1e05fb5cd395d488d0e0cc2f2f90ce0fd248e31a03595da5ccb47') version('4.4.1', sha256='8f2a5512d6cc2ffb08988aef639330a2f0378e4ac3ee0e1fbbdb64d9fff56246') version('4.1.2', sha256='09415253fb409a77e19b9951532a3c22c4e07e74bab80652527064617daab194') version('3.9.1', sha256='625e4fc7e85ec2278c2828bdc547fce74091b3bbe4d9eeeba2d61af51195df74') @@ -31,12 +32,20 @@ class Mercurial(PythonPackage): version('3.8.2', sha256='cb78b16956140625266a8a6d1fadc7c868969d994086e1ec60279a66bf20bffd') version('3.8.1', sha256='face1f058de5530b56b0dfd3b4d0b23d89590c588605c06f3d18b79e8c30d594') - depends_on('python@2.6:2.8', when='@:4.2.99') - depends_on('python@2.7:2.8,3.5:3.5.999,3.6.2:', when='@4.3:') + depends_on('python@2.6:2.8', when='@:4.2.99', type=('build', 'run')) + depends_on('python@2.7:2.8,3.5.3:3.5.999,3.6.2:', when='@4.3:', type=('build', 'run')) + depends_on('py-setuptools', when='@3.6:', type='build') depends_on('py-docutils', type='build') depends_on('py-pygments', type=('build', 'run')) depends_on('py-certifi', type=('build', 'run')) + def setup_environment(self, spack_env, run_env): + # Python 3 support is still experimental, explicitly allow + spack_env.set('HGALLOWPYTHON3', True) + spack_env.set('HGPYTHON3', True) + # Setuptools is still opt-in, explicitly enable + spack_env.set('FORCE_SETUPTOOLS', True) + @run_after('install') def post_install(self): prefix = self.prefix From b3fcfc1cb25884f668466816be08a2a68cee256a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:50:44 -0500 Subject: [PATCH 234/499] Add lz4 1.9.2 (#13155) --- var/spack/repos/builtin/packages/lz4/package.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/lz4/package.py b/var/spack/repos/builtin/packages/lz4/package.py index 0f01a59743b..b062c25b260 100644 --- a/var/spack/repos/builtin/packages/lz4/package.py +++ b/var/spack/repos/builtin/packages/lz4/package.py @@ -7,15 +7,16 @@ import sys -class Lz4(Package): +class Lz4(MakefilePackage): """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.""" homepage = "http://lz4.github.io/lz4/" - url = "https://github.com/lz4/lz4/archive/v1.7.5.tar.gz" + url = "https://github.com/lz4/lz4/archive/v1.9.2.tar.gz" + version('1.9.2', sha256='658ba6191fa44c92280d4aa2c271b0f4fbc0e34d249578dd05e50e76d0e5efcc') version('1.9.0', sha256='f8b6d5662fa534bd61227d313535721ae41a68c9d84058b7b7d86e143572dcfb') version('1.8.3', sha256='33af5936ac06536805f9745e0b6d61da606a1f8b4cc5c04dd3cbaca3b9b4fc43') version('1.8.1.2', sha256='12f3a9e776a923275b2dc78ae138b4967ad6280863b77ff733028ce89b8123f9') @@ -32,13 +33,13 @@ def url_for_version(self, version): else: return "{0}/r{1}.tar.gz".format(url, version.joined) - def install(self, spec, prefix): + def build(self, spec, prefix): if sys.platform != "darwin": make('MOREFLAGS=-lrt') # fixes make error on CentOS6 else: make() - if self.run_tests: - make('test') # requires valgrind to be installed + + def install(self, spec, prefix): make('install', 'PREFIX={0}'.format(prefix)) @run_after('install') From 518a7c5bb95b6f2919ff775616f9c3ba97c4a81e Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:51:04 -0500 Subject: [PATCH 235/499] Add libpng 1.6.37 (#13153) --- .../repos/builtin/packages/libpng/package.py | 23 ++++++------------- 1 file changed, 7 insertions(+), 16 deletions(-) diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index d9547786000..1b699fff015 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -10,25 +10,16 @@ class Libpng(AutotoolsPackage): """libpng is the official PNG reference library.""" homepage = "http://www.libpng.org/pub/png/libpng.html" - url = "http://download.sourceforge.net/libpng/libpng-1.6.34.tar.gz" + url = "http://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz" list_url = "https://sourceforge.net/projects/libpng/files/" list_depth = 2 - version('1.6.34', sha256='574623a4901a9969080ab4a2df9437026c8a87150dfd5c235e28c94b212964a7') - version('1.6.29', sha256='e30bf36cd5882e017c23a5c6a79a9aa1a744dd5841bb45ff7035ec6e3b3096b8') - version('1.6.28', sha256='b6cec903e74e9fdd7b5bbcde0ab2415dd12f2f9e84d9e4d9ddd2ba26a41623b2') - version('1.6.27', sha256='c9d164ec247f426a525a7b89936694aefbc91fb7a50182b198898b8fc91174b4') - # From http://www.libpng.org/pub/png/libpng.html (2017-01-04) - # Virtually all libpng versions through 1.6.26, 1.5.27, - # 1.4.19, 1.2.56, and 1.0.66, respectively, have a - # null-pointer-dereference bug in png_set_text_2() when an - # image-editing application adds, removes, and re-adds text - # chunks to a PNG image. (This bug does not affect pure - # viewers, nor are there any known editors that could trigger - # it without interactive user input. It has been assigned ID - # CVE-2016-10087.) The vulnerability is fixed in versions - # 1.6.27, 1.5.28, 1.4.20, 1.2.57, and 1.0.67, released on 29 - # December 2016. + version('1.6.37', sha256='daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4') + # From http://www.libpng.org/pub/png/libpng.html (2019-04-15) + # libpng versions 1.6.36 and earlier have a use-after-free bug in the + # simplified libpng API png_image_free(). It has been assigned ID + # CVE-2019-7317. The vulnerability is fixed in version 1.6.37, + # released on 15 April 2019. # Required for qt@3 version('1.2.57', sha256='09ec37869fc5b130f5eb06ffb9bf949796e8d2d78e0788f78ab1c78624c6e9da') From 30c5f882554936a7422f43e87d76c30901bfa14d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:51:53 -0500 Subject: [PATCH 236/499] Add freetype 2.10.1 (#13149) --- var/spack/repos/builtin/packages/freetype/package.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/freetype/package.py b/var/spack/repos/builtin/packages/freetype/package.py index 507228b2cce..0f522ab2c84 100644 --- a/var/spack/repos/builtin/packages/freetype/package.py +++ b/var/spack/repos/builtin/packages/freetype/package.py @@ -13,12 +13,13 @@ class Freetype(AutotoolsPackage): of most vector and bitmap font formats.""" homepage = "https://www.freetype.org/index.html" - url = "https://download.savannah.gnu.org/releases/freetype/freetype-2.9.1.tar.gz" + url = "https://download.savannah.gnu.org/releases/freetype/freetype-2.10.1.tar.gz" - version('2.9.1', sha256='ec391504e55498adceb30baceebd147a6e963f636eb617424bcfc47a169898ce') - version('2.7.1', sha256='162ef25aa64480b1189cdb261228e6c5c44f212aac4b4621e28cf2157efb59f5') - version('2.7', sha256='7b657d5f872b0ab56461f3bd310bd1c5ec64619bd15f0d8e08282d494d9cfea4') - version('2.5.3', sha256='41217f800d3f40d78ef4eb99d6a35fd85235b64f81bc56e4812d7672fca7b806') + version('2.10.1', sha256='3a60d391fd579440561bf0e7f31af2222bc610ad6ce4d9d7bd2165bca8669110') + version('2.9.1', sha256='ec391504e55498adceb30baceebd147a6e963f636eb617424bcfc47a169898ce') + version('2.7.1', sha256='162ef25aa64480b1189cdb261228e6c5c44f212aac4b4621e28cf2157efb59f5') + version('2.7', sha256='7b657d5f872b0ab56461f3bd310bd1c5ec64619bd15f0d8e08282d494d9cfea4') + version('2.5.3', sha256='41217f800d3f40d78ef4eb99d6a35fd85235b64f81bc56e4812d7672fca7b806') depends_on('libpng') depends_on('bzip2') From 7b21ac3188f879eb98d6de1996cd95eb3459522b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:52:10 -0500 Subject: [PATCH 237/499] Add bison 3.4.2 (#13147) --- var/spack/repos/builtin/packages/bison/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index f1eb5503879..02abd3e4fa8 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -13,9 +13,10 @@ class Bison(AutotoolsPackage): an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - homepage = "http://www.gnu.org/software/bison/" - url = "https://ftpmirror.gnu.org/bison/bison-3.0.4.tar.gz" + homepage = "https://www.gnu.org/software/bison/" + url = "https://ftpmirror.gnu.org/bison/bison-3.4.2.tar.gz" + version('3.4.2', sha256='ff3922af377d514eca302a6662d470e857bd1a591e96a2050500df5a9d59facf') version('3.0.5', sha256='cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566') version('3.0.4', sha256='b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e') version('2.7', sha256='19bbe7374fd602f7a6654c131c21a15aebdc06cc89493e8ff250cb7f9ed0a831') From c121ddb300352fe23764f29b5012011c3a536edb Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:52:40 -0500 Subject: [PATCH 238/499] Add apr 1.7.0 (#13146) --- var/spack/repos/builtin/packages/apr/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py index 9efefa1002f..97e615834bd 100644 --- a/var/spack/repos/builtin/packages/apr/package.py +++ b/var/spack/repos/builtin/packages/apr/package.py @@ -10,7 +10,8 @@ class Apr(AutotoolsPackage): """Apache portable runtime.""" homepage = 'https://apr.apache.org/' - url = 'http://archive.apache.org/dist/apr/apr-1.6.2.tar.gz' + url = 'https://archive.apache.org/dist/apr/apr-1.7.0.tar.gz' + version('1.7.0', sha256='48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2') version('1.6.2', sha256='4fc24506c968c5faf57614f5d0aebe0e9d0b90afa47a883e1a1ca94f15f4a42e') version('1.5.2', sha256='1af06e1720a58851d90694a984af18355b65bb0d047be03ec7d659c746d6dbdb') From ce6bf5fba1bbbff36f36ba88aaa8faa1f3a7f618 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 19:52:58 -0500 Subject: [PATCH 239/499] Add apr-util 1.6.1 (#13145) --- var/spack/repos/builtin/packages/apr-util/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py index bebce244fa3..849cac0495b 100644 --- a/var/spack/repos/builtin/packages/apr-util/package.py +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -10,8 +10,9 @@ class AprUtil(AutotoolsPackage): """Apache Portable Runtime Utility""" homepage = 'https://apr.apache.org/' - url = 'http://archive.apache.org/dist/apr/apr-util-1.6.0.tar.gz' + url = 'https://archive.apache.org/dist/apr/apr-util-1.6.1.tar.gz' + version('1.6.1', sha256='b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459') version('1.6.0', sha256='483ef4d59e6ac9a36c7d3fd87ad7b9db7ad8ae29c06b9dd8ff22dda1cc416389') version('1.5.4', sha256='976a12a59bc286d634a21d7be0841cc74289ea9077aa1af46be19d1a6e844c19') From 1f29785b887cf2fdeb589b5e749e60c73091e77c Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Sun, 13 Oct 2019 19:54:41 -0500 Subject: [PATCH 240/499] omega-h: add version 9.29.0 (#13208) --- var/spack/repos/builtin/packages/omega-h/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/omega-h/package.py b/var/spack/repos/builtin/packages/omega-h/package.py index f8296a8811b..e4594061648 100644 --- a/var/spack/repos/builtin/packages/omega-h/package.py +++ b/var/spack/repos/builtin/packages/omega-h/package.py @@ -18,6 +18,7 @@ class OmegaH(CMakePackage): maintainers = ['ibaned'] version('develop', branch='master') + version('9.29.0', sha256='b41964b018909ffe9cea91c23a0509b259bfbcf56874fcdf6bd9f6a179938014') version('9.27.0', sha256='aa51f83508cbd14a41ae953bda7da98a6ad2979465c76e5b3a3d9a7a651cb34a') version('9.22.2', sha256='ab5636be9dc171a514a7015df472bd85ab86fa257806b41696170842eabea37d') version('9.19.1', sha256='60ef65c2957ce03ef9d1b995d842fb65c32c5659d064de002c071effe66b1b1f') From 20c2fa62aaa788c30bc868005daf1520a5677b26 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Sun, 13 Oct 2019 19:56:27 -0500 Subject: [PATCH 241/499] slepc: use spack specified python in configure (#13207) --- var/spack/repos/builtin/packages/slepc/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index dd9774a2eaf..8313705cbf9 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -93,7 +93,7 @@ def install(self, spec, prefix): if '+blopex' in spec: options.append('--download-blopex') - configure('--prefix=%s' % prefix, *options) + python('configure', '--prefix=%s' % prefix, *options) make('MAKE_NP=%s' % make_jobs, parallel=False) if self.run_tests: From 846daa0404b887a218529834daee326c209e150c Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Sun, 13 Oct 2019 19:57:11 -0500 Subject: [PATCH 242/499] amrex: add version 19.10 (#13206) --- var/spack/repos/builtin/packages/amrex/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py index cea0d5fd61b..234584927b6 100644 --- a/var/spack/repos/builtin/packages/amrex/package.py +++ b/var/spack/repos/builtin/packages/amrex/package.py @@ -17,6 +17,7 @@ class Amrex(CMakePackage): maintainers = ['mic84', 'asalmgren'] version('develop', branch='development') + version('19.10', commit='52844b32b7da11e9733b9a7f4a782e51de7f5e1e') # tag:19.10 version('19.08', commit='bdd1146139e8727a513d451075f900c172eb81fd') # tag:19.08 version('18.10.1', commit='260b53169badaa760b91dfc60ea6b2ea3d9ccf06') # tag:18.10.1 version('18.10', commit='d37a266c38092e1174096e245326e9eead1f4e03') # tag:18.10 From 27ad28e51a33dcb0cc14b3400c8dcb246d53b21c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 13 Oct 2019 22:26:49 -0700 Subject: [PATCH 243/499] Add py-kiwisolver 1.1.0 (#13170) --- var/spack/repos/builtin/packages/py-kiwisolver/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-kiwisolver/package.py b/var/spack/repos/builtin/packages/py-kiwisolver/package.py index 0afcec72c65..fb8509f1db7 100644 --- a/var/spack/repos/builtin/packages/py-kiwisolver/package.py +++ b/var/spack/repos/builtin/packages/py-kiwisolver/package.py @@ -10,8 +10,10 @@ class PyKiwisolver(PythonPackage): """A fast implementation of the Cassowary constraint solver""" homepage = "https://github.com/nucleic/kiwi" - url = "https://pypi.io/packages/source/k/kiwisolver/kiwisolver-1.0.1.tar.gz" + url = "https://pypi.io/packages/source/k/kiwisolver/kiwisolver-1.1.0.tar.gz" + version('1.1.0', sha256='53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75') version('1.0.1', sha256='ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') From 04af0eb5a2e4bf91d63825b33cff62f36176c5f3 Mon Sep 17 00:00:00 2001 From: wspear Date: Mon, 14 Oct 2019 01:34:37 -0700 Subject: [PATCH 244/499] py-redis: added new package at version 3.3.8 (#13134) --- .../repos/builtin/packages/py-redis/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-redis/package.py diff --git a/var/spack/repos/builtin/packages/py-redis/package.py b/var/spack/repos/builtin/packages/py-redis/package.py new file mode 100644 index 00000000000..fbfc0757e95 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-redis/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyRedis(PythonPackage): + """The Python interface to the Redis key-value store.""" + + homepage = "https://pypi.org/project/redis/" + url = "https://pypi.io/packages/source/r/redis/redis-3.3.8.tar.gz" + + version('3.3.8', sha256='98a22fb750c9b9bb46e75e945dc3f61d0ab30d06117cbb21ff9cd1d315fedd3b') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') From bdcf9ba5cd7af40c25009c2551d337eb80059379 Mon Sep 17 00:00:00 2001 From: wspear Date: Mon, 14 Oct 2019 01:35:41 -0700 Subject: [PATCH 245/499] py-python-memcached: added new package at version 1.59 (#13133) * Added package py-python-memcached, a dependency of python-oauth2 * Fixed line lengths --- .../packages/py-python-memcached/package.py | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-python-memcached/package.py diff --git a/var/spack/repos/builtin/packages/py-python-memcached/package.py b/var/spack/repos/builtin/packages/py-python-memcached/package.py new file mode 100644 index 00000000000..13c14d38a65 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-memcached/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonMemcached(PythonPackage): + """This software is a 100% Python interface to the memcached memory cache + daemon. It is the client side software which allows storing values in one + or more, possibly remote, memcached servers. Search google for memcached + for more information.""" + + homepage = "https://pypi.org/project/python-memcached/" + url = "https://pypi.io/packages/source/p/python-memcached/python-memcached-1.59.tar.gz" + + version('1.59', sha256='a2e28637be13ee0bf1a8b6843e7490f9456fd3f2a4cb60471733c7b5d5557e4f') + + depends_on('py-setuptools', type='build') + depends_on('py-six@1.4.0:', type=('build', 'run')) From e1cf35a82b04bd31dff64c260a4a30c741217723 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 14 Oct 2019 01:40:20 -0700 Subject: [PATCH 246/499] Fix svn tests, skip if svnadmin not found (#13137) --- lib/spack/spack/test/mirror.py | 3 ++- lib/spack/spack/test/svn_fetch.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py index a8697fd029a..2f80bae4081 100644 --- a/lib/spack/spack/test/mirror.py +++ b/lib/spack/spack/test/mirror.py @@ -109,7 +109,8 @@ def test_git_mirror(mock_git_repository): @pytest.mark.skipif( - not which('svn'), reason='requires subversion to be installed') + not which('svn') or not which('svnadmin'), + reason='requires subversion to be installed') def test_svn_mirror(mock_svn_repository): set_up_package('svn-test', mock_svn_repository, 'svn') check_mirror() diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py index a915a82874a..eb0d22ee7cd 100644 --- a/lib/spack/spack/test/svn_fetch.py +++ b/lib/spack/spack/test/svn_fetch.py @@ -19,7 +19,8 @@ pytestmark = pytest.mark.skipif( - not which('svn'), reason='requires subversion to be installed') + not which('svn') or not which('svnadmin'), + reason='requires subversion to be installed') @pytest.mark.parametrize("type_of_test", ['default', 'rev0']) From c851cfd1226c6a5db69813d06c82d7631dadbb71 Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Mon, 14 Oct 2019 03:42:49 -0500 Subject: [PATCH 247/499] py-smart-open: new package at 1.8.4 (#13135) --- .../builtin/packages/py-smart-open/package.py | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-smart-open/package.py diff --git a/var/spack/repos/builtin/packages/py-smart-open/package.py b/var/spack/repos/builtin/packages/py-smart-open/package.py new file mode 100644 index 00000000000..483e55a6b42 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-smart-open/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySmartOpen(PythonPackage): + """smart_open is a Python 2 & Python 3 library for efficient streaming of + very large files from/to S3, HDFS, WebHDFS, HTTP, or local storage. It + supports transparent, on-the-fly (de-)compression for a variety of + different formats.""" + + homepage = "https://github.com/piskvorky/smart_open" + url = "https://github.com/RaRe-Technologies/smart_open/archive/1.8.4.tar.gz" + + version('1.8.4', sha256='788e07f035defcbb62e3c1e313329a70b0976f4f65406ee767db73ad5d2d04f9') + + depends_on('py-setuptools', type='build') + depends_on('py-boto3', type=('build', 'run')) From 2bb1bae2ae42770bcc122816f22a2a3a7031ef78 Mon Sep 17 00:00:00 2001 From: Jeffrey Salmond Date: Mon, 14 Oct 2019 09:49:31 +0100 Subject: [PATCH 248/499] dialign: added new package at version 2.2.1 (#13130) Co-Authored-By: Adam J. Stewart --- .../repos/builtin/packages/dialign/package.py | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/repos/builtin/packages/dialign/package.py diff --git a/var/spack/repos/builtin/packages/dialign/package.py b/var/spack/repos/builtin/packages/dialign/package.py new file mode 100644 index 00000000000..5a8e6b7d7c0 --- /dev/null +++ b/var/spack/repos/builtin/packages/dialign/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Dialign(MakefilePackage): + """DIALIGN is a software program for multiple sequence alignment developed + by Burkhard Morgenstern et al..""" + + homepage = "https://bibiserv.cebitec.uni-bielefeld.de/dialign" + url = "https://bibiserv.cebitec.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz" + + version('2.2.1', sha256='046361bb4ca6e4ab2ac5e634cfcd673f964a887006c09c1b8bd3310fac86f519') + + build_directory = 'src' + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install(join_path('src', 'dialign2-2'), prefix.bin) + + mkdirp(prefix.share) + install_tree('dialign2_dir', prefix.share) + + def setup_environment(self, spack_env, run_env): + run_env.set('DIALIGN2_DIR', self.prefix.share) From 8a1e5f68f4185b87875f28435bccc7fb44e9fe5f Mon Sep 17 00:00:00 2001 From: wspear Date: Mon, 14 Oct 2019 01:53:01 -0700 Subject: [PATCH 249/499] py-alembic: fixed missing dependencies. (#13127) --- var/spack/repos/builtin/packages/py-alembic/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/py-alembic/package.py b/var/spack/repos/builtin/packages/py-alembic/package.py index 397dd40accb..c3ccdf23c59 100644 --- a/var/spack/repos/builtin/packages/py-alembic/package.py +++ b/var/spack/repos/builtin/packages/py-alembic/package.py @@ -15,3 +15,7 @@ class PyAlembic(PythonPackage): version('1.0.7', sha256='16505782b229007ae905ef9e0ae6e880fddafa406f086ac7d442c1aaf712f8c2') depends_on('py-setuptools', type='build') + depends_on('py-sqlalchemy@1.1.0:', type=('build', 'run')) + depends_on('py-mako', type=('build', 'run')) + depends_on('py-python-dateutil', type=('build', 'run')) + depends_on('py-python-editor@0.3:', type=('build', 'run')) From 385d2bf3fa5f99782fbdea5d8951c29a4bf2a91b Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 14 Oct 2019 08:58:01 -0700 Subject: [PATCH 250/499] commands: add resource stats to `spack url stats` (#13205) `spack url stats` now also looks at packages' resources when outputting statistics. Example: ``` $ spack url stats ==> URL stats for 3531 packages: -------------------------------------------------------------- stat versions % resources % -------------------------------------------------------------- url 8335 89.3% 339 89.0% schemes https 6489 69.5% 93 24.4% ftp 32 0.3% 8 2.1% http 1763 18.9% 237 62.2% file 51 0.5% 1 0.3% checksums md5 26 0.3% 0 0.0% sha256 8306 89.0% 336 88.2% no checksum 3 0.0% 3 0.8% -------------------------------------------------------------- go 1 0.0% 0 0.0% -------------------------------------------------------------- hg 7 0.1% 0 0.0% -------------------------------------------------------------- no code 4 0.0% 0 0.0% -------------------------------------------------------------- svn 4 0.0% 16 4.2% -------------------------------------------------------------- git 981 10.5% 26 6.8% branch 442 4.7% 4 1.0% commit 362 3.9% 14 3.7% no ref 36 0.4% 2 0.5% tag 141 1.5% 6 1.6% -------------------------------------------------------------- ``` --- lib/spack/spack/cmd/url.py | 150 ++++++++++++++++++-------------- lib/spack/spack/test/cmd/url.py | 6 +- 2 files changed, 92 insertions(+), 64 deletions(-) diff --git a/lib/spack/spack/cmd/url.py b/lib/spack/spack/cmd/url.py index 3fe4e0ac6a2..10257b26086 100644 --- a/lib/spack/spack/cmd/url.py +++ b/lib/spack/spack/cmd/url.py @@ -239,80 +239,104 @@ def url_summary(args): def url_stats(args): - stats = {} # stats about fetchers in packages. - nvers = 0 # total number of versions - npkgs = 0 # total number of packages + class UrlStats(object): + def __init__(self): + self.total = 0 + self.schemes = defaultdict(lambda: 0) + self.checksums = defaultdict(lambda: 0) + self.url_type = defaultdict(lambda: 0) + self.git_type = defaultdict(lambda: 0) - def inc(fstype, category, attr=None): - """Increment statistics in the stats dict.""" - categories = stats.setdefault(fstype, {}) - if attr: - cat_stats = categories.setdefault(category, {}) - val = cat_stats.setdefault(attr, 0) - stats[fstype][category][attr] = val + 1 - else: - val = categories.setdefault(category, 0) - stats[fstype][category] = val + 1 + def add(self, fetcher): + self.total += 1 - # over all packages - for pkg in spack.repo.path.all_packages(): - npkgs += 1 + url_type = fetcher.url_attr + self.url_type[url_type or 'no code'] += 1 - if not pkg.has_code: - for _ in pkg.versions: - inc('No code', 'total') - nvers += 1 - continue - - # look at each version - for v, args in pkg.versions.items(): - # figure out what type of fetcher it is - fetcher = fs.for_package_version(pkg, v) - nvers += 1 - - fstype = fetcher.url_attr - inc(fstype, 'total') - - # put some special stats in for particular types of fetchers. - if fstype == 'git': - if 'commit' in args: - inc('git', 'security', 'commit') + if url_type == 'url': + digest = getattr(fetcher, 'digest', None) + if digest: + algo = crypto.hash_algo_for_digest(digest) else: - inc('git', 'security', 'no commit') - elif fstype == 'url': - for h in crypto.hashes: - if h in args: - inc('url', 'checksums', h) - break - else: - if 'checksum' in args: - h = crypto.hash_algo_for_digest(args['checksum']) - inc('url', 'checksums', h) - else: - inc('url', 'checksums', 'no checksum') + algo = 'no checksum' + self.checksums[algo] += 1 # parse out the URL scheme (https/http/ftp/etc.) urlinfo = urlparse(fetcher.url) - inc('url', 'schemes', urlinfo.scheme) + self.schemes[urlinfo.scheme] += 1 + + elif url_type == 'git': + if getattr(fetcher, 'commit', None): + self.git_type['commit'] += 1 + elif getattr(fetcher, 'branch', None): + self.git_type['branch'] += 1 + elif getattr(fetcher, 'tag', None): + self.git_type['tag'] += 1 + else: + self.git_type['no ref'] += 1 + + npkgs = 0 + version_stats = UrlStats() + resource_stats = UrlStats() + + for pkg in spack.repo.path.all_packages(): + npkgs += 1 + + for v, args in pkg.versions.items(): + fetcher = fs.for_package_version(pkg, v) + version_stats.add(fetcher) + + for _, resources in pkg.resources.items(): + for resource in resources: + resource_stats.add(resource.fetcher) # print a nice summary table - tty.msg("%d total versions for %d packages:" % (nvers, npkgs)) - line_width = 36 - print("-" * line_width) - for fetcher, fetcher_stats in sorted(stats.items(), reverse=True): - fs_total = fetcher_stats['total'] - fs_pct = float(fs_total) / nvers * 100 - print("%-22s%5d%8.1f%%" % (fetcher, fs_total, fs_pct)) + tty.msg("URL stats for %d packages:" % npkgs) - for category, cat_stats in sorted(fetcher_stats.items(), reverse=True): - if category == 'total': - continue - print(" %s" % category) + def print_line(): + print("-" * 62) - for name, number in sorted(cat_stats.items(), reverse=True): - pct = float(number) / fs_total * 100 - print(" %-18s%5d%8.1f%%" % (name, number, pct)) - print("-" * line_width) + def print_stat(indent, name, stat_name=None): + width = 20 - indent + fmt = " " * indent + fmt += "%%-%ds" % width + if stat_name is None: + print(fmt % name) + else: + fmt += "%12d%8.1f%%%12d%8.1f%%" + v = getattr(version_stats, stat_name).get(name, 0) + r = getattr(resource_stats, stat_name).get(name, 0) + print(fmt % (name, + v, v / version_stats.total * 100, + r, r / resource_stats.total * 100)) + + print_line() + print("%-20s%12s%9s%12s%9s" % ("stat", "versions", "%", "resources", "%")) + print_line() + print_stat(0, "url", "url_type") + + print_stat(4, "schemes") + schemes = set(version_stats.schemes) | set(resource_stats.schemes) + for scheme in schemes: + print_stat(8, scheme, "schemes") + + print_stat(4, "checksums") + checksums = set(version_stats.checksums) | set(resource_stats.checksums) + for checksum in checksums: + print_stat(8, checksum, "checksums") + print_line() + + types = set(version_stats.url_type) | set(resource_stats.url_type) + types -= set(["url", "git"]) + for url_type in sorted(types): + print_stat(0, url_type, "url_type") + print_line() + + print_stat(0, "git", "url_type") + git_types = set(version_stats.git_type) | set(resource_stats.git_type) + for git_type in sorted(git_types): + print_stat(4, git_type, "git_type") + print_line() def print_name_and_version(url): diff --git a/lib/spack/spack/test/cmd/url.py b/lib/spack/spack/test/cmd/url.py index e147f842917..6593c94d980 100644 --- a/lib/spack/spack/test/cmd/url.py +++ b/lib/spack/spack/test/cmd/url.py @@ -131,4 +131,8 @@ def test_url_stats(capfd): output = url('stats') npkgs = '%d packages' % len(spack.repo.all_package_names()) assert npkgs in output - assert 'total versions' in output + assert 'url' in output + assert 'git' in output + assert 'schemes' in output + assert 'versions' in output + assert 'resources' in output From 48b73702651d206b81cd7df12c93f92c75e0c113 Mon Sep 17 00:00:00 2001 From: wspear Date: Mon, 14 Oct 2019 11:57:54 -0700 Subject: [PATCH 251/499] py-pymongo: added new package at version 3.9.0 (#13132) --- .../builtin/packages/py-pymongo/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pymongo/package.py diff --git a/var/spack/repos/builtin/packages/py-pymongo/package.py b/var/spack/repos/builtin/packages/py-pymongo/package.py new file mode 100644 index 00000000000..8e28001e4ce --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pymongo/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPymongo(PythonPackage): + """The PyMongo distribution contains tools for interacting with + MongoDB database from Python. The bson package is an implementation + of the BSON format for Python. The pymongo package is a native + Python driver for MongoDB. The gridfs package is a gridfs + implementation on top of pymongo. + + PyMongo supports MongoDB 2.6, 3.0, 3.2, 3.4, 3.6, 4.0 and 4.2.""" + + homepage = "https://pypi.org/project/pymongo/" + url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.9.0.tar.gz" + + version('3.9.0', sha256='4249c6ba45587b959292a727532826c5032d59171f923f7f823788f413c2a5a3') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') From be8f8856ce8a8d72cd2309af3ad77c4ab52d43bc Mon Sep 17 00:00:00 2001 From: Hadrien G Date: Mon, 14 Oct 2019 21:01:53 +0200 Subject: [PATCH 252/499] New ACTS versions (#12484) * Add new ACTS releases * Update ACTS dependency requirements * We can actually be more specific here * The material plugin is gone as of ACTS v0.10.0 * Add 0.10.4 release * Remove material mapping plugin It was merged into core as of 0.10.x, and given ACTS' youth it is unlikely to have actual users at this point in time. --- .../repos/builtin/packages/acts-core/package.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts-core/package.py index bad166660ec..30cba1eaa82 100644 --- a/var/spack/repos/builtin/packages/acts-core/package.py +++ b/var/spack/repos/builtin/packages/acts-core/package.py @@ -33,8 +33,14 @@ class ActsCore(CMakePackage): git = "https://gitlab.cern.ch/acts/acts-core.git" version('develop', branch='master') + version('0.10.4', commit='42cbc359c209f5cf386e620b5a497192c024655e') + version('0.10.3', commit='a3bb86b79a65b3d2ceb962b60411fd0df4cf274c') + version('0.10.2', commit='64cbf28c862d8b0f95232b00c0e8c38949d5015d') version('0.10.1', commit='0692dcf7824efbc504fb16f7aa00a50df395adbc') version('0.10.0', commit='30ef843cb00427f9959b7de4d1b9843413a13f02') + version('0.09.5', commit='12b11fe8b0d428ccb8e92dda7dc809198f828672') + version('0.09.4', commit='e5dd9fbe179201e70347d1a3b9fa1899c226798f') + version('0.09.3', commit='a8f31303ee8720ed2946bfe2d59e81d0f70e307e') version('0.09.2', commit='4e1f7fa73ffe07457080d787e206bf6466fe1680') version('0.09.1', commit='69c451035516cb683b8f7bc0bab1a25893e9113d') version('0.09.0', commit='004888b0a412f5bbaeef2ffaaeaf2aa182511494') @@ -53,13 +59,11 @@ class ActsCore(CMakePackage): variant('dd4hep', default=False, description='Build the DD4hep plugin') variant('identification', default=False, description='Build the Identification plugin') variant('json', default=False, description='Build the Json plugin') - variant('material', default=False, description='Build the material plugin') variant('tgeo', default=False, description='Build the TGeo plugin') - depends_on('cmake @3.7:', type='build') - # Currently incompatible with boost 1.70.0, see also discussion at - # https://gitlab.cern.ch/acts/acts-core/issues/592#note_2618474 - depends_on('boost @1.62:1.69.99 +program_options +test') + depends_on('cmake @3.9:', type='build') + depends_on('boost @1.62:1.69.99 +program_options +test', when='@:0.10.3') + depends_on('boost @1.62: +program_options +test', when='@0.10.4:') depends_on('eigen @3.2.9:', type='build') depends_on('root @6.10: cxxstd=14', when='+tgeo @:0.8.0') depends_on('root @6.10:', when='+tgeo @0.8.1:') @@ -81,7 +85,6 @@ def cmake_variant(cmake_label, spack_variant): cmake_variant("DD4HEP_PLUGIN", "dd4hep"), cmake_variant("IDENTIFICATION", "identification"), cmake_variant("JSON_PLUGIN", "json"), - cmake_variant("MATERIAL_PLUGIN", "material"), cmake_variant("TGEO_PLUGIN", "tgeo") ] From dafee9df3199af365a8dfb58952b8fde6116c105 Mon Sep 17 00:00:00 2001 From: William F Godoy Date: Mon, 14 Oct 2019 15:47:55 -0400 Subject: [PATCH 253/499] Complete cleanup of the adios2 package configuration (#13107) Provide up to date specs for build options Remove non-production versions Format using autopep8 and flake8 Separate cmake options in adios2 2.4.0 version Keep default as True as much as possible Support for Python 2 and 3 for adios2 versions <= 2.4.0 Starting v2.5.0 only Python 3 is supported Addressing review suggestions --- .../repos/builtin/packages/adios2/package.py | 102 +++++++++--------- 1 file changed, 49 insertions(+), 53 deletions(-) diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index 2a3d3698df3..3d7339da41a 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -7,57 +7,58 @@ class Adios2(CMakePackage): - """Next generation of ADIOS developed in the Exascale Computing Program""" + """The Adaptable Input Output System version 2, + developed in the Exascale Computing Program""" - homepage = "https://www.olcf.ornl.gov/center-projects/adios/" - url = "https://github.com/ornladios/ADIOS2/archive/v2.0.0.tar.gz" - git = "https://github.com/ornladios/ADIOS2.git" + homepage = "https://csmd.ornl.gov/software/adios2" + url = "https://github.com/ornladios/ADIOS2/archive/v2.5.0.tar.gz" + git = "https://github.com/ornladios/ADIOS2.git" - maintainers = ['ax3l', 'chuckatkins'] + maintainers = ['ax3l', 'chuckatkins', 'williamfgc'] version('develop', branch='master') version('2.5.0', sha256='7c8ff3bf5441dd662806df9650c56a669359cb0185ea232ecb3578de7b065329') version('2.4.0', sha256='50ecea04b1e41c88835b4b3fd4e7bf0a0a2a3129855c9cc4ba6cf6a1575106e2') version('2.3.1', sha256='3bf81ccc20a7f2715935349336a76ba4c8402355e1dc3848fcd6f4c3c5931893') - version('2.2.0', sha256='77058ea2ff7224dc02ea519733de42d89112cf21ffe7474fb2fa3c5696152948') - version('2.1.0', sha256='d4df3b3035b4236b51c77b59d68e756e825834b2ea3cb17439927a027831453b') - version('2.0.0', sha256='4eeedf4404824d8de6e4ef580b8a703c0aedb5c03f900f5ce6f85f0b35980135') + # general build options + variant('mpi', default=True, description='Enable MPI') + variant('build_type', default='Release', + description='CMake build type', + values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel')) variant('shared', default=True, description='Also build shared libraries') variant('pic', default=True, description='Enable position independent code ' '(for usage of static in shared downstream deps)') - variant('mpi', default=True, - description='Enable MPI') + variant('endian_reverse', default=False, + description='Enable Endian Interoperability') - # transforms + # compression libraries variant('blosc', default=True, - description='Enable Blosc transforms') + description='Enable Blosc compression') variant('bzip2', default=True, - description='Enable BZip2 transforms') + description='Enable BZip2 compression') variant('zfp', default=True, - description='Enable ZFP transforms') + description='Enable ZFP compression') variant('png', default=True, - description='Enable ZFP transforms') + description='Enable PNG compression') + variant('sz', default=True, + description='Enable SZ compression') - # sz is broken in 2.2.0: https://github.com/ornladios/ADIOS2/issues/705 - # variant('sz', default=True, - # description='Enable SZ compression') # transport engines + variant('sst', default=True, + description='Enable the SST staging engine') variant('dataman', default=True, description='Enable the DataMan engine for WAN transports') - # currently required by DataMan, optional in the future - # variant('zeromq', default=False, - # description='Enable ZeroMQ for the DataMan engine') + variant('ssc', default=True, + description='Enable the SSC staging engine') variant('hdf5', default=False, description='Enable the HDF5 engine') - variant('adios1', default=False, - description='Enable the ADIOS 1.x engine ' - '(in 2.3.0+ integrated in BPFile engine)') - # language bindings - variant('python', default=False, - description='Enable the Python >= 2.7 bindings') + + # optional language bindings, C++11 and C always provided + variant('python', default=True, + description='Enable the Python bindings') variant('fortran', default=True, description='Enable the Fortran bindings') @@ -72,33 +73,26 @@ class Adios2(CMakePackage): # DataMan needs dlopen conflicts('+dataman', when='~shared') - # BPFile engine was emulated via a ADIOS1 engine prior to v2.3.0 - conflicts('+adios1', when='@2.3.0:') - depends_on('cmake@3.6.0:', type='build') - depends_on('pkgconfig', type='build', when='@2.2.0:') - # The included ffs requires bison and flex but using them makes - # the build fail due to an undefined reference. - # depends_on('bison', type='build', when='@2.2.0:') - # depends_on('flex', when='@2.2.0:') + depends_on('pkgconfig', type='build') depends_on('mpi', when='+mpi') depends_on('zeromq', when='+dataman') + depends_on('zeromq', when='@2.4: +ssc') depends_on('hdf5', when='+hdf5') depends_on('hdf5+mpi', when='+hdf5+mpi') - depends_on('adios', when='@:2.2.99 +adios1') - depends_on('adios+mpi', when='@:2.2.99 +adios1+mpi') - depends_on('c-blosc', when='@2.4.0: +blosc') - depends_on('bzip2', when='+bzip2') - depends_on('libpng@1.6:', when='@2.4.0: +png') - # depends_on('mgard', when='@2.3.0: +mgard') + depends_on('c-blosc', when='@2.4: +blosc') + depends_on('bzip2', when='@2.4: +bzip2') + depends_on('libpng@1.6:', when='@2.4: +png') depends_on('zfp@0.5.1:', when='+zfp') - # depends_on('sz@:1.4.12', when='+sz') + depends_on('sz@:2.0.2.0', when='+sz') extends('python', when='+python') - depends_on('python@2.7:', type=('build', 'run'), when='+python') + depends_on('python@2.7:2.8,3.5:', + when='@:2.4.0 +python', type=('build', 'run')) + depends_on('python@3.5:', when='@2.5.0: +python', type=('build', 'run')) depends_on('py-numpy@1.6.1:', type=('build', 'run'), when='+python') depends_on('py-mpi4py@2.0.0:', type=('build', 'run'), when='+mpi +python') @@ -113,10 +107,9 @@ def cmake_args(self): '-DBUILD_SHARED_LIBS:BOOL={0}'.format( 'ON' if '+shared' in spec else 'OFF'), '-DADIOS2_BUILD_TESTING=OFF', + '-DADIOS2_BUILD_EXAMPLES=OFF', '-DADIOS2_USE_MPI={0}'.format( 'ON' if '+mpi' in spec else 'OFF'), - '-DADIOS2_USE_BZip2={0}'.format( - 'ON' if '+bzip2' in spec else 'OFF'), '-DADIOS2_USE_MGARD=OFF', '-DADIOS2_USE_ZFP={0}'.format( 'ON' if '+zfp' in spec else 'OFF'), @@ -124,31 +117,34 @@ def cmake_args(self): 'ON' if '+sz' in spec else 'OFF'), '-DADIOS2_USE_DataMan={0}'.format( 'ON' if '+dataman' in spec else 'OFF'), - '-DADIOS2_USE_ZeroMQ={0}'.format( - 'ON' if '+dataman' in spec else 'OFF'), + '-DADIOS2_USE_SST={0}'.format( + 'ON' if '+sst' in spec else 'OFF'), '-DADIOS2_USE_HDF5={0}'.format( 'ON' if '+hdf5' in spec else 'OFF'), '-DADIOS2_USE_Python={0}'.format( 'ON' if '+python' in spec else 'OFF'), '-DADIOS2_USE_Fortran={0}'.format( - 'ON' if '+fortran' in spec else 'OFF') + 'ON' if '+fortran' in spec else 'OFF'), + '-DADIOS2_USE_Endian_Reverse={0}'.format( + 'ON' if '+endian_reverse' in spec else 'OFF'), ] - # option removed and integrated in internal BPFile engine - if self.spec.version < Version('2.3.0'): - args.append('-DADIOS2_USE_ADIOS1={0}'.format( - 'ON' if '+adios1' in spec else 'OFF')) - if self.spec.version >= Version('2.4.0'): args.append('-DADIOS2_USE_Blosc={0}'.format( 'ON' if '+blosc' in spec else 'OFF')) + args.append('-DADIOS2_USE_BZip2={0}'.format( + 'ON' if '+bzip2' in spec else 'OFF')) args.append('-DADIOS2_USE_PNG={0}'.format( 'ON' if '+png' in spec else 'OFF')) + args.append('-DADIOS2_USE_SSC={0}'.format( + 'ON' if '+ssc' in spec else 'OFF')) if spec.satisfies('~shared'): args.append('-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL={0}'.format( 'ON' if '+pic' in spec else 'OFF')) + if spec.satisfies('+python'): args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s' % self.spec['python'].command.path) + return args From a63e64f1c4f2f96d68daa1916ca77d4986b60cf1 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Mon, 14 Oct 2019 15:27:28 -0500 Subject: [PATCH 254/499] py-petsc4py: add version 3.12.0 (#13209) * py-petsc4py: add version 3.12.0 * fix typo wrt maintainer --- var/spack/repos/builtin/packages/py-petsc4py/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-petsc4py/package.py b/var/spack/repos/builtin/packages/py-petsc4py/package.py index e9c7ebe24de..b2626f5378f 100644 --- a/var/spack/repos/builtin/packages/py-petsc4py/package.py +++ b/var/spack/repos/builtin/packages/py-petsc4py/package.py @@ -14,9 +14,10 @@ class PyPetsc4py(PythonPackage): url = "https://bitbucket.org/petsc/petsc4py/get/3.10.0.tar.gz" git = "https://bitbucket.org/petsc/petsc4py.git" - maintainers = ['dalcin', 'balay'] + maintainers = ['dalcinl', 'balay'] version('develop', branch='master') + version('3.12.0', sha256='1ddffc35163ec81de50ca43b8a82fdbe73baf02d9e24d594685d5f4a6c17a8cb') version('3.11.0', sha256='50a7bbca76000da287d5b18969ddf4743b360bda1f6ee3b43b5829095569cc46') version('3.10.1', sha256='4eae5eaf459875b1329cae36fa1e5e185f603e8b01a4e05b59b0983c02b5a174') version('3.10.0', sha256='737e7812ccc54b1e0d6e8de4bdcd886c8ce287129297831f1f0e33089fa352f2') @@ -34,6 +35,7 @@ class PyPetsc4py(PythonPackage): depends_on('petsc+mpi') depends_on('petsc@develop+mpi', when='@develop') + depends_on('petsc@3.12:3.12.99+mpi', when='@3.12:3.12.99') depends_on('petsc@3.11:3.11.99+mpi', when='@3.11:3.11.99') depends_on('petsc@3.10.3:3.10.99+mpi', when='@3.10.1:3.10.99') depends_on('petsc@3.10:3.10.2+mpi', when='@3.10.0') From 3f46f03c837da9959b4257c710e521fc9bf777bb Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Mon, 14 Oct 2019 17:50:38 -0700 Subject: [PATCH 255/499] bugfix: install --only dependencies works in env (#13090) * bugfix: install --only dependents works in env includes regression testing --- lib/spack/spack/cmd/install.py | 28 ++++------- lib/spack/spack/package.py | 12 +++++ lib/spack/spack/test/cmd/install.py | 48 +++++++++++++++++++ .../packages/dependent-install/package.py | 4 +- 4 files changed, 73 insertions(+), 19 deletions(-) diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py index b625078a0bf..876fb58f512 100644 --- a/lib/spack/spack/cmd/install.py +++ b/lib/spack/spack/cmd/install.py @@ -39,8 +39,15 @@ def update_kwargs_from_args(args, kwargs): 'fake': args.fake, 'dirty': args.dirty, 'use_cache': args.use_cache, - 'cache_only': args.cache_only + 'cache_only': args.cache_only, + 'explicit': True # Always true for install command }) + + kwargs.update({ + 'install_dependencies': ('dependencies' in args.things_to_install), + 'install_package': ('package' in args.things_to_install) + }) + if hasattr(args, 'setup'): setups = set() for arglist_s in args.setup: @@ -188,8 +195,8 @@ def default_log_file(spec): def install_spec(cli_args, kwargs, abstract_spec, spec): """Do the actual installation.""" - # handle active environment, if any - def install(spec, kwargs): + try: + # handle active environment, if any env = ev.get_env(cli_args, 'install') if env: env.install(abstract_spec, spec, **kwargs) @@ -197,17 +204,6 @@ def install(spec, kwargs): else: spec.package.do_install(**kwargs) - try: - if cli_args.things_to_install == 'dependencies': - # Install dependencies as-if they were installed - # for root (explicit=False in the DB) - kwargs['explicit'] = False - for s in spec.dependencies(): - install(s, kwargs) - else: - kwargs['explicit'] = True - install(spec, kwargs) - except spack.build_environment.InstallError as e: if cli_args.show_log_on_error: e.print_context() @@ -242,10 +238,6 @@ def install(parser, args, **kwargs): # Parse cli arguments and construct a dictionary # that will be passed to Package.do_install API update_kwargs_from_args(args, kwargs) - kwargs.update({ - 'install_dependencies': ('dependencies' in args.things_to_install), - 'install_package': ('package' in args.things_to_install) - }) if args.run_tests: tty.warn("Deprecated option: --run-tests: use --test=all instead") diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 686bbc2e1e9..b6a2d2de8d5 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1519,6 +1519,15 @@ def do_install(self, **kwargs): dirty = kwargs.get('dirty', False) restage = kwargs.get('restage', False) + # install_self defaults True and is popped so that dependencies are + # always installed regardless of whether the root was installed + install_self = kwargs.pop('install_package', True) + # explicit defaults False so that dependents are implicit regardless + # of whether their dependents are implicitly or explicitly installed. + # Spack ensures root packages of install commands are always marked to + # install explicit + explicit = kwargs.pop('explicit', False) + # For external packages the workflow is simplified, and basically # consists in module file generation and registration in the DB if self.spec.external: @@ -1568,6 +1577,9 @@ def do_install(self, **kwargs): if install_deps: Package._install_bootstrap_compiler(self, **kwargs) + if not install_self: + return + # Then, install the package proper tty.msg(colorize('@*{Installing} @*g{%s}' % self.name)) diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py index 3892a1da7b3..3be548907ab 100644 --- a/lib/spack/spack/test/cmd/install.py +++ b/lib/spack/spack/test/cmd/install.py @@ -21,10 +21,13 @@ from spack.error import SpackError from spack.spec import Spec from spack.main import SpackCommand +import spack.environment as ev from six.moves.urllib.error import HTTPError, URLError install = SpackCommand('install') +env = SpackCommand('env') +add = SpackCommand('add') @pytest.fixture(scope='module') @@ -600,3 +603,48 @@ def test_cache_only_fails(tmpdir, mock_fetch, install_mockery, capfd): assert False except spack.main.SpackCommandError: pass + + +def test_install_only_dependencies(tmpdir, mock_fetch, install_mockery): + dep = Spec('dependency-install').concretized() + root = Spec('dependent-install').concretized() + + install('--only', 'dependencies', 'dependent-install') + + assert os.path.exists(dep.prefix) + assert not os.path.exists(root.prefix) + + +@pytest.mark.regression('12002') +def test_install_only_dependencies_in_env(tmpdir, mock_fetch, install_mockery, + mutable_mock_env_path): + env('create', 'test') + + with ev.read('test'): + dep = Spec('dependency-install').concretized() + root = Spec('dependent-install').concretized() + + install('-v', '--only', 'dependencies', 'dependent-install') + + assert os.path.exists(dep.prefix) + assert not os.path.exists(root.prefix) + + +@pytest.mark.regression('12002') +def test_install_only_dependencies_of_all_in_env( + tmpdir, mock_fetch, install_mockery, mutable_mock_env_path +): + env('create', '--without-view', 'test') + + with ev.read('test'): + roots = [Spec('dependent-install@1.0').concretized(), + Spec('dependent-install@2.0').concretized()] + + add('dependent-install@1.0') + add('dependent-install@2.0') + install('--only', 'dependencies') + + for root in roots: + assert not os.path.exists(root.prefix) + for dep in root.traverse(root=False): + assert os.path.exists(dep.prefix) diff --git a/var/spack/repos/builtin.mock/packages/dependent-install/package.py b/var/spack/repos/builtin.mock/packages/dependent-install/package.py index 1a0f13ffea9..54c60ce99e8 100644 --- a/var/spack/repos/builtin.mock/packages/dependent-install/package.py +++ b/var/spack/repos/builtin.mock/packages/dependent-install/package.py @@ -13,8 +13,10 @@ class DependentInstall(Package): url = "http://www.example.com/a-1.0.tar.gz" version('1.0', '0123456789abcdef0123456789abcdef') + version('2.0', '0123456789abcdef0123456789abcdef') - depends_on('dependency-install') + depends_on('dependency-install@2.0', when='@2.0') + depends_on('dependency-install@1.0', when='@1.0') def install(self, spec, prefix): touch(join_path(prefix, 'an_installation_file')) From 5cd28847e81b3a1bf659d184c990ba9144974624 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 15 Oct 2019 05:35:14 +0200 Subject: [PATCH 256/499] filter_file uses "surrogateescape" error handling (#12765) From Python docs: -- 'surrogateescape' will represent any incorrect bytes as code points in the Unicode Private Use Area ranging from U+DC80 to U+DCFF. These private code points will then be turned back into the same bytes when the surrogateescape error handler is used when writing data. This is useful for processing files in an unknown encoding. -- This will allow us to process files with unknown encodings. To accommodate the case of self-extracting bash scripts, filter_file can now stop filtering text input if a certain marker is found. The marker must be passed at call time via the "stop_at" function argument. At that point the file will be reopened in binary mode and copied verbatim. * use "surrogateescape" error handling to ignore unknown chars * permit to stop filtering if a marker is found * add unit tests for non-ASCII and mixed text/binary files --- lib/spack/llnl/util/filesystem.py | 38 +- .../test/data/filter_file/selfextract.bsx | Bin 0 -> 585 bytes .../test/data/filter_file/x86_cpuid_info.c | 1531 +++++++++++++++++ lib/spack/spack/test/llnl/util/filesystem.py | 38 +- .../builtin/packages/aspera-cli/package.py | 3 +- 5 files changed, 1603 insertions(+), 7 deletions(-) create mode 100644 lib/spack/spack/test/data/filter_file/selfextract.bsx create mode 100644 lib/spack/spack/test/data/filter_file/x86_cpuid_info.c diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 762d851ec5c..45914be60ea 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -6,7 +6,6 @@ import collections import errno import hashlib -import fileinput import glob import grp import itertools @@ -123,10 +122,15 @@ def filter_file(regex, repl, *filenames, **kwargs): backup (bool): Make backup file(s) suffixed with ``~``. Default is True ignore_absent (bool): Ignore any files that don't exist. Default is False + stop_at (str): Marker used to stop scanning the file further. If a text + line matches this marker filtering is stopped and the rest of the + file is copied verbatim. Default is to filter until the end of the + file. """ string = kwargs.get('string', False) backup = kwargs.get('backup', True) ignore_absent = kwargs.get('ignore_absent', False) + stop_at = kwargs.get('stop_at', None) # Allow strings to use \1, \2, etc. for replacement, like sed if not callable(repl): @@ -159,8 +163,36 @@ def groupid_to_group(x): shutil.copy(filename, backup_filename) try: - for line in fileinput.input(filename, inplace=True): - print(re.sub(regex, repl, line.rstrip('\n'))) + extra_kwargs = {} + if sys.version_info > (3, 0): + extra_kwargs = {'errors': 'surrogateescape'} + + # Open as a text file and filter until the end of the file is + # reached or we found a marker in the line if it was specified + with open(backup_filename, mode='r', **extra_kwargs) as input_file: + with open(filename, mode='w', **extra_kwargs) as output_file: + # Using iter and readline is a workaround needed not to + # disable input_file.tell(), which will happen if we call + # input_file.next() implicitly via the for loop + for line in iter(input_file.readline, ''): + if stop_at is not None: + current_position = input_file.tell() + if stop_at == line.strip(): + output_file.write(line) + break + filtered_line = re.sub(regex, repl, line) + output_file.write(filtered_line) + else: + current_position = None + + # If we stopped filtering at some point, reopen the file in + # binary mode and copy verbatim the remaining part + if current_position and stop_at: + with open(backup_filename, mode='rb') as input_file: + input_file.seek(current_position) + with open(filename, mode='ab') as output_file: + output_file.writelines(input_file.readlines()) + except BaseException: # clean up the original file on failure. shutil.move(backup_filename, filename) diff --git a/lib/spack/spack/test/data/filter_file/selfextract.bsx b/lib/spack/spack/test/data/filter_file/selfextract.bsx new file mode 100644 index 0000000000000000000000000000000000000000..7c0a436a56b6c9584241e228c1a5dcf21e369d22 GIT binary patch literal 585 zcmY#Z)KALH(@#n)&frQ-&d66#Qi9UKsX1v1t`#LkiOD6IdFcwCdBr7(IXS6CFa=6n zT&WcW`9&oPA-(}Fo`<-W013lXPB#P zLSlKgg1UZOd^}Vn-pSR+KRiBOU!l67C^N4_!7oTbTfxv;A+;j2M8UvXp;lc%#Qf^MF+3RELdRG~(pB(X@LqN+?m*I7XY;vOz8XRxaZ%2N`!l2hQqdit3#uW*6I zLCUy_ausxo(%_1KUIW?6#f9NMF8OW_j_A`%Vi}kV5-W4^6I1knb~C)a<>=pRAaShl zTuqnN`Ahqj-nDD!>FL8CBEM8kN~24z z8qV(aoOX_P^_o4B>pM$dPV#)Yx8rlzCA*Dky;Ent?REQQCL6ml=dyYG-y{3xKdZmu z>=objZtv`ml9zwhTRqoby5!H%^*TS}4^7zr*Y~G&@u~eP^$f^hM$ij^+v~Ds{fhc~ zz9jkX&i|oN_FwE%J^#N~%FF*^<+69(t=zc$ZPi;VUM2H<47IKME8bo6{hLgmSNZP4 kD|P4a&tLN+k8kzv-ygr+N@qeg`Cm7GM%2Y`3;_%b08*yl_5c6? literal 0 HcmV?d00001 diff --git a/lib/spack/spack/test/data/filter_file/x86_cpuid_info.c b/lib/spack/spack/test/data/filter_file/x86_cpuid_info.c new file mode 100644 index 00000000000..c7431fef367 --- /dev/null +++ b/lib/spack/spack/test/data/filter_file/x86_cpuid_info.c @@ -0,0 +1,1531 @@ +/****************************/ +/* THIS IS OPEN SOURCE CODE */ +/****************************/ + +/* +* File: x86_cpuid_info.c +* Author: Dan Terpstra +* terpstra@eecs.utk.edu +* complete rewrite of linux-memory.c to conform to latest docs +* and convert Intel to a table driven implementation. +* Now also supports multiple TLB descriptors +*/ + +#include +#include +#include +#include "papi.h" +#include "papi_internal.h" + +static void init_mem_hierarchy( PAPI_mh_info_t * mh_info ); +static int init_amd( PAPI_mh_info_t * mh_info, int *levels ); +static short int _amd_L2_L3_assoc( unsigned short int pattern ); +static int init_intel( PAPI_mh_info_t * mh_info , int *levels); + +#if defined( __amd64__ ) || defined (__x86_64__) +static inline void +cpuid( unsigned int *a, unsigned int *b, unsigned int *c, unsigned int *d ) +{ + unsigned int op = *a; + __asm__("cpuid;" + : "=a" (*a), "=b" (*b), "=c" (*c), "=d" (*d) + : "a" (op) ); +} +#else +static inline void +cpuid( unsigned int *a, unsigned int *b, unsigned int *c, unsigned int *d ) +{ + unsigned int op = *a; + // .byte 0x53 == push ebx. it's universal for 32 and 64 bit + // .byte 0x5b == pop ebx. + // Some gcc's (4.1.2 on Core2) object to pairing push/pop and ebx in 64 bit mode. + // Using the opcode directly avoids this problem. + __asm__ __volatile__( ".byte 0x53\n\tcpuid\n\tmovl %%ebx, %%esi\n\t.byte 0x5b":"=a"( *a ), "=S"( *b ), "=c"( *c ), + "=d" + ( *d ) + : "a"( op ) ); +} +#endif + +int +_x86_cache_info( PAPI_mh_info_t * mh_info ) +{ + int retval = 0; + union + { + struct + { + unsigned int ax, bx, cx, dx; + } e; + char vendor[20]; /* leave room for terminator bytes */ + } reg; + + /* Don't use cpu_type to determine the processor. + * get the information directly from the chip. + */ + reg.e.ax = 0; /* function code 0: vendor string */ + /* The vendor string is composed of EBX:EDX:ECX. + * by swapping the register addresses in the call below, + * the string is correctly composed in the char array. + */ + cpuid( ®.e.ax, ®.e.bx, ®.e.dx, ®.e.cx ); + reg.vendor[16] = 0; + MEMDBG( "Vendor: %s\n", ®.vendor[4] ); + + init_mem_hierarchy( mh_info ); + + if ( !strncmp( "GenuineIntel", ®.vendor[4], 12 ) ) { + init_intel( mh_info, &mh_info->levels); + } else if ( !strncmp( "AuthenticAMD", ®.vendor[4], 12 ) ) { + init_amd( mh_info, &mh_info->levels ); + } else { + MEMDBG( "Unsupported cpu type; Not Intel or AMD x86\n" ); + return PAPI_ENOIMPL; + } + + /* This works only because an empty cache element is initialized to 0 */ + MEMDBG( "Detected L1: %d L2: %d L3: %d\n", + mh_info->level[0].cache[0].size + mh_info->level[0].cache[1].size, + mh_info->level[1].cache[0].size + mh_info->level[1].cache[1].size, + mh_info->level[2].cache[0].size + mh_info->level[2].cache[1].size ); + return retval; +} + +static void +init_mem_hierarchy( PAPI_mh_info_t * mh_info ) +{ + int i, j; + PAPI_mh_level_t *L = mh_info->level; + + /* initialize entire memory hierarchy structure to benign values */ + for ( i = 0; i < PAPI_MAX_MEM_HIERARCHY_LEVELS; i++ ) { + for ( j = 0; j < PAPI_MH_MAX_LEVELS; j++ ) { + L[i].tlb[j].type = PAPI_MH_TYPE_EMPTY; + L[i].tlb[j].num_entries = 0; + L[i].tlb[j].associativity = 0; + L[i].cache[j].type = PAPI_MH_TYPE_EMPTY; + L[i].cache[j].size = 0; + L[i].cache[j].line_size = 0; + L[i].cache[j].num_lines = 0; + L[i].cache[j].associativity = 0; + } + } +} + +static short int +_amd_L2_L3_assoc( unsigned short int pattern ) +{ + /* From "CPUID Specification" #25481 Rev 2.28, April 2008 */ + short int assoc[16] = + { 0, 1, 2, -1, 4, -1, 8, -1, 16, -1, 32, 48, 64, 96, 128, SHRT_MAX }; + if ( pattern > 0xF ) + return -1; + return ( assoc[pattern] ); +} + +/* Cache configuration for AMD Athlon/Duron */ +static int +init_amd( PAPI_mh_info_t * mh_info, int *num_levels ) +{ + union + { + struct + { + unsigned int ax, bx, cx, dx; + } e; + unsigned char byt[16]; + } reg; + int i, j, levels = 0; + PAPI_mh_level_t *L = mh_info->level; + + /* + * Layout of CPU information taken from : + * "CPUID Specification" #25481 Rev 2.28, April 2008 for most current info. + */ + + MEMDBG( "Initializing AMD memory info\n" ); + /* AMD level 1 cache info */ + reg.e.ax = 0x80000005; /* extended function code 5: L1 Cache and TLB Identifiers */ + cpuid( ®.e.ax, ®.e.bx, ®.e.cx, ®.e.dx ); + + MEMDBG( "e.ax=%#8.8x e.bx=%#8.8x e.cx=%#8.8x e.dx=%#8.8x\n", + reg.e.ax, reg.e.bx, reg.e.cx, reg.e.dx ); + MEMDBG + ( ":\neax: %#x %#x %#x %#x\nebx: %#x %#x %#x %#x\necx: %#x %#x %#x %#x\nedx: %#x %#x %#x %#x\n", + reg.byt[0], reg.byt[1], reg.byt[2], reg.byt[3], reg.byt[4], + reg.byt[5], reg.byt[6], reg.byt[7], reg.byt[8], reg.byt[9], + reg.byt[10], reg.byt[11], reg.byt[12], reg.byt[13], reg.byt[14], + reg.byt[15] ); + + /* NOTE: We assume L1 cache and TLB always exists */ + /* L1 TLB info */ + + /* 4MB memory page information; half the number of entries as 2MB */ + L[0].tlb[0].type = PAPI_MH_TYPE_INST; + L[0].tlb[0].num_entries = reg.byt[0] / 2; + L[0].tlb[0].page_size = 4096 << 10; + L[0].tlb[0].associativity = reg.byt[1]; + + L[0].tlb[1].type = PAPI_MH_TYPE_DATA; + L[0].tlb[1].num_entries = reg.byt[2] / 2; + L[0].tlb[1].page_size = 4096 << 10; + L[0].tlb[1].associativity = reg.byt[3]; + + /* 2MB memory page information */ + L[0].tlb[2].type = PAPI_MH_TYPE_INST; + L[0].tlb[2].num_entries = reg.byt[0]; + L[0].tlb[2].page_size = 2048 << 10; + L[0].tlb[2].associativity = reg.byt[1]; + + L[0].tlb[3].type = PAPI_MH_TYPE_DATA; + L[0].tlb[3].num_entries = reg.byt[2]; + L[0].tlb[3].page_size = 2048 << 10; + L[0].tlb[3].associativity = reg.byt[3]; + + /* 4k page information */ + L[0].tlb[4].type = PAPI_MH_TYPE_INST; + L[0].tlb[4].num_entries = reg.byt[4]; + L[0].tlb[4].page_size = 4 << 10; + L[0].tlb[4].associativity = reg.byt[5]; + + L[0].tlb[5].type = PAPI_MH_TYPE_DATA; + L[0].tlb[5].num_entries = reg.byt[6]; + L[0].tlb[5].page_size = 4 << 10; + L[0].tlb[5].associativity = reg.byt[7]; + + for ( i = 0; i < PAPI_MH_MAX_LEVELS; i++ ) { + if ( L[0].tlb[i].associativity == 0xff ) + L[0].tlb[i].associativity = SHRT_MAX; + } + + /* L1 D-cache info */ + L[0].cache[0].type = + PAPI_MH_TYPE_DATA | PAPI_MH_TYPE_WB | PAPI_MH_TYPE_PSEUDO_LRU; + L[0].cache[0].size = reg.byt[11] << 10; + L[0].cache[0].associativity = reg.byt[10]; + L[0].cache[0].line_size = reg.byt[8]; + /* Byt[9] is "Lines per tag" */ + /* Is that == lines per cache? */ + /* L[0].cache[1].num_lines = reg.byt[9]; */ + if ( L[0].cache[0].line_size ) + L[0].cache[0].num_lines = L[0].cache[0].size / L[0].cache[0].line_size; + MEMDBG( "D-Cache Line Count: %d; Computed: %d\n", reg.byt[9], + L[0].cache[0].num_lines ); + + /* L1 I-cache info */ + L[0].cache[1].type = PAPI_MH_TYPE_INST; + L[0].cache[1].size = reg.byt[15] << 10; + L[0].cache[1].associativity = reg.byt[14]; + L[0].cache[1].line_size = reg.byt[12]; + /* Byt[13] is "Lines per tag" */ + /* Is that == lines per cache? */ + /* L[0].cache[1].num_lines = reg.byt[13]; */ + if ( L[0].cache[1].line_size ) + L[0].cache[1].num_lines = L[0].cache[1].size / L[0].cache[1].line_size; + MEMDBG( "I-Cache Line Count: %d; Computed: %d\n", reg.byt[13], + L[0].cache[1].num_lines ); + + for ( i = 0; i < 2; i++ ) { + if ( L[0].cache[i].associativity == 0xff ) + L[0].cache[i].associativity = SHRT_MAX; + } + + /* AMD L2/L3 Cache and L2 TLB info */ + /* NOTE: For safety we assume L2 and L3 cache and TLB may not exist */ + + reg.e.ax = 0x80000006; /* extended function code 6: L2/L3 Cache and L2 TLB Identifiers */ + cpuid( ®.e.ax, ®.e.bx, ®.e.cx, ®.e.dx ); + + MEMDBG( "e.ax=%#8.8x e.bx=%#8.8x e.cx=%#8.8x e.dx=%#8.8x\n", + reg.e.ax, reg.e.bx, reg.e.cx, reg.e.dx ); + MEMDBG + ( ":\neax: %#x %#x %#x %#x\nebx: %#x %#x %#x %#x\necx: %#x %#x %#x %#x\nedx: %#x %#x %#x %#x\n", + reg.byt[0], reg.byt[1], reg.byt[2], reg.byt[3], reg.byt[4], + reg.byt[5], reg.byt[6], reg.byt[7], reg.byt[8], reg.byt[9], + reg.byt[10], reg.byt[11], reg.byt[12], reg.byt[13], reg.byt[14], + reg.byt[15] ); + + /* L2 TLB info */ + + if ( reg.byt[0] | reg.byt[1] ) { /* Level 2 ITLB exists */ + /* 4MB ITLB page information; half the number of entries as 2MB */ + L[1].tlb[0].type = PAPI_MH_TYPE_INST; + L[1].tlb[0].num_entries = + ( ( ( short ) ( reg.byt[1] & 0xF ) << 8 ) + reg.byt[0] ) / 2; + L[1].tlb[0].page_size = 4096 << 10; + L[1].tlb[0].associativity = + _amd_L2_L3_assoc( ( reg.byt[1] & 0xF0 ) >> 4 ); + + /* 2MB ITLB page information */ + L[1].tlb[2].type = PAPI_MH_TYPE_INST; + L[1].tlb[2].num_entries = L[1].tlb[0].num_entries * 2; + L[1].tlb[2].page_size = 2048 << 10; + L[1].tlb[2].associativity = L[1].tlb[0].associativity; + } + + if ( reg.byt[2] | reg.byt[3] ) { /* Level 2 DTLB exists */ + /* 4MB DTLB page information; half the number of entries as 2MB */ + L[1].tlb[1].type = PAPI_MH_TYPE_DATA; + L[1].tlb[1].num_entries = + ( ( ( short ) ( reg.byt[3] & 0xF ) << 8 ) + reg.byt[2] ) / 2; + L[1].tlb[1].page_size = 4096 << 10; + L[1].tlb[1].associativity = + _amd_L2_L3_assoc( ( reg.byt[3] & 0xF0 ) >> 4 ); + + /* 2MB DTLB page information */ + L[1].tlb[3].type = PAPI_MH_TYPE_DATA; + L[1].tlb[3].num_entries = L[1].tlb[1].num_entries * 2; + L[1].tlb[3].page_size = 2048 << 10; + L[1].tlb[3].associativity = L[1].tlb[1].associativity; + } + + /* 4k page information */ + if ( reg.byt[4] | reg.byt[5] ) { /* Level 2 ITLB exists */ + L[1].tlb[4].type = PAPI_MH_TYPE_INST; + L[1].tlb[4].num_entries = + ( ( short ) ( reg.byt[5] & 0xF ) << 8 ) + reg.byt[4]; + L[1].tlb[4].page_size = 4 << 10; + L[1].tlb[4].associativity = + _amd_L2_L3_assoc( ( reg.byt[5] & 0xF0 ) >> 4 ); + } + if ( reg.byt[6] | reg.byt[7] ) { /* Level 2 DTLB exists */ + L[1].tlb[5].type = PAPI_MH_TYPE_DATA; + L[1].tlb[5].num_entries = + ( ( short ) ( reg.byt[7] & 0xF ) << 8 ) + reg.byt[6]; + L[1].tlb[5].page_size = 4 << 10; + L[1].tlb[5].associativity = + _amd_L2_L3_assoc( ( reg.byt[7] & 0xF0 ) >> 4 ); + } + + /* AMD Level 2 cache info */ + if ( reg.e.cx ) { + L[1].cache[0].type = + PAPI_MH_TYPE_UNIFIED | PAPI_MH_TYPE_WT | PAPI_MH_TYPE_PSEUDO_LRU; + L[1].cache[0].size = ( int ) ( ( reg.e.cx & 0xffff0000 ) >> 6 ); /* right shift by 16; multiply by 2^10 */ + L[1].cache[0].associativity = + _amd_L2_L3_assoc( ( reg.byt[9] & 0xF0 ) >> 4 ); + L[1].cache[0].line_size = reg.byt[8]; +/* L[1].cache[0].num_lines = reg.byt[9]&0xF; */ + if ( L[1].cache[0].line_size ) + L[1].cache[0].num_lines = + L[1].cache[0].size / L[1].cache[0].line_size; + MEMDBG( "U-Cache Line Count: %d; Computed: %d\n", reg.byt[9] & 0xF, + L[1].cache[0].num_lines ); + } + + /* AMD Level 3 cache info (shared across cores) */ + if ( reg.e.dx ) { + L[2].cache[0].type = + PAPI_MH_TYPE_UNIFIED | PAPI_MH_TYPE_WT | PAPI_MH_TYPE_PSEUDO_LRU; + L[2].cache[0].size = ( int ) ( reg.e.dx & 0xfffc0000 ) << 1; /* in blocks of 512KB (2^19) */ + L[2].cache[0].associativity = + _amd_L2_L3_assoc( ( reg.byt[13] & 0xF0 ) >> 4 ); + L[2].cache[0].line_size = reg.byt[12]; +/* L[2].cache[0].num_lines = reg.byt[13]&0xF; */ + if ( L[2].cache[0].line_size ) + L[2].cache[0].num_lines = + L[2].cache[0].size / L[2].cache[0].line_size; + MEMDBG( "U-Cache Line Count: %d; Computed: %d\n", reg.byt[13] & 0xF, + L[1].cache[0].num_lines ); + } + for ( i = 0; i < PAPI_MAX_MEM_HIERARCHY_LEVELS; i++ ) { + for ( j = 0; j < PAPI_MH_MAX_LEVELS; j++ ) { + /* Compute the number of levels of hierarchy actually used */ + if ( L[i].tlb[j].type != PAPI_MH_TYPE_EMPTY || + L[i].cache[j].type != PAPI_MH_TYPE_EMPTY ) + levels = i + 1; + } + } + *num_levels = levels; + return PAPI_OK; +} + + /* + * The data from this table now comes from figure 3-17 in + * the Intel Architectures Software Reference Manual 2A + * (cpuid instruction section) + * + * Pretviously the information was provided by + * "Intel® Processor Identification and the CPUID Instruction", + * Application Note, AP-485, Nov 2008, 241618-033 + * Updated to AP-485, Aug 2009, 241618-036 + * + * The following data structure and its instantiation trys to + * capture all the information in Section 2.1.3 of the above + * document. Not all of it is used by PAPI, but it could be. + * As the above document is revised, this table should be + * updated. + */ + +#define TLB_SIZES 3 /* number of different page sizes for a single TLB descriptor */ +struct _intel_cache_info +{ + int descriptor; /* 0x00 - 0xFF: register descriptor code */ + int level; /* 1 to PAPI_MH_MAX_LEVELS */ + int type; /* Empty, instr, data, vector, unified | TLB */ + int size[TLB_SIZES]; /* cache or TLB page size(s) in kB */ + int associativity; /* SHRT_MAX == fully associative */ + int sector; /* 1 if cache is sectored; else 0 */ + int line_size; /* for cache */ + int entries; /* for TLB */ +}; + +static struct _intel_cache_info intel_cache[] = { +// 0x01 + {.descriptor = 0x01, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size[0] = 4, + .associativity = 4, + .entries = 32, + }, +// 0x02 + {.descriptor = 0x02, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size[0] = 4096, + .associativity = SHRT_MAX, + .entries = 2, + }, +// 0x03 + {.descriptor = 0x03, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4, + .associativity = 4, + .entries = 64, + }, +// 0x04 + {.descriptor = 0x04, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4096, + .associativity = 4, + .entries = 8, + }, +// 0x05 + {.descriptor = 0x05, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4096, + .associativity = 4, + .entries = 32, + }, +// 0x06 + {.descriptor = 0x06, + .level = 1, + .type = PAPI_MH_TYPE_INST, + .size[0] = 8, + .associativity = 4, + .line_size = 32, + }, +// 0x08 + {.descriptor = 0x08, + .level = 1, + .type = PAPI_MH_TYPE_INST, + .size[0] = 16, + .associativity = 4, + .line_size = 32, + }, +// 0x09 + {.descriptor = 0x09, + .level = 1, + .type = PAPI_MH_TYPE_INST, + .size[0] = 32, + .associativity = 4, + .line_size = 64, + }, +// 0x0A + {.descriptor = 0x0A, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 8, + .associativity = 2, + .line_size = 32, + }, +// 0x0B + {.descriptor = 0x0B, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size[0] = 4096, + .associativity = 4, + .entries = 4, + }, +// 0x0C + {.descriptor = 0x0C, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 16, + .associativity = 4, + .line_size = 32, + }, +// 0x0D + {.descriptor = 0x0D, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 16, + .associativity = 4, + .line_size = 64, + }, +// 0x0E + {.descriptor = 0x0E, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 24, + .associativity = 6, + .line_size = 64, + }, +// 0x21 + {.descriptor = 0x21, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 256, + .associativity = 8, + .line_size = 64, + }, +// 0x22 + {.descriptor = 0x22, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 4, + .sector = 1, + .line_size = 64, + }, +// 0x23 + {.descriptor = 0x23, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x25 + {.descriptor = 0x25, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 2048, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x29 + {.descriptor = 0x29, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 4096, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x2C + {.descriptor = 0x2C, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 32, + .associativity = 8, + .line_size = 64, + }, +// 0x30 + {.descriptor = 0x30, + .level = 1, + .type = PAPI_MH_TYPE_INST, + .size[0] = 32, + .associativity = 8, + .line_size = 64, + }, +// 0x39 + {.descriptor = 0x39, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 128, + .associativity = 4, + .sector = 1, + .line_size = 64, + }, +// 0x3A + {.descriptor = 0x3A, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 192, + .associativity = 6, + .sector = 1, + .line_size = 64, + }, +// 0x3B + {.descriptor = 0x3B, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 128, + .associativity = 2, + .sector = 1, + .line_size = 64, + }, +// 0x3C + {.descriptor = 0x3C, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 256, + .associativity = 4, + .sector = 1, + .line_size = 64, + }, +// 0x3D + {.descriptor = 0x3D, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 384, + .associativity = 6, + .sector = 1, + .line_size = 64, + }, +// 0x3E + {.descriptor = 0x3E, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 4, + .sector = 1, + .line_size = 64, + }, +// 0x40: no last level cache (??) +// 0x41 + {.descriptor = 0x41, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 128, + .associativity = 4, + .line_size = 32, + }, +// 0x42 + {.descriptor = 0x42, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 256, + .associativity = 4, + .line_size = 32, + }, +// 0x43 + {.descriptor = 0x43, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 4, + .line_size = 32, + }, +// 0x44 + {.descriptor = 0x44, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 4, + .line_size = 32, + }, +// 0x45 + {.descriptor = 0x45, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 2048, + .associativity = 4, + .line_size = 32, + }, +// 0x46 + {.descriptor = 0x46, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 4096, + .associativity = 4, + .line_size = 64, + }, +// 0x47 + {.descriptor = 0x47, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 8192, + .associativity = 8, + .line_size = 64, + }, +// 0x48 + {.descriptor = 0x48, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 3072, + .associativity = 12, + .line_size = 64, + }, +// 0x49 NOTE: for family 0x0F model 0x06 this is level 3 + {.descriptor = 0x49, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 4096, + .associativity = 16, + .line_size = 64, + }, +// 0x4A + {.descriptor = 0x4A, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 6144, + .associativity = 12, + .line_size = 64, + }, +// 0x4B + {.descriptor = 0x4B, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 8192, + .associativity = 16, + .line_size = 64, + }, +// 0x4C + {.descriptor = 0x4C, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 12288, + .associativity = 12, + .line_size = 64, + }, +// 0x4D + {.descriptor = 0x4D, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 16384, + .associativity = 16, + .line_size = 64, + }, +// 0x4E + {.descriptor = 0x4E, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 6144, + .associativity = 24, + .line_size = 64, + }, +// 0x4F + {.descriptor = 0x4F, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size[0] = 4, + .associativity = SHRT_MAX, + .entries = 32, + }, +// 0x50 + {.descriptor = 0x50, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size = {4, 2048, 4096}, + .associativity = SHRT_MAX, + .entries = 64, + }, +// 0x51 + {.descriptor = 0x51, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size = {4, 2048, 4096}, + .associativity = SHRT_MAX, + .entries = 128, + }, +// 0x52 + {.descriptor = 0x52, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size = {4, 2048, 4096}, + .associativity = SHRT_MAX, + .entries = 256, + }, +// 0x55 + {.descriptor = 0x55, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size = {2048, 4096, 0}, + .associativity = SHRT_MAX, + .entries = 7, + }, +// 0x56 + {.descriptor = 0x56, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4096, + .associativity = 4, + .entries = 16, + }, +// 0x57 + {.descriptor = 0x57, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4, + .associativity = 4, + .entries = 16, + }, +// 0x59 + {.descriptor = 0x59, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4, + .associativity = SHRT_MAX, + .entries = 16, + }, +// 0x5A + {.descriptor = 0x5A, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size = {2048, 4096, 0}, + .associativity = 4, + .entries = 32, + }, +// 0x5B + {.descriptor = 0x5B, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size = {4, 4096, 0}, + .associativity = SHRT_MAX, + .entries = 64, + }, +// 0x5C + {.descriptor = 0x5C, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size = {4, 4096, 0}, + .associativity = SHRT_MAX, + .entries = 128, + }, +// 0x5D + {.descriptor = 0x5D, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size = {4, 4096, 0}, + .associativity = SHRT_MAX, + .entries = 256, + }, +// 0x60 + {.descriptor = 0x60, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 16, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x66 + {.descriptor = 0x66, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 8, + .associativity = 4, + .sector = 1, + .line_size = 64, + }, +// 0x67 + {.descriptor = 0x67, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 16, + .associativity = 4, + .sector = 1, + .line_size = 64, + }, +// 0x68 + {.descriptor = 0x68, + .level = 1, + .type = PAPI_MH_TYPE_DATA, + .size[0] = 32, + .associativity = 4, + .sector = 1, + .line_size = 64, + }, +// 0x70 + {.descriptor = 0x70, + .level = 1, + .type = PAPI_MH_TYPE_TRACE, + .size[0] = 12, + .associativity = 8, + }, +// 0x71 + {.descriptor = 0x71, + .level = 1, + .type = PAPI_MH_TYPE_TRACE, + .size[0] = 16, + .associativity = 8, + }, +// 0x72 + {.descriptor = 0x72, + .level = 1, + .type = PAPI_MH_TYPE_TRACE, + .size[0] = 32, + .associativity = 8, + }, +// 0x73 + {.descriptor = 0x73, + .level = 1, + .type = PAPI_MH_TYPE_TRACE, + .size[0] = 64, + .associativity = 8, + }, +// 0x78 + {.descriptor = 0x78, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 4, + .line_size = 64, + }, +// 0x79 + {.descriptor = 0x79, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 128, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x7A + {.descriptor = 0x7A, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 256, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x7B + {.descriptor = 0x7B, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x7C + {.descriptor = 0x7C, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 8, + .sector = 1, + .line_size = 64, + }, +// 0x7D + {.descriptor = 0x7D, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 2048, + .associativity = 8, + .line_size = 64, + }, +// 0x7F + {.descriptor = 0x7F, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 2, + .line_size = 64, + }, +// 0x80 + {.descriptor = 0x80, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 8, + .line_size = 64, + }, +// 0x82 + {.descriptor = 0x82, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 256, + .associativity = 8, + .line_size = 32, + }, +// 0x83 + {.descriptor = 0x83, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 8, + .line_size = 32, + }, +// 0x84 + {.descriptor = 0x84, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 8, + .line_size = 32, + }, +// 0x85 + {.descriptor = 0x85, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 2048, + .associativity = 8, + .line_size = 32, + }, +// 0x86 + {.descriptor = 0x86, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 4, + .line_size = 64, + }, +// 0x87 + {.descriptor = 0x87, + .level = 2, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 8, + .line_size = 64, + }, +// 0xB0 + {.descriptor = 0xB0, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size[0] = 4, + .associativity = 4, + .entries = 128, + }, +// 0xB1 NOTE: This is currently the only instance where .entries +// is dependent on .size. It's handled as a code exception. +// If other instances appear in the future, the structure +// should probably change to accomodate it. + {.descriptor = 0xB1, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size = {2048, 4096, 0}, + .associativity = 4, + .entries = 8, /* or 4 if size = 4096 */ + }, +// 0xB2 + {.descriptor = 0xB2, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_INST, + .size[0] = 4, + .associativity = 4, + .entries = 64, + }, +// 0xB3 + {.descriptor = 0xB3, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4, + .associativity = 4, + .entries = 128, + }, +// 0xB4 + {.descriptor = 0xB4, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4, + .associativity = 4, + .entries = 256, + }, +// 0xBA + {.descriptor = 0xBA, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size[0] = 4, + .associativity = 4, + .entries = 64, + }, +// 0xC0 + {.descriptor = 0xBA, + .level = 1, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_DATA, + .size = {4,4096}, + .associativity = 4, + .entries = 8, + }, +// 0xCA + {.descriptor = 0xCA, + .level = 2, + .type = PAPI_MH_TYPE_TLB | PAPI_MH_TYPE_UNIFIED, + .size[0] = 4, + .associativity = 4, + .entries = 512, + }, +// 0xD0 + {.descriptor = 0xD0, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 512, + .associativity = 4, + .line_size = 64, + }, +// 0xD1 + {.descriptor = 0xD1, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 4, + .line_size = 64, + }, +// 0xD2 + {.descriptor = 0xD2, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 2048, + .associativity = 4, + .line_size = 64, + }, +// 0xD6 + {.descriptor = 0xD6, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1024, + .associativity = 8, + .line_size = 64, + }, +// 0xD7 + {.descriptor = 0xD7, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 2048, + .associativity = 8, + .line_size = 64, + }, +// 0xD8 + {.descriptor = 0xD8, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 4096, + .associativity = 8, + .line_size = 64, + }, +// 0xDC + {.descriptor = 0xDC, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 1536, + .associativity = 12, + .line_size = 64, + }, +// 0xDD + {.descriptor = 0xDD, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 3072, + .associativity = 12, + .line_size = 64, + }, +// 0xDE + {.descriptor = 0xDE, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 6144, + .associativity = 12, + .line_size = 64, + }, +// 0xE2 + {.descriptor = 0xE2, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 2048, + .associativity = 16, + .line_size = 64, + }, +// 0xE3 + {.descriptor = 0xE3, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 4096, + .associativity = 16, + .line_size = 64, + }, +// 0xE4 + {.descriptor = 0xE4, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 8192, + .associativity = 16, + .line_size = 64, + }, +// 0xEA + {.descriptor = 0xEA, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 12288, + .associativity = 24, + .line_size = 64, + }, +// 0xEB + {.descriptor = 0xEB, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 18432, + .associativity = 24, + .line_size = 64, + }, +// 0xEC + {.descriptor = 0xEC, + .level = 3, + .type = PAPI_MH_TYPE_UNIFIED, + .size[0] = 24576, + .associativity = 24, + .line_size = 64, + }, +// 0xF0 + {.descriptor = 0xF0, + .level = 1, + .type = PAPI_MH_TYPE_PREF, + .size[0] = 64, + }, +// 0xF1 + {.descriptor = 0xF1, + .level = 1, + .type = PAPI_MH_TYPE_PREF, + .size[0] = 128, + }, +}; + +#ifdef DEBUG +static void +print_intel_cache_table( ) +{ + int i, j, k = + ( int ) ( sizeof ( intel_cache ) / + sizeof ( struct _intel_cache_info ) ); + for ( i = 0; i < k; i++ ) { + printf( "%d.\tDescriptor: %#x\n", i, intel_cache[i].descriptor ); + printf( "\t Level: %d\n", intel_cache[i].level ); + printf( "\t Type: %d\n", intel_cache[i].type ); + printf( "\t Size(s): " ); + for ( j = 0; j < TLB_SIZES; j++ ) + printf( "%d, ", intel_cache[i].size[j] ); + printf( "\n" ); + printf( "\t Assoc: %d\n", intel_cache[i].associativity ); + printf( "\t Sector: %d\n", intel_cache[i].sector ); + printf( "\t Line Size: %d\n", intel_cache[i].line_size ); + printf( "\t Entries: %d\n", intel_cache[i].entries ); + printf( "\n" ); + } +} +#endif + +/* Given a specific cache descriptor, this routine decodes the information from a table + * of such descriptors and fills out one or more records in a PAPI data structure. + * Called only by init_intel() + */ +static void +intel_decode_descriptor( struct _intel_cache_info *d, PAPI_mh_level_t * L ) +{ + int i, next; + int level = d->level - 1; + PAPI_mh_tlb_info_t *t; + PAPI_mh_cache_info_t *c; + + if ( d->descriptor == 0x49 ) { /* special case */ + unsigned int r_eax, r_ebx, r_ecx, r_edx; + r_eax = 0x1; /* function code 1: family & model */ + cpuid( &r_eax, &r_ebx, &r_ecx, &r_edx ); + /* override table for Family F, model 6 only */ + if ( ( r_eax & 0x0FFF3FF0 ) == 0xF60 ) + level = 3; + } + if ( d->type & PAPI_MH_TYPE_TLB ) { + for ( next = 0; next < PAPI_MH_MAX_LEVELS - 1; next++ ) { + if ( L[level].tlb[next].type == PAPI_MH_TYPE_EMPTY ) + break; + } + /* expand TLB entries for multiple possible page sizes */ + for ( i = 0; i < TLB_SIZES && next < PAPI_MH_MAX_LEVELS && d->size[i]; + i++, next++ ) { +// printf("Level %d Descriptor: %#x TLB type %#x next: %d, i: %d\n", level, d->descriptor, d->type, next, i); + t = &L[level].tlb[next]; + t->type = PAPI_MH_CACHE_TYPE( d->type ); + t->num_entries = d->entries; + t->page_size = d->size[i] << 10; /* minimum page size in KB */ + t->associativity = d->associativity; + /* another special case */ + if ( d->descriptor == 0xB1 && d->size[i] == 4096 ) + t->num_entries = d->entries / 2; + } + } else { + for ( next = 0; next < PAPI_MH_MAX_LEVELS - 1; next++ ) { + if ( L[level].cache[next].type == PAPI_MH_TYPE_EMPTY ) + break; + } +// printf("Level %d Descriptor: %#x Cache type %#x next: %d\n", level, d->descriptor, d->type, next); + c = &L[level].cache[next]; + c->type = PAPI_MH_CACHE_TYPE( d->type ); + c->size = d->size[0] << 10; /* convert from KB to bytes */ + c->associativity = d->associativity; + if ( d->line_size ) { + c->line_size = d->line_size; + c->num_lines = c->size / c->line_size; + } + } +} + +#if defined(__amd64__) || defined(__x86_64__) +static inline void +cpuid2( unsigned int*eax, unsigned int* ebx, + unsigned int*ecx, unsigned int *edx, + unsigned int index, unsigned int ecx_in ) +{ + __asm__ __volatile__ ("cpuid;" + : "=a" (*eax), "=b" (*ebx), "=c" (*ecx), "=d" (*edx) + : "0" (index), "2"(ecx_in) ); +} +#else +static inline void +cpuid2 ( unsigned int* eax, unsigned int* ebx, + unsigned int* ecx, unsigned int* edx, + unsigned int index, unsigned int ecx_in ) +{ + unsigned int a,b,c,d; + __asm__ __volatile__ (".byte 0x53\n\tcpuid\n\tmovl %%ebx, %%esi\n\t.byte 0x5b" + : "=a" (a), "=S" (b), "=c" (c), "=d" (d) \ + : "0" (index), "2"(ecx_in) ); + *eax = a; *ebx = b; *ecx = c; *edx = d; +} +#endif + + +static int +init_intel_leaf4( PAPI_mh_info_t * mh_info, int *num_levels ) +{ + + unsigned int eax, ebx, ecx, edx; + unsigned int maxidx, ecx_in; + int next; + + int cache_type,cache_level,cache_selfinit,cache_fullyassoc; + int cache_linesize,cache_partitions,cache_ways,cache_sets; + + PAPI_mh_cache_info_t *c; + + *num_levels=0; + + cpuid2(&eax,&ebx,&ecx,&edx, 0, 0); + maxidx = eax; + + if (maxidx<4) { + MEMDBG("Warning! CPUID Index 4 not supported!\n"); + return PAPI_ENOSUPP; + } + + ecx_in=0; + while(1) { + cpuid2(&eax,&ebx,&ecx,&edx, 4, ecx_in); + + + + /* decoded as per table 3-12 in Intel Software Developer's Manual Volume 2A */ + + cache_type=eax&0x1f; + if (cache_type==0) break; + + cache_level=(eax>>5)&0x3; + cache_selfinit=(eax>>8)&0x1; + cache_fullyassoc=(eax>>9)&0x1; + + cache_linesize=(ebx&0xfff)+1; + cache_partitions=((ebx>>12)&0x3ff)+1; + cache_ways=((ebx>>22)&0x3ff)+1; + + cache_sets=(ecx)+1; + + /* should we export this info? + + cache_maxshare=((eax>>14)&0xfff)+1; + cache_maxpackage=((eax>>26)&0x3f)+1; + + cache_wb=(edx)&1; + cache_inclusive=(edx>>1)&1; + cache_indexing=(edx>>2)&1; + */ + + if (cache_level>*num_levels) *num_levels=cache_level; + + /* find next slot available to hold cache info */ + for ( next = 0; next < PAPI_MH_MAX_LEVELS - 1; next++ ) { + if ( mh_info->level[cache_level-1].cache[next].type == PAPI_MH_TYPE_EMPTY ) break; + } + + c=&(mh_info->level[cache_level-1].cache[next]); + + switch(cache_type) { + case 1: MEMDBG("L%d Data Cache\n",cache_level); + c->type=PAPI_MH_TYPE_DATA; + break; + case 2: MEMDBG("L%d Instruction Cache\n",cache_level); + c->type=PAPI_MH_TYPE_INST; + break; + case 3: MEMDBG("L%d Unified Cache\n",cache_level); + c->type=PAPI_MH_TYPE_UNIFIED; + break; + } + + if (cache_selfinit) { MEMDBG("\tSelf-init\n"); } + if (cache_fullyassoc) { MEMDBG("\tFully Associtative\n"); } + + //MEMDBG("\tMax logical processors sharing cache: %d\n",cache_maxshare); + //MEMDBG("\tMax logical processors sharing package: %d\n",cache_maxpackage); + + MEMDBG("\tCache linesize: %d\n",cache_linesize); + + MEMDBG("\tCache partitions: %d\n",cache_partitions); + MEMDBG("\tCache associaticity: %d\n",cache_ways); + + MEMDBG("\tCache sets: %d\n",cache_sets); + MEMDBG("\tCache size = %dkB\n", + (cache_ways*cache_partitions*cache_linesize*cache_sets)/1024); + + //MEMDBG("\tWBINVD/INVD acts on lower caches: %d\n",cache_wb); + //MEMDBG("\tCache is not inclusive: %d\n",cache_inclusive); + //MEMDBG("\tComplex cache indexing: %d\n",cache_indexing); + + c->line_size=cache_linesize; + if (cache_fullyassoc) { + c->associativity=SHRT_MAX; + } + else { + c->associativity=cache_ways; + } + c->size=(cache_ways*cache_partitions*cache_linesize*cache_sets); + c->num_lines=cache_ways*cache_partitions*cache_sets; + + ecx_in++; + } + return PAPI_OK; +} + +static int +init_intel_leaf2( PAPI_mh_info_t * mh_info , int *num_levels) +{ + /* cpuid() returns memory copies of 4 32-bit registers + * this union allows them to be accessed as either registers + * or individual bytes. Remember that Intel is little-endian. + */ + union + { + struct + { + unsigned int ax, bx, cx, dx; + } e; + unsigned char descrip[16]; + } reg; + + int r; /* register boundary index */ + int b; /* byte index into a register */ + int i; /* byte index into the descrip array */ + int t; /* table index into the static descriptor table */ + int count; /* how many times to call cpuid; from eax:lsb */ + int size; /* size of the descriptor table */ + int last_level = 0; /* how many levels in the cache hierarchy */ + + /* All of Intel's cache info is in 1 call to cpuid + * however it is a table lookup :( + */ + MEMDBG( "Initializing Intel Cache and TLB descriptors\n" ); + +#ifdef DEBUG + if ( ISLEVEL( DEBUG_MEMORY ) ) + print_intel_cache_table( ); +#endif + + reg.e.ax = 0x2; /* function code 2: cache descriptors */ + cpuid( ®.e.ax, ®.e.bx, ®.e.cx, ®.e.dx ); + + MEMDBG( "e.ax=%#8.8x e.bx=%#8.8x e.cx=%#8.8x e.dx=%#8.8x\n", + reg.e.ax, reg.e.bx, reg.e.cx, reg.e.dx ); + MEMDBG + ( ":\nd0: %#x %#x %#x %#x\nd1: %#x %#x %#x %#x\nd2: %#x %#x %#x %#x\nd3: %#x %#x %#x %#x\n", + reg.descrip[0], reg.descrip[1], reg.descrip[2], reg.descrip[3], + reg.descrip[4], reg.descrip[5], reg.descrip[6], reg.descrip[7], + reg.descrip[8], reg.descrip[9], reg.descrip[10], reg.descrip[11], + reg.descrip[12], reg.descrip[13], reg.descrip[14], reg.descrip[15] ); + + count = reg.descrip[0]; /* # times to repeat CPUID call. Not implemented. */ + + /* Knights Corner at least returns 0 here */ + if (count==0) goto early_exit; + + size = ( sizeof ( intel_cache ) / sizeof ( struct _intel_cache_info ) ); /* # descriptors */ + MEMDBG( "Repeat cpuid(2,...) %d times. If not 1, code is broken.\n", + count ); + if (count!=1) { + fprintf(stderr,"Warning: Unhandled cpuid count of %d\n",count); + } + + for ( r = 0; r < 4; r++ ) { /* walk the registers */ + if ( ( reg.descrip[r * 4 + 3] & 0x80 ) == 0 ) { /* only process if high order bit is 0 */ + for ( b = 3; b >= 0; b-- ) { /* walk the descriptor bytes from high to low */ + i = r * 4 + b; /* calculate an index into the array of descriptors */ + if ( i ) { /* skip the low order byte in eax [0]; it's the count (see above) */ + if ( reg.descrip[i] == 0xff ) { + MEMDBG("Warning! PAPI x86_cache: must implement cpuid leaf 4\n"); + return PAPI_ENOSUPP; + /* we might continue instead */ + /* in order to get TLB info */ + /* continue; */ + } + for ( t = 0; t < size; t++ ) { /* walk the descriptor table */ + if ( reg.descrip[i] == intel_cache[t].descriptor ) { /* find match */ + if ( intel_cache[t].level > last_level ) + last_level = intel_cache[t].level; + intel_decode_descriptor( &intel_cache[t], + mh_info->level ); + } + } + } + } + } + } +early_exit: + MEMDBG( "# of Levels: %d\n", last_level ); + *num_levels=last_level; + return PAPI_OK; +} + + +static int +init_intel( PAPI_mh_info_t * mh_info, int *levels ) +{ + + int result; + int num_levels; + + /* try using the oldest leaf2 method first */ + result=init_intel_leaf2(mh_info, &num_levels); + + if (result!=PAPI_OK) { + /* All Core2 and newer also support leaf4 detection */ + /* Starting with Westmere *only* leaf4 is supported */ + result=init_intel_leaf4(mh_info, &num_levels); + } + + *levels=num_levels; + return PAPI_OK; +} + + +/* Returns 1 if hypervisor detected */ +/* Returns 0 if none found. */ +int +_x86_detect_hypervisor(char *vendor_name) +{ + unsigned int eax, ebx, ecx, edx; + char hyper_vendor_id[13]; + + cpuid2(&eax, &ebx, &ecx, &edx,0x1,0); + /* This is the hypervisor bit, ecx bit 31 */ + if (ecx&0x80000000) { + /* There are various values in the 0x4000000X range */ + /* It is questionable how standard they are */ + /* For now we just return the name. */ + cpuid2(&eax, &ebx, &ecx, &edx, 0x40000000,0); + memcpy(hyper_vendor_id + 0, &ebx, 4); + memcpy(hyper_vendor_id + 4, &ecx, 4); + memcpy(hyper_vendor_id + 8, &edx, 4); + hyper_vendor_id[12] = '\0'; + strncpy(vendor_name,hyper_vendor_id,PAPI_MAX_STR_LEN); + return 1; + } + else { + strncpy(vendor_name,"none",PAPI_MAX_STR_LEN); + } + return 0; +} diff --git a/lib/spack/spack/test/llnl/util/filesystem.py b/lib/spack/spack/test/llnl/util/filesystem.py index 0a8dc074fe4..cdc50f9df25 100644 --- a/lib/spack/spack/test/llnl/util/filesystem.py +++ b/lib/spack/spack/test/llnl/util/filesystem.py @@ -5,10 +5,14 @@ """Tests for ``llnl/util/filesystem.py``""" -import llnl.util.filesystem as fs -import os -import stat import pytest +import os +import shutil +import stat +import sys + +import llnl.util.filesystem as fs +import spack.paths @pytest.fixture() @@ -306,3 +310,31 @@ def test_headers_directory_setter(): # Setting directories to None also returns an empty list hl.directories = None assert hl.directories == [] + + +@pytest.mark.regression('7358') +@pytest.mark.parametrize('regex,replacement,filename,keyword_args', [ + (r"\", "", 'x86_cpuid_info.c', {}), + (r"CDIR", "CURRENT_DIRECTORY", 'selfextract.bsx', + {'stop_at': '__ARCHIVE_BELOW__'}) +]) +def test_filter_files_with_different_encodings( + regex, replacement, filename, tmpdir, keyword_args +): + # All files given as input to this test must satisfy the pre-requisite + # that the 'replacement' string is not present in the file initially and + # that there's at least one match for the regex + original_file = os.path.join( + spack.paths.test_path, 'data', 'filter_file', filename + ) + target_file = os.path.join(str(tmpdir), filename) + shutil.copy(original_file, target_file) + # This should not raise exceptions + fs.filter_file(regex, replacement, target_file, **keyword_args) + # Check the strings have been replaced + extra_kwargs = {} + if sys.version_info > (3, 0): + extra_kwargs = {'errors': 'surrogateescape'} + + with open(target_file, mode='r', **extra_kwargs) as f: + assert replacement in f.read() diff --git a/var/spack/repos/builtin/packages/aspera-cli/package.py b/var/spack/repos/builtin/packages/aspera-cli/package.py index f0a2debfa6e..00253a19738 100644 --- a/var/spack/repos/builtin/packages/aspera-cli/package.py +++ b/var/spack/repos/builtin/packages/aspera-cli/package.py @@ -26,7 +26,8 @@ def install(self, spec, prefix): filter_file('INSTALL_DIR=~/.aspera', 'INSTALL_DIR=%s' % prefix, runfile, - string=True) + string=True, + stop_at='__ARCHIVE_FOLLOWS__') # Install chmod = which('chmod') chmod('+x', runfile) From 8f69c9d3340b96ccbd3c4a7ae2e0f49cd212f8bc Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Tue, 15 Oct 2019 14:20:52 +0900 Subject: [PATCH 257/499] ntpoly: Define module directry when compiling with Fujitsu compiler. (#13120) * ntpoly: Define module directry when compiling with Fujitsu compiler. * Delete quotes. --- var/spack/repos/builtin/packages/ntpoly/package.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/var/spack/repos/builtin/packages/ntpoly/package.py b/var/spack/repos/builtin/packages/ntpoly/package.py index 1fb459a6104..d390e19dba9 100644 --- a/var/spack/repos/builtin/packages/ntpoly/package.py +++ b/var/spack/repos/builtin/packages/ntpoly/package.py @@ -26,4 +26,7 @@ class Ntpoly(CMakePackage): def cmake_args(self): args = ["-DNOSWIG=Yes"] + if self.spec.satisfies('%fj'): + args.append('-DCMAKE_Fortran_MODDIR_FLAG=-M') + return args From 27a339eeb28007bf0844e4c331bdd7d9da13da2e Mon Sep 17 00:00:00 2001 From: Tim Haines Date: Tue, 15 Oct 2019 00:22:11 -0500 Subject: [PATCH 258/499] Add version 0.177 of elfutils (#13129) * Add version 0.177 * Fix spacing --- var/spack/repos/builtin/packages/elfutils/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py index f8d6048bf68..80e39e3e8fc 100644 --- a/var/spack/repos/builtin/packages/elfutils/package.py +++ b/var/spack/repos/builtin/packages/elfutils/package.py @@ -17,10 +17,11 @@ class Elfutils(AutotoolsPackage): version of elfutils.""" homepage = "https://fedorahosted.org/elfutils/" - url = "https://sourceware.org/elfutils/ftp/0.176/elfutils-0.176.tar.bz2" + url = "https://sourceware.org/elfutils/ftp/0.177/elfutils-0.177.tar.bz2" list_url = "https://sourceware.org/elfutils/ftp" list_depth = 1 + version('0.177', sha256='fa489deccbcae7d8c920f60d85906124c1989c591196d90e0fd668e3dc05042e') version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023') version('0.175', sha256='f7ef925541ee32c6d15ae5cb27da5f119e01a5ccdbe9fe57bf836730d7b7a65b') version('0.174', sha256='cdf27e70076e10a29539d89e367101d516bc4aa11b0d7777fe52139e3fcad08a') From ce5333c1fd248ad078f3712774c57a94143b17bd Mon Sep 17 00:00:00 2001 From: Andrey Prokopenko Date: Tue, 15 Oct 2019 05:14:37 -0400 Subject: [PATCH 259/499] kokkos: add cxxstd variant (#13142) --- var/spack/repos/builtin/packages/kokkos/package.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py index e6b61c51b20..dc971737554 100644 --- a/var/spack/repos/builtin/packages/kokkos/package.py +++ b/var/spack/repos/builtin/packages/kokkos/package.py @@ -72,7 +72,11 @@ class Kokkos(Package): 'Pascal60', 'Pascal61', 'Volta70', 'Volta72') - cuda_options = ('force_uvm', 'use_ldg', 'rdc', 'enable_lambda') + # C++ standard variant + variant('cxxstd', default='none', + values=('c++11', 'c++14', 'c++17', 'c++1y', 'c++1z', 'c++2a'), + multi=False, + description='set cxxstandard Kokkos option') # Host architecture variant variant( @@ -151,6 +155,11 @@ def install(self, spec, prefix): if '+pic' in spec: g_args.append('--cxxflags=-fPIC') + # C++ standard + cxxstandard = spec.variants['cxxstd'].value + if cxxstandard != 'none': + g_args.append('--cxxstandard=%s' % cxxstandard) + # Build Debug if '+debug' in spec: g_args.append('--debug') From 41e7e5693e86dba94ed4237a3962c311887aa5a8 Mon Sep 17 00:00:00 2001 From: Andrey Prokopenko Date: Tue, 15 Oct 2019 05:19:16 -0400 Subject: [PATCH 260/499] arborx: update v0.8-beta to v0.8-beta2 (#13143) - Require Kokkos with c++14 - Update the case of CMake options --- .../repos/builtin/packages/arborx/package.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/arborx/package.py b/var/spack/repos/builtin/packages/arborx/package.py index 55e064f8bbf..45e368884e0 100644 --- a/var/spack/repos/builtin/packages/arborx/package.py +++ b/var/spack/repos/builtin/packages/arborx/package.py @@ -10,11 +10,11 @@ class Arborx(CMakePackage): """ArborX is a performance-portable library for geometric search""" homepage = "http://github.com/arborx/arborx" - url = "https://github.com/arborx/arborx/archive/v0.8-beta.tar.gz" + url = "https://github.com/arborx/arborx/archive/v0.8-beta2.tar.gz" git = "https://github.com/arborx/arborx.git" version('master', branch='master') - version('0.8-beta', sha256='d90254656df089b1321bf26d55f69d0db465fff12a972c446562ceaca5f090ad') + version('0.8-beta2', sha256='e68733bc77fbb84313f3ff059f746fa79ab2ffe24a0a391126eefa47ec4fd2df') variant('cuda', default=False, description='enable Cuda backend') variant('openmp', default=False, description='enable OpenMP backend') @@ -28,18 +28,19 @@ class Arborx(CMakePackage): # ArborX relies on Kokkos to provide devices, thus having one-to-one match # The only way to disable those devices is to make sure Kokkos does not # provide them - depends_on('kokkos@2.7.00:+cuda+enable_lambda', when='+cuda') - depends_on('kokkos@2.7.00:+openmp', when='+openmp') - depends_on('kokkos@2.7.00:+serial', when='+serial') + depends_on('kokkos@2.7.00:+cuda+enable_lambda cxxstd=c++14', when='+cuda') + depends_on('kokkos@2.7.00:+openmp cxxstd=c++14', when='+openmp') + depends_on('kokkos@2.7.00:+serial cxxstd=c++14', when='+serial') def cmake_args(self): spec = self.spec options = [ '-DCMAKE_PREFIX_PATH=%s' % spec['kokkos'].prefix, - '-DArborX_ENABLE_TESTS=OFF', - '-DArborX_ENABLE_EXAMPLES=OFF', - '-DArborX_ENABLE_MPI=%s' % ('ON' if '+mpi' in spec else 'OFF') + '-DARBORX_ENABLE_TESTS=OFF', + '-DARBORX_ENABLE_EXAMPLES=OFF', + '-DARBORX_ENABLE_BENCHMARKS=OFF', + '-DARBORX_ENABLE_MPI=%s' % ('ON' if '+mpi' in spec else 'OFF') ] if '+cuda' in spec: From d33b0ffc50248ee1c099875830838b41e2d4ad12 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 15 Oct 2019 20:20:49 +0200 Subject: [PATCH 261/499] lmod: module files are written in a root folder named by target family (#13121) fixes #13005 This commit fixes an issue with the name of the root directory for module file hierarchies. Since #3206 the root folder was named after the microarchitecture used for the spec, which is too specific and not backward compatible for lmod hierarchies. Here we compute the root folder name using the target family instead of the target name itself and we add target information in the 'whatis' portion of the module file. --- lib/spack/spack/modules/lmod.py | 6 +++++- lib/spack/spack/test/modules/lmod.py | 16 ++++++++++++++++ share/spack/templates/modules/modulefile.lua | 1 + 3 files changed, 22 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/modules/lmod.py b/lib/spack/spack/modules/lmod.py index a381e08ca9e..e45b97773bf 100644 --- a/lib/spack/spack/modules/lmod.py +++ b/lib/spack/spack/modules/lmod.py @@ -198,7 +198,11 @@ class LmodFileLayout(BaseFileLayout): @property def arch_dirname(self): """Returns the root folder for THIS architecture""" - arch_folder = str(self.spec.architecture) + arch_folder = '-'.join([ + str(self.spec.platform), + str(self.spec.os), + str(self.spec.target.family) + ]) return os.path.join( self.dirname(), # root for lmod module files arch_folder, # architecture relative path diff --git a/lib/spack/spack/test/modules/lmod.py b/lib/spack/spack/test/modules/lmod.py index 7ee173d660f..e480d22601a 100644 --- a/lib/spack/spack/test/modules/lmod.py +++ b/lib/spack/spack/test/modules/lmod.py @@ -262,3 +262,19 @@ def no_op_set(*args, **kwargs): # Assert we have core compilers now writer, _ = factory(mpileaks_spec_string) assert writer.conf.core_compilers + + @pytest.mark.parametrize('spec_str', [ + 'mpileaks target=haswell', + 'mpileaks target=core2', + 'mpileaks target=x86_64', + ]) + @pytest.mark.regression('13005') + def test_only_generic_microarchitectures_in_root( + self, spec_str, factory, module_configuration + ): + module_configuration('complex_hierarchy') + writer, spec = factory(spec_str) + + assert str(spec.target.family) in writer.layout.arch_dirname + if spec.target.family != spec.target: + assert str(spec.target) not in writer.layout.arch_dirname diff --git a/share/spack/templates/modules/modulefile.lua b/share/spack/templates/modules/modulefile.lua index a8eae9bef14..2149c8bfaf7 100644 --- a/share/spack/templates/modules/modulefile.lua +++ b/share/spack/templates/modules/modulefile.lua @@ -8,6 +8,7 @@ {% if short_description %} whatis([[Name : {{ spec.name }}]]) whatis([[Version : {{ spec.version }}]]) +whatis([[Target : {{ spec.target }}]]) whatis([[Short description : {{ short_description }}]]) {% endif %} {% if configure_options %} From dc3a9618a0c9aad91e08267c264694860bacf536 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 15 Oct 2019 11:55:45 -0700 Subject: [PATCH 262/499] ADIOS2: Default no Python (#13220) Turn off the python variant by default. --- var/spack/repos/builtin/packages/adios2/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index 3d7339da41a..b1bc7c11dae 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -57,7 +57,7 @@ class Adios2(CMakePackage): description='Enable the HDF5 engine') # optional language bindings, C++11 and C always provided - variant('python', default=True, + variant('python', default=False, description='Enable the Python bindings') variant('fortran', default=True, description='Enable the Fortran bindings') From 5ea0eed2876b272b06861c5697c5ba8627842dd7 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Tue, 15 Oct 2019 15:05:51 -0500 Subject: [PATCH 263/499] hypre: add version 2.18.1 (#13224) --- var/spack/repos/builtin/packages/hypre/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 3cd57ef6ba3..a2444370571 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -20,6 +20,7 @@ class Hypre(Package): maintainers = ['ulrikeyang', 'osborn9', 'balay'] version('develop', branch='master') + version('2.18.1', sha256='220f9c4ad024e815add8dad8950eaa2d8f4f231104788cf2a3c5d9da8f94ba6e') version('2.18.0', sha256='62591ac69f9cc9728bd6d952b65bcadd2dfe52b521081612609804a413f49b07') version('2.17.0', sha256='4674f938743aa29eb4d775211b13b089b9de84bfe5e9ea00c7d8782ed84a46d7') version('2.16.0', sha256='33f8a27041e697343b820d0426e74694670f955e21bbf3fcb07ee95b22c59e90') From 94e80933f0fc77055635f35795f4ab02251c2cdf Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Tue, 15 Oct 2019 14:24:52 -0700 Subject: [PATCH 264/499] Feature: installed file verification (#12841) This feature generates a verification manifest for each installed package and provides a command, "spack verify", which can be used to compare the current file checksums/permissions with those calculated at installed time. Verification includes * Checksums of files * File permissions * Modification time * File size Packages installed before this PR will be skipped during verification. To verify such a package you must reinstall it. The spack verify command has three modes. * With the -a,--all option it will check every installed package. * With the -f,--files option, it will check some specific files, determine which package they belong to, and confirm that they have not been changed. * With the -s,--specs option or by default, it will check some specific packages that no files havae changed. --- lib/spack/docs/basic_usage.rst | 34 +++ lib/spack/llnl/util/filesystem.py | 13 +- lib/spack/spack/binary_distribution.py | 9 +- lib/spack/spack/cmd/__init__.py | 8 +- lib/spack/spack/cmd/verify.py | 95 +++++++ lib/spack/spack/directory_layout.py | 6 + lib/spack/spack/filesystem_view.py | 56 ++-- lib/spack/spack/hooks/__init__.py | 8 +- .../spack/hooks/write_install_manifest.py | 11 + lib/spack/spack/test/cmd/install.py | 40 ++- lib/spack/spack/test/cmd/verify.py | 89 +++++++ lib/spack/spack/test/verification.py | 232 +++++++++++++++++ lib/spack/spack/verify.py | 244 ++++++++++++++++++ 13 files changed, 791 insertions(+), 54 deletions(-) create mode 100644 lib/spack/spack/cmd/verify.py create mode 100644 lib/spack/spack/hooks/write_install_manifest.py create mode 100644 lib/spack/spack/test/cmd/verify.py create mode 100644 lib/spack/spack/test/verification.py create mode 100644 lib/spack/spack/verify.py diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index f6ceb2a9e69..f86724e1405 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -277,6 +277,40 @@ the tarballs in question to it (see :ref:`mirrors`): $ spack install galahad +----------------------- +Verifying installations +----------------------- + +The ``spack verify`` command can be used to verify the validity of +Spack-installed packages any time after installation. + +At installation time, Spack creates a manifest of every file in the +installation prefix. For links, Spack tracks the mode, ownership, and +destination. For directories, Spack tracks the mode, and +ownership. For files, Spack tracks the mode, ownership, modification +time, hash, and size. The Spack verify command will check, for every +file in each package, whether any of those attributes have changed. It +will also check for newly added files or deleted files from the +installation prefix. Spack can either check all installed packages +using the `-a,--all` or accept specs listed on the command line to +verify. + +The ``spack verify`` command can also verify for individual files that +they haven't been altered since installation time. If the given file +is not in a Spack installation prefix, Spack will report that it is +not owned by any package. To check individual files instead of specs, +use the ``-f,--files`` option. + +Spack installation manifests are part of the tarball signed by Spack +for binary package distribution. When installed from a binary package, +Spack uses the packaged installation manifest instead of creating one +at install time. + +The ``spack verify`` command also accepts the ``-l,--local`` option to +check only local packages (as opposed to those used transparently from +``upstream`` spack instances) and the ``-j,--json`` option to output +machine-readable json data for any errors. + ------------------------- Seeing installed packages ------------------------- diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 45914be60ea..06925bec487 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -653,7 +653,7 @@ def replace_directory_transaction(directory_name, tmp_root=None): tty.debug('TEMPORARY DIRECTORY DELETED [{0}]'.format(tmp_dir)) -def hash_directory(directory): +def hash_directory(directory, ignore=[]): """Hashes recursively the content of a directory. Args: @@ -670,11 +670,12 @@ def hash_directory(directory): for root, dirs, files in os.walk(directory): for name in sorted(files): filename = os.path.join(root, name) - # TODO: if caching big files becomes an issue, convert this to - # TODO: read in chunks. Currently it's used only for testing - # TODO: purposes. - with open(filename, 'rb') as f: - md5_hash.update(f.read()) + if filename not in ignore: + # TODO: if caching big files becomes an issue, convert this to + # TODO: read in chunks. Currently it's used only for testing + # TODO: purposes. + with open(filename, 'rb') as f: + md5_hash.update(f.read()) return md5_hash.hexdigest() diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index ca8fbd31d16..cbc0f22327c 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -585,8 +585,13 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False, except Exception as e: shutil.rmtree(spec.prefix) tty.die(e) - # Delay creating spec.prefix until verification is complete - # and any relocation has been done. + else: + manifest_file = os.path.join(spec.prefix, + spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) + if not os.path.exists(manifest_file): + spec_id = spec.format('{name}/{hash:7}') + tty.warn('No manifest file in tarball for spec %s' % spec_id) finally: shutil.rmtree(tmpdir) diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index cefec644a26..52e20614a1a 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -174,16 +174,20 @@ def elide_list(line_list, max_num=10): return line_list -def disambiguate_spec(spec, env): +def disambiguate_spec(spec, env, local=False): """Given a spec, figure out which installed package it refers to. Arguments: spec (spack.spec.Spec): a spec to disambiguate env (spack.environment.Environment): a spack environment, if one is active, or None if no environment is active + local (boolean, default False): do not search chained spack instances """ hashes = env.all_hashes() if env else None - matching_specs = spack.store.db.query(spec, hashes=hashes) + if local: + matching_specs = spack.store.db.query_local(spec, hashes=hashes) + else: + matching_specs = spack.store.db.query(spec, hashes=hashes) if not matching_specs: tty.die("Spec '%s' matches no installed packages." % spec) diff --git a/lib/spack/spack/cmd/verify.py b/lib/spack/spack/cmd/verify.py new file mode 100644 index 00000000000..4bd7b39fea8 --- /dev/null +++ b/lib/spack/spack/cmd/verify.py @@ -0,0 +1,95 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from __future__ import print_function +import argparse + +import llnl.util.tty as tty + +import spack.store +import spack.verify +import spack.environment as ev + +description = "Check that all spack packages are on disk as installed" +section = "admin" +level = "long" + + +def setup_parser(subparser): + setup_parser.parser = subparser + + subparser.add_argument('-l', '--local', action='store_true', + help="Verify only locally installed packages") + subparser.add_argument('-j', '--json', action='store_true', + help="Ouptut json-formatted errors") + subparser.add_argument('-a', '--all', action='store_true', + help="Verify all packages") + subparser.add_argument('files_or_specs', nargs=argparse.REMAINDER, + help="Files or specs to verify") + + type = subparser.add_mutually_exclusive_group() + type.add_argument( + '-s', '--specs', + action='store_const', const='specs', dest='type', default='specs', + help='Treat entries as specs (default)') + type.add_argument( + '-f', '--files', + action='store_const', const='files', dest='type', default='specs', + help="Treat entries as absolute filenames. Cannot be used with '-a'") + + +def verify(parser, args): + local = args.local + + if args.type == 'files': + if args.all: + setup_parser.parser.print_help() + return 1 + + for file in args.files_or_specs: + results = spack.verify.check_file_manifest(file) + if results.has_errors(): + if args.json: + print(results.json_string()) + else: + print(results) + + return 0 + else: + spec_args = spack.cmd.parse_specs(args.files_or_specs) + + if args.all: + query = spack.store.db.query_local if local else spack.store.db.query + + # construct spec list + if spec_args: + spec_list = spack.cmd.parse_specs(args.files_or_specs) + specs = [] + for spec in spec_list: + specs += query(spec, installed=True) + else: + specs = query(installed=True) + + elif args.files_or_specs: + # construct disambiguated spec list + env = ev.get_env(args, 'verify') + specs = list(map(lambda x: spack.cmd.disambiguate_spec(x, env, + local=local), + spec_args)) + else: + setup_parser.parser.print_help() + return 1 + + for spec in specs: + tty.debug("Verifying package %s") + results = spack.verify.check_spec_manifest(spec) + if results.has_errors(): + if args.json: + print(results.json_string()) + else: + tty.msg("In package %s" % spec.format('{name}/{hash:7}')) + print(results) + return 1 + else: + tty.debug(results) diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index 01ddd0e1f70..a48b8411476 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -194,6 +194,7 @@ def __init__(self, root, **kwargs): self.spec_file_name = 'spec.yaml' self.extension_file_name = 'extensions.yaml' self.packages_dir = 'repos' # archive of package.py files + self.manifest_file_name = 'install_manifest.json' @property def hidden_file_paths(self): @@ -430,6 +431,11 @@ def _extension_map(self, spec): def _write_extensions(self, spec, extensions): path = self.extension_file_path(spec) + if not extensions: + # Remove the empty extensions file + os.remove(path) + return + # Create a temp file in the same directory as the actual file. dirname, basename = os.path.split(path) mkdirp(dirname) diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py index 1701af55014..417466cd837 100644 --- a/lib/spack/spack/filesystem_view.py +++ b/lib/spack/spack/filesystem_view.py @@ -188,47 +188,41 @@ def __init__(self, root, layout, **kwargs): # Super class gets projections from the kwargs # YAML specific to get projections from YAML file - projections_path = os.path.join(self._root, _projections_path) + self.projections_path = os.path.join(self._root, _projections_path) if not self.projections: - if os.path.exists(projections_path): - # Read projections file from view - with open(projections_path, 'r') as f: - projections_data = s_yaml.load(f) - spack.config.validate(projections_data, - spack.schema.projections.schema) - self.projections = projections_data['projections'] - else: - # Write projections file to new view - # Not strictly necessary as the empty file is the empty - # projection but it makes sense for consistency - try: - mkdirp(os.path.dirname(projections_path)) - with open(projections_path, 'w') as f: - f.write(s_yaml.dump({'projections': self.projections})) - except OSError as e: - if self.projections: - raise e - elif not os.path.exists(projections_path): + # Read projections file from view + self.projections = self.read_projections() + elif not os.path.exists(self.projections_path): # Write projections file to new view - mkdirp(os.path.dirname(projections_path)) - with open(projections_path, 'w') as f: - f.write(s_yaml.dump({'projections': self.projections})) + self.write_projections() else: # Ensure projections are the same from each source # Read projections file from view - with open(projections_path, 'r') as f: - projections_data = s_yaml.load(f) - spack.config.validate(projections_data, - spack.schema.projections.schema) - if self.projections != projections_data['projections']: - msg = 'View at %s has projections file' % self._root - msg += ' which does not match projections passed manually.' - raise ConflictingProjectionsError(msg) + if self.projections != self.read_projections(): + msg = 'View at %s has projections file' % self._root + msg += ' which does not match projections passed manually.' + raise ConflictingProjectionsError(msg) self.extensions_layout = YamlViewExtensionsLayout(self, layout) self._croot = colorize_root(self._root) + " " + def write_projections(self): + if self.projections: + mkdirp(os.path.dirname(self.projections_path)) + with open(self.projections_path, 'w') as f: + f.write(s_yaml.dump({'projections': self.projections})) + + def read_projections(self): + if os.path.exists(self.projections_path): + with open(self.projections_path, 'r') as f: + projections_data = s_yaml.load(f) + spack.config.validate(projections_data, + spack.schema.projections.schema) + return projections_data['projections'] + else: + return {} + def add_specs(self, *specs, **kwargs): assert all((s.concrete for s in specs)) specs = set(specs) diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py index 3938f9e6d3d..860134112e1 100644 --- a/lib/spack/spack/hooks/__init__.py +++ b/lib/spack/spack/hooks/__init__.py @@ -36,8 +36,14 @@ def all_hook_modules(): mod_name = __name__ + '.' + name path = os.path.join(spack.paths.hooks_path, name) + ".py" mod = simp.load_source(mod_name, path) - modules.append(mod) + if name == 'write_install_manifest': + last_mod = mod + else: + modules.append(mod) + + # put `write_install_manifest` as the last hook to run + modules.append(last_mod) return modules diff --git a/lib/spack/spack/hooks/write_install_manifest.py b/lib/spack/spack/hooks/write_install_manifest.py new file mode 100644 index 00000000000..8118caae244 --- /dev/null +++ b/lib/spack/spack/hooks/write_install_manifest.py @@ -0,0 +1,11 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import spack.verify + + +def post_install(spec): + if not spec.external: + spack.verify.write_manifest(spec) diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py index 3be548907ab..db8cf01f484 100644 --- a/lib/spack/spack/test/cmd/install.py +++ b/lib/spack/spack/test/cmd/install.py @@ -197,22 +197,26 @@ def test_install_overwrite( install('libdwarf') + manifest = os.path.join(spec.prefix, spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) + assert os.path.exists(spec.prefix) - expected_md5 = fs.hash_directory(spec.prefix) + expected_md5 = fs.hash_directory(spec.prefix, ignore=[manifest]) # Modify the first installation to be sure the content is not the same # as the one after we reinstalled with open(os.path.join(spec.prefix, 'only_in_old'), 'w') as f: f.write('This content is here to differentiate installations.') - bad_md5 = fs.hash_directory(spec.prefix) + bad_md5 = fs.hash_directory(spec.prefix, ignore=[manifest]) assert bad_md5 != expected_md5 install('--overwrite', '-y', 'libdwarf') + assert os.path.exists(spec.prefix) - assert fs.hash_directory(spec.prefix) == expected_md5 - assert fs.hash_directory(spec.prefix) != bad_md5 + assert fs.hash_directory(spec.prefix, ignore=[manifest]) == expected_md5 + assert fs.hash_directory(spec.prefix, ignore=[manifest]) != bad_md5 def test_install_overwrite_not_installed( @@ -242,11 +246,20 @@ def test_install_overwrite_multiple( install('cmake') + ld_manifest = os.path.join(libdwarf.prefix, + spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) + assert os.path.exists(libdwarf.prefix) - expected_libdwarf_md5 = fs.hash_directory(libdwarf.prefix) + expected_libdwarf_md5 = fs.hash_directory(libdwarf.prefix, + ignore=[ld_manifest]) + + cm_manifest = os.path.join(cmake.prefix, + spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) assert os.path.exists(cmake.prefix) - expected_cmake_md5 = fs.hash_directory(cmake.prefix) + expected_cmake_md5 = fs.hash_directory(cmake.prefix, ignore=[cm_manifest]) # Modify the first installation to be sure the content is not the same # as the one after we reinstalled @@ -255,8 +268,8 @@ def test_install_overwrite_multiple( with open(os.path.join(cmake.prefix, 'only_in_old'), 'w') as f: f.write('This content is here to differentiate installations.') - bad_libdwarf_md5 = fs.hash_directory(libdwarf.prefix) - bad_cmake_md5 = fs.hash_directory(cmake.prefix) + bad_libdwarf_md5 = fs.hash_directory(libdwarf.prefix, ignore=[ld_manifest]) + bad_cmake_md5 = fs.hash_directory(cmake.prefix, ignore=[cm_manifest]) assert bad_libdwarf_md5 != expected_libdwarf_md5 assert bad_cmake_md5 != expected_cmake_md5 @@ -264,10 +277,13 @@ def test_install_overwrite_multiple( install('--overwrite', '-y', 'libdwarf', 'cmake') assert os.path.exists(libdwarf.prefix) assert os.path.exists(cmake.prefix) - assert fs.hash_directory(libdwarf.prefix) == expected_libdwarf_md5 - assert fs.hash_directory(cmake.prefix) == expected_cmake_md5 - assert fs.hash_directory(libdwarf.prefix) != bad_libdwarf_md5 - assert fs.hash_directory(cmake.prefix) != bad_cmake_md5 + + ld_hash = fs.hash_directory(libdwarf.prefix, ignore=[ld_manifest]) + cm_hash = fs.hash_directory(cmake.prefix, ignore=[cm_manifest]) + assert ld_hash == expected_libdwarf_md5 + assert cm_hash == expected_cmake_md5 + assert ld_hash != bad_libdwarf_md5 + assert cm_hash != bad_cmake_md5 @pytest.mark.usefixtures( diff --git a/lib/spack/spack/test/cmd/verify.py b/lib/spack/spack/test/cmd/verify.py new file mode 100644 index 00000000000..4896cb05c88 --- /dev/null +++ b/lib/spack/spack/test/cmd/verify.py @@ -0,0 +1,89 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +"""Tests for the `spack verify` command""" +import os + +import llnl.util.filesystem as fs + +import spack.util.spack_json as sjson +import spack.verify +import spack.spec +import spack.store +from spack.main import SpackCommand + +verify = SpackCommand('verify') +install = SpackCommand('install') + + +def test_single_file_verify_cmd(tmpdir): + # Test the verify command interface to verifying a single file. + filedir = os.path.join(str(tmpdir), 'a', 'b', 'c', 'd') + filepath = os.path.join(filedir, 'file') + metadir = os.path.join(str(tmpdir), spack.store.layout.metadata_dir) + + fs.mkdirp(filedir) + fs.mkdirp(metadir) + + with open(filepath, 'w') as f: + f.write("I'm a file") + + data = spack.verify.create_manifest_entry(filepath) + + manifest_file = os.path.join(metadir, + spack.store.layout.manifest_file_name) + + with open(manifest_file, 'w') as f: + sjson.dump({filepath: data}, f) + + results = verify('-f', filepath, fail_on_error=False) + print(results) + assert not results + + os.utime(filepath, (0, 0)) + with open(filepath, 'w') as f: + f.write("I changed.") + + results = verify('-f', filepath, fail_on_error=False) + + expected = ['hash'] + mtime = os.stat(filepath).st_mtime + if mtime != data['time']: + expected.append('mtime') + + assert results + assert filepath in results + assert all(x in results for x in expected) + + results = verify('-fj', filepath, fail_on_error=False) + res = sjson.load(results) + assert len(res) == 1 + errors = res.pop(filepath) + assert sorted(errors) == sorted(expected) + + +def test_single_spec_verify_cmd(tmpdir, mock_packages, mock_archive, + mock_fetch, config, install_mockery): + # Test the verify command interface to verify a single spec + install('libelf') + s = spack.spec.Spec('libelf').concretized() + prefix = s.prefix + hash = s.dag_hash() + + results = verify('/%s' % hash, fail_on_error=False) + assert not results + + new_file = os.path.join(prefix, 'new_file_for_verify_test') + with open(new_file, 'w') as f: + f.write('New file') + + results = verify('/%s' % hash, fail_on_error=False) + assert new_file in results + assert 'added' in results + + results = verify('-j', '/%s' % hash, fail_on_error=False) + res = sjson.load(results) + assert len(res) == 1 + assert res[new_file] == ['added'] diff --git a/lib/spack/spack/test/verification.py b/lib/spack/spack/test/verification.py new file mode 100644 index 00000000000..dbc76e6268c --- /dev/null +++ b/lib/spack/spack/test/verification.py @@ -0,0 +1,232 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +"""Tests for the `spack.verify` module""" +import os +import shutil + +import llnl.util.filesystem as fs + +import spack.util.spack_json as sjson +import spack.verify +import spack.spec +import spack.store + + +def test_link_manifest_entry(tmpdir): + # Test that symlinks are properly checked against the manifest. + # Test that the appropriate errors are generated when the check fails. + file = str(tmpdir.join('file')) + open(file, 'a').close() + link = str(tmpdir.join('link')) + os.symlink(file, link) + + data = spack.verify.create_manifest_entry(link) + assert data['type'] == 'link' + assert data['dest'] == file + assert all(x in data for x in ('mode', 'owner', 'group')) + + results = spack.verify.check_entry(link, data) + assert not results.has_errors() + + data['type'] = 'garbage' + + results = spack.verify.check_entry(link, data) + assert results.has_errors() + assert link in results.errors + assert results.errors[link] == ['type'] + + data['type'] = 'link' + + file2 = str(tmpdir.join('file2')) + open(file2, 'a').close() + os.remove(link) + os.symlink(file2, link) + + results = spack.verify.check_entry(link, data) + assert results.has_errors() + assert link in results.errors + assert results.errors[link] == ['link'] + + +def test_dir_manifest_entry(tmpdir): + # Test that directories are properly checked against the manifest. + # Test that the appropriate errors are generated when the check fails. + dirent = str(tmpdir.join('dir')) + fs.mkdirp(dirent) + + data = spack.verify.create_manifest_entry(dirent) + assert data['type'] == 'dir' + assert all(x in data for x in ('mode', 'owner', 'group')) + + results = spack.verify.check_entry(dirent, data) + assert not results.has_errors() + + data['type'] = 'garbage' + + results = spack.verify.check_entry(dirent, data) + assert results.has_errors() + assert dirent in results.errors + assert results.errors[dirent] == ['type'] + + +def test_file_manifest_entry(tmpdir): + # Test that files are properly checked against the manifest. + # Test that the appropriate errors are generated when the check fails. + orig_str = 'This is a file' + new_str = 'The file has changed' + + file = str(tmpdir.join('dir')) + with open(file, 'w') as f: + f.write(orig_str) + + data = spack.verify.create_manifest_entry(file) + assert data['type'] == 'file' + assert data['size'] == len(orig_str) + assert all(x in data for x in ('mode', 'owner', 'group')) + + results = spack.verify.check_entry(file, data) + assert not results.has_errors() + + data['type'] = 'garbage' + + results = spack.verify.check_entry(file, data) + assert results.has_errors() + assert file in results.errors + assert results.errors[file] == ['type'] + + data['type'] = 'file' + + with open(file, 'w') as f: + f.write(new_str) + + results = spack.verify.check_entry(file, data) + + expected = ['size', 'hash'] + mtime = os.stat(file).st_mtime + if mtime != data['time']: + expected.append('mtime') + + assert results.has_errors() + assert file in results.errors + assert sorted(results.errors[file]) == sorted(expected) + + +def test_check_chmod_manifest_entry(tmpdir): + # Check that the verification properly identifies errors for files whose + # permissions have been modified. + file = str(tmpdir.join('dir')) + with open(file, 'w') as f: + f.write('This is a file') + + data = spack.verify.create_manifest_entry(file) + + os.chmod(file, data['mode'] - 1) + + results = spack.verify.check_entry(file, data) + assert results.has_errors() + assert file in results.errors + assert results.errors[file] == ['mode'] + + +def test_check_prefix_manifest(tmpdir): + # Test the verification of an entire prefix and its contents + prefix_path = tmpdir.join('prefix') + prefix = str(prefix_path) + + spec = spack.spec.Spec('libelf') + spec._mark_concrete() + spec.prefix = prefix + + results = spack.verify.check_spec_manifest(spec) + assert results.has_errors() + assert prefix in results.errors + assert results.errors[prefix] == ['manifest missing'] + + metadata_dir = str(prefix_path.join('.spack')) + bin_dir = str(prefix_path.join('bin')) + other_dir = str(prefix_path.join('other')) + + for d in (metadata_dir, bin_dir, other_dir): + fs.mkdirp(d) + + file = os.path.join(other_dir, 'file') + with open(file, 'w') as f: + f.write("I'm a little file short and stout") + + link = os.path.join(bin_dir, 'run') + os.symlink(file, link) + + spack.verify.write_manifest(spec) + results = spack.verify.check_spec_manifest(spec) + assert not results.has_errors() + + os.remove(link) + malware = os.path.join(metadata_dir, 'hiddenmalware') + with open(malware, 'w') as f: + f.write("Foul evil deeds") + + results = spack.verify.check_spec_manifest(spec) + assert results.has_errors() + assert all(x in results.errors for x in (malware, link)) + assert len(results.errors) == 2 + + assert results.errors[link] == ['deleted'] + assert results.errors[malware] == ['added'] + + manifest_file = os.path.join(spec.prefix, + spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) + with open(manifest_file, 'w') as f: + f.write("{This) string is not proper json") + + results = spack.verify.check_spec_manifest(spec) + assert results.has_errors() + assert results.errors[spec.prefix] == ['manifest corrupted'] + + +def test_single_file_verification(tmpdir): + # Test the API to verify a single file, including finding the package + # to which it belongs + filedir = os.path.join(str(tmpdir), 'a', 'b', 'c', 'd') + filepath = os.path.join(filedir, 'file') + metadir = os.path.join(str(tmpdir), spack.store.layout.metadata_dir) + + fs.mkdirp(filedir) + fs.mkdirp(metadir) + + with open(filepath, 'w') as f: + f.write("I'm a file") + + data = spack.verify.create_manifest_entry(filepath) + + manifest_file = os.path.join(metadir, + spack.store.layout.manifest_file_name) + + with open(manifest_file, 'w') as f: + sjson.dump({filepath: data}, f) + + results = spack.verify.check_file_manifest(filepath) + assert not results.has_errors() + + os.utime(filepath, (0, 0)) + with open(filepath, 'w') as f: + f.write("I changed.") + + results = spack.verify.check_file_manifest(filepath) + + expected = ['hash'] + mtime = os.stat(filepath).st_mtime + if mtime != data['time']: + expected.append('mtime') + + assert results.has_errors() + assert filepath in results.errors + assert sorted(results.errors[filepath]) == sorted(expected) + + shutil.rmtree(metadir) + results = spack.verify.check_file_manifest(filepath) + assert results.has_errors() + assert results.errors[filepath] == ['not owned by any package'] diff --git a/lib/spack/spack/verify.py b/lib/spack/spack/verify.py new file mode 100644 index 00000000000..ec604a32405 --- /dev/null +++ b/lib/spack/spack/verify.py @@ -0,0 +1,244 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os +import hashlib +import base64 +import sys + +import llnl.util.tty as tty + +import spack.util.spack_json as sjson +import spack.util.file_permissions as fp +import spack.store +import spack.filesystem_view + + +def compute_hash(path): + with open(path, 'rb') as f: + sha1 = hashlib.sha1(f.read()).digest() + b32 = base64.b32encode(sha1) + + if sys.version_info[0] >= 3: + b32 = b32.decode() + + return b32 + + +def create_manifest_entry(path): + data = {} + stat = os.stat(path) + + data['mode'] = stat.st_mode + data['owner'] = stat.st_uid + data['group'] = stat.st_gid + + if os.path.islink(path): + data['type'] = 'link' + data['dest'] = os.readlink(path) + + elif os.path.isdir(path): + data['type'] = 'dir' + + else: + data['type'] = 'file' + data['hash'] = compute_hash(path) + data['time'] = stat.st_mtime + data['size'] = stat.st_size + + return data + + +def write_manifest(spec): + manifest_file = os.path.join(spec.prefix, + spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) + + if not os.path.exists(manifest_file): + tty.debug("Writing manifest file: No manifest from binary") + + manifest = {} + for root, dirs, files in os.walk(spec.prefix): + for entry in list(dirs + files): + path = os.path.join(root, entry) + manifest[path] = create_manifest_entry(path) + manifest[spec.prefix] = create_manifest_entry(spec.prefix) + + with open(manifest_file, 'w') as f: + sjson.dump(manifest, f) + + fp.set_permissions_by_spec(manifest_file, spec) + + +def check_entry(path, data): + res = VerificationResults() + + if not data: + res.add_error(path, 'added') + return res + + stat = os.stat(path) + + # Check for all entries + if stat.st_mode != data['mode']: + res.add_error(path, 'mode') + if stat.st_uid != data['owner']: + res.add_error(path, 'owner') + if stat.st_gid != data['group']: + res.add_error(path, 'group') + + # Check for symlink targets and listed as symlink + if os.path.islink(path): + if data['type'] != 'link': + res.add_error(path, 'type') + if os.readlink(path) != data.get('dest', ''): + res.add_error(path, 'link') + + # Check directories are listed as directory + elif os.path.isdir(path): + if data['type'] != 'dir': + res.add_error(path, 'type') + + else: + # Check file contents against hash and listed as file + # Check mtime and size as well + if stat.st_size != data['size']: + res.add_error(path, 'size') + if stat.st_mtime != data['time']: + res.add_error(path, 'mtime') + if data['type'] != 'file': + res.add_error(path, 'type') + if compute_hash(path) != data.get('hash', ''): + res.add_error(path, 'hash') + + return res + + +def check_file_manifest(file): + dirname = os.path.dirname(file) + + results = VerificationResults() + while spack.store.layout.metadata_dir not in os.listdir(dirname): + if dirname == os.path.sep: + results.add_error(file, 'not owned by any package') + return results + dirname = os.path.dirname(dirname) + + manifest_file = os.path.join(dirname, + spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) + + if not os.path.exists(manifest_file): + results.add_error(file, "manifest missing") + return results + + try: + with open(manifest_file, 'r') as f: + manifest = sjson.load(f) + except Exception: + results.add_error(file, "manifest corrupted") + return results + + if file in manifest: + results += check_entry(file, manifest[file]) + else: + results.add_error(file, 'not owned by any package') + return results + + +def check_spec_manifest(spec): + prefix = spec.prefix + + results = VerificationResults() + manifest_file = os.path.join(prefix, + spack.store.layout.metadata_dir, + spack.store.layout.manifest_file_name) + + if not os.path.exists(manifest_file): + results.add_error(prefix, "manifest missing") + return results + + try: + with open(manifest_file, 'r') as f: + manifest = sjson.load(f) + except Exception: + results.add_error(prefix, "manifest corrupted") + return results + + # Get extensions active in spec + view = spack.filesystem_view.YamlFilesystemView(prefix, + spack.store.layout) + active_exts = view.extensions_layout.extension_map(spec).values() + ext_file = '' + if active_exts: + # No point checking contents of this file as it is the only source of + # truth for that information. + ext_file = view.extensions_layout.extension_file_path(spec) + + def is_extension_artifact(p): + if os.path.islink(p): + if any(os.readlink(p).startswith(e.prefix) for e in active_exts): + # This file is linked in by an extension. Belongs to extension + return True + elif os.path.isdir(p) and p not in manifest: + if all(is_extension_artifact(os.path.join(p, f)) + for f in os.listdir(p)): + return True + return False + + for root, dirs, files in os.walk(prefix): + for entry in list(dirs + files): + path = os.path.join(root, entry) + + # Do not check links from prefix to active extension + # TODO: make this stricter for non-linux systems that use symlink + # permissions + # Do not check directories that only exist for extensions + if is_extension_artifact(path): + continue + + # Do not check manifest file. Can't store your own hash + # Nothing to check for ext_file + if path == manifest_file or path == ext_file: + continue + + data = manifest.pop(path, {}) + results += check_entry(path, data) + + results += check_entry(prefix, manifest.pop(prefix, {})) + + for path in manifest: + results.add_error(path, 'deleted') + + return results + + +class VerificationResults(object): + def __init__(self): + self.errors = {} + + def add_error(self, path, field): + self.errors[path] = self.errors.get(path, []) + [field] + + def __add__(self, vr): + for path, fields in vr.errors.items(): + self.errors[path] = self.errors.get(path, []) + fields + return self + + def has_errors(self): + return bool(self.errors) + + def json_string(self): + return sjson.dump(self.errors) + + def __str__(self): + res = '' + for path, fields in self.errors.items(): + res += '%s verification failed with error(s):\n' % path + for error in fields: + res += ' %s\n' % error + + if not res: + res += 'No Errors' + return res From f08f4201c739ebc5a9f6258668471afb007e1827 Mon Sep 17 00:00:00 2001 From: Jeffrey Salmond Date: Wed, 16 Oct 2019 04:43:03 +0100 Subject: [PATCH 265/499] add latest version of vim (#13203) --- var/spack/repos/builtin/packages/vim/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py index d59f8372db3..fe514c97d03 100644 --- a/var/spack/repos/builtin/packages/vim/package.py +++ b/var/spack/repos/builtin/packages/vim/package.py @@ -18,6 +18,7 @@ class Vim(AutotoolsPackage): homepage = "http://www.vim.org" url = "https://github.com/vim/vim/archive/v8.1.0338.tar.gz" + version('8.1.2141', sha256='7be3c3d88a6c871121230ffb9b7371b1d2ab462118dedb967c7265473af1144b') version('8.1.0338', sha256='3febcc4e49eaca458be1a1e8055a3a52887aa2054b03e24d5f38d192c3de51a0') version('8.1.0001', sha256='c342acaa26589f371fa34a5ca213b95811f26185c12443f8f48ad2868dee2935') version('8.0.1376', sha256='1ad8b5a0b9b63df5abc3f8050e31e1cb49379ffcfd2662a56daeff8bd3d780b9') From b0543005b264553bda28dedc1c0914bb1aab6e2e Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 16 Oct 2019 05:59:51 -0700 Subject: [PATCH 266/499] expat: don't pick up external docbook (#13228) --- var/spack/repos/builtin/packages/expat/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index 8e992491d61..da3aa5b0eb6 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -37,7 +37,7 @@ def url_for_version(self, version): def configure_args(self): spec = self.spec - args = [] + args = ['--without-docbook'] if '+libbsd' in spec and '@2.2.1:' in spec: - args = ['--with-libbsd'] + args.append('--with-libbsd') return args From e17df2e8f5dd46ef1c08252c08bdda191b64d911 Mon Sep 17 00:00:00 2001 From: Jeffrey Salmond Date: Wed, 16 Oct 2019 22:42:36 +0100 Subject: [PATCH 267/499] add python version 3.8.0 (#13218) --- var/spack/repos/builtin/packages/python/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 35a99bc31f1..d3537611815 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -25,12 +25,13 @@ class Python(AutotoolsPackage): """The Python programming language.""" homepage = "https://www.python.org/" - url = "https://www.python.org/ftp/python/3.7.4/Python-3.7.4.tgz" + url = "https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tgz" list_url = "https://www.python.org/downloads/" list_depth = 1 maintainers = ['adamjstewart'] + version('3.8.0', sha256='f1069ad3cae8e7ec467aa98a6565a62a48ef196cb8f1455a245a08db5e1792df') version('3.7.4', sha256='d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3') version('3.7.3', sha256='d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff') version('3.7.2', sha256='f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d') From 1ef71376f2e2b41229471501e91448858f2df61d Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Wed, 16 Oct 2019 14:55:37 -0700 Subject: [PATCH 268/499] Bugfix: stage directory permissions and cleaning (#12733) * This updates stage names to use "spack-stage-" as a prefix. This avoids removing non-Spack directories in "spack clean" as c141e99 did (in this case so long as they don't contain the prefix "spack-stage-"), and also addresses a follow-up issue where Spack stage directories were not removed. * Spack now does more-stringent checking of expected permissions for staging directories. For a given stage root that includes a user component, all directories before the user component that are created by Spack are expected to match the permissions of their parent; the user component and all deeper directories are expected to be accessible to the user (read/write/execute). --- lib/spack/docs/config_yaml.rst | 7 +- lib/spack/docs/tutorial_configuration.rst | 9 +- lib/spack/llnl/util/filesystem.py | 69 +++++++++ lib/spack/spack/package.py | 5 +- lib/spack/spack/stage.py | 85 ++++++----- lib/spack/spack/test/cmd/env.py | 4 +- lib/spack/spack/test/conftest.py | 25 +++- lib/spack/spack/test/llnl/util/filesystem.py | 24 +++ lib/spack/spack/test/stage.py | 146 +++++++++++++++---- 9 files changed, 294 insertions(+), 80 deletions(-) diff --git a/lib/spack/docs/config_yaml.rst b/lib/spack/docs/config_yaml.rst index 53398f55c2d..525f829c9ef 100644 --- a/lib/spack/docs/config_yaml.rst +++ b/lib/spack/docs/config_yaml.rst @@ -91,9 +91,10 @@ the selected ``build_stage`` path. .. warning:: We highly recommend specifying ``build_stage`` paths that distinguish between staging and other activities to ensure ``spack clean`` does not inadvertently remove unrelated files. - This can be accomplished by using a combination of ``spack`` and or - ``stage`` in each path as shown in the default settings and documented - examples. + Spack prepends ``spack-stage-`` to temporary staging directory names to + reduce this risk. Using a combination of ``spack`` and or ``stage`` in + each specified path, as shown in the default settings and documented + examples, will add another layer of protection. By default, Spack's ``build_stage`` is configured like this: diff --git a/lib/spack/docs/tutorial_configuration.rst b/lib/spack/docs/tutorial_configuration.rst index 565a6c02b55..879bb949670 100644 --- a/lib/spack/docs/tutorial_configuration.rst +++ b/lib/spack/docs/tutorial_configuration.rst @@ -856,10 +856,11 @@ from this file system with the following ``config.yaml``: It is important to distinguish the build stage directory from other directories in your scratch space to ensure ``spack clean`` does not - inadvertently remove unrelated files. This can be accomplished by - including a combination of ``spack`` and or ``stage`` in each path - as shown in the default settings and documented examples. See - :ref:`config-yaml` for details. + inadvertently remove unrelated files. Spack prepends ``spack-stage-`` + to temporary staging directory names to reduce this risk. Using a + combination of ``spack`` and or ``stage`` in each specified path, as + shown in the default settings and documented examples, will add + another layer of protection. See :ref:`config-yaml` for details. On systems with compilers that absolutely *require* environment variables diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 06925bec487..0af9c915b6a 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -49,6 +49,8 @@ 'is_exe', 'join_path', 'mkdirp', + 'partition_path', + 'prefixes', 'remove_dead_links', 'remove_if_dead_link', 'remove_linked_tree', @@ -1608,3 +1610,70 @@ def search_paths_for_executables(*path_hints): executable_paths.append(bin_dir) return executable_paths + + +def partition_path(path, entry=None): + """ + Split the prefixes of the path at the first occurrence of entry and + return a 3-tuple containing a list of the prefixes before the entry, a + string of the prefix ending with the entry, and a list of the prefixes + after the entry. + + If the entry is not a node in the path, the result will be the prefix list + followed by an empty string and an empty list. + """ + paths = prefixes(path) + + if entry is not None: + # Derive the index of entry within paths, which will correspond to + # the location of the entry in within the path. + try: + entries = path.split(os.sep) + i = entries.index(entry) + if '' in entries: + i -= 1 + return paths[:i], paths[i], paths[i + 1:] + except ValueError: + pass + + return paths, '', [] + + +def prefixes(path): + """ + Returns a list containing the path and its ancestors, top-to-bottom. + + The list for an absolute path will not include an ``os.sep`` entry. + For example, assuming ``os.sep`` is ``/``, given path ``/ab/cd/efg`` + the resulting paths will be, in order: ``/ab``, ``/ab/cd``, and + ``/ab/cd/efg`` + + The list for a relative path starting ``./`` will not include ``.``. + For example, path ``./hi/jkl/mn`` results in a list with the following + paths, in order: ``./hi``, ``./hi/jkl``, and ``./hi/jkl/mn``. + + Parameters: + path (str): the string used to derive ancestor paths + + Returns: + A list containing ancestor paths in order and ending with the path + """ + if not path: + return [] + + parts = path.strip(os.sep).split(os.sep) + if path.startswith(os.sep): + parts.insert(0, os.sep) + paths = [os.path.join(*parts[:i + 1]) for i in range(len(parts))] + + try: + paths.remove(os.sep) + except ValueError: + pass + + try: + paths.remove('.') + except ValueError: + pass + + return paths diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index b6a2d2de8d5..dbe6e38fa69 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -56,7 +56,7 @@ from llnl.util.tty.color import colorize from spack.filesystem_view import YamlFilesystemView from spack.util.executable import which -from spack.stage import Stage, ResourceStage, StageComposite +from spack.stage import stage_prefix, Stage, ResourceStage, StageComposite from spack.util.environment import dump_environment from spack.util.package_hash import package_hash from spack.version import Version @@ -753,7 +753,8 @@ def _make_root_stage(self, fetcher): mp = spack.mirror.mirror_archive_path(self.spec, fetcher) # Construct a path where the stage should build.. s = self.spec - stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash()) + stage_name = "{0}{1}-{2}-{3}".format(stage_prefix, s.name, s.version, + s.dag_hash()) def download_search(): dynamic_fetcher = fs.from_list_url(self) diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index 537a97b10e9..6b27d37adf9 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -4,7 +4,6 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os -import re import stat import sys import errno @@ -17,7 +16,7 @@ import llnl.util.tty as tty from llnl.util.filesystem import mkdirp, can_access, install, install_tree -from llnl.util.filesystem import remove_linked_tree +from llnl.util.filesystem import partition_path, remove_linked_tree import spack.paths import spack.caches @@ -34,40 +33,63 @@ _source_path_subdir = 'spack-src' # The temporary stage name prefix. -_stage_prefix = 'spack-stage-' +stage_prefix = 'spack-stage-' def _create_stage_root(path): """Create the stage root directory and ensure appropriate access perms.""" assert path.startswith(os.path.sep) and len(path.strip()) > 1 - curr_dir = os.path.sep - parts = path.strip(os.path.sep).split(os.path.sep) - for i, part in enumerate(parts): - curr_dir = os.path.join(curr_dir, part) - if not os.path.exists(curr_dir): - rest = os.path.join(os.path.sep, *parts[i + 1:]) - user_parts = rest.partition(os.path.sep + getpass.getuser()) - if len(user_parts[0]) > 0: - # Ensure access controls of subdirs created above `$user` - # inherit from the parent and share the group. - stats = os.stat(os.path.dirname(curr_dir)) - curr_dir = ''.join([curr_dir, user_parts[0]]) - mkdirp(curr_dir, group=stats.st_gid, mode=stats.st_mode) + err_msg = 'Cannot create stage root {0}: Access to {1} is denied' - user_subdirs = ''.join(user_parts[1:]) - if len(user_subdirs) > 0: - # Ensure access controls of subdirs from `$user` on down are - # restricted to the user. - curr_dir = ''.join([curr_dir, user_subdirs]) - mkdirp(curr_dir, mode=stat.S_IRWXU) + user_uid = os.getuid() - assert os.getuid() == os.stat(curr_dir).st_uid - break + # Obtain lists of ancestor and descendant paths of the $user node, if any. + group_paths, user_node, user_paths = partition_path(path, + getpass.getuser()) - if not can_access(path): - raise OSError(errno.EACCES, - 'Cannot access %s: Permission denied' % curr_dir) + for p in group_paths: + if not os.path.exists(p): + # Ensure access controls of subdirs created above `$user` inherit + # from the parent and share the group. + par_stat = os.stat(os.path.dirname(p)) + mkdirp(p, group=par_stat.st_gid, mode=par_stat.st_mode) + + p_stat = os.stat(p) + if par_stat.st_gid != p_stat.st_gid: + tty.warn("Expected {0} to have group {1}, but it is {2}" + .format(p, par_stat.st_gid, p_stat.st_gid)) + + if par_stat.st_mode & p_stat.st_mode != par_stat.st_mode: + tty.warn("Expected {0} to support mode {1}, but it is {2}" + .format(p, par_stat.st_mode, p_stat.st_mode)) + + if not can_access(p): + raise OSError(errno.EACCES, err_msg.format(path, p)) + + # Add the path ending with the $user node to the user paths to ensure paths + # from $user (on down) meet the ownership and permission requirements. + if user_node: + user_paths.insert(0, user_node) + + for p in user_paths: + # Ensure access controls of subdirs from `$user` on down are + # restricted to the user. + if not os.path.exists(p): + mkdirp(p, mode=stat.S_IRWXU) + + p_stat = os.stat(p) + if p_stat.st_mode & stat.S_IRWXU != stat.S_IRWXU: + tty.error("Expected {0} to support mode {1}, but it is {2}" + .format(p, stat.S_IRWXU, p_stat.st_mode)) + + raise OSError(errno.EACCES, err_msg.format(path, p)) + else: + p_stat = os.stat(p) + + if user_uid != p_stat.st_uid: + tty.warn("Expected user {0} to own {1}, but it is owned by {2}" + .format(user_uid, p, p_stat.st_uid)) def _first_accessible_path(paths): @@ -106,7 +128,7 @@ def _resolve_paths(candidates): # Remove the extra `$user` node from a `$tempdir/$user` entry for # hosts that automatically append `$user` to `$tempdir`. if path.startswith(os.path.join('$tempdir', '$user')) and tmp_has_usr: - path = os.path.join('$tempdir', path[15:]) + path = path.replace("/$user", "", 1) # Ensure the path is unique per user. can_path = sup.canonicalize_path(path) @@ -250,7 +272,7 @@ def __init__( # TODO: temporary stage area in _stage_root. self.name = name if name is None: - self.name = _stage_prefix + next(tempfile._get_candidate_names()) + self.name = stage_prefix + next(tempfile._get_candidate_names()) self.mirror_path = mirror_path # Use the provided path or construct an optionally named stage path. @@ -680,11 +702,8 @@ def purge(): """Remove all build directories in the top-level stage path.""" root = get_stage_root() if os.path.isdir(root): - # TODO: Figure out a "standard" way to identify the hash length - # TODO: Should this support alternate base represenations? - dir_expr = re.compile(r'.*-[0-9a-f]{32}$') for stage_dir in os.listdir(root): - if re.match(dir_expr, stage_dir) or stage_dir == '.lock': + if stage_dir.startswith(stage_prefix) or stage_dir == '.lock': stage_path = os.path.join(root, stage_dir) remove_linked_tree(stage_path) diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py index b7f3e5e325d..232da811a36 100644 --- a/lib/spack/spack/test/cmd/env.py +++ b/lib/spack/spack/test/cmd/env.py @@ -17,6 +17,7 @@ from spack.cmd.env import _env_create from spack.spec import Spec from spack.main import SpackCommand +from spack.stage import stage_prefix from spack.spec_list import SpecListError from spack.test.conftest import MockPackage, MockPackageMultiRepo @@ -576,7 +577,8 @@ def test_stage(mock_stage, mock_fetch, install_mockery): def check_stage(spec): spec = Spec(spec).concretized() for dep in spec.traverse(): - stage_name = "%s-%s-%s" % (dep.name, dep.version, dep.dag_hash()) + stage_name = "{0}{1}-{2}-{3}".format(stage_prefix, dep.name, + dep.version, dep.dag_hash()) assert os.path.isdir(os.path.join(root, stage_name)) check_stage('mpileaks') diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py index 7795303edae..969e2471e41 100644 --- a/lib/spack/spack/test/conftest.py +++ b/lib/spack/spack/test/conftest.py @@ -5,6 +5,7 @@ import collections import copy +import errno import inspect import itertools import os @@ -41,6 +42,14 @@ from spack.version import Version +@pytest.fixture +def no_path_access(monkeypatch): + def _can_access(path, perms): + return False + + monkeypatch.setattr(os, 'access', _can_access) + + # # Disable any activate Spack environment BEFORE all tests # @@ -184,23 +193,29 @@ def working_env(): @pytest.fixture(scope='function', autouse=True) def check_for_leftover_stage_files(request, mock_stage, ignore_stage_files): - """Ensure that each test leaves a clean stage when done. + """ + Ensure that each (mock_stage) test leaves a clean stage when done. - This can be disabled for tests that are expected to dirty the stage - by adding:: + Tests that are expected to dirty the stage can disable the check by + adding:: @pytest.mark.disable_clean_stage_check - to tests that need it. + and the associated stage files will be removed. """ stage_path = mock_stage yield files_in_stage = set() - if os.path.exists(stage_path): + try: stage_files = os.listdir(stage_path) files_in_stage = set(stage_files) - ignore_stage_files + except OSError as err: + if err.errno == errno.ENOENT: + pass + else: + raise if 'disable_clean_stage_check' in request.keywords: # clean up after tests that are expected to be dirty diff --git a/lib/spack/spack/test/llnl/util/filesystem.py b/lib/spack/spack/test/llnl/util/filesystem.py index cdc50f9df25..f6d8845800d 100644 --- a/lib/spack/spack/test/llnl/util/filesystem.py +++ b/lib/spack/spack/test/llnl/util/filesystem.py @@ -312,6 +312,30 @@ def test_headers_directory_setter(): assert hl.directories == [] +@pytest.mark.parametrize('path,entry,expected', [ + ('/tmp/user/root', None, + (['/tmp', '/tmp/user', '/tmp/user/root'], '', [])), + ('/tmp/user/root', 'tmp', ([], '/tmp', ['/tmp/user', '/tmp/user/root'])), + ('/tmp/user/root', 'user', (['/tmp'], '/tmp/user', ['/tmp/user/root'])), + ('/tmp/user/root', 'root', (['/tmp', '/tmp/user'], '/tmp/user/root', [])), + ('relative/path', None, (['relative', 'relative/path'], '', [])), + ('relative/path', 'relative', ([], 'relative', ['relative/path'])), + ('relative/path', 'path', (['relative'], 'relative/path', [])) +]) +def test_partition_path(path, entry, expected): + assert fs.partition_path(path, entry) == expected + + +@pytest.mark.parametrize('path,expected', [ + ('', []), + ('/tmp/user/dir', ['/tmp', '/tmp/user', '/tmp/user/dir']), + ('./some/sub/dir', ['./some', './some/sub', './some/sub/dir']), + ('another/sub/dir', ['another', 'another/sub', 'another/sub/dir']) +]) +def test_prefixes(path, expected): + assert fs.prefixes(path) == expected + + @pytest.mark.regression('7358') @pytest.mark.parametrize('regex,replacement,filename,keyword_args', [ (r"\", "", 'x86_cpuid_info.c', {}), diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py index cb3204bc5ff..66b358435fe 100644 --- a/lib/spack/spack/test/stage.py +++ b/lib/spack/spack/test/stage.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) """Test that the Stage class works correctly.""" +import errno import os import collections import shutil @@ -13,7 +14,7 @@ import pytest -from llnl.util.filesystem import mkdirp, touch, working_dir +from llnl.util.filesystem import mkdirp, partition_path, touch, working_dir import spack.paths import spack.stage @@ -354,23 +355,34 @@ def check_stage_dir_perms(prefix, path): # Ensure the path's subdirectories -- to `$user` -- have their parent's # perms while those from `$user` on are owned and restricted to the # user. - status = os.stat(prefix) - gid = status.st_gid - uid = os.getuid() + assert path.startswith(prefix) + user = getpass.getuser() - parts = path[len(prefix) + 1:].split(os.path.sep) - have_user = False - for part in parts: - if part == user: - have_user = True - prefix = os.path.join(prefix, part) - prefix_status = os.stat(prefix) - if not have_user: - assert gid == prefix_status.st_gid - assert status.st_mode == prefix_status.st_mode - else: - assert uid == status.st_uid - assert status.st_mode & stat.S_IRWXU == stat.S_IRWXU + prefix_status = os.stat(prefix) + uid = os.getuid() + + # Obtain lists of ancestor and descendant paths of the $user node, if any. + # + # Skip processing prefix ancestors since no guarantee they will be in the + # required group (e.g. $TEMPDIR on HPC machines). + skip = prefix if prefix.endswith(os.sep) else prefix + os.sep + group_paths, user_node, user_paths = partition_path(path.replace(skip, ""), + user) + + for p in group_paths: + p_status = os.stat(os.path.join(prefix, p)) + assert p_status.st_gid == prefix_status.st_gid + assert p_status.st_mode == prefix_status.st_mode + + # Add the path ending with the $user node to the user paths to ensure paths + # from $user (on down) meet the ownership and permission requirements. + if user_node: + user_paths.insert(0, user_node) + + for p in user_paths: + p_status = os.stat(os.path.join(prefix, p)) + assert uid == p_status.st_uid + assert p_status.st_mode & stat.S_IRWXU == stat.S_IRWXU @pytest.mark.usefixtures('mock_packages') @@ -643,7 +655,7 @@ def test_source_path_available(self, mock_stage_archive): def test_first_accessible_path(self, tmpdir): """Test _first_accessible_path names.""" - spack_dir = tmpdir.join('spack-test-fap') + spack_dir = tmpdir.join('paths') name = str(spack_dir) files = [os.path.join(os.path.sep, 'no', 'such', 'path'), name] @@ -671,9 +683,75 @@ def test_first_accessible_path(self, tmpdir): # Cleanup shutil.rmtree(str(name)) + def test_create_stage_root(self, tmpdir, no_path_access): + """Test _create_stage_root permissions.""" + test_dir = tmpdir.join('path') + test_path = str(test_dir) + + try: + if getpass.getuser() in str(test_path).split(os.sep): + # Simply ensure directory created if tmpdir includes user + spack.stage._create_stage_root(test_path) + assert os.path.exists(test_path) + + p_stat = os.stat(test_path) + assert p_stat.st_mode & stat.S_IRWXU == stat.S_IRWXU + else: + # Ensure an OS Error is raised on created, non-user directory + with pytest.raises(OSError) as exc_info: + spack.stage._create_stage_root(test_path) + + assert exc_info.value.errno == errno.EACCES + finally: + try: + shutil.rmtree(test_path) + except OSError: + pass + + @pytest.mark.nomockstage + def test_create_stage_root_bad_uid(self, tmpdir, monkeypatch): + """ + Test the code path that uses an existing user path -- whether `$user` + in `$tempdir` or not -- and triggers the generation of the UID + mismatch warning. + + This situation can happen with some `config:build_stage` settings + for teams using a common service account for installing software. + """ + orig_stat = os.stat + + class MinStat: + st_mode = -1 + st_uid = -1 + + def _stat(path): + p_stat = orig_stat(path) + + fake_stat = MinStat() + fake_stat.st_mode = p_stat.st_mode + return fake_stat + + user_dir = tmpdir.join(getpass.getuser()) + user_dir.ensure(dir=True) + user_path = str(user_dir) + + # TODO: If we could guarantee access to the monkeypatch context + # function (i.e., 3.6.0 on), the call and assertion could be moved + # to a with block, such as: + # + # with monkeypatch.context() as m: + # m.setattr(os, 'stat', _stat) + # spack.stage._create_stage_root(user_path) + # assert os.stat(user_path).st_uid != os.getuid() + monkeypatch.setattr(os, 'stat', _stat) + spack.stage._create_stage_root(user_path) + + # The following check depends on the patched os.stat as a poor + # substitute for confirming the generated warnings. + assert os.stat(user_path).st_uid != os.getuid() + def test_resolve_paths(self): """Test _resolve_paths.""" - assert spack.stage._resolve_paths([]) == [] # resolved path without user appends user @@ -686,19 +764,24 @@ def test_resolve_paths(self): paths = [os.path.join(os.path.sep, 'spack-{0}'.format(user), 'stage')] assert spack.stage._resolve_paths(paths) == paths - # resolve paths where user - tmp = '$tempdir' - can_tmpdir = canonicalize_path(tmp) - temp_has_user = user in can_tmpdir.split(os.sep) - paths = [os.path.join(tmp, 'stage'), os.path.join(tmp, '$user')] - can_paths = [canonicalize_path(p) for p in paths] + tempdir = '$tempdir' + can_tempdir = canonicalize_path(tempdir) + user = getpass.getuser() + temp_has_user = user in can_tempdir.split(os.sep) + paths = [os.path.join(tempdir, 'stage'), + os.path.join(tempdir, '$user'), + os.path.join(tempdir, '$user', '$user'), + os.path.join(tempdir, '$user', 'stage', '$user')] + res_paths = [canonicalize_path(p) for p in paths] if temp_has_user: - can_paths[1] = can_tmpdir + res_paths[1] = can_tempdir + res_paths[2] = os.path.join(can_tempdir, user) + res_paths[3] = os.path.join(can_tempdir, 'stage', user) else: - can_paths[0] = os.path.join(can_paths[0], user) + res_paths[0] = os.path.join(res_paths[0], user) - assert spack.stage._resolve_paths(paths) == can_paths + assert spack.stage._resolve_paths(paths) == res_paths def test_get_stage_root_bad_path(self, clear_stage_root): """Ensure an invalid stage path root raises a StageError.""" @@ -711,9 +794,9 @@ def test_get_stage_root_bad_path(self, clear_stage_root): assert spack.stage._stage_root is None @pytest.mark.parametrize( - 'path,purged', [('stage-1234567890abcdef1234567890abcdef', True), - ('stage-abcdef12345678900987654321fedcba', True), - ('stage-a1b2c3', False)]) + 'path,purged', [('spack-stage-1234567890abcdef1234567890abcdef', True), + ('spack-stage-anything-goes-here', True), + ('stage-spack', False)]) def test_stage_purge(self, tmpdir, clear_stage_root, path, purged): """Test purging of stage directories.""" stage_dir = tmpdir.join('stage') @@ -737,7 +820,6 @@ def test_stage_purge(self, tmpdir, clear_stage_root, path, purged): def test_get_stage_root_in_spack(self, clear_stage_root): """Ensure an instance path is an accessible build stage path.""" - base = canonicalize_path(os.path.join('$spack', '.spack-test-stage')) mkdirp(base) test_path = tempfile.mkdtemp(dir=base) From ffe87ed49f928035bc0bafa5f2b834a38e694b51 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Thu, 17 Oct 2019 00:15:24 +0200 Subject: [PATCH 269/499] filter_file: fix multiple invocations on the same file (#13234) Since the backup file is only created on the first invocation, it will contain the original file without any modifications. Further invocations will then read the backup file, effectively reverting prior invocations. This can be reproduced easily by trying to install likwid, which will try to install into /usr/local. Work around this by creating a temporary file to read from. --- lib/spack/llnl/util/filesystem.py | 11 +++++++-- lib/spack/spack/test/llnl/util/filesystem.py | 24 ++++++++++++++++++++ 2 files changed, 33 insertions(+), 2 deletions(-) diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 0af9c915b6a..0095e3fd215 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -153,6 +153,7 @@ def groupid_to_group(x): tty.debug(msg.format(filename, regex)) backup_filename = filename + "~" + tmp_filename = filename + ".spack~" if ignore_absent and not os.path.exists(filename): msg = 'FILTER FILE: file "{0}" not found. Skipping to next file.' @@ -164,6 +165,10 @@ def groupid_to_group(x): if not os.path.exists(backup_filename): shutil.copy(filename, backup_filename) + # Create a temporary file to read from. We cannot use backup_filename + # in case filter_file is invoked multiple times on the same file. + shutil.copy(filename, tmp_filename) + try: extra_kwargs = {} if sys.version_info > (3, 0): @@ -171,7 +176,7 @@ def groupid_to_group(x): # Open as a text file and filter until the end of the file is # reached or we found a marker in the line if it was specified - with open(backup_filename, mode='r', **extra_kwargs) as input_file: + with open(tmp_filename, mode='r', **extra_kwargs) as input_file: with open(filename, mode='w', **extra_kwargs) as output_file: # Using iter and readline is a workaround needed not to # disable input_file.tell(), which will happen if we call @@ -190,17 +195,19 @@ def groupid_to_group(x): # If we stopped filtering at some point, reopen the file in # binary mode and copy verbatim the remaining part if current_position and stop_at: - with open(backup_filename, mode='rb') as input_file: + with open(tmp_filename, mode='rb') as input_file: input_file.seek(current_position) with open(filename, mode='ab') as output_file: output_file.writelines(input_file.readlines()) except BaseException: + os.remove(tmp_filename) # clean up the original file on failure. shutil.move(backup_filename, filename) raise finally: + os.remove(tmp_filename) if not backup and os.path.exists(backup_filename): os.remove(backup_filename) diff --git a/lib/spack/spack/test/llnl/util/filesystem.py b/lib/spack/spack/test/llnl/util/filesystem.py index f6d8845800d..6c26c5fb43b 100644 --- a/lib/spack/spack/test/llnl/util/filesystem.py +++ b/lib/spack/spack/test/llnl/util/filesystem.py @@ -362,3 +362,27 @@ def test_filter_files_with_different_encodings( with open(target_file, mode='r', **extra_kwargs) as f: assert replacement in f.read() + + +def test_filter_files_multiple(tmpdir): + # All files given as input to this test must satisfy the pre-requisite + # that the 'replacement' string is not present in the file initially and + # that there's at least one match for the regex + original_file = os.path.join( + spack.paths.test_path, 'data', 'filter_file', 'x86_cpuid_info.c' + ) + target_file = os.path.join(str(tmpdir), 'x86_cpuid_info.c') + shutil.copy(original_file, target_file) + # This should not raise exceptions + fs.filter_file(r'\', '', target_file) + fs.filter_file(r'\', '', target_file) + fs.filter_file(r'\', '', target_file) + # Check the strings have been replaced + extra_kwargs = {} + if sys.version_info > (3, 0): + extra_kwargs = {'errors': 'surrogateescape'} + + with open(target_file, mode='r', **extra_kwargs) as f: + assert '' not in f.read() + assert '' not in f.read() + assert '' not in f.read() From e65b7f8ebfe62feb95205e5fc4da559e4eabe88d Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 16 Oct 2019 17:07:18 -0700 Subject: [PATCH 270/499] importing: make importlib_importer recognize .pyc cache (#13239) Our importer was always parsing from source (which is considerably slower) because the source size recorded in the .pyc file differed from the size of the input file. Override path_stats in the prepending importer to fool it into thinking that the source size is the size *with* the prepended code. --- lib/spack/spack/util/imp/importlib_importer.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/lib/spack/spack/util/imp/importlib_importer.py b/lib/spack/spack/util/imp/importlib_importer.py index 9eec5695748..33c50cb601a 100644 --- a/lib/spack/spack/util/imp/importlib_importer.py +++ b/lib/spack/spack/util/imp/importlib_importer.py @@ -15,6 +15,12 @@ def __init__(self, full_name, path, prepend=None): super(PrependFileLoader, self).__init__(full_name, path) self.prepend = prepend + def path_stats(self, path): + stats = super(PrependFileLoader, self).path_stats(path) + if self.prepend: + stats["size"] += len(self.prepend) + 1 + return stats + def get_data(self, path): data = super(PrependFileLoader, self).get_data(path) if path != self.path or self.prepend is None: From 6cd997e74379a2dd8719748095bd13a26dfbf74f Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 16 Oct 2019 18:46:26 -0700 Subject: [PATCH 271/499] eospac: avoid conflict with linux's getopt (#13241) * eospac: avoid conflict with linux's getopt * Update package.py --- var/spack/repos/builtin/packages/eospac/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/eospac/package.py b/var/spack/repos/builtin/packages/eospac/package.py index 4399ef60398..1ee01f6f218 100644 --- a/var/spack/repos/builtin/packages/eospac/package.py +++ b/var/spack/repos/builtin/packages/eospac/package.py @@ -43,3 +43,8 @@ def install(self, spec, prefix): 'INSTALLED_INCLUDE_DIR={0}'.format(prefix.include), 'INSTALLED_EXAMPLE_DIR={0}'.format(prefix.example), 'INSTALLED_BIN_DIR={0}'.format(prefix.bin)) + + # fix conflict with linux's getopt for 6.4.0beta.2 + if spec.satisfies('@6.4.0beta.2'): + with working_dir(prefix.bin): + move('getopt', 'driver_getopt') From 93c34039e488937e6803d20316c1d3607869067e Mon Sep 17 00:00:00 2001 From: wspear Date: Wed, 16 Oct 2019 23:46:34 -0700 Subject: [PATCH 272/499] python-editor: added new package at v1.0.4 (#13126) --- .../packages/py-python-editor/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-python-editor/package.py diff --git a/var/spack/repos/builtin/packages/py-python-editor/package.py b/var/spack/repos/builtin/packages/py-python-editor/package.py new file mode 100644 index 00000000000..0a4fada91da --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-editor/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonEditor(PythonPackage): + """python-editor is a library that provides the editor module for + programmatically interfacing with your system's EDITOR variable.""" + + homepage = "https://pypi.org/project/python-editor/" + url = "https://pypi.io/packages/source/p/python-editor/python-editor-1.0.4.tar.gz" + + version('1.0.4', sha256='51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b') + + depends_on('python@2.7:2.7.999,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') From cf9de058aaa6bfde635868422b504e4fb1413359 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Thu, 17 Oct 2019 06:40:23 -0700 Subject: [PATCH 273/499] multimethods: avoid calling caller_locals() in Python 3 (#13238) Python 3 metaclasses have a `__prepare__` method that lets us save the class's dictionary before it is constructed. In Python 2 we had to walk up the stack using our `caller_locals()` method to get at this. Using `__prepare__` is much faster as it doesn't require us to use `inspect`. This makes multimethods use the faster `__prepare__` method in Python3, while still using `caller_locals()` in Python 2. We try to reduce the use of caller locals using caching to speed up Python 2 a little bit. --- lib/spack/spack/multimethod.py | 39 +++++++++++++++++++++++++++------- lib/spack/spack/package.py | 4 +++- 2 files changed, 34 insertions(+), 9 deletions(-) diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py index 085f2431748..e0854a01c9c 100644 --- a/lib/spack/spack/multimethod.py +++ b/lib/spack/spack/multimethod.py @@ -24,6 +24,7 @@ depending on the scenario, regular old conditionals might be clearer, so package authors should use their judgement. """ + import functools import inspect @@ -34,6 +35,24 @@ from spack.spec import Spec +class MultiMethodMeta(type): + """This allows us to track the class's dict during instantiation.""" + + #: saved dictionary of attrs on the class being constructed + _locals = None + + @classmethod + def __prepare__(cls, name, bases, **kwargs): + """Save the dictionary that will be used for the class namespace.""" + MultiMethodMeta._locals = dict() + return MultiMethodMeta._locals + + def __init__(cls, name, bases, attr_dict): + """Clear out the cached locals dict once the class is built.""" + MultiMethodMeta._locals = None + super(MultiMethodMeta, cls).__init__(name, bases, attr_dict) + + class SpecMultiMethod(object): """This implements a multi-method for Spack specs. Packages are instantiated with a particular spec, and you may want to @@ -149,14 +168,15 @@ class SomePackage(Package): def install(self, prefix): # Do default install - @when('arch=chaos_5_x86_64_ib') + @when('target=x86_64:') def install(self, prefix): # This will be executed instead of the default install if - # the package's platform() is chaos_5_x86_64_ib. + # the package's target is in the x86_64 family. - @when('arch=bgqos_0") + @when('target=ppc64:') def install(self, prefix): - # This will be executed if the package's sys_type is bgqos_0 + # This will be executed if the package's target is in + # the ppc64 family This allows each package to have a default version of install() AND specialized versions for particular platforms. The version that is @@ -202,11 +222,14 @@ def __init__(self, condition): self.spec = Spec(condition) def __call__(self, method): - # Get the first definition of the method in the calling scope - original_method = caller_locals().get(method.__name__) + # In Python 2, Get the first definition of the method in the + # calling scope by looking at the caller's locals. In Python 3, + # we handle this using MultiMethodMeta.__prepare__. + if MultiMethodMeta._locals is None: + MultiMethodMeta._locals = caller_locals() - # Create a multimethod out of the original method if it - # isn't one already. + # Create a multimethod with this name if there is not one already + original_method = MultiMethodMeta._locals.get(method.__name__) if not type(original_method) == SpecMultiMethod: original_method = SpecMultiMethod(original_method) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index dbe6e38fa69..ecff265508f 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -42,6 +42,7 @@ import spack.hooks import spack.mirror import spack.mixins +import spack.multimethod import spack.repo import spack.url import spack.util.web @@ -138,7 +139,8 @@ def copy(self): class PackageMeta( spack.directives.DirectiveMeta, - spack.mixins.PackageMixinsMeta + spack.mixins.PackageMixinsMeta, + spack.multimethod.MultiMethodMeta ): """ Package metaclass for supporting directives (e.g., depends_on) and phases From 9ddc98e46a73d53e9937cad1a430a34522d241de Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 17 Oct 2019 19:17:21 +0200 Subject: [PATCH 274/499] Separate setting build environment and run environment in packages (#11115) * Methods setting the environment now do it separately for build and run Before this commit the `*_environment` methods were setting modifications to both the build-time and run-time environment simultaneously. This might cause issues as the two environments inherently rely on different preconditions: 1. The build-time environment is set before building a package, thus the package prefix doesn't exist and can't be inspected 2. The run-time environment instead is set assuming the target package has been already installed Here we split each of these functions into two: one setting the build-time environment, one the run-time. We also adopt a fallback strategy that inspects for old methods and executes them as before, but prints a deprecation warning to tty. This permits to port packages to use the new methods in a distributed way, rather than having to modify all the packages at once. * Added a test that fails if any package uses the old API Marked the test xfail for now as we have a lot of packages in that state. * Added a test to check that a package modified by a PR is up to date This test can be used any time we deprecate a method call to ensure that during the first modification of the package we update also the deprecated calls. * Updated documentation --- lib/spack/docs/module_file_support.rst | 14 +- lib/spack/docs/packaging_guide.rst | 73 ++++----- .../docs/tutorial_advanced_packaging.rst | 79 +++++----- lib/spack/spack/build_environment.py | 64 +++++--- lib/spack/spack/cmd/flake8.py | 9 +- lib/spack/spack/modules/common.py | 17 +-- lib/spack/spack/package.py | 143 +++++++++++------- lib/spack/spack/test/package_sanity.py | 50 ++++++ .../builtin/packages/docbook-xml/package.py | 4 +- .../repos/builtin/packages/elpa/package.py | 14 +- .../repos/builtin/packages/mpich/package.py | 35 +++-- .../repos/builtin/packages/python/package.py | 15 +- .../repos/builtin/packages/qt/package.py | 12 +- var/spack/repos/builtin/packages/r/package.py | 27 ++-- 14 files changed, 337 insertions(+), 219 deletions(-) diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst index 7ce2398af2c..1b5de3a0e81 100644 --- a/lib/spack/docs/module_file_support.rst +++ b/lib/spack/docs/module_file_support.rst @@ -303,8 +303,7 @@ content of the module files generated by Spack. The first one: .. code-block:: python - def setup_environment(self, spack_env, run_env): - """Set up the compile and runtime environments for a package.""" + def setup_run_environment(self, env): pass can alter the content of the module file associated with the same package where it is overridden. @@ -312,16 +311,15 @@ The second method: .. code-block:: python - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - """Set up the environment of packages that depend on this one""" + def setup_dependent_run_environment(self, env, dependent_spec): pass can instead inject run-time environment modifications in the module files of packages that depend on it. In both cases you need to fill ``run_env`` with the desired list of environment modifications. -.. note:: - The ``r`` package and callback APIs +.. admonition:: The ``r`` package and callback APIs + An example in which it is crucial to override both methods is given by the ``r`` package. This package installs libraries and headers in non-standard locations and it is possible to prepend the appropriate directory @@ -336,14 +334,14 @@ list of environment modifications. with the following snippet: .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py - :pyobject: R.setup_environment + :pyobject: R.setup_run_environment The ``r`` package also knows which environment variable should be modified to make language extensions provided by other packages available, and modifies it appropriately in the override of the second method: .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py - :pyobject: R.setup_dependent_environment + :pyobject: R.setup_dependent_run_environment .. _modules-yaml: diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 5adb9962325..767a744baa9 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -2032,55 +2032,58 @@ appear in the package file (or in this case, in the list). .. _setup-dependent-environment: -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -``setup_dependent_environment()`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Influence how dependents are built or run +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Spack provides a mechanism for dependencies to provide variables that -can be used in their dependents' build. Any package can declare a -``setup_dependent_environment()`` function, and this function will be -called before the ``install()`` method of any dependent packages. -This allows dependencies to set up environment variables and other -properties to be used by dependents. - -The function declaration should look like this: +Spack provides a mechanism for dependencies to influence the +environment of their dependents by overriding the +:meth:`setup_dependent_run_environment ` +or the +:meth:`setup_dependent_build_environment ` +methods. +The Qt package, for instance, uses this call: .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/qt/package.py - :pyobject: Qt.setup_dependent_environment + :pyobject: Qt.setup_dependent_build_environment :linenos: -Here, the Qt package sets the ``QTDIR`` environment variable so that -packages that depend on a particular Qt installation will find it. - -The arguments to this function are: - -* **spack_env**: List of environment modifications to be applied when - the dependent package is built within Spack. -* **run_env**: List of environment modifications to be applied when - the dependent package is run outside of Spack. These are added to the - resulting module file. -* **dependent_spec**: The spec of the dependent package about to be - built. This allows the extendee (self) to query the dependent's state. - Note that *this* package's spec is available as ``self.spec``. - -A good example of using these is in the Python package: +to set the ``QTDIR`` environment variable so that packages +that depend on a particular Qt installation will find it. +Another good example of how a dependency can influence +the build environment of dependents is the Python package: .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py - :pyobject: Python.setup_dependent_environment + :pyobject: Python.setup_dependent_build_environment :linenos: -The first thing that happens here is that the ``python`` command is -inserted into module scope of the dependent. This allows most python -packages to have a very simple install method, like this: +In the method above it is ensured that any package that depends on Python +will have the ``PYTHONPATH``, ``PYTHONHOME`` and ``PATH`` environment +variables set appropriately before starting the installation. To make things +even simpler the ``python setup.py`` command is also inserted into the module +scope of dependents by overriding a third method called +:meth:`setup_dependent_package ` +: + +.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py + :pyobject: Python.setup_dependent_package + :linenos: + +This allows most python packages to have a very simple install procedure, +like the following: .. code-block:: python def install(self, spec, prefix): - python('setup.py', 'install', '--prefix={0}'.format(prefix)) + setup_py('install', '--prefix={0}'.format(prefix)) + +Finally the Python package takes also care of the modifications to ``PYTHONPATH`` +to allow dependencies to run correctly: + +.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py + :pyobject: Python.setup_dependent_run_environment + :linenos: -Python's ``setup_dependent_environment`` method also sets up some -other variables, creates a directory, and sets up the ``PYTHONPATH`` -so that dependent packages can find their dependencies at build time. .. _packaging_conflicts: diff --git a/lib/spack/docs/tutorial_advanced_packaging.rst b/lib/spack/docs/tutorial_advanced_packaging.rst index bd90f724a74..876a6e8f70a 100644 --- a/lib/spack/docs/tutorial_advanced_packaging.rst +++ b/lib/spack/docs/tutorial_advanced_packaging.rst @@ -90,21 +90,23 @@ like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH`` so it is available at build time; this is required because the default setup that spack does is not sufficient for python to import modules. -To provide environment setup for a dependent, a package can implement the -:py:func:`setup_dependent_environment ` -function. This function takes as a parameter a :py:class:`EnvironmentModifications ` +Any package can override the +:py:func:`setup_dependent_build_environment ` +method to setup the build environment for a dependent. +This method takes as an argument a :py:class:`EnvironmentModifications ` object which includes convenience methods to update the environment. For example, an MPI implementation can set ``MPICC`` for packages that depend on it: .. code-block:: python - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) In this case packages that depend on ``mpi`` will have ``MPICC`` defined in -their environment when they build. This section is focused on modifying the -build-time environment represented by ``spack_env``, but it's worth noting that -modifications to ``run_env`` are included in Spack's automatically-generated +their environment when they build. This section is focused on setting up the +build-time environment but it's worth noting that a similar method called +:py:func:`setup_dependent_run_environment ` +can be used to code modifications that will be included in Spack's automatically-generated module files. We can practice by editing the ``mpich`` package to set the ``MPICC`` @@ -118,17 +120,17 @@ Once you're finished, the method should look like this: .. code-block:: python - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) - spack_env.set('MPICH_CC', spack_cc) - spack_env.set('MPICH_CXX', spack_cxx) - spack_env.set('MPICH_F77', spack_f77) - spack_env.set('MPICH_F90', spack_fc) - spack_env.set('MPICH_FC', spack_fc) + env.set('MPICH_CC', spack_cc) + env.set('MPICH_CXX', spack_cxx) + env.set('MPICH_F77', spack_f77) + env.set('MPICH_F90', spack_fc) + env.set('MPICH_FC', spack_fc) At this point we can, for instance, install ``netlib-scalapack`` with ``mpich``: @@ -155,25 +157,32 @@ set to the correct value. Set environment variables in your own package ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Packages can modify their own build-time environment by implementing the -:py:func:`setup_environment ` function. -For ``qt`` this looks like: +Packages can override the +:py:func:`setup_build_environment ` +or the +:py:func:`setup_run_environment ` +methods to modify their own build-time or run-time environment respectively. +An example of a package that overrides both methods is ``qt``: .. code-block:: python - def setup_environment(self, spack_env, run_env): - spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) - run_env.set('QTDIR', self.prefix) + def setup_build_environment(self, env): + env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) -When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment. + def setup_run_environment(self, env): + env.set('QTDIR', self.prefix) -To contrast with ``qt``'s :py:func:`setup_dependent_environment ` +When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment. Likewise, when a +module file is created for ``qt`` it will contain commands to define ``QTDIR`` appropriately. + +To contrast with ``qt``'s +:py:func:`setup_dependent_build_environment ` function: .. code-block:: python - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('QTDIR', self.prefix) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('QTDIR', self.prefix) Let's see how it works by completing the ``elpa`` package: @@ -185,16 +194,16 @@ In the end your method should look like: .. code-block:: python - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('FC', spec['mpi'].mpifc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) + env.set('CC', spec['mpi'].mpicc) + env.set('FC', spec['mpi'].mpifc) + env.set('CXX', spec['mpi'].mpicxx) + env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) - spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) - spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags) + env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) + env.append_flags('LIBS', spec['lapack'].libs.link_flags) At this point it's possible to proceed with the installation of ``elpa ^mpich`` diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 3702a989c35..db99a7a4c10 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -673,35 +673,26 @@ def load_external_modules(pkg): def setup_package(pkg, dirty): """Execute all environment setup routines.""" - spack_env = EnvironmentModifications() - run_env = EnvironmentModifications() + build_env = EnvironmentModifications() if not dirty: clean_environment() - set_compiler_environment_variables(pkg, spack_env) - set_build_environment_variables(pkg, spack_env, dirty) - pkg.architecture.platform.setup_platform_environment(pkg, spack_env) + set_compiler_environment_variables(pkg, build_env) + set_build_environment_variables(pkg, build_env, dirty) + pkg.architecture.platform.setup_platform_environment(pkg, build_env) - # traverse in postorder so package can use vars from its dependencies - spec = pkg.spec - for dspec in pkg.spec.traverse(order='post', root=False, - deptype=('build', 'test')): - spkg = dspec.package - set_module_variables_for_package(spkg) + build_env.extend( + modifications_from_dependencies(pkg.spec, context='build') + ) - # Allow dependencies to modify the module - dpkg = dspec.package - dpkg.setup_dependent_package(pkg.module, spec) - dpkg.setup_dependent_environment(spack_env, run_env, spec) - - if (not dirty) and (not spack_env.is_unset('CPATH')): + if (not dirty) and (not build_env.is_unset('CPATH')): tty.debug("A dependency has updated CPATH, this may lead pkg-config" " to assume that the package is part of the system" " includes and omit it when invoked with '--cflags'.") set_module_variables_for_package(pkg) - pkg.setup_environment(spack_env, run_env) + pkg.setup_build_environment(build_env) # Loading modules, in particular if they are meant to be used outside # of Spack, can change environment variables that are relevant to the @@ -711,7 +702,7 @@ def setup_package(pkg, dirty): # unnecessary. Modules affecting these variables will be overwritten anyway with preserve_environment('CC', 'CXX', 'FC', 'F77'): # All module loads that otherwise would belong in previous - # functions have to occur after the spack_env object has its + # functions have to occur after the build_env object has its # modifications applied. Otherwise the environment modifications # could undo module changes, such as unsetting LD_LIBRARY_PATH # after a module changes it. @@ -727,8 +718,39 @@ def setup_package(pkg, dirty): load_external_modules(pkg) # Make sure nothing's strange about the Spack environment. - validate(spack_env, tty.warn) - spack_env.apply_modifications() + validate(build_env, tty.warn) + build_env.apply_modifications() + + +def modifications_from_dependencies(spec, context): + """Returns the environment modifications that are required by + the dependencies of a spec and also applies modifications + to this spec's package at module scope, if need be. + + Args: + spec (Spec): spec for which we want the modifications + context (str): either 'build' for build-time modifications or 'run' + for run-time modifications + """ + env = EnvironmentModifications() + pkg = spec.package + + # Maps the context to deptype and method to be called + deptype_and_method = { + 'build': (('build', 'link', 'test'), + 'setup_dependent_build_environment'), + 'run': (('link', 'run'), 'setup_dependent_run_environment') + } + deptype, method = deptype_and_method[context] + + for dspec in spec.traverse(order='post', root=False, deptype=deptype): + dpkg = dspec.package + set_module_variables_for_package(dpkg) + # Allow dependencies to modify the module + dpkg.setup_dependent_package(pkg.module, spec) + getattr(dpkg, method)(env, spec) + + return env def fork(pkg, function, dirty, fake): diff --git a/lib/spack/spack/cmd/flake8.py b/lib/spack/spack/cmd/flake8.py index ebcad88a063..61f7dd567f1 100644 --- a/lib/spack/spack/cmd/flake8.py +++ b/lib/spack/spack/cmd/flake8.py @@ -93,12 +93,11 @@ def is_package(f): for file_pattern, error_dict in pattern_exemptions.items()) -def changed_files(args): +def changed_files(base=None, untracked=True, all_files=False): """Get list of changed files in the Spack repository.""" git = which('git', required=True) - base = args.base if base is None: base = os.environ.get('TRAVIS_BRANCH', 'develop') @@ -114,11 +113,11 @@ def changed_files(args): ] # Add new files that are untracked - if args.untracked: + if untracked: git_args.append(['ls-files', '--exclude-standard', '--other']) # add everything if the user asked for it - if args.all: + if all_files: git_args.append(['ls-files', '--exclude-standard']) excludes = [os.path.realpath(f) for f in exclude_directories] @@ -246,7 +245,7 @@ def prefix_relative(path): with working_dir(spack.paths.prefix): if not file_list: - file_list = changed_files(args) + file_list = changed_files(args.base, args.untracked, args.all) print('=======================================================') print('flake8: running flake8 code checks on spack.') diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py index 116d4f5471b..d38ede1385e 100644 --- a/lib/spack/spack/modules/common.py +++ b/lib/spack/spack/modules/common.py @@ -634,23 +634,16 @@ def environment_modifications(self): exclude=spack.util.environment.is_system_path ) - # Modifications that are coded at package level - _ = spack.util.environment.EnvironmentModifications() - # TODO : the code down below is quite similar to - # TODO : build_environment.setup_package and needs to be factored out - # TODO : to a single place # Let the extendee/dependency modify their extensions/dependencies # before asking for package-specific modifications - for item in dependencies(self.spec, 'all'): - package = self.spec[item.name].package - build_environment.set_module_variables_for_package(package) - package.setup_dependent_package( - self.spec.package.module, self.spec + env.extend( + build_environment.modifications_from_dependencies( + self.spec, context='run' ) - package.setup_dependent_environment(_, env, self.spec) + ) # Package specific modifications build_environment.set_module_variables_for_package(self.spec.package) - self.spec.package.setup_environment(_, env) + self.spec.package.setup_run_environment(env) # Modifications required from modules.yaml env.extend(self.conf.env) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index ecff265508f..e3d4f1b6e99 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -45,6 +45,7 @@ import spack.multimethod import spack.repo import spack.url +import spack.util.environment import spack.util.web import spack.multimethod import spack.binary_distribution as binary_distribution @@ -1951,68 +1952,108 @@ def build_system_flags(cls, name, flags): """ return (None, None, flags) - def setup_environment(self, spack_env, run_env): - """Set up the compile and runtime environments for a package. + def _get_legacy_environment_method(self, method_name): + legacy_fn = getattr(self, method_name, None) + name_prefix = method_name.split('_environment')[0] + if legacy_fn: + msg = '[DEPRECATED METHOD]\n"{0}" ' \ + 'still defines the deprecated method "{1}" ' \ + '[should be split into "{2}_build_environment" and ' \ + '"{2}_run_environment"]' + tty.debug(msg.format(self.name, method_name, name_prefix)) + return legacy_fn - ``spack_env`` and ``run_env`` are ``EnvironmentModifications`` - objects. Package authors can call methods on them to alter - the environment within Spack and at runtime. + def setup_build_environment(self, env): + """Sets up the build environment for a package. - Both ``spack_env`` and ``run_env`` are applied within the build - process, before this package's ``install()`` method is called. - - Modifications in ``run_env`` will *also* be added to the - generated environment modules for this package. - - Default implementation does nothing, but this can be - overridden if the package needs a particular environment. - - Example: - - 1. Qt extensions need ``QTDIR`` set. + This method will be called before the current package prefix exists in + Spack's store. Args: - spack_env (EnvironmentModifications): List of environment - modifications to be applied when this package is built - within Spack. - run_env (EnvironmentModifications): List of environment - modifications to be applied when this package is run outside - of Spack. These are added to the resulting module file. + env (EnvironmentModifications): environment modifications to be + applied when the package is built. Package authors can call + methods on it to alter the build environment. """ - pass + legacy_fn = self._get_legacy_environment_method('setup_environment') + if legacy_fn: + _ = spack.util.environment.EnvironmentModifications() + legacy_fn(env, _) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - """Set up the environment of packages that depend on this one. - - This is similar to ``setup_environment``, but it is used to - modify the compile and runtime environments of packages that - *depend* on this one. This gives packages like Python and - others that follow the extension model a way to implement - common environment or compile-time settings for dependencies. - - This is useful if there are some common steps to installing - all extensions for a certain package. - - Example: - - 1. Installing python modules generally requires ``PYTHONPATH`` to point - to the ``lib/pythonX.Y/site-packages`` directory in the module's - install prefix. This method could be used to set that variable. + def setup_run_environment(self, env): + """Sets up the run environment for a package. Args: - spack_env (EnvironmentModifications): List of environment - modifications to be applied when the dependent package is - built within Spack. - run_env (EnvironmentModifications): List of environment - modifications to be applied when the dependent package is - run outside of Spack. These are added to the resulting - module file. - dependent_spec (Spec): The spec of the dependent package + env (EnvironmentModifications): environment modifications to be + applied when the package is run. Package authors can call + methods on it to alter the run environment. + """ + legacy_fn = self._get_legacy_environment_method('setup_environment') + if legacy_fn: + _ = spack.util.environment.EnvironmentModifications() + legacy_fn(_, env) + + def setup_dependent_build_environment(self, env, dependent_spec): + """Sets up the build environment of packages that depend on this one. + + This is similar to ``setup_build_environment``, but it is used to + modify the build environments of packages that *depend* on this one. + + This gives packages like Python and others that follow the extension + model a way to implement common environment or compile-time settings + for dependencies. + + This method will be called before the dependent package prefix exists + in Spack's store. + + Examples: + 1. Installing python modules generally requires ``PYTHONPATH`` + to point to the ``lib/pythonX.Y/site-packages`` directory in the + module's install prefix. This method could be used to set that + variable. + + Args: + env (EnvironmentModifications): environment modifications to be + applied when the dependent package is built. Package authors + can call methods on it to alter the build environment. + + dependent_spec (Spec): the spec of the dependent package about to be built. This allows the extendee (self) to query the dependent's state. Note that *this* package's spec is - available as ``self.spec``. + available as ``self.spec`` """ - pass + legacy_fn = self._get_legacy_environment_method( + 'setup_dependent_environment' + ) + if legacy_fn: + _ = spack.util.environment.EnvironmentModifications() + legacy_fn(env, _, dependent_spec) + + def setup_dependent_run_environment(self, env, dependent_spec): + """Sets up the run environment of packages that depend on this one. + + This is similar to ``setup_run_environment``, but it is used to + modify the run environments of packages that *depend* on this one. + + This gives packages like Python and others that follow the extension + model a way to implement common environment or run-time settings + for dependencies. + + Args: + env (EnvironmentModifications): environment modifications to be + applied when the dependent package is run. Package authors + can call methods on it to alter the build environment. + + dependent_spec (Spec): The spec of the dependent package + about to be run. This allows the extendee (self) to query + the dependent's state. Note that *this* package's spec is + available as ``self.spec`` + """ + legacy_fn = self._get_legacy_environment_method( + 'setup_dependent_environment' + ) + if legacy_fn: + _ = spack.util.environment.EnvironmentModifications() + legacy_fn(_, env, dependent_spec) def setup_dependent_package(self, module, dependent_spec): """Set up Python module-scope variables for dependent packages. diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py index 1dd96dccecd..f83a2dbb8ee 100644 --- a/lib/spack/spack/test/package_sanity.py +++ b/lib/spack/spack/test/package_sanity.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) """This test does sanity checks on Spack's builtin package database.""" +import os.path import re import pytest @@ -11,6 +12,10 @@ import spack.fetch_strategy import spack.paths import spack.repo +import spack.util.executable as executable +# A few functions from this module are used to +# do sanity checks only on packagess modified by a PR +import spack.cmd.flake8 as flake8 import spack.util.crypto as crypto @@ -134,3 +139,48 @@ def invalid_sha256_digest(fetcher): ) assert [] == errors + + +@pytest.mark.xfail +def test_api_for_build_and_run_environment(): + """Ensure that every package uses the correct API to set build and + run environment, and not the old one. + """ + failing = [] + for pkg in spack.repo.path.all_packages(): + add_to_list = (hasattr(pkg, 'setup_environment') or + hasattr(pkg, 'setup_dependent_environment')) + if add_to_list: + failing.append(pkg) + + msg = ('there are {0} packages using the old API to set build ' + 'and run environment [{1}]') + assert not failing, msg.format( + len(failing), ','.join(x.name for x in failing) + ) + + +@pytest.mark.skipif( + not executable.which('git'), reason='requires git to be installed' +) +def test_prs_update_old_api(): + """Ensures that every package modified in a PR doesn't contain + deprecated calls to any method. + """ + changed_package_files = [ + x for x in flake8.changed_files() if flake8.is_package(x) + ] + failing = [] + for file in changed_package_files: + name = os.path.basename(os.path.dirname(file)) + pkg = spack.repo.get(name) + + # Check for old APIs + failed = (hasattr(pkg, 'setup_environment') or + hasattr(pkg, 'setup_dependent_environment')) + if failed: + failing.append(pkg) + msg = 'there are {0} packages still using old APIs in this PR [{1}]' + assert not failing, msg.format( + len(failing), ','.join(x.name for x in failing) + ) diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py index d654f790eaf..0a24a5d2b6a 100644 --- a/var/spack/repos/builtin/packages/docbook-xml/package.py +++ b/var/spack/repos/builtin/packages/docbook-xml/package.py @@ -20,6 +20,6 @@ class DocbookXml(Package): def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): catalog = os.path.join(self.prefix, 'catalog.xml') - run_env.set('XML_CATALOG_FILES', catalog, separator=' ') + env.set('XML_CATALOG_FILES', catalog, separator=' ') diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py index 19fdf7a3830..5633594c8f4 100644 --- a/var/spack/repos/builtin/packages/elpa/package.py +++ b/var/spack/repos/builtin/packages/elpa/package.py @@ -61,16 +61,16 @@ def headers(self): build_directory = 'spack-build' - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('FC', spec['mpi'].mpifc) - spack_env.set('CXX', spec['mpi'].mpicxx) + env.set('CC', spec['mpi'].mpicc) + env.set('FC', spec['mpi'].mpifc) + env.set('CXX', spec['mpi'].mpicxx) - spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) - spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags) - spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) + env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) + env.append_flags('LIBS', spec['lapack'].libs.link_flags) + env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) def configure_args(self): # TODO: set optimum flags for platform+compiler combo, see diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 5b92fbafee4..5d7a74cb59b 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -110,29 +110,28 @@ class Mpich(AutotoolsPackage): conflicts('pmi=pmi2', when='device=ch3 netmod=ofi') conflicts('pmi=pmix', when='device=ch3') - def setup_environment(self, spack_env, run_env): - # mpich configure fails when F90 and F90FLAGS are set - spack_env.unset('F90') - spack_env.unset('F90FLAGS') + def setup_build_environment(self, env): + env.unset('F90') + env.unset('F90FLAGS') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # On Cray, the regular compiler wrappers *are* the MPI wrappers. if 'platform=cray' in self.spec: - spack_env.set('MPICC', spack_cc) - spack_env.set('MPICXX', spack_cxx) - spack_env.set('MPIF77', spack_fc) - spack_env.set('MPIF90', spack_fc) + env.set('MPICC', spack_cc) + env.set('MPICXX', spack_cxx) + env.set('MPIF77', spack_fc) + env.set('MPIF90', spack_fc) else: - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) - spack_env.set('MPICH_CC', spack_cc) - spack_env.set('MPICH_CXX', spack_cxx) - spack_env.set('MPICH_F77', spack_f77) - spack_env.set('MPICH_F90', spack_fc) - spack_env.set('MPICH_FC', spack_fc) + env.set('MPICH_CC', spack_cc) + env.set('MPICH_CXX', spack_cxx) + env.set('MPICH_F77', spack_f77) + env.set('MPICH_F90', spack_fc) + env.set('MPICH_FC', spack_fc) def setup_dependent_package(self, module, dependent_spec): if 'platform=cray' in self.spec: diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index d3537611815..b05bd6dd9b8 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -183,7 +183,7 @@ def patch(self): r'\1setup.py\2 --no-user-cfg \3\6' ) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec # TODO: The '--no-user-cfg' option for Python installation is only in @@ -195,7 +195,7 @@ def setup_environment(self, spack_env, run_env): 'user configurations are present.').format(self.version)) # Need this to allow python build to find the Python installation. - spack_env.set('MACOSX_DEPLOYMENT_TARGET', platform.mac_ver()[0]) + env.set('MACOSX_DEPLOYMENT_TARGET', platform.mac_ver()[0]) def configure_args(self): spec = self.spec @@ -672,7 +672,7 @@ def site_packages_dir(self): def easy_install_file(self): return join_path(self.site_packages_dir, "easy-install.pth") - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Set PYTHONPATH to include the site-packages directory for the extension and any other python extensions it depends on.""" @@ -680,11 +680,11 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # python is found in the build environment. This to prevent cases # where a system provided python is run against the standard libraries # of a Spack built python. See issue #7128 - spack_env.set('PYTHONHOME', self.home) + env.set('PYTHONHOME', self.home) path = os.path.dirname(self.command.path) if not is_system_path(path): - spack_env.prepend_path('PATH', path) + env.prepend_path('PATH', path) python_paths = [] for d in dependent_spec.traverse( @@ -694,12 +694,13 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec): self.site_packages_dir)) pythonpath = ':'.join(python_paths) - spack_env.set('PYTHONPATH', pythonpath) + env.set('PYTHONPATH', pythonpath) + def setup_dependent_run_environment(self, env, dependent_spec): # For run time environment set only the path for # dependent_spec and prepend it to PYTHONPATH if dependent_spec.package.extends(self.spec): - run_env.prepend_path('PYTHONPATH', join_path( + env.prepend_path('PYTHONPATH', join_path( dependent_spec.prefix, self.site_packages_dir)) def setup_dependent_package(self, module, dependent_spec): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 7a4232ee228..0405aa49027 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -206,12 +206,14 @@ def url_for_version(self, version): return url - def setup_environment(self, spack_env, run_env): - spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) - run_env.set('QTDIR', self.prefix) + def setup_build_environment(self, env): + env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('QTDIR', self.prefix) + def setup_run_environment(self, env): + env.set('QTDIR', self.prefix) + + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('QTDIR', self.prefix) def setup_dependent_package(self, module, dependent_spec): module.qmake = Executable(join_path(self.spec.prefix.bin, 'qmake')) diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index 6d68e72bc3e..3755fb594f2 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -168,7 +168,7 @@ def copy_makeconf(self): def r_lib_dir(self): return join_path('rlib', 'R', 'library') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # Set R_LIBS to include the library dir for the # extension and any other R extensions it depends on. r_libs_path = [] @@ -178,27 +178,28 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec): r_libs_path.append(join_path(d.prefix, self.r_lib_dir)) r_libs_path = ':'.join(r_libs_path) - spack_env.set('R_LIBS', r_libs_path) - spack_env.set('R_MAKEVARS_SITE', - join_path(self.etcdir, 'Makeconf.spack')) + env.set('R_LIBS', r_libs_path) + env.set('R_MAKEVARS_SITE', + join_path(self.etcdir, 'Makeconf.spack')) # Use the number of make_jobs set in spack. The make program will # determine how many jobs can actually be started. - spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) + env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) + def setup_dependent_run_environment(self, env, dependent_spec): # For run time environment set only the path for dependent_spec and # prepend it to R_LIBS if dependent_spec.package.extends(self.spec): - run_env.prepend_path('R_LIBS', join_path( + env.prepend_path('R_LIBS', join_path( dependent_spec.prefix, self.r_lib_dir)) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('LIBRARY_PATH', - join_path(self.prefix, 'rlib', 'R', 'lib')) - run_env.prepend_path('LD_LIBRARY_PATH', - join_path(self.prefix, 'rlib', 'R', 'lib')) - run_env.prepend_path('CPATH', - join_path(self.prefix, 'rlib', 'R', 'include')) + def setup_run_environment(self, env): + env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'rlib', 'R', 'lib')) + env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'rlib', 'R', 'lib')) + env.prepend_path('CPATH', + join_path(self.prefix, 'rlib', 'R', 'include')) def setup_dependent_package(self, module, dependent_spec): """Called before R modules' install() methods. In most cases, From fd88f8fefa578518e51db88c67ed8c4cfc16c66c Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Thu, 17 Oct 2019 11:02:14 -0700 Subject: [PATCH 275/499] satisfaction checks on dependencies should be strict when the parent check is strict (#13243) --- lib/spack/spack/spec.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 0cde672de25..1a6cc5f6bd7 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -2899,7 +2899,7 @@ def satisfies_dependencies(self, other, strict=False): selfdeps = self.traverse(root=False) otherdeps = other.traverse(root=False) - if not all(any(d.satisfies(dep) for d in selfdeps) + if not all(any(d.satisfies(dep, strict=True) for d in selfdeps) for dep in otherdeps): return False From af3c238c3162c1c2bf0ec95e0ba362873d5b5c87 Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Thu, 17 Oct 2019 20:52:54 -0500 Subject: [PATCH 276/499] interproscan: add 5.38-76.0 (#13253) --- var/spack/repos/builtin/packages/interproscan/package.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/interproscan/package.py b/var/spack/repos/builtin/packages/interproscan/package.py index dcd09fa54a4..981e85ccb53 100644 --- a/var/spack/repos/builtin/packages/interproscan/package.py +++ b/var/spack/repos/builtin/packages/interproscan/package.py @@ -15,6 +15,7 @@ class Interproscan(Package): homepage = "https://www.ebi.ac.uk/interpro/interproscan.html" url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz" + version('5.38-76.0', sha256='cb191ff8eee275689b789167a57b368ea5c06bbcd36b4de23e8bbbbdc0fc7434') version('5.36-75.0', sha256='383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb') version('4.8', sha256='f1cb0ae1218eb05ed59ad7f94883f474eb9a6185a56ad3a93a364acb73506a3f', @@ -27,10 +28,11 @@ class Interproscan(Package): sha256='551610a4682b112522f3ded5268f76ba9a47399a72e726fafb17cc938a50e7ee', ) - depends_on('java@8.0:8.9', when='@5:', type=('build', 'run')) - depends_on('maven', when='@5:', type='build') - depends_on('python@3:', when='@5:', type=('build', 'run')) + depends_on('java@8.0:8.9', type=('build', 'run'), when='@5:5.36-99.0') + depends_on('java@11.0:', type=('build', 'run'), when='@5.37-76.0:') + depends_on('maven', type='build', when='@5:') depends_on('perl@5:', type=('build', 'run')) + depends_on('python@3:', when='@5:', type=('build', 'run')) depends_on('perl-cgi', when='@:4.8', type=('build', 'run')) depends_on('perl-mailtools', when='@:4.8', type=('build', 'run')) depends_on('perl-xml-quote', when='@:4.8', type=('build', 'run')) From 40a11c6bf6f99eff333c7483c695bdb1aab523c9 Mon Sep 17 00:00:00 2001 From: wspear Date: Fri, 18 Oct 2019 09:29:26 -0700 Subject: [PATCH 277/499] =?UTF-8?q?Added=20package=20py-python-oauth2,=20a?= =?UTF-8?q?=20dependency=20of=20py-jupyterhub@0.9.4.=20=E2=80=A6=20(#13140?= =?UTF-8?q?)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added package py-python-oauth2, a dependency of py-jupyterhub@0.9.4. Depends on #13132, #13133 and #13134 * Remove optional dependencies --- .../packages/py-python-oauth2/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-python-oauth2/package.py diff --git a/var/spack/repos/builtin/packages/py-python-oauth2/package.py b/var/spack/repos/builtin/packages/py-python-oauth2/package.py new file mode 100644 index 00000000000..6c0c7231839 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-oauth2/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonOauth2(PythonPackage): + """python-oauth2 is a framework that aims at making it easy to + provide authentication via OAuth 2.0 within an application stack.""" + + homepage = "https://pypi.org/project/python-oauth2/" + url = "https://pypi.io/packages/source/p/python-oauth2/python-oauth2-1.1.1.tar.gz" + + version('1.1.1', sha256='d7a8544927ac18215ba5317edd8f640a5f1f0593921bcf3ce862178312c8c9a4') + + depends_on('py-setuptools', type='build') From b4383825be628e3493da316937995df4fef9ab00 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Fri, 18 Oct 2019 10:36:40 -0600 Subject: [PATCH 278/499] fftw: altivec only works for float (#13242) --- .../repos/builtin/packages/fftw/package.py | 23 ++++++++++++++----- 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py index 82bd0c7aa72..895bb53c3ea 100644 --- a/var/spack/repos/builtin/packages/fftw/package.py +++ b/var/spack/repos/builtin/packages/fftw/package.py @@ -137,19 +137,21 @@ def configure(self, spec, prefix): if '+mpi' in spec: options.append('--enable-mpi') - # Specific SIMD support. Note there's SSE support too for float, but - # given that it can be activated only for float and that most machines - # are new enough to have SSE2 it has been skipped not to complicate the - # recipe further. + # Specific SIMD support. + # all precisions simd_features = ['sse2', 'avx', 'avx2', 'avx512', 'avx-128-fma', - 'kcvi', 'altivec', 'vsx', 'neon'] + 'kcvi', 'vsx', 'neon'] + # float only + float_simd_features = ['altivec', 'sse'] + simd_options = [] for feature in simd_features: msg = '--enable-{0}' if feature in spec.target else '--disable-{0}' simd_options.append(msg.format(feature)) # If no features are found, enable the generic ones - if not any(f in spec.target for f in simd_features): + if not any(f in spec.target for f in + simd_features + float_simd_features): simd_options += [ '--enable-generic-simd128', '--enable-generic-simd256' @@ -178,6 +180,15 @@ def configure(self, spec, prefix): if precision in ('float', 'double') and spec.satisfies('@3:'): opts += simd_options + # float-only acceleration + if precision == 'float': + for feature in float_simd_features: + if feature in spec.target: + msg = '--enable-{0}' + else: + msg = '--disable-{0}' + opts.append(msg.format(feature)) + with working_dir(precision, create=True): configure(*opts) From f9e7bf295c4aa0666f9f4e5ec45fea1ac597f702 Mon Sep 17 00:00:00 2001 From: wspear Date: Fri, 18 Oct 2019 10:53:47 -0700 Subject: [PATCH 279/499] Updated to latest version. Removed dependency on node-js (#13055) * Updated to latest version. Removed dependency on node-js * Refined dependencies * Added dependencies, including version-specific ones. Re-added 0.9.4. * Updated py-jupyterhub requirements. Enabled version 0.9.4 and 1.0.0 --- .../builtin/packages/py-jupyterhub/package.py | 38 ++++++++++--------- 1 file changed, 21 insertions(+), 17 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-jupyterhub/package.py b/var/spack/repos/builtin/packages/py-jupyterhub/package.py index cfde53c23d5..2b3e39a3891 100644 --- a/var/spack/repos/builtin/packages/py-jupyterhub/package.py +++ b/var/spack/repos/builtin/packages/py-jupyterhub/package.py @@ -10,22 +10,26 @@ class PyJupyterhub(PythonPackage): """Multi-user server for Jupyter notebooks.""" homepage = "https://pypi.org/project/jupyterhub" - url = "https://pypi.io/packages/source/j/jupyterhub/jupyterhub-0.9.4.tar.gz" + url = "https://pypi.io/packages/source/j/jupyterhub/jupyterhub-1.0.0.tar.gz" - version('0.9.4', sha256='86b1cce446d4e8347e26913878858fc8964d103fde19b606fe37ccc5188d629d') + version('1.0.0', sha256='33541a515a041b9a518ca057c1c4ab4215a7450fdddc206401713ee8137fa67f') + version('0.9.4', sha256='7848bbb299536641a59eb1977ec3c7c95d931bace4a2803d7e9b28b9256714da') - depends_on('python@3.5:') - depends_on('node-js', type=('build', 'run')) - depends_on('py-setuptools', type='build') - depends_on('py-python-dateutil', type='run') - depends_on('py-jinja2', type='run') - depends_on('py-sqlalchemy', type='run') - depends_on('py-tornado', type='run') - depends_on('py-traitlets', type='run') - depends_on('py-alembic', type='run') - depends_on('py-mako', type='run') - depends_on('py-async-generator', type='run') - depends_on('py-jupyter-notebook', type='run') - depends_on('py-prometheus-client', type='run') - depends_on('py-send2trash', type='run') - depends_on('py-requests', type='run') + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-python-dateutil', type=('build', 'run')) + depends_on('py-jinja2', type=('build', 'run')) + depends_on('py-sqlalchemy@1.1:', type=('build', 'run')) + depends_on('py-tornado@5.0:', type=('build', 'run')) + depends_on('py-traitlets@4.3.2:', type=('build', 'run')) + depends_on('py-alembic', type=('build', 'run')) + depends_on('py-mako', type=('build', 'run')) + depends_on('py-async-generator@1.8:', type=('build', 'run')) + depends_on('py-requests', type=('build', 'run')) + depends_on('py-certipy@0.1.2:', when='@1.0.0:', type=('build', 'run')) + depends_on('py-entrypoints', when='@1.0.0:', type=('build', 'run')) + depends_on('py-oauthlib@3.0:', when='@1.0.0:', type=('build', 'run')) + depends_on('py-python-oauth2@1.0:', when='@:9.4', type=('build', 'run')) + depends_on('py-pamela', type=('build', 'run')) + depends_on('py-jupyter-notebook', type=('build', 'run')) + depends_on('py-prometheus-client@0.0.21:', type=('build', 'run')) From 327a7368e91cb1763531e0154ccabf04005a090c Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Fri, 18 Oct 2019 13:26:56 -0700 Subject: [PATCH 280/499] ADIOS2: Dataspaces, libffi, libfabric (#13230) * DataSpaces: 1.8.0 Add a newer release of DataSpaces for ADIOS2. Also add missing `-fPIC` flags since this is a static library. * ADIOS2: Dataspaces, libffi, libfabric Add missing dependencies to ADIOS2. Without explicit control, those dependencies might get picked up from the system environment and will cause unstable builds. * Hide transitive SST dependencies * ADIOS2: Simplify SST CMake Flags As proposed by Chuck --- .../repos/builtin/packages/adios2/package.py | 24 +++++++++++++++++++ .../builtin/packages/dataspaces/package.py | 2 ++ 2 files changed, 26 insertions(+) diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index b1bc7c11dae..4be02170f4d 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -51,6 +51,8 @@ class Adios2(CMakePackage): description='Enable the SST staging engine') variant('dataman', default=True, description='Enable the DataMan engine for WAN transports') + variant('dataspaces', default=False, + description='Enable support for DATASPACES') variant('ssc', default=True, description='Enable the SSC staging engine') variant('hdf5', default=False, @@ -76,9 +78,15 @@ class Adios2(CMakePackage): depends_on('cmake@3.6.0:', type='build') depends_on('pkgconfig', type='build') + depends_on('libffi', when='+sst') # optional in DILL + depends_on('libfabric@1.6.0:', when='+sst') # optional in EVPath and SST + # depends_on('bison', when='+sst') # optional in FFS, broken package + # depends_on('flex', when='+sst') # optional in FFS, depends on BISON + depends_on('mpi', when='+mpi') depends_on('zeromq', when='+dataman') depends_on('zeromq', when='@2.4: +ssc') + depends_on('dataspaces@1.8.0:', when='+dataspaces') depends_on('hdf5', when='+hdf5') depends_on('hdf5+mpi', when='+hdf5+mpi') @@ -139,6 +147,22 @@ def cmake_args(self): args.append('-DADIOS2_USE_SSC={0}'.format( 'ON' if '+ssc' in spec else 'OFF')) + if self.spec.version >= Version('2.5.0'): + args.append('-DADIOS2_USE_DataSpaces={0}'.format( + 'ON' if '+dataspaces' in spec else 'OFF')) + + if '+sst' in spec: + args.extend([ + # Broken dependency package + '-DCMAKE_DISABLE_FIND_PACKAGE_BISON=TRUE', + # Depends on ^ + '-DCMAKE_DISABLE_FIND_PACKAGE_FLEX=TRUE', + + # Not yet packaged + '-DCMAKE_DISABLE_FIND_PACKAGE_CrayDRC=TRUE', + '-DCMAKE_DISABLE_FIND_PACKAGE_NVSTREAM=TRUE' + ]) + if spec.satisfies('~shared'): args.append('-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL={0}'.format( 'ON' if '+pic' in spec else 'OFF')) diff --git a/var/spack/repos/builtin/packages/dataspaces/package.py b/var/spack/repos/builtin/packages/dataspaces/package.py index 5bfa513ddeb..d227d4ea3cc 100644 --- a/var/spack/repos/builtin/packages/dataspaces/package.py +++ b/var/spack/repos/builtin/packages/dataspaces/package.py @@ -23,6 +23,7 @@ class Dataspaces(AutotoolsPackage): git = "https://github.com/melrom/dataspaces.git" version('develop', branch='master') + version('1.8.0', sha256='7f204bb3c03c2990f5a2d76a29185466b584793c63ada03e5e694627e6060605') version('1.6.2', sha256='3c43d551c1e8198a4ab269c83928e1dc6f8054e6d41ceaee45155d91a48cf9bf') variant('dimes', @@ -57,6 +58,7 @@ def configure_args(self): args = [] cookie = self.spec.variants['gni-cookie'].value ptag = self.spec.variants['ptag'].value + args.append('CFLAGS={0}'.format(self.compiler.pic_flag)) if self.spec.satisfies('+dimes'): args.append('--enable-dimes') if self.spec.satisfies('+cray-drc'): From 306346356caefcd683b469200527dff7437458b0 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 19 Oct 2019 12:18:06 -0500 Subject: [PATCH 281/499] brotli: fix darwin install name (#13258) --- var/spack/repos/builtin/packages/brotli/package.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/var/spack/repos/builtin/packages/brotli/package.py b/var/spack/repos/builtin/packages/brotli/package.py index 81c736e033a..e11c6810298 100644 --- a/var/spack/repos/builtin/packages/brotli/package.py +++ b/var/spack/repos/builtin/packages/brotli/package.py @@ -13,3 +13,9 @@ class Brotli(CMakePackage): url = "https://github.com/google/brotli/archive/v1.0.7.tar.gz" version('1.0.7', sha256='4c61bfb0faca87219ea587326c467b95acb25555b53d1a421ffa3c8a9296ee2c') + + @run_after('install') + def darwin_fix(self): + # The shared library is not installed correctly on Darwin; fix this + if self.spec.satisfies('platform=darwin'): + fix_darwin_install_name(self.prefix.lib) From 0fb563f3d9f944f25f3badbf91d53754ef075aaa Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 19 Oct 2019 12:18:31 -0500 Subject: [PATCH 282/499] GCC: fix build on macOS Catalina (#13202) * GCC: speed up build * Add back 3-stage bootstrapping --- .../repos/builtin/packages/gcc/package.py | 34 +++++++++++-------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 5551ba0cac1..836c018604b 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -100,6 +100,7 @@ class Gcc(AutotoolsPackage): depends_on('isl@0.15:0.18', when='@6:8.9') depends_on('isl@0.15:0.20', when='@9:') depends_on('zlib', when='@6:') + depends_on('libiconv') depends_on('gnat', when='languages=ada') depends_on('binutils~libiberty', when='+binutils') depends_on('zip', type='build', when='languages=java') @@ -195,6 +196,14 @@ class Gcc(AutotoolsPackage): # https://trac.macports.org/ticket/56502#no1 # see also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83531 patch('darwin/headers-10.13-fix.patch', when='@5.5.0') + if macos_version() >= Version('10.15'): + # Fix system headers for Catalina SDK + # (otherwise __OSX_AVAILABLE_STARTING ends up undefined) + patch('https://raw.githubusercontent.com/Homebrew/formula-patches/b8b8e65e/gcc/9.2.0-catalina.patch', + sha256='0b8d14a7f3c6a2f0d2498526e86e088926671b5da50a554ffa6b7f73ac4f132b', when='@9.2.0:') + # Use -headerpad_max_install_names in the build, + # otherwise updated load commands won't fit in the Mach-O header. + # This is needed because `gcc` avoids the superenv shim. patch('darwin/gcc-7.1.0-headerpad.patch', when='@5:') patch('darwin/gcc-6.1.0-jit.patch', when='@5:7') patch('darwin/gcc-4.9.patch1', when='@4.9.0:4.9.3') @@ -255,18 +264,24 @@ def patch(self): '-I{0}'.format(spec['zlib'].prefix.include), 'gcc/Makefile.in') + # https://gcc.gnu.org/install/configure.html def configure_args(self): spec = self.spec # Generic options to compile GCC options = [ + # Distributor options + '--with-pkgversion=Spack GCC', + '--with-bugurl=https://github.com/spack/spack/issues', + # Xcode 10 dropped 32-bit support '--disable-multilib', '--enable-languages={0}'.format( ','.join(spec.variants['languages'].value)), + # Drop gettext dependency + '--disable-nls', + '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix), '--with-mpfr={0}'.format(spec['mpfr'].prefix), '--with-gmp={0}'.format(spec['gmp'].prefix), - '--enable-lto', - '--with-quad' ] # Use installed libz @@ -280,7 +295,7 @@ def configure_args(self): # Binutils if spec.satisfies('+binutils'): static_bootstrap_flags = '-static-libstdc++ -static-libgcc' - binutils_options = [ + options.extend([ '--with-sysroot=/', '--with-stage1-ldflags={0} {1}'.format( self.rpath_args, static_bootstrap_flags), @@ -290,8 +305,7 @@ def configure_args(self): '--with-ld={0}/ld'.format(spec['binutils'].prefix.bin), '--with-gnu-as', '--with-as={0}/as'.format(spec['binutils'].prefix.bin), - ] - options.extend(binutils_options) + ]) # MPC if 'mpc' in spec: @@ -301,10 +315,6 @@ def configure_args(self): if 'isl' in spec: options.append('--with-isl={0}'.format(spec['isl'].prefix)) - # macOS - if sys.platform == 'darwin': - options.append('--with-build-config=bootstrap-debug') - # nvptx-none offloading for host compiler if spec.satisfies('+nvptx'): options.extend(['--enable-offload-targets=nvptx-none', @@ -382,12 +392,6 @@ def nvptx_install(self): make() make('install') - @property - def build_targets(self): - if sys.platform == 'darwin': - return ['bootstrap'] - return [] - @property def install_targets(self): if '+strip' in self.spec: From 41fb0395a61093373eb8942b257308bbcc49c2dc Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Sat, 19 Oct 2019 22:19:29 +0200 Subject: [PATCH 283/499] Microarchitecture specific optimizations for LLVM (#13250) * Added architecture specific optimization flags for Clang / LLVM * Disallow compiler optimizations for mixed toolchains * We emit a warning when building for a mixed toolchain * Fixed issues with suffixed versions of compilers; Apple's Clang will, for the time being, fall back on x86-64 for every compilation. --- lib/spack/llnl/util/cpu/microarchitecture.py | 3 +- .../llnl/util/cpu/microarchitectures.json | 187 +++++++++++++++++- lib/spack/spack/architecture.py | 16 ++ lib/spack/spack/compilers/__init__.py | 38 ++++ lib/spack/spack/test/architecture.py | 18 ++ lib/spack/spack/test/compilers.py | 8 + lib/spack/spack/test/concretize.py | 4 +- lib/spack/spack/test/data/compilers.yaml | 21 ++ lib/spack/spack/test/llnl/util/cpu.py | 7 + 9 files changed, 292 insertions(+), 10 deletions(-) diff --git a/lib/spack/llnl/util/cpu/microarchitecture.py b/lib/spack/llnl/util/cpu/microarchitecture.py index 319eec28c72..e14e1a8c668 100644 --- a/lib/spack/llnl/util/cpu/microarchitecture.py +++ b/lib/spack/llnl/util/cpu/microarchitecture.py @@ -224,7 +224,8 @@ def satisfies_constraint(entry, version): version, _, suffix = version.partition('-') # If the suffixes are not all equal there's no match - if suffix != min_suffix or suffix != max_suffix: + if ((suffix != min_suffix and min_version) or + (suffix != max_suffix and max_version)): return False # Assume compiler versions fit into semver diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 88e2bb665f1..02f507fa6d7 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -60,7 +60,12 @@ "name": "x86-64", "flags": "-march={name} -mtune={name}" } - ] + ], + "clang": { + "versions": ":", + "family": "x86-64", + "flags": "-march={family} -mcpu=generic" + } } }, "nocona": { @@ -76,6 +81,11 @@ "gcc": { "versions": "4:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -92,6 +102,11 @@ "gcc": { "versions": "4:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -118,7 +133,12 @@ "name": "corei7", "flags": "-march={name} -mtune={name}" } - ] + ], + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" + } } }, "westmere": { @@ -139,6 +159,11 @@ "gcc": { "versions": "4.9:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -168,7 +193,12 @@ "name": "corei7-avx", "flags": "-march={name} -mtune={name}" } - ] + ], + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" + } } }, "ivybridge": { @@ -199,7 +229,12 @@ "name": "core-avx-i", "flags": "-march={name} -mtune={name}" } - ] + ], + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" + } } }, "haswell": { @@ -235,7 +270,12 @@ "name": "core-avx2", "flags": "-march={name} -mtune={name}" } - ] + ], + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" + } } }, "broadwell": { @@ -266,6 +306,11 @@ "gcc": { "versions": "4.9:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -300,6 +345,11 @@ "gcc": { "versions": "5.3:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -337,6 +387,12 @@ "versions": "5.1:", "name": "knl", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "name": "knl", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -378,6 +434,12 @@ "name": "skylake-avx512", "versions": "5.3:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "name": "skylake-avx512", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -421,6 +483,11 @@ "gcc": { "versions": "8:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -462,6 +529,11 @@ "gcc": { "versions": "9:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "8.0:", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -518,7 +590,20 @@ "name": "icelake-client", "versions": "8:", "flags": "-march={name} -mtune={name}" - } + }, + "clang": [ + { + "versions": "7.0:", + "name": "icelake-client", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" + }, + { + "versions": "6.0:6.9", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" + } + ] } }, "bulldozer": { @@ -545,6 +630,12 @@ "name": "bdver1", "versions": "4.6:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "name": "bdver1", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -576,6 +667,12 @@ "name": "bdver2", "versions": "4.7:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "name": "bdver2", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -608,6 +705,12 @@ "name": "bdver3", "versions": "4.8:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "name": "bdver3", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -643,6 +746,12 @@ "name": "bdver4", "versions": "4.9:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "name": "bdver4", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -681,6 +790,12 @@ "name": "znver1", "versions": "6:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "4.0:", + "name": "znver1", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -720,6 +835,12 @@ "name": "znver2", "versions": "9:", "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "9.0:", + "name": "znver2", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" } } }, @@ -732,6 +853,11 @@ "name": "powerpc64", "versions": "4:", "flags": "-mcpu={name} -mtune={name}" + }, + "clang": { + "versions": ":", + "family": "ppc64", + "flags": "-march={family} -mcpu=generic" } } }, @@ -744,6 +870,12 @@ "gcc": { "versions": "4.5:", "flags": "-mcpu={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "ppc64", + "name": "pwr7", + "flags": "-march={family} -mcpu={name}" } } }, @@ -763,7 +895,13 @@ "warnings": "Using GCC 4.8 to optimize for Power 8 might not work if you are not on Red Hat Enterprise Linux 7, where a custom backport of the feature has been done. Upstream support from GCC starts in version 4.9", "flags": "-mcpu={name} -mtune={name}" } - ] + ], + "clang": { + "versions": "3.9:", + "family": "ppc64", + "name": "pwr8", + "flags": "-march={family} -mcpu={name}" + } } }, "power9": { @@ -775,6 +913,12 @@ "gcc": { "versions": "6:", "flags": "-mcpu={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "ppc64", + "name": "pwr9", + "flags": "-march={family} -mcpu={name}" } } }, @@ -787,6 +931,11 @@ "name": "powerpc64le", "versions": "4:", "flags": "-mcpu={name} -mtune={name}" + }, + "clang": { + "versions": ":", + "family": "ppc64le", + "flags": "-march={family} -mcpu=generic" } } }, @@ -808,7 +957,13 @@ "name": "power8", "flags": "-mcpu={name} -mtune={name}" } - ] + ], + "clang": { + "versions": "3.9:", + "family": "ppc64le", + "name": "pwr8", + "flags": "-march={family} -mcpu={name}" + } } }, "power9le": { @@ -821,6 +976,12 @@ "name": "power9", "versions": "6:", "flags": "-mcpu={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "family": "ppc64le", + "name": "pwr9", + "flags": "-march={family} -mcpu={name}" } } }, @@ -832,6 +993,11 @@ "gcc": { "versions": "4:", "flags": "-march=armv8-a -mtune=generic" + }, + "clang": { + "versions": ":", + "family": "aarch64", + "flags": "-march={family} -mcpu=generic" } } }, @@ -840,6 +1006,11 @@ "vendor": "generic", "features": [], "compilers": { + "clang": { + "versions": ":", + "family": "arm", + "flags": "-march={family} -mcpu=generic" + } } }, "ppc": { diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index 53cbc44ca53..dd99cfa1e3b 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -58,6 +58,7 @@ """ import functools import inspect +import warnings import six @@ -184,6 +185,21 @@ def __contains__(self, cpu_flag): return cpu_flag in self.microarchitecture def optimization_flags(self, compiler): + """Returns the flags needed to optimize for this target using + the compiler passed as argument. + + Args: + compiler (CompilerSpec or Compiler): object that contains both the + name and the version of the compiler we want to use + """ + if isinstance(compiler, spack.compiler.Compiler): + if spack.compilers.is_mixed_toolchain(compiler): + msg = ('microarchitecture specific optimizations are not ' + 'supported yet on mixed compiler toolchains [check' + ' {0.name}@{0.version} for further details]') + warnings.warn(msg.format(compiler)) + return '' + return self.microarchitecture.optimization_flags( compiler.name, str(compiler.version) ) diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py index 206aa17e1b1..bc2e4df391f 100644 --- a/lib/spack/spack/compilers/__init__.py +++ b/lib/spack/spack/compilers/__init__.py @@ -676,6 +676,44 @@ def _default(cmp_id, paths): return compilers +def is_mixed_toolchain(compiler): + """Returns True if the current compiler is a mixed toolchain, + False otherwise. + + Args: + compiler (Compiler): a valid compiler object + """ + cc = os.path.basename(compiler.cc or '') + cxx = os.path.basename(compiler.cxx or '') + f77 = os.path.basename(compiler.f77 or '') + fc = os.path.basename(compiler.fc or '') + + toolchains = set() + for compiler_cls in all_compiler_types(): + # Inspect all the compiler toolchain we know. If a compiler is the + # only compiler supported there it belongs to that toolchain. + def name_matches(name, name_list): + # This is such that 'gcc' matches variations + # like 'ggc-9' etc that are found in distros + name, _, _ = name.partition('-') + return len(name_list) == 1 and name and name in name_list + + if any([ + name_matches(cc, compiler_cls.cc_names), + name_matches(cxx, compiler_cls.cxx_names), + name_matches(f77, compiler_cls.f77_names), + name_matches(fc, compiler_cls.fc_names) + ]): + tty.debug("[TOOLCHAIN] MATCH {0}".format(compiler_cls.__name__)) + toolchains.add(compiler_cls.__name__) + + if len(toolchains) > 1: + tty.debug("[TOOLCHAINS] {0}".format(toolchains)) + return True + + return False + + class InvalidCompilerConfigurationError(spack.error.SpackError): def __init__(self, compiler_spec): diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index b36219aa761..7e120000d42 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -169,3 +169,21 @@ def test_target_container_semantic(cpu_flag, target_name): def test_arch_spec_container_semantic(item, architecture_str): architecture = spack.spec.ArchSpec(architecture_str) assert item in architecture + + +@pytest.mark.parametrize('compiler_spec,target_name,expected_flags', [ + # Check compilers with version numbers from a single toolchain + ('gcc@4.7.2', 'haswell', '-march=core-avx2 -mtune=core-avx2'), + # Check mixed toolchains + ('clang@8.0.0', 'broadwell', ''), + # Check clang compilers with 'apple' suffix + ('clang@9.1.0-apple', 'x86_64', '-march=x86-64 -mcpu=generic') +]) +@pytest.mark.filterwarnings("ignore:microarchitecture specific") +def test_optimization_flags( + compiler_spec, target_name, expected_flags, config +): + target = spack.architecture.Target(target_name) + compiler = spack.compilers.compilers_for_spec(compiler_spec).pop() + opt_flags = target.optimization_flags(compiler) + assert opt_flags == expected_flags diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py index dc104225f12..ac107170b07 100644 --- a/lib/spack/spack/test/compilers.py +++ b/lib/spack/spack/test/compilers.py @@ -469,3 +469,11 @@ def test_cce_version_detection(version_str, expected_version): def test_fj_version_detection(version_str, expected_version): version = spack.compilers.fj.Fj.extract_version_from_output(version_str) assert version == expected_version + + +@pytest.mark.parametrize('compiler_spec,expected_result', [ + ('gcc@4.7.2', False), ('clang@3.3', False), ('clang@8.0.0', True) +]) +def test_detecting_mixed_toolchains(compiler_spec, expected_result, config): + compiler = spack.compilers.compilers_for_spec(compiler_spec).pop() + assert spack.compilers.is_mixed_toolchain(compiler) is expected_result diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index 5243ba76815..f0c8e93bcfe 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -585,7 +585,9 @@ def test_noversion_pkg(self, spec): @pytest.mark.parametrize('spec, best_achievable', [ ('mpileaks%gcc@4.8', 'haswell'), - ('mpileaks%gcc@5.3.0', 'skylake_avx512') + ('mpileaks%gcc@5.3.0', 'skylake_avx512'), + # Apple's clang always falls back to x86-64 for now + ('mpileaks%clang@9.1.0-apple', 'x86_64') ]) def test_adjusting_default_target_based_on_compiler( self, spec, best_achievable, current_host diff --git a/lib/spack/spack/test/data/compilers.yaml b/lib/spack/spack/test/data/compilers.yaml index d7092945d5b..f619c8d351c 100644 --- a/lib/spack/spack/test/data/compilers.yaml +++ b/lib/spack/spack/test/data/compilers.yaml @@ -114,3 +114,24 @@ compilers: cflags: -O3 cxxflags: -O3 modules: 'None' +- compiler: + spec: clang@8.0.0 + operating_system: redhat7 + paths: + cc: /path/to/clang-8 + cxx: /path/to/clang++-8 + f77: /path/to/gfortran-9 + fc: /path/to/gfortran-9 + flags: + cflags: -O3 + cxxflags: -O3 + modules: 'None' +- compiler: + spec: clang@9.1.0-apple + operating_system: elcapitan + paths: + cc: /path/to/clang + cxx: /path/to/clang++ + f77: None + fc: None + modules: 'None' diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 9c65825a52c..5713580a72f 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -191,6 +191,7 @@ def test_target_json_schema(): @pytest.mark.parametrize('target_name,compiler,version,expected_flags', [ + # Test GCC ('x86_64', 'gcc', '4.9.3', '-march=x86-64 -mtune=generic'), ('x86_64', 'gcc', '4.2.0', '-march=x86-64 -mtune=generic'), ('x86_64', 'gcc', '4.1.1', '-march=x86-64 -mtune=x86-64'), @@ -198,6 +199,12 @@ def test_target_json_schema(): ('nehalem', 'gcc', '4.9.3', '-march=nehalem -mtune=nehalem'), ('nehalem', 'gcc', '4.8.5', '-march=corei7 -mtune=corei7'), ('sandybridge', 'gcc', '4.8.5', '-march=corei7-avx -mtune=corei7-avx'), + # Test Clang / LLVM + ('sandybridge', 'clang', '3.9.0', '-march=x86-64 -mcpu=sandybridge'), + ('icelake', 'clang', '6.0.0', '-march=x86-64 -mcpu=icelake'), + ('icelake', 'clang', '8.0.0', '-march=x86-64 -mcpu=icelake-client'), + ('zen2', 'clang', '9.0.0', '-march=x86-64 -mcpu=znver2'), + ('power9le', 'clang', '8.0.0', '-march=ppc64le -mcpu=pwr9'), # Test that an unknown compiler returns an empty string ('sandybridge', 'unknown', '4.8.5', ''), ]) From 20bb6fd733977187e733842de70b04bfcfe68602 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 19 Oct 2019 14:09:25 -0700 Subject: [PATCH 284/499] shebangs: don't warn when patching long shebangs (#13266) We've been doing this for quite a while now, and it does not seem to cause issues. - [x] Switch the noisy warning to a debug to make Spack a bit quieter while building. --- lib/spack/spack/hooks/sbang.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py index f40e8d40d58..6987815bc87 100644 --- a/lib/spack/spack/hooks/sbang.py +++ b/lib/spack/spack/hooks/sbang.py @@ -69,7 +69,7 @@ def filter_shebang(path): if saved_mode is not None: os.chmod(path, saved_mode) - tty.warn("Patched overlong shebang in %s" % path) + tty.debug("Patched overlong shebang in %s" % path) def filter_shebangs_in_directory(directory, filenames=None): From 596f3f1d61d9e00e61e0c056821bfd33cacaffb7 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:05:54 -0500 Subject: [PATCH 285/499] spack create: http -> https (#13269) --- lib/spack/spack/cmd/create.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index c2dd143ce05..527a7a883c5 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -56,7 +56,7 @@ class {class_name}({base_class_name}): """FIXME: Put a proper description of your package here.""" # FIXME: Add a proper url for your package's homepage here. - homepage = "http://www.example.com" + homepage = "https://www.example.com" {url_def} {versions} From 4f56bcc790cbf8260ed7255a2a596209c4c3b22d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:06:18 -0500 Subject: [PATCH 286/499] Add py-brotlipy package (#13270) --- .../builtin/packages/py-brotlipy/package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-brotlipy/package.py diff --git a/var/spack/repos/builtin/packages/py-brotlipy/package.py b/var/spack/repos/builtin/packages/py-brotlipy/package.py new file mode 100644 index 00000000000..82f63e77641 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-brotlipy/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyBrotlipy(PythonPackage): + """Python binding to the Brotli library.""" + + homepage = "https://github.com/python-hyper/brotlipy/" + url = "https://pypi.io/packages/source/b/brotlipy/brotlipy-0.7.0.tar.gz" + + version('0.7.0', sha256='36def0b859beaf21910157b4c33eb3b06d8ce459c942102f16988cca6ea164df') + + depends_on('py-setuptools', type='build') + depends_on('py-cffi@1.0.0:', type=('build', 'run')) + depends_on('py-enum34@1.0.4:1.999', when='^python@:3.3', type=('build', 'run')) + + # TODO: Builds against internal copy of headers, doesn't seem to be a way + # to use external brotli installation + # depends_on('brotli') From 95b7f31112bb8cffd1f620ca50b39c9de03b3baf Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:06:38 -0500 Subject: [PATCH 287/499] Add py-docutils-stubs package (#13271) --- .../packages/py-docutils-stubs/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-docutils-stubs/package.py diff --git a/var/spack/repos/builtin/packages/py-docutils-stubs/package.py b/var/spack/repos/builtin/packages/py-docutils-stubs/package.py new file mode 100644 index 00000000000..81ddf8e97c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-docutils-stubs/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyDocutilsStubs(PythonPackage): + """PEP 561 based Type information for docutils.""" + + homepage = "https://github.com/tk0miya/docutils-stubs" + url = "https://pypi.io/packages/source/d/docutils-stubs/docutils-stubs-0.0.21.tar.gz" + + version('0.0.21', sha256='e0d3d2588a0c0b47bf66b917bf4ff2c100cf4cf77bbe2f518d97b8f4d63e735c') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-docutils@0.14', type=('build', 'run')) From 3e18e664fc10485e0101cf09374844e199e1d821 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:07:01 -0500 Subject: [PATCH 288/499] Add py-typed-ast package (#13272) --- .../builtin/packages/py-typed-ast/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-typed-ast/package.py diff --git a/var/spack/repos/builtin/packages/py-typed-ast/package.py b/var/spack/repos/builtin/packages/py-typed-ast/package.py new file mode 100644 index 00000000000..492d63cbc23 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-typed-ast/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTypedAst(PythonPackage): + """A fork of Python 2 and 3 ast modules with type comment support.""" + + homepage = "https://github.com/python/typed_ast" + url = "https://pypi.io/packages/source/t/typed-ast/typed_ast-1.4.0.tar.gz" + + version('1.4.0', sha256='66480f95b8167c9c5c5c87f32cf437d585937970f3fc24386f313a4c97b44e34') + + depends_on('python@3.3:', type=('build', 'run')) + depends_on('py-setuptools', type='build') From f35bcaf83bcf6cdd9e1d46e0ca7597af20810c5a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:07:31 -0500 Subject: [PATCH 289/499] Add py-sphinxcontrib-serializinghtml package (#13274) --- .../package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py new file mode 100644 index 00000000000..ba431272227 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySphinxcontribSerializinghtml(PythonPackage): + """sphinxcontrib-serializinghtml is a sphinx extension which outputs + "serialized" HTML files (json and pickle).""" + + homepage = "http://sphinx-doc.org/" + url = "https://pypi.io/packages/source/s/sphinxcontrib-serializinghtml/sphinxcontrib-serializinghtml-1.1.3.tar.gz" + + version('1.1.3', sha256='c0efb33f8052c04fd7a26c0a07f1678e8512e0faec19f4aa8f2473a8b81d5227') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + + def test(self): + # Requires sphinx, creating a circular dependency + pass From d4ac57f3a328dd98b76f6c8924ddc9d735c32c04 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:07:54 -0500 Subject: [PATCH 290/499] Add py-sphinxcontrib-qthelp package (#13275) --- .../py-sphinxcontrib-qthelp/package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py new file mode 100644 index 00000000000..17c2ba1e959 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySphinxcontribQthelp(PythonPackage): + """sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp + document.""" + + homepage = "http://sphinx-doc.org/" + url = "https://pypi.io/packages/source/s/sphinxcontrib-qthelp/sphinxcontrib-qthelp-1.0.2.tar.gz" + + version('1.0.2', sha256='79465ce11ae5694ff165becda529a600c754f4bc459778778c7017374d4d406f') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + + def test(self): + # Requires sphinx, creating a circular dependency + pass From 7bda2fe2925fa67e2c7e48e13c395d1a0a9e1e63 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:08:16 -0500 Subject: [PATCH 291/499] Add py-sphinxcontrib-jsmath package (#13276) --- .../py-sphinxcontrib-jsmath/package.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py new file mode 100644 index 00000000000..213dca354dd --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySphinxcontribJsmath(PythonPackage): + """A sphinx extension which renders display math in HTML via JavaScript.""" + + homepage = "http://sphinx-doc.org/" + url = "https://pypi.io/packages/source/s/sphinxcontrib-jsmath/sphinxcontrib-jsmath-1.0.1.tar.gz" + + version('1.0.1', sha256='a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + + def test(self): + # Requires sphinx, creating a circular dependency + pass From d37c95b80b4b329722d2426b3187c677549da85f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:08:34 -0500 Subject: [PATCH 292/499] Add py-sphinxcontrib-htmlhelp package (#13277) --- .../py-sphinxcontrib-htmlhelp/package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py new file mode 100644 index 00000000000..b4c8961d2c0 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySphinxcontribHtmlhelp(PythonPackage): + """sphinxcontrib-htmlhelp is a sphinx extension which outputs htmlhelp + document.""" + + homepage = "http://sphinx-doc.org/" + url = "https://pypi.io/packages/source/s/sphinxcontrib-htmlhelp/sphinxcontrib-htmlhelp-1.0.2.tar.gz" + + version('1.0.2', sha256='4670f99f8951bd78cd4ad2ab962f798f5618b17675c35c5ac3b2132a14ea8422') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + + def test(self): + # Requires sphinx, creating a circular dependency + pass From c8285da8e7bfa92c541943fb79e0eacf95c513eb Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:08:51 -0500 Subject: [PATCH 293/499] Add py-sphinxcontrib-applehelp package (#13279) --- .../py-sphinxcontrib-applehelp/package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py new file mode 100644 index 00000000000..089ef152cf1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySphinxcontribApplehelp(PythonPackage): + """sphinxcontrib-applehelp is a sphinx extension which outputs Apple + help books.""" + + homepage = "http://sphinx-doc.org/" + url = "https://pypi.io/packages/source/s/sphinxcontrib-applehelp/sphinxcontrib-applehelp-1.0.1.tar.gz" + + version('1.0.1', sha256='edaa0ab2b2bc74403149cb0209d6775c96de797dfd5b5e2a71981309efab3897') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + + def test(self): + # Requires sphinx, creating a circular dependency + pass From 00f766b24865e8010411105794f20bc0ef39a6dc Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:09:04 -0500 Subject: [PATCH 294/499] Add py-sphinxcontrib-devhelp package (#13278) --- .../py-sphinxcontrib-devhelp/package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py new file mode 100644 index 00000000000..244fd13b780 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySphinxcontribDevhelp(PythonPackage): + """sphinxcontrib-devhelp is a sphinx extension which outputs + Devhelp document.""" + + homepage = "http://sphinx-doc.org/" + url = "https://pypi.io/packages/source/s/sphinxcontrib-devhelp/sphinxcontrib-devhelp-1.0.1.tar.gz" + + version('1.0.1', sha256='6c64b077937330a9128a4da74586e8c2130262f014689b4b89e2d08ee7294a34') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + + def test(self): + # Requires sphinx, creating a circular dependency + pass From a6bc0c7ee0575287fb2fd2da6546b3741b5814d8 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:09:23 -0500 Subject: [PATCH 295/499] Add py-flake8-import-order package (#13273) --- .../py-flake8-import-order/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-flake8-import-order/package.py diff --git a/var/spack/repos/builtin/packages/py-flake8-import-order/package.py b/var/spack/repos/builtin/packages/py-flake8-import-order/package.py new file mode 100644 index 00000000000..453b5ef3808 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-flake8-import-order/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyFlake8ImportOrder(PythonPackage): + """Flake8 and pylama plugin that checks the ordering of import statements. + """ + + homepage = "https://github.com/PyCQA/flake8-import-order" + url = "https://pypi.io/packages/source/f/flake8-import-order/flake8-import-order-0.18.1.tar.gz" + + version('0.18.1', sha256='a28dc39545ea4606c1ac3c24e9d05c849c6e5444a50fb7e9cdd430fc94de6e92') + + depends_on('py-enum34', when='^python@:2', type=('build', 'run')) + depends_on('py-pycodestyle', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) From 1dc99765e94a7f148af7c45d290e381f0ed3d458 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:09:44 -0500 Subject: [PATCH 296/499] Add py-raven package (#13280) --- .../builtin/packages/py-raven/package.py | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-raven/package.py diff --git a/var/spack/repos/builtin/packages/py-raven/package.py b/var/spack/repos/builtin/packages/py-raven/package.py new file mode 100644 index 00000000000..9236d7a5f84 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-raven/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyRaven(PythonPackage): + """Raven is a client for Sentry.""" + + homepage = "https://github.com/getsentry/raven-python" + url = "https://pypi.io/packages/source/r/raven/raven-6.10.0.tar.gz" + + version('6.10.0', sha256='3fa6de6efa2493a7c827472e984ce9b020797d0da16f1db67197bcc23c8fae54') + + variant('flask', default=False, description='Build flask backend') + + depends_on('py-setuptools', type='build') + depends_on('py-flask@0.8:', when='+flask', type=('build', 'run')) + depends_on('py-blinker@1.1:', when='+flask', type=('build', 'run')) From 9ac7e098d90726749e8375a43e57ff7fdfe02150 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:10:04 -0500 Subject: [PATCH 297/499] Add py-pytest-forked package (#13281) --- .../packages/py-pytest-forked/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pytest-forked/package.py diff --git a/var/spack/repos/builtin/packages/py-pytest-forked/package.py b/var/spack/repos/builtin/packages/py-pytest-forked/package.py new file mode 100644 index 00000000000..ac70de01486 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pytest-forked/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPytestForked(PythonPackage): + """Run tests in isolated forked subprocesses.""" + + homepage = "https://github.com/pytest-dev/pytest-forked" + url = "https://pypi.io/packages/source/p/pytest-forked/pytest-forked-1.1.1.tar.gz" + + version('1.1.1', sha256='e2d46f319c8063a3a0536b18f9cdea6eea3bc9fe2cb16c94e1d6fad3abc37300') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm', type='build') + depends_on('py-pytest@3.1.0:', type=('build', 'run')) From 92a359e4ba41b99279999187bebfb4a2502c1578 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:10:22 -0500 Subject: [PATCH 298/499] Add py-mypy package (#13282) --- .../repos/builtin/packages/py-mypy/package.py | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-mypy/package.py diff --git a/var/spack/repos/builtin/packages/py-mypy/package.py b/var/spack/repos/builtin/packages/py-mypy/package.py new file mode 100644 index 00000000000..887964fe5b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-mypy/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyMypy(PythonPackage): + """Optional static typing for Python.""" + + homepage = "http://www.mypy-lang.org/" + url = "https://pypi.io/packages/source/m/mypy/mypy-0.740.tar.gz" + + version('0.740', sha256='48c8bc99380575deb39f5d3400ebb6a8a1cb5cc669bbba4d3bb30f904e0a0e7d') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-typed-ast@1.4.0:1.4.999', type=('build', 'run')) + depends_on('py-typing-extensions@3.7.4:', type=('build', 'run')) + depends_on('py-mypy-extensions@0.4.0:0.4.999', type=('build', 'run')) + depends_on('py-pytest', type='test') + depends_on('py-virtualenv', type='test') + depends_on('py-pip', type='test') + depends_on('py-lxml', type='test') + depends_on('googletest', type='test') From 0443581a2018b6c1449f5b77afec0bb1c640876a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:10:40 -0500 Subject: [PATCH 299/499] Add py-mypy-extensions package (#13283) --- .../packages/py-mypy-extensions/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-mypy-extensions/package.py diff --git a/var/spack/repos/builtin/packages/py-mypy-extensions/package.py b/var/spack/repos/builtin/packages/py-mypy-extensions/package.py new file mode 100644 index 00000000000..f0ee060789c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-mypy-extensions/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyMypyExtensions(PythonPackage): + """Experimental type system extensions for programs checked with the + mypy typechecker.""" + + homepage = "https://github.com/python/mypy_extensions" + url = "https://pypi.io/packages/source/m/mypy-extensions/mypy_extensions-0.4.3.tar.gz" + + version('0.4.3', sha256='2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8') + + depends_on('py-setuptools', type='build') + depends_on('py-typing@3.5.3:', when='^python@:3.4', type=('build', 'run')) From 78942c7840e5d22ed9848ce21cc9929763f35845 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:11:06 -0500 Subject: [PATCH 300/499] Add latest version of py-werkzeug (#13284) --- var/spack/repos/builtin/packages/py-werkzeug/package.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-werkzeug/package.py b/var/spack/repos/builtin/packages/py-werkzeug/package.py index 43f200fb02c..058d3e74d21 100644 --- a/var/spack/repos/builtin/packages/py-werkzeug/package.py +++ b/var/spack/repos/builtin/packages/py-werkzeug/package.py @@ -10,9 +10,14 @@ class PyWerkzeug(PythonPackage): """The Swiss Army knife of Python web development""" homepage = "http://werkzeug.pocoo.org" - url = "https://pypi.io/packages/source/W/Werkzeug/Werkzeug-0.11.11.tar.gz" + url = "https://pypi.io/packages/source/W/Werkzeug/Werkzeug-0.16.0.tar.gz" + version('0.16.0', sha256='7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7') version('0.11.15', sha256='455d7798ac263266dbd38d4841f7534dd35ca9c3da4a8df303f8488f38f3bcc0') version('0.11.11', sha256='e72c46bc14405cba7a26bd2ce28df734471bc9016bc8b4cb69466c2c14c2f7e5') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') + depends_on('py-pytest', type='test') + depends_on('py-hypothesis', type='test') + depends_on('py-requests', type='test') From d2202f6d98cdac9c438b710f853b93430d42f7ad Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:11:23 -0500 Subject: [PATCH 301/499] Add latest version of py-virtualenv (#13285) --- var/spack/repos/builtin/packages/py-virtualenv/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index db0baa73466..d8e45ede312 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -10,8 +10,9 @@ class PyVirtualenv(PythonPackage): """virtualenv is a tool to create isolated Python environments.""" homepage = "https://virtualenv.pypa.io/" - url = "https://pypi.io/packages/source/v/virtualenv/virtualenv-15.1.0.tar.gz" + url = "https://pypi.io/packages/source/v/virtualenv/virtualenv-16.7.6.tar.gz" + version('16.7.6', sha256='5d370508bf32e522d79096e8cbea3499d47e624ac7e11e9089f9397a0b3318df') version('16.4.1', sha256='5a3ecdfbde67a4a3b3111301c4d64a5b71cf862c8c42958d30cf3253df1f29dd') version('16.0.0', sha256='ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752') version('15.1.0', sha256='02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a') @@ -19,7 +20,7 @@ class PyVirtualenv(PythonPackage): version('13.0.1', sha256='36c2cfae0f9c6462264bb19c478fc6bab3478cf0575f1027452e975a1ed84dbd') version('1.11.6', sha256='3e7a4c151e2ee97f51db0215bfd2a073b04a91e9786df6cb67c916f16abe04f7') - depends_on('python@2.6:') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) # not just build-time, requires pkg_resources - depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-setuptools@40.6.3:', type=('build', 'run')) From 4e2cce2c9f8fbf36cb642c7389692b90926f75f4 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:11:41 -0500 Subject: [PATCH 302/499] Add latest version of py-urllib3 (#13286) --- .../repos/builtin/packages/py-urllib3/package.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-urllib3/package.py b/var/spack/repos/builtin/packages/py-urllib3/package.py index 542df740761..2cfadd5c117 100644 --- a/var/spack/repos/builtin/packages/py-urllib3/package.py +++ b/var/spack/repos/builtin/packages/py-urllib3/package.py @@ -11,10 +11,15 @@ class PyUrllib3(PythonPackage): more.""" homepage = "https://urllib3.readthedocs.io/" - url = "https://pypi.io/packages/source/u/urllib3/urllib3-1.20.tar.gz" + url = "https://pypi.io/packages/source/u/urllib3/urllib3-1.25.6.tar.gz" + version('1.25.6', sha256='9a107b99a5393caf59c7aa3c1249c16e6879447533d0887f4336dde834c7be86') version('1.21.1', sha256='b14486978518ca0901a76ba973d7821047409d7f726f22156b24e83fd71382a5') - version('1.20', sha256='97ef2b6e2878d84c0126b9f4e608e37a951ca7848e4855a7f7f4437d5c34a72f') - version('1.14', sha256='dd4fb13a4ce50b18338c7e4d665b21fd38632c5d4b1d9f1a1379276bd3c08d37') + version('1.20', sha256='97ef2b6e2878d84c0126b9f4e608e37a951ca7848e4855a7f7f4437d5c34a72f') + version('1.14', sha256='dd4fb13a4ce50b18338c7e4d665b21fd38632c5d4b1d9f1a1379276bd3c08d37') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') + depends_on('py-pytest', type='test') + depends_on('py-mock', type='test') + depends_on('py-tornado', type='test') From 5995c3f85bf7b3066ea7e0cd485654ed4164b5cf Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:12:27 -0500 Subject: [PATCH 303/499] Add latest version of py-typing-extensions (#13288) --- .../repos/builtin/packages/py-typing-extensions/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-typing-extensions/package.py b/var/spack/repos/builtin/packages/py-typing-extensions/package.py index 35f1c4288da..bb981b85198 100644 --- a/var/spack/repos/builtin/packages/py-typing-extensions/package.py +++ b/var/spack/repos/builtin/packages/py-typing-extensions/package.py @@ -13,9 +13,11 @@ class PyTypingExtensions(PythonPackage): details about protocols and static duck typing).""" homepage = "https://github.com/python/typing/tree/master/typing_extensions" - url = "https://pypi.io/packages/source/t/typing_extensions/typing_extensions-3.7.2.tar.gz" + url = "https://pypi.io/packages/source/t/typing_extensions/typing_extensions-3.7.4.tar.gz" + version('3.7.4', sha256='2ed632b30bb54fc3941c382decfd0ee4148f5c591651c9272473fea2c6397d95') version('3.7.2', sha256='fb2cd053238d33a8ec939190f30cfd736c00653a85a2919415cecf7dc3d9da71') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-typing@3.6.4:', type=('build', 'run')) + depends_on('py-typing@3.7.4:', when='^python@:3.4', type=('build', 'run')) From de6d53b626eca8ed140d34fc3c43f2660748cd4c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:12:43 -0500 Subject: [PATCH 304/499] Add latest version of py-torchvision (#13289) --- var/spack/repos/builtin/packages/py-torchvision/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-torchvision/package.py b/var/spack/repos/builtin/packages/py-torchvision/package.py index c322ac8f55e..d369cef54bd 100644 --- a/var/spack/repos/builtin/packages/py-torchvision/package.py +++ b/var/spack/repos/builtin/packages/py-torchvision/package.py @@ -11,7 +11,7 @@ class PyTorchvision(PythonPackage): architectures, and common image transformations for computer vision.""" homepage = "https://github.com/pytorch/vision" - url = "https://github.com/pytorch/vision/archive/v0.3.0.tar.gz" + url = "https://github.com/pytorch/vision/archive/v0.4.0.tar.gz" maintainers = ['adamjstewart'] import_modules = [ @@ -21,13 +21,16 @@ class PyTorchvision(PythonPackage): 'torchvision.models.detection' ] + version('0.4.0', sha256='c270d74e568bad4559fed4544f6dd1e22e2eb1c60b088e04a5bd5787c4150589') version('0.3.0', sha256='c205f0618c268c6ed2f8abb869ef6eb83e5339c1336c243ad321a2f2a85195f0') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) + depends_on('py-torch@1.2.0:', when='@0.4.0:', type=('build', 'run')) depends_on('py-torch@1.1.0:', type=('build', 'run')) depends_on('py-pillow@4.1.1:', type=('build', 'run')) # or py-pillow-simd # Many of the datasets require additional dependencies to use. # These can be installed after the fact. + depends_on('py-scipy', type='test') From db8f83d3333d81b636661be2e293fbd78777fbdd Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:13:55 -0500 Subject: [PATCH 305/499] Add latest version of py-flask (#13316) --- .../repos/builtin/packages/py-flask/package.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-flask/package.py b/var/spack/repos/builtin/packages/py-flask/package.py index bb7f5781837..b2b68ec05fe 100644 --- a/var/spack/repos/builtin/packages/py-flask/package.py +++ b/var/spack/repos/builtin/packages/py-flask/package.py @@ -7,17 +7,19 @@ class PyFlask(PythonPackage): - """A microframework based on Werkzeug, Jinja2 and good intentions""" + """A simple framework for building complex web applications.""" - homepage = "http://github.com/pallets/flask" - url = "https://pypi.io/packages/source/F/Flask/Flask-0.11.1.tar.gz" + homepage = "https://palletsprojects.com/p/flask/" + url = "https://pypi.io/packages/source/F/Flask/Flask-1.1.1.tar.gz" + version('1.1.1', sha256='13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52') version('0.12.2', sha256='49f44461237b69ecd901cc7ce66feea0319b9158743dd27a2899962ab214dac1') version('0.12.1', sha256='9dce4b6bfbb5b062181d3f7da8f727ff70c1156cbb4024351eafd426deb5fb88') version('0.11.1', sha256='b4713f2bfb9ebc2966b8a49903ae0d3984781d5c878591cf2f7b484d28756b0e') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-werkzeug@0.7:', type=('build', 'run')) - depends_on('py-jinja2@2.4:', type=('build', 'run')) - depends_on('py-itsdangerous@0.21:', type=('build', 'run')) - depends_on('py-click@2.0:', type=('build', 'run')) + depends_on('py-werkzeug@0.15:', type=('build', 'run')) + depends_on('py-jinja2@2.10.1:', type=('build', 'run')) + depends_on('py-itsdangerous@0.24:', type=('build', 'run')) + depends_on('py-click@5.1:', type=('build', 'run')) From 5aea70e733dcaa6ab06e36be4adcff1f3e0440aa Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:14:17 -0500 Subject: [PATCH 306/499] Add latest version of py-httpbin (#13315) --- .../builtin/packages/py-httpbin/package.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-httpbin/package.py b/var/spack/repos/builtin/packages/py-httpbin/package.py index 3933c8c4601..7c3078ed09d 100644 --- a/var/spack/repos/builtin/packages/py-httpbin/package.py +++ b/var/spack/repos/builtin/packages/py-httpbin/package.py @@ -10,13 +10,17 @@ class PyHttpbin(PythonPackage): """HTTP Request and Response Service""" homepage = "https://github.com/Runscope/httpbin" - url = "https://pypi.io/packages/source/h/httpbin/httpbin-0.5.0.tar.gz" + url = "https://pypi.io/packages/source/h/httpbin/httpbin-0.7.0.tar.gz" + version('0.7.0', sha256='cbb37790c91575f4f15757f42ad41d9f729eb227d5edbe89e4ec175486db8dfa') version('0.5.0', sha256='79fbc5d27e4194ea908b0fa18e09a59d95d287c91667aa69bcd010342d1589b5') - depends_on('py-setuptools', type='build') - depends_on('py-decorator@3.4.0:', type=('build', 'run')) - depends_on('py-flask@0.10.1:', type=('build', 'run')) - depends_on('py-itsdangerous@0.24:', type=('build', 'run')) - depends_on('py-markupsafe@0.23:', type=('build', 'run')) - depends_on('py-six@1.6.1:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-flask', type=('build', 'run')) + depends_on('py-markupsafe', type=('build', 'run')) + depends_on('py-decorator', type=('build', 'run')) + depends_on('py-itsdangerous', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-brotlipy', type=('build', 'run')) + depends_on('py-raven+flask', type=('build', 'run')) + depends_on('py-werkzeug@0.14.1:', type=('build', 'run')) From ac0fee0f345e8f9e4cfcda372670c4eb6ead1a23 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:14:32 -0500 Subject: [PATCH 307/499] Add latest version of py-hypothesis (#13314) --- .../repos/builtin/packages/py-hypothesis/package.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-hypothesis/package.py b/var/spack/repos/builtin/packages/py-hypothesis/package.py index cc50b5b85b3..2820ddcd7e2 100644 --- a/var/spack/repos/builtin/packages/py-hypothesis/package.py +++ b/var/spack/repos/builtin/packages/py-hypothesis/package.py @@ -10,18 +10,20 @@ class PyHypothesis(PythonPackage): """A library for property based testing.""" homepage = "https://github.com/HypothesisWorks/hypothesis-python" - url = "https://pypi.io/packages/source/h/hypothesis/hypothesis-3.7.0.tar.gz" + url = "https://pypi.io/packages/source/h/hypothesis/hypothesis-4.41.2.tar.gz" import_modules = [ 'hypothesis', 'hypothesis.searchstrategy', 'hypothesis.extra', - 'hypothesis.tools', 'hypothesis.utils', 'hypothesis.vendor', - 'hypothesis.internal', 'hypothesis.internal.conjecture' + 'hypothesis.utils', 'hypothesis.vendor', 'hypothesis.internal', + 'hypothesis.internal.conjecture' ] # TODO: Add missing dependency required to import hypothesis.extra.django + version('4.41.2', sha256='6847df3ffb4aa52798621dd007e6b61dbcf2d76c30ba37dc2699720e2c734b7a') version('4.7.2', sha256='87944c6379f77634474b88abbf1e5ed5fe966637cc926131eda5e2af5b54a608') - version('3.7.0', sha256='0fea49d08f2d5884f014151a5af6fb48d862f6ad567ffc4a2e84abf2f186c423') + version('3.7.0', sha256='0fea49d08f2d5884f014151a5af6fb48d862f6ad567ffc4a2e84abf2f186c423') depends_on('py-setuptools', type='build') + depends_on('py-attrs@19.2.0:', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run'), when='^python@:2') From e05d165f92a684e6f1299f90ece87d3f7befa3f2 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:14:46 -0500 Subject: [PATCH 308/499] Add latest version of py-idna (#13313) --- var/spack/repos/builtin/packages/py-idna/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-idna/package.py b/var/spack/repos/builtin/packages/py-idna/package.py index 6d4aa05f2ce..26850800569 100644 --- a/var/spack/repos/builtin/packages/py-idna/package.py +++ b/var/spack/repos/builtin/packages/py-idna/package.py @@ -11,9 +11,10 @@ class PyIdna(PythonPackage): """Internationalized Domain Names for Python (IDNA 2008 and UTS #46) """ homepage = "https://github.com/kjd/idna" - url = "https://pypi.io/packages/source/i/idna/idna-2.5.tar.gz" + url = "https://pypi.io/packages/source/i/idna/idna-2.8.tar.gz" + version('2.8', sha256='c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407') version('2.5', sha256='3cb5ce08046c4e3a560fc02f138d0ac63e00f8ce5901a56b32ec8b7994082aab') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type=('build', 'link')) - depends_on('python@2.6:', type=('build', 'run')) From d61b5125c5fc979c3ccdbcdaa926af660f585352 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:15:01 -0500 Subject: [PATCH 309/499] Add latest version of py-itsdangerous (#13312) --- var/spack/repos/builtin/packages/py-itsdangerous/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-itsdangerous/package.py b/var/spack/repos/builtin/packages/py-itsdangerous/package.py index e7098c2d85c..e92393d1765 100644 --- a/var/spack/repos/builtin/packages/py-itsdangerous/package.py +++ b/var/spack/repos/builtin/packages/py-itsdangerous/package.py @@ -10,8 +10,10 @@ class PyItsdangerous(PythonPackage): """Various helpers to pass trusted data to untrusted environments.""" homepage = "http://github.com/mitsuhiko/itsdangerous" - url = "https://pypi.io/packages/source/i/itsdangerous/itsdangerous-0.24.tar.gz" + url = "https://pypi.io/packages/source/i/itsdangerous/itsdangerous-1.1.0.tar.gz" - version('0.24', sha256='cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519') + version('1.1.0', sha256='321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19') + version('0.24', sha256='cbb3fcf8d3e33df861709ecaf89d9e6629cff0a217bc2848f1b41cd30d360519') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') From 51432aa92e233ba3c9db500e4e3d55b7067e906c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:15:16 -0500 Subject: [PATCH 310/499] Add latest version of py-jinja2 (#13311) --- .../builtin/packages/py-jinja2/package.py | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py index 530a2503788..b0daeaa1af8 100644 --- a/var/spack/repos/builtin/packages/py-jinja2/package.py +++ b/var/spack/repos/builtin/packages/py-jinja2/package.py @@ -11,19 +11,20 @@ class PyJinja2(PythonPackage): a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" - homepage = "http://jinja.pocoo.org/" - url = "https://pypi.io/packages/source/J/Jinja2/Jinja2-2.9.6.tar.gz" + homepage = "https://palletsprojects.com/p/jinja/" + url = "https://pypi.io/packages/source/J/Jinja2/Jinja2-2.10.3.tar.gz" import_modules = ['jinja2'] - version('2.10', sha256='f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4') - version('2.9.6', sha256='ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff') - version('2.8', sha256='bc1ff2ff88dbfacefde4ddde471d1417d3b304e8df103a7a9437d47269201bf4') - version('2.7.3', sha256='2e24ac5d004db5714976a04ac0e80c6df6e47e98c354cb2c0d82f8879d4f8fdb') - version('2.7.2', sha256='310a35fbccac3af13ebf927297f871ac656b9da1d248b1fe6765affa71b53235') - version('2.7.1', sha256='5cc0a087a81dca1c08368482fb7a92fe2bdd8cfbb22bc0fccfe6c85affb04c8b') - version('2.7', sha256='474f1518d189ae7e318b139fecc1d30b943f124448cfa0f09582ca23e069fa4d') + version('2.10.3', sha256='9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de') + version('2.10', sha256='f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4') + version('2.9.6', sha256='ddaa01a212cd6d641401cb01b605f4a4d9f37bfc93043d7f760ec70fb99ff9ff') + version('2.8', sha256='bc1ff2ff88dbfacefde4ddde471d1417d3b304e8df103a7a9437d47269201bf4') + version('2.7.3', sha256='2e24ac5d004db5714976a04ac0e80c6df6e47e98c354cb2c0d82f8879d4f8fdb') + version('2.7.2', sha256='310a35fbccac3af13ebf927297f871ac656b9da1d248b1fe6765affa71b53235') + version('2.7.1', sha256='5cc0a087a81dca1c08368482fb7a92fe2bdd8cfbb22bc0fccfe6c85affb04c8b') + version('2.7', sha256='474f1518d189ae7e318b139fecc1d30b943f124448cfa0f09582ca23e069fa4d') depends_on('py-setuptools', type='build') - depends_on('py-markupsafe', type=('build', 'run')) + depends_on('py-markupsafe@0.23:', type=('build', 'run')) depends_on('py-babel@0.8:', type=('build', 'run')) # optional, required for i18n From 30fdff4ff94489ddd7da317c565db461edf84050 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:15:32 -0500 Subject: [PATCH 311/499] Add latest version of py-lxml (#13310) --- var/spack/repos/builtin/packages/py-lxml/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-lxml/package.py b/var/spack/repos/builtin/packages/py-lxml/package.py index e045f9597d9..86dcd9181be 100644 --- a/var/spack/repos/builtin/packages/py-lxml/package.py +++ b/var/spack/repos/builtin/packages/py-lxml/package.py @@ -11,13 +11,14 @@ class PyLxml(PythonPackage): XML and HTML in the Python language.""" homepage = "http://lxml.de/" - url = "https://pypi.io/packages/source/l/lxml/lxml-2.3.tar.gz" + url = "https://pypi.io/packages/source/l/lxml/lxml-4.4.1.tar.gz" + version('4.4.1', sha256='c81cb40bff373ab7a7446d6bbca0190bccc5be3448b47b51d729e37799bb5692') version('4.2.5', sha256='36720698c29e7a9626a0dc802ef8885f8f0239bfd1689628ecd459a061f2807f') version('3.7.3', sha256='aa502d78a51ee7d127b4824ff96500f0181d3c7826e6ee7b800d068be79361c7') version('2.3', sha256='eea1b8d29532739c1383cb4794c5eacd6176f0972b59e8d29348335b87ff2e66') - depends_on('py-setuptools@0.6c5:', type='build') - depends_on('py-cython@0.20:', type='build') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') depends_on('libxml2', type=('build', 'run')) depends_on('libxslt', type=('build', 'run')) From 0d189e779a902cc66ce8524fb800142e6168c00f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:15:51 -0500 Subject: [PATCH 312/499] Add latest version of py-markupsafe (#13309) --- .../builtin/packages/py-markupsafe/package.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py index dcae1c3ae9f..d962c3615a6 100644 --- a/var/spack/repos/builtin/packages/py-markupsafe/package.py +++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py @@ -13,15 +13,17 @@ class PyMarkupsafe(PythonPackage): Mako templating engine, the Pylons web framework and many more.""" homepage = "http://www.pocoo.org/projects/markupsafe/" - url = "https://pypi.io/packages/source/M/MarkupSafe/MarkupSafe-1.0.tar.gz" + url = "https://pypi.io/packages/source/M/MarkupSafe/MarkupSafe-1.1.1.tar.gz" import_modules = ['markupsafe'] - version('1.0', sha256='a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665') - version('0.23', sha256='a4ec1aff59b95a14b45eb2e23761a0179e98319da5a7eb76b56ea8cdc7b871c3') - version('0.22', sha256='7642852b6d1e55c9e12e00a552c0b8943880f2172e55141ccb41eb5f8675dfa5') - version('0.21', sha256='c6465cd6ed2b96509ef0100e7fff8718ed52c2affab1860ed5a9b67f604dd59a') - version('0.20', sha256='f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8') - version('0.19', sha256='62fcc5d641df8b5ad271ebbd6b77a19cd92eceba1e1a990de4e96c867789f037') + version('1.1.1', sha256='29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b') + version('1.0', sha256='a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665') + version('0.23', sha256='a4ec1aff59b95a14b45eb2e23761a0179e98319da5a7eb76b56ea8cdc7b871c3') + version('0.22', sha256='7642852b6d1e55c9e12e00a552c0b8943880f2172e55141ccb41eb5f8675dfa5') + version('0.21', sha256='c6465cd6ed2b96509ef0100e7fff8718ed52c2affab1860ed5a9b67f604dd59a') + version('0.20', sha256='f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8') + version('0.19', sha256='62fcc5d641df8b5ad271ebbd6b77a19cd92eceba1e1a990de4e96c867789f037') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') From c130a2980f5b618da8ba9aa2c30b6caac5900e15 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:16:07 -0500 Subject: [PATCH 313/499] Add latest version of py-mock (#13308) --- .../repos/builtin/packages/py-mock/package.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py index 516f1aff2df..90fecff01e5 100644 --- a/var/spack/repos/builtin/packages/py-mock/package.py +++ b/var/spack/repos/builtin/packages/py-mock/package.py @@ -12,14 +12,16 @@ class PyMock(PythonPackage): they have been used.""" homepage = "https://github.com/testing-cabal/mock" - url = "https://pypi.io/packages/source/m/mock/mock-1.3.0.tar.gz" + url = "https://pypi.io/packages/source/m/mock/mock-3.0.5.tar.gz" + version('3.0.5', sha256='83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3') version('2.0.0', sha256='b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba') version('1.3.0', sha256='1e247dbecc6ce057299eb7ee019ad68314bb93152e81d9a6110d35f4d5eca0f6') - depends_on('py-pbr@0.11:', type=('build', 'run')) - depends_on('py-six@1.7:', type=('build', 'run')) - depends_on('py-six@1.9:', type=('build', 'run'), when='@2.0.0:') - # requirements.txt references @1:, but 0.4 is newest available.. - depends_on('py-funcsigs', type=('build', 'run'), when='^python@:3.2.99') - depends_on('py-setuptools@17.1:', type='build') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-six@1.7:', type=('build', 'run')) + depends_on('py-six@1.9:', type=('build', 'run'), when='@2.0.0:') + depends_on('py-funcsigs@1:', type=('build', 'run'), when='^python@:3.2') + depends_on('py-pytest', type='test') + depends_on('py-pytest-cov', type='test') From 04af812e032e58f4cff858fc67a95f22e59b305b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:16:36 -0500 Subject: [PATCH 314/499] Add latest version of py-pip (#13306) --- var/spack/repos/builtin/packages/py-pip/package.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pip/package.py b/var/spack/repos/builtin/packages/py-pip/package.py index 28a58dea5f0..24883e0712b 100644 --- a/var/spack/repos/builtin/packages/py-pip/package.py +++ b/var/spack/repos/builtin/packages/py-pip/package.py @@ -10,14 +10,15 @@ class PyPip(PythonPackage): """The PyPA recommended tool for installing Python packages.""" homepage = "https://pypi.python.org/pypi/pip" - url = "https://pypi.io/packages/source/p/pip/pip-9.0.1.tar.gz" + url = "https://pypi.io/packages/source/p/pip/pip-19.3.tar.gz" + version('19.3', sha256='324d234b8f6124846b4e390df255cacbe09ce22791c3b714aa1ea6e44a4f2861') version('19.0.3', sha256='6e6f197a1abfb45118dbb878b5c859a0edbdd33fd250100bc015b67fded4b9f2') - version('18.1', sha256='c0a292bd977ef590379a3f05d7b7f65135487b67470f6281289a94e015650ea1') + version('18.1', sha256='c0a292bd977ef590379a3f05d7b7f65135487b67470f6281289a94e015650ea1') version('10.0.1', sha256='f2bd08e0cd1b06e10218feaf6fef299f473ba706582eb3bd9d52203fdbd7ee68') - version('9.0.1', sha256='09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d') + version('9.0.1', sha256='09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d') - depends_on('python@2.6:2.8,3.3:') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) # Most Python packages only require setuptools as a build dependency. # However, pip requires setuptools during runtime as well. From d4f409ea5159e2828bce0b3834187a003b2c46a3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:16:53 -0500 Subject: [PATCH 315/499] Add latest version of py-psutil (#13305) --- var/spack/repos/builtin/packages/py-psutil/package.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-psutil/package.py b/var/spack/repos/builtin/packages/py-psutil/package.py index 2e4abedf6cf..6c3720bc622 100644 --- a/var/spack/repos/builtin/packages/py-psutil/package.py +++ b/var/spack/repos/builtin/packages/py-psutil/package.py @@ -12,11 +12,15 @@ class PyPsutil(PythonPackage): in Python.""" homepage = "https://pypi.python.org/pypi/psutil" - url = "https://pypi.io/packages/source/p/psutil/psutil-5.4.5.tar.gz" + url = "https://pypi.io/packages/source/p/psutil/psutil-5.6.3.tar.gz" + version('5.6.3', sha256='863a85c1c0a5103a12c05a35e59d336e1d665747e531256e061213e2e90f63f3') version('5.5.1', sha256='72cebfaa422b7978a1d3632b65ff734a34c6b34f4578b68a5c204d633756b810') version('5.4.5', sha256='ebe293be36bb24b95cdefc5131635496e88b17fabbcf1e4bc9b5c01f5e489cfe') version('5.0.1', sha256='9d8b7f8353a2b2eb6eb7271d42ec99d0d264a9338a37be46424d56b4e473b39e') - depends_on('python@2.6:') + depends_on('python@2.6:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') + depends_on('py-unittest2', when='^python@:2.6', type='test') + depends_on('py-mock', when='^python@:2.7', type='test') + depends_on('py-ipaddress', when='^python@:3.2', type='test') From 10065b325dc119bbf32771527f454471cc2de9bd Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:17:11 -0500 Subject: [PATCH 316/499] Add latest version of py-pycparser (#13304) --- var/spack/repos/builtin/packages/py-pycparser/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py index e93ff6879f9..d82b4e3c86d 100644 --- a/var/spack/repos/builtin/packages/py-pycparser/package.py +++ b/var/spack/repos/builtin/packages/py-pycparser/package.py @@ -8,13 +8,16 @@ class PyPycparser(PythonPackage): """A complete parser of the C language, written in pure python.""" + homepage = "https://github.com/eliben/pycparser" - url = "https://pypi.io/packages/source/p/pycparser/pycparser-2.17.tar.gz" + url = "https://pypi.io/packages/source/p/pycparser/pycparser-2.19.tar.gz" import_modules = ['pycparser', 'pycparser.ply'] + version('2.19', sha256='a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3') version('2.18', sha256='99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226') version('2.17', sha256='0aac31e917c24cb3357f5a4d5566f2cc91a19ca41862f6c3c22dc60a629673b6') version('2.13', sha256='b399599a8a0e386bfcbc5e01a38d79dd6e926781f9e358cd5512f41ab7d20eb7') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') From 03b1af0d960d164ec9fb2494dc9de45955d46bea Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:17:27 -0500 Subject: [PATCH 317/499] Add latest version of py-pysocks (#13303) --- var/spack/repos/builtin/packages/py-pysocks/package.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pysocks/package.py b/var/spack/repos/builtin/packages/py-pysocks/package.py index da0c2f620a0..32e781b2c0e 100644 --- a/var/spack/repos/builtin/packages/py-pysocks/package.py +++ b/var/spack/repos/builtin/packages/py-pysocks/package.py @@ -10,7 +10,13 @@ class PyPysocks(PythonPackage): """A Python SOCKS client module.""" homepage = "https://github.com/Anorov/PySocks" - url = "https://pypi.io/packages/source/P/PySocks/PySocks-1.6.6.tar.gz" + url = "https://pypi.io/packages/source/P/PySocks/PySocks-1.7.1.tar.gz" + version('1.7.1', sha256='3f8804571ebe159c380ac6de37643bb4685970655d3bba243530d6558b799aa0') version('1.6.6', sha256='02419a225ff5dcfc3c9695ef8fc9b4d8cc99658e650c6d4718d4c8f451e63f41') version('1.5.7', sha256='e51c7694b10288e6fd9a28e15c0bcce9aca0327e7b32ebcd9af05fcd56f38b88') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-psutil', type='test') + depends_on('py-pytest', type='test') From 63dd97f84ecb7a84c54575e4a67125d7aa5e9139 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:17:47 -0500 Subject: [PATCH 318/499] Add latest version of py-pytest-cov (#13302) --- .../repos/builtin/packages/py-pytest-cov/package.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pytest-cov/package.py b/var/spack/repos/builtin/packages/py-pytest-cov/package.py index c70dad68b8a..91a9d5be461 100644 --- a/var/spack/repos/builtin/packages/py-pytest-cov/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-cov/package.py @@ -10,12 +10,14 @@ class PyPytestCov(PythonPackage): """Pytest plugin for measuring coverage.""" homepage = "https://github.com/pytest-dev/pytest-cov" - url = "https://pypi.io/packages/source/p/pytest-cov/pytest-cov-2.3.1.tar.gz" + url = "https://pypi.io/packages/source/p/pytest-cov/pytest-cov-2.8.1.tar.gz" + version('2.8.1', sha256='cc6742d8bac45070217169f5f72ceee1e0e55b0221f54bcf24845972d3a47f2b') version('2.3.1', sha256='fa0a212283cdf52e2eecc24dd6459bb7687cc29adb60cb84258fab73be8dda0f') extends('python', ignore=r'bin/*') - depends_on('py-setuptools', type='build') - depends_on('py-pytest@2.6.0:', type=('build', 'run')) - depends_on('py-coverage@3.7.1:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-pytest@3.6:', type=('build', 'run')) + depends_on('py-coverage@4.4:', type=('build', 'run')) From 4d7226e56128637041bcd35e27b147d6559c59be Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:18:04 -0500 Subject: [PATCH 319/499] Add latest version of py-pytest-httpbin (#13301) --- .../builtin/packages/py-pytest-httpbin/package.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py index 02fdaeddd30..8d5cf502505 100644 --- a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py @@ -10,14 +10,17 @@ class PyPytestHttpbin(PythonPackage): """Easily test your HTTP library against a local copy of httpbin""" homepage = "https://github.com/kevin1024/pytest-httpbin" - url = "https://pypi.io/packages/source/p/pytest-httpbin/pytest-httpbin-0.2.3.tar.gz" + url = "https://pypi.io/packages/source/p/pytest-httpbin/pytest-httpbin-1.0.0.tar.gz" + version('1.0.0', sha256='d8ce547f42423026550ed7765f6c6d50c033b43025e8592270a7abf970e19b72') version('0.2.3', sha256='c5b698dfa474ffc9caebcb35e34346b753eb226aea5c2e1b69fefedbcf161bf8') + version('0.0.7', sha256='03af8a7055c8bbcb68b14d9a14c103c82c97aeb86a8f1b29cd63d83644c2f021') extends('python', ignore=r'bin/flask') depends_on('py-setuptools', type='build') - depends_on('py-flask', type=('build', 'run')) - depends_on('py-decorator', type=('build', 'run')) - depends_on('py-httpbin', type=('build', 'run')) - depends_on('py-six', type=('build', 'run')) + depends_on('py-flask', when='@:0.2', type=('build', 'run')) + depends_on('py-decorator', when='@:0.2', type=('build', 'run')) + depends_on('py-httpbin', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-pytest', type='test') From 3a2eeedf208bc562188fb6ec17cd0322d2cf1417 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:18:39 -0500 Subject: [PATCH 320/499] Add latest version of py-pytest-mock (#13300) --- .../repos/builtin/packages/py-pytest-mock/package.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pytest-mock/package.py b/var/spack/repos/builtin/packages/py-pytest-mock/package.py index 45a3ffb163b..32c89a10ba0 100644 --- a/var/spack/repos/builtin/packages/py-pytest-mock/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-mock/package.py @@ -10,12 +10,15 @@ class PyPytestMock(PythonPackage): """Thin-wrapper around the mock package for easier use with py.test""" homepage = "https://github.com/pytest-dev/pytest-mock" - url = "https://pypi.io/packages/source/p/pytest-mock/pytest-mock-1.2.zip" + url = "https://pypi.io/packages/source/p/pytest-mock/pytest-mock-1.11.1.tar.gz" - version('1.2', sha256='f78971ed376fcb265255d1e4bb313731b3a1be92d7f3ecb19ea7fedc4a56fd0f') + version('1.11.1', sha256='f1ab8aefe795204efe7a015900296d1719e7bf0f4a0558d71e8599da1d1309d0') + version('1.2', sha256='f78971ed376fcb265255d1e4bb313731b3a1be92d7f3ecb19ea7fedc4a56fd0f', + url='https://pypi.io/packages/source/p/pytest-mock/pytest-mock-1.2.zip') extends('python', ignore=r'bin/*') - depends_on('py-setuptools', type='build') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm', type='build') depends_on('py-pytest@2.7:', type=('build', 'run')) - depends_on('py-mock', type=('build', 'run')) From f832f12ca687622ea3db45a91378de2ae30ef3b3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:18:55 -0500 Subject: [PATCH 321/499] Add latest version of py-pytest-runner (#13299) --- var/spack/repos/builtin/packages/py-pytest-runner/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pytest-runner/package.py b/var/spack/repos/builtin/packages/py-pytest-runner/package.py index a2826ae4f8f..415efa0703f 100644 --- a/var/spack/repos/builtin/packages/py-pytest-runner/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-runner/package.py @@ -10,10 +10,11 @@ class PyPytestRunner(PythonPackage): """Invoke py.test as distutils command with dependency resolution.""" homepage = "https://github.com/pytest-dev/pytest-runner" - url = "https://pypi.io/packages/source/p/pytest-runner/pytest-runner-2.11.1.tar.gz" + url = "https://pypi.io/packages/source/p/pytest-runner/pytest-runner-5.1.tar.gz" import_modules = ['ptr'] + version('5.1', sha256='25a013c8d84f0ca60bb01bd11913a3bcab420f601f0f236de4423074af656e7a') version('2.11.1', sha256='983a31eab45e375240e250161a556163bc8d250edaba97960909338c273a89b3') depends_on('py-setuptools', type='build') From b76f1687fb61f4879ece5f3b177c0c6ed2753325 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:19:11 -0500 Subject: [PATCH 322/499] Add latest version of py-pytest-xdist (#13298) --- .../repos/builtin/packages/py-pytest-xdist/package.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py index 688e19878c0..a35d8995e4d 100644 --- a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py @@ -10,11 +10,14 @@ class PyPytestXdist(PythonPackage): """py.test xdist plugin for distributed testing and loop-on-failing mode""" homepage = "https://github.com/pytest-dev/pytest-xdist" - url = "https://pypi.io/packages/source/p/pytest-xdist/pytest-xdist-1.16.0.tar.gz" + url = "https://pypi.io/packages/source/p/pytest-xdist/pytest-xdist-1.30.0.tar.gz" + version('1.30.0', sha256='5d1b1d4461518a6023d56dab62fb63670d6f7537f23e2708459a557329accf48') version('1.16.0', sha256='42e5a1e5da9d7cff3e74b07f8692598382f95624f234ff7e00a3b1237e0feba2') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-execnet@1.1:', type=('build', 'run')) - depends_on('py-pytest@2.7.0:', type=('build', 'run')) - depends_on('py-py@1.4.22:', type=('build', 'run')) + depends_on('py-pytest@4.4.0:', type=('build', 'run')) + depends_on('py-pytest-forked', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) From 35362adb978419aa060283416e73a766d2f03c31 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:19:29 -0500 Subject: [PATCH 323/499] Add latest version of py-pyyaml (#13297) --- .../repos/builtin/packages/py-pyyaml/package.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py index 3761663c1de..980d5fae516 100644 --- a/var/spack/repos/builtin/packages/py-pyyaml/package.py +++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py @@ -9,8 +9,12 @@ class PyPyyaml(PythonPackage): """PyYAML is a YAML parser and emitter for Python.""" homepage = "http://pyyaml.org/wiki/PyYAML" - url = "http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz" + url = "http://pyyaml.org/download/pyyaml/PyYAML-5.1.2.tar.gz" - version('3.13', sha256='3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf') - version('3.12', sha256='592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab') - version('3.11', sha256='c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8') + version('5.1.2', sha256='01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4') + version('3.13', sha256='3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf') + version('3.12', sha256='592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab') + version('3.11', sha256='c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('libyaml') From a2e7f0e9d2439ad7403cc8edbb179d4da538dd08 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:19:51 -0500 Subject: [PATCH 324/499] Add latest version of py-requests (#13296) --- .../builtin/packages/py-requests/package.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-requests/package.py b/var/spack/repos/builtin/packages/py-requests/package.py index 8a76d9622f7..f93ad6d9523 100644 --- a/var/spack/repos/builtin/packages/py-requests/package.py +++ b/var/spack/repos/builtin/packages/py-requests/package.py @@ -10,7 +10,7 @@ class PyRequests(PythonPackage): """Python HTTP for Humans.""" homepage = "http://python-requests.org" - url = "https://pypi.io/packages/source/r/requests/requests-2.14.2.tar.gz" + url = "https://pypi.io/packages/source/r/requests/requests-2.22.0.tar.gz" import_modules = [ 'requests', 'requests.packages', 'requests.packages.chardet', @@ -23,20 +23,24 @@ class PyRequests(PythonPackage): 'requests.packages.urllib3.contrib._securetransport' ] + version('2.22.0', sha256='11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4') version('2.21.0', sha256='502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e') version('2.14.2', sha256='a274abba399a23e8713ffd2b5706535ae280ebe2b8069ee6a941cb089440d153') version('2.13.0', sha256='5722cd09762faa01276230270ff16af7acf7c5c45d623868d9ba116f15791ce8') version('2.11.1', sha256='5acf980358283faba0b897c73959cecf8b841205bb4b2ad3ef545f46eae1a133') version('2.3.0', sha256='1c1473875d846fe563d70868acf05b1953a4472f4695b7b3566d1d978957b8fc') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-chardet@3.0.2:3.0.999', type=('build', 'run'), when='@2.16.0:') - depends_on('py-idna@2.5', type=('build', 'run'), when='@2.16.0:') - depends_on('py-urllib3@1.21.1:1.21.999', type=('build', 'run'), when='@2.16.0:') - depends_on('py-certifi@2017.4.17', type=('build', 'run'), when='@2.16.0:') + depends_on('py-idna@2.5:2.8', type=('build', 'run'), when='@2.16.0:') + depends_on('py-urllib3@1.21.1:1.24,1.25.2:1.25.999', type=('build', 'run'), when='@2.16.0:') + depends_on('py-certifi@2017.4.17:', type=('build', 'run'), when='@2.16.0:') - depends_on('py-pytest@2.8.0:', type='test') - depends_on('py-pytest-cov', type='test') depends_on('py-pytest-httpbin@0.0.7', type='test') + depends_on('py-pytest-cov', type='test') depends_on('py-pytest-mock', type='test') + depends_on('py-pytest-xdist', type='test') + depends_on('py-pysocks@1.5.6,1.5.8:', type='test') + depends_on('py-pytest@2.8.0:', type='test') From 2268dd9e8f8bdbfe2750d7f4df767b271bcccb60 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:20:21 -0500 Subject: [PATCH 325/499] Add latest version of py-snowballstemmer (#13294) --- .../repos/builtin/packages/py-snowballstemmer/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py index 19a26ca5cf5..20a65a1b457 100644 --- a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py +++ b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py @@ -11,8 +11,11 @@ class PySnowballstemmer(PythonPackage): English stemmer) generated from Snowball algorithms.""" homepage = "https://github.com/shibukawa/snowball_py" - url = "https://pypi.io/packages/source/s/snowballstemmer/snowballstemmer-1.2.1.tar.gz" + url = "https://pypi.io/packages/source/s/snowballstemmer/snowballstemmer-2.0.0.tar.gz" import_modules = ['snowballstemmer'] + version('2.0.0', sha256='df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52') version('1.2.1', sha256='919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128') + + depends_on('py-setuptools', type='build') From 21d14a19f656e8de2eb76f201900545265147f5f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:20:46 -0500 Subject: [PATCH 326/499] Add latest version of py-sphinx (#13293) --- .../builtin/packages/py-sphinx/package.py | 64 ++++++++++--------- 1 file changed, 33 insertions(+), 31 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py index aaf21e6eec6..291b064b5db 100644 --- a/var/spack/repos/builtin/packages/py-sphinx/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx/package.py @@ -8,8 +8,9 @@ class PySphinx(PythonPackage): """Sphinx Documentation Generator.""" + homepage = "http://sphinx-doc.org" - url = "https://pypi.io/packages/source/S/Sphinx/Sphinx-1.6.1.tar.gz" + url = "https://pypi.io/packages/source/S/Sphinx/Sphinx-2.2.0.tar.gz" import_modules = [ 'sphinx', 'sphinx.testing', 'sphinx.ext', 'sphinx.pycode', @@ -21,8 +22,9 @@ class PySphinx(PythonPackage): 'sphinx.environment.collectors', 'sphinx.environment.adapters' ] - version('1.8.4', sha256='c1c00fc4f6e8b101a0d037065043460dffc2d507257f2f11acaed71fd2b0c83c') - version('1.8.2', sha256='120732cbddb1b2364471c3d9f8bfd4b0c5b550862f99a65736c77f970b142aea') + version('2.2.0', sha256='0d586b0f8c2fc3cc6559c5e8fd6124628110514fda0e5d7c82e682d749d2e845') + version('1.8.4', sha256='c1c00fc4f6e8b101a0d037065043460dffc2d507257f2f11acaed71fd2b0c83c') + version('1.8.2', sha256='120732cbddb1b2364471c3d9f8bfd4b0c5b550862f99a65736c77f970b142aea') version('1.7.4', sha256='e9b1a75a3eae05dded19c80eb17325be675e0698975baae976df603b6ed1eb10') version('1.6.3', sha256='af8bdb8c714552b77d01d4536e3d6d2879d6cb9d25423d29163d5788e27046e6') version('1.6.1', sha256='7581d82c3f206f0ac380edeeba890a2e2d2be011e5abe94684ceb0df4b6acc3f') @@ -32,39 +34,39 @@ class PySphinx(PythonPackage): extends('python', ignore='bin/(pybabel|pygmentize)') - # Sphinx requires at least Python 2.7 or 3.4 to run - depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) - # See here for upstream list of dependencies: # https://github.com/sphinx-doc/sphinx/blob/master/setup.py + # See http://www.sphinx-doc.org/en/stable/changes.html for when each + # dependency was added or removed. + depends_on('python@3.5:', when='@2:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', when='@:1', type=('build', 'run')) - # Most Python packages only require py-setuptools as a build dependency. - # However, py-sphinx requires py-setuptools during runtime as well. - depends_on('py-setuptools', type=('build', 'run')) - - depends_on('py-six@1.5:', type=('build', 'run')) - depends_on('py-jinja2@2.3:', type=('build', 'run')) - depends_on('py-pygments@2.0:', type=('build', 'run')) - depends_on('py-docutils@0.11:', type=('build', 'run')) - depends_on('py-snowballstemmer@1.1:', type=('build', 'run')) - depends_on('py-babel@1.3:', type=('build', 'run')) # not 2.0 - depends_on('py-alabaster@0.7.0:0.7.999', type=('build', 'run')) - depends_on('py-imagesize', when='@1.4:', type=('build', 'run')) - depends_on('py-requests@2.0.0:', type=('build', 'run')) - depends_on('py-sphinx-rtd-theme@0.1:', type=('build', 'run')) # optional as of 1.4 - # See: https://github.com/sphinx-doc/sphinx/commit/854a227501a7582510eba41a208d25816f754e0c - depends_on('py-packaging', type=('build', 'run'), when='@1.7.4:') - - # Sphinx v1.6+ no longer includes websupport by default: - # http://www.sphinx-doc.org/en/stable/changes.html - depends_on('py-sphinxcontrib-websupport', when='@1.6:', - type=('build', 'run')) - # Build dep for 1.6.1 all python (bug), see: - # https://github.com/sphinx-doc/sphinx/pull/3789 + depends_on('py-sphinxcontrib-websupport', when='@1.6:1.999', type=('build', 'run')) + depends_on('py-sphinxcontrib-applehelp', when='@2:', type=('build', 'run')) + depends_on('py-sphinxcontrib-devhelp', when='@2:', type=('build', 'run')) + depends_on('py-sphinxcontrib-jsmath', when='@2:', type=('build', 'run')) + depends_on('py-sphinxcontrib-htmlhelp', when='@2:', type=('build', 'run')) + depends_on('py-sphinxcontrib-serializinghtml', when='@2:', type=('build', 'run')) + depends_on('py-sphinxcontrib-qthelp', when='@2:', type=('build', 'run')) + depends_on('py-six@1.5:', when='@:1', type=('build', 'run')) + depends_on('py-jinja2@2.3:', type=('build', 'run')) + depends_on('py-pygments@2.0:', type=('build', 'run')) + depends_on('py-docutils@0.12:', type=('build', 'run')) + depends_on('py-snowballstemmer@1.1:', type=('build', 'run')) + depends_on('py-babel@1.3:1.999,2.1:', type=('build', 'run')) + depends_on('py-alabaster@0.7.0:0.7.999', type=('build', 'run')) + depends_on('py-imagesize', when='@1.4:', type=('build', 'run')) + depends_on('py-requests@2.5.0:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-sphinx-rtd-theme@0.1:', when='@:1.3', type=('build', 'run')) + depends_on('py-packaging', when='@1.7.4:', type=('build', 'run')) depends_on('py-typing', when='@1.6.1', type=('build', 'run')) depends_on('py-typing', when='@1.6.2:^python@2.7:3.4', type=('build', 'run')) depends_on('py-pytest', type='test') - depends_on('py-mock', type='test') - depends_on('py-simplejson', type='test') + depends_on('py-pytest-cov', type='test') depends_on('py-html5lib', type='test') + depends_on('py-flake8@3.5.0:', type='test') + depends_on('py-flake8-import-order', type='test') + depends_on('py-mypy@0.720:', type='test') + depends_on('py-docutils-stubs', type='test') From b421c97110e5fa411ac5697c39a6eb1db86eae4a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:21:03 -0500 Subject: [PATCH 327/499] Add latest version of py-sphinxcontrib-websupport (#13292) --- .../packages/py-sphinxcontrib-websupport/package.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py index 0d3ba39c5d8..4346ec4bff2 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py @@ -11,7 +11,7 @@ class PySphinxcontribWebsupport(PythonPackage): Sphinx documentation into your Web application.""" homepage = "http://sphinx-doc.org/" - url = "https://pypi.io/packages/source/s/sphinxcontrib-websupport/sphinxcontrib-websupport-1.0.1.tar.gz" + url = "https://pypi.io/packages/source/s/sphinxcontrib-websupport/sphinxcontrib-websupport-1.1.2.tar.gz" # FIXME: These import tests don't work for some reason # import_modules = [ @@ -19,10 +19,13 @@ class PySphinxcontribWebsupport(PythonPackage): # 'sphinxcontrib.websupport.storage', 'sphinxcontrib.websupport.search' # ] + version('1.1.2', sha256='1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc') version('1.1.0', sha256='9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9') version('1.0.1', sha256='7a85961326aa3a400cd4ad3c816d70ed6f7c740acd7ce5d78cd0a67825072eb9') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-pytest', type='test') - depends_on('py-mock', type='test') + def test(self): + # Unit tests require sphinx, creating a circular dependency + pass From 47831a95e106ef7f8e2a9579969b5966e65fc1ee Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:21:32 -0500 Subject: [PATCH 328/499] Add latest version of py-coverage (#13319) --- var/spack/repos/builtin/packages/py-coverage/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py index a8075f18f7d..fa1c7a9b81c 100644 --- a/var/spack/repos/builtin/packages/py-coverage/package.py +++ b/var/spack/repos/builtin/packages/py-coverage/package.py @@ -10,9 +10,11 @@ class PyCoverage(PythonPackage): """ Testing coverage checker for python """ homepage = "http://nedbatchelder.com/code/coverage/" - url = "https://pypi.io/packages/source/c/coverage/coverage-4.3.4.tar.gz" + url = "https://pypi.io/packages/source/c/coverage/coverage-4.5.4.tar.gz" + version('4.5.4', sha256='e07d9f1a23e9e93ab5c62902833bf3e4b1f65502927379148b6622686223125c') version('4.3.4', sha256='eaaefe0f6aa33de5a65f48dd0040d7fe08cac9ac6c35a56d0a7db109c3e733df') version('4.0a6', sha256='85c7f3efceb3724ab066a3fcccc05b9b89afcaefa5b669a7e2222d31eac4728d') + depends_on('python@2.6:2.8,3.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') From 1007a0f7e5a72bd9939c79f80951b2a475bfa8fc Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:21:46 -0500 Subject: [PATCH 329/499] Add latest version of py-decorator (#13318) --- var/spack/repos/builtin/packages/py-decorator/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py index 2c85de8f028..7902a3074e0 100644 --- a/var/spack/repos/builtin/packages/py-decorator/package.py +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -10,10 +10,13 @@ class PyDecorator(PythonPackage): """The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples.""" - homepage = "https://github.com/micheles/decorator" - url = "https://pypi.io/packages/source/d/decorator/decorator-4.0.9.tar.gz" + homepage = "https://github.com/micheles/decorator" + url = "https://pypi.io/packages/source/d/decorator/decorator-4.4.0.tar.gz" + + version('4.4.0', sha256='86156361c50488b84a3f148056ea716ca587df2f0de1d34750d35c21312725de') version('4.3.0', sha256='c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c') version('4.0.9', sha256='90022e83316363788a55352fe39cfbed357aa3a71d90e5f2803a35471de4bba8') + depends_on('python@2.6:2.8,3.2:', type=('build', 'run')) depends_on('py-setuptools', type='build') From 41126d457fc6ae7d1817651522861c8c9ba2d60b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:21:59 -0500 Subject: [PATCH 330/499] Add latest version of py-execnet (#13317) --- var/spack/repos/builtin/packages/py-execnet/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-execnet/package.py b/var/spack/repos/builtin/packages/py-execnet/package.py index 7c44ca40f79..5b70292a2a0 100644 --- a/var/spack/repos/builtin/packages/py-execnet/package.py +++ b/var/spack/repos/builtin/packages/py-execnet/package.py @@ -12,10 +12,12 @@ class PyExecnet(PythonPackage): across version, platform and network barriers.""" homepage = "http://codespeak.net/execnet" - url = "https://pypi.io/packages/source/e/execnet/execnet-1.4.1.tar.gz" + url = "https://pypi.io/packages/source/e/execnet/execnet-1.7.1.tar.gz" + version('1.7.1', sha256='cacb9df31c9680ec5f95553976c4da484d407e85e41c83cb812aa014f0eddc50') version('1.4.1', sha256='f66dd4a7519725a1b7e14ad9ae7d3df8e09b2da88062386e08e941cafc0ef3e6') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-setuptools-scm', type='build') depends_on('py-apipkg@1.4:', type=('build', 'run')) From d2744a072bb97bb8d20b539e4686df6234bc9c8f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:43:56 -0500 Subject: [PATCH 331/499] Add latest version of py-click (#13320) --- var/spack/repos/builtin/packages/py-click/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-click/package.py b/var/spack/repos/builtin/packages/py-click/package.py index 6fc6c79f621..70f58ed0770 100644 --- a/var/spack/repos/builtin/packages/py-click/package.py +++ b/var/spack/repos/builtin/packages/py-click/package.py @@ -10,8 +10,11 @@ class PyClick(PythonPackage): """A simple wrapper around optparse for powerful command line utilities.""" homepage = "http://github.com/mitsuhiko/click" - url = "https://pypi.io/packages/source/c/click/click-6.6.tar.gz" + url = "https://pypi.io/packages/source/c/click/Click-7.0.tar.gz" - version('6.6', sha256='cc6a19da8ebff6e7074f731447ef7e112bd23adf3de5c597cf9989f2fd8defe9') + version('7.0', sha256='5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7') + version('6.6', sha256='cc6a19da8ebff6e7074f731447ef7e112bd23adf3de5c597cf9989f2fd8defe9', + url='https://pypi.io/packages/source/c/click/click-6.6.tar.gz') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') From ea90d2b88a77e70fe25da894ccbc639062b7799e Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 11:44:12 -0500 Subject: [PATCH 332/499] Add latest version of py-chardet (#13321) --- var/spack/repos/builtin/packages/py-chardet/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-chardet/package.py b/var/spack/repos/builtin/packages/py-chardet/package.py index eaa64eda36b..d8d640d3ac6 100644 --- a/var/spack/repos/builtin/packages/py-chardet/package.py +++ b/var/spack/repos/builtin/packages/py-chardet/package.py @@ -10,10 +10,13 @@ class PyChardet(PythonPackage): """Universal encoding detector for Python 2 and 3""" homepage = "https://github.com/chardet/chardet" - url = "https://pypi.io/packages/source/c/chardet/chardet-2.3.0.tar.gz" + url = "https://pypi.io/packages/source/c/chardet/chardet-3.0.4.tar.gz" + version('3.0.4', sha256='84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae') version('3.0.2', sha256='4f7832e7c583348a9eddd927ee8514b3bf717c061f57b21dbe7697211454d9bb') version('2.3.0', sha256='e53e38b3a4afe6d1132de62b7400a4ac363452dc5dfcf8d88e8e0cce663c68aa') depends_on('py-setuptools', type='build') depends_on('py-pytest-runner', type='build') + depends_on('py-pytest', type='test') + depends_on('py-hypothesis', type='test') From 32879df9d056666dd0545b426641ffa876b4b884 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 13:17:28 -0500 Subject: [PATCH 333/499] Add latest version of py-babel (#13323) --- var/spack/repos/builtin/packages/py-babel/package.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-babel/package.py b/var/spack/repos/builtin/packages/py-babel/package.py index ed90f2efe64..8208ac3d722 100644 --- a/var/spack/repos/builtin/packages/py-babel/package.py +++ b/var/spack/repos/builtin/packages/py-babel/package.py @@ -12,13 +12,17 @@ class PyBabel(PythonPackage): emphasis on web-based applications.""" homepage = "http://babel.pocoo.org/en/latest/" - url = "https://pypi.io/packages/source/B/Babel/Babel-2.4.0.tar.gz" + url = "https://pypi.io/packages/source/B/Babel/Babel-2.7.0.tar.gz" import_modules = ['babel', 'babel.localtime', 'babel.messages'] + version('2.7.0', sha256='e86135ae101e31e2c8ec20a4e0c5220f4eed12487d5cf3f78be7e98d3a57fc28') version('2.6.0', sha256='8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23') version('2.4.0', sha256='8c98f5e5f8f5f088571f2c6bd88d530e331cbbcb95a7311a0db69d3dca7ec563') version('2.3.4', sha256='c535c4403802f6eb38173cd4863e419e2274921a01a8aad8a5b497c131c62875') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-pytz', type=('build', 'run')) + depends_on('py-pytz@2015.7:', type=('build', 'run')) + depends_on('py-pytest', type='test') + depends_on('py-freezegun', type='test') From d462749b597791b3719db913de315b4a09e48916 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 13:17:44 -0500 Subject: [PATCH 334/499] Add missing dependencies to py-apipkg (#13324) --- var/spack/repos/builtin/packages/py-apipkg/package.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/var/spack/repos/builtin/packages/py-apipkg/package.py b/var/spack/repos/builtin/packages/py-apipkg/package.py index 676462d5cbe..36881719ef4 100644 --- a/var/spack/repos/builtin/packages/py-apipkg/package.py +++ b/var/spack/repos/builtin/packages/py-apipkg/package.py @@ -16,4 +16,7 @@ class PyApipkg(PythonPackage): version('1.4', sha256='2e38399dbe842891fe85392601aab8f40a8f4cc5a9053c326de35a1cc0297ac6') depends_on('py-setuptools@30.3.0:', type='build') + depends_on('py-setuptools-scm', type='build') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-py', type='test') + depends_on('py-pytest', type='test') From a602ed873d71253723f07dfa043d959cd247d734 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 13:18:02 -0500 Subject: [PATCH 335/499] Add latest version of py-typing (#13287) --- var/spack/repos/builtin/packages/py-typing/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-typing/package.py b/var/spack/repos/builtin/packages/py-typing/package.py index 6dd46be526f..bfa9a2d49ad 100644 --- a/var/spack/repos/builtin/packages/py-typing/package.py +++ b/var/spack/repos/builtin/packages/py-typing/package.py @@ -11,13 +11,13 @@ class PyTyping(PythonPackage): versions older than 3.6.""" homepage = "https://docs.python.org/3/library/typing.html" - url = "https://pypi.io/packages/source/t/typing/typing-3.6.1.tar.gz" + url = "https://pypi.io/packages/source/t/typing/typing-3.7.4.1.tar.gz" import_modules = ['typing'] + version('3.7.4.1', sha256='91dfe6f3f706ee8cc32d38edbbf304e9b7583fb37108fef38229617f8b3eba23') version('3.6.4', sha256='d400a9344254803a2368533e4533a4200d21eb7b6b729c173bc38201a74db3f2') version('3.6.1', sha256='c36dec260238e7464213dcd50d4b5ef63a507972f5780652e835d0228d0edace') - # You need Python 2.7 or 3.3+ to install the typing package - depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') From c767444f883374bd49b2e74801d60768b7af6023 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 14:44:14 -0500 Subject: [PATCH 336/499] Add missing test dependency to py-alabaster (#13325) --- var/spack/repos/builtin/packages/py-alabaster/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-alabaster/package.py b/var/spack/repos/builtin/packages/py-alabaster/package.py index d661750cffb..d28f2085a03 100644 --- a/var/spack/repos/builtin/packages/py-alabaster/package.py +++ b/var/spack/repos/builtin/packages/py-alabaster/package.py @@ -20,3 +20,4 @@ class PyAlabaster(PythonPackage): version('0.7.9', sha256='47afd43b08a4ecaa45e3496e139a193ce364571e7e10c6a87ca1a4c57eb7ea08') depends_on('py-setuptools', type='build') + depends_on('py-pygments', type='test') From 1673dc5aebb4871fbe5bbace1de2a9565ee2ee58 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 14:44:28 -0500 Subject: [PATCH 337/499] GEOS: http -> https (#13327) --- var/spack/repos/builtin/packages/geos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py index 7d241198d2d..2100b95d207 100644 --- a/var/spack/repos/builtin/packages/geos/package.py +++ b/var/spack/repos/builtin/packages/geos/package.py @@ -14,7 +14,7 @@ class Geos(AutotoolsPackage): operators, as well as specific JTS enhanced topology functions.""" homepage = "http://trac.osgeo.org/geos/" - url = "http://download.osgeo.org/geos/geos-3.7.2.tar.bz2" + url = "https://download.osgeo.org/geos/geos-3.7.2.tar.bz2" maintainers = ['adamjstewart'] From 73c5a9c736d1b2c3f5e9680f3ff8e0dc69933afa Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 14:44:43 -0500 Subject: [PATCH 338/499] Add latest version of googletest (#13328) --- .../repos/builtin/packages/googletest/package.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py index 06e89691596..26cd097149f 100644 --- a/var/spack/repos/builtin/packages/googletest/package.py +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -9,12 +9,13 @@ class Googletest(CMakePackage): """Google test framework for C++. Also called gtest.""" homepage = "https://github.com/google/googletest" - url = "https://github.com/google/googletest/tarball/release-1.7.0" + url = "https://github.com/google/googletest/tarball/release-1.10.0" - version('1.8.1', sha256='8e40a005e098b1ba917d64104549e3da274e31261dedc57d6250fe91391b2e84') - version('1.8.0', sha256='d8c33605d23d303b08a912eaee7f84c4e091d6e3d90e9a8ec8aaf7450dfe2568') - version('1.7.0', sha256='9639cf8b7f37a4d0c6575f52c01ef167c5f11faee65252296b3ffc2d9acd421b') - version('1.6.0', sha256='a61e20c65819eb39a2da85c88622bac703b865ca7fe2bfdcd3da734d87d5521a') + version('1.10.0', sha256='e4a7cd97c903818abe7ddb129db9c41cc9fd9e2ded654be57ced26d45c72e4c9') + version('1.8.1', sha256='8e40a005e098b1ba917d64104549e3da274e31261dedc57d6250fe91391b2e84') + version('1.8.0', sha256='d8c33605d23d303b08a912eaee7f84c4e091d6e3d90e9a8ec8aaf7450dfe2568') + version('1.7.0', sha256='9639cf8b7f37a4d0c6575f52c01ef167c5f11faee65252296b3ffc2d9acd421b') + version('1.6.0', sha256='a61e20c65819eb39a2da85c88622bac703b865ca7fe2bfdcd3da734d87d5521a') variant('gmock', default=False, description='Build with gmock') conflicts('+gmock', when='@:1.7.0') From 04e999162d485ea7c43dce3043e0a6262e1d399e Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 14:45:00 -0500 Subject: [PATCH 339/499] Add latest version of libgcrypt (#13329) --- .../repos/builtin/packages/libgcrypt/package.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py index 46ba7ab7039..07161ff08c5 100644 --- a/var/spack/repos/builtin/packages/libgcrypt/package.py +++ b/var/spack/repos/builtin/packages/libgcrypt/package.py @@ -8,13 +8,15 @@ class Libgcrypt(AutotoolsPackage): """Libgcrypt is a general purpose cryptographic library based on - the code from GnuPG. It provides functions for all cryptographic - building blocks: symmetric ciphers, hash algorithms, MACs, public - key algorithms, large integer functions, random numbers and a lot - of supporting functions. """ - homepage = "http://www.gnu.org/software/libgcrypt/" - url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.8.1.tar.bz2" + the code from GnuPG. It provides functions for all cryptographic + building blocks: symmetric ciphers, hash algorithms, MACs, public + key algorithms, large integer functions, random numbers and a lot + of supporting functions.""" + homepage = "http://www.gnu.org/software/libgcrypt/" + url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.8.5.tar.bz2" + + version('1.8.5', sha256='3b4a2a94cb637eff5bdebbcaf46f4d95c4f25206f459809339cdada0eb577ac3') version('1.8.4', sha256='f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227') version('1.8.1', sha256='7a2875f8b1ae0301732e878c0cca2c9664ff09ef71408f085c50e332656a78b3') version('1.7.6', sha256='626aafee84af9d2ce253d2c143dc1c0902dda045780cc241f39970fc60be05bc') From f1e595cb61793e12461a3110c14288537182c2b3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 15:50:48 -0500 Subject: [PATCH 340/499] Add latest version of libyaml (#13333) --- .../repos/builtin/packages/libyaml/package.py | 47 +++++++++---------- 1 file changed, 22 insertions(+), 25 deletions(-) diff --git a/var/spack/repos/builtin/packages/libyaml/package.py b/var/spack/repos/builtin/packages/libyaml/package.py index 2179472eb7a..4289751cc17 100644 --- a/var/spack/repos/builtin/packages/libyaml/package.py +++ b/var/spack/repos/builtin/packages/libyaml/package.py @@ -6,34 +6,31 @@ from spack import * -class Libyaml(Package): +class Libyaml(AutotoolsPackage): """A C library for parsing and emitting YAML.""" - homepage = "https://github.com/yaml/libyaml" - url = "https://github.com/yaml/libyaml/archive/0.2.1.tar.gz" + homepage = "https://pyyaml.org/wiki/LibYAML" + url = "https://pyyaml.org/download/libyaml/yaml-0.2.2.tar.gz" git = "https://github.com/yaml/libyaml.git" - version('master', branch='master') - version('0.2.1', sha256='1d2aeb87f7d317f1496e4c39410d913840714874a354970300f375eec9303dc4') - version('0.1.7', sha256='e1884d0fa1eec8cf869ac6bebbf25391e81956aa2970267f974a9fa5e0b968e2') - version('0.1.6', sha256='a0ad4b8cfa4b26c669c178af08147449ea7e6d50374cc26503edc56f3be894cf') - version('0.1.5', sha256='79511ce3c1195e3c83157b7243bc98c48f945662ed75d8606aea9182eb8dccd5') - version('0.1.4', sha256='6406d298a7889ad8e107239d3154c3540dbc0820ff4c5e889c60019fc2bf672b') - version('0.1.3', sha256='87bd8237880ccf3f993cfa5718c1081673813d11572ca469b24cfc3df5a425f5') - version('0.1.2', sha256='fa395384d1964ea2039744087fa825ed3ac321222df17ad66f198fecc48e39cd') - version('0.1.1', sha256='1183790fc59795a77bf4c8193aa24439dc0f8712ac37e4639be2e821c9d4e463') + version('master', branch='master') + version('0.2.2', sha256='4a9100ab61047fd9bd395bcef3ce5403365cafd55c1e0d0299cde14958e47be9') + version('0.2.1', sha256='78281145641a080fb32d6e7a87b9c0664d611dcb4d542e90baf731f51cbb59cd') + version('0.1.7', sha256='8088e457264a98ba451a90b8661fcb4f9d6f478f7265d48322a196cec2480729') + version('0.1.6', sha256='7da6971b4bd08a986dd2a61353bc422362bd0edcc67d7ebaac68c95f74182749') + version('0.1.5', sha256='fa87ee8fb7b936ec04457bc044cd561155e1000a4d25029867752e543c2d3bef') + version('0.1.4', sha256='7bf81554ae5ab2d9b6977da398ea789722e0db75b86bffdaeb4e66d961de6a37') + version('0.1.3', sha256='a8bbad7e5250b3735126b7e3bd9f6fce9db19d6be7cc13abad17a24b59ec144a') + version('0.1.2', sha256='5beb94529cc7ac79b17e354f9b03aea311f5af17be5d48bc39e6f1db5059f70f') + version('0.1.1', sha256='76444692a94de4e6776a1bdf3b735e8f016bb374ae7c60496f8032fdc6085889') - depends_on('automake') - depends_on('autoconf') - depends_on('libtool') + depends_on('automake', when='@master') + depends_on('autoconf', when='@master') + depends_on('libtool', when='@master') + depends_on('m4', when='@master') - phases = ['bootstrap', 'install'] - - def bootstrap(self, spec, prefix): - bootstrap = Executable('./bootstrap') - bootstrap() - - def install(self, spec, prefix): - configure('--disable-dependency-tracking', - '--prefix=%s' % self.spec.prefix) - make('install') + @run_before('configure') + def bootstrap(self): + if self.spec.satisfies('@master'): + bootstrap = Executable('./bootstrap') + bootstrap() From b56e46ece8e5e25d191844a0ce975cdb75182724 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 15:51:08 -0500 Subject: [PATCH 341/499] libgeotiff: http -> https (#13330) --- var/spack/repos/builtin/packages/libgeotiff/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/libgeotiff/package.py b/var/spack/repos/builtin/packages/libgeotiff/package.py index 07c8d549744..c3a2e1913c7 100644 --- a/var/spack/repos/builtin/packages/libgeotiff/package.py +++ b/var/spack/repos/builtin/packages/libgeotiff/package.py @@ -13,7 +13,7 @@ class Libgeotiff(AutotoolsPackage): """ homepage = "https://trac.osgeo.org/geotiff/" - url = "http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-1.5.1.tar.gz" + url = "https://download.osgeo.org/geotiff/libgeotiff/libgeotiff-1.5.1.tar.gz" maintainers = ['adamjstewart'] From 529d1246f648f4305f69afc38be7598ae7e38aa0 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 15:51:23 -0500 Subject: [PATCH 342/499] libtiff: http -> https (#13332) --- var/spack/repos/builtin/packages/libtiff/package.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py index 3d23210b563..f24cd86844b 100644 --- a/var/spack/repos/builtin/packages/libtiff/package.py +++ b/var/spack/repos/builtin/packages/libtiff/package.py @@ -10,14 +10,14 @@ class Libtiff(AutotoolsPackage): """LibTIFF - Tag Image File Format (TIFF) Library and Utilities.""" homepage = "http://www.simplesystems.org/libtiff/" - url = "http://download.osgeo.org/libtiff/tiff-4.0.10.tar.gz" + url = "https://download.osgeo.org/libtiff/tiff-4.0.10.tar.gz" version('4.0.10', sha256='2c52d11ccaf767457db0c46795d9c7d1a8d8f76f68b0b800a3dfe45786b996e4') - version('4.0.9', sha256='6e7bdeec2c310734e734d19aae3a71ebe37a4d842e0e23dbb1b8921c0026cfcd') - version('4.0.8', sha256='59d7a5a8ccd92059913f246877db95a2918e6c04fb9d43fd74e5c3390dac2910') - version('4.0.7', sha256='9f43a2cfb9589e5cecaa66e16bf87f814c945f22df7ba600d63aac4632c4f019') - version('4.0.6', sha256='4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c') - version('3.9.7', sha256='f5d64dd4ce61c55f5e9f6dc3920fbe5a41e02c2e607da7117a35eb5c320cef6a') + version('4.0.9', sha256='6e7bdeec2c310734e734d19aae3a71ebe37a4d842e0e23dbb1b8921c0026cfcd') + version('4.0.8', sha256='59d7a5a8ccd92059913f246877db95a2918e6c04fb9d43fd74e5c3390dac2910') + version('4.0.7', sha256='9f43a2cfb9589e5cecaa66e16bf87f814c945f22df7ba600d63aac4632c4f019') + version('4.0.6', sha256='4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c') + version('3.9.7', sha256='f5d64dd4ce61c55f5e9f6dc3920fbe5a41e02c2e607da7117a35eb5c320cef6a') depends_on('jpeg') depends_on('zlib') From 4789ac956cffa03ccbc6cddee8dc5b0757638a33 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 15:51:35 -0500 Subject: [PATCH 343/499] liblas: http -> https (#13331) --- var/spack/repos/builtin/packages/liblas/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/liblas/package.py b/var/spack/repos/builtin/packages/liblas/package.py index 99d7c3b7b9a..380d27f710f 100644 --- a/var/spack/repos/builtin/packages/liblas/package.py +++ b/var/spack/repos/builtin/packages/liblas/package.py @@ -12,7 +12,7 @@ class Liblas(CMakePackage): """ homepage = "https://liblas.org/" - url = "http://download.osgeo.org/liblas/libLAS-1.8.1.tar.bz2" + url = "https://download.osgeo.org/liblas/libLAS-1.8.1.tar.bz2" version('1.8.1', sha256='9adb4a98c63b461ed2bc82e214ae522cbd809cff578f28511122efe6c7ea4e76') From 785d5d9ca3603a4ac4916b82860ce17bbc2fd659 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 16:31:55 -0500 Subject: [PATCH 344/499] mapserver: http -> https (#13334) --- var/spack/repos/builtin/packages/mapserver/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/mapserver/package.py b/var/spack/repos/builtin/packages/mapserver/package.py index a2bb66053b7..245ea1c714e 100644 --- a/var/spack/repos/builtin/packages/mapserver/package.py +++ b/var/spack/repos/builtin/packages/mapserver/package.py @@ -14,7 +14,7 @@ class Mapserver(CMakePackage): to content""" homepage = "http://www.mapserver.org/" - url = "http://download.osgeo.org/mapserver/mapserver-7.2.1.tar.gz" + url = "https://download.osgeo.org/mapserver/mapserver-7.2.1.tar.gz" version('7.2.1', sha256='9459a7057d5a85be66a41096a5d804f74665381186c37077c94b56e784db6102') From 0cfc88c7d7458fd62408d92636c9c264f338364a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 17:06:30 -0500 Subject: [PATCH 345/499] openblas: http -> https (#13335) --- var/spack/repos/builtin/packages/openblas/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index d0655b793c5..97242ee45d0 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -13,8 +13,8 @@ class Openblas(MakefilePackage): """OpenBLAS: An optimized BLAS library""" - homepage = 'http://www.openblas.net' - url = 'http://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz' + homepage = 'https://www.openblas.net' + url = 'https://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz' git = 'https://github.com/xianyi/OpenBLAS.git' version('develop', branch='develop') From 030b2f8657b7511f13a4f3fe97ada20af00ee3d3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 17:06:43 -0500 Subject: [PATCH 346/499] Add missing zlib dependency to openjpeg (#13336) --- var/spack/repos/builtin/packages/openjpeg/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py index d4617b00284..980819c8bbe 100644 --- a/var/spack/repos/builtin/packages/openjpeg/package.py +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -30,6 +30,8 @@ class Openjpeg(CMakePackage): version('1.5.2', sha256='3734e95edd0bef6e056815591755efd822228dc3cd866894e00a2c929026b16d') version('1.5.1', sha256='6a42fcc23cb179f69a1e94429089e5a5926aee1ffe582a0a6bd91299d297e61a') + depends_on('zlib') + # The problem with install name of the library on MacOs was fixed starting # version 2.1.1: https://github.com/uclouvain/openjpeg/commit/b9a247b559e62e55f5561624cf4a19aee3c8afdc # The solution works for the older versions (at least starting 1.5.1) too. From 7f2aacfffcd6c8fa3daa2d2ea47e14c7ff472b86 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 17:56:37 -0500 Subject: [PATCH 347/499] Add latest version of proj (#13337) --- var/spack/repos/builtin/packages/proj/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py index 795462742d2..6c3febcd7b2 100644 --- a/var/spack/repos/builtin/packages/proj/package.py +++ b/var/spack/repos/builtin/packages/proj/package.py @@ -13,13 +13,14 @@ class Proj(AutotoolsPackage): transformations.""" homepage = "https://proj.org/" - url = "http://download.osgeo.org/proj/proj-6.1.0.tar.gz" + url = "https://download.osgeo.org/proj/proj-6.2.0.tar.gz" maintainers = ['adamjstewart'] # Version 6 removes projects.h, while version 7 removes proj_api.h. # Many packages that depend on proj do not yet support the newer API. # See https://github.com/OSGeo/PROJ/wiki/proj.h-adoption-status + version('6.2.0', sha256='b300c0f872f632ad7f8eb60725edbf14f0f8f52db740a3ab23e7b94f1cd22a50') version('6.1.0', sha256='676165c54319d2f03da4349cbd7344eb430b225fe867a90191d848dc64788008') version('6.0.0', sha256='4510a2c1c8f9056374708a867c51b1192e8d6f9a5198dd320bf6a168e44a3657') version('5.2.0', sha256='ef919499ffbc62a4aae2659a55e2b25ff09cccbbe230656ba71c6224056c7e60') From 01e64886acaa87319d2613ea179510bda55c1e34 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 19:08:04 -0500 Subject: [PATCH 348/499] Tut cannot be built with Python 3.7+ (#13341) --- var/spack/repos/builtin/packages/tut/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/tut/package.py b/var/spack/repos/builtin/packages/tut/package.py index 286e813c6dc..41c86909c92 100644 --- a/var/spack/repos/builtin/packages/tut/package.py +++ b/var/spack/repos/builtin/packages/tut/package.py @@ -16,6 +16,10 @@ class Tut(WafPackage): patch('python3-octal.patch', when='@2016-12-19') + # Python 3.7 support is currently broken + # https://github.com/mrzechonek/tut-framework/issues/18 + depends_on('python@:3.6', type='build') + def build_args(self): args = [] From f2d91f7e3c826011e1e6a47a598cda4acca8c8a6 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 20 Oct 2019 19:08:23 -0500 Subject: [PATCH 349/499] Use specific version of googletest for uriparser (#13339) --- var/spack/repos/builtin/packages/uriparser/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/uriparser/package.py b/var/spack/repos/builtin/packages/uriparser/package.py index aaa7143b725..4171d257c90 100644 --- a/var/spack/repos/builtin/packages/uriparser/package.py +++ b/var/spack/repos/builtin/packages/uriparser/package.py @@ -18,7 +18,7 @@ class Uriparser(CMakePackage): variant('docs', default=False, description='Build API documentation') depends_on('cmake@3.3:', type='build') - depends_on('googletest@1.8.1:', type='link') + depends_on('googletest@1.8.1', type='link') depends_on('doxygen', when='+docs', type='build') depends_on('graphviz', when='+docs', type='build') From 509007169381f4898a70febfb70a48ca7c35d994 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 21 Oct 2019 11:17:15 -0500 Subject: [PATCH 350/499] Add latest version of py-torch (#13290) * Add latest version of py-torch * setup_environment -> setup_build_environment --- .../builtin/packages/py-torch/package.py | 58 ++++++++++--------- 1 file changed, 30 insertions(+), 28 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py index ce432ee33be..9325b2504cb 100644 --- a/var/spack/repos/builtin/packages/py-torch/package.py +++ b/var/spack/repos/builtin/packages/py-torch/package.py @@ -50,6 +50,7 @@ class PyTorch(PythonPackage): ] version('master', branch='master', submodules=True) + version('1.3.0', tag='v1.3.0', submodules=True) version('1.2.0', tag='v1.2.0', submodules=True) version('1.1.0', tag='v1.1.0', submodules=True) version('1.0.1', tag='v1.0.1', submodules=True) @@ -135,7 +136,13 @@ class PyTorch(PythonPackage): depends_on('zstd', when='+zstd') depends_on('tbb', when='+tbb') - def setup_environment(self, build_env, run_env): + # Test dependencies + depends_on('ninja', type='test') + depends_on('py-hypothesis', type='test') + depends_on('py-six', type='test') + depends_on('py-psutil', type='test') + + def setup_build_environment(self, env): def enable_or_disable(variant, keyword='USE', var=None, newer=False): """Set environment variable to enable or disable support for a particular variant. @@ -153,43 +160,39 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False): # But some newer variants have always used USE_* or BUILD_* if self.spec.satisfies('@1.1:') or newer: if '+' + variant in self.spec: - build_env.set(keyword + '_' + var, 'ON') + env.set(keyword + '_' + var, 'ON') else: - build_env.set(keyword + '_' + var, 'OFF') + env.set(keyword + '_' + var, 'OFF') else: if '+' + variant in self.spec: - build_env.unset('NO_' + var) + env.unset('NO_' + var) else: - build_env.set('NO_' + var, 'ON') + env.set('NO_' + var, 'ON') - build_env.set('MAX_JOBS', make_jobs) + env.set('MAX_JOBS', make_jobs) enable_or_disable('cuda') if '+cuda' in self.spec: - build_env.set('CUDA_HOME', self.spec['cuda'].prefix) + env.set('CUDA_HOME', self.spec['cuda'].prefix) enable_or_disable('cudnn') if '+cudnn' in self.spec: - build_env.set('CUDNN_LIB_DIR', - self.spec['cudnn'].libs.directories[0]) - build_env.set('CUDNN_INCLUDE_DIR', - self.spec['cudnn'].prefix.include) - build_env.set('CUDNN_LIBRARY', self.spec['cudnn'].libs[0]) + env.set('CUDNN_LIB_DIR', self.spec['cudnn'].libs.directories[0]) + env.set('CUDNN_INCLUDE_DIR', self.spec['cudnn'].prefix.include) + env.set('CUDNN_LIBRARY', self.spec['cudnn'].libs[0]) enable_or_disable('fbgemm') enable_or_disable('test', keyword='BUILD') enable_or_disable('miopen') if '+miopen' in self.spec: - build_env.set('MIOPEN_LIB_DIR', - self.spec['miopen'].libs.directories[0]) - build_env.set('MIOPEN_INCLUDE_DIR', - self.spec['miopen'].prefix.include) - build_env.set('MIOPEN_LIBRARY', self.spec['miopen'].libs[0]) + env.set('MIOPEN_LIB_DIR', self.spec['miopen'].libs.directories[0]) + env.set('MIOPEN_INCLUDE_DIR', self.spec['miopen'].prefix.include) + env.set('MIOPEN_LIBRARY', self.spec['miopen'].libs[0]) enable_or_disable('mkldnn') if '+mkldnn' in self.spec: - build_env.set('MKLDNN_HOME', self.spec['intel-mkl'].prefix) + env.set('MKLDNN_HOME', self.spec['intel-mkl'].prefix) enable_or_disable('nnpack') enable_or_disable('qnnpack') @@ -198,10 +201,9 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False): enable_or_disable('nccl') enable_or_disable('nccl', var='SYSTEM_NCCL') if '+nccl' in self.spec: - build_env.set('NCCL_ROOT', self.spec['nccl'].prefix) - build_env.set('NCCL_LIB_DIR', - self.spec['nccl'].libs.directories[0]) - build_env.set('NCCL_INCLUDE_DIR', self.spec['nccl'].prefix.include) + env.set('NCCL_ROOT', self.spec['nccl'].prefix) + env.set('NCCL_LIB_DIR', self.spec['nccl'].libs.directories[0]) + env.set('NCCL_INCLUDE_DIR', self.spec['nccl'].prefix.include) enable_or_disable('caffe2', keyword='BUILD', var='CAFFE2_OPS') enable_or_disable('gloo', newer=True) @@ -213,18 +215,18 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False): enable_or_disable('lmdb', newer=True) enable_or_disable('binary', keyword='BUILD', newer=True) - build_env.set('PYTORCH_BUILD_VERSION', self.version) - build_env.set('PYTORCH_BUILD_NUMBER', 0) + env.set('PYTORCH_BUILD_VERSION', self.version) + env.set('PYTORCH_BUILD_NUMBER', 0) # BLAS to be used by Caffe2. Can be MKL, Eigen, ATLAS, or OpenBLAS. if '^mkl' in self.spec: - build_env.set('BLAS', 'MKL') + env.set('BLAS', 'MKL') elif '^eigen' in self.spec: - build_env.set('BLAS', 'Eigen') + env.set('BLAS', 'Eigen') elif '^atlas' in self.spec: - build_env.set('BLAS', 'ATLAS') + env.set('BLAS', 'ATLAS') elif '^openblas' in self.spec: - build_env.set('BLAS', 'OpenBLAS') + env.set('BLAS', 'OpenBLAS') enable_or_disable('redis', newer=True) enable_or_disable('zstd', newer=True) From 72177b6e97ed00449fe19474b477e268860d9a8b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 21 Oct 2019 11:17:52 -0500 Subject: [PATCH 351/499] Add latest version of py-tables (#13291) * Add latest version of py-tables * setup_environment -> setup_build_environment --- .../builtin/packages/py-tables/package.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-tables/package.py b/var/spack/repos/builtin/packages/py-tables/package.py index e837cc9d7df..2fcb494c6ce 100644 --- a/var/spack/repos/builtin/packages/py-tables/package.py +++ b/var/spack/repos/builtin/packages/py-tables/package.py @@ -11,12 +11,13 @@ class PyTables(PythonPackage): efficiently and easily cope with extremely large amounts of data.""" homepage = "http://www.pytables.org/" - url = "https://github.com/PyTables/PyTables/archive/v3.5.2.tar.gz" + url = "https://github.com/PyTables/PyTables/archive/v3.6.0.tar.gz" import_modules = [ 'tables', 'tables.misc', 'tables.nodes', 'tables.scripts' ] + version('3.6.0', sha256='2dcd077f42b195f48aa00f5a720b79189ea92fba0d16ad35e2881e403ba6914e') version('3.5.2', sha256='e4fc6f1194f02a8b10ff923e77364fb70710592f620d7de35f4d4e064dc70e91') version('3.4.4', sha256='c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114') version('3.3.0', sha256='dceb15fef556a2775121bcc695561df4ff0e09248e0ce3a2d58f5244a9f61421') @@ -28,12 +29,13 @@ class PyTables(PythonPackage): variant('lzo', default=False, description='Support for lzo compression') # requirements.txt + depends_on('python@3.5:', when='@3.4:', type=('build', 'run')) depends_on('python@2.6:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-cython', type='build') + depends_on('py-cython@0.21:', type='build') depends_on('py-numpy@1.9.3:', type=('build', 'run')) depends_on('py-numexpr@2.6.2:', type=('build', 'run')) - depends_on('py-six@1.9.0:', type=('build', 'run')) + depends_on('py-six@1.9.0:', when='@:3.5', type=('build', 'run')) depends_on('py-mock@2.0:', type='test') # tables/req_versions.py depends_on('hdf5@1.8.4:1.8.999', when='@:3.3.99') @@ -45,11 +47,11 @@ class PyTables(PythonPackage): depends_on('bzip2', when='+bzip2') depends_on('lzo', when='+lzo') - def setup_environment(self, spack_env, run_env): - spack_env.set('HDF5_DIR', self.spec['hdf5'].prefix) + def setup_build_environment(self, env): + env.set('HDF5_DIR', self.spec['hdf5'].prefix) if '+bzip2' in self.spec: - spack_env.set('BZIP2_DIR', self.spec['bzip2'].prefix) + env.set('BZIP2_DIR', self.spec['bzip2'].prefix) if '+lzo' in self.spec: - spack_env.set('LZO_DIR', self.spec['lzo'].prefix) + env.set('LZO_DIR', self.spec['lzo'].prefix) if '^c-blosc' in self.spec: - spack_env.set('BLOSC_DIR', self.spec['c-blosc'].prefix) + env.set('BLOSC_DIR', self.spec['c-blosc'].prefix) From 038f7b1b666e6f4d92e0837e344aca0d72eb74de Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 21 Oct 2019 11:19:05 -0500 Subject: [PATCH 352/499] Add latest version of py-numpy (#13307) * Add latest version of py-numpy * setup_environment -> setup_build_environment --- var/spack/repos/builtin/packages/py-numpy/package.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 8dc9db262d6..e1ca99d7496 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -15,7 +15,7 @@ class PyNumpy(PythonPackage): number capabilities""" homepage = "http://www.numpy.org/" - url = "https://pypi.io/packages/source/n/numpy/numpy-1.17.2.zip" + url = "https://pypi.io/packages/source/n/numpy/numpy-1.17.3.zip" maintainers = ['adamjstewart'] install_time_test_callbacks = ['install_test', 'import_module_test'] @@ -27,6 +27,7 @@ class PyNumpy(PythonPackage): 'numpy.distutils.command', 'numpy.distutils.fcompiler' ] + version('1.17.3', sha256='a0678793096205a4d784bd99f32803ba8100f639cf3b932dc63b21621390ea7e') version('1.17.2', sha256='73615d3edc84dd7c4aeb212fa3748fb83217e00d201875a47327f55363cef2df') version('1.17.1', sha256='f11331530f0eff69a758d62c2461cd98cdc2eae0147279d8fc86e0464eb7e8ca') version('1.17.0', sha256='951fefe2fb73f84c620bec4e001e80a80ddaa1b84dce244ded7f1e0cbe0ed34a') @@ -196,7 +197,7 @@ def write_library_dirs(f, dirs): write_library_dirs(f, lapack_lib_dirs) f.write('include_dirs = {0}\n'.format(lapack_header_dirs)) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Tell numpy which BLAS/LAPACK libraries we want to use. # https://github.com/numpy/numpy/pull/13132 # https://numpy.org/devdocs/user/building.html#accelerated-blas-lapack-libraries @@ -219,7 +220,7 @@ def setup_environment(self, spack_env, run_env): else: blas = 'blas' - spack_env.set('NPY_BLAS_ORDER', blas) + env.set('NPY_BLAS_ORDER', blas) # https://numpy.org/devdocs/user/building.html#lapack if 'lapack' not in spec: @@ -238,7 +239,7 @@ def setup_environment(self, spack_env, run_env): else: lapack = 'lapack' - spack_env.set('NPY_LAPACK_ORDER', lapack) + env.set('NPY_LAPACK_ORDER', lapack) def build_args(self, spec, prefix): args = [] From 4d99663ef91faee04bfdc1042d3d7796c7734f45 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 21 Oct 2019 11:19:48 -0500 Subject: [PATCH 353/499] Add latest version of py-cffi (#13322) * Add latest version of py-cffi * setup_environment -> setup_build_environment --- .../repos/builtin/packages/py-cffi/package.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py index 2010aa1431c..e61aa14c677 100644 --- a/var/spack/repos/builtin/packages/py-cffi/package.py +++ b/var/spack/repos/builtin/packages/py-cffi/package.py @@ -9,11 +9,13 @@ class PyCffi(PythonPackage): """Foreign Function Interface for Python calling C code""" - homepage = "http://cffi.readthedocs.org/en/latest/" - url = "https://pypi.io/packages/source/c/cffi/cffi-1.10.0.tar.gz" + + homepage = "https://cffi.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/c/cffi/cffi-1.13.0.tar.gz" import_modules = ['cffi'] + version('1.13.0', sha256='8fe230f612c18af1df6f348d02d682fe2c28ca0a6c3856c99599cdacae7cf226') version('1.12.2', sha256='e113878a446c6228669144ae8a56e268c91b7f1fafae927adc4879d9849e0ea7') version('1.11.5', sha256='e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4') version('1.10.0', sha256='b3b02911eb1f6ada203b0763ba924234629b51586f72a21faacc638269f4ced5') @@ -22,14 +24,17 @@ class PyCffi(PythonPackage): depends_on('pkgconfig', type='build') depends_on('py-setuptools', type='build') depends_on('py-pycparser', type=('build', 'run')) + depends_on('py-pycparser@2.19:', when='^python@:2.6', type=('build', 'run')) depends_on('libffi') + depends_on('py-py', type='test') + depends_on('py-pytest', type='test') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # This sets the compiler (and flags) that distutils will use # to create the final shared library. It will use the # compiler specified by the environment variable 'CC' for all - # other compilation. We are setting the 'LDSHARED" to the + # other compilation. We are setting 'LDSHARED' to the # spack compiler wrapper plus a few extra flags necessary for # building the shared library. if not sys.platform == 'darwin': - spack_env.set('LDSHARED', "{0} -shared -pthread".format(spack_cc)) + env.set('LDSHARED', '{0} -shared -pthread'.format(spack_cc)) From 4ab63c17d58c7d24ec6a446daf784f95bc818f49 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 21 Oct 2019 11:21:47 -0500 Subject: [PATCH 354/499] Fix Python 3.8 build on macOS (#13338) --- .../repos/builtin/packages/python/package.py | 318 +++++++++--------- 1 file changed, 167 insertions(+), 151 deletions(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index b05bd6dd9b8..2813121ddab 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -40,21 +40,21 @@ class Python(AutotoolsPackage): version('3.6.8', sha256='7f5b1f08b3b0a595387ef6c64c85b1b13b38abef0dd871835ee923262e4f32f0') version('3.6.7', sha256='b7c36f7ed8f7143b2c46153b7332db2227669f583ea0cce753facf549d1a4239') version('3.6.6', sha256='7d56dadf6c7d92a238702389e80cfe66fbfae73e584189ed6f89c75bbf3eda58') - version('3.6.5', sha256='53a3e17d77cd15c5230192b6a8c1e031c07cd9f34a2f089a731c6f6bd343d5c6') - version('3.6.4', sha256='7dc453e1a93c083388eb1a23a256862407f8234a96dc4fae0fc7682020227486') - version('3.6.3', sha256='ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91') - version('3.6.2', sha256='7919489310a5f17f7acbab64d731e46dca0702874840dadce8bd4b2b3b8e7a82') - version('3.6.1', sha256='aa50b0143df7c89ce91be020fe41382613a817354b33acdc6641b44f8ced3828') - version('3.6.0', sha256='aa472515800d25a3739833f76ca3735d9f4b2fe77c3cb21f69275e0cce30cb2b') - version('3.5.7', sha256='542d94920a2a06a471a73b51614805ad65366af98145b0369bc374cf248b521b') - version('3.5.2', sha256='1524b840e42cf3b909e8f8df67c1724012c7dc7f9d076d4feef2d3eff031e8a0') - version('3.5.1', sha256='687e067d9f391da645423c7eda8205bae9d35edc0c76ef5218dcbe4cc770d0d7') - version('3.5.0', sha256='584e3d5a02692ca52fce505e68ecd77248a6f2c99adf9db144a39087336b0fe0') + version('3.6.5', sha256='53a3e17d77cd15c5230192b6a8c1e031c07cd9f34a2f089a731c6f6bd343d5c6') + version('3.6.4', sha256='7dc453e1a93c083388eb1a23a256862407f8234a96dc4fae0fc7682020227486') + version('3.6.3', sha256='ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91') + version('3.6.2', sha256='7919489310a5f17f7acbab64d731e46dca0702874840dadce8bd4b2b3b8e7a82') + version('3.6.1', sha256='aa50b0143df7c89ce91be020fe41382613a817354b33acdc6641b44f8ced3828') + version('3.6.0', sha256='aa472515800d25a3739833f76ca3735d9f4b2fe77c3cb21f69275e0cce30cb2b') + version('3.5.7', sha256='542d94920a2a06a471a73b51614805ad65366af98145b0369bc374cf248b521b') + version('3.5.2', sha256='1524b840e42cf3b909e8f8df67c1724012c7dc7f9d076d4feef2d3eff031e8a0') + version('3.5.1', sha256='687e067d9f391da645423c7eda8205bae9d35edc0c76ef5218dcbe4cc770d0d7') + version('3.5.0', sha256='584e3d5a02692ca52fce505e68ecd77248a6f2c99adf9db144a39087336b0fe0') version('3.4.10', sha256='217757699249ab432571b381386d441e12b433100ab5f908051fcb7cced2539d') - version('3.4.3', sha256='8b743f56e9e50bf0923b9e9c45dd927c071d7aa56cd46569d8818add8cf01147') - version('3.3.6', sha256='0a58ad1f1def4ecc90b18b0c410a3a0e1a48cf7692c75d1f83d0af080e5d2034') - version('3.2.6', sha256='fc1e41296e29d476f696303acae293ae7a2310f0f9d0d637905e722a3f16163e') - version('3.1.5', sha256='d12dae6d06f52ef6bf1271db4d5b4d14b5dd39813e324314e72b648ef1bc0103') + version('3.4.3', sha256='8b743f56e9e50bf0923b9e9c45dd927c071d7aa56cd46569d8818add8cf01147') + version('3.3.6', sha256='0a58ad1f1def4ecc90b18b0c410a3a0e1a48cf7692c75d1f83d0af080e5d2034') + version('3.2.6', sha256='fc1e41296e29d476f696303acae293ae7a2310f0f9d0d637905e722a3f16163e') + version('3.1.5', sha256='d12dae6d06f52ef6bf1271db4d5b4d14b5dd39813e324314e72b648ef1bc0103') version('2.7.16', sha256='01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5', preferred=True) version('2.7.15', sha256='18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db') version('2.7.14', sha256='304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8') @@ -62,8 +62,8 @@ class Python(AutotoolsPackage): version('2.7.12', sha256='3cb522d17463dfa69a155ab18cffa399b358c966c0363d6c8b5b3bf1384da4b6') version('2.7.11', sha256='82929b96fd6afc8da838b149107078c02fa1744b7e60999a8babbc0d3fa86fc6') version('2.7.10', sha256='eda8ce6eec03e74991abb5384170e7c65fcd7522e409b8e83d7e6372add0f12a') - version('2.7.9', sha256='c8bba33e66ac3201dabdc556f0ea7cfe6ac11946ec32d357c4c6f9b018c12c5b') - version('2.7.8', sha256='74d70b914da4487aa1d97222b29e9554d042f825f26cb2b93abd20fdda56b557') + version('2.7.9', sha256='c8bba33e66ac3201dabdc556f0ea7cfe6ac11946ec32d357c4c6f9b018c12c5b') + version('2.7.8', sha256='74d70b914da4487aa1d97222b29e9554d042f825f26cb2b93abd20fdda56b557') extendable = True @@ -135,7 +135,7 @@ class Python(AutotoolsPackage): # a Mac. depends_on('libuuid', when='+uuid') - patch('tkinter.patch', when='@:2.8,3.3: platform=darwin') + patch('tkinter.patch', when='@:2.8,3.3:3.7 platform=darwin') # Ensure that distutils chooses correct compiler option for RPATH on cray: patch('cray-rpath-2.3.patch', when='@2.3:3.0.1 platform=cray') @@ -190,7 +190,7 @@ def setup_build_environment(self, env): # Python v2.7 and v3.4+ (see https://bugs.python.org/issue1180) and # adding support for ignoring user configuration will require # significant changes to this package for other Python versions. - if not spec.satisfies('@2.7,3.4:'): + if not spec.satisfies('@2.7:2.8,3.4:'): tty.warn(('Python v{0} may not install properly if Python ' 'user configurations are present.').format(self.version)) @@ -290,21 +290,112 @@ def configure_args(self): return config_args @run_after('install') - def post_install(self): + def _save_distutil_vars(self): + """ + Run before changing automatically generated contents of the + _sysconfigdata.py, which is used by distutils to figure out what + executables to use while compiling and linking extensions. If we build + extensions with spack those executables should be spack's wrappers. + Spack partially covers this by setting environment variables that + are also accounted for by distutils. Currently there is one more known + variable that must be set, which is LDSHARED, so the method saves its + autogenerated value to pass it to the dependent package's setup script. + """ + + self._distutil_vars = {} + + input_filename = self.get_sysconfigdata_name() + input_dict = None + try: + with open(input_filename) as input_file: + match = re.search(r'build_time_vars\s*=\s*(?P{.*})', + input_file.read(), + flags=re.DOTALL) + + if match: + input_dict = ast.literal_eval(match.group('dict')) + except (IOError, SyntaxError): + pass + + if not input_dict: + tty.warn("Failed to find 'build_time_vars' dictionary in file " + "'%s'. This might cause the extensions that are " + "installed with distutils to call compilers directly " + "avoiding Spack's wrappers." % input_filename) + return + + for var_name in Python._DISTUTIL_VARS_TO_SAVE: + if var_name in input_dict: + self._distutil_vars[var_name] = input_dict[var_name] + else: + tty.warn("Failed to find key '%s' in 'build_time_vars' " + "dictionary in file '%s'. This might cause the " + "extensions that are installed with distutils to " + "call compilers directly avoiding Spack's wrappers." + % (var_name, input_filename)) + + if len(self._distutil_vars) > 0: + output_filename = None + try: + output_filename = join_path( + spack.store.layout.metadata_path(self.spec), + Python._DISTUTIL_CACHE_FILENAME) + with open(output_filename, 'w') as output_file: + sjson.dump(self._distutil_vars, output_file) + except Exception: + tty.warn("Failed to save metadata for distutils. This might " + "cause the extensions that are installed with " + "distutils to call compilers directly avoiding " + "Spack's wrappers.") + # We make the cache empty if we failed to save it to file + # to provide the same behaviour as in the case when the cache + # is initialized by the method load_distutils_data(). + self._distutil_vars = {} + if output_filename: + force_remove(output_filename) + + def _load_distutil_vars(self): + # We update and keep the cache unchanged only if the package is + # installed. + if not self._distutil_vars and self.installed: + try: + input_filename = join_path( + spack.store.layout.metadata_path(self.spec), + Python._DISTUTIL_CACHE_FILENAME) + if os.path.isfile(input_filename): + with open(input_filename) as input_file: + self._distutil_vars = sjson.load(input_file) + except Exception: + pass + + if not self._distutil_vars: + self._distutil_vars = {} + + return self._distutil_vars + + @run_after('install') + def filter_compilers(self): + """Run after install to tell the configuration files and Makefiles + to use the compilers that Spack built the package with. + + If this isn't done, they'll have CC and CXX set to Spack's generic + cc and c++. We want them to be bound to whatever compiler + they were built with.""" + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + + filenames = [ + self.get_sysconfigdata_name(), self.get_makefile_filename() + ] + + filter_file(spack_cc, self.compiler.cc, *filenames, **kwargs) + filter_file(spack_cxx, self.compiler.cxx, *filenames, **kwargs) + + @run_after('install') + def symlink(self): spec = self.spec prefix = self.prefix - self.sysconfigfilename = '_sysconfigdata.py' - if spec.satisfies('@3.6:'): - # Python 3.6.0 renamed the sys config file - sc = 'import sysconfig; print(sysconfig._get_sysconfigdata_name())' - cf = self.command('-c', sc, output=str).strip() - self.sysconfigfilename = '{0}.py'.format(cf) - - self._save_distutil_vars(prefix) - - self.filter_compilers(prefix) - # TODO: # On OpenSuse 13, python uses /lib64/python2.7/lib-dynload/*.so # instead of /lib/python2.7/lib-dynload/*.so. Oddly enough the @@ -398,125 +489,6 @@ def import_tests(self): if '+uuid' in spec: self.command('-c', 'import uuid') - def _save_distutil_vars(self, prefix): - """ - Run before changing automatically generated contents of the - _sysconfigdata.py, which is used by distutils to figure out what - executables to use while compiling and linking extensions. If we build - extensions with spack those executables should be spack's wrappers. - Spack partially covers this by setting environment variables that - are also accounted for by distutils. Currently there is one more known - variable that must be set, which is LDSHARED, so the method saves its - autogenerated value to pass it to the dependent package's setup script. - """ - - self._distutil_vars = {} - - input_filename = None - for filename in [join_path(lib_dir, - 'python{0}'.format(self.version.up_to(2)), - self.sysconfigfilename) - for lib_dir in [prefix.lib, prefix.lib64]]: - if os.path.isfile(filename): - input_filename = filename - break - if not input_filename: - return - - input_dict = None - try: - with open(input_filename) as input_file: - match = re.search(r'build_time_vars\s*=\s*(?P{.*})', - input_file.read(), - flags=re.DOTALL) - - if match: - input_dict = ast.literal_eval(match.group('dict')) - except (IOError, SyntaxError): - pass - - if not input_dict: - tty.warn("Failed to find 'build_time_vars' dictionary in file " - "'%s'. This might cause the extensions that are " - "installed with distutils to call compilers directly " - "avoiding Spack's wrappers." % input_filename) - return - - for var_name in Python._DISTUTIL_VARS_TO_SAVE: - if var_name in input_dict: - self._distutil_vars[var_name] = input_dict[var_name] - else: - tty.warn("Failed to find key '%s' in 'build_time_vars' " - "dictionary in file '%s'. This might cause the " - "extensions that are installed with distutils to " - "call compilers directly avoiding Spack's wrappers." - % (var_name, input_filename)) - - if len(self._distutil_vars) > 0: - output_filename = None - try: - output_filename = join_path( - spack.store.layout.metadata_path(self.spec), - Python._DISTUTIL_CACHE_FILENAME) - with open(output_filename, 'w') as output_file: - sjson.dump(self._distutil_vars, output_file) - except Exception: - tty.warn("Failed to save metadata for distutils. This might " - "cause the extensions that are installed with " - "distutils to call compilers directly avoiding " - "Spack's wrappers.") - # We make the cache empty if we failed to save it to file - # to provide the same behaviour as in the case when the cache - # is initialized by the method load_distutils_data(). - self._distutil_vars = {} - if output_filename: - force_remove(output_filename) - - def _load_distutil_vars(self): - # We update and keep the cache unchanged only if the package is - # installed. - if not self._distutil_vars and self.installed: - try: - input_filename = join_path( - spack.store.layout.metadata_path(self.spec), - Python._DISTUTIL_CACHE_FILENAME) - if os.path.isfile(input_filename): - with open(input_filename) as input_file: - self._distutil_vars = sjson.load(input_file) - except Exception: - pass - - if not self._distutil_vars: - self._distutil_vars = {} - - return self._distutil_vars - - def filter_compilers(self, prefix): - """Run after install to tell the configuration files and Makefiles - to use the compilers that Spack built the package with. - - If this isn't done, they'll have CC and CXX set to Spack's generic - cc and c++. We want them to be bound to whatever compiler - they were built with.""" - - kwargs = {'ignore_absent': True, 'backup': False, 'string': True} - - lib_dirnames = [ - join_path(lib_dir, 'python{0}'.format(self.version.up_to(2))) for - lib_dir in [prefix.lib, prefix.lib64]] - - config_dirname = 'config-{0}m'.format( - self.version.up_to(2)) if self.spec.satisfies('@3:') else 'config' - - rel_filenames = [self.sysconfigfilename, - join_path(config_dirname, 'Makefile')] - - abs_filenames = [join_path(dirname, filename) for dirname in - lib_dirnames for filename in rel_filenames] - - filter_file(env['CC'], self.compiler.cc, *abs_filenames, **kwargs) - filter_file(env['CXX'], self.compiler.cxx, *abs_filenames, **kwargs) - # ======================================================================== # Set up environment to make install easy for python extensions. # ======================================================================== @@ -579,7 +551,7 @@ def print_string(self, string): return 'print({0})'.format(string) def get_config_var(self, key): - """Returns the value of a single variable. Wrapper around + """Return the value of a single variable. Wrapper around ``distutils.sysconfig.get_config_var()``.""" cmd = 'from distutils.sysconfig import get_config_var; ' @@ -588,7 +560,7 @@ def get_config_var(self, key): return self.command('-c', cmd, output=str).strip() def get_config_h_filename(self): - """Returns the full path name of the configuration header. + """Return the full path name of the configuration header. Wrapper around ``distutils.sysconfig.get_config_h_filename()``.""" cmd = 'from distutils.sysconfig import get_config_h_filename; ' @@ -596,6 +568,50 @@ def get_config_h_filename(self): return self.command('-c', cmd, output=str).strip() + def get_makefile_filename(self): + """Return the full path name of ``Makefile`` used to build Python. + Wrapper around ``distutils.sysconfig.get_makefile_filename()``.""" + + cmd = 'from distutils.sysconfig import get_makefile_filename; ' + cmd += self.print_string('get_makefile_filename()') + + return self.command('-c', cmd, output=str).strip() + + def get_python_inc(self): + """Return the directory for either the general or platform-dependent C + include files. Wrapper around ``distutils.sysconfig.get_python_inc()``. + """ + + cmd = 'from distutils.sysconfig import get_python_inc; ' + cmd += self.print_string('get_python_inc()') + + return self.command('-c', cmd, output=str).strip() + + def get_python_lib(self): + """Return the directory for either the general or platform-dependent + library installation. Wrapper around + ``distutils.sysconfig.get_python_lib()``.""" + + cmd = 'from distutils.sysconfig import get_python_lib; ' + cmd += self.print_string('get_python_lib()') + + return self.command('-c', cmd, output=str).strip() + + def get_sysconfigdata_name(self): + """Return the full path name of the sysconfigdata file.""" + + libdest = self.get_config_var('LIBDEST') + + filename = '_sysconfigdata.py' + if self.spec.satisfies('@3.6:'): + # Python 3.6.0 renamed the sys config file + cmd = 'from sysconfig import _get_sysconfigdata_name; ' + cmd += self.print_string('_get_sysconfigdata_name()') + filename = self.command('-c', cmd, output=str).strip() + filename += '.py' + + return join_path(libdest, filename) + @property def home(self): """Most of the time, ``PYTHONHOME`` is simply From 498f448ef353eed906a100752b2c1598423a7276 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Mon, 21 Oct 2019 19:24:57 +0200 Subject: [PATCH 355/499] microarchitectures: fix custom compiler versions (#13222) Custom string versions for compilers were raising a ValueError on conversion to int. This commit fixes the behavior by trying to detect the underlying compiler version when in presence of a custom string version. * Refactor code that deals with custom versions for better readability * Partition version components with a regex * Fix semantic of custom compiler versions with a suffix * clang@x.y-apple has been special-cased * Add unit tests --- lib/spack/llnl/util/cpu/__init__.py | 4 ++- lib/spack/llnl/util/cpu/microarchitecture.py | 27 +++++++++++++++++--- lib/spack/spack/architecture.py | 18 ++++++++++++- lib/spack/spack/test/architecture.py | 26 +++++++++++++++++++ lib/spack/spack/test/data/compilers.yaml | 18 +++++++++++++ lib/spack/spack/test/llnl/util/cpu.py | 12 +++++++++ 6 files changed, 100 insertions(+), 5 deletions(-) diff --git a/lib/spack/llnl/util/cpu/__init__.py b/lib/spack/llnl/util/cpu/__init__.py index eda6fa9c369..cf3c3ef50c5 100644 --- a/lib/spack/llnl/util/cpu/__init__.py +++ b/lib/spack/llnl/util/cpu/__init__.py @@ -5,6 +5,7 @@ from .microarchitecture import Microarchitecture, UnsupportedMicroarchitecture from .microarchitecture import targets, generic_microarchitecture +from .microarchitecture import version_components from .detect import host __all__ = [ @@ -12,5 +13,6 @@ 'UnsupportedMicroarchitecture', 'targets', 'generic_microarchitecture', - 'host' + 'host', + 'version_components' ] diff --git a/lib/spack/llnl/util/cpu/microarchitecture.py b/lib/spack/llnl/util/cpu/microarchitecture.py index e14e1a8c668..3d1590376a0 100644 --- a/lib/spack/llnl/util/cpu/microarchitecture.py +++ b/lib/spack/llnl/util/cpu/microarchitecture.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import functools import platform +import re import warnings try: @@ -219,9 +220,9 @@ def satisfies_constraint(entry, version): min_version, max_version = entry['versions'].split(':') # Check version suffixes - min_version, _, min_suffix = min_version.partition('-') - max_version, _, max_suffix = max_version.partition('-') - version, _, suffix = version.partition('-') + min_version, min_suffix = version_components(min_version) + max_version, max_suffix = version_components(max_version) + version, suffix = version_components(version) # If the suffixes are not all equal there's no match if ((suffix != min_suffix and min_version) or @@ -277,6 +278,26 @@ def generic_microarchitecture(name): ) +def version_components(version): + """Decomposes the version passed as input in version number and + suffix and returns them. + + If the version number of the suffix are not present, an empty + string is returned. + + Args: + version (str): version to be decomposed into its components + """ + match = re.match(r'([\d.]*)(-?)(.*)', str(version)) + if not match: + return '', '' + + version_number = match.group(1) + suffix = match.group(3) + + return version_number, suffix + + def _known_microarchitectures(): """Returns a dictionary of the known micro-architectures. If the current host platform is unknown adds it too as a generic target. diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index dd99cfa1e3b..0e318bbccf9 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -192,6 +192,8 @@ def optimization_flags(self, compiler): compiler (CompilerSpec or Compiler): object that contains both the name and the version of the compiler we want to use """ + # Mixed toolchains are not supported yet + import spack.compilers if isinstance(compiler, spack.compiler.Compiler): if spack.compilers.is_mixed_toolchain(compiler): msg = ('microarchitecture specific optimizations are not ' @@ -200,8 +202,22 @@ def optimization_flags(self, compiler): warnings.warn(msg.format(compiler)) return '' + # Try to check if the current compiler comes with a version number or + # has an unexpected suffix. If so, treat it as a compiler with a + # custom spec. + compiler_version = compiler.version + version_number, suffix = cpu.version_components(compiler.version) + if not version_number or suffix not in ('', 'apple'): + # Try to deduce the correct version. Depending on where this + # function is called we might get either a CompilerSpec or a + # fully fledged compiler object + import spack.spec + if isinstance(compiler, spack.spec.CompilerSpec): + compiler = spack.compilers.compilers_for_spec(compiler).pop() + compiler_version = compiler.cc_version(compiler.cc) + return self.microarchitecture.optimization_flags( - compiler.name, str(compiler.version) + compiler.name, str(compiler_version) ) diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index 7e120000d42..35980d8a863 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -187,3 +187,29 @@ def test_optimization_flags( compiler = spack.compilers.compilers_for_spec(compiler_spec).pop() opt_flags = target.optimization_flags(compiler) assert opt_flags == expected_flags + + +@pytest.mark.parametrize('compiler,real_version,target_str,expected_flags', [ + (spack.spec.CompilerSpec('gcc@9.2.0'), None, 'haswell', + '-march=haswell -mtune=haswell'), + # Check that custom string versions are accepted + (spack.spec.CompilerSpec('gcc@foo'), '9.2.0', 'icelake', + '-march=icelake-client -mtune=icelake-client'), + # Check that we run version detection (4.4.0 doesn't support icelake) + (spack.spec.CompilerSpec('gcc@4.4.0-special'), '9.2.0', 'icelake', + '-march=icelake-client -mtune=icelake-client'), + # Check that the special case for Apple's clang is treated correctly + # i.e. it won't try to dtect the version again + (spack.spec.CompilerSpec('clang@9.1.0-apple'), None, 'x86_64', + '-march=x86-64 -mcpu=generic'), +]) +def test_optimization_flags_with_custom_versions( + compiler, real_version, target_str, expected_flags, monkeypatch, config +): + target = spack.architecture.Target(target_str) + if real_version: + monkeypatch.setattr( + spack.compiler.Compiler, 'cc_version', lambda x, y: real_version + ) + opt_flags = target.optimization_flags(compiler) + assert opt_flags == expected_flags diff --git a/lib/spack/spack/test/data/compilers.yaml b/lib/spack/spack/test/data/compilers.yaml index f619c8d351c..7aec1384736 100644 --- a/lib/spack/spack/test/data/compilers.yaml +++ b/lib/spack/spack/test/data/compilers.yaml @@ -135,3 +135,21 @@ compilers: f77: None fc: None modules: 'None' +- compiler: + spec: gcc@foo + operating_system: redhat6 + paths: + cc: /path/to/gcc + cxx: /path/to/g++ + f77: /path/to/gfortran + fc: /path/to/gfortran + modules: 'None' +- compiler: + spec: gcc@4.4.0-special + operating_system: redhat6 + paths: + cc: /path/to/gcc + cxx: /path/to/g++ + f77: /path/to/gfortran + fc: /path/to/gfortran + modules: 'None' diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 5713580a72f..68185532b44 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -242,3 +242,15 @@ def test_automatic_conversion_on_comparisons(operation, expected_result): target = llnl.util.cpu.targets[target] code = 'target ' + operator + 'other_target' assert eval(code) is expected_result + + +@pytest.mark.parametrize('version,expected_number,expected_suffix', [ + ('4.2.0', '4.2.0', ''), + ('4.2.0-apple', '4.2.0', 'apple'), + ('my-funny-name-with-dashes', '', 'my-funny-name-with-dashes'), + ('10.3.56~svnr64537', '10.3.56', '~svnr64537') +]) +def test_version_components(version, expected_number, expected_suffix): + number, suffix = llnl.util.cpu.version_components(version) + assert number == expected_number + assert suffix == expected_suffix From 3d77ecd92e0ccc950daf30468ec2ef591668d8eb Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Mon, 21 Oct 2019 20:20:05 +0200 Subject: [PATCH 356/499] Bootstrap environment modules optimizing for generic architectures (#13105) fixes #13073 Since #3206 was merged bootstrapping environment-modules was using the architecture of the current host or the best match supported by the default compiler. The former case is an issue since shell integration was looking for a spec targeted at the host microarchitecture. 1. Bootstrap an env modules targeted at generic architectures 2. Look for generic targets in shell integration scripts 3. Add a new entry in Travis to test shell integration --- .travis.yml | 5 ++++ lib/spack/spack/cmd/bootstrap.py | 8 ++++++- lib/spack/spack/main.py | 6 +++-- share/spack/qa/run-bootstrap-tests | 37 ++++++++++++++++++++++++++++++ 4 files changed, 53 insertions(+), 3 deletions(-) create mode 100755 share/spack/qa/run-bootstrap-tests diff --git a/.travis.yml b/.travis.yml index 33c0346eaf7..1f5b82c811e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,6 +22,11 @@ jobs: os: linux language: python env: TEST_SUITE=flake8 +# Shell integration with module files + - python: '3.7' + os: linux + language: python + env: [ TEST_SUITE=bootstrap ] - stage: 'unit tests + documentation' python: '2.6' dist: trusty diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index 71db75c788a..96cb8ccaa95 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -3,6 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import llnl.util.cpu import llnl.util.tty as tty import spack.repo @@ -56,7 +57,12 @@ def bootstrap(parser, args, **kwargs): # Define requirement dictionary defining general specs which need # to be satisfied, and the specs to install when the general spec # isn't satisfied. - requirement_dict = {'environment-modules': 'environment-modules~X'} + requirement_dict = { + # Install environment-modules with generic optimizations + 'environment-modules': 'environment-modules~X target={0}'.format( + llnl.util.cpu.host().family + ) + } for requirement in requirement_dict: installed_specs = spack.store.db.query(requirement) diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py index 89b4d3dc85e..ff2ff74da3c 100644 --- a/lib/spack/spack/main.py +++ b/lib/spack/spack/main.py @@ -20,6 +20,7 @@ import warnings from six import StringIO +import llnl.util.cpu import llnl.util.tty as tty import llnl.util.tty.color as color from llnl.util.tty.log import log_output @@ -621,8 +622,9 @@ def shell_set(var, value): # print environment module system if available. This can be expensive # on clusters, so skip it if not needed. if 'modules' in info: - specs = spack.store.db.query( - 'environment-modules arch=%s' % spack.architecture.sys_type()) + generic_arch = llnl.util.cpu.host().family + module_spec = 'environment-modules target={0}'.format(generic_arch) + specs = spack.store.db.query(module_spec) if specs: shell_set('_sp_module_prefix', specs[-1].prefix) else: diff --git a/share/spack/qa/run-bootstrap-tests b/share/spack/qa/run-bootstrap-tests new file mode 100755 index 00000000000..346122c529a --- /dev/null +++ b/share/spack/qa/run-bootstrap-tests @@ -0,0 +1,37 @@ +#!/bin/bash -e +# +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# +# Description: +# Checks that Spack shell integration with modules works correctly. +# +# Usage: +# run-bootstrap-tests +# +. "$(dirname $0)/setup.sh" +check_dependencies ${coverage} git hg svn + +# Fetch the sources in a mirror, and add it to Spack +mkdir -p ~/.mirror +bin/spack mirror add travis ~/.mirror +bin/spack mirror create -D -d ~/.mirror environment-modules~X + + +# Move to root directory of Spack +# Allows script to be run from anywhere +cd "$SPACK_ROOT" + +# Print compiler information +spack config get compilers + +# Run some build smoke tests, potentially with code coverage +${coverage_run} bin/spack bootstrap + +# Check module integration +. "share/spack/setup-env.sh" +module av || exit 1 +spack load tcl || exit 1 From 26687988eb7328023b69c277c280b2f485d74961 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?= Date: Tue, 22 Oct 2019 03:04:00 +0800 Subject: [PATCH 357/499] New package: Fl (#12877) --- .../repos/builtin/packages/fl/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/fl/package.py diff --git a/var/spack/repos/builtin/packages/fl/package.py b/var/spack/repos/builtin/packages/fl/package.py new file mode 100644 index 00000000000..3b60495a533 --- /dev/null +++ b/var/spack/repos/builtin/packages/fl/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Fl(Package): + """Fawlty Language is an IDL8 + (Interactive Data Language) compatible compiler.""" + + homepage = "https://www.flxpert.hu/fl/" + url = "https://www.flxpert.hu/fl/fl_0.79.47-amd64-linux.tar.gz" + + version('0.79.47', sha256='b8a4a74118c1a024313bf912261fbc016a53f2d15adb1226217f2a10a9f7ca9a') + + def install(self, spec, prefix): + if (self.spec.satisfies('platform=linux') and + self.spec.satisfies('target=x86_64')): + with working_dir('fl_{0}'.format(spec.version)): + install_tree('.', prefix) + else: + raise InstallError('fl is built for Linux x86_64 platform only.') From edf56d8ac42d491f0d86e3e5210cbc080f61d2be Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Tue, 22 Oct 2019 01:23:03 +0200 Subject: [PATCH 358/499] qt: Fix build for newer versions (#13262) For some reason, newer versions of qt fail to build because they cannot find certain system libraries such as libatomic and libdl. Leaving the qmake compiler set to gcc seems to fix the problem. Fixes #13221 --- var/spack/repos/builtin/packages/qt/package.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 0405aa49027..55e59cb7882 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -294,8 +294,6 @@ def patch(self): @when('@5') def patch(self): # Fix qmake compilers in the default mkspec - filter_file('^QMAKE_COMPILER .*', 'QMAKE_COMPILER = cc', - 'qtbase/mkspecs/common/g++-base.conf') filter_file('^QMAKE_CC .*', 'QMAKE_CC = cc', 'qtbase/mkspecs/common/g++-base.conf') filter_file('^QMAKE_CXX .*', 'QMAKE_CXX = c++', From 26141ad489e4d6f4f67a2b638b6fd5b84a117fb1 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Tue, 22 Oct 2019 08:24:10 +0900 Subject: [PATCH 359/499] bpp-core: Clarify 'isnan' function's namespace. (#13260) --- .../packages/bpp-core/clarify_isnan.patch | 42 +++++++++++++++++++ .../builtin/packages/bpp-core/package.py | 4 ++ 2 files changed, 46 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch diff --git a/var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch b/var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch new file mode 100644 index 00000000000..6038c15e42e --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch @@ -0,0 +1,42 @@ +diff -ur bpp-core-2.2.0_org/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp bpp-core-2.2.0/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp +--- bpp-core-2.2.0_org/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp 2019-10-18 14:13:47.041015700 +0900 ++++ bpp-core-2.2.0/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp 2019-10-18 15:32:41.888978173 +0900 +@@ -53,7 +53,7 @@ + function2_->enableSecondOrderDerivatives(false); + function_->setParameters(parameters); + f2_ = function_->getValue(); +- if ((abs(f2_) >= NumConstants::VERY_BIG()) || isnan(f2_)) ++ if ((abs(f2_) >= NumConstants::VERY_BIG()) || std::isnan(f2_)) + { + for (size_t i = 0; i < variables_.size(); ++i) + { +@@ -103,7 +103,7 @@ + + p = p.subList(0); + f1_ = function_->getValue(); +- if ((abs(f1_) >= NumConstants::VERY_BIG()) || isnan(f1_)) ++ if ((abs(f1_) >= NumConstants::VERY_BIG()) || std::isnan(f1_)) + throw ConstraintException("f1_ too large", &p[0], f1_); + else + hf1 = h; +@@ -137,7 +137,7 @@ + + p = p.subList(0); + f3_ = function_->getValue(); +- if ((abs(f3_) >= NumConstants::VERY_BIG()) || isnan(f3_)) ++ if ((abs(f3_) >= NumConstants::VERY_BIG()) || std::isnan(f3_)) + throw ConstraintException("f3_ too large", &p[0], f3_); + else + hf3 = h; +diff -ur bpp-core-2.2.0_org/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp bpp-core-2.2.0/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp +--- bpp-core-2.2.0_org/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp 2019-10-18 14:13:47.051016751 +0900 ++++ bpp-core-2.2.0/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp 2019-10-18 15:40:33.218550564 +0900 +@@ -124,7 +124,7 @@ + size_t ii = i * nbStates_; + for (size_t j = 0; j < nbStates_; j++) { + trans[ii + j] = transitionMatrix_->Pij(j, i); +- if (isnan(trans[ii + j])) ++ if (std::isnan(trans[ii + j])) + throw Exception("RescaledHmmLikelihood::computeForward_. NaN transition probability"); + if (trans[ii + j] < 0) + throw Exception("RescaledHmmLikelihood::computeForward_. Negative transition probability: " + TextTools::toString(trans[ii + j])); diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py index da9473e2aec..86326ccc1b8 100644 --- a/var/spack/repos/builtin/packages/bpp-core/package.py +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -16,5 +16,9 @@ class BppCore(CMakePackage): depends_on('cmake@2.6:', type='build') + # Clarify isnan's namespace, because Fujitsu compiler can't + # resolve ambiguous of 'isnan' function. + patch('clarify_isnan.patch', when='%fj') + def cmake_args(self): return ['-DBUILD_TESTING=FALSE'] From 0e3e1836ff9f19664766299314f4afd1fbde08c0 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Tue, 22 Oct 2019 08:27:39 +0900 Subject: [PATCH 360/499] arpack-ng: Fixed error that is not compatible with isnan. (#13246) --- .../arpack-ng/incompatible_isnan_fix.patch | 22 +++++++++++++++++++ .../builtin/packages/arpack-ng/package.py | 4 ++++ 2 files changed, 26 insertions(+) create mode 100644 var/spack/repos/builtin/packages/arpack-ng/incompatible_isnan_fix.patch diff --git a/var/spack/repos/builtin/packages/arpack-ng/incompatible_isnan_fix.patch b/var/spack/repos/builtin/packages/arpack-ng/incompatible_isnan_fix.patch new file mode 100644 index 00000000000..a2290e4cc56 --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/incompatible_isnan_fix.patch @@ -0,0 +1,22 @@ +diff -ur arpack-ng-3.7.0_org/TESTS/bug_58_double.f arpack-ng-3.7.0/TESTS/bug_58_double.f +--- arpack-ng-3.7.0_org/TESTS/bug_58_double.f 2019-10-17 12:17:22.496987817 +0900 ++++ arpack-ng-3.7.0/TESTS/bug_58_double.f 2019-10-17 17:12:37.669353870 +0900 +@@ -69,7 +69,7 @@ + & workev(3*maxncv), + & workl(3*maxncv*maxncv+6*maxncv), + & dd(maxn), dl(maxn), du(maxn), +- & du2(maxn), a(maxn,maxn), c(maxn,maxn) ++ & du2(maxn), a(maxn,maxn), c(maxn,maxn), rslt + c + c %---------------% + c | Local Scalars | +@@ -417,7 +417,8 @@ + print *, ' ' + c + end if +- if (isnan(v(1,1))) then ++ rslt = v(1,1) ++ if (rslt .ne. rslt) then + stop 1 + end if + c diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index f7628cc5aec..d2834035152 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -59,6 +59,10 @@ class ArpackNg(Package): patch('make_install.patch', when='@3.4.0') patch('parpack_cmake.patch', when='@3.4.0') + # Fujitsu compiler does not support 'isnan' function. + # isnan: function that determines whether it is NaN. + patch('incompatible_isnan_fix.patch', when='%fj') + depends_on('blas') depends_on('lapack') depends_on('automake', when='@3.3.0', type='build') From 7b62b64b031f27a5317818f0246f9bb844862b39 Mon Sep 17 00:00:00 2001 From: noguchi-k <55966120+noguchi-k@users.noreply.github.com> Date: Tue, 22 Oct 2019 08:28:38 +0900 Subject: [PATCH 361/499] elsi:add CMAKE Fortran MODDIR FLAG for Fujitsu compiler (#13244) * add CMAKE Fortran MODDIR FLAG for Fujitsu compiler * elsi:remove extra fix --- var/spack/repos/builtin/packages/elsi/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/elsi/package.py b/var/spack/repos/builtin/packages/elsi/package.py index 8d28f15133d..34aeacffbea 100644 --- a/var/spack/repos/builtin/packages/elsi/package.py +++ b/var/spack/repos/builtin/packages/elsi/package.py @@ -71,6 +71,7 @@ class Elsi(CMakePackage): def cmake_args(self): from os.path import dirname + spec = self.spec args = [] # Compiler Information @@ -105,4 +106,8 @@ def cmake_args(self): if '-use_mpi_iallgather' in self.spec: args += ["-DUSE_MPI_IALLGATHER=OFF"] + # Only when using fujitsu compiler + if spec.satisfies('%fj'): + args += ["-DCMAKE_Fortran_MODDIR_FLAG=-M"] + return args From 98c0d59a0c9963286fb5eb0cdbc63f3a8321916a Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Tue, 22 Oct 2019 08:38:05 +0900 Subject: [PATCH 362/499] sniffles: fix zlib header lookup directory. (#13063) * sniffles: fix zlib header lookup directory. * use bamtools and zlib to spack installed package. * remove unneeded patch. --- .../builtin/packages/sniffles/package.py | 9 ++++ .../packages/sniffles/unused_libs.patch | 41 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 var/spack/repos/builtin/packages/sniffles/unused_libs.patch diff --git a/var/spack/repos/builtin/packages/sniffles/package.py b/var/spack/repos/builtin/packages/sniffles/package.py index 03da487df18..b6dca88203f 100644 --- a/var/spack/repos/builtin/packages/sniffles/package.py +++ b/var/spack/repos/builtin/packages/sniffles/package.py @@ -15,6 +15,15 @@ class Sniffles(CMakePackage): version('1.0.7', sha256='03fa703873bdf9c32055c584448e1eece45f94b4bc68e60c9624cf3841e6d8a9') version('1.0.5', sha256='386c6536bdaa4637579e235bac48444c08297337c490652d1e165accd34b258f') + depends_on('zlib', type='link') + depends_on('bamtools', type='link') + + patch('unused_libs.patch') + + def cmake_args(self): + i = self.spec['bamtools'].prefix.include.bamtools + return ['-DCMAKE_CXX_FLAGS=-I{0}'.format(i)] + # the build process doesn't actually install anything, do it by hand def install(self, spec, prefix): mkdir(prefix.bin) diff --git a/var/spack/repos/builtin/packages/sniffles/unused_libs.patch b/var/spack/repos/builtin/packages/sniffles/unused_libs.patch new file mode 100644 index 00000000000..3a1813c4549 --- /dev/null +++ b/var/spack/repos/builtin/packages/sniffles/unused_libs.patch @@ -0,0 +1,41 @@ +--- spack-src.org/CMakeLists.txt 2017-11-14 04:24:46.000000000 +0900 ++++ spack-src/CMakeLists.txt 2019-10-08 09:10:10.409449275 +0900 +@@ -29,8 +29,4 @@ + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") + endif() + +- +-add_subdirectory(lib/zlib-1.2.7) +-add_subdirectory(lib/bamtools-2.3.0) +- + add_subdirectory(src) +--- spack-src.org/src/CMakeLists.txt 2017-11-14 04:24:46.000000000 +0900 ++++ spack-src/src/CMakeLists.txt 2019-10-08 09:21:52.569644934 +0900 +@@ -1,7 +1,6 @@ + cmake_minimum_required(VERSION 2.8) + project(Sniffles) + +-include_directories (../lib/bamtools-2.3.0/src) + include_directories(../lib/tclap-1.2.1/include) + + configure_file( Version.h.in ${CMAKE_SOURCE_DIR}/src/Version.h ) +@@ -32,8 +31,8 @@ + ) + + #target_link_libraries(ngm-core pthread) +-TARGET_LINK_LIBRARIES(sniffles BamTools-static) +-TARGET_LINK_LIBRARIES(sniffles zlibstatic) ++TARGET_LINK_LIBRARIES(sniffles bamtools) ++TARGET_LINK_LIBRARIES(sniffles z) + + add_executable(sniffles-debug + tree/Breakpoint_Tree.cpp +@@ -63,6 +62,6 @@ + SET_TARGET_PROPERTIES(sniffles-debug PROPERTIES COMPILE_FLAGS "-g3 -O0") + + #target_link_libraries(sniffles-debug pthread) +-TARGET_LINK_LIBRARIES(sniffles-debug BamTools-static) +-TARGET_LINK_LIBRARIES(sniffles-debug zlibstatic) ++TARGET_LINK_LIBRARIES(sniffles-debug bamtools) ++TARGET_LINK_LIBRARIES(sniffles-debug z) + From 5e6dc7ab4ba8121f0cd5bbc865b75b749886f7cb Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 21 Oct 2019 21:45:48 -0500 Subject: [PATCH 363/499] Add latest version of zstd (#13340) * Add latest version of zstd * setup_environment -> setup_build_environment --- var/spack/repos/builtin/packages/zstd/package.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py index 03e43c5400f..bfdd5d0d1a9 100644 --- a/var/spack/repos/builtin/packages/zstd/package.py +++ b/var/spack/repos/builtin/packages/zstd/package.py @@ -12,8 +12,9 @@ class Zstd(MakefilePackage): better compression ratios.""" homepage = "http://facebook.github.io/zstd/" - url = "https://github.com/facebook/zstd/archive/v1.4.2.tar.gz" + url = "https://github.com/facebook/zstd/archive/v1.4.3.tar.gz" + version('1.4.3', sha256='5eda3502ecc285c3c92ee0cc8cd002234dee39d539b3f692997a0e80de1d33de') version('1.4.2', sha256='7a6e1dad34054b35e2e847eb3289be8820a5d378228802239852f913c6dcf6a7') version('1.4.0', sha256='63be339137d2b683c6d19a9e34f4fb684790e864fee13c7dd40e197a64c705c1') version('1.3.8', sha256='90d902a1282cc4e197a8023b6d6e8d331c1fd1dfe60f7f8e4ee9da40da886dc3') @@ -22,9 +23,11 @@ class Zstd(MakefilePackage): variant('pic', default=True, description='Build position independent code') - def setup_environment(self, spack_env, run_env): + depends_on('zlib') + + def setup_build_environment(self, env): if '+pic' in self.spec: - spack_env.append_flags('CFLAGS', self.compiler.pic_flag) + env.append_flags('CFLAGS', self.compiler.pic_flag) def build(self, spec, prefix): make('PREFIX={0}'.format(prefix)) From 326db657da3f0c3111131c0d27be26e53c84245c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 00:42:40 -0500 Subject: [PATCH 364/499] Add latest version of patchelf (#13348) --- var/spack/repos/builtin/packages/patchelf/package.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/patchelf/package.py b/var/spack/repos/builtin/packages/patchelf/package.py index 73328f3c01a..6d4d979b16e 100644 --- a/var/spack/repos/builtin/packages/patchelf/package.py +++ b/var/spack/repos/builtin/packages/patchelf/package.py @@ -11,10 +11,10 @@ class Patchelf(AutotoolsPackage): ELF executables.""" homepage = "https://nixos.org/patchelf.html" - url = "http://nixos.org/releases/patchelf/patchelf-0.8/patchelf-0.8.tar.gz" - - list_url = "http://nixos.org/releases/patchelf/" + url = "https://nixos.org/releases/patchelf/patchelf-0.10/patchelf-0.10.tar.gz" + list_url = "https://nixos.org/releases/patchelf/" list_depth = 1 - version('0.9', sha256='f2aa40a6148cb3b0ca807a1bf836b081793e55ec9e5540a5356d800132be7e0a') - version('0.8', sha256='14af06a2da688d577d64ff8dac065bb8903bbffbe01d30c62df7af9bf4ce72fe') + version('0.10', sha256='b2deabce05c34ce98558c0efb965f209de592197b2c88e930298d740ead09019') + version('0.9', sha256='f2aa40a6148cb3b0ca807a1bf836b081793e55ec9e5540a5356d800132be7e0a') + version('0.8', sha256='14af06a2da688d577d64ff8dac065bb8903bbffbe01d30c62df7af9bf4ce72fe') From fb219cd91c45b03b47067914e55f68cf00e15520 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 00:42:56 -0500 Subject: [PATCH 365/499] Add latest version of gnupg (#13349) --- .../repos/builtin/packages/gnupg/package.py | 36 ++++++++++++------- 1 file changed, 23 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/gnupg/package.py b/var/spack/repos/builtin/packages/gnupg/package.py index b05f468dee3..255b9e0b4b4 100644 --- a/var/spack/repos/builtin/packages/gnupg/package.py +++ b/var/spack/repos/builtin/packages/gnupg/package.py @@ -11,24 +11,34 @@ class Gnupg(AutotoolsPackage): standard as defined by RFC4880 """ homepage = "https://gnupg.org/index.html" - url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.2.3.tar.bz2" + url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.2.17.tar.bz2" + version('2.2.17', sha256='afa262868e39b651a2db4c071fba90415154243e83a830ca00516f9a807fd514') version('2.2.15', sha256='cb8ce298d7b36558ffc48aec961b14c830ff1783eef7a623411188b5e0f5d454') - version('2.2.3', sha256='cbd37105d139f7aa74f92b6f65d136658682094b0e308666b820ae4b984084b4') + version('2.2.3', sha256='cbd37105d139f7aa74f92b6f65d136658682094b0e308666b820ae4b984084b4') version('2.1.21', sha256='7aead8a8ba75b69866f583b6c747d91414d523bfdfbe9a8e0fe026b16ba427dd') - depends_on('libgcrypt') + depends_on('libgcrypt@1.7.0:') depends_on('libassuan@2.4:', when='@:2.2.3') depends_on('libassuan@2.5:', when='@2.2.15:') - depends_on('libksba') - depends_on('libgpg-error') - depends_on('npth') + depends_on('libksba@1.3.4:') + depends_on('libgpg-error@1.24:') + depends_on('npth@1.2:') + depends_on('zlib') + depends_on('libiconv') def configure_args(self): - args = ['--with-npth-prefix=%s' % self.spec['npth'].prefix, - '--with-libgcrypt-prefix=%s' % self.spec['libgcrypt'].prefix, - '--with-libksba-prefixx=%s' % self.spec['libksba'].prefix, - '--with-libassuan-prefix=%s' % self.spec['libassuan'].prefix, - '--with-libpgp-error-prefix=%s' % - self.spec['libgpg-error'].prefix] - return args + return [ + '--without-tar', + '--with-libgpg-error-prefix=' + self.spec['libgpg-error'].prefix, + '--with-libgcrypt-prefix=' + self.spec['libgcrypt'].prefix, + '--with-libassuan-prefix=' + self.spec['libassuan'].prefix, + '--with-ksba-prefix=' + self.spec['libksba'].prefix, + '--with-npth-prefix=' + self.spec['npth'].prefix, + '--without-ldap', + '--with-libiconv-prefix=' + self.spec['libiconv'].prefix, + '--without-regex', + '--with-zlib=' + self.spec['zlib'].prefix, + '--without-bzip2', + '--without-readline', + ] From 598274a278351b508a01232f3bcb8da359129297 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 00:43:11 -0500 Subject: [PATCH 366/499] Fix configure arg to libksba (#13352) --- var/spack/repos/builtin/packages/libksba/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/libksba/package.py b/var/spack/repos/builtin/packages/libksba/package.py index 23d0c1509f7..70da99d6821 100644 --- a/var/spack/repos/builtin/packages/libksba/package.py +++ b/var/spack/repos/builtin/packages/libksba/package.py @@ -15,8 +15,9 @@ class Libksba(AutotoolsPackage): version('1.3.5', sha256='41444fd7a6ff73a79ad9728f985e71c9ba8cd3e5e53358e70d5f066d35c1a340') - depends_on('libgpg-error') + depends_on('libgpg-error@1.8:') def configure_args(self): - args = ['--with-libgpp-error=%s' % self.spec['libgpg-error'].prefix] - return args + return [ + '--with-libgpg-error-prefix=' + self.spec['libgpg-error'].prefix + ] From 2aa51697c55ff06d2c6a4bf027b3cdbc1f7d5c11 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 00:43:29 -0500 Subject: [PATCH 367/499] Fix configure arg to libassuan (#13350) --- var/spack/repos/builtin/packages/libassuan/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/libassuan/package.py b/var/spack/repos/builtin/packages/libassuan/package.py index 2ecccdbbab1..4f7ee1da193 100644 --- a/var/spack/repos/builtin/packages/libassuan/package.py +++ b/var/spack/repos/builtin/packages/libassuan/package.py @@ -17,8 +17,9 @@ class Libassuan(AutotoolsPackage): version('2.4.5', sha256='fbfea5d1dbcdee34f2597b0afb3d8bb4eda96c924a1e01b01c2acde68b81625f') version('2.4.3', sha256='22843a3bdb256f59be49842abf24da76700354293a066d82ade8134bb5aa2b71') - depends_on('libgpg-error') + depends_on('libgpg-error@1.17:') def configure_args(self): - args = ['--with-libgpp-error=%s' % self.spec['libgpg-error'].prefix] - return args + return [ + '--with-libgpg-error-prefix=' + self.spec['libgpg-error'].prefix + ] From 6cb972a9d25cee6ed8b92195cccd8ad2255e98a9 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 00:43:44 -0500 Subject: [PATCH 368/499] Add dependency version constraint to libgcrypt (#13351) --- var/spack/repos/builtin/packages/libgcrypt/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py index 07161ff08c5..0edc1a0d203 100644 --- a/var/spack/repos/builtin/packages/libgcrypt/package.py +++ b/var/spack/repos/builtin/packages/libgcrypt/package.py @@ -22,4 +22,4 @@ class Libgcrypt(AutotoolsPackage): version('1.7.6', sha256='626aafee84af9d2ce253d2c143dc1c0902dda045780cc241f39970fc60be05bc') version('1.6.2', sha256='de084492a6b38cdb27b67eaf749ceba76bf7029f63a9c0c3c1b05c88c9885c4c') - depends_on("libgpg-error") + depends_on('libgpg-error@1.25:') From fd58c98b0edd198e2b1bc8c9f81208d7d6010178 Mon Sep 17 00:00:00 2001 From: Omar Padron Date: Tue, 22 Oct 2019 03:32:04 -0400 Subject: [PATCH 369/499] fetching: S3 upload and download (#11117) This extends Spack functionality so that it can fetch sources and binaries from-, push sources and binaries to-, and index the contents of- mirrors hosted on an S3 bucket. High level to-do list: - [x] Extend mirrors configuration to add support for `file://`, and `s3://` URLs. - [x] Ensure all fetching, pushing, and indexing operations work for `file://` URLs. - [x] Implement S3 source fetching - [x] Implement S3 binary mirror indexing - [x] Implement S3 binary package fetching - [x] Implement S3 source pushing - [x] Implement S3 binary package pushing Important details: * refactor URL handling to handle S3 URLs and mirror URLs more gracefully. - updated parse() to accept already-parsed URL objects. an equivalent object is returned with any extra s3-related attributes intact. Objects created with urllib can also be passed, and the additional s3 handling logic will still be applied. * update mirror schema/parsing (mirror can have separate fetch/push URLs) * implement s3_fetch_strategy/several utility changes * provide more feature-complete S3 fetching * update buildcache create command to support S3 * Move the core logic for reading data from S3 out of the s3 fetch strategy and into the s3 URL handler. The s3 fetch strategy now calls into `read_from_url()` Since read_from_url can now handle S3 URLs, the S3 fetch strategy is redundant. It's not clear whether the ideal design is to have S3 fetching functionality in a fetch strategy, directly implemented in read_from_url, or both. * expanded what can be passed to `spack buildcache` via the -d flag: In addition to a directory on the local filesystem, the name of a configured mirror can be passed, or a push URL can be passed directly. --- .gitlab-ci.yml | 5 + bin/rebuild-index.sh | 2 +- lib/spack/spack/binary_distribution.py | 229 +++++++----- lib/spack/spack/caches.py | 16 +- lib/spack/spack/cmd/buildcache.py | 28 ++ lib/spack/spack/cmd/checksum.py | 4 +- lib/spack/spack/cmd/create.py | 3 +- lib/spack/spack/cmd/mirror.py | 125 +++++-- lib/spack/spack/cmd/url.py | 8 +- lib/spack/spack/fetch_strategy.py | 104 +++++- lib/spack/spack/mirror.py | 230 +++++++++++- lib/spack/spack/s3_handler.py | 92 +++++ lib/spack/spack/schema/mirrors.py | 14 +- lib/spack/spack/stage.py | 118 +++++- lib/spack/spack/test/cmd/pkg.py | 2 + lib/spack/spack/test/config.py | 1 + lib/spack/spack/test/llnl/util/lock.py | 2 + lib/spack/spack/test/stage.py | 2 + lib/spack/spack/util/s3.py | 44 +++ lib/spack/spack/util/url.py | 175 +++++++++ lib/spack/spack/util/web.py | 487 ++++++++++++++++++------- 21 files changed, 1411 insertions(+), 280 deletions(-) create mode 100644 lib/spack/spack/s3_handler.py create mode 100644 lib/spack/spack/util/s3.py create mode 100644 lib/spack/spack/util/url.py diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c4d6bcaab6d..f0cfd456ff2 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,3 +1,8 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + generate ci jobs: script: - "./bin/generate-gitlab-ci-yml.sh" diff --git a/bin/rebuild-index.sh b/bin/rebuild-index.sh index 09e14a9ceeb..009010baf11 100755 --- a/bin/rebuild-index.sh +++ b/bin/rebuild-index.sh @@ -10,4 +10,4 @@ set -x SPACK_BIN_DIR="${CI_PROJECT_DIR}/bin" export PATH="${SPACK_BIN_DIR}:${PATH}" -spack upload-s3 index +spack buildcache update-index -d "$MIRROR_URL" diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index cbc0f22327c..aab07b8a845 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -3,6 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import codecs import os import re import tarfile @@ -23,14 +24,32 @@ import spack.util.gpg as gpg_util import spack.relocate as relocate import spack.util.spack_yaml as syaml +import spack.mirror +import spack.util.url as url_util +import spack.util.web as web_util + from spack.spec import Spec from spack.stage import Stage from spack.util.gpg import Gpg -from spack.util.web import spider, read_from_url from spack.util.executable import ProcessError _build_cache_relative_path = 'build_cache' +BUILD_CACHE_INDEX_TEMPLATE = ''' + + + {title} + + +
    +{path_list} +
+ + +''' + +BUILD_CACHE_INDEX_ENTRY_TEMPLATE = '
  • {path}
    • ' + class NoOverwriteException(Exception): """ @@ -101,7 +120,7 @@ def build_cache_relative_path(): return _build_cache_relative_path -def build_cache_directory(prefix): +def build_cache_prefix(prefix): return os.path.join(prefix, build_cache_relative_path()) @@ -246,29 +265,36 @@ def sign_tarball(key, force, specfile_path): Gpg.sign(key, specfile_path, '%s.asc' % specfile_path) -def _generate_html_index(path_list, output_path): - f = open(output_path, 'w') - header = """\n -\n\n -\n""" - footer = "\n\n" - f.write(header) - for path in path_list: - rel = os.path.basename(path) - f.write('
  • %s\n' % (rel, rel)) - f.write(footer) - f.close() +def generate_package_index(cache_prefix): + """Create the build cache index page. + Creates (or replaces) the "index.html" page at the location given in + cache_prefix. This page contains a link for each binary package (*.yaml) + and signing key (*.key) under cache_prefix. + """ + tmpdir = tempfile.mkdtemp() + try: + index_html_path = os.path.join(tmpdir, 'index.html') + file_list = ( + entry + for entry in web_util.list_url(cache_prefix) + if (entry.endswith('.yaml') + or entry.endswith('.key'))) -def generate_package_index(build_cache_dir): - yaml_list = os.listdir(build_cache_dir) - path_list = [os.path.join(build_cache_dir, l) for l in yaml_list] + with open(index_html_path, 'w') as f: + f.write(BUILD_CACHE_INDEX_TEMPLATE.format( + title='Spack Package Index', + path_list='\n'.join( + BUILD_CACHE_INDEX_ENTRY_TEMPLATE.format(path=path) + for path in file_list))) - index_html_path_tmp = os.path.join(build_cache_dir, 'index.html.tmp') - index_html_path = os.path.join(build_cache_dir, 'index.html') - - _generate_html_index(path_list, index_html_path_tmp) - shutil.move(index_html_path_tmp, index_html_path) + web_util.push_to_url( + index_html_path, + url_util.join(cache_prefix, 'index.html'), + keep_original=False, + extra_args={'ContentType': 'text/html'}) + finally: + shutil.rmtree(tmpdir) def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, @@ -281,33 +307,41 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, raise ValueError('spec must be concrete to build tarball') # set up some paths - build_cache_dir = build_cache_directory(outdir) + tmpdir = tempfile.mkdtemp() + cache_prefix = build_cache_prefix(tmpdir) tarfile_name = tarball_name(spec, '.tar.gz') - tarfile_dir = os.path.join(build_cache_dir, - tarball_directory_name(spec)) + tarfile_dir = os.path.join(cache_prefix, tarball_directory_name(spec)) tarfile_path = os.path.join(tarfile_dir, tarfile_name) - mkdirp(tarfile_dir) spackfile_path = os.path.join( - build_cache_dir, tarball_path_name(spec, '.spack')) - if os.path.exists(spackfile_path): + cache_prefix, tarball_path_name(spec, '.spack')) + + remote_spackfile_path = url_util.join( + outdir, os.path.relpath(spackfile_path, tmpdir)) + + mkdirp(tarfile_dir) + if web_util.url_exists(remote_spackfile_path): if force: - os.remove(spackfile_path) + web_util.remove_url(remote_spackfile_path) else: - raise NoOverwriteException(str(spackfile_path)) + raise NoOverwriteException(url_util.format(remote_spackfile_path)) + # need to copy the spec file so the build cache can be downloaded # without concretizing with the current spack packages # and preferences spec_file = os.path.join(spec.prefix, ".spack", "spec.yaml") specfile_name = tarball_name(spec, '.spec.yaml') specfile_path = os.path.realpath( - os.path.join(build_cache_dir, specfile_name)) + os.path.join(cache_prefix, specfile_name)) - if os.path.exists(specfile_path): + remote_specfile_path = url_util.join( + outdir, os.path.relpath(specfile_path, os.path.realpath(tmpdir))) + + if web_util.url_exists(remote_specfile_path): if force: - os.remove(specfile_path) + web_util.remove_url(remote_specfile_path) else: - raise NoOverwriteException(str(specfile_path)) + raise NoOverwriteException(url_util.format(remote_specfile_path)) # make a copy of the install directory to work with workdir = os.path.join(tempfile.mkdtemp(), os.path.basename(spec.prefix)) @@ -324,6 +358,7 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, except Exception as e: shutil.rmtree(workdir) shutil.rmtree(tarfile_dir) + shutil.rmtree(tmpdir) tty.die(e) else: try: @@ -331,7 +366,9 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, except Exception as e: shutil.rmtree(workdir) shutil.rmtree(tarfile_dir) + shutil.rmtree(tmpdir) tty.die(e) + # create compressed tarball of the install prefix with closing(tarfile.open(tarfile_path, 'w:gz')) as tar: tar.add(name='%s' % workdir, @@ -360,7 +397,9 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, spec_dict['full_hash'] = spec.full_hash() tty.debug('The full_hash ({0}) of {1} will be written into {2}'.format( - spec_dict['full_hash'], spec.name, specfile_path)) + spec_dict['full_hash'], + spec.name, + url_util.format(remote_specfile_path))) tty.debug(spec.tree()) with open(specfile_path, 'w') as outfile: @@ -382,9 +421,19 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, if not unsigned: os.remove('%s.asc' % specfile_path) - # create an index.html for the build_cache directory so specs can be found - if regenerate_index: - generate_package_index(build_cache_dir) + web_util.push_to_url( + spackfile_path, remote_spackfile_path, keep_original=False) + web_util.push_to_url( + specfile_path, remote_specfile_path, keep_original=False) + + try: + # create an index.html for the build_cache directory so specs can be + # found + if regenerate_index: + generate_package_index(url_util.join( + outdir, os.path.relpath(cache_prefix, tmpdir))) + finally: + shutil.rmtree(tmpdir) return None @@ -394,13 +443,16 @@ def download_tarball(spec): Download binary tarball for given package into stage area Return True if successful """ - mirrors = spack.config.get('mirrors') - if len(mirrors) == 0: + if not spack.mirror.MirrorCollection(): tty.die("Please add a spack mirror to allow " + "download of pre-compiled packages.") + tarball = tarball_path_name(spec, '.spack') - for mirror_name, mirror_url in mirrors.items(): - url = mirror_url + '/' + _build_cache_relative_path + '/' + tarball + + for mirror in spack.mirror.MirrorCollection().values(): + url = url_util.join( + mirror.fetch_url, _build_cache_relative_path, tarball) + # stage the tarball into standard place stage = Stage(url, name="build_cache", keep=True) try: @@ -408,6 +460,7 @@ def download_tarball(spec): return stage.save_filename except fs.FetchError: continue + return None @@ -610,26 +663,29 @@ def get_specs(force=False): tty.debug("Using previously-retrieved specs") return _cached_specs - mirrors = spack.config.get('mirrors') - if len(mirrors) == 0: - tty.debug("No Spack mirrors are currently configured") + if not spack.mirror.MirrorCollection(): + tty.warn("No Spack mirrors are currently configured") return {} urls = set() - for mirror_name, mirror_url in mirrors.items(): - if mirror_url.startswith('file'): - mirror = mirror_url.replace( - 'file://', '') + "/" + _build_cache_relative_path - tty.msg("Finding buildcaches in %s" % mirror) - if os.path.exists(mirror): - files = os.listdir(mirror) + for mirror in spack.mirror.MirrorCollection().values(): + fetch_url_build_cache = url_util.join( + mirror.fetch_url, _build_cache_relative_path) + + mirror_dir = url_util.local_file_path(fetch_url_build_cache) + if mirror_dir: + tty.msg("Finding buildcaches in %s" % mirror_dir) + if os.path.exists(mirror_dir): + files = os.listdir(mirror_dir) for file in files: if re.search('spec.yaml', file): - link = 'file://' + mirror + '/' + file + link = url_util.join(fetch_url_build_cache, file) urls.add(link) else: - tty.msg("Finding buildcaches on %s" % mirror_url) - p, links = spider(mirror_url + "/" + _build_cache_relative_path) + tty.msg("Finding buildcaches at %s" % + url_util.format(fetch_url_build_cache)) + p, links = web_util.spider( + url_util.join(fetch_url_build_cache, 'index.html')) for link in links: if re.search("spec.yaml", link): urls.add(link) @@ -659,28 +715,33 @@ def get_keys(install=False, trust=False, force=False): """ Get pgp public keys available on mirror """ - mirrors = spack.config.get('mirrors') - if len(mirrors) == 0: + if not spack.mirror.MirrorCollection(): tty.die("Please add a spack mirror to allow " + "download of build caches.") keys = set() - for mirror_name, mirror_url in mirrors.items(): - if mirror_url.startswith('file'): - mirror = os.path.join( - mirror_url.replace('file://', ''), _build_cache_relative_path) - tty.msg("Finding public keys in %s" % mirror) - files = os.listdir(mirror) + + for mirror in spack.mirror.MirrorCollection().values(): + fetch_url_build_cache = url_util.join( + mirror.fetch_url, _build_cache_relative_path) + + mirror_dir = url_util.local_file_path(fetch_url_build_cache) + if mirror_dir: + tty.msg("Finding public keys in %s" % mirror_dir) + files = os.listdir(mirror_dir) for file in files: if re.search(r'\.key', file): - link = 'file://' + mirror + '/' + file + link = url_util.join(fetch_url_build_cache, file) keys.add(link) else: - tty.msg("Finding public keys on %s" % mirror_url) - p, links = spider(mirror_url + "/build_cache", depth=1) + tty.msg("Finding public keys at %s" % + url_util.format(fetch_url_build_cache)) + p, links = web_util.spider(fetch_url_build_cache, depth=1) + for link in links: if re.search(r'\.key', link): keys.add(link) + for link in keys: with Stage(link, name="build_cache", keep=True) as stage: if os.path.exists(stage.save_filename) and force: @@ -717,15 +778,16 @@ def needs_rebuild(spec, mirror_url, rebuild_on_errors=False): # Try to retrieve the .spec.yaml directly, based on the known # format of the name, in order to determine if the package # needs to be rebuilt. - build_cache_dir = build_cache_directory(mirror_url) + cache_prefix = build_cache_prefix(mirror_url) spec_yaml_file_name = tarball_name(spec, '.spec.yaml') - file_path = os.path.join(build_cache_dir, spec_yaml_file_name) + file_path = os.path.join(cache_prefix, spec_yaml_file_name) result_of_error = 'Package ({0}) will {1}be rebuilt'.format( spec.short_spec, '' if rebuild_on_errors else 'not ') try: - yaml_contents = read_from_url(file_path) + _, _, yaml_file = web_util.read_from_url(file_path) + yaml_contents = codecs.getreader('utf-8')(yaml_file).read() except URLError as url_err: err_msg = [ 'Unable to determine whether {0} needs rebuilding,', @@ -782,22 +844,22 @@ def check_specs_against_mirrors(mirrors, specs, output_file=None, """ rebuilds = {} - for mirror_name, mirror_url in mirrors.items(): - tty.msg('Checking for built specs at %s' % mirror_url) + for mirror in spack.mirror.MirrorCollection(mirrors).values(): + tty.msg('Checking for built specs at %s' % mirror.fetch_url) rebuild_list = [] for spec in specs: - if needs_rebuild(spec, mirror_url, rebuild_on_errors): + if needs_rebuild(spec, mirror.fetch_url, rebuild_on_errors): rebuild_list.append({ 'short_spec': spec.short_spec, 'hash': spec.dag_hash() }) if rebuild_list: - rebuilds[mirror_url] = { - 'mirrorName': mirror_name, - 'mirrorUrl': mirror_url, + rebuilds[mirror.fetch_url] = { + 'mirrorName': mirror.name, + 'mirrorUrl': mirror.fetch_url, 'rebuildSpecs': rebuild_list } @@ -810,33 +872,36 @@ def check_specs_against_mirrors(mirrors, specs, output_file=None, def _download_buildcache_entry(mirror_root, descriptions): for description in descriptions: - url = os.path.join(mirror_root, description['url']) + description_url = os.path.join(mirror_root, description['url']) path = description['path'] fail_if_missing = description['required'] mkdirp(path) - stage = Stage(url, name="build_cache", path=path, keep=True) + stage = Stage( + description_url, name="build_cache", path=path, keep=True) try: stage.fetch() except fs.FetchError as e: tty.debug(e) if fail_if_missing: - tty.error('Failed to download required url {0}'.format(url)) + tty.error('Failed to download required url {0}'.format( + description_url)) return False return True def download_buildcache_entry(file_descriptions): - mirrors = spack.config.get('mirrors') - if len(mirrors) == 0: + if not spack.mirror.MirrorCollection(): tty.die("Please add a spack mirror to allow " + "download of buildcache entries.") - for mirror_name, mirror_url in mirrors.items(): - mirror_root = os.path.join(mirror_url, _build_cache_relative_path) + for mirror in spack.mirror.MirrorCollection().values(): + mirror_root = os.path.join( + mirror.fetch_url, + _build_cache_relative_path) if _download_buildcache_entry(mirror_root, file_descriptions): return True diff --git a/lib/spack/spack/caches.py b/lib/spack/spack/caches.py index dfd750fa825..e2352b2fcc0 100644 --- a/lib/spack/spack/caches.py +++ b/lib/spack/spack/caches.py @@ -9,11 +9,13 @@ import llnl.util.lang from llnl.util.filesystem import mkdirp +import spack.error import spack.paths import spack.config import spack.fetch_strategy import spack.util.file_cache -from spack.util.path import canonicalize_path +import spack.util.path +import spack.util.url as url_util def _misc_cache(): @@ -25,7 +27,7 @@ def _misc_cache(): path = spack.config.get('config:misc_cache') if not path: path = os.path.join(spack.paths.user_config_path, 'cache') - path = canonicalize_path(path) + path = spack.util.path.canonicalize_path(path) return spack.util.file_cache.FileCache(path) @@ -43,22 +45,26 @@ def _fetch_cache(): path = spack.config.get('config:source_cache') if not path: path = os.path.join(spack.paths.var_path, "cache") - path = canonicalize_path(path) + path = spack.util.path.canonicalize_path(path) return spack.fetch_strategy.FsCache(path) class MirrorCache(object): def __init__(self, root): - self.root = os.path.abspath(root) + self.root = url_util.local_file_path(root) + if not self.root: + raise spack.error.SpackError( + 'MirrorCaches only work with file:// URLs') + self.new_resources = set() self.existing_resources = set() def store(self, fetcher, relative_dest): # Note this will archive package sources even if they would not # normally be cached (e.g. the current tip of an hg/git branch) - dst = os.path.join(self.root, relative_dest) + if os.path.exists(dst): self.existing_resources.add(relative_dest) else: diff --git a/lib/spack/spack/cmd/buildcache.py b/lib/spack/spack/cmd/buildcache.py index 121a6f4aa50..ee09a33f396 100644 --- a/lib/spack/spack/cmd/buildcache.py +++ b/lib/spack/spack/cmd/buildcache.py @@ -14,6 +14,7 @@ import spack.cmd.common.arguments as arguments import spack.environment as ev import spack.hash_types as ht +import spack.mirror import spack.relocate import spack.repo import spack.spec @@ -21,6 +22,8 @@ import spack.config import spack.repo import spack.store +import spack.util.url as url_util + from spack.error import SpecError from spack.spec import Spec, save_dependency_spec_yamls @@ -205,6 +208,13 @@ def setup_parser(subparser): help='Destination mirror url') copy.set_defaults(func=buildcache_copy) + # Update buildcache index without copying any additional packages + update_index = subparsers.add_parser( + 'update-index', help=buildcache_update_index.__doc__) + update_index.add_argument( + '-d', '--mirror-url', default=None, help='Destination mirror url') + update_index.set_defaults(func=buildcache_update_index) + def find_matching_specs(pkgs, allow_multiple_matches=False, env=None): """Returns a list of specs matching the not necessarily @@ -312,9 +322,14 @@ def createtarball(args): " yaml file containing a spec to install") pkgs = set(packages) specs = set() + outdir = '.' if args.directory: outdir = args.directory + + mirror = spack.mirror.MirrorCollection().lookup(outdir) + outdir = url_util.format(mirror.push_url) + signkey = None if args.key: signkey = args.key @@ -649,6 +664,19 @@ def buildcache_copy(args): shutil.copyfile(cdashid_src_path, cdashid_dest_path) +def buildcache_update_index(args): + """Update a buildcache index.""" + outdir = '.' + if args.mirror_url: + outdir = args.mirror_url + + mirror = spack.mirror.MirrorCollection().lookup(outdir) + outdir = url_util.format(mirror.push_url) + + bindist.generate_package_index( + url_util.join(outdir, bindist.build_cache_relative_path())) + + def buildcache(parser, args): if args.func: args.func(args) diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py index ecc71d3060b..2518dfef9f0 100644 --- a/lib/spack/spack/cmd/checksum.py +++ b/lib/spack/spack/cmd/checksum.py @@ -11,8 +11,8 @@ import spack.cmd import spack.repo +import spack.stage import spack.util.crypto -import spack.util.web from spack.util.naming import valid_fully_qualified_module_name from spack.version import ver, Version @@ -56,7 +56,7 @@ def checksum(parser, args): if not url_dict: tty.die("Could not find any versions for {0}".format(pkg.name)) - version_lines = spack.util.web.get_checksums_for_versions( + version_lines = spack.stage.get_checksums_for_versions( url_dict, pkg.name, keep_stage=args.keep_stage) print() diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index 527a7a883c5..6c68617acd6 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -13,6 +13,7 @@ import spack.util.web import spack.repo +import spack.stage from spack.spec import Spec from spack.util.editor import editor from spack.util.executable import which, ProcessError @@ -618,7 +619,7 @@ def get_versions(args, name): version = parse_version(args.url) url_dict = {version: args.url} - versions = spack.util.web.get_checksums_for_versions( + versions = spack.stage.get_checksums_for_versions( url_dict, name, first_stage_function=guesser, keep_stage=args.keep_stage) else: diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py index 723e310ad68..91ed40a4c58 100644 --- a/lib/spack/spack/cmd/mirror.py +++ b/lib/spack/spack/cmd/mirror.py @@ -4,20 +4,21 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import sys -import os -from datetime import datetime import argparse import llnl.util.tty as tty from llnl.util.tty.colify import colify import spack.cmd +import spack.cmd.common.arguments as arguments import spack.concretize import spack.config +import spack.environment as ev import spack.mirror import spack.repo -import spack.cmd.common.arguments as arguments -import spack.environment as ev +import spack.util.url as url_util +import spack.util.web as web_util + from spack.spec import Spec from spack.error import SpackError from spack.util.spack_yaml import syaml_dict @@ -73,6 +74,19 @@ def setup_parser(subparser): default=spack.config.default_modify_scope(), help="configuration scope to modify") + # Set-Url + set_url_parser = sp.add_parser('set-url', help=mirror_set_url.__doc__) + set_url_parser.add_argument('name', help="mnemonic name for mirror") + set_url_parser.add_argument( + 'url', help="url of mirror directory from 'spack mirror create'") + set_url_parser.add_argument( + '--push', action='store_true', + help="set only the URL used for uploading new packages") + set_url_parser.add_argument( + '--scope', choices=scopes, metavar=scopes_metavar, + default=spack.config.default_modify_scope(), + help="configuration scope to modify") + # List list_parser = sp.add_parser('list', help=mirror_list.__doc__) list_parser.add_argument( @@ -83,20 +97,14 @@ def setup_parser(subparser): def mirror_add(args): """Add a mirror to Spack.""" - url = args.url - if url.startswith('/'): - url = 'file://' + url + url = url_util.format(args.url) mirrors = spack.config.get('mirrors', scope=args.scope) if not mirrors: mirrors = syaml_dict() - for name, u in mirrors.items(): - if name == args.name: - tty.die("Mirror with name %s already exists." % name) - if u == url: - tty.die("Mirror with url %s already exists." % url) - # should only be one item per mirror dict. + if args.name in mirrors: + tty.die("Mirror with name %s already exists." % args.name) items = [(n, u) for n, u in mirrors.items()] items.insert(0, (args.name, url)) @@ -117,21 +125,86 @@ def mirror_remove(args): old_value = mirrors.pop(name) spack.config.set('mirrors', mirrors, scope=args.scope) - tty.msg("Removed mirror %s with url %s" % (name, old_value)) + + debug_msg_url = "url %s" + debug_msg = ["Removed mirror %s with"] + values = [name] + + try: + fetch_value = old_value['fetch'] + push_value = old_value['push'] + + debug_msg.extend(("fetch", debug_msg_url, "and push", debug_msg_url)) + values.extend((fetch_value, push_value)) + except TypeError: + debug_msg.append(debug_msg_url) + values.append(old_value) + + tty.debug(" ".join(debug_msg) % tuple(values)) + tty.msg("Removed mirror %s." % name) + + +def mirror_set_url(args): + """Change the URL of a mirror.""" + url = url_util.format(args.url) + + mirrors = spack.config.get('mirrors', scope=args.scope) + if not mirrors: + mirrors = syaml_dict() + + if args.name not in mirrors: + tty.die("No mirror found with name %s." % args.name) + + entry = mirrors[args.name] + + try: + fetch_url = entry['fetch'] + push_url = entry['push'] + except TypeError: + fetch_url, push_url = entry, entry + + changes_made = False + + if args.push: + changes_made = changes_made or push_url != url + push_url = url + else: + changes_made = ( + changes_made or fetch_url != push_url or push_url != url) + + fetch_url, push_url = url, url + + items = [ + ( + (n, u) + if n != args.name else ( + (n, {"fetch": fetch_url, "push": push_url}) + if fetch_url != push_url else (n, fetch_url) + ) + ) + for n, u in mirrors.items() + ] + + mirrors = syaml_dict(items) + spack.config.set('mirrors', mirrors, scope=args.scope) + + if changes_made: + tty.msg( + "Changed%s url for mirror %s." % + ((" (push)" if args.push else ""), args.name)) + else: + tty.msg("Url already set for mirror %s." % args.name) def mirror_list(args): """Print out available mirrors to the console.""" - mirrors = spack.config.get('mirrors', scope=args.scope) + + mirrors = spack.mirror.MirrorCollection(scope=args.scope) if not mirrors: tty.msg("No mirrors configured.") return - max_len = max(len(n) for n in mirrors.keys()) - fmt = "%%-%ds%%s" % (max_len + 4) - - for name in mirrors: - print(fmt % (name, mirrors[name])) + mirrors.display() def _read_specs_from_file(filename): @@ -188,14 +261,13 @@ def mirror_create(args): msg = 'Skipping {0} as it is an external spec.' tty.msg(msg.format(spec.cshort_spec)) - # Default name for directory is spack-mirror- - directory = args.directory - if not directory: - timestamp = datetime.now().strftime("%Y-%m-%d") - directory = 'spack-mirror-' + timestamp + mirror = spack.mirror.Mirror( + args.directory or spack.config.get('config:source_cache')) + + directory = url_util.format(mirror.push_url) # Make sure nothing is in the way. - existed = os.path.isdir(directory) + existed = web_util.url_exists(directory) # Actually do the work to create the mirror present, mirrored, error = spack.mirror.create( @@ -220,6 +292,7 @@ def mirror(parser, args): 'add': mirror_add, 'remove': mirror_remove, 'rm': mirror_remove, + 'set-url': mirror_set_url, 'list': mirror_list} if args.no_checksum: diff --git a/lib/spack/spack/cmd/url.py b/lib/spack/spack/cmd/url.py index 10257b26086..f1ce050a904 100644 --- a/lib/spack/spack/cmd/url.py +++ b/lib/spack/spack/cmd/url.py @@ -5,10 +5,8 @@ from __future__ import division, print_function from collections import defaultdict -try: - from urllib.parse import urlparse -except ImportError: - from urlparse import urlparse + +import six.moves.urllib.parse as urllib_parse import spack.fetch_strategy as fs import spack.repo @@ -262,7 +260,7 @@ def add(self, fetcher): self.checksums[algo] += 1 # parse out the URL scheme (https/http/ftp/etc.) - urlinfo = urlparse(fetcher.url) + urlinfo = urllib_parse.urlparse(fetcher.url) self.schemes[urlinfo.scheme] += 1 elif url_type == 'git': diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 32239d81ceb..48122118127 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -23,6 +23,7 @@ Archive a source directory, e.g. for creating a mirror. """ import os +import os.path import sys import re import shutil @@ -30,6 +31,7 @@ import xml.etree.ElementTree from functools import wraps from six import string_types, with_metaclass +import six.moves.urllib.parse as urllib_parse import llnl.util.tty as tty from llnl.util.filesystem import ( @@ -39,6 +41,9 @@ import spack.error import spack.util.crypto as crypto import spack.util.pattern as pattern +import spack.util.web as web_util +import spack.util.url as url_util + from spack.util.executable import which from spack.util.string import comma_and, quote from spack.version import Version, ver @@ -48,6 +53,17 @@ #: List of all fetch strategies, created by FetchStrategy metaclass. all_strategies = [] +CONTENT_TYPE_MISMATCH_WARNING_TEMPLATE = ( + "The contents of {subject} look like {content_type}. Either the URL" + " you are trying to use does not exist or you have an internet gateway" + " issue. You can remove the bad archive using 'spack clean" + " ', then try again using the correct URL.") + + +def warn_content_type_mismatch(subject, content_type='HTML'): + tty.warn(CONTENT_TYPE_MISMATCH_WARNING_TEMPLATE.format( + subject=subject, content_type=content_type)) + def _needs_stage(fun): """Many methods on fetch strategies require a stage to be set @@ -351,12 +367,7 @@ def fetch(self): content_types = re.findall(r'Content-Type:[^\r\n]+', headers, flags=re.IGNORECASE) if content_types and 'text/html' in content_types[-1]: - msg = ("The contents of {0} look like HTML. Either the URL " - "you are trying to use does not exist or you have an " - "internet gateway issue. You can remove the bad archive " - "using 'spack clean ', then try again using " - "the correct URL.") - tty.warn(msg.format(self.archive_file or "the archive")) + warn_content_type_mismatch(self.archive_file or "the archive") if save_file: os.rename(partial_file, save_file) @@ -449,7 +460,10 @@ def archive(self, destination): if not self.archive_file: raise NoArchiveFileError("Cannot call archive() before fetching.") - shutil.copyfile(self.archive_file, destination) + web_util.push_to_url( + self.archive_file, + destination, + keep_original=True) @_needs_stage def check(self): @@ -1063,6 +1077,54 @@ def __str__(self): return "[hg] %s" % self.url +class S3FetchStrategy(URLFetchStrategy): + """FetchStrategy that pulls from an S3 bucket.""" + enabled = True + url_attr = 's3' + + def __init__(self, *args, **kwargs): + try: + super(S3FetchStrategy, self).__init__(*args, **kwargs) + except ValueError: + if not kwargs.get('url'): + raise ValueError( + "S3FetchStrategy requires a url for fetching.") + + @_needs_stage + def fetch(self): + if self.archive_file: + tty.msg("Already downloaded %s" % self.archive_file) + return + + parsed_url = url_util.parse(self.url) + if parsed_url.scheme != 's3': + raise ValueError( + 'S3FetchStrategy can only fetch from s3:// urls.') + + tty.msg("Fetching %s" % self.url) + + basename = os.path.basename(parsed_url.path) + + with working_dir(self.stage.path): + _, headers, stream = web_util.read_from_url(self.url) + + with open(basename, 'wb') as f: + shutil.copyfileobj(stream, f) + + content_type = headers['Content-type'] + + if content_type == 'text/html': + warn_content_type_mismatch(self.archive_file or "the archive") + + if self.stage.save_filename: + os.rename( + os.path.join(self.stage.path, basename), + self.stage.save_filename) + + if not self.archive_file: + raise FailedDownloadError(self.url) + + def from_url(url): """Given a URL, find an appropriate fetch strategy for it. Currently just gives you a URLFetchStrategy that uses curl. @@ -1206,6 +1268,34 @@ def for_package_version(pkg, version): raise InvalidArgsError(pkg, version, **args) +def from_url_scheme(url, *args, **kwargs): + """Finds a suitable FetchStrategy by matching its url_attr with the scheme + in the given url.""" + + url = kwargs.get('url', url) + parsed_url = urllib_parse.urlparse(url, scheme='file') + + scheme_mapping = ( + kwargs.get('scheme_mapping') or + { + 'file': 'url', + 'http': 'url', + 'https': 'url' + }) + + scheme = parsed_url.scheme + scheme = scheme_mapping.get(scheme, scheme) + + for fetcher in all_strategies: + url_attr = getattr(fetcher, 'url_attr', None) + if url_attr and url_attr == scheme: + return fetcher(url, *args, **kwargs) + + raise ValueError( + 'No FetchStrategy found for url with scheme: "{SCHEME}"'.format( + SCHEME=parsed_url.scheme)) + + def from_list_url(pkg): """If a package provides a URL which lists URLs for resources by version, this can can create a fetcher for a URL discovered for diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py index 45aa779c69d..e2329b68615 100644 --- a/lib/spack/spack/mirror.py +++ b/lib/spack/spack/mirror.py @@ -13,6 +13,18 @@ """ import sys import os +import os.path +import operator + +import six + +import ruamel.yaml.error as yaml_error + +try: + from collections.abc import Mapping +except ImportError: + from collections import Mapping + import llnl.util.tty as tty from llnl.util.filesystem import mkdirp @@ -20,9 +32,205 @@ import spack.error import spack.url as url import spack.fetch_strategy as fs -from spack.spec import Spec +import spack.util.spack_json as sjson +import spack.util.spack_yaml as syaml +import spack.util.url as url_util +import spack.spec from spack.version import VersionList from spack.util.compression import allowed_archive +from spack.util.spack_yaml import syaml_dict + + +def _display_mirror_entry(size, name, url, type_=None): + if type_: + type_ = "".join((" (", type_, ")")) + else: + type_ = "" + + print("%-*s%s%s" % (size + 4, name, url, type_)) + + +class Mirror(object): + """Represents a named location for storing source tarballs and binary + packages. + + Mirrors have a fetch_url that indicate where and how artifacts are fetched + from them, and a push_url that indicate where and how artifacts are pushed + to them. These two URLs are usually the same. + """ + + def __init__(self, fetch_url, push_url=None, name=None): + self._fetch_url = fetch_url + self._push_url = push_url + self._name = name + + def to_json(self, stream=None): + return sjson.dump(self.to_dict(), stream) + + def to_yaml(self, stream=None): + return syaml.dump(self.to_dict(), stream) + + @staticmethod + def from_yaml(stream, name=None): + try: + data = syaml.load(stream) + return Mirror.from_dict(data, name) + except yaml_error.MarkedYAMLError as e: + raise syaml.SpackYAMLError("error parsing YAML spec:", str(e)) + + @staticmethod + def from_json(stream, name=None): + d = sjson.load(stream) + return Mirror.from_dict(d, name) + + def to_dict(self): + if self._push_url is None: + return self._fetch_url + else: + return syaml_dict([ + ('fetch', self._fetch_url), + ('push', self._push_url)]) + + @staticmethod + def from_dict(d, name=None): + if isinstance(d, six.string_types): + return Mirror(d, name=name) + else: + return Mirror(d['fetch'], d['push'], name) + + def display(self, max_len=0): + if self._push_url is None: + _display_mirror_entry(max_len, self._name, self._fetch_url) + else: + _display_mirror_entry( + max_len, self._name, self._fetch_url, "fetch") + _display_mirror_entry( + max_len, self._name, self._push_url, "push") + + def __str__(self): + name = self._name + if name is None: + name = '' + else: + name = ' "%s"' % name + + if self._push_url is None: + return "[Mirror%s (%s)]" % (name, self._fetch_url) + + return "[Mirror%s (fetch: %s, push: %s)]" % ( + name, self._fetch_url, self._push_url) + + def __repr__(self): + return ''.join(( + 'Mirror(', + ', '.join( + '%s=%s' % (k, repr(v)) + for k, v in ( + ('fetch_url', self._fetch_url), + ('push_url', self._push_url), + ('name', self._name)) + if k == 'fetch_url' or v), + ')' + )) + + @property + def name(self): + return self._name or "" + + @property + def fetch_url(self): + return self._fetch_url + + @fetch_url.setter + def fetch_url(self, url): + self._fetch_url = url + self._normalize() + + @property + def push_url(self): + if self._push_url is None: + return self._fetch_url + return self._push_url + + @push_url.setter + def push_url(self, url): + self._push_url = url + self._normalize() + + def _normalize(self): + if self._push_url is not None and self._push_url == self._fetch_url: + self._push_url = None + + +class MirrorCollection(Mapping): + """A mapping of mirror names to mirrors.""" + + def __init__(self, mirrors=None, scope=None): + self._mirrors = dict( + (name, Mirror.from_dict(mirror, name)) + for name, mirror in ( + mirrors.items() if mirrors is not None else + spack.config.get('mirrors', scope=scope).items())) + + def to_json(self, stream=None): + return sjson.dump(self.to_dict(True), stream) + + def to_yaml(self, stream=None): + return syaml.dump(self.to_dict(True), stream) + + @staticmethod + def from_yaml(stream, name=None): + try: + data = syaml.load(stream) + return MirrorCollection(data) + except yaml_error.MarkedYAMLError as e: + raise syaml.SpackYAMLError("error parsing YAML spec:", str(e)) + + @staticmethod + def from_json(stream, name=None): + d = sjson.load(stream) + return MirrorCollection(d) + + def to_dict(self, recursive=False): + return syaml_dict(sorted( + ( + (k, (v.to_dict() if recursive else v)) + for (k, v) in self._mirrors.items() + ), key=operator.itemgetter(0) + )) + + @staticmethod + def from_dict(d): + return MirrorCollection(d) + + def __getitem__(self, item): + return self._mirrors[item] + + def display(self): + max_len = max(len(mirror.name) for mirror in self._mirrors.values()) + for mirror in self._mirrors.values(): + mirror.display(max_len) + + def lookup(self, name_or_url): + """Looks up and returns a Mirror. + + If this MirrorCollection contains a named Mirror under the name + [name_or_url], then that mirror is returned. Otherwise, [name_or_url] + is assumed to be a mirror URL, and an anonymous mirror with the given + URL is returned. + """ + result = self.get(name_or_url) + + if result is None: + result = Mirror(fetch_url=name_or_url) + + return result + + def __iter__(self): + return iter(self._mirrors) + + def __len__(self): + return len(self._mirrors) def mirror_archive_filename(spec, fetcher, resource_id=None): @@ -114,7 +322,7 @@ def get_matching_versions(specs, **kwargs): # Generate only versions that satisfy the spec. if spec.concrete or v.satisfies(spec.versions): - s = Spec(pkg.name) + s = spack.spec.Spec(pkg.name) s.versions = VersionList([v]) s.variants = spec.variants.copy() # This is needed to avoid hanging references during the @@ -166,12 +374,17 @@ def create(path, specs, **kwargs): it creates specs for those versions. If the version satisfies any spec in the specs list, it is downloaded and added to the mirror. """ + parsed = url_util.parse(path) + mirror_root = url_util.local_file_path(parsed) + # Make sure nothing is in the way. - if os.path.isfile(path): - raise MirrorError("%s already exists and is a file." % path) + if mirror_root and os.path.isfile(mirror_root): + raise MirrorError("%s already exists and is a file." % mirror_root) # automatically spec-ify anything in the specs array. - specs = [s if isinstance(s, Spec) else Spec(s) for s in specs] + specs = [ + s if isinstance(s, spack.spec.Spec) else spack.spec.Spec(s) + for s in specs] # Get concrete specs for each matching version of these specs. version_specs = get_matching_versions( @@ -180,8 +393,7 @@ def create(path, specs, **kwargs): s.concretize() # Get the absolute path of the root before we start jumping around. - mirror_root = os.path.abspath(path) - if not os.path.isdir(mirror_root): + if mirror_root and not os.path.isdir(mirror_root): try: mkdirp(mirror_root) except OSError as e: @@ -195,12 +407,12 @@ def create(path, specs, **kwargs): 'error': [] } - mirror_cache = spack.caches.MirrorCache(mirror_root) + mirror_cache = spack.caches.MirrorCache(parsed) try: spack.caches.mirror_cache = mirror_cache # Iterate through packages and download all safe tarballs for each for spec in version_specs: - add_single_spec(spec, mirror_root, categories, **kwargs) + add_single_spec(spec, parsed, categories, **kwargs) finally: spack.caches.mirror_cache = None diff --git a/lib/spack/spack/s3_handler.py b/lib/spack/spack/s3_handler.py new file mode 100644 index 00000000000..2a54b9ecb1b --- /dev/null +++ b/lib/spack/spack/s3_handler.py @@ -0,0 +1,92 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from io import BufferedReader + +import six.moves.urllib.response as urllib_response +import six.moves.urllib.request as urllib_request +import six.moves.urllib.error as urllib_error + +import spack.util.s3 as s3_util +import spack.util.url as url_util +import spack.util.web as web_util + + +# NOTE(opadron): Workaround issue in boto where its StreamingBody +# implementation is missing several APIs expected from IOBase. These missing +# APIs prevent the streams returned by boto from being passed as-are along to +# urllib. +# +# https://github.com/boto/botocore/issues/879 +# https://github.com/python/cpython/pull/3249 +class WrapStream(BufferedReader): + def __init__(self, raw): + raw.readable = lambda: True + raw.writable = lambda: False + raw.seekable = lambda: False + raw.closed = False + raw.flush = lambda: None + super(WrapStream, self).__init__(raw) + + def detach(self): + self.raw = None + + def read(self, *args, **kwargs): + return self.raw.read(*args, **kwargs) + + def __getattr__(self, key): + return getattr(self.raw, key) + + +def _s3_open(url): + parsed = url_util.parse(url) + s3 = s3_util.create_s3_session(parsed) + + bucket = parsed.netloc + key = parsed.path + + if key.startswith('/'): + key = key[1:] + + obj = s3.get_object(Bucket=bucket, Key=key) + + # NOTE(opadron): Apply workaround here (see above) + stream = WrapStream(obj['Body']) + headers = web_util.standardize_header_names( + obj['ResponseMetadata']['HTTPHeaders']) + + return url, headers, stream + + +class UrllibS3Handler(urllib_request.HTTPSHandler): + def s3_open(self, req): + orig_url = req.get_full_url() + from botocore.exceptions import ClientError + try: + url, headers, stream = _s3_open(orig_url) + return urllib_response.addinfourl(stream, headers, url) + except ClientError as err: + # if no such [KEY], but [KEY]/index.html exists, + # return that, instead. + if err.response['Error']['Code'] == 'NoSuchKey': + try: + _, headers, stream = _s3_open( + url_util.join(orig_url, 'index.html')) + return urllib_response.addinfourl( + stream, headers, orig_url) + + except ClientError as err2: + if err.response['Error']['Code'] == 'NoSuchKey': + # raise original error + raise urllib_error.URLError(err) + + raise urllib_error.URLError(err2) + + raise urllib_error.URLError(err) + + +S3OpenerDirector = urllib_request.build_opener(UrllibS3Handler()) + +open = S3OpenerDirector.open diff --git a/lib/spack/spack/schema/mirrors.py b/lib/spack/spack/schema/mirrors.py index 551267bd4f0..92e6c9bca1a 100644 --- a/lib/spack/spack/schema/mirrors.py +++ b/lib/spack/spack/schema/mirrors.py @@ -17,7 +17,19 @@ 'default': {}, 'additionalProperties': False, 'patternProperties': { - r'\w[\w-]*': {'type': 'string'}, + r'\w[\w-]*': { + 'anyOf': [ + {'type': 'string'}, + { + 'type': 'object', + 'required': ['fetch', 'push'], + 'properties': { + 'fetch': {'type': 'string'}, + 'push': {'type': 'string'} + } + } + ] + }, }, }, } diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index 6b27d37adf9..9621938bcd1 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -12,7 +12,6 @@ import getpass from six import string_types from six import iteritems -from six.moves.urllib.parse import urljoin import llnl.util.tty as tty from llnl.util.filesystem import mkdirp, can_access, install, install_tree @@ -20,12 +19,16 @@ import spack.paths import spack.caches +import spack.cmd import spack.config import spack.error +import spack.mirror import spack.util.lock import spack.fetch_strategy as fs import spack.util.pattern as pattern import spack.util.path as sup +import spack.util.url as url_util + from spack.util.crypto import prefix_bits, bit_length @@ -252,7 +255,7 @@ def __init__( # TODO: fetch/stage coupling needs to be reworked -- the logic # TODO: here is convoluted and not modular enough. if isinstance(url_or_fetch_strategy, string_types): - self.fetcher = fs.from_url(url_or_fetch_strategy) + self.fetcher = fs.from_url_scheme(url_or_fetch_strategy) elif isinstance(url_or_fetch_strategy, fs.FetchStrategy): self.fetcher = url_or_fetch_strategy else: @@ -397,16 +400,9 @@ def fetch(self, mirror_only=False): # TODO: CompositeFetchStrategy here. self.skip_checksum_for_mirror = True if self.mirror_path: - mirrors = spack.config.get('mirrors') - - # Join URLs of mirror roots with mirror paths. Because - # urljoin() will strip everything past the final '/' in - # the root, so we add a '/' if it is not present. - mir_roots = [ - sup.substitute_path_variables(root) if root.endswith(os.sep) - else sup.substitute_path_variables(root) + os.sep - for root in mirrors.values()] - urls = [urljoin(root, self.mirror_path) for root in mir_roots] + urls = [ + url_util.join(mirror.fetch_url, self.mirror_path) + for mirror in spack.mirror.MirrorCollection().values()] # If this archive is normally fetched from a tarball URL, # then use the same digest. `spack mirror` ensures that @@ -425,9 +421,12 @@ def fetch(self, mirror_only=False): # Add URL strategies for all the mirrors with the digest for url in urls: - fetchers.insert( - 0, fs.URLFetchStrategy( - url, digest, expand=expand, extension=extension)) + fetchers.append(fs.from_url_scheme( + url, digest, expand=expand, extension=extension)) + # fetchers.insert( + # 0, fs.URLFetchStrategy( + # url, digest, expand=expand, extension=extension)) + if self.default_fetcher.cachable: fetchers.insert( 0, spack.caches.fetch_cache.fetcher( @@ -708,6 +707,91 @@ def purge(): remove_linked_tree(stage_path) +def get_checksums_for_versions( + url_dict, name, first_stage_function=None, keep_stage=False): + """Fetches and checksums archives from URLs. + + This function is called by both ``spack checksum`` and ``spack + create``. The ``first_stage_function`` argument allows the caller to + inspect the first downloaded archive, e.g., to determine the build + system. + + Args: + url_dict (dict): A dictionary of the form: version -> URL + name (str): The name of the package + first_stage_function (callable): function that takes a Stage and a URL; + this is run on the stage of the first URL downloaded + keep_stage (bool): whether to keep staging area when command completes + + Returns: + (str): A multi-line string containing versions and corresponding hashes + + """ + sorted_versions = sorted(url_dict.keys(), reverse=True) + + # Find length of longest string in the list for padding + max_len = max(len(str(v)) for v in sorted_versions) + num_ver = len(sorted_versions) + + tty.msg("Found {0} version{1} of {2}:".format( + num_ver, '' if num_ver == 1 else 's', name), + "", + *spack.cmd.elide_list( + ["{0:{1}} {2}".format(str(v), max_len, url_dict[v]) + for v in sorted_versions])) + tty.msg('') + + archives_to_fetch = tty.get_number( + "How many would you like to checksum?", default=1, abort='q') + + if not archives_to_fetch: + tty.die("Aborted.") + + versions = sorted_versions[:archives_to_fetch] + urls = [url_dict[v] for v in versions] + + tty.msg("Downloading...") + version_hashes = [] + i = 0 + for url, version in zip(urls, versions): + try: + with Stage(url, keep=keep_stage) as stage: + # Fetch the archive + stage.fetch() + if i == 0 and first_stage_function: + # Only run first_stage_function the first time, + # no need to run it every time + first_stage_function(stage, url) + + # Checksum the archive and add it to the list + version_hashes.append((version, spack.util.crypto.checksum( + hashlib.sha256, stage.archive_file))) + i += 1 + except FailedDownloadError: + tty.msg("Failed to fetch {0}".format(url)) + except Exception as e: + tty.msg("Something failed on {0}, skipping.".format(url), + " ({0})".format(e)) + + if not version_hashes: + tty.die("Could not fetch any versions for {0}".format(name)) + + # Find length of longest string in the list for padding + max_len = max(len(str(v)) for v, h in version_hashes) + + # Generate the version directives to put in a package.py + version_lines = "\n".join([ + " version('{0}', {1}sha256='{2}')".format( + v, ' ' * (max_len - len(str(v))), h) for v, h in version_hashes + ]) + + num_hash = len(version_hashes) + tty.msg("Checksummed {0} version{1} of {2}".format( + num_hash, '' if num_hash == 1 else 's', name)) + + return version_lines + + class StageError(spack.error.SpackError): """"Superclass for all errors encountered during staging.""" @@ -720,5 +804,9 @@ class RestageError(StageError): """"Error encountered during restaging.""" +class VersionFetchError(StageError): + """Raised when we can't determine a URL to fetch a package.""" + + # Keep this in namespace for convenience FailedDownloadError = fs.FailedDownloadError diff --git a/lib/spack/spack/test/cmd/pkg.py b/lib/spack/spack/test/cmd/pkg.py index c9e8e74c4ae..e7d1006cc19 100644 --- a/lib/spack/spack/test/cmd/pkg.py +++ b/lib/spack/spack/test/cmd/pkg.py @@ -53,6 +53,8 @@ def mock_pkg_git_repo(tmpdir_factory): # initial commit with mock packages git('add', '.') + git('config', 'user.email', 'testing@spack.io') + git('config', 'user.name', 'Spack Testing') git('commit', '-m', 'initial mock repo commit') # add commit with pkg-a, pkg-b, pkg-c packages diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index 2de4e552811..3b85bb2a23c 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -595,6 +595,7 @@ def test_bad_config_section(mock_config): spack.config.get('foobar') +@pytest.mark.skipif(os.getuid() == 0, reason='user is root') def test_bad_command_line_scopes(tmpdir, mock_config): cfg = spack.config.Configuration() diff --git a/lib/spack/spack/test/llnl/util/lock.py b/lib/spack/spack/test/llnl/util/lock.py index cf962ada4ff..d8081d108c4 100644 --- a/lib/spack/spack/test/llnl/util/lock.py +++ b/lib/spack/spack/test/llnl/util/lock.py @@ -546,6 +546,7 @@ def test_write_lock_timeout_with_multiple_readers_3_2_ranges(lock_path): timeout_write(lock_path, 5, 1)) +@pytest.mark.skipif(os.getuid() == 0, reason='user is root') def test_read_lock_on_read_only_lockfile(lock_dir, lock_path): """read-only directory, read-only lockfile.""" touch(lock_path) @@ -573,6 +574,7 @@ def test_read_lock_read_only_dir_writable_lockfile(lock_dir, lock_path): pass +@pytest.mark.skipif(os.getuid() == 0, reason='user is root') def test_read_lock_no_lockfile(lock_dir, lock_path): """read-only directory, no lockfile (so can't create).""" with read_only(lock_dir): diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py index 66b358435fe..cc4f9448673 100644 --- a/lib/spack/spack/test/stage.py +++ b/lib/spack/spack/test/stage.py @@ -653,6 +653,7 @@ def test_source_path_available(self, mock_stage_archive): assert source_path.endswith(spack.stage._source_path_subdir) assert not os.path.exists(source_path) + @pytest.mark.skipif(os.getuid() == 0, reason='user is root') def test_first_accessible_path(self, tmpdir): """Test _first_accessible_path names.""" spack_dir = tmpdir.join('paths') @@ -783,6 +784,7 @@ def test_resolve_paths(self): assert spack.stage._resolve_paths(paths) == res_paths + @pytest.mark.skipif(os.getuid() == 0, reason='user is root') def test_get_stage_root_bad_path(self, clear_stage_root): """Ensure an invalid stage path root raises a StageError.""" with spack.config.override('config:build_stage', '/no/such/path'): diff --git a/lib/spack/spack/util/s3.py b/lib/spack/spack/util/s3.py new file mode 100644 index 00000000000..ee6b3d56cf2 --- /dev/null +++ b/lib/spack/spack/util/s3.py @@ -0,0 +1,44 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import os + +import six.moves.urllib.parse as urllib_parse + +import spack +import spack.util.url as url_util + + +def create_s3_session(url): + url = url_util.parse(url) + if url.scheme != 's3': + raise ValueError( + 'Can not create S3 session from URL with scheme: {SCHEME}'.format( + SCHEME=url.scheme)) + + # NOTE(opadron): import boto and friends as late as possible. We don't + # want to require boto as a dependency unless the user actually wants to + # access S3 mirrors. + from boto3 import Session + + session = Session() + + s3_client_args = {"use_ssl": spack.config.get('config:verify_ssl')} + + endpoint_url = os.environ.get('S3_ENDPOINT_URL') + if endpoint_url: + if urllib_parse.urlparse(endpoint_url, scheme=None).scheme is None: + endpoint_url = '://'.join(('https', endpoint_url)) + + s3_client_args['endpoint_url'] = endpoint_url + + # if no access credentials provided above, then access anonymously + if not session.get_credentials(): + from botocore import UNSIGNED + from botocore.client import Config + + s3_client_args["config"] = Config(signature_version=UNSIGNED) + + return session.client('s3', **s3_client_args) diff --git a/lib/spack/spack/util/url.py b/lib/spack/spack/util/url.py new file mode 100644 index 00000000000..6b2786f244a --- /dev/null +++ b/lib/spack/spack/util/url.py @@ -0,0 +1,175 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +""" +Utility functions for parsing, formatting, and manipulating URLs. +""" + +import itertools +import os.path + +from six import string_types +import six.moves.urllib.parse as urllib_parse + +import spack.util.path + + +def _split_all(path): + """Split path into its atomic components. + + Returns the shortest list, L, of strings such that os.path.join(*L) == path + and os.path.split(element) == ('', element) for every element in L except + possibly the first. This first element may possibly have the value of '/', + or some other OS-dependent path root. + """ + result = [] + a = path + old_a = None + while a != old_a: + (old_a, (a, b)) = a, os.path.split(a) + + if a or b: + result.insert(0, b or '/') + + return result + + +def local_file_path(url): + """Get a local file path from a url. + + If url is a file:// URL, return the absolute path to the local + file or directory referenced by it. Otherwise, return None. + """ + if isinstance(url, string_types): + url = parse(url) + + if url.scheme == 'file': + return url.path + return None + + +def parse(url, scheme='file'): + """Parse a mirror url. + + For file:// URLs, the netloc and path components are concatenated and + passed through spack.util.path.canoncalize_path(). + + Otherwise, the returned value is the same as urllib's urlparse() with + allow_fragments=False. + """ + + url_obj = ( + urllib_parse.urlparse(url, scheme=scheme, allow_fragments=False) + if isinstance(url, string_types) else url) + + (scheme, netloc, path, params, query, _) = url_obj + scheme = (scheme or 'file').lower() + + if scheme == 'file': + path = spack.util.path.canonicalize_path(netloc + path) + while path.startswith('//'): + path = path[1:] + netloc = '' + + return urllib_parse.ParseResult(scheme=scheme, + netloc=netloc, + path=path, + params=params, + query=query, + fragment=None) + + +def format(parsed_url): + """Format a URL string + + Returns a canonicalized format of the given URL as a string. + """ + if isinstance(parsed_url, string_types): + parsed_url = parse(parsed_url) + + return parsed_url.geturl() + + +def join(base_url, path, *extra, **kwargs): + """Joins a base URL with one or more local URL path components + + If resolve_href is True, treat the base URL as though it where the locator + of a web page, and the remaining URL path components as though they formed + a relative URL to be resolved against it (i.e.: as in os.path.join(...)). + The result is an absolute URL to the resource to which a user's browser + would navigate if they clicked on a link with an "href" attribute equal to + the relative URL. + + If resolve_href is False (default), then the URL path components are joined + as in os.path.join(). + + Examples: + base_url = 's3://bucket/index.html' + body = fetch_body(prefix) + link = get_href(body) # link == '../other-bucket/document.txt' + + # wrong - link is a local URL that needs to be resolved against base_url + spack.util.url.join(base_url, link) + 's3://bucket/other_bucket/document.txt' + + # correct - resolve local URL against base_url + spack.util.url.join(base_url, link, resolve_href=True) + 's3://other_bucket/document.txt' + + prefix = 'https://mirror.spack.io/build_cache' + + # wrong - prefix is just a URL prefix + spack.util.url.join(prefix, 'my-package', resolve_href=True) + 'https://mirror.spack.io/my-package' + + # correct - simply append additional URL path components + spack.util.url.join(prefix, 'my-package', resolve_href=False) # default + 'https://mirror.spack.io/build_cache/my-package' + """ + base_url = parse(base_url) + resolve_href = kwargs.get('resolve_href', False) + + (scheme, netloc, base_path, params, query, _) = base_url + scheme = scheme.lower() + + path_tokens = [ + part for part in itertools.chain( + _split_all(path), + itertools.chain.from_iterable( + _split_all(extra_path) for extra_path in extra)) + if part and part != '/'] + + base_path_args = ['/fake-root'] + if scheme == 's3': + if netloc: + base_path_args.append(netloc) + + if base_path.startswith('/'): + base_path = base_path[1:] + + base_path_args.append(base_path) + + if resolve_href: + new_base_path, _ = os.path.split(os.path.join(*base_path_args)) + base_path_args = [new_base_path] + + base_path_args.extend(path_tokens) + base_path = os.path.relpath(os.path.join(*base_path_args), '/fake-root') + + if scheme == 's3': + path_tokens = [ + part for part in _split_all(base_path) + if part and part != '/'] + + if path_tokens: + netloc = path_tokens.pop(0) + base_path = os.path.join('', *path_tokens) + + return format(urllib_parse.ParseResult(scheme=scheme, + netloc=netloc, + path=base_path, + params=params, + query=query, + fragment=None)) diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py index da2d5bbeb95..e0a23fb444a 100644 --- a/lib/spack/spack/util/web.py +++ b/lib/spack/spack/util/web.py @@ -5,16 +5,21 @@ from __future__ import print_function +import codecs +import errno import re import os +import os.path +import shutil import ssl import sys import traceback -import hashlib +from itertools import product + +import six from six.moves.urllib.request import urlopen, Request from six.moves.urllib.error import URLError -from six.moves.urllib.parse import urljoin import multiprocessing.pool try: @@ -28,20 +33,47 @@ class HTMLParseError(Exception): pass +from llnl.util.filesystem import mkdirp import llnl.util.tty as tty -import spack.config import spack.cmd -import spack.url -import spack.stage +import spack.config import spack.error +import spack.url import spack.util.crypto +import spack.util.s3 as s3_util +import spack.util.url as url_util + from spack.util.compression import ALLOWED_ARCHIVE_TYPES # Timeout in seconds for web requests _timeout = 10 +# See docstring for standardize_header_names() +_separators = ('', ' ', '_', '-') +HTTP_HEADER_NAME_ALIASES = { + "Accept-ranges": set( + ''.join((A, 'ccept', sep, R, 'anges')) + for A, sep, R in product('Aa', _separators, 'Rr')), + + "Content-length": set( + ''.join((C, 'ontent', sep, L, 'ength')) + for C, sep, L in product('Cc', _separators, 'Ll')), + + "Content-type": set( + ''.join((C, 'ontent', sep, T, 'ype')) + for C, sep, T in product('Cc', _separators, 'Tt')), + + "Date": set(('Date', 'date')), + + "Last-modified": set( + ''.join((L, 'ast', sep, M, 'odified')) + for L, sep, M in product('Ll', _separators, 'Mm')), + + "Server": set(('Server', 'server')) +} + class LinkParser(HTMLParser): """This parser just takes an HTML page and strips out the hrefs on the @@ -59,7 +91,7 @@ def handle_starttag(self, tag, attrs): class NonDaemonProcess(multiprocessing.Process): - """Process tha allows sub-processes, so pools can have sub-pools.""" + """Process that allows sub-processes, so pools can have sub-pools.""" @property def daemon(self): return False @@ -86,25 +118,53 @@ def __init__(self, *args, **kwargs): super(NonDaemonPool, self).__init__(*args, **kwargs) -def _read_from_url(url, accept_content_type=None): +def uses_ssl(parsed_url): + if parsed_url.scheme == 'https': + return True + + if parsed_url.scheme == 's3': + endpoint_url = os.environ.get('S3_ENDPOINT_URL') + if not endpoint_url: + return True + + if url_util.parse(endpoint_url, scheme='https').scheme == 'https': + return True + + return False + + +__UNABLE_TO_VERIFY_SSL = ( + lambda pyver: ( + (pyver < (2, 7, 9)) or + ((3,) < pyver < (3, 4, 3)) + ))(sys.version_info) + + +def read_from_url(url, accept_content_type=None): + url = url_util.parse(url) context = None + verify_ssl = spack.config.get('config:verify_ssl') - pyver = sys.version_info - if (pyver < (2, 7, 9) or (3,) < pyver < (3, 4, 3)): + + # Don't even bother with a context unless the URL scheme is one that uses + # SSL certs. + if uses_ssl(url): if verify_ssl: - tty.warn("Spack will not check SSL certificates. You need to " - "update your Python to enable certificate " - "verification.") - elif verify_ssl: - # without a defined context, urlopen will not verify the ssl cert for - # python 3.x - context = ssl.create_default_context() - else: - context = ssl._create_unverified_context() + if __UNABLE_TO_VERIFY_SSL: + # User wants SSL verification, but it cannot be provided. + warn_no_ssl_cert_checking() + else: + # User wants SSL verification, and it *can* be provided. + context = ssl.create_default_context() + else: + # User has explicitly indicated that they do not want SSL + # verification. + context = ssl._create_unverified_context() - req = Request(url) - - if accept_content_type: + req = Request(url_util.format(url)) + content_type = None + is_web_url = url.scheme in ('http', 'https') + if accept_content_type and is_web_url: # Make a HEAD request first to check the content type. This lets # us ignore tarballs and gigantic files. # It would be nice to do this with the HTTP Accept header to avoid @@ -113,29 +173,179 @@ def _read_from_url(url, accept_content_type=None): req.get_method = lambda: "HEAD" resp = _urlopen(req, timeout=_timeout, context=context) - if "Content-type" not in resp.headers: - tty.debug("ignoring page " + url) - return None, None - - if not resp.headers["Content-type"].startswith(accept_content_type): - tty.debug("ignoring page " + url + " with content type " + - resp.headers["Content-type"]) - return None, None + content_type = resp.headers.get('Content-type') # Do the real GET request when we know it's just HTML. req.get_method = lambda: "GET" response = _urlopen(req, timeout=_timeout, context=context) - response_url = response.geturl() - # Read the page and and stick it in the map we'll return - page = response.read().decode('utf-8') + if accept_content_type and not is_web_url: + content_type = response.headers.get('Content-type') - return response_url, page + reject_content_type = ( + accept_content_type and ( + content_type is None or + not content_type.startswith(accept_content_type))) + + if reject_content_type: + tty.debug("ignoring page {0}{1}{2}".format( + url_util.format(url), + " with content type " if content_type is not None else "", + content_type or "")) + + return None, None, None + + return response.geturl(), response.headers, response -def read_from_url(url, accept_content_type=None): - resp_url, contents = _read_from_url(url, accept_content_type) - return contents +def warn_no_ssl_cert_checking(): + tty.warn("Spack will not check SSL certificates. You need to update " + "your Python to enable certificate verification.") + + +def push_to_url(local_path, remote_path, **kwargs): + keep_original = kwargs.get('keep_original', True) + + local_url = url_util.parse(local_path) + local_file_path = url_util.local_file_path(local_url) + if local_file_path is None: + raise ValueError('local path must be a file:// url') + + remote_url = url_util.parse(remote_path) + verify_ssl = spack.config.get('config:verify_ssl') + + if __UNABLE_TO_VERIFY_SSL and verify_ssl and uses_ssl(remote_url): + warn_no_ssl_cert_checking() + + remote_file_path = url_util.local_file_path(remote_url) + if remote_file_path is not None: + mkdirp(os.path.dirname(remote_file_path)) + if keep_original: + shutil.copy(local_file_path, remote_file_path) + else: + try: + os.rename(local_file_path, remote_file_path) + except OSError as e: + if e.errno == errno.EXDEV: + # NOTE(opadron): The above move failed because it crosses + # filesystem boundaries. Copy the file (plus original + # metadata), and then delete the original. This operation + # needs to be done in separate steps. + shutil.copy2(local_file_path, remote_file_path) + os.remove(local_file_path) + + elif remote_url.scheme == 's3': + extra_args = kwargs.get('extra_args', {}) + + remote_path = remote_url.path + while remote_path.startswith('/'): + remote_path = remote_path[1:] + + s3 = s3_util.create_s3_session(remote_url) + s3.upload_file(local_file_path, remote_url.netloc, + remote_path, ExtraArgs=extra_args) + + if not keep_original: + os.remove(local_file_path) + + else: + raise NotImplementedError( + 'Unrecognized URL scheme: {SCHEME}'.format( + SCHEME=remote_url.scheme)) + + +def url_exists(url): + url = url_util.parse(url) + local_path = url_util.local_file_path(url) + if local_path: + return os.path.exists(local_path) + + if url.scheme == 's3': + s3 = s3_util.create_s3_session(url) + from botocore.exceptions import ClientError + try: + s3.get_object(Bucket=url.netloc, Key=url.path) + return True + except ClientError as err: + if err.response['Error']['Code'] == 'NoSuchKey': + return False + raise err + + # otherwise, just try to "read" from the URL, and assume that *any* + # non-throwing response contains the resource represented by the URL + try: + read_from_url(url) + return True + except URLError: + return False + + +def remove_url(url): + url = url_util.parse(url) + + local_path = url_util.local_file_path(url) + if local_path: + os.remove(local_path) + return + + if url.scheme == 's3': + s3 = s3_util.create_s3_session(url) + s3.delete_object(Bucket=url.s3_bucket, Key=url.path) + return + + # Don't even try for other URL schemes. + + +def _list_s3_objects(client, url, num_entries, start_after=None): + list_args = dict( + Bucket=url.netloc, + Prefix=url.path, + MaxKeys=num_entries) + + if start_after is not None: + list_args['StartAfter'] = start_after + + result = client.list_objects_v2(**list_args) + + last_key = None + if result['IsTruncated']: + last_key = result['Contents'][-1]['Key'] + + iter = (key for key in + ( + os.path.relpath(entry['Key'], url.path) + for entry in result['Contents'] + ) + if key != '.') + + return iter, last_key + + +def _iter_s3_prefix(client, url, num_entries=1024): + key = None + while True: + contents, key = _list_s3_objects( + client, url, num_entries, start_after=key) + + for x in contents: + yield x + + if not key: + break + + +def list_url(url): + url = url_util.parse(url) + + local_path = url_util.local_file_path(url) + if local_path: + return os.listdir(local_path) + + if url.scheme == 's3': + s3 = s3_util.create_s3_session(url) + return list(set( + key.split('/', 1)[0] + for key in _iter_s3_prefix(s3, url))) def _spider(url, visited, root, depth, max_depth, raise_on_error): @@ -154,16 +364,12 @@ def _spider(url, visited, root, depth, max_depth, raise_on_error): pages = {} # dict from page URL -> text content. links = set() # set of all links seen on visited pages. - # root may end with index.html -- chop that off. - if root.endswith('/index.html'): - root = re.sub('/index.html$', '', root) - try: - response_url, page = _read_from_url(url, 'text/html') - - if not response_url or not page: + response_url, _, response = read_from_url(url, 'text/html') + if not response_url or not response: return pages, links + page = codecs.getreader('utf-8')(response).read() pages[response_url] = page # Parse out the links in the page @@ -173,8 +379,10 @@ def _spider(url, visited, root, depth, max_depth, raise_on_error): while link_parser.links: raw_link = link_parser.links.pop() - abs_link = urljoin(response_url, raw_link.strip()) - + abs_link = url_util.join( + response_url, + raw_link.strip(), + resolve_href=True) links.add(abs_link) # Skip stuff that looks like an archive @@ -243,16 +451,28 @@ def _spider_wrapper(args): return _spider(*args) -def _urlopen(*args, **kwargs): +def _urlopen(req, *args, **kwargs): """Wrapper for compatibility with old versions of Python.""" - # We don't pass 'context' parameter to urlopen because it - # was introduces only starting versions 2.7.9 and 3.4.3 of Python. - if 'context' in kwargs and kwargs['context'] is None: + url = req + try: + url = url.get_full_url() + except AttributeError: + pass + + # We don't pass 'context' parameter because it was only introduced starting + # with versions 2.7.9 and 3.4.3 of Python. + if 'context' in kwargs: del kwargs['context'] - return urlopen(*args, **kwargs) + + opener = urlopen + if url_util.parse(url).scheme == 's3': + import spack.s3_handler + opener = spack.s3_handler.open + + return opener(req, *args, **kwargs) -def spider(root_url, depth=0): +def spider(root, depth=0): """Gets web pages from a root URL. If depth is specified (e.g., depth=2), then this will also follow @@ -262,7 +482,9 @@ def spider(root_url, depth=0): performance over a sequential fetch. """ - pages, links = _spider(root_url, set(), root_url, 0, depth, False) + + root = url_util.parse(root) + pages, links = _spider(root, set(), root, 0, depth, False) return pages, links @@ -356,99 +578,112 @@ def find_versions_of_archive(archive_urls, list_url=None, list_depth=0): return versions -def get_checksums_for_versions( - url_dict, name, first_stage_function=None, keep_stage=False): - """Fetches and checksums archives from URLs. +def standardize_header_names(headers): + """Replace certain header names with standardized spellings. - This function is called by both ``spack checksum`` and ``spack - create``. The ``first_stage_function`` argument allows the caller to - inspect the first downloaded archive, e.g., to determine the build - system. + Standardizes the spellings of the following header names: + - Accept-ranges + - Content-length + - Content-type + - Date + - Last-modified + - Server - Args: - url_dict (dict): A dictionary of the form: version -> URL - name (str): The name of the package - first_stage_function (callable): function that takes a Stage and a URL; - this is run on the stage of the first URL downloaded - keep_stage (bool): whether to keep staging area when command completes + Every name considered is translated to one of the above names if the only + difference between the two is how the first letters of each word are + capitalized; whether words are separated; or, if separated, whether they + are so by a dash (-), underscore (_), or space ( ). Header names that + cannot be mapped as described above are returned unaltered. - Returns: - (str): A multi-line string containing versions and corresponding hashes + For example: The standard spelling of "Content-length" would be substituted + for any of the following names: + - Content-length + - content_length + - contentlength + - content_Length + - contentLength + - content Length + ... and any other header name, such as "Content-encoding", would not be + altered, regardless of spelling. + + If headers is a string, then it (or an appropriate substitute) is returned. + + If headers is a non-empty tuple, headers[0] is a string, and there exists a + standardized spelling for header[0] that differs from it, then a new tuple + is returned. This tuple has the same elements as headers, except the first + element is the standardized spelling for headers[0]. + + If headers is a sequence, then a new list is considered, where each element + is its corresponding element in headers, but mapped as above if a string or + tuple. This new list is returned if at least one of its elements differ + from their corrsponding element in headers. + + If headers is a mapping, then a new dict is considered, where the key in + each item is the key of its corresponding item in headers, mapped as above + if a string or tuple. The value is taken from the corresponding item. If + the keys of multiple items in headers map to the same key after being + standardized, then the value for the resulting item is undefined. The new + dict is returned if at least one of its items has a key that differs from + that of their corresponding item in headers, or if the keys of multiple + items in headers map to the same key after being standardized. + + In all other cases headers is returned unaltered. """ - sorted_versions = sorted(url_dict.keys(), reverse=True) + if isinstance(headers, six.string_types): + for standardized_spelling, other_spellings in ( + HTTP_HEADER_NAME_ALIASES.items()): + if headers in other_spellings: + if headers == standardized_spelling: + return headers + return standardized_spelling + return headers - # Find length of longest string in the list for padding - max_len = max(len(str(v)) for v in sorted_versions) - num_ver = len(sorted_versions) + if isinstance(headers, tuple): + if not headers: + return headers + old = headers[0] + if isinstance(old, six.string_types): + new = standardize_header_names(old) + if old is not new: + return (new,) + headers[1:] + return headers - tty.msg("Found {0} version{1} of {2}:".format( - num_ver, '' if num_ver == 1 else 's', name), - "", - *spack.cmd.elide_list( - ["{0:{1}} {2}".format(str(v), max_len, url_dict[v]) - for v in sorted_versions])) - print() + try: + changed = False + new_dict = {} + for key, value in headers.items(): + if isinstance(key, (tuple, six.string_types)): + old_key, key = key, standardize_header_names(key) + changed = changed or key is not old_key - archives_to_fetch = tty.get_number( - "How many would you like to checksum?", default=1, abort='q') + new_dict[key] = value - if not archives_to_fetch: - tty.die("Aborted.") + return new_dict if changed else headers + except (AttributeError, TypeError, ValueError): + pass - versions = sorted_versions[:archives_to_fetch] - urls = [url_dict[v] for v in versions] + try: + changed = False + new_list = [] + for item in headers: + if isinstance(item, (tuple, six.string_types)): + old_item, item = item, standardize_header_names(item) + changed = changed or item is not old_item - tty.msg("Downloading...") - version_hashes = [] - i = 0 - for url, version in zip(urls, versions): - try: - with spack.stage.Stage(url, keep=keep_stage) as stage: - # Fetch the archive - stage.fetch() - if i == 0 and first_stage_function: - # Only run first_stage_function the first time, - # no need to run it every time - first_stage_function(stage, url) + new_list.append(item) - # Checksum the archive and add it to the list - version_hashes.append((version, spack.util.crypto.checksum( - hashlib.sha256, stage.archive_file))) - i += 1 - except spack.stage.FailedDownloadError: - tty.msg("Failed to fetch {0}".format(url)) - except Exception as e: - tty.msg("Something failed on {0}, skipping.".format(url), - " ({0})".format(e)) + return new_list if changed else headers + except TypeError: + pass - if not version_hashes: - tty.die("Could not fetch any versions for {0}".format(name)) - - # Find length of longest string in the list for padding - max_len = max(len(str(v)) for v, h in version_hashes) - - # Generate the version directives to put in a package.py - version_lines = "\n".join([ - " version('{0}', {1}sha256='{2}')".format( - v, ' ' * (max_len - len(str(v))), h) for v, h in version_hashes - ]) - - num_hash = len(version_hashes) - tty.msg("Checksummed {0} version{1} of {2}".format( - num_hash, '' if num_hash == 1 else 's', name)) - - return version_lines + return headers class SpackWebError(spack.error.SpackError): """Superclass for Spack web spidering errors.""" -class VersionFetchError(SpackWebError): - """Raised when we can't determine a URL to fetch a package.""" - - class NoNetworkConnectionError(SpackWebError): """Raised when an operation can't get an internet connection.""" def __init__(self, message, url): From cfbdd2179e83c0e900dca0e43183e10c0e2a373a Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 22 Oct 2019 09:33:59 +0200 Subject: [PATCH 370/499] microarchitectures: add optimization flags for Intel compilers (#13345) * Added optimization flags for Intel compilers with Intel CPUs * Added optimization flags for Intel compilers with AMD CPUs --- .../llnl/util/cpu/microarchitectures.json | 129 +++++++++++++++++- lib/spack/spack/test/llnl/util/cpu.py | 9 ++ 2 files changed, 134 insertions(+), 4 deletions(-) diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 02f507fa6d7..28734e1da90 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -65,6 +65,11 @@ "versions": ":", "family": "x86-64", "flags": "-march={family} -mcpu=generic" + }, + "intel": { + "versions": ":", + "name": "pentium4", + "flags": "-march={name} -mtune=generic" } } }, @@ -86,6 +91,11 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "name": "pentium4", + "flags": "-march={name} -mtune=generic" } } }, @@ -107,6 +117,10 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "flags": "-march={name} -mtune={name}}" } } }, @@ -138,6 +152,11 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "name": "corei7", + "flags": "-march={name} -mtune={name}" } } }, @@ -164,6 +183,11 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "name": "corei7", + "flags": "-march={name} -mtune={name}" } } }, @@ -198,7 +222,18 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" - } + }, + "intel": [ + { + "versions": "16.0:17.9.0", + "name": "corei7-avx", + "flags": "-march={name} -mtune={name}" + }, + { + "versions": "18.0:", + "flags": "-march={name} -mtune={name}" + } + ] } }, "ivybridge": { @@ -234,7 +269,18 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" - } + }, + "intel": [ + { + "versions": "16.0:17.9.0", + "name": "core-avx-i", + "flags": "-march={name} -mtune={name}" + }, + { + "versions": "18.0:", + "flags": "-march={name} -mtune={name}" + } + ] } }, "haswell": { @@ -275,7 +321,18 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" - } + }, + "intel": [ + { + "versions": "16.0:17.9.0", + "name": "core-avx2", + "flags": "-march={name} -mtune={name}" + }, + { + "versions": "18.0:", + "flags": "-march={name} -mtune={name}" + } + ] } }, "broadwell": { @@ -311,6 +368,10 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "18.0:", + "flags": "-march={name} -mtune={name}" } } }, @@ -350,6 +411,10 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "18.0:", + "flags": "-march={name} -mtune={name}" } } }, @@ -393,6 +458,11 @@ "name": "knl", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "18.0:", + "name": "knl", + "flags": "-march={name} -mtune={name}" } } }, @@ -440,6 +510,11 @@ "name": "skylake-avx512", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "18.0:", + "name": "skylake-avx512", + "flags": "-march={name} -mtune={name}" } } }, @@ -488,6 +563,10 @@ "versions": "3.9:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "18.0:", + "flags": "-march={name} -mtune={name}" } } }, @@ -534,6 +613,10 @@ "versions": "8.0:", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "19.0:", + "flags": "-march={name} -mtune={name}" } } }, @@ -603,7 +686,12 @@ "family": "x86-64", "flags": "-march={family} -mcpu={name}" } - ] + ], + "intel": { + "versions": "18.0:", + "name": "icelake-client", + "flags": "-march={name} -mtune={name}" + } } }, "bulldozer": { @@ -636,6 +724,11 @@ "name": "bdver1", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "warnings": "Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors", + "flags": "-msse3" } } }, @@ -673,6 +766,11 @@ "name": "bdver2", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "warnings": "Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors", + "flags": "-msse3" } } }, @@ -711,6 +809,11 @@ "name": "bdver3", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "warnings": "Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors", + "flags": "-msse4.2" } } }, @@ -752,6 +855,12 @@ "name": "bdver4", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "warnings": "Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors", + "name": "core-avx2", + "flags": "-march={name} -mtune={name}" } } }, @@ -796,6 +905,12 @@ "name": "znver1", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "warnings": "Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors", + "name": "core-avx2", + "flags": "-march={name} -mtune={name}" } } }, @@ -841,6 +956,12 @@ "name": "znver2", "family": "x86-64", "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "warnings": "Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors", + "name": "core-avx2", + "flags": "-march={name} -mtune={name}" } } }, diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 68185532b44..fe1209c8c86 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -205,6 +205,15 @@ def test_target_json_schema(): ('icelake', 'clang', '8.0.0', '-march=x86-64 -mcpu=icelake-client'), ('zen2', 'clang', '9.0.0', '-march=x86-64 -mcpu=znver2'), ('power9le', 'clang', '8.0.0', '-march=ppc64le -mcpu=pwr9'), + # Test Intel on Intel CPUs + ('sandybridge', 'intel', '17.0.2', '-march=corei7-avx -mtune=corei7-avx'), + ('sandybridge', 'intel', '18.0.5', + '-march=sandybridge -mtune=sandybridge'), + # Test Intel on AMD CPUs + pytest.param('steamroller', 'intel', '17.0.2', '-msse4.2', + marks=pytest.mark.filterwarnings('ignore::UserWarning')), + pytest.param('zen', 'intel', '17.0.2', '-march=core-avx2 -mtune=core-avx2', + marks=pytest.mark.filterwarnings('ignore::UserWarning')), # Test that an unknown compiler returns an empty string ('sandybridge', 'unknown', '4.8.5', ''), ]) From 809733c7e6861e56d3a4ab4107e3afd4b4a65dd9 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 09:15:11 -0500 Subject: [PATCH 371/499] Restrict parallel build of py-astropy to Python 3 (#13360) --- var/spack/repos/builtin/packages/py-astropy/package.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py index 26e995985a5..1eb605e2d6b 100644 --- a/var/spack/repos/builtin/packages/py-astropy/package.py +++ b/var/spack/repos/builtin/packages/py-astropy/package.py @@ -60,11 +60,15 @@ class PyAstropy(PythonPackage): depends_on('expat') def build_args(self, spec, prefix): - return [ - '-j', str(make_jobs), + args = [ '--use-system-libraries', '--use-system-erfa', '--use-system-wcslib', '--use-system-cfitsio', '--use-system-expat' ] + + if spec.satisfies('^python@3:'): + args.extend(['-j', str(make_jobs)]) + + return args From e0c310bfd322a311ba534bd5107972907532c07d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 09:15:39 -0500 Subject: [PATCH 372/499] Add latest version of py-sphinxcontrib-programoutput (#13359) --- .../packages/py-sphinxcontrib-programoutput/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py index cc50f20af18..30ec4a0aba9 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py @@ -11,12 +11,14 @@ class PySphinxcontribProgramoutput(PythonPackage): into documents, helping you to keep your command examples up to date.""" homepage = "https://sphinxcontrib-programoutput.readthedocs.org/" - url = "https://pypi.io/packages/source/s/sphinxcontrib-programoutput/sphinxcontrib-programoutput-0.10.tar.gz" + url = "https://pypi.io/packages/source/s/sphinxcontrib-programoutput/sphinxcontrib-programoutput-0.15.tar.gz" # FIXME: These import tests don't work for some reason # import_modules = ['sphinxcontrib', 'sphinxcontrib.programoutput'] + version('0.15', sha256='80dd5b4eab780a13ff2c23500cac3dbf0e04ef9976b409ef25a47c263ef8ab94') version('0.10', sha256='fdee94fcebb0d8fddfccac5c4fa560f6177d5340c4349ee447c890bea8857094') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-sphinx@1.3.5:', type=('build', 'run')) + depends_on('py-sphinx@1.7.0:', type=('build', 'run')) From 2de807d4cb4ad6559e381ee6dd0e0281c60d557f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 09:16:07 -0500 Subject: [PATCH 373/499] Add latest version of py-macs2 (#13358) --- var/spack/repos/builtin/packages/py-macs2/package.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-macs2/package.py b/var/spack/repos/builtin/packages/py-macs2/package.py index 3db1a170673..9e2e4f3d3f8 100644 --- a/var/spack/repos/builtin/packages/py-macs2/package.py +++ b/var/spack/repos/builtin/packages/py-macs2/package.py @@ -11,13 +11,17 @@ class PyMacs2(PythonPackage): """MACS2 Model-based Analysis of ChIP-Seq""" homepage = "https://github.com/taoliu/MACS" - url = "https://pypi.io/packages/source/M/MACS2/MACS2-2.1.1.20160309.tar.gz" + url = "https://pypi.io/packages/source/M/MACS2/MACS2-2.2.4.tar.gz" + version('2.2.4', sha256='b131aadc8f5fd94bec35308b821e1f7585def788d2e7c756fc8cac402ffee25b') + version('2.1.4', sha256='e4966d001914320829ab859c7bc8e92c6410aa7bdbddfd00b7625e9a0fb15c97') version('2.1.1.20160309', sha256='2008ba838f83f34f8e0fddefe2a3a0159f4a740707c68058f815b31ddad53d26') - depends_on('python@2.7:2.8') + depends_on('python@3.5:', when='@2.2:', type=('build', 'run')) + depends_on('python@2.7:2.8', when='@:2.1', type=('build', 'run')) # Most Python packages only require py-setuptools as a build dependency. # However, py-macs2 requires py-setuptools during runtime as well. depends_on('py-setuptools', type=('build', 'run')) - depends_on('py-numpy@1.6:', type=('build', 'run')) + depends_on('py-numpy@1.17:', when='@2.2:', type=('build', 'run')) + depends_on('py-numpy@1.16:', type=('build', 'run')) From 09070b0c9be23be4b2db7665615faca092b4fe14 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 09:16:33 -0500 Subject: [PATCH 374/499] Add latest version of npth (#13353) --- var/spack/repos/builtin/packages/npth/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/npth/package.py b/var/spack/repos/builtin/packages/npth/package.py index 5d2a6e95d14..3cc30fea6c1 100644 --- a/var/spack/repos/builtin/packages/npth/package.py +++ b/var/spack/repos/builtin/packages/npth/package.py @@ -11,7 +11,8 @@ class Npth(AutotoolsPackage): non-preemptive threads implementation.""" homepage = "https://gnupg.org/software/npth/index.html" - url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.5.tar.bz2" + url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.6.tar.bz2" + version('1.6', sha256='1393abd9adcf0762d34798dc34fdcf4d0d22a8410721e76f1e3afcd1daa4e2d1') version('1.5', sha256='294a690c1f537b92ed829d867bee537e46be93fbd60b16c04630fbbfcd9db3c2') version('1.4', sha256='8915141836a3169a502d65c1ebd785fcc6d406cae5ee84474272ebf2fa96f1f2') From 48e8029fb16ec6a1b4882b03791715f8c7650144 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 09:16:58 -0500 Subject: [PATCH 375/499] Add latest version of py-scikit-learn (#13295) * Add latest version of py-scikit-learn * setup_environment -> setup_build_environment --- .../packages/py-scikit-learn/package.py | 51 +++++++------------ 1 file changed, 19 insertions(+), 32 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py index 13137c0da01..02d85c33cda 100644 --- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py @@ -10,7 +10,7 @@ class PyScikitLearn(PythonPackage): """A set of python modules for machine learning and data mining.""" homepage = "https://pypi.python.org/pypi/scikit-learn" - url = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.21.2.tar.gz" + url = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.21.3.tar.gz" git = "https://github.com/scikit-learn/scikit-learn.git" maintainers = ['adamjstewart'] @@ -33,6 +33,7 @@ class PyScikitLearn(PythonPackage): ] version('master', branch='master') + version('0.21.3', sha256='eb9b8ebf59eddd8b96366428238ab27d05a19e89c5516ce294abc35cea75d003') version('0.21.2', sha256='0aafc312a55ebf58073151b9308761a5fcfa45b7f7730cea4b1f066f824c72db') version('0.21.1', sha256='228d0611e69e5250946f8cd7bbefec75347950f0ca426d0c518db8f06583f660') version('0.20.2', sha256='bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6') @@ -46,18 +47,18 @@ class PyScikitLearn(PythonPackage): variant('openmp', default=True, description='Build with OpenMP support') - depends_on('python@2.6:2.8,3.3:', when='@:0.19') - depends_on('python@2.7:2.8,3.4:', when='@0.20.0:0.20.999') - depends_on('python@3.5:', when='@0.21:') - depends_on('py-numpy@1.6.1:', type=('build', 'run'), when='@:0.19') - depends_on('py-numpy@1.8.2:', type=('build', 'run'), when='@0.20.0:0.20.999') - depends_on('py-numpy@1.11.0:', type=('build', 'run'), when='@0.21:') - depends_on('py-scipy@0.9:', type=('build', 'run'), when='@:0.19') - depends_on('py-scipy@0.13.3:', type=('build', 'run'), when='@0.20.0:0.20.999') - depends_on('py-scipy@0.17.0:', type=('build', 'run'), when='@0.21:') + depends_on('python@2.6:2.8,3.3:', when='@:0.19', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', when='@0.20.0:0.20.999', type=('build', 'run')) + depends_on('python@3.5:', when='@0.21:', type=('build', 'run')) + depends_on('py-numpy@1.6.1:', when='@:0.19', type=('build', 'run')) + depends_on('py-numpy@1.8.2:', when='@0.20.0:0.20.999', type=('build', 'run')) + depends_on('py-numpy@1.11.0:', when='@0.21:', type=('build', 'run')) + depends_on('py-scipy@0.9:', when='@:0.19', type=('build', 'run')) + depends_on('py-scipy@0.13.3:', when='@0.20.0:0.20.999', type=('build', 'run')) + depends_on('py-scipy@0.17.0:', when='@0.21:', type=('build', 'run')) depends_on('py-joblib@0.11:', type=('build', 'run')) depends_on('py-cython@0.23:', type='build') - depends_on('py-cython@0.28.5:', type='build', when='@0.21:') + depends_on('py-cython@0.28.5:', when='@0.21:', type='build') depends_on('py-pytest@3.3.0:', type='test') depends_on('py-pandas', type='test') depends_on('py-setuptools', type='build') @@ -71,34 +72,20 @@ class PyScikitLearn(PythonPackage): # See https://github.com/scikit-learn/scikit-learn/issues/14332 conflicts('~openmp', when='@:999', msg='Only master supports ~openmp') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # https://scikit-learn.org/stable/developers/advanced_installation.html#building-from-source if self.spec.satisfies('~openmp'): - spack_env.set('SKLEARN_NO_OPENMP', 'True') + env.set('SKLEARN_NO_OPENMP', 'True') # https://scikit-learn.org/stable/developers/advanced_installation.html#mac-osx elif self.spec.satisfies('@0.21: %clang platform=darwin +openmp'): - spack_env.append_flags( + env.append_flags( 'CPPFLAGS', '-Xpreprocessor -fopenmp') - spack_env.append_flags( + env.append_flags( 'CFLAGS', self.spec['llvm-openmp'].headers.include_flags) - spack_env.append_flags( - 'CXXFLAGS', - self.spec['llvm-openmp'].headers.include_flags) - spack_env.append_flags( + env.append_flags( + 'CXXFLAGS', self.spec['llvm-openmp'].headers.include_flags) + env.append_flags( 'LDFLAGS', self.spec['llvm-openmp'].libs.ld_flags) - spack_env.append_flags( - 'DYLD_LIBRARY_PATH', - self.spec['llvm-openmp'].libs.directories[0]) - - run_env.append_flags( - 'DYLD_LIBRARY_PATH', - self.spec['llvm-openmp'].libs.directories[0]) - - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - if self.spec.satisfies('@0.21: %clang platform=darwin +openmp'): - spack_env.append_flags( - 'DYLD_LIBRARY_PATH', - self.spec['llvm-openmp'].libs.directories[0]) def install_test(self): # https://scikit-learn.org/stable/developers/advanced_installation.html#testing From 526ee113ea4c8003650d7d0611cd736eef01732a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 22 Oct 2019 10:22:32 -0500 Subject: [PATCH 376/499] Default to Python 3.7 (#10319) * Default to Python 3 * Fix build with Intel compilers --- .../builtin/packages/python/intel-3.6.7.patch | 38 +++++++++++++++++++ .../repos/builtin/packages/python/package.py | 13 +++---- 2 files changed, 44 insertions(+), 7 deletions(-) create mode 100644 var/spack/repos/builtin/packages/python/intel-3.6.7.patch diff --git a/var/spack/repos/builtin/packages/python/intel-3.6.7.patch b/var/spack/repos/builtin/packages/python/intel-3.6.7.patch new file mode 100644 index 00000000000..f2277624af2 --- /dev/null +++ b/var/spack/repos/builtin/packages/python/intel-3.6.7.patch @@ -0,0 +1,38 @@ +From 87ed388f41d761ddddc8447e5104569f2436c005 Mon Sep 17 00:00:00 2001 +From: Victor Stinner +Date: Fri, 11 Oct 2019 15:13:51 +0200 +Subject: [PATCH] bpo-37415: Fix stdatomic.h header check for ICC compiler + +Fix stdatomic.h header check for ICC compiler: the ICC implementation +lacks atomic_uintptr_t type which is needed by Python. + +Test: + +* atomic_int and atomic_uintptr_t types +* atomic_load_explicit() and atomic_store_explicit() +* memory_order_relaxed and memory_order_seq_cst constants + +But don't test ATOMIC_VAR_INIT(): it's not used in Python. +--- + configure | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/configure b/configure +index f1979c1b8124c..1b30a848a77e7 100755 +--- a/configure ++++ b/configure +@@ -16734,9 +16722,12 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext + + + #include +- atomic_int value = ATOMIC_VAR_INIT(1); ++ atomic_int int_var; ++ atomic_uintptr_t uintptr_var; + int main() { +- int loaded_value = atomic_load(&value); ++ atomic_store_explicit(&int_var, 5, memory_order_relaxed); ++ atomic_store_explicit(&uintptr_var, 0, memory_order_relaxed); ++ int loaded_value = atomic_load_explicit(&int_var, memory_order_seq_cst); + return 0; + } + diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 2813121ddab..6087ff5be8d 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -32,7 +32,7 @@ class Python(AutotoolsPackage): maintainers = ['adamjstewart'] version('3.8.0', sha256='f1069ad3cae8e7ec467aa98a6565a62a48ef196cb8f1455a245a08db5e1792df') - version('3.7.4', sha256='d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3') + version('3.7.4', sha256='d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3', preferred=True) version('3.7.3', sha256='d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff') version('3.7.2', sha256='f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d') version('3.7.1', sha256='36c1b81ac29d0f8341f727ef40864d99d8206897be96be73dc34d4739c9c9f06') @@ -55,7 +55,7 @@ class Python(AutotoolsPackage): version('3.3.6', sha256='0a58ad1f1def4ecc90b18b0c410a3a0e1a48cf7692c75d1f83d0af080e5d2034') version('3.2.6', sha256='fc1e41296e29d476f696303acae293ae7a2310f0f9d0d637905e722a3f16163e') version('3.1.5', sha256='d12dae6d06f52ef6bf1271db4d5b4d14b5dd39813e324314e72b648ef1bc0103') - version('2.7.16', sha256='01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5', preferred=True) + version('2.7.16', sha256='01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5') version('2.7.15', sha256='18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db') version('2.7.14', sha256='304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8') version('2.7.13', sha256='a4f05a0720ce0fd92626f0278b6b433eee9a6173ddf2bced7957dfb599a5ece1') @@ -145,6 +145,10 @@ class Python(AutotoolsPackage): # https://github.com/python/cpython/commit/0b91f8a668201fc58fa732b8acc496caedfdbae0 patch('gcc-8-2.7.14.patch', when='@2.7.14 %gcc@8:') + # Fixes build with the Intel compilers + # https://github.com/python/cpython/pull/16717 + patch('intel-3.6.7.patch', when='@3.6.7:3.6.8,3.7.1: %intel') + # For more information refer to this bug report: # https://bugs.python.org/issue29712 conflicts( @@ -155,11 +159,6 @@ class Python(AutotoolsPackage): conflicts('+tix', when='~tkinter', msg='python+tix requires python+tix+tkinter') - # Python 3.6.7 and above can not be compiled with the Intel compiler - # https://bugs.python.org/issue35473 - # https://bugs.python.org/issue37415 - conflicts('%intel', when='@3.6.7:') - _DISTUTIL_VARS_TO_SAVE = ['LDSHARED'] _DISTUTIL_CACHE_FILENAME = 'sysconfig.json' _distutil_vars = None From 49291d5a401421ec8637da06a2608c44072fe3b8 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Tue, 22 Oct 2019 17:45:45 +0200 Subject: [PATCH 377/499] git-lfs: Add new version (#13356) PS: The old versions do not work: it's likely that they changed git history on submodules --- var/spack/repos/builtin/packages/git-lfs/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py index 4308a38c817..180e01b97d9 100644 --- a/var/spack/repos/builtin/packages/git-lfs/package.py +++ b/var/spack/repos/builtin/packages/git-lfs/package.py @@ -16,6 +16,7 @@ class GitLfs(MakefilePackage): homepage = "https://git-lfs.github.com" url = "https://github.com/git-lfs/git-lfs/archive/v2.6.1.tar.gz" + version('2.9.0', sha256='f1963ad88747577ffeeb854649aeacaa741c59be74683da4d46b129a72d111b7') version('2.8.0', sha256='10b476bb8862ebceddc6f0a55f5fb63e2c1e5bed6554f6e3b207dd0155a196ad') version('2.7.2', sha256='e65659f12ec557ae8c778c01ca62d921413221864b68bd93cfa41399028ae67f') version('2.7.1', sha256='af60c2370d135ab13724d302a0b1c226ec9fb0ee6d29ecc335e9add4c86497b4') From 0f931cfc87f48321ce91f815590e32a6d503137f Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 22 Oct 2019 12:06:06 -0400 Subject: [PATCH 378/499] ADIOS2: Document endian_reverse variant (#13226) Update the documentation of the `endian_reverse` variant in ADIOS2. The short description caused some confusion (for me) :-) --- var/spack/repos/builtin/packages/adios2/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index 4be02170f4d..e5e10db9966 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -32,7 +32,8 @@ class Adios2(CMakePackage): description='Enable position independent code ' '(for usage of static in shared downstream deps)') variant('endian_reverse', default=False, - description='Enable Endian Interoperability') + description='Enable endian conversion if a different ' + 'endianness is detected between write and read.') # compression libraries variant('blosc', default=True, From ab5135db1cb29eaef9c766c6d3372b5fdbe81c5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= Date: Tue, 22 Oct 2019 23:25:03 +0200 Subject: [PATCH 379/499] Boost package: Fix iostream autodetect libraries (#12440) Boost iostream autodetects the compression libraries libzstd and liblzma outside of the Spack environment. This commit disables mentioned libraries. In the future if the Spack zstd/lzma packages were added as dependencies of the Spack Boost package, additional work could be done to build Boost with the Spack-built versions of these libraries. --- var/spack/repos/builtin/packages/boost/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 40fda7c362d..094a96954c2 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -305,7 +305,9 @@ def determine_b2_options(self, spec, options): '-s', 'BZIP2_INCLUDE=%s' % spec['bzip2'].prefix.include, '-s', 'BZIP2_LIBPATH=%s' % spec['bzip2'].prefix.lib, '-s', 'ZLIB_INCLUDE=%s' % spec['zlib'].prefix.include, - '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib]) + '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib, + '-s', 'NO_LZMA=1', + '-s', 'NO_ZSTD=1']) link_types = ['static'] if '+shared' in spec: From 73387305286a058a8017431bc2caf07137f5be53 Mon Sep 17 00:00:00 2001 From: Benjamin Fovet <45510885+bfovet@users.noreply.github.com> Date: Wed, 23 Oct 2019 01:18:19 +0200 Subject: [PATCH 380/499] gmsh: add version 4.4.1 (#13366) --- var/spack/repos/builtin/packages/gmsh/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 05afa72aa11..1e1d1972958 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -19,6 +19,7 @@ class Gmsh(CMakePackage): homepage = 'http://gmsh.info' url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz' + version('4.4.1', sha256='853c6438fc4e4b765206e66a514b09182c56377bb4b73f1d0d26eda7eb8af0dc') version('4.2.2', sha256='e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc') version('4.0.0', sha256='fb0c8afa37425c6f4315ab3b3124e9e102fcf270a35198423a4002796f04155f') version('3.0.6', sha256='9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b') From a942d2dd3d76216d51b85e2bc0a4675fd8523dc7 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 22 Oct 2019 20:40:47 -0700 Subject: [PATCH 381/499] Disable macOS builds on PRs while we wait for Travis to catch up. (#13389) Travis macOS builds are taking too long to run, so we'll only run them on `develop` until they get faster. --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 1f5b82c811e..a79a5126b19 100644 --- a/.travis.yml +++ b/.travis.yml @@ -56,6 +56,7 @@ jobs: - os: osx language: generic env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ] + if: type != pull_request # mpich (AutotoolsPackage) - stage: 'build tests' python: '2.7' From 8808207ddf711a63a67ead632f6dd7457bc22616 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 23 Oct 2019 06:40:45 +0200 Subject: [PATCH 382/499] Fixed optimization flags support for old GCC versions (#13362) These changes update our gcc microarchitecture descriptions based on manuals found here https://gcc.gnu.org/onlinedocs/ and assuming that new architectures are not added during patch releases. --- .../llnl/util/cpu/microarchitectures.json | 38 +++++++++---------- lib/spack/spack/test/architecture.py | 2 +- lib/spack/spack/test/concretize.py | 4 +- lib/spack/spack/test/modules/lmod.py | 2 +- 4 files changed, 24 insertions(+), 22 deletions(-) diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 28734e1da90..6873fc9676a 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -56,7 +56,7 @@ "flags": "-march={name} -mtune=generic" }, { - "versions": "4.0:4.1.2", + "versions": ":4.1.2", "name": "x86-64", "flags": "-march={name} -mtune={name}" } @@ -84,7 +84,7 @@ ], "compilers": { "gcc": { - "versions": "4:", + "versions": "4.0.4:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -110,7 +110,7 @@ ], "compilers": { "gcc": { - "versions": "4:", + "versions": "4.3.0:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -260,7 +260,7 @@ "flags": "-march={name} -mtune={name}" }, { - "versions": ":4.8.5", + "versions": "4.6:4.8.5", "name": "core-avx-i", "flags": "-march={name} -mtune={name}" } @@ -312,7 +312,7 @@ "flags": "-march={name} -mtune={name}" }, { - "versions": ":4.8.5", + "versions": "4.8:4.8.5", "name": "core-avx2", "flags": "-march={name} -mtune={name}" } @@ -404,7 +404,7 @@ ], "compilers": { "gcc": { - "versions": "5.3:", + "versions": "6.0:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -502,7 +502,7 @@ "compilers": { "gcc": { "name": "skylake-avx512", - "versions": "5.3:", + "versions": "6.0:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -556,7 +556,7 @@ ], "compilers": { "gcc": { - "versions": "8:", + "versions": "8.0:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -606,7 +606,7 @@ ], "compilers": { "gcc": { - "versions": "9:", + "versions": "9.0:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -671,7 +671,7 @@ "compilers": { "gcc": { "name": "icelake-client", - "versions": "8:", + "versions": "8.0:", "flags": "-march={name} -mtune={name}" }, "clang": [ @@ -716,7 +716,7 @@ "compilers": { "gcc": { "name": "bdver1", - "versions": "4.6:", + "versions": "4.7:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -897,7 +897,7 @@ "compilers": { "gcc": { "name": "znver1", - "versions": "6:", + "versions": "6.0:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -948,7 +948,7 @@ "compilers": { "gcc": { "name": "znver2", - "versions": "9:", + "versions": "9.0:", "flags": "-march={name} -mtune={name}" }, "clang": { @@ -972,7 +972,7 @@ "compilers": { "gcc": { "name": "powerpc64", - "versions": "4:", + "versions": ":", "flags": "-mcpu={name} -mtune={name}" }, "clang": { @@ -989,7 +989,7 @@ "features": [], "compilers": { "gcc": { - "versions": "4.5:", + "versions": "4.4:", "flags": "-mcpu={name} -mtune={name}" }, "clang": { @@ -1032,7 +1032,7 @@ "features": [], "compilers": { "gcc": { - "versions": "6:", + "versions": "6.0:", "flags": "-mcpu={name} -mtune={name}" }, "clang": { @@ -1050,7 +1050,7 @@ "compilers": { "gcc": { "name": "powerpc64le", - "versions": "4:", + "versions": "4.8:", "flags": "-mcpu={name} -mtune={name}" }, "clang": { @@ -1095,7 +1095,7 @@ "compilers": { "gcc": { "name": "power9", - "versions": "6:", + "versions": "6.0:", "flags": "-mcpu={name} -mtune={name}" }, "clang": { @@ -1112,7 +1112,7 @@ "features": [], "compilers": { "gcc": { - "versions": "4:", + "versions": "4.8.0:", "flags": "-march=armv8-a -mtune=generic" }, "clang": { diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index 35980d8a863..30aba652143 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -173,7 +173,7 @@ def test_arch_spec_container_semantic(item, architecture_str): @pytest.mark.parametrize('compiler_spec,target_name,expected_flags', [ # Check compilers with version numbers from a single toolchain - ('gcc@4.7.2', 'haswell', '-march=core-avx2 -mtune=core-avx2'), + ('gcc@4.7.2', 'ivybridge', '-march=core-avx-i -mtune=core-avx-i'), # Check mixed toolchains ('clang@8.0.0', 'broadwell', ''), # Check clang compilers with 'apple' suffix diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index f0c8e93bcfe..592b515dbf0 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -584,11 +584,13 @@ def test_noversion_pkg(self, spec): Spec(spec).concretized() @pytest.mark.parametrize('spec, best_achievable', [ + ('mpileaks%gcc@4.4.7', 'core2'), ('mpileaks%gcc@4.8', 'haswell'), - ('mpileaks%gcc@5.3.0', 'skylake_avx512'), + ('mpileaks%gcc@5.3.0', 'broadwell'), # Apple's clang always falls back to x86-64 for now ('mpileaks%clang@9.1.0-apple', 'x86_64') ]) + @pytest.mark.regression('13361') def test_adjusting_default_target_based_on_compiler( self, spec, best_achievable, current_host ): diff --git a/lib/spack/spack/test/modules/lmod.py b/lib/spack/spack/test/modules/lmod.py index e480d22601a..34ba63c3734 100644 --- a/lib/spack/spack/test/modules/lmod.py +++ b/lib/spack/spack/test/modules/lmod.py @@ -264,7 +264,7 @@ def no_op_set(*args, **kwargs): assert writer.conf.core_compilers @pytest.mark.parametrize('spec_str', [ - 'mpileaks target=haswell', + 'mpileaks target=nocona', 'mpileaks target=core2', 'mpileaks target=x86_64', ]) From b14f18acda23c3299bea060b4d3424b8c72052a3 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 23 Oct 2019 06:42:38 +0200 Subject: [PATCH 383/499] microarchitectures: look in /sbin and /usr/sbin for sysctl (#13365) This PR ensures that on Darwin we always append /sbin and /usr/sbin to PATH, if they are not already present, when looking for sysctl. * Make sure we look into /sbin and /usr/sbin for sysctl * Refactor sysctl for better readability * Remove marker to make test pass --- lib/spack/llnl/util/cpu/detect.py | 46 ++++++++++++-------- lib/spack/spack/test/cmd/compiler_command.py | 2 +- lib/spack/spack/test/llnl/util/cpu.py | 2 +- 3 files changed, 29 insertions(+), 21 deletions(-) diff --git a/lib/spack/llnl/util/cpu/detect.py b/lib/spack/llnl/util/cpu/detect.py index 7744d5acd23..92b75e9653b 100644 --- a/lib/spack/llnl/util/cpu/detect.py +++ b/lib/spack/llnl/util/cpu/detect.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import collections import functools +import os import platform import re import subprocess @@ -75,31 +76,38 @@ def proc_cpuinfo(): return info -def check_output(args): - output = subprocess.Popen(args, stdout=subprocess.PIPE).communicate()[0] +def check_output(args, env): + output = subprocess.Popen( + args, stdout=subprocess.PIPE, env=env + ).communicate()[0] return six.text_type(output.decode('utf-8')) @info_dict(operating_system='Darwin') -def sysctl(): +def sysctl_info_dict(): """Returns a raw info dictionary parsing the output of sysctl.""" + # Make sure that /sbin and /usr/sbin are in PATH as sysctl is + # usually found there + child_environment = dict(os.environ.items()) + search_paths = child_environment.get('PATH', '').split(os.pathsep) + for additional_path in ('/sbin', '/usr/sbin'): + if additional_path not in search_paths: + search_paths.append(additional_path) + child_environment['PATH'] = os.pathsep.join(search_paths) - info = {} - info['vendor_id'] = check_output( - ['sysctl', '-n', 'machdep.cpu.vendor'] - ).strip() - info['flags'] = check_output( - ['sysctl', '-n', 'machdep.cpu.features'] - ).strip().lower() - info['flags'] += ' ' + check_output( - ['sysctl', '-n', 'machdep.cpu.leaf7_features'] - ).strip().lower() - info['model'] = check_output( - ['sysctl', '-n', 'machdep.cpu.model'] - ).strip() - info['model name'] = check_output( - ['sysctl', '-n', 'machdep.cpu.brand_string'] - ).strip() + def sysctl(*args): + return check_output( + ['sysctl'] + list(args), env=child_environment + ).strip() + + flags = (sysctl('-n', 'machdep.cpu.features').lower() + ' ' + + sysctl('-n', 'machdep.cpu.leaf7_features').lower()) + info = { + 'vendor_id': sysctl('-n', 'machdep.cpu.vendor'), + 'flags': flags, + 'model': sysctl('-n', 'machdep.cpu.model'), + 'model name': sysctl('-n', 'machdep.cpu.brand_string') + } # Super hacky way to deal with slight representation differences # Would be better to somehow consider these "identical" diff --git a/lib/spack/spack/test/cmd/compiler_command.py b/lib/spack/spack/test/cmd/compiler_command.py index e40e49544dc..a4ceb638226 100644 --- a/lib/spack/spack/test/cmd/compiler_command.py +++ b/lib/spack/spack/test/cmd/compiler_command.py @@ -24,7 +24,7 @@ def no_compilers_yaml(mutable_config, monkeypatch): os.remove(compilers_yaml) -@pytest.mark.regression('11678') +@pytest.mark.regression('11678,13138') def test_compiler_find_without_paths(no_compilers_yaml, working_env, tmpdir): with tmpdir.as_cwd(): with open('gcc', 'w') as f: diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index fe1209c8c86..2e03772d193 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -67,7 +67,7 @@ def _open(not_used_arg): key, value = line.split(':') info[key.strip()] = value.strip() - def _check_output(args): + def _check_output(args, env): current_key = args[-1] return info[current_key] From 95a48b27ec09b691d4107d48854126c045b03188 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Tue, 22 Oct 2019 23:27:40 -0700 Subject: [PATCH 384/499] env activation: use package defined env setup methods (#13249) This PR ensures that environment activation sets all environment variables set by the equivalent `module load` operations, except that the spec prefixes are "rebased" to the view associated with the environment. Currently, Spack blindly adds paths relative to the environment view root to the user environment on activation. Issue #12731 points out ways in which this behavior is insufficient. This PR changes that behavior to use the `setup_run_environment` logic for each package to augment the prefix inspections (as in Spack's modulefile generation logic) to ensure that all necessary variables are set to make use of the packages in the environment. See #12731 for details on the previous problems in behavior. This PR also updates the `ViewDescriptor` object in `spack.environment` to have a `__contains__` method. This allows for checks like `if spec in self.default_view`. The `__contains__` operator for `ViewDescriptor` objects checks whether the spec satisfies the filters of the View descriptor, not whether the spec is already linked into the underlying `FilesystemView` object. --- lib/spack/spack/environment.py | 119 +++++++++++++----- lib/spack/spack/test/cmd/env.py | 2 + lib/spack/spack/test/package_sanity.py | 17 +-- lib/spack/spack/test/util/environment.py | 31 +++++ lib/spack/spack/util/environment.py | 62 ++++++++- .../packages/cmake-client/package.py | 4 +- 6 files changed, 190 insertions(+), 45 deletions(-) diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index ab8d7e14f18..5204f7d288e 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -28,9 +28,11 @@ import spack.spec import spack.util.spack_json as sjson import spack.config +import spack.build_environment as build_env +from spack.util.prefix import Prefix from spack.filesystem_view import YamlFilesystemView -from spack.util.environment import EnvironmentModifications +import spack.util.environment import spack.architecture as architecture from spack.spec import Spec from spack.spec_list import SpecList, InvalidSpecConstraintError @@ -468,6 +470,23 @@ def view(self): ignore_conflicts=True, projections=self.projections) + def __contains__(self, spec): + """Is the spec described by the view descriptor + + Note: This does not claim the spec is already linked in the view. + It merely checks that the spec is selected if a select operation is + specified and is not excluded if an exclude operator is specified. + """ + if self.select: + if not self.select_fn(spec): + return False + + if self.exclude: + if not self.exclude_fn(spec): + return False + + return True + def regenerate(self, all_specs, roots): specs_for_view = [] specs = all_specs if self.link == 'all' else roots @@ -478,14 +497,8 @@ def regenerate(self, all_specs, roots): if spec.concrete: # Do not link unconcretized roots specs_for_view.append(spec.copy(deps=('link', 'run'))) - if self.select: - specs_for_view = list(filter(self.select_fn, specs_for_view)) - - if self.exclude: - specs_for_view = list(filter(self.exclude_fn, specs_for_view)) - installed_specs_for_view = set(s for s in specs_for_view - if s.package.installed) + if s in self and s.package.installed) view = self.view() @@ -1009,38 +1022,76 @@ def regenerate_views(self): for view in self.views.values(): view.regenerate(specs, self.roots()) - def _shell_vars(self): - updates = [ - ('PATH', ['bin']), - ('MANPATH', ['man', 'share/man']), - ('ACLOCAL_PATH', ['share/aclocal']), - ('LD_LIBRARY_PATH', ['lib', 'lib64']), - ('LIBRARY_PATH', ['lib', 'lib64']), - ('CPATH', ['include']), - ('PKG_CONFIG_PATH', ['lib/pkgconfig', 'lib64/pkgconfig', - 'share/pkgconfig']), - ('CMAKE_PREFIX_PATH', ['']), - ] + prefix_inspections = { + 'bin': ['PATH'], + 'lib': ['LD_LIBRARY_PATH', 'LIBRARY_PATH', 'DYLD_LIBRARY_PATH'], + 'lib64': ['LD_LIBRARY_PATH', 'LIBRARY_PATH', 'DYLD_LIBRARY_PATH'], + 'man': ['MANPATH'], + 'share/man': ['MANPATH'], + 'share/aclocal': ['ACLOCAL_PATH'], + 'include': ['CPATH'], + 'lib/pkgconfig': ['PKG_CONFIG_PATH'], + 'lib64/pkgconfig': ['PKG_CONFIG_PATH'], + '': ['CMAKE_PREFIX_PATH'] + } - path_updates = list() - if default_view_name in self.views: - for var, dirs in updates: - paths = [os.path.join(self.default_view.root, x) for x in dirs] - path_updates.append((var, paths)) - return path_updates + def environment_modifications_for_spec(self, spec, view=None): + """List of environment modifications to be processed.""" + spec = spec.copy() + if view: + spec.prefix = Prefix(view.view().get_projection_for_spec(spec)) + + # generic environment modifications determined by inspecting the spec + # prefix + env = spack.util.environment.inspect_path( + spec.prefix, + self.prefix_inspections, + exclude=spack.util.environment.is_system_path + ) + + # Let the extendee/dependency modify their extensions/dependents + # before asking for package-specific modifications + env.extend( + build_env.modifications_from_dependencies( + spec, context='run' + ) + ) + # Package specific modifications + build_env.set_module_variables_for_package(spec.package) + spec.package.setup_run_environment(env) + + return env def add_default_view_to_shell(self, shell): - env_mod = EnvironmentModifications() - for var, paths in self._shell_vars(): - for path in paths: - env_mod.prepend_path(var, path) + env_mod = spack.util.environment.EnvironmentModifications() + + if default_view_name not in self.views: + # No default view to add to shell + return env_mod.shell_modifications(shell) + + for _, spec in self.concretized_specs(): + if spec in self.default_view: + env_mod.extend(self.environment_modifications_for_spec( + spec, self.default_view)) + + # deduplicate paths from specs mapped to the same location + for env_var in env_mod.group_by_name(): + env_mod.prune_duplicate_paths(env_var) + return env_mod.shell_modifications(shell) def rm_default_view_from_shell(self, shell): - env_mod = EnvironmentModifications() - for var, paths in self._shell_vars(): - for path in paths: - env_mod.remove_path(var, path) + env_mod = spack.util.environment.EnvironmentModifications() + + if default_view_name not in self.views: + # No default view to add to shell + return env_mod.shell_modifications(shell) + + for _, spec in self.concretized_specs(): + if spec in self.default_view: + env_mod.extend( + self.environment_modifications_for_spec( + spec, self.default_view).reversed()) return env_mod.shell_modifications(shell) def _add_concrete_spec(self, spec, concrete, new=True): diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py index 232da811a36..f2912f3ec0d 100644 --- a/lib/spack/spack/test/cmd/env.py +++ b/lib/spack/spack/test/cmd/env.py @@ -1577,8 +1577,10 @@ def test_stack_view_activate_from_default(tmpdir, mock_fetch, mock_packages, install() shell = env('activate', '--sh', 'test') + assert 'PATH' in shell assert os.path.join(viewdir, 'bin') in shell + assert 'FOOBAR=mpileaks' in shell def test_stack_view_no_activate_without_default(tmpdir, mock_fetch, diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py index f83a2dbb8ee..290d21b85f8 100644 --- a/lib/spack/spack/test/package_sanity.py +++ b/lib/spack/spack/test/package_sanity.py @@ -172,15 +172,16 @@ def test_prs_update_old_api(): ] failing = [] for file in changed_package_files: - name = os.path.basename(os.path.dirname(file)) - pkg = spack.repo.get(name) + if 'builtin.mock' not in file: # don't restrict packages for tests + name = os.path.basename(os.path.dirname(file)) + pkg = spack.repo.get(name) + + failed = (hasattr(pkg, 'setup_environment') or + hasattr(pkg, 'setup_dependent_environment')) + if failed: + failing.append(name) - # Check for old APIs - failed = (hasattr(pkg, 'setup_environment') or - hasattr(pkg, 'setup_dependent_environment')) - if failed: - failing.append(pkg) msg = 'there are {0} packages still using old APIs in this PR [{1}]' assert not failing, msg.format( - len(failing), ','.join(x.name for x in failing) + len(failing), ','.join(failing) ) diff --git a/lib/spack/spack/test/util/environment.py b/lib/spack/spack/test/util/environment.py index cb1748fa280..e34fc95f334 100644 --- a/lib/spack/spack/test/util/environment.py +++ b/lib/spack/spack/test/util/environment.py @@ -103,3 +103,34 @@ def test_dump_environment(prepare_environment_for_tests, tmpdir): with open(dumpfile_path, 'r') as dumpfile: assert('TEST_ENV_VAR={0}; export TEST_ENV_VAR\n'.format(test_paths) in list(dumpfile)) + + +def test_reverse_environment_modifications(working_env): + start_env = { + 'PREPEND_PATH': '/path/to/prepend/to', + 'APPEND_PATH': '/path/to/append/to', + 'UNSET': 'var_to_unset', + 'APPEND_FLAGS': 'flags to append to', + } + + to_reverse = envutil.EnvironmentModifications() + + to_reverse.prepend_path('PREPEND_PATH', '/new/path/prepended') + to_reverse.append_path('APPEND_PATH', '/new/path/appended') + to_reverse.set_path('SET_PATH', ['/one/set/path', '/two/set/path']) + to_reverse.set('SET', 'a var') + to_reverse.unset('UNSET') + to_reverse.append_flags('APPEND_FLAGS', 'more_flags') + + reversal = to_reverse.reversed() + + os.environ = start_env.copy() + + print(os.environ) + to_reverse.apply_modifications() + print(os.environ) + reversal.apply_modifications() + print(os.environ) + + start_env.pop('UNSET') + assert os.environ == start_env diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py index 63f428dd06f..b85ec963e25 100644 --- a/lib/spack/spack/util/environment.py +++ b/lib/spack/spack/util/environment.py @@ -226,6 +226,16 @@ def execute(self, env): env.pop(self.name, None) +class RemoveFlagsEnv(NameValueModifier): + + def execute(self, env): + environment_value = env.get(self.name, '') + flags = environment_value.split( + self.separator) if environment_value else [] + flags = [f for f in flags if f != self.value] + env[self.name] = self.separator.join(flags) + + class SetPath(NameValueModifier): def execute(self, env): @@ -372,6 +382,21 @@ def unset(self, name, **kwargs): item = UnsetEnv(name, **kwargs) self.env_modifications.append(item) + def remove_flags(self, name, value, sep=' ', **kwargs): + """ + Stores in the current object a request to remove flags from an + env variable + + Args: + name: name of the environment variable to be removed from + value: value to remove to the environment variable + sep: separator to assume for environment variable + """ + kwargs.update(self._get_outside_caller_attributes()) + kwargs.update({'separator': sep}) + item = RemoveFlagsEnv(name, value, **kwargs) + self.env_modifications.append(item) + def set_path(self, name, elements, **kwargs): """Stores a request to set a path generated from a list. @@ -467,6 +492,40 @@ def clear(self): """ self.env_modifications = [] + def reversed(self): + """ + Returns the EnvironmentModifications object that will reverse self + + Only creates reversals for additions to the environment, as reversing + ``unset`` and ``remove_path`` modifications is impossible. + + Reversable operations are set(), prepend_path(), append_path(), + set_path(), and append_flags(). + """ + rev = EnvironmentModifications() + + for envmod in reversed(self.env_modifications): + if type(envmod) == SetEnv: + tty.warn("Reversing `Set` environment operation may lose " + "original value") + rev.unset(envmod.name) + elif type(envmod) == AppendPath: + rev.remove_path(envmod.name, envmod.value) + elif type(envmod) == PrependPath: + rev.remove_path(envmod.name, envmod.value) + elif type(envmod) == SetPath: + tty.warn("Reversing `SetPath` environment operation may lose " + "original value") + rev.unset(envmod.name) + elif type(envmod) == AppendFlagsEnv: + rev.remove_flags(envmod.name, envmod.value) + else: + # This is an un-reversable operation + tty.warn("Skipping reversal of unreversable operation" + "%s %s" % (type(envmod), envmod.name)) + + return rev + def apply_modifications(self): """Applies the modifications and clears the list.""" modifications = self.group_by_name() @@ -485,7 +544,8 @@ def shell_modifications(self, shell='sh'): x.execute(new_env) cmds = '' - for name in set(new_env) & set(os.environ): + + for name in set(new_env) | set(os.environ): new = new_env.get(name, None) old = os.environ.get(name, None) if new != old: diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py index e5cadb5d61a..40e1c9f9ed9 100644 --- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -43,7 +43,7 @@ def flip(self): def do_not_execute(self): self.did_something = True - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, spack_env): spack_cc # Ensure spack module-scope variable is avaiabl check(from_cmake == "from_cmake", "setup_environment couldn't read global set by cmake.") @@ -52,7 +52,7 @@ def setup_environment(self, spack_env, run_env): "link arg on dependency spec not readable from " "setup_environment.") - def setup_dependent_environment(self, spack_env, run_env, dspec): + def setup_dependent_build_environment(self, spack_env, dspec): spack_cc # Ensure spack module-scope variable is avaiable check(from_cmake == "from_cmake", "setup_dependent_environment couldn't read global set by cmake.") From b3f5084b96f1458e5ec041f197e0b0dabbc0ecff Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 22 Oct 2019 23:59:28 -0700 Subject: [PATCH 385/499] tests: avoid extra output in `env status` test (#13344) `test_envoronment_status()` was printing extra output during tests. - [x] disable output only for `env('status')` calls instead of disabling it for the whole test. --- lib/spack/spack/test/cmd/env.py | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py index f2912f3ec0d..c3fb9113360 100644 --- a/lib/spack/spack/test/cmd/env.py +++ b/lib/spack/spack/test/cmd/env.py @@ -218,21 +218,24 @@ def test_remove_command(): assert 'mpileaks@' not in find('--show-concretized') -def test_environment_status(capfd, tmpdir): - with capfd.disabled(): - with tmpdir.as_cwd(): +def test_environment_status(capsys, tmpdir): + with tmpdir.as_cwd(): + with capsys.disabled(): assert 'No active environment' in env('status') - with ev.create('test'): + with ev.create('test'): + with capsys.disabled(): assert 'In environment test' in env('status') - with ev.Environment('local_dir'): + with ev.Environment('local_dir'): + with capsys.disabled(): assert os.path.join(os.getcwd(), 'local_dir') in env('status') - e = ev.Environment('myproject') - e.write() - with tmpdir.join('myproject').as_cwd(): - with e: + e = ev.Environment('myproject') + e.write() + with tmpdir.join('myproject').as_cwd(): + with e: + with capsys.disabled(): assert 'in current directory' in env('status') From af65146ef69fcde10d53b2ee12f82a9c28361e23 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 22 Oct 2019 23:50:31 -0700 Subject: [PATCH 386/499] Preserve comments for Spack YAML objects (#11602) This updates the configuration loading/dumping logic (now called load_config/dump_config) in spack_yaml to preserve comments (by using ruamel.yaml's RoundTripLoader). This has two effects: * environment spack.yaml files expect to retain comments, which load_config now supports. By using load_config, users can now use the ':' override syntax that was previously unavailable for environment configs (but was available for other config files). * config files now retain user comments by default (although in cases where Spack updates/overwrites config, the comments can still be removed). Details: * Subclasses `RoundTripLoader`/`RoundTripDumper` to parse yaml into ruamel's `CommentedMap` and analogous data structures * Applies filename info directly to ruamel objects in cases where the updated loader returns those * Copies management of sections in `SingleFileScope` from #10651 to allow overrides to occur * Updates the loader/dumper to handle the processing of overrides by specifically checking for the `:` character * Possibly the most controversial aspect, but without that, the parsed objects have to be reconstructed (i.e. as was done in `mark_overrides`). It is possible that `mark_overrides` could remain and a deep copy will not cause problems, but IMO that's generally worth avoiding. * This is also possibly controversial because Spack YAML strings can include `:`. My reckoning is that this only occurs for version specifications, so it is safe to check for `endswith(':') and not ('@' in string)` * As a consequence, this PR ends up reserving spack yaml functions load_config/dump_config exclusively for the purpose of storing spack config --- lib/spack/spack/binary_distribution.py | 6 +- lib/spack/spack/cmd/release_jobs.py | 2 +- lib/spack/spack/config.py | 79 +++----- lib/spack/spack/environment.py | 7 +- lib/spack/spack/filesystem_view.py | 2 +- lib/spack/spack/hooks/yaml_version_check.py | 2 +- lib/spack/spack/modules/common.py | 2 +- lib/spack/spack/spec.py | 11 +- lib/spack/spack/test/cmd/release_jobs.py | 5 +- .../spack/test/concretize_preferences.py | 10 +- lib/spack/spack/test/config.py | 39 +++- lib/spack/spack/test/spack_yaml.py | 2 +- lib/spack/spack/util/spack_yaml.py | 182 ++++++++---------- 13 files changed, 171 insertions(+), 178 deletions(-) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index aab07b8a845..eafa1dcdb10 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -11,6 +11,7 @@ import tempfile import hashlib from contextlib import closing +import ruamel.yaml as yaml import json @@ -139,7 +140,7 @@ def read_buildinfo_file(prefix): filename = buildinfo_file_name(prefix) with open(filename, 'r') as inputfile: content = inputfile.read() - buildinfo = syaml.load(content) + buildinfo = yaml.load(content) return buildinfo @@ -380,10 +381,9 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, checksum = checksum_tarball(tarfile_path) # add sha256 checksum to spec.yaml - spec_dict = {} with open(spec_file, 'r') as inputfile: content = inputfile.read() - spec_dict = syaml.load(content) + spec_dict = yaml.load(content) bchecksum = {} bchecksum['hash_algorithm'] = 'sha256' bchecksum['hash'] = checksum diff --git a/lib/spack/spack/cmd/release_jobs.py b/lib/spack/spack/cmd/release_jobs.py index 65ba42053d1..c5acc4ee2d2 100644 --- a/lib/spack/spack/cmd/release_jobs.py +++ b/lib/spack/spack/cmd/release_jobs.py @@ -655,4 +655,4 @@ def release_jobs(parser, args): output_object['stages'] = stage_names with open(args.output_file, 'w') as outf: - outf.write(syaml.dump(output_object)) + outf.write(syaml.dump_config(output_object, default_flow_style=True)) diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index 1af8ad757b4..3f536f37935 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -36,7 +36,6 @@ import sys import multiprocessing from contextlib import contextmanager -from six import string_types from six import iteritems from ordereddict_backport import OrderedDict @@ -155,7 +154,7 @@ def write_section(self, section): mkdirp(self.path) with open(filename, 'w') as f: validate(data, section_schemas[section]) - syaml.dump(data, stream=f, default_flow_style=False) + syaml.dump_config(data, stream=f, default_flow_style=False) except (yaml.YAMLError, IOError) as e: raise ConfigFileError( "Error writing to config file: '%s'" % str(e)) @@ -200,6 +199,22 @@ def get_section(self, section): # ... data ... # }, # } + # + # To preserve overrides up to the section level (e.g. to override + # the "packages" section with the "::" syntax), data in self.sections + # looks like this: + # { + # 'config': { + # 'config': { + # ... data ... + # } + # }, + # 'packages': { + # 'packages': { + # ... data ... + # } + # } + # } if self._raw_data is None: self._raw_data = _read_config_file(self.path, self.schema) if self._raw_data is None: @@ -215,29 +230,10 @@ def get_section(self, section): self._raw_data = self._raw_data[key] - # data in self.sections looks (awkwardly) like this: - # { - # 'config': { - # 'config': { - # ... data ... - # } - # }, - # 'packages': { - # 'packages': { - # ... data ... - # } - # } - # } - # - # UNLESS there is no section, in which case it is stored as: - # { - # 'config': None, - # ... - # } - value = self._raw_data.get(section) - self.sections.setdefault( - section, None if value is None else {section: value}) - return self.sections[section] + for section_key, data in self._raw_data.items(): + self.sections[section_key] = {section_key: data} + + return self.sections.get(section, None) def write_section(self, section): validate(self.sections, self.schema) @@ -247,7 +243,8 @@ def write_section(self, section): tmp = os.path.join(parent, '.%s.tmp' % self.path) with open(tmp, 'w') as f: - syaml.dump(self.sections, stream=f, default_flow_style=False) + syaml.dump_config(self.sections, stream=f, + default_flow_style=False) os.path.move(tmp, self.path) except (yaml.YAMLError, IOError) as e: raise ConfigFileError( @@ -533,7 +530,7 @@ def print_section(self, section, blame=False): try: data = syaml.syaml_dict() data[section] = self.get_config(section) - syaml.dump( + syaml.dump_config( data, stream=sys.stdout, default_flow_style=False, blame=blame) except (yaml.YAMLError, IOError): raise ConfigError("Error reading configuration: %s" % section) @@ -708,7 +705,7 @@ def _read_config_file(filename, schema): try: tty.debug("Reading config file %s" % filename) with open(filename) as f: - data = _mark_overrides(syaml.load(f)) + data = syaml.load_config(f) if data: validate(data, schema) @@ -734,23 +731,6 @@ def _override(string): return hasattr(string, 'override') and string.override -def _mark_overrides(data): - if isinstance(data, list): - return syaml.syaml_list(_mark_overrides(elt) for elt in data) - - elif isinstance(data, dict): - marked = syaml.syaml_dict() - for key, val in iteritems(data): - if isinstance(key, string_types) and key.endswith(':'): - key = syaml.syaml_str(key[:-1]) - key.override = True - marked[key] = _mark_overrides(val) - return marked - - else: - return data - - def _mark_internal(data, name): """Add a simple name mark to raw YAML/JSON data. @@ -820,9 +800,14 @@ def they_are(t): # ensure that keys are marked in the destination. the key_marks dict # ensures we can get the actual source key objects from dest keys - for dk in dest.keys(): - if dk in key_marks: + for dk in list(dest.keys()): + if dk in key_marks and syaml.markable(dk): syaml.mark(dk, key_marks[dk]) + elif dk in key_marks: + # The destination key may not be markable if it was derived + # from a schema default. In this case replace the key. + val = dest.pop(dk) + dest[key_marks[dk]] = val return dest diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 5204f7d288e..b6b1814819b 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -11,7 +11,6 @@ import copy import socket -import ruamel.yaml import six from ordereddict_backport import OrderedDict @@ -27,6 +26,7 @@ import spack.schema.env import spack.spec import spack.util.spack_json as sjson +import spack.util.spack_yaml as syaml import spack.config import spack.build_environment as build_env @@ -401,7 +401,7 @@ def validate(data, filename=None): def _read_yaml(str_or_file): """Read YAML from a file for round-trip parsing.""" - data = ruamel.yaml.load(str_or_file, ruamel.yaml.RoundTripLoader) + data = syaml.load_config(str_or_file) filename = getattr(str_or_file, 'name', None) validate(data, filename) return data @@ -411,8 +411,7 @@ def _write_yaml(data, str_or_file): """Write YAML to a file preserving comments and dict order.""" filename = getattr(str_or_file, 'name', None) validate(data, filename) - ruamel.yaml.dump(data, str_or_file, Dumper=ruamel.yaml.RoundTripDumper, - default_flow_style=False) + syaml.dump_config(data, str_or_file, default_flow_style=False) def _eval_conditional(string): diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py index 417466cd837..448254f26b3 100644 --- a/lib/spack/spack/filesystem_view.py +++ b/lib/spack/spack/filesystem_view.py @@ -211,7 +211,7 @@ def write_projections(self): if self.projections: mkdirp(os.path.dirname(self.projections_path)) with open(self.projections_path, 'w') as f: - f.write(s_yaml.dump({'projections': self.projections})) + f.write(s_yaml.dump_config({'projections': self.projections})) def read_projections(self): if os.path.exists(self.projections_path): diff --git a/lib/spack/spack/hooks/yaml_version_check.py b/lib/spack/spack/hooks/yaml_version_check.py index 76ebceab79c..ff8be584811 100644 --- a/lib/spack/spack/hooks/yaml_version_check.py +++ b/lib/spack/spack/hooks/yaml_version_check.py @@ -24,7 +24,7 @@ def check_compiler_yaml_version(): data = None if os.path.isfile(file_name): with open(file_name) as f: - data = syaml.load(f) + data = syaml.load_config(f) if data: compilers = data.get('compilers') diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py index d38ede1385e..434d09c1254 100644 --- a/lib/spack/spack/modules/common.py +++ b/lib/spack/spack/modules/common.py @@ -235,7 +235,7 @@ def generate_module_index(root, modules): index_path = os.path.join(root, 'module-index.yaml') llnl.util.filesystem.mkdirp(root) with open(index_path, 'w') as index_file: - syaml.dump(index, index_file, default_flow_style=False) + syaml.dump(index, default_flow_style=False, stream=index_file) def _generate_upstream_module_index(): diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 1a6cc5f6bd7..cb4942b157c 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -79,7 +79,6 @@ import base64 import sys import collections -import ctypes import hashlib import itertools import os @@ -88,6 +87,7 @@ import six from operator import attrgetter +import ruamel.yaml as yaml from llnl.util.filesystem import find_headers, find_libraries, is_exe from llnl.util.lang import key_ordering, HashableMap, ObjectWrapper, dedupe @@ -185,9 +185,6 @@ #: every time we call str() _any_version = VersionList([':']) -#: Max integer helps avoid passing too large a value to cyaml. -maxint = 2 ** (ctypes.sizeof(ctypes.c_int) * 8 - 1) - 1 - default_format = '{name}{@version}' default_format += '{%compiler.name}{@compiler.version}{compiler_flags}' default_format += '{variants}{arch=architecture}' @@ -1366,8 +1363,8 @@ def _spec_hash(self, hash): """ # TODO: curently we strip build dependencies by default. Rethink # this when we move to using package hashing on all specs. - yaml_text = syaml.dump(self.to_node_dict(hash=hash), - default_flow_style=True, width=maxint) + yaml_text = syaml.dump( + self.to_node_dict(hash=hash), default_flow_style=True) sha = hashlib.sha1(yaml_text.encode('utf-8')) b32_hash = base64.b32encode(sha.digest()).lower() @@ -1937,7 +1934,7 @@ def from_yaml(stream): stream -- string or file object to read from. """ try: - data = syaml.load(stream) + data = yaml.load(stream) return Spec.from_dict(data) except MarkedYAMLError as e: raise syaml.SpackYAMLError("error parsing YAML spec:", str(e)) diff --git a/lib/spack/spack/test/cmd/release_jobs.py b/lib/spack/spack/test/cmd/release_jobs.py index c4f44308d9a..0dbe8c5d5c6 100644 --- a/lib/spack/spack/test/cmd/release_jobs.py +++ b/lib/spack/spack/test/cmd/release_jobs.py @@ -5,6 +5,7 @@ import os import pytest +import re import spack import spack.environment as ev @@ -122,6 +123,6 @@ def test_release_jobs_with_env(tmpdir, mutable_mock_env_path, env_deactivate, release_jobs('--output-file', outputfile) with open(outputfile) as f: - contents = f.read() + contents = f.read().replace(os.linesep, '') assert('archive-files' in contents) - assert('stages: [stage-0' in contents) + assert(re.search(r'stages:\s*\[\s*stage-0', contents)) diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py index 5563bad75b0..e5fa4a851d7 100644 --- a/lib/spack/spack/test/concretize_preferences.py +++ b/lib/spack/spack/test/concretize_preferences.py @@ -29,7 +29,7 @@ def concretize_scope(config, tmpdir): @pytest.fixture() def configure_permissions(): - conf = syaml.load("""\ + conf = syaml.load_config("""\ all: permissions: read: group @@ -182,9 +182,9 @@ def test_no_virtuals_in_packages_yaml(self): """Verify that virtuals are not allowed in packages.yaml.""" # set up a packages.yaml file with a vdep as a key. We use - # syaml.load here to make sure source lines in the config are + # syaml.load_config here to make sure source lines in the config are # attached to parsed strings, as the error message uses them. - conf = syaml.load("""\ + conf = syaml.load_config("""\ mpi: paths: mpi-with-lapack@2.1: /path/to/lapack @@ -197,7 +197,7 @@ def test_no_virtuals_in_packages_yaml(self): def test_all_is_not_a_virtual(self): """Verify that `all` is allowed in packages.yaml.""" - conf = syaml.load("""\ + conf = syaml.load_config("""\ all: variants: [+mpi] """) @@ -214,7 +214,7 @@ def test_external_mpi(self): assert not spec['mpi'].external # load config - conf = syaml.load("""\ + conf = syaml.load_config("""\ all: providers: mpi: [mpich] diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index 3b85bb2a23c..605c37d468f 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -12,7 +12,6 @@ from llnl.util.filesystem import touch, mkdirp import pytest -import ruamel.yaml as yaml import spack.paths import spack.config @@ -57,7 +56,7 @@ def _write(config, data, scope): config_yaml = tmpdir.join(scope, config + '.yaml') config_yaml.ensure() with config_yaml.open('w') as f: - yaml.dump(data, f) + syaml.dump_config(data, f) return _write @@ -721,10 +720,44 @@ def test_single_file_scope(tmpdir, config): '/x/y/z', '$spack/var/spack/repos/builtin'] +def test_single_file_scope_section_override(tmpdir, config): + """Check that individual config sections can be overridden in an + environment config. The config here primarily differs in that the + ``packages`` section is intended to override all other scopes (using the + "::" syntax). + """ + env_yaml = str(tmpdir.join("env.yaml")) + with open(env_yaml, 'w') as f: + f.write("""\ +env: + config: + verify_ssl: False + packages:: + libelf: + compiler: [ 'gcc@4.5.3' ] + repos: + - /x/y/z +""") + + scope = spack.config.SingleFileScope( + 'env', env_yaml, spack.schema.env.schema, ['env']) + + with spack.config.override(scope): + # from the single-file config + assert spack.config.get('config:verify_ssl') is False + assert spack.config.get('packages:libelf:compiler') == ['gcc@4.5.3'] + + # from the lower config scopes + assert spack.config.get('config:checksum') is True + assert not spack.config.get('packages:externalmodule') + assert spack.config.get('repos') == [ + '/x/y/z', '$spack/var/spack/repos/builtin'] + + def check_schema(name, file_contents): """Check a Spack YAML schema against some data""" f = StringIO(file_contents) - data = syaml.load(f) + data = syaml.load_config(f) spack.config.validate(data, name) diff --git a/lib/spack/spack/test/spack_yaml.py b/lib/spack/spack/test/spack_yaml.py index 41a7c0e0155..2166d294e97 100644 --- a/lib/spack/spack/test/spack_yaml.py +++ b/lib/spack/spack/test/spack_yaml.py @@ -27,7 +27,7 @@ def data(): [ 1, 2, 3 ] some_key: some_string """ - return syaml.load(test_file) + return syaml.load_config(test_file) def test_parse(data): diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py index f08be5fdb56..c4910be8bda 100644 --- a/lib/spack/spack/util/spack_yaml.py +++ b/lib/spack/spack/util/spack_yaml.py @@ -12,13 +12,14 @@ default unorderd dict. """ +import ctypes + + from ordereddict_backport import OrderedDict from six import string_types, StringIO import ruamel.yaml as yaml -from ruamel.yaml import Loader, Dumper -from ruamel.yaml.nodes import MappingNode, SequenceNode, ScalarNode -from ruamel.yaml.constructor import ConstructorError +from ruamel.yaml import RoundTripLoader, RoundTripDumper from llnl.util.tty.color import colorize, clen, cextra @@ -58,6 +59,11 @@ class syaml_int(int): } +markable_types = set(syaml_types) | set([ + yaml.comments.CommentedSeq, + yaml.comments.CommentedMap]) + + def syaml_type(obj): """Get the corresponding syaml wrapper type for a primitive type. @@ -72,19 +78,15 @@ def syaml_type(obj): def markable(obj): """Whether an object can be marked.""" - return type(obj) in syaml_types + return type(obj) in markable_types def mark(obj, node): """Add start and end markers to an object.""" - if not markable(obj): - return - if hasattr(node, 'start_mark'): obj._start_mark = node.start_mark elif hasattr(node, '_start_mark'): obj._start_mark = node._start_mark - if hasattr(node, 'end_mark'): obj._end_mark = node.end_mark elif hasattr(node, '_end_mark'): @@ -97,8 +99,11 @@ def marked(obj): hasattr(obj, '_end_mark') and obj._end_mark) -class OrderedLineLoader(Loader): - """YAML loader that preserves order and line numbers. +class OrderedLineLoader(RoundTripLoader): + """YAML loader specifically intended for reading Spack configuration + files. It preserves order and line numbers. It also has special-purpose + logic for handling dictionary keys that indicate a Spack config + override: namely any key that contains an "extra" ':' character. Mappings read in by this loader behave like an ordered dict. Sequences, mappings, and strings also have new attributes, @@ -107,74 +112,46 @@ class OrderedLineLoader(Loader): """ # - # Override construct_yaml_* so that they build our derived types, - # which allows us to add new attributes to them. + # Override construct_yaml_* so that we can apply _start_mark/_end_mark to + # them. The superclass returns CommentedMap/CommentedSeq objects that we + # can add attributes to (and we depend on their behavior to preserve + # comments). # - # The standard YAML constructors return empty instances and fill - # in with mappings later. We preserve this behavior. + # The inherited sequence/dictionary constructors return empty instances + # and fill in with mappings later. We preserve this behavior. # def construct_yaml_str(self, node): - value = self.construct_scalar(node) - value = syaml_str(value) + value = super(OrderedLineLoader, self).construct_yaml_str(node) + # There is no specific marker to indicate that we are parsing a key, + # so this assumes we are talking about a Spack config override key if + # it ends with a ':' and does not contain a '@' (which can appear + # in config values that refer to Spack specs) + if value and value.endswith(':') and '@' not in value: + value = syaml_str(value[:-1]) + value.override = True + else: + value = syaml_str(value) mark(value, node) return value def construct_yaml_seq(self, node): - data = syaml_list() - mark(data, node) + gen = super(OrderedLineLoader, self).construct_yaml_seq(node) + data = next(gen) + if markable(data): + mark(data, node) yield data - data.extend(self.construct_sequence(node)) + for x in gen: + pass def construct_yaml_map(self, node): - data = syaml_dict() - mark(data, node) + gen = super(OrderedLineLoader, self).construct_yaml_map(node) + data = next(gen) + if markable(data): + mark(data, node) yield data - value = self.construct_mapping(node) - data.update(value) - - # - # Override the ``construct_*`` routines. These fill in empty - # objects after yielded by the above ``construct_yaml_*`` methods. - # - def construct_sequence(self, node, deep=False): - if not isinstance(node, SequenceNode): - raise ConstructorError( - None, None, - "expected a sequence node, but found %s" % node.id, - node.start_mark) - value = syaml_list(self.construct_object(child, deep=deep) - for child in node.value) - mark(value, node) - return value - - def construct_mapping(self, node, deep=False): - """Store mappings as OrderedDicts instead of as regular python - dictionaries to preserve file ordering.""" - if not isinstance(node, MappingNode): - raise ConstructorError( - None, None, - "expected a mapping node, but found %s" % node.id, - node.start_mark) - - mapping = syaml_dict() - for key_node, value_node in node.value: - key = self.construct_object(key_node, deep=deep) - try: - hash(key) - except TypeError as exc: - raise ConstructorError( - "while constructing a mapping", node.start_mark, - "found unacceptable key (%s)" % exc, key_node.start_mark) - value = self.construct_object(value_node, deep=deep) - if key in mapping: - raise ConstructorError( - "while constructing a mapping", node.start_mark, - "found already in-use key (%s)" % key, key_node.start_mark) - mapping[key] = value - - mark(mapping, node) - return mapping + for x in gen: + pass # register above new constructors @@ -186,7 +163,7 @@ def construct_mapping(self, node, deep=False): 'tag:yaml.org,2002:str', OrderedLineLoader.construct_yaml_str) -class OrderedLineDumper(Dumper): +class OrderedLineDumper(RoundTripDumper): """Dumper that preserves ordering and formats ``syaml_*`` objects. This dumper preserves insertion ordering ``syaml_dict`` objects @@ -196,41 +173,15 @@ class OrderedLineDumper(Dumper): """ - def represent_mapping(self, tag, mapping, flow_style=None): - value = [] - node = MappingNode(tag, value, flow_style=flow_style) - if self.alias_key is not None: - self.represented_objects[self.alias_key] = node - best_style = True - if hasattr(mapping, 'items'): - # if it's a syaml_dict, preserve OrderedDict order. - # Otherwise do the default thing. - sort = not isinstance(mapping, syaml_dict) - mapping = list(mapping.items()) - if sort: - mapping.sort() - - for item_key, item_value in mapping: - node_key = self.represent_data(item_key) - node_value = self.represent_data(item_value) - if not (isinstance(node_key, ScalarNode) and not node_key.style): - best_style = False - if not (isinstance(node_value, ScalarNode) and - not node_value.style): - best_style = False - value.append((node_key, node_value)) - if flow_style is None: - if self.default_flow_style is not None: - node.flow_style = self.default_flow_style - else: - node.flow_style = best_style - - return node - def ignore_aliases(self, _data): """Make the dumper NEVER print YAML aliases.""" return True + def represent_str(self, data): + if hasattr(data, 'override') and data.override: + data = data + ':' + return super(OrderedLineDumper, self).represent_str(data) + # Make our special objects look like normal YAML ones. OrderedLineDumper.add_representer(syaml_dict, OrderedLineDumper.represent_dict) @@ -239,6 +190,28 @@ def ignore_aliases(self, _data): OrderedLineDumper.add_representer(syaml_int, OrderedLineDumper.represent_int) +class SafeDumper(RoundTripDumper): + + def ignore_aliases(self, _data): + """Make the dumper NEVER print YAML aliases.""" + return True + + +# Allow syaml_dict objects to be represented by ruamel.yaml.dump. With this, +# syaml_dict allows a user to provide an ordered dictionary to yaml.dump when +# the RoundTripDumper is used. +RoundTripDumper.add_representer(syaml_dict, RoundTripDumper.represent_dict) + + +#: Max integer helps avoid passing too large a value to cyaml. +maxint = 2 ** (ctypes.sizeof(ctypes.c_int) * 8 - 1) - 1 + + +def dump(obj, default_flow_style=False, stream=None): + return yaml.dump(obj, default_flow_style=default_flow_style, width=maxint, + Dumper=SafeDumper, stream=stream) + + def file_line(mark): """Format a mark as : information.""" result = mark.name @@ -288,7 +261,8 @@ def represent_data(self, data): result = super(LineAnnotationDumper, self).represent_data(data) if isinstance(result.value, string_types): result.value = syaml_str(data) - mark(result.value, data) + if markable(result.value): + mark(result.value, data) return result def write_stream_start(self): @@ -319,14 +293,18 @@ def write_line_break(self): _annotations.append('') -def load(*args, **kwargs): +def load_config(*args, **kwargs): """Load but modify the loader instance so that it will add __line__ - atrributes to the returned object.""" + attributes to the returned object.""" kwargs['Loader'] = OrderedLineLoader return yaml.load(*args, **kwargs) -def dump(*args, **kwargs): +def load(*args, **kwargs): + return yaml.load(*args, **kwargs) + + +def dump_config(*args, **kwargs): blame = kwargs.pop('blame', False) if blame: From 25d63aa44c240ef22c57bbcbec47ff1d247f6a46 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Wed, 23 Oct 2019 09:29:28 -0500 Subject: [PATCH 387/499] petsc: add version 3.12.1 [and variant: batch] (#13390) * petsc: add version 3.12.1 [and variant: batch] * fix test_prs_update_old_api errors --- .../repos/builtin/packages/petsc/package.py | 22 ++++++++++++------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 72f331b1369..e436ffd02fd 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -24,6 +24,7 @@ class Petsc(Package): version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') + version('3.12.1', sha256='b72d895d0f4a79acb13ebc782b47b26d10d4e5706d399f533afcd5b3dba13737') version('3.12.0', sha256='ba9ecf69783c7ebf05bd1c91dd1d4b38bf09b7a2d5f9a774aa6bb46deff7cb14') version('3.11.4', sha256='319cb5a875a692a67fe5b1b90009ba8f182e21921ae645d38106544aff20c3c1') version('3.11.3', sha256='199ad9650a9f58603b49e7fff7cd003ceb03aa231e5d37d0bf0496c6348eca81') @@ -94,6 +95,8 @@ class Petsc(Package): description='Build for KNL') variant('X', default=False, description='Activate X support') + variant('batch', default=False, + description='Enable when mpiexec is not available to run binaries') # 3.8.0 has a build issue with MKL - so list this conflict explicitly conflicts('^intel-mkl', when='@3.8.0') @@ -240,6 +243,8 @@ def install(self, spec, prefix): '--with-blas-lapack-lib=%s' % lapack_blas.joined() ]) + if '+batch' in spec: + options.append('--with-batch=1') if '+knl' in spec: options.append('--with-avx-512-kernels') options.append('--with-memalign=64') @@ -372,19 +377,20 @@ def install(self, spec, prefix): '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # configure fails if these env vars are set outside of Spack - spack_env.unset('PETSC_DIR') - spack_env.unset('PETSC_ARCH') + env.unset('PETSC_DIR') + env.unset('PETSC_ARCH') + def setup_run_environment(self, env): # Set PETSC_DIR in the module file - run_env.set('PETSC_DIR', self.prefix) - run_env.unset('PETSC_ARCH') + env.set('PETSC_DIR', self.prefix) + env.unset('PETSC_ARCH') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # Set up PETSC_DIR for everyone using PETSc package - spack_env.set('PETSC_DIR', self.prefix) - spack_env.unset('PETSC_ARCH') + env.set('PETSC_DIR', self.prefix) + env.unset('PETSC_ARCH') @property def headers(self): From 464ce2795a6790f67ef65bb6f921855b43bd3305 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 23 Oct 2019 16:30:46 +0200 Subject: [PATCH 388/499] glib: Use correct python command (#13392) python~pythoncmd does not provide a python symlink for python3, so make sure we pick the right command. --- var/spack/repos/builtin/packages/glib/package.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index f6265771d7c..f883508449d 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -100,7 +100,8 @@ def fix_python_path(self): files = ['gobject/glib-genmarshal.in', 'gobject/glib-mkenums.in'] filter_file('^#!/usr/bin/env @PYTHON@', - '#!/usr/bin/env python', + '#!/usr/bin/env {0}'.format( + os.path.basename(self.spec['python'].command.path)), *files) @run_before('configure') @@ -119,7 +120,8 @@ def fix_dtrace_usr_bin_path(self): copy(dtrace, dtrace_copy) filter_file( '^#!/usr/bin/python', - '#!/usr/bin/env python', + '#!/usr/bin/env {0}'.format( + os.path.basename(self.spec['python'].command.path)), dtrace_copy ) @@ -135,7 +137,8 @@ def filter_sbang(self): # this after install because otherwise the install target will try # to rebuild files as filter_file updates the timestamps) if self.spec.satisfies('@2.53.4:'): - pattern = '^#!/usr/bin/env python' + pattern = '^#!/usr/bin/env {0}'.format( + os.path.basename(self.spec['python'].command.path)) repl = '#!{0}'.format(self.spec['python'].command.path) files = ['glib-genmarshal', 'glib-mkenums'] else: From 44f859849baa679652eedb7bbd10f471ddf4935a Mon Sep 17 00:00:00 2001 From: carlabguillen Date: Wed, 23 Oct 2019 16:31:06 +0200 Subject: [PATCH 389/499] Ace package. Initial commit (#13211) * Ace package. Initial commit * Correcting header now with licence. * Using sha256 * Making requested changes:removing import line, urls and checksums in one line, and making it an MakefilePackage. * Removing extra line --- .../repos/builtin/packages/ace/package.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ace/package.py diff --git a/var/spack/repos/builtin/packages/ace/package.py b/var/spack/repos/builtin/packages/ace/package.py new file mode 100644 index 00000000000..0c57bb6dbff --- /dev/null +++ b/var/spack/repos/builtin/packages/ace/package.py @@ -0,0 +1,44 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Ace(MakefilePackage): + """ACE is an open-source framework that provides many components and + patterns for developing high-performance, distributed real-time and + embedded systems. ACE provides powerful, yet efficient abstractions + for sockets, demultiplexing loops, threads, synchronization + primitives.""" + + homepage = "http://www.dre.vanderbilt.edu/~schmidt/ACE.html" + url = "http://download.dre.vanderbilt.edu/previous_versions/ACE-6.5.1.tar.gz" + + version('6.5.6', '7717cad84d4a9c3d6b2c47963eb555d96de0be657870bcab6fcef4c0423af0de') + version('6.5.1', '1f318adadb19da23c9be570a9c600a330056b18950fe0bf0eb1cf5cac8b72a32') + version('6.5.0', 'b6f9ec922fbdcecb4348e16d851d0d1f135df1836dfe77d2e0b64295ddb83066') + + def edit(self, spec, prefix): + + # Dictionary mapping: compiler-name : ACE config-label + supported = {'intel': '_icc', 'gcc': ''} + + if not(self.compiler.name in supported): + raise Exception('compiler ' + self.compiler.name + + ' not supported in ace spack-package') + + env['ACE_ROOT'] = self.stage.source_path + + with working_dir('./ace'): + with open('config.h', 'w') as f: + f.write('#include "ace/config-linux.h"\n') + + with working_dir(join_path(self.stage.source_path, + 'include/makeinclude')): + with open('platform_macros.GNU', 'w') as f: + f.write("include $(ACE_ROOT)/include/makeinclude/" + "platform_linux" + supported[self.compiler.name] + + ".GNU\n") + f.write("INSTALL_PREFIX=%s" % prefix) From 466d07558d2016ecd844653b95aca29b3c848b24 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 23 Oct 2019 16:33:09 +0200 Subject: [PATCH 390/499] bracken: Use correct python command (#13395) python~pythoncmd does not provide a python symlink for python3, so make sure we pick the right command. --- var/spack/repos/builtin/packages/bracken/package.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py index b971f099691..35846909374 100644 --- a/var/spack/repos/builtin/packages/bracken/package.py +++ b/var/spack/repos/builtin/packages/bracken/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os class Bracken(Package): @@ -16,8 +17,8 @@ class Bracken(Package): version('1.0.0', sha256='8ee736535ad994588339d94d0db4c0b1ba554a619f5f96332ee09f2aabdfe176') - depends_on('perl') - depends_on('python@2.7:') + depends_on('perl', type=('build', 'link', 'run')) + depends_on('python@2.7:', type=('build', 'link', 'run')) depends_on('perl-exporter-tiny') depends_on('perl-list-moreutils') depends_on('perl-parallel-forkmanager') @@ -34,13 +35,15 @@ def install(self, spec, prefix): filter_file( r'#!/usr/bin/python', - '#!/usr/bin/env python', + '#!/usr/bin/env {0}'.format( + os.path.basename(self.spec['python'].command.path)), 'est_abundance.py' ) filter_file( r'#!/usr/bin/python', - '#!/usr/bin/env python', + '#!/usr/bin/env {0}'.format( + os.path.basename(self.spec['python'].command.path)), 'generate_kmer_distribution.py' ) From 64694dfaf8281265e99c6ab88004f94582ec02ee Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 23 Oct 2019 16:33:42 +0200 Subject: [PATCH 391/499] magics: Use correct python path (#13394) python~pythoncmd does not provide a python symlink for python3, so make sure we pick the right command. --- var/spack/repos/builtin/packages/magics/package.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py index d2f3a99003f..b281df021b7 100644 --- a/var/spack/repos/builtin/packages/magics/package.py +++ b/var/spack/repos/builtin/packages/magics/package.py @@ -5,6 +5,7 @@ from spack import * import glob +import os class Magics(CMakePackage): @@ -105,7 +106,11 @@ def patch(self): for plfile in glob.glob('*/*.pl'): filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', plfile) for pyfile in glob.glob('*/*.py'): - filter_file('#!/usr/bin/python', '#!/usr/bin/env python', pyfile) + filter_file('#!/usr/bin/python', + '#!/usr/bin/env {0}'.format( + os.path.basename( + self.spec['python'].command.path)), + pyfile) def cmake_args(self): args = [ From 6f41987500cf9bd4b9b28dd1f282326d0a3d7323 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Wed, 23 Oct 2019 23:36:01 +0900 Subject: [PATCH 392/499] bpp-phyl: Clarify namespace of 'isnan' function. (#13386) --- .../packages/bpp-phyl/clarify_isnan.patch | 75 +++++++++++++++++++ .../builtin/packages/bpp-phyl/package.py | 4 + 2 files changed, 79 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch diff --git a/var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch b/var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch new file mode 100644 index 00000000000..705e4ead97c --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch @@ -0,0 +1,75 @@ +diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionReward.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionReward.cpp +--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionReward.cpp 2019-10-21 14:56:59.567938605 +0900 ++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionReward.cpp 2019-10-21 14:59:43.645224219 +0900 +@@ -137,7 +137,7 @@ + for (size_t j = 0; j < nbStates_; j++) { + for (size_t k = 0; k < nbStates_; k++) { + rewards_(j, k) /= P(j, k); +- if (isnan(rewards_(j, k))) ++ if (std::isnan(rewards_(j, k))) + rewards_(j, k) = 0.; + } + } +diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp +--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp 2019-10-21 14:56:59.567938605 +0900 ++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp 2019-10-21 15:00:02.147173408 +0900 +@@ -166,7 +166,7 @@ + for (size_t j = 0; j < nbStates_; j++) { + for (size_t k = 0; k < nbStates_; k++) { + counts_[i](j, k) /= P(j, k); +- if (isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.) { ++ if (std::isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.) { + counts_[i](j, k) = 0.; + //Weights: + if (weights_) +diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp +--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp 2019-10-21 14:56:59.567938605 +0900 ++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp 2019-10-21 15:00:45.601751367 +0900 +@@ -1427,7 +1427,7 @@ + for (size_t t = 0; t < nbTypes; ++t) + { + tmp[t] = (*mapping)(mapping->getNodeIndex(ids[k]), i, t); +- error = isnan(tmp[t]); ++ error = std::isnan(tmp[t]); + if (error) + goto ERROR; + s += tmp[t]; +@@ -1509,7 +1509,7 @@ + for (size_t t = 0; t < nbTypes; ++t) + { + tmp[t] = (*mapping)(mapping->getNodeIndex(ids[k]), i, t); +- error = isnan(tmp[t]); ++ error = std::isnan(tmp[t]); + if (error) + goto ERROR; + s += tmp[t]; +@@ -1609,7 +1609,7 @@ + for (size_t i = 0; i < nbSites; ++i) + { + double tmp = (*mapping)(k, i); +- if (isnan(tmp)) ++ if (std::isnan(tmp)) + { + if (verbose) + ApplicationTools::displayWarning("On branch " + TextTools::toString(ids[k]) + ", reward for type " + reg.getTypeName(nbt + 1) + " could not be computed."); +@@ -1689,7 +1689,7 @@ + for (size_t i = 0; i < nbSites; ++i) + { + double tmp = (*mapping)(mapping->getNodeIndex(mids[k]), i); +- if (isnan(tmp)) ++ if (std::isnan(tmp)) + { + if (verbose) + ApplicationTools::displayWarning("On branch " + TextTools::toString(mids[k]) + ", reward for type " + reg.getTypeName(nbt + 1) + " could not be computed."); +diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp +--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp 2019-10-21 14:56:59.567938605 +0900 ++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp 2019-10-21 15:01:30.276461683 +0900 +@@ -163,7 +163,7 @@ + for (size_t j = 0; j < nbStates_; j++) { + for(size_t k = 0; k < nbStates_; k++) { + counts_[i](j, k) /= P(j, k); +- if (isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.) ++ if (std::isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.) + counts_[i](j, k) = 0; + //Weights: + if (weights_) diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py index f48889a8821..e2b8f0588a9 100644 --- a/var/spack/repos/builtin/packages/bpp-phyl/package.py +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -18,5 +18,9 @@ class BppPhyl(CMakePackage): depends_on('bpp-core') depends_on('bpp-seq') + # Clarify isnan's namespace, because Fujitsu compiler can't + # resolve ambiguous of 'isnan' function. + patch('clarify_isnan.patch', when='%fj') + def cmake_args(self): return ['-DBUILD_TESTING=FALSE'] From 79c28331d2fe61569b73b60464671a94bdb415cc Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 23 Oct 2019 09:36:45 -0500 Subject: [PATCH 393/499] Add py-codecov package (#13383) --- .../builtin/packages/py-codecov/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-codecov/package.py diff --git a/var/spack/repos/builtin/packages/py-codecov/package.py b/var/spack/repos/builtin/packages/py-codecov/package.py new file mode 100644 index 00000000000..0415ceccaed --- /dev/null +++ b/var/spack/repos/builtin/packages/py-codecov/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCodecov(PythonPackage): + """Hosted coverage reports for Github, Bitbucket and Gitlab.""" + + homepage = "https://github.com/codecov/codecov-python" + url = "https://pypi.io/packages/source/c/codecov/codecov-2.0.15.tar.gz" + + import_modules = ['codecov'] + + version('2.0.15', sha256='8ed8b7c6791010d359baed66f84f061bba5bd41174bf324c31311e8737602788') + + depends_on('py-setuptools', type='build') + depends_on('py-requests@2.7.9:', type=('build', 'run')) + depends_on('py-coverage', type=('build', 'run')) + depends_on('py-argparse', when='^python@:2.6', type=('build', 'run')) + depends_on('py-unittest2', type='test') + depends_on('py-linecache2', type='test') From baeec6a94efb87d0446f0b008da9ade2d17d21f0 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 23 Oct 2019 09:37:03 -0500 Subject: [PATCH 394/499] py-unittest2: fix dependencies (#13382) --- var/spack/repos/builtin/packages/py-unittest2/package.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py index 828b12f117e..7961a2e2f7c 100644 --- a/var/spack/repos/builtin/packages/py-unittest2/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2/package.py @@ -16,7 +16,6 @@ class PyUnittest2(PythonPackage): version('1.1.0', sha256='22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579') depends_on('py-setuptools', type='build') - depends_on('py-enum34', when='^python@:3.3', type=('build', 'run')) depends_on('py-traceback2', type=('build', 'run')) - depends_on('py-six', type=('build', 'run')) + depends_on('py-six@1.4:', type=('build', 'run')) depends_on('py-argparse', type=('build', 'run')) From 4bd0a9b286605a9aae6eec90b92671e31f419032 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 23 Oct 2019 09:38:05 -0500 Subject: [PATCH 395/499] py-linecache2: pbr is only a build dependency (#13379) --- var/spack/repos/builtin/packages/py-linecache2/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-linecache2/package.py b/var/spack/repos/builtin/packages/py-linecache2/package.py index e05e540e942..e23bc0d20bb 100644 --- a/var/spack/repos/builtin/packages/py-linecache2/package.py +++ b/var/spack/repos/builtin/packages/py-linecache2/package.py @@ -15,4 +15,6 @@ class PyLinecache2(PythonPackage): version('1.0.0', sha256='4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c') depends_on('py-setuptools', type='build') - depends_on('py-pbr', type=('build', 'run')) + depends_on('py-pbr', type='build') + depends_on('py-fixtures', type='test') + depends_on('py-unittest2', type='test') From b75f506a1a3c67950e361676900bedd8aae18f7e Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 23 Oct 2019 17:07:22 +0200 Subject: [PATCH 396/499] bison: Fix build (#13231) It seems that 3.4.2 includes a change that is supposed to fix parallel builds (https://lists.gnu.org/archive/html/bug-bison/2019-08/msg00000.html). Instead, it actually breaks it for me (with -j48) with errors such as: ``` mv: cannot stat 'examples/c/reccalc/scan.stamp.tmp': No such file or directory Makefile:9323: recipe for target 'examples/c/reccalc/scan.stamp' failed ``` --- var/spack/repos/builtin/packages/bison/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index 02abd3e4fa8..7444400d00b 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -32,3 +32,7 @@ class Bison(AutotoolsPackage): patch('secure_snprintf.patch', level=0, when='@3.0.4') build_directory = 'spack-build' + + @property + def parallel(self): + return not self.spec.satisfies('@3.4.2') From bc6c76baf90d7954f60ab6d43aa17efeea2c931c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 23 Oct 2019 10:13:11 -0500 Subject: [PATCH 397/499] py-traceback2: fix dependencies (#13381) --- .../repos/builtin/packages/py-traceback2/package.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-traceback2/package.py b/var/spack/repos/builtin/packages/py-traceback2/package.py index 1f76eefac0f..cdd22129630 100644 --- a/var/spack/repos/builtin/packages/py-traceback2/package.py +++ b/var/spack/repos/builtin/packages/py-traceback2/package.py @@ -15,5 +15,10 @@ class PyTraceback2(PythonPackage): version('1.4.0', sha256='05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030') depends_on('py-setuptools', type='build') - depends_on('py-linecache2', type=('build', 'run')) - depends_on('py-pbr', type=('build', 'run')) + depends_on('py-pbr', type='build') + + # test-requirements.txt + depends_on('py-contextlib2', type='test') + depends_on('py-fixtures', type='test') + depends_on('py-testtools', type='test') + depends_on('py-unittest2', type='test') From df3b23334a730aeb8a59c22749552984ff0691ea Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 23 Oct 2019 10:13:39 -0500 Subject: [PATCH 398/499] py-argparse: remove Python dependency version (#13378) --- var/spack/repos/builtin/packages/py-argparse/package.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-argparse/package.py b/var/spack/repos/builtin/packages/py-argparse/package.py index a1257333828..63f726ad566 100644 --- a/var/spack/repos/builtin/packages/py-argparse/package.py +++ b/var/spack/repos/builtin/packages/py-argparse/package.py @@ -14,6 +14,4 @@ class PyArgparse(PythonPackage): version('1.4.0', sha256='62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4') - depends_on('python@2.3:') - depends_on('py-setuptools', type='build') From 33499681a49e0c07c490cd075e485ac48acaaf46 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 23 Oct 2019 10:14:04 -0500 Subject: [PATCH 399/499] Add latest version of py-pbr (#13380) --- .../repos/builtin/packages/py-pbr/package.py | 30 ++++++++++++++----- 1 file changed, 23 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py index 4d737ffbcde..be84096ed6b 100644 --- a/var/spack/repos/builtin/packages/py-pbr/package.py +++ b/var/spack/repos/builtin/packages/py-pbr/package.py @@ -9,15 +9,31 @@ class PyPbr(PythonPackage): """PBR is a library that injects some useful and sensible default behaviors into your setuptools run.""" + homepage = "https://pypi.python.org/pypi/pbr" - url = "https://pypi.io/packages/source/p/pbr/pbr-1.10.0.tar.gz" + url = "https://pypi.io/packages/source/p/pbr/pbr-5.4.3.tar.gz" - version('3.1.1', sha256='05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1') - version('2.0.0', sha256='0ccd2db529afd070df815b1521f01401d43de03941170f8a800e7531faba265d') + version('5.4.3', sha256='2c8e420cd4ed4cec4e7999ee47409e876af575d4c35a45840d59e8b5f3155ab8') + version('3.1.1', sha256='05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1') + version('2.0.0', sha256='0ccd2db529afd070df815b1521f01401d43de03941170f8a800e7531faba265d') version('1.10.0', sha256='186428c270309e6fdfe2d5ab0949ab21ae5f7dea831eab96701b86bd666af39c') - version('1.8.1', sha256='e2127626a91e6c885db89668976db31020f0af2da728924b56480fc7ccf09649') + version('1.8.1', sha256='e2127626a91e6c885db89668976db31020f0af2da728924b56480fc7ccf09649') + depends_on('python@2.6:', type=('build', 'run')) depends_on('py-setuptools', type='build') - # Only needed for py<3.4, however when='^python@:3.4.2' syntax might be - # broken, if this fails, remove the when-clause - depends_on('py-enum34', type='build', when='^python@:3.3') + + # test-requirements.txt + depends_on('py-wheel@0.32.0:', type='test') + depends_on('py-fixtures@3.0.0:', type='test') + depends_on('py-hacking@0.12.0:0.12.999,0.13.1:0.13.999', type='test') + depends_on('py-mock@2.0.0:', type='test') + depends_on('py-six@1.10.0:', type='test') + depends_on('py-stestr@2.1.0:', type='test') + depends_on('py-testresources@2.0.0:', type='test') + depends_on('py-testscenarios@0.4:', type='test') + depends_on('py-testtools@2.2.0:', type='test') + depends_on('py-virtualenv@14.0.6:', type='test') + depends_on('py-coverage@4.0:4.3,4.5:', type='test') + depends_on('py-sphinx@1.6.2:1.6.5,1.6.8:1.999', when='^python@:2', type='test') + depends_on('py-sphinx@1.6.2:1.6.5,1.6.8:', type='test') + depends_on('py-testrepository@0.0.18:', type='test') From 26ec644fc8718f134900e613780669c0c9b9e951 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 23 Oct 2019 00:46:35 -0700 Subject: [PATCH 400/499] url summary: show right and wrong parse counts for each regex Previously this command only showed total counts for each regular expression. This doesn't give you a sense of which regexes are working well and which ones are not. We now display the number of right, wrong, and total URL parses per regex. It's easier to see where we might improve the URL parsing with this change. --- lib/spack/spack/cmd/url.py | 43 ++++++++++++++++++++++++++------------ 1 file changed, 30 insertions(+), 13 deletions(-) diff --git a/lib/spack/spack/cmd/url.py b/lib/spack/spack/cmd/url.py index f1ce050a904..a24fcc575c6 100644 --- a/lib/spack/spack/cmd/url.py +++ b/lib/spack/spack/cmd/url.py @@ -160,10 +160,13 @@ def url_summary(args): correct_versions = 0 # Collect statistics on which regexes were matched and how often - name_regex_dict = dict() - name_count_dict = defaultdict(int) - version_regex_dict = dict() - version_count_dict = defaultdict(int) + name_regex_dict = dict() + right_name_count = defaultdict(int) + wrong_name_count = defaultdict(int) + + version_regex_dict = dict() + right_version_count = defaultdict(int) + wrong_version_count = defaultdict(int) tty.msg('Generating a summary of URL parsing in Spack...') @@ -189,9 +192,11 @@ def url_summary(args): try: version, vs, vl, vi, vregex = parse_version_offset(url) version_regex_dict[vi] = vregex - version_count_dict[vi] += 1 if version_parsed_correctly(pkg, version): correct_versions += 1 + right_version_count[vi] += 1 + else: + wrong_version_count[vi] += 1 except UndetectableVersionError: pass @@ -199,9 +204,11 @@ def url_summary(args): try: name, ns, nl, ni, nregex = parse_name_offset(url, version) name_regex_dict[ni] = nregex - name_count_dict[ni] += 1 if name_parsed_correctly(pkg, name): correct_names += 1 + right_name_count[ni] += 1 + else: + wrong_name_count[ni] += 1 except UndetectableNameError: pass @@ -216,24 +223,34 @@ def url_summary(args): tty.msg('Statistics on name regular expressions:') print() - print(' Index Count Regular Expression') + print(' Index Right Wrong Total Regular Expression') for ni in sorted(name_regex_dict.keys()): - print(' {0:>3}: {1:>6} r{2!r}'.format( - ni, name_count_dict[ni], name_regex_dict[ni])) + print(' {0:>5} {1:>5} {2:>5} {3:>5} r{4!r}'.format( + ni, + right_name_count[ni], + wrong_name_count[ni], + right_name_count[ni] + wrong_name_count[ni], + name_regex_dict[ni]) + ) print() tty.msg('Statistics on version regular expressions:') print() - print(' Index Count Regular Expression') + print(' Index Right Wrong Total Regular Expression') for vi in sorted(version_regex_dict.keys()): - print(' {0:>3}: {1:>6} r{2!r}'.format( - vi, version_count_dict[vi], version_regex_dict[vi])) + print(' {0:>5} {1:>5} {2:>5} {3:>5} r{4!r}'.format( + vi, + right_version_count[vi], + wrong_version_count[vi], + right_version_count[vi] + wrong_version_count[vi], + version_regex_dict[vi]) + ) print() # Return statistics, only for testing purposes return (total_urls, correct_names, correct_versions, - name_count_dict, version_count_dict) + right_name_count, right_version_count) def url_stats(args): From b7536eb3323309b47a2f17883f0ad75cf1fa1e90 Mon Sep 17 00:00:00 2001 From: Sarah Osborn <30503782+osborn9@users.noreply.github.com> Date: Wed, 23 Oct 2019 12:13:21 -0700 Subject: [PATCH 401/499] hypre: Add new variants to expose existing features. (#13373) * hypre: Add new variants to expost existing features. * hypre: Add new variants to expose existing features. * hypre: Shorten description line. * hypre: Add an explicit else clause to disable some features. --- .../repos/builtin/packages/hypre/package.py | 41 ++++++++++++++++--- 1 file changed, 36 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index a2444370571..44ff3efc16a 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -41,14 +41,18 @@ class Hypre(Package): # between versions 2.12.1 and 2.13.0. variant('shared', default=(sys.platform != 'darwin'), description="Build shared library (disables static library)") - # SuperluDist have conflicting headers with those in Hypre - variant('internal-superlu', default=True, - description="Use internal Superlu routines") + # Use internal SuperLU routines for FEI - version 2.12.1 and below + variant('internal-superlu', default=False, + description="Use internal SuperLU routines") variant('superlu-dist', default=False, - description='Activates support for SuperluDist') + description='Activates support for SuperLU_Dist library') variant('int64', default=False, description="Use 64bit integers") + variant('mixedint', default=False, + description="Use 64bit integers while reducing memory use") + variant('complex', default=False, description='Use complex values') variant('mpi', default=True, description='Enable MPI support') + variant('openmp', default=False, description='Enable OpenMP support') variant('debug', default=False, description='Build debug instead of optimized version') @@ -71,6 +75,16 @@ class Hypre(Package): # versions before 2.13.0 conflicts("+shared@:2.12.99 platform=darwin") + # Conflicts + # Option added in v2.13.0 + conflicts('+superlu-dist', when='@:2.12.99') + + # Internal SuperLU Option removed in v2.13.0 + conflicts('+internal-superlu', when='@2.13.0:') + + # Option added in v2.16.0 + conflicts('+mixedint', when='@:2.15.99') + def url_for_version(self, version): if version >= Version('2.12.0'): url = 'https://github.com/hypre-space/hypre/archive/v{0}.tar.gz' @@ -100,8 +114,25 @@ def install(self, spec, prefix): else: configure_args.append('--without-MPI') + if '+openmp' in self.spec: + configure_args.append('--with-openmp') + else: + configure_args.append('--without-openmp') + if '+int64' in self.spec: configure_args.append('--enable-bigint') + else: + configure_args.append('--disable-bigint') + + if '+mixedint' in self.spec: + configure_args.append('--enable-mixedint') + else: + configure_args.append('--disable-mixedint') + + if '+complex' in self.spec: + configure_args.append('--enable-complex') + else: + configure_args.append('--disable-complex') if '+shared' in self.spec: configure_args.append("--enable-shared") @@ -112,7 +143,7 @@ def install(self, spec, prefix): configure_args.append("--without-mli") configure_args.append("--without-fei") - if 'superlu-dist' in self.spec: + if '+superlu-dist' in self.spec: configure_args.append('--with-dsuperlu-include=%s' % spec['superlu-dist'].prefix.include) configure_args.append('--with-dsuperlu-lib=%s' % From 420346b275c19806bc83e4f421109ee8edded369 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 23 Oct 2019 21:15:30 +0200 Subject: [PATCH 402/499] mysql: Use correct python command (#13393) * mysql: Use correct python command python~pythoncmd does not provide a python symlink for python3, so make sure we pick the right command. * mysql: Adapt to build env changes --- .../repos/builtin/packages/mysql/package.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/var/spack/repos/builtin/packages/mysql/package.py b/var/spack/repos/builtin/packages/mysql/package.py index ec5d7d183da..497b8568a8f 100644 --- a/var/spack/repos/builtin/packages/mysql/package.py +++ b/var/spack/repos/builtin/packages/mysql/package.py @@ -122,7 +122,7 @@ def cmake_args(self): options.append('-DWITHOUT_SERVER:BOOL=ON') return options - def _fix_dtrace_shebang(self, spack_env): + def _fix_dtrace_shebang(self, build_env): # dtrace may cause build to fail because it uses # '/usr/bin/python' in the shebang. To work around that we copy # the original script into a temporary folder, and change the @@ -135,27 +135,28 @@ def _fix_dtrace_shebang(self, spack_env): copy(dtrace, dtrace_copy) filter_file( '^#!/usr/bin/python', - '#!/usr/bin/env python', + '#!/usr/bin/env {0}'.format( + os.path.basename(self.spec['python'].command)), dtrace_copy ) # To have our own copy of dtrace in PATH, we need to # prepend to PATH the temporary folder where it resides. - spack_env.prepend_path('PATH', dtrace_copy_path) + build_env.prepend_path('PATH', dtrace_copy_path) @run_before('cmake') def _maybe_fix_dtrace_shebang(self): if 'python' in self.spec.flat_dependencies() and \ self.spec.satisfies('@:7.99.99'): - self._fix_dtrace_shebang(spack_env) + self._fix_dtrace_shebang(build_env) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): cxxstd = self.spec.variants['cxxstd'].value flag = getattr(self.compiler, 'cxx{0}_flag'.format(cxxstd)) if flag: - spack_env.append_flags('CXXFLAGS', flag) + env.append_flags('CXXFLAGS', flag) if cxxstd != '98': if int(cxxstd) > 11: - spack_env.append_flags('CXXFLAGS', - '-Wno-deprecated-declarations') + env.append_flags('CXXFLAGS', + '-Wno-deprecated-declarations') if int(cxxstd) > 14: - spack_env.append_flags('CXXFLAGS', '-Wno-error=register') + env.append_flags('CXXFLAGS', '-Wno-error=register') From cd185c3d284b8086735db11e9ca77ba29f84c753 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Wed, 23 Oct 2019 15:11:35 -0500 Subject: [PATCH 403/499] commands: add `spack deprecate` command (#12933) `spack deprecate` allows for the removal of insecure packages with minimal impact to their dependents. It allows one package to be symlinked into the prefix of another to provide seamless transition for rpath'd and hard-coded applications using the old version. Example usage: spack deprecate /hash-of-old-openssl /hash-of-new-openssl The spack deprecate command is designed for use only in extroardinary circumstances. The spack deprecate command makes no promises about binary compatibility. It is up to the user to ensure the replacement is suitable for the deprecated package. --- lib/spack/docs/basic_usage.rst | 58 +++++++- lib/spack/spack/cmd/__init__.py | 11 +- lib/spack/spack/cmd/deprecate.py | 129 +++++++++++++++++ lib/spack/spack/cmd/find.py | 23 ++- lib/spack/spack/cmd/uninstall.py | 5 +- lib/spack/spack/database.py | 200 +++++++++++++++++++++----- lib/spack/spack/directory_layout.py | 52 ++++++- lib/spack/spack/package.py | 87 +++++++++-- lib/spack/spack/spec.py | 19 +++ lib/spack/spack/test/cmd/deprecate.py | 192 +++++++++++++++++++++++++ lib/spack/spack/test/cmd/find.py | 4 +- lib/spack/spack/test/cmd/reindex.py | 53 +++++++ lib/spack/spack/test/database.py | 19 +++ 13 files changed, 789 insertions(+), 63 deletions(-) create mode 100644 lib/spack/spack/cmd/deprecate.py create mode 100644 lib/spack/spack/test/cmd/deprecate.py create mode 100644 lib/spack/spack/test/cmd/reindex.py diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index f86724e1405..0d2d74b43fb 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -277,6 +277,52 @@ the tarballs in question to it (see :ref:`mirrors`): $ spack install galahad +----------------------------- +Deprecating insecure packages +----------------------------- + +``spack deprecate`` allows for the removal of insecure packages with +minimal impact to their dependents. + +.. warning:: + + The ``spack deprecate`` command is designed for use only in + extraordinary circumstances. This is a VERY big hammer to be used + with care. + +The ``spack deprecate`` command will remove one package and replace it +with another by replacing the deprecated package's prefix with a link +to the deprecator package's prefix. + +.. warning:: + + The ``spack deprecate`` command makes no promises about binary + compatibility. It is up to the user to ensure the deprecator is + suitable for the deprecated package. + +Spack tracks concrete deprecated specs and ensures that no future packages +concretize to a deprecated spec. + +The first spec given to the ``spack deprecate`` command is the package +to deprecate. It is an abstract spec that must describe a single +installed package. The second spec argument is the deprecator +spec. By default it must be an abstract spec that describes a single +installed package, but with the ``-i/--install-deprecator`` it can be +any abstract spec that Spack will install and then use as the +deprecator. The ``-I/--no-install-deprecator`` option will ensure +the default behavior. + +By default, ``spack deprecate`` will deprecate all dependencies of the +deprecated spec, replacing each by the dependency of the same name in +the deprecator spec. The ``-d/--dependencies`` option will ensure the +default, while the ``-D/--no-dependencies`` option will deprecate only +the root of the deprecate spec in favor of the root of the deprecator +spec. + +``spack deprecate`` can use symbolic links or hard links. The default +behavior is symbolic links, but the ``-l/--link-type`` flag can take +options ``hard`` or ``soft``. + ----------------------- Verifying installations ----------------------- @@ -372,11 +418,13 @@ only shows the version of installed packages. Viewing more metadata """""""""""""""""""""""""""""""" -``spack find`` can filter the package list based on the package name, spec, or -a number of properties of their installation status. For example, missing -dependencies of a spec can be shown with ``--missing``, packages which were -explicitly installed with ``spack install `` can be singled out with -``--explicit`` and those which have been pulled in only as dependencies with +``spack find`` can filter the package list based on the package name, +spec, or a number of properties of their installation status. For +example, missing dependencies of a spec can be shown with +``--missing``, deprecated packages can be included with +``--deprecated``, packages which were explicitly installed with +``spack install `` can be singled out with ``--explicit`` and +those which have been pulled in only as dependencies with ``--implicit``. In some cases, there may be different configurations of the *same* diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index 52e20614a1a..9dd6dc4c6ec 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -174,7 +174,7 @@ def elide_list(line_list, max_num=10): return line_list -def disambiguate_spec(spec, env, local=False): +def disambiguate_spec(spec, env, local=False, installed=True): """Given a spec, figure out which installed package it refers to. Arguments: @@ -182,12 +182,17 @@ def disambiguate_spec(spec, env, local=False): env (spack.environment.Environment): a spack environment, if one is active, or None if no environment is active local (boolean, default False): do not search chained spack instances + installed (boolean or any, or spack.database.InstallStatus or iterable + of spack.database.InstallStatus): install status argument passed to + database query. See ``spack.database.Database._query`` for details. """ hashes = env.all_hashes() if env else None if local: - matching_specs = spack.store.db.query_local(spec, hashes=hashes) + matching_specs = spack.store.db.query_local(spec, hashes=hashes, + installed=installed) else: - matching_specs = spack.store.db.query(spec, hashes=hashes) + matching_specs = spack.store.db.query(spec, hashes=hashes, + installed=installed) if not matching_specs: tty.die("Spec '%s' matches no installed packages." % spec) diff --git a/lib/spack/spack/cmd/deprecate.py b/lib/spack/spack/cmd/deprecate.py new file mode 100644 index 00000000000..286d2e995a0 --- /dev/null +++ b/lib/spack/spack/cmd/deprecate.py @@ -0,0 +1,129 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +'''Deprecate one Spack install in favor of another + +Spack packages of different configurations cannot be installed to the same +location. However, in some circumstances (e.g. security patches) old +installations should never be used again. In these cases, we will mark the old +installation as deprecated, remove it, and link another installation into its +place. + +It is up to the user to ensure binary compatibility between the deprecated +installation and its deprecator. +''' +from __future__ import print_function +import argparse +import os + +import llnl.util.tty as tty + +import spack.cmd +import spack.store +import spack.cmd.common.arguments as arguments +import spack.environment as ev + +from spack.error import SpackError +from spack.database import InstallStatuses + +description = "Replace one package with another via symlinks" +section = "admin" +level = "long" + +# Arguments for display_specs when we find ambiguity +display_args = { + 'long': True, + 'show_flags': True, + 'variants': True, + 'indent': 4, +} + + +def setup_parser(sp): + setup_parser.parser = sp + + arguments.add_common_arguments(sp, ['yes_to_all']) + + deps = sp.add_mutually_exclusive_group() + deps.add_argument('-d', '--dependencies', action='store_true', + default=True, dest='dependencies', + help='Deprecate dependencies (default)') + deps.add_argument('-D', '--no-dependencies', action='store_false', + default=True, dest='dependencies', + help='Do not deprecate dependencies') + + install = sp.add_mutually_exclusive_group() + install.add_argument('-i', '--install-deprecator', action='store_true', + default=False, dest='install', + help='Concretize and install deprecator spec') + install.add_argument('-I', '--no-install-deprecator', + action='store_false', default=False, dest='install', + help='Deprecator spec must already be installed (default)') # noqa 501 + + sp.add_argument('-l', '--link-type', type=str, + default='soft', choices=['soft', 'hard'], + help="Type of filesystem link to use for deprecation (default soft)") # noqa 501 + + sp.add_argument('specs', nargs=argparse.REMAINDER, + help="spec to deprecate and spec to use as deprecator") + + +def deprecate(parser, args): + """Deprecate one spec in favor of another""" + env = ev.get_env(args, 'deprecate') + specs = spack.cmd.parse_specs(args.specs) + + if len(specs) != 2: + raise SpackError('spack deprecate requires exactly two specs') + + install_query = [InstallStatuses.INSTALLED, InstallStatuses.DEPRECATED] + deprecate = spack.cmd.disambiguate_spec(specs[0], env, local=True, + installed=install_query) + + if args.install: + deprecator = specs[1].concretized() + else: + deprecator = spack.cmd.disambiguate_spec(specs[1], env, local=True) + + # calculate all deprecation pairs for errors and warning message + all_deprecate = [] + all_deprecators = [] + + generator = deprecate.traverse( + order='post', type='link', root=True + ) if args.dependencies else [deprecate] + for spec in generator: + all_deprecate.append(spec) + all_deprecators.append(deprecator[spec.name]) + # This will throw a key error if deprecator does not have a dep + # that matches the name of a dep of the spec + + if not args.yes_to_all: + tty.msg('The following packages will be deprecated:\n') + spack.cmd.display_specs(all_deprecate, **display_args) + tty.msg("In favor of (respectively):\n") + spack.cmd.display_specs(all_deprecators, **display_args) + print() + + already_deprecated = [] + already_deprecated_for = [] + for spec in all_deprecate: + deprecated_for = spack.store.db.deprecator(spec) + if deprecated_for: + already_deprecated.append(spec) + already_deprecated_for.append(deprecated_for) + + tty.msg('The following packages are already deprecated:\n') + spack.cmd.display_specs(already_deprecated, **display_args) + tty.msg('In favor of (respectively):\n') + spack.cmd.display_specs(already_deprecated_for, **display_args) + + answer = tty.get_yes_or_no('Do you want to proceed?', default=False) + if not answer: + tty.die('Will not deprecate any packages.') + + link_fn = os.link if args.link_type == 'hard' else os.symlink + + for dcate, dcator in zip(all_deprecate, all_deprecators): + dcate.package.do_deprecate(dcator, link_fn) diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py index 5d6b07f45f4..ed8f2ed2bf4 100644 --- a/lib/spack/spack/cmd/find.py +++ b/lib/spack/spack/cmd/find.py @@ -14,6 +14,7 @@ import spack.cmd as cmd import spack.cmd.common.arguments as arguments from spack.util.string import plural +from spack.database import InstallStatuses description = "list and search installed packages" section = "basic" @@ -83,6 +84,12 @@ def setup_parser(subparser): action='store_true', dest='only_missing', help='show only missing dependencies') + subparser.add_argument( + '--deprecated', action='store_true', + help='show deprecated packages as well as installed specs') + subparser.add_argument( + '--only-deprecated', action='store_true', + help='show only deprecated packages') subparser.add_argument('-N', '--namespace', action='store_true', help='show fully qualified package names') @@ -100,18 +107,24 @@ def setup_parser(subparser): def query_arguments(args): # Set up query arguments. - installed, known = True, any - if args.only_missing: - installed = False - elif args.missing: - installed = any + installed = [] + if not (args.only_missing or args.only_deprecated): + installed.append(InstallStatuses.INSTALLED) + if (args.deprecated or args.only_deprecated) and not args.only_missing: + installed.append(InstallStatuses.DEPRECATED) + if (args.missing or args.only_missing) and not args.only_deprecated: + installed.append(InstallStatuses.MISSING) + + known = any if args.unknown: known = False + explicit = any if args.explicit: explicit = True if args.implicit: explicit = False + q_args = {'installed': installed, 'known': known, "explicit": explicit} # Time window of installation diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index 8ad8dcb4b53..2d903fdd474 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -14,6 +14,7 @@ import spack.cmd.common.arguments as arguments import spack.repo import spack.store +from spack.database import InstallStatuses from llnl.util import tty from llnl.util.tty.colify import colify @@ -81,7 +82,9 @@ def find_matching_specs(env, specs, allow_multiple_matches=False, force=False): specs_from_cli = [] has_errors = False for spec in specs: - matching = spack.store.db.query_local(spec, hashes=hashes) + install_query = [InstallStatuses.INSTALLED, InstallStatuses.DEPRECATED] + matching = spack.store.db.query_local(spec, hashes=hashes, + installed=install_query) # For each spec provided, make sure it refers to only one package. # Fail and ask user to be unambiguous if it doesn't if not allow_multiple_matches and len(matching) > 1: diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 4d532d1f00c..5110e66c7a0 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -46,7 +46,6 @@ from spack.version import Version from spack.util.lock import Lock, WriteTransaction, ReadTransaction, LockError - # DB goes in this directory underneath the root _db_dirname = '.spack-db' @@ -77,6 +76,36 @@ def converter(self, spec_like, *args, **kwargs): return converter +class InstallStatus(str): + pass + + +class InstallStatuses(object): + INSTALLED = InstallStatus('installed') + DEPRECATED = InstallStatus('deprecated') + MISSING = InstallStatus('missing') + + @classmethod + def canonicalize(cls, query_arg): + if query_arg is True: + return [cls.INSTALLED] + elif query_arg is False: + return [cls.MISSING] + elif query_arg is any: + return [cls.INSTALLED, cls.DEPRECATED, cls.MISSING] + elif isinstance(query_arg, InstallStatus): + return [query_arg] + else: + try: # Try block catches if it is not an iterable at all + if any(type(x) != InstallStatus for x in query_arg): + raise TypeError + except TypeError: + raise TypeError( + 'installation query must be `any`, boolean, ' + 'InstallStatus, or iterable of InstallStatus') + return query_arg + + class InstallRecord(object): """A record represents one installation in the DB. @@ -109,7 +138,8 @@ def __init__( installed, ref_count=0, explicit=False, - installation_time=None + installation_time=None, + deprecated_for=None ): self.spec = spec self.path = str(path) if path else None @@ -117,16 +147,29 @@ def __init__( self.ref_count = ref_count self.explicit = explicit self.installation_time = installation_time or _now() + self.deprecated_for = deprecated_for + + def install_type_matches(self, installed): + installed = InstallStatuses.canonicalize(installed) + if self.installed: + return InstallStatuses.INSTALLED in installed + elif self.deprecated_for: + return InstallStatuses.DEPRECATED in installed + else: + return InstallStatuses.MISSING in installed def to_dict(self): - return { + rec_dict = { 'spec': self.spec.to_node_dict(), 'path': self.path, 'installed': self.installed, 'ref_count': self.ref_count, 'explicit': self.explicit, - 'installation_time': self.installation_time + 'installation_time': self.installation_time, } + if self.deprecated_for: + rec_dict.update({'deprecated_for': self.deprecated_for}) + return rec_dict @classmethod def from_dict(cls, spec, dictionary): @@ -136,6 +179,7 @@ def from_dict(cls, spec, dictionary): # Old databases may have "None" for path for externals if d['path'] == 'None': d['path'] = None + return InstallRecord(spec, **d) @@ -533,13 +577,37 @@ def _read_suppress_error(): self._data = old_data raise + def _construct_entry_from_directory_layout(self, directory_layout, + old_data, spec, + deprecator=None): + # Try to recover explicit value from old DB, but + # default it to True if DB was corrupt. This is + # just to be conservative in case a command like + # "autoremove" is run by the user after a reindex. + tty.debug( + 'RECONSTRUCTING FROM SPEC.YAML: {0}'.format(spec)) + explicit = True + inst_time = os.stat(spec.prefix).st_ctime + if old_data is not None: + old_info = old_data.get(spec.dag_hash()) + if old_info is not None: + explicit = old_info.explicit + inst_time = old_info.installation_time + + extra_args = { + 'explicit': explicit, + 'installation_time': inst_time + } + self._add(spec, directory_layout, **extra_args) + if deprecator: + self._deprecate(spec, deprecator) + def _construct_from_directory_layout(self, directory_layout, old_data): # Read first the `spec.yaml` files in the prefixes. They should be # considered authoritative with respect to DB reindexing, as # entries in the DB may be corrupted in a way that still makes # them readable. If we considered DB entries authoritative # instead, we would perpetuate errors over a reindex. - with directory_layout.disable_upstream_check(): # Initialize data in the reconstructed DB self._data = {} @@ -548,26 +616,14 @@ def _construct_from_directory_layout(self, directory_layout, old_data): processed_specs = set() for spec in directory_layout.all_specs(): - # Try to recover explicit value from old DB, but - # default it to True if DB was corrupt. This is - # just to be conservative in case a command like - # "autoremove" is run by the user after a reindex. - tty.debug( - 'RECONSTRUCTING FROM SPEC.YAML: {0}'.format(spec)) - explicit = True - inst_time = os.stat(spec.prefix).st_ctime - if old_data is not None: - old_info = old_data.get(spec.dag_hash()) - if old_info is not None: - explicit = old_info.explicit - inst_time = old_info.installation_time - - extra_args = { - 'explicit': explicit, - 'installation_time': inst_time - } - self._add(spec, directory_layout, **extra_args) + self._construct_entry_from_directory_layout(directory_layout, + old_data, spec) + processed_specs.add(spec) + for spec, deprecator in directory_layout.all_deprecated_specs(): + self._construct_entry_from_directory_layout(directory_layout, + old_data, spec, + deprecator) processed_specs.add(spec) for key, entry in old_data.items(): @@ -625,6 +681,10 @@ def _check_ref_counts(self): counts.setdefault(dep_key, 0) counts[dep_key] += 1 + if rec.deprecated_for: + counts.setdefault(rec.deprecated_for, 0) + counts[rec.deprecated_for] += 1 + for rec in self._data.values(): key = rec.spec.dag_hash() expected = counts[key] @@ -761,7 +821,7 @@ def _add( installed = True except DirectoryLayoutError as e: tty.warn( - 'Dependency missing due to corrupt install directory:', + 'Dependency missing: may be deprecated or corrupted:', path, str(e)) elif spec.external_path: path = spec.external_path @@ -840,6 +900,15 @@ def _decrement_ref_count(self, spec): for dep in spec.dependencies(_tracked_deps): self._decrement_ref_count(dep) + def _increment_ref_count(self, spec): + key = spec.dag_hash() + + if key not in self._data: + return + + rec = self._data[key] + rec.ref_count += 1 + def _remove(self, spec): """Non-locking version of remove(); does real work. """ @@ -854,6 +923,10 @@ def _remove(self, spec): for dep in rec.spec.dependencies(_tracked_deps): self._decrement_ref_count(dep) + if rec.deprecated_for: + new_spec = self._data[rec.deprecated_for].spec + self._decrement_ref_count(new_spec) + # Returns the concrete spec so we know it in the case where a # query spec was passed in. return rec.spec @@ -874,6 +947,46 @@ def remove(self, spec): with self.write_transaction(): return self._remove(spec) + def deprecator(self, spec): + """Return the spec that the given spec is deprecated for, or None""" + with self.read_transaction(): + spec_key = self._get_matching_spec_key(spec) + spec_rec = self._data[spec_key] + + if spec_rec.deprecated_for: + return self._data[spec_rec.deprecated_for].spec + else: + return None + + def specs_deprecated_by(self, spec): + """Return all specs deprecated in favor of the given spec""" + with self.read_transaction(): + return [rec.spec for rec in self._data.values() + if rec.deprecated_for == spec.dag_hash()] + + def _deprecate(self, spec, deprecator): + spec_key = self._get_matching_spec_key(spec) + spec_rec = self._data[spec_key] + + deprecator_key = self._get_matching_spec_key(deprecator) + + self._increment_ref_count(deprecator) + + # If spec was already deprecated, update old deprecator's ref count + if spec_rec.deprecated_for: + old_repl_rec = self._data[spec_rec.deprecated_for] + self._decrement_ref_count(old_repl_rec.spec) + + spec_rec.deprecated_for = deprecator_key + spec_rec.installed = False + self._data[spec_key] = spec_rec + + @_autospec + def deprecate(self, spec, deprecator): + """Marks a spec as deprecated in favor of its deprecator""" + with self.write_transaction(): + return self._deprecate(spec, deprecator) + @_autospec def installed_relatives(self, spec, direction='children', transitive=True, deptype='all'): @@ -944,9 +1057,13 @@ def get_by_hash_local(self, dag_hash, default=None, installed=any): dag_hash (str): hash (or hash prefix) to look up default (object, optional): default value to return if dag_hash is not in the DB (default: None) - installed (bool or any, optional): if ``True``, includes only - installed specs in the search; if ``False`` only missing specs, - and if ``any``, either installed or missing (default: any) + installed (bool or any, or InstallStatus or iterable of + InstallStatus, optional): if ``True``, includes only installed + specs in the search; if ``False`` only missing specs, and if + ``any``, all specs in database. If an InstallStatus or iterable + of InstallStatus, returns specs whose install status + (installed, deprecated, or missing) matches (one of) the + InstallStatus. (default: any) ``installed`` defaults to ``any`` so that we can refer to any known hash. Note that ``query()`` and ``query_one()`` differ in @@ -960,7 +1077,7 @@ def get_by_hash_local(self, dag_hash, default=None, installed=any): # hash is a full hash and is in the data somewhere if dag_hash in self._data: rec = self._data[dag_hash] - if installed is any or rec.installed == installed: + if rec.install_type_matches(installed): return [rec.spec] else: return default @@ -969,7 +1086,7 @@ def get_by_hash_local(self, dag_hash, default=None, installed=any): # installed) spec. matches = [record.spec for h, record in self._data.items() if h.startswith(dag_hash) and - (installed is any or installed == record.installed)] + record.install_type_matches(installed)] if matches: return matches @@ -983,9 +1100,13 @@ def get_by_hash(self, dag_hash, default=None, installed=any): dag_hash (str): hash (or hash prefix) to look up default (object, optional): default value to return if dag_hash is not in the DB (default: None) - installed (bool or any, optional): if ``True``, includes only - installed specs in the search; if ``False`` only missing specs, - and if ``any``, either installed or missing (default: any) + installed (bool or any, or InstallStatus or iterable of + InstallStatus, optional): if ``True``, includes only installed + specs in the search; if ``False`` only missing specs, and if + ``any``, all specs in database. If an InstallStatus or iterable + of InstallStatus, returns specs whose install status + (installed, deprecated, or missing) matches (one of) the + InstallStatus. (default: any) ``installed`` defaults to ``any`` so that we can refer to any known hash. Note that ``query()`` and ``query_one()`` differ in @@ -1030,10 +1151,13 @@ def _query( Spack, but have since either changed their name or been removed - installed (bool or any, optional): Specs for which a prefix exists - are "installed". A spec that is NOT installed will be in the - database if some other spec depends on it but its installation - has gone away since Spack installed it. + installed (bool or any, or InstallStatus or iterable of + InstallStatus, optional): if ``True``, includes only installed + specs in the search; if ``False`` only missing specs, and if + ``any``, all specs in database. If an InstallStatus or iterable + of InstallStatus, returns specs whose install status + (installed, deprecated, or missing) matches (one of) the + InstallStatus. (default: True) explicit (bool or any, optional): A spec that was installed following a specific user request is marked as explicit. If @@ -1078,7 +1202,7 @@ def _query( if hashes is not None and rec.spec.dag_hash() not in hashes: continue - if installed is not any and rec.installed != installed: + if not rec.install_type_matches(installed): continue if explicit is not any and rec.explicit != explicit: diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index a48b8411476..f8a42bf42b9 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -90,14 +90,23 @@ def path_for_spec(self, spec): assert(not path.startswith(self.root)) return os.path.join(self.root, path) - def remove_install_directory(self, spec): + def remove_install_directory(self, spec, deprecated=False): """Removes a prefix and any empty parent directories from the root. Raised RemoveFailedError if something goes wrong. """ path = self.path_for_spec(spec) assert(path.startswith(self.root)) - if os.path.exists(path): + if deprecated: + if os.path.exists(path): + try: + metapath = self.deprecated_file_path(spec) + os.unlink(path) + os.remove(metapath) + except OSError as e: + raise RemoveFailedError(spec, path, e) + + elif os.path.exists(path): try: shutil.rmtree(path) except OSError as e: @@ -191,6 +200,7 @@ def __init__(self, root, **kwargs): # If any of these paths change, downstream databases may not be able to # locate files in older upstream databases self.metadata_dir = '.spack' + self.deprecated_dir = 'deprecated' self.spec_file_name = 'spec.yaml' self.extension_file_name = 'extensions.yaml' self.packages_dir = 'repos' # archive of package.py files @@ -232,6 +242,30 @@ def spec_file_path(self, spec): _check_concrete(spec) return os.path.join(self.metadata_path(spec), self.spec_file_name) + def deprecated_file_name(self, spec): + """Gets name of deprecated spec file in deprecated dir""" + _check_concrete(spec) + return spec.dag_hash() + '_' + self.spec_file_name + + def deprecated_file_path(self, deprecated_spec, deprecator_spec=None): + """Gets full path to spec file for deprecated spec + + If the deprecator_spec is provided, use that. Otherwise, assume + deprecated_spec is already deprecated and its prefix links to the + prefix of its deprecator.""" + _check_concrete(deprecated_spec) + if deprecator_spec: + _check_concrete(deprecator_spec) + + # If deprecator spec is None, assume deprecated_spec already deprecated + # and use its link to find the file. + base_dir = self.path_for_spec( + deprecator_spec + ) if deprecator_spec else os.readlink(deprecated_spec.prefix) + + return os.path.join(base_dir, self.metadata_dir, self.deprecated_dir, + self.deprecated_file_name(deprecated_spec)) + @contextmanager def disable_upstream_check(self): self.check_upstream = False @@ -307,6 +341,20 @@ def all_specs(self): spec_files = glob.glob(pattern) return [self.read_spec(s) for s in spec_files] + def all_deprecated_specs(self): + if not os.path.isdir(self.root): + return [] + + path_elems = ["*"] * len(self.path_scheme.split(os.sep)) + path_elems += [self.metadata_dir, self.deprecated_dir, + '*_' + self.spec_file_name] + pattern = os.path.join(self.root, *path_elems) + spec_files = glob.glob(pattern) + get_depr_spec_file = lambda x: os.path.join( + os.path.dirname(os.path.dirname(x)), self.spec_file_name) + return set((self.read_spec(s), self.read_spec(get_depr_spec_file(s))) + for s in spec_files) + def specs_by_hash(self): by_hash = {} for spec in self.all_specs(): diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index e3d4f1b6e99..b49c8c1a231 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -2112,14 +2112,19 @@ def flags_to_build_system_args(self, flags): raise NotImplementedError(msg) @staticmethod - def uninstall_by_spec(spec, force=False): + def uninstall_by_spec(spec, force=False, deprecator=None): if not os.path.isdir(spec.prefix): # prefix may not exist, but DB may be inconsistent. Try to fix by # removing, but omit hooks. specs = spack.store.db.query(spec, installed=True) if specs: - spack.store.db.remove(specs[0]) - tty.msg("Removed stale DB entry for %s" % spec.short_spec) + if deprecator: + spack.store.db.deprecate(specs[0], deprecator) + tty.msg("Deprecating stale DB entry for " + "%s" % spec.short_spec) + else: + spack.store.db.remove(specs[0]) + tty.msg("Removed stale DB entry for %s" % spec.short_spec) return else: raise InstallError(str(spec) + " is not installed.") @@ -2130,7 +2135,7 @@ def uninstall_by_spec(spec, force=False): if dependents: raise PackageStillNeededError(spec, dependents) - # Try to get the pcakage for the spec + # Try to get the package for the spec try: pkg = spec.package except spack.repo.UnknownEntityError: @@ -2146,11 +2151,19 @@ def uninstall_by_spec(spec, force=False): if not spec.external: msg = 'Deleting package prefix [{0}]' tty.debug(msg.format(spec.short_spec)) - spack.store.layout.remove_install_directory(spec) + # test if spec is already deprecated, not whether we want to + # deprecate it now + deprecated = bool(spack.store.db.deprecator(spec)) + spack.store.layout.remove_install_directory(spec, deprecated) # Delete DB entry - msg = 'Deleting DB entry [{0}]' - tty.debug(msg.format(spec.short_spec)) - spack.store.db.remove(spec) + if deprecator: + msg = 'deprecating DB entry [{0}] in favor of [{1}]' + tty.debug(msg.format(spec.short_spec, deprecator.short_spec)) + spack.store.db.deprecate(spec, deprecator) + else: + msg = 'Deleting DB entry [{0}]' + tty.debug(msg.format(spec.short_spec)) + spack.store.db.remove(spec) if pkg is not None: spack.hooks.post_uninstall(spec) @@ -2162,6 +2175,64 @@ def do_uninstall(self, force=False): # delegate to instance-less method. Package.uninstall_by_spec(self.spec, force) + def do_deprecate(self, deprecator, link_fn): + """Deprecate this package in favor of deprecator spec""" + spec = self.spec + + # Check whether package to deprecate has active extensions + if self.extendable: + view = spack.filesystem_view.YamlFilesystemView(spec.prefix, + spack.store.layout) + active_exts = view.extensions_layout.extension_map(spec).values() + if active_exts: + short = spec.format('{name}/{hash:7}') + m = "Spec %s has active extensions\n" % short + for active in active_exts: + m += ' %s\n' % active.format('{name}/{hash:7}') + m += "Deactivate extensions before deprecating %s" % short + tty.die(m) + + # Check whether package to deprecate is an active extension + if self.is_extension: + extendee = self.extendee_spec + view = spack.filesystem_view.YamlFilesystemView(extendee.prefix, + spack.store.layout) + + if self.is_activated(view): + short = spec.format('{name}/{hash:7}') + short_ext = extendee.format('{name}/{hash:7}') + msg = "Spec %s is an active extension of %s\n" % (short, + short_ext) + msg += "Deactivate %s to be able to deprecate it" % short + tty.die(msg) + + # Install deprecator if it isn't installed already + if not spack.store.db.query(deprecator): + deprecator.package.do_install() + + old_deprecator = spack.store.db.deprecator(spec) + if old_deprecator: + # Find this specs yaml file from its old deprecation + self_yaml = spack.store.layout.deprecated_file_path(spec, + old_deprecator) + else: + self_yaml = spack.store.layout.spec_file_path(spec) + + # copy spec metadata to "deprecated" dir of deprecator + depr_yaml = spack.store.layout.deprecated_file_path(spec, + deprecator) + fs.mkdirp(os.path.dirname(depr_yaml)) + shutil.copy2(self_yaml, depr_yaml) + + # Any specs deprecated in favor of this spec are re-deprecated in + # favor of its new deprecator + for deprecated in spack.store.db.specs_deprecated_by(spec): + deprecated.package.do_deprecate(deprecator, link_fn) + + # Now that we've handled metadata, uninstall and replace with link + Package.uninstall_by_spec(spec, force=True, deprecator=deprecator) + link_fn(deprecator.prefix, spec.prefix) + def _check_extendable(self): if not self.extendable: raise ValueError("Package %s is not extendable!" % self.name) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index cb4942b157c..050f0276795 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -2241,6 +2241,21 @@ def concretize(self, tests=False): # Mark everything in the spec as concrete, as well. self._mark_concrete() + # If any spec in the DAG is deprecated, throw an error + deprecated = [] + for x in self.traverse(): + _, rec = spack.store.db.query_by_spec_hash(x.dag_hash()) + if rec and rec.deprecated_for: + deprecated.append(rec) + if deprecated: + msg = "\n The following specs have been deprecated" + msg += " in favor of specs with the hashes shown:\n" + for rec in deprecated: + msg += ' %s --> %s\n' % (rec.spec, rec.deprecated_for) + msg += '\n' + msg += " For each package listed, choose another spec\n" + raise SpecDeprecatedError(msg) + # Now that the spec is concrete we should check if # there are declared conflicts # @@ -4493,3 +4508,7 @@ def __init__(self, spec, matches): class SpecDependencyNotFoundError(SpecError): """Raised when a failure is encountered writing the dependencies of a spec.""" + + +class SpecDeprecatedError(SpecError): + """Raised when a spec concretizes to a deprecated spec or dependency.""" diff --git a/lib/spack/spack/test/cmd/deprecate.py b/lib/spack/spack/test/cmd/deprecate.py new file mode 100644 index 00000000000..6bc87fa5e3b --- /dev/null +++ b/lib/spack/spack/test/cmd/deprecate.py @@ -0,0 +1,192 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import pytest +from spack.main import SpackCommand +import spack.store +from spack.database import InstallStatuses + +install = SpackCommand('install') +uninstall = SpackCommand('uninstall') +deprecate = SpackCommand('deprecate') +find = SpackCommand('find') +activate = SpackCommand('activate') + + +def test_deprecate(mock_packages, mock_archive, mock_fetch, install_mockery): + install('libelf@0.8.13') + install('libelf@0.8.10') + + all_installed = spack.store.db.query() + assert len(all_installed) == 2 + + deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.13') + + non_deprecated = spack.store.db.query() + all_available = spack.store.db.query(installed=any) + assert all_available == all_installed + assert non_deprecated == spack.store.db.query('libelf@0.8.13') + + +def test_deprecate_fails_no_such_package(mock_packages, mock_archive, + mock_fetch, install_mockery): + """Tests that deprecating a spec that is not installed fails. + + Tests that deprecating without the ``-i`` option in favor of a spec that + is not installed fails.""" + output = deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.13', + fail_on_error=False) + assert "Spec 'libelf@0.8.10' matches no installed packages" in output + + install('libelf@0.8.10') + + output = deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.13', + fail_on_error=False) + assert "Spec 'libelf@0.8.13' matches no installed packages" in output + + +def test_deprecate_install(mock_packages, mock_archive, mock_fetch, + install_mockery): + """Tests that the ```-i`` option allows us to deprecate in favor of a spec + that is not yet installed.""" + install('libelf@0.8.10') + + to_deprecate = spack.store.db.query() + assert len(to_deprecate) == 1 + + deprecate('-y', '-i', 'libelf@0.8.10', 'libelf@0.8.13') + + non_deprecated = spack.store.db.query() + deprecated = spack.store.db.query(installed=InstallStatuses.DEPRECATED) + assert deprecated == to_deprecate + assert len(non_deprecated) == 1 + assert non_deprecated[0].satisfies('libelf@0.8.13') + + +def test_deprecate_deps(mock_packages, mock_archive, mock_fetch, + install_mockery): + """Test that the deprecate command deprecates all dependencies properly.""" + install('libdwarf@20130729 ^libelf@0.8.13') + install('libdwarf@20130207 ^libelf@0.8.10') + + new_spec = spack.spec.Spec('libdwarf@20130729^libelf@0.8.13').concretized() + old_spec = spack.spec.Spec('libdwarf@20130207^libelf@0.8.10').concretized() + + all_installed = spack.store.db.query() + + deprecate('-y', '-d', 'libdwarf@20130207', 'libdwarf@20130729') + + non_deprecated = spack.store.db.query() + all_available = spack.store.db.query(installed=any) + deprecated = spack.store.db.query(installed=InstallStatuses.DEPRECATED) + + assert all_available == all_installed + assert sorted(all_available) == sorted(deprecated + non_deprecated) + + assert sorted(non_deprecated) == sorted(list(new_spec.traverse())) + assert sorted(deprecated) == sorted(list(old_spec.traverse())) + + +def test_deprecate_fails_active_extensions(mock_packages, mock_archive, + mock_fetch, install_mockery): + """Tests that active extensions and their extendees cannot be + deprecated.""" + install('extendee') + install('extension1') + activate('extension1') + + output = deprecate('-yi', 'extendee', 'extendee@nonexistent', + fail_on_error=False) + assert 'extension1' in output + assert "Deactivate extensions before deprecating" in output + + output = deprecate('-yiD', 'extension1', 'extension1@notaversion', + fail_on_error=False) + assert 'extendee' in output + assert 'is an active extension of' in output + + +def test_uninstall_deprecated(mock_packages, mock_archive, mock_fetch, + install_mockery): + """Tests that we can still uninstall deprecated packages.""" + install('libelf@0.8.13') + install('libelf@0.8.10') + + deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.13') + + non_deprecated = spack.store.db.query() + + uninstall('-y', 'libelf@0.8.10') + + assert spack.store.db.query() == spack.store.db.query(installed=any) + assert spack.store.db.query() == non_deprecated + + +def test_deprecate_already_deprecated(mock_packages, mock_archive, mock_fetch, + install_mockery): + """Tests that we can re-deprecate a spec to change its deprecator.""" + install('libelf@0.8.13') + install('libelf@0.8.12') + install('libelf@0.8.10') + + deprecated_spec = spack.spec.Spec('libelf@0.8.10').concretized() + + deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.12') + + deprecator = spack.store.db.deprecator(deprecated_spec) + assert deprecator == spack.spec.Spec('libelf@0.8.12').concretized() + + deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.13') + + non_deprecated = spack.store.db.query() + all_available = spack.store.db.query(installed=any) + assert len(non_deprecated) == 2 + assert len(all_available) == 3 + + deprecator = spack.store.db.deprecator(deprecated_spec) + assert deprecator == spack.spec.Spec('libelf@0.8.13').concretized() + + +def test_deprecate_deprecator(mock_packages, mock_archive, mock_fetch, + install_mockery): + """Tests that when a deprecator spec is deprecated, its deprecatee specs + are updated to point to the new deprecator.""" + install('libelf@0.8.13') + install('libelf@0.8.12') + install('libelf@0.8.10') + + first_deprecated_spec = spack.spec.Spec('libelf@0.8.10').concretized() + second_deprecated_spec = spack.spec.Spec('libelf@0.8.12').concretized() + final_deprecator = spack.spec.Spec('libelf@0.8.13').concretized() + + deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.12') + + deprecator = spack.store.db.deprecator(first_deprecated_spec) + assert deprecator == second_deprecated_spec + + deprecate('-y', 'libelf@0.8.12', 'libelf@0.8.13') + + non_deprecated = spack.store.db.query() + all_available = spack.store.db.query(installed=any) + assert len(non_deprecated) == 1 + assert len(all_available) == 3 + + first_deprecator = spack.store.db.deprecator(first_deprecated_spec) + assert first_deprecator == final_deprecator + second_deprecator = spack.store.db.deprecator(second_deprecated_spec) + assert second_deprecator == final_deprecator + + +def test_concretize_deprecated(mock_packages, mock_archive, mock_fetch, + install_mockery): + """Tests that the concretizer throws an error if we concretize to a + deprecated spec""" + install('libelf@0.8.13') + install('libelf@0.8.10') + + deprecate('-y', 'libelf@0.8.10', 'libelf@0.8.13') + + spec = spack.spec.Spec('libelf@0.8.10') + with pytest.raises(spack.spec.SpecDeprecatedError): + spec.concretize() diff --git a/lib/spack/spack/test/cmd/find.py b/lib/spack/spack/test/cmd/find.py index 55706c264c2..45b065fce99 100644 --- a/lib/spack/spack/test/cmd/find.py +++ b/lib/spack/spack/test/cmd/find.py @@ -50,6 +50,8 @@ def test_query_arguments(): args = Bunch( only_missing=False, missing=False, + only_deprecated=False, + deprecated=False, unknown=False, explicit=False, implicit=False, @@ -61,7 +63,7 @@ def test_query_arguments(): assert 'installed' in q_args assert 'known' in q_args assert 'explicit' in q_args - assert q_args['installed'] is True + assert q_args['installed'] == ['installed'] assert q_args['known'] is any assert q_args['explicit'] is any assert 'start_date' in q_args diff --git a/lib/spack/spack/test/cmd/reindex.py b/lib/spack/spack/test/cmd/reindex.py new file mode 100644 index 00000000000..0ee36b3001d --- /dev/null +++ b/lib/spack/spack/test/cmd/reindex.py @@ -0,0 +1,53 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os +from spack.main import SpackCommand +import spack.store + +install = SpackCommand('install') +deprecate = SpackCommand('deprecate') +reindex = SpackCommand('reindex') + + +def test_reindex_basic(mock_packages, mock_archive, mock_fetch, + install_mockery): + install('libelf@0.8.13') + install('libelf@0.8.12') + + all_installed = spack.store.db.query() + + reindex() + + assert spack.store.db.query() == all_installed + + +def test_reindex_db_deleted(mock_packages, mock_archive, mock_fetch, + install_mockery): + install('libelf@0.8.13') + install('libelf@0.8.12') + + all_installed = spack.store.db.query() + + os.remove(spack.store.db._index_path) + reindex() + + assert spack.store.db.query() == all_installed + + +def test_reindex_with_deprecated_packages(mock_packages, mock_archive, + mock_fetch, install_mockery): + install('libelf@0.8.13') + install('libelf@0.8.12') + + deprecate('-y', 'libelf@0.8.12', 'libelf@0.8.13') + + all_installed = spack.store.db.query(installed=any) + non_deprecated = spack.store.db.query(installed=True) + + os.remove(spack.store.db._index_path) + reindex() + + assert spack.store.db.query(installed=any) == all_installed + assert spack.store.db.query(installed=True) == non_deprecated diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py index 6938b5d0f0b..099894e0d21 100644 --- a/lib/spack/spack/test/database.py +++ b/lib/spack/spack/test/database.py @@ -437,6 +437,16 @@ def test_025_reindex(mutable_database): _check_db_sanity(mutable_database) +def test_026_reindex_after_deprecate(mutable_database): + """Make sure reindex works and ref counts are valid after deprecation.""" + mpich = mutable_database.query_one('mpich') + zmpi = mutable_database.query_one('zmpi') + mutable_database.deprecate(mpich, zmpi) + + spack.store.store.reindex() + _check_db_sanity(mutable_database) + + def test_030_db_sanity_from_another_process(mutable_database): def read_and_modify(): # check that other process can read DB @@ -458,6 +468,15 @@ def test_040_ref_counts(database): database._check_ref_counts() +def test_041_ref_counts_deprecate(mutable_database): + """Ensure that we have appropriate ref counts after deprecating""" + mpich = mutable_database.query_one('mpich') + zmpi = mutable_database.query_one('zmpi') + + mutable_database.deprecate(mpich, zmpi) + mutable_database._check_ref_counts() + + def test_050_basic_query(database): """Ensure querying database is consistent with what is installed.""" # query everything From b29eb4212e8d9077e0c01911c5448a5900210954 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 23 Oct 2019 22:22:24 +0200 Subject: [PATCH 404/499] Users can configure use of RPATH or RUNPATH (#9168) Add a new entry in `config.yaml`: config: shared_linking: 'rpath' If this variable is set to `rpath` (the default) Spack will set RPATH in ELF binaries. If set to `runpath` it will set RUNPATH. Details: * Spack cc wrapper explicitly adds `--disable-new-dtags` when linking * cc wrapper also strips `--enable-new-dtags` from the compile line when disabling (and vice versa) * We specifically do *not* add any dtags flags on macOS, which uses Mach-O binaries, not ELF, so there's no RUNPATH) --- etc/spack/defaults/config.yaml | 5 +++ lib/spack/docs/config_yaml.rst | 21 +++++++++++ lib/spack/env/cc | 34 ++++++++++++++++- lib/spack/spack/build_environment.py | 9 +++++ lib/spack/spack/compiler.py | 18 +++++++++ lib/spack/spack/compilers/nag.py | 4 ++ lib/spack/spack/schema/config.py | 4 ++ lib/spack/spack/test/build_environment.py | 33 ++++++++++++++++ lib/spack/spack/test/cc.py | 46 ++++++++++++++++++++++- 9 files changed, 172 insertions(+), 2 deletions(-) diff --git a/etc/spack/defaults/config.yaml b/etc/spack/defaults/config.yaml index d6c9551d93b..6be1d9770b8 100644 --- a/etc/spack/defaults/config.yaml +++ b/etc/spack/defaults/config.yaml @@ -138,3 +138,8 @@ config: # anticipates that a significant delay indicates that the lock attempt will # never succeed. package_lock_timeout: null + + # Control whether Spack embeds RPATH or RUNPATH attributes in ELF binaries. + # Has no effect on macOS. DO NOT MIX these within the same install tree. + # See the Spack documentation for details. + shared_linking: 'rpath' diff --git a/lib/spack/docs/config_yaml.rst b/lib/spack/docs/config_yaml.rst index 525f829c9ef..d8d07b505af 100644 --- a/lib/spack/docs/config_yaml.rst +++ b/lib/spack/docs/config_yaml.rst @@ -226,3 +226,24 @@ ccache`` to learn more about the default settings and how to change them). Please note that we currently disable ccache's ``hash_dir`` feature to avoid an issue with the stage directory (see https://github.com/LLNL/spack/pull/3761#issuecomment-294352232). + +------------------ +``shared_linking`` +------------------ + +Control whether Spack embeds ``RPATH`` or ``RUNPATH`` attributes in ELF binaries +so that they can find their dependencies. Has no effect on macOS. +Two options are allowed: + + 1. ``rpath`` uses ``RPATH`` and forces the ``--disable-new-tags`` flag to be passed to the linker + 2. ``runpath`` uses ``RUNPATH`` and forces the ``--enable-new-tags`` flag to be passed to the linker + +``RPATH`` search paths have higher precedence than ``LD_LIBRARY_PATH`` +and ld.so will search for libraries in transitive ``RPATHs`` of +parent objects. + +``RUNPATH`` search paths have lower precedence than ``LD_LIBRARY_PATH``, +and ld.so will ONLY search for dependencies in the ``RUNPATH`` of +the loading object. + +DO NOT MIX the two options within the same install tree. diff --git a/lib/spack/env/cc b/lib/spack/env/cc index 8246539a001..2d6fe9998a1 100755 --- a/lib/spack/env/cc +++ b/lib/spack/env/cc @@ -33,6 +33,9 @@ parameters=( SPACK_F77_RPATH_ARG SPACK_FC_RPATH_ARG SPACK_TARGET_ARGS + SPACK_DTAGS_TO_ADD + SPACK_DTAGS_TO_STRIP + SPACK_LINKER_ARG SPACK_SHORT_SPEC SPACK_SYSTEM_DIRS ) @@ -167,6 +170,25 @@ if [[ -z $mode ]]; then done fi +# This is needed to ensure we set RPATH instead of RUNPATH +# (or the opposite, depending on the configuration in config.yaml) +# +# Documentation on this mechanism is lacking at best. A few sources +# of information are (note that some of them take explicitly the +# opposite stance that Spack does): +# +# http://blog.qt.io/blog/2011/10/28/rpath-and-runpath/ +# https://wiki.debian.org/RpathIssue +# +# The only discussion I could find on enabling new dynamic tags by +# default on ld is the following: +# +# https://sourceware.org/ml/binutils/2013-01/msg00307.html +# +dtags_to_add="${SPACK_DTAGS_TO_ADD}" +dtags_to_strip="${SPACK_DTAGS_TO_STRIP}" +linker_arg="${SPACK_LINKER_ARG}" + # Set up rpath variable according to language. eval rpath=\$SPACK_${comp}_RPATH_ARG @@ -293,6 +315,8 @@ while [ -n "$1" ]; do die "-Wl,-rpath was not followed by -Wl,*" fi rp="${arg#-Wl,}" + elif [[ "$arg" = "$dtags_to_strip" ]] ; then + : # We want to remove explicitly this flag else other_args+=("-Wl,$arg") fi @@ -319,12 +343,18 @@ while [ -n "$1" ]; do fi shift 3; rp="$1" + elif [[ "$2" = "$dtags_to_strip" ]] ; then + shift # We want to remove explicitly this flag else other_args+=("$1") fi ;; *) - other_args+=("$1") + if [[ "$1" = "$dtags_to_strip" ]] ; then + : # We want to remove explicitly this flag + else + other_args+=("$1") + fi ;; esac @@ -462,10 +492,12 @@ for dir in "${system_libdirs[@]}"; do args+=("-L$dir"); done # RPATHs arguments case "$mode" in ccld) + if [ ! -z "$dtags_to_add" ] ; then args+=("$linker_arg$dtags_to_add") ; fi for dir in "${rpaths[@]}"; do args+=("$rpath$dir"); done for dir in "${system_rpaths[@]}"; do args+=("$rpath$dir"); done ;; ld) + if [ ! -z "$dtags_to_add" ] ; then args+=("$dtags_to_add") ; fi for dir in "${rpaths[@]}"; do args+=("-rpath" "$dir"); done for dir in "${system_rpaths[@]}"; do args+=("-rpath" "$dir"); done ;; diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index db99a7a4c10..84fc58587ea 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -199,6 +199,15 @@ def set_compiler_environment_variables(pkg, env): env.set('SPACK_CXX_RPATH_ARG', compiler.cxx_rpath_arg) env.set('SPACK_F77_RPATH_ARG', compiler.f77_rpath_arg) env.set('SPACK_FC_RPATH_ARG', compiler.fc_rpath_arg) + env.set('SPACK_LINKER_ARG', compiler.linker_arg) + + # Check whether we want to force RPATH or RUNPATH + if spack.config.get('config:shared_linking') == 'rpath': + env.set('SPACK_DTAGS_TO_STRIP', compiler.enable_new_dtags) + env.set('SPACK_DTAGS_TO_ADD', compiler.disable_new_dtags) + else: + env.set('SPACK_DTAGS_TO_STRIP', compiler.disable_new_dtags) + env.set('SPACK_DTAGS_TO_ADD', compiler.enable_new_dtags) # Set the target parameters that the compiler will add isa_arg = spec.architecture.target.optimization_flags(compiler) diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py index 21521522554..f2b62dc3f90 100644 --- a/lib/spack/spack/compiler.py +++ b/lib/spack/spack/compiler.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os +import platform import re import itertools import shutil @@ -222,6 +223,23 @@ def f77_rpath_arg(self): def fc_rpath_arg(self): return '-Wl,-rpath,' + @property + def linker_arg(self): + """Flag that need to be used to pass an argument to the linker.""" + return '-Wl,' + + @property + def disable_new_dtags(self): + if platform.system() == 'Darwin': + return '' + return '--disable-new-dtags' + + @property + def enable_new_dtags(self): + if platform.system() == 'Darwin': + return '' + return '--enable-new-dtags' + # Cray PrgEnv name that can be used to load this compiler PrgEnv = None # Name of module used to switch versions of this compiler diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py index 5b0a79bcd94..bd0040c9a9f 100644 --- a/lib/spack/spack/compilers/nag.py +++ b/lib/spack/spack/compilers/nag.py @@ -54,3 +54,7 @@ def f77_rpath_arg(self): @property def fc_rpath_arg(self): return '-Wl,-Wl,,-rpath,,' + + @property + def linker_arg(self): + return '-Wl,-Wl,,' diff --git a/lib/spack/spack/schema/config.py b/lib/spack/spack/schema/config.py index 4c49cbca6ad..6eb127a3595 100644 --- a/lib/spack/spack/schema/config.py +++ b/lib/spack/spack/schema/config.py @@ -16,6 +16,10 @@ 'type': 'object', 'default': {}, 'properties': { + 'shared_linking': { + 'type': 'string', + 'enum': ['rpath', 'runpath'] + }, 'install_tree': {'type': 'string'}, 'install_hash_length': {'type': 'integer', 'minimum': 1}, 'install_path_scheme': {'type': 'string'}, diff --git a/lib/spack/spack/test/build_environment.py b/lib/spack/spack/test/build_environment.py index e30e4a7c165..b6a0f4b441d 100644 --- a/lib/spack/spack/test/build_environment.py +++ b/lib/spack/spack/test/build_environment.py @@ -4,9 +4,12 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os +import platform + import pytest import spack.build_environment +import spack.config import spack.spec from spack.paths import build_env_path from spack.build_environment import dso_suffix, _static_to_shared_library @@ -42,6 +45,9 @@ def build_environment(working_env): os.environ['SPACK_CXX_RPATH_ARG'] = "-Wl,-rpath," os.environ['SPACK_F77_RPATH_ARG'] = "-Wl,-rpath," os.environ['SPACK_FC_RPATH_ARG'] = "-Wl,-rpath," + os.environ['SPACK_LINKER_ARG'] = '-Wl,' + os.environ['SPACK_DTAGS_TO_ADD'] = '--disable-new-dtags' + os.environ['SPACK_DTAGS_TO_STRIP'] = '--enable-new-dtags' os.environ['SPACK_SYSTEM_DIRS'] = '/usr/include /usr/lib' os.environ['SPACK_TARGET_ARGS'] = '' @@ -64,9 +70,11 @@ def test_static_to_shared_library(build_environment): expected = { 'linux': ('/bin/mycc -shared' + ' -Wl,--disable-new-dtags' ' -Wl,-soname,{2} -Wl,--whole-archive {0}' ' -Wl,--no-whole-archive -o {1}'), 'darwin': ('/bin/mycc -dynamiclib' + ' -Wl,--disable-new-dtags' ' -install_name {1} -Wl,-force_load,{0} -o {1}') } @@ -304,3 +312,28 @@ class AttributeHolder(object): m = AttributeHolder() spack.build_environment._set_variables_for_single_module(s.package, m) assert m.make_jobs == expected_jobs + + +@pytest.mark.parametrize('config_setting,expected_flag', [ + ('runpath', '' if platform.system() == 'Darwin' else '--enable-new-dtags'), + ('rpath', '' if platform.system() == 'Darwin' else '--disable-new-dtags'), +]) +def test_setting_dtags_based_on_config( + config_setting, expected_flag, config, mock_packages +): + # Pick a random package to be able to set compiler's variables + s = spack.spec.Spec('cmake') + s.concretize() + pkg = s.package + + env = EnvironmentModifications() + with spack.config.override('config:shared_linking', config_setting): + spack.build_environment.set_compiler_environment_variables(pkg, env) + modifications = env.group_by_name() + assert 'SPACK_DTAGS_TO_STRIP' in modifications + assert 'SPACK_DTAGS_TO_ADD' in modifications + assert len(modifications['SPACK_DTAGS_TO_ADD']) == 1 + assert len(modifications['SPACK_DTAGS_TO_STRIP']) == 1 + + dtags_to_add = modifications['SPACK_DTAGS_TO_ADD'][0] + assert dtags_to_add.value == expected_flag diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py index a24f2b7d4e8..e3c962b9d7e 100644 --- a/lib/spack/spack/test/cc.py +++ b/lib/spack/spack/test/cc.py @@ -103,7 +103,10 @@ def wrapper_environment(): SPACK_LINK_DIRS=None, SPACK_INCLUDE_DIRS=None, SPACK_RPATH_DIRS=None, - SPACK_TARGET_ARGS=''): + SPACK_TARGET_ARGS='', + SPACK_LINKER_ARG='-Wl,', + SPACK_DTAGS_TO_ADD='--disable-new-dtags', + SPACK_DTAGS_TO_STRIP='--enable-new-dtags'): yield @@ -180,6 +183,7 @@ def test_ld_flags(wrapper_flags): spack_ldflags + test_include_paths + test_library_paths + + ['--disable-new-dtags'] + test_rpaths + test_args_without_paths + spack_ldlibs) @@ -204,6 +208,7 @@ def test_cc_flags(wrapper_flags): spack_ldflags + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths + spack_ldlibs) @@ -218,6 +223,7 @@ def test_cxx_flags(wrapper_flags): spack_ldflags + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths + spack_ldlibs) @@ -232,6 +238,7 @@ def test_fc_flags(wrapper_flags): spack_ldflags + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths + spack_ldlibs) @@ -244,6 +251,7 @@ def test_dep_rpath(): [real_cc] + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths) @@ -257,6 +265,7 @@ def test_dep_include(): test_include_paths + ['-Ix'] + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths) @@ -271,6 +280,7 @@ def test_dep_lib(): test_include_paths + test_library_paths + ['-Lx'] + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + ['-Wl,-rpath,x'] + test_args_without_paths) @@ -285,6 +295,7 @@ def test_dep_lib_no_rpath(): test_include_paths + test_library_paths + ['-Lx'] + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths) @@ -297,6 +308,7 @@ def test_dep_lib_no_lib(): [real_cc] + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + ['-Wl,-rpath,x'] + test_args_without_paths) @@ -318,6 +330,7 @@ def test_ccld_deps(): ['-Lxlib', '-Lylib', '-Lzlib'] + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + ['-Wl,-rpath,xlib', '-Wl,-rpath,ylib', @@ -368,6 +381,7 @@ def test_ccld_with_system_dirs(): '-Lzlib'] + ['-L/usr/local/lib', '-L/lib64/'] + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + ['-Wl,-rpath,xlib', '-Wl,-rpath,ylib', @@ -389,6 +403,7 @@ def test_ld_deps(): ['-Lxlib', '-Lylib', '-Lzlib'] + + ['--disable-new-dtags'] + test_rpaths + ['-rpath', 'xlib', '-rpath', 'ylib', @@ -408,6 +423,7 @@ def test_ld_deps_no_rpath(): ['-Lxlib', '-Lylib', '-Lzlib'] + + ['--disable-new-dtags'] + test_rpaths + test_args_without_paths) @@ -421,6 +437,7 @@ def test_ld_deps_no_link(): ['ld'] + test_include_paths + test_library_paths + + ['--disable-new-dtags'] + test_rpaths + ['-rpath', 'xlib', '-rpath', 'ylib', @@ -444,6 +461,7 @@ def test_ld_deps_partial(): test_include_paths + test_library_paths + ['-Lxlib'] + + ['--disable-new-dtags'] + test_rpaths + ['-rpath', 'xlib'] + ['-r'] + @@ -459,6 +477,7 @@ def test_ld_deps_partial(): test_include_paths + test_library_paths + ['-Lxlib'] + + ['--disable-new-dtags'] + test_rpaths + ['-r'] + test_args_without_paths) @@ -473,6 +492,7 @@ def test_ccache_prepend_for_cc(): [real_cc] + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths) os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=darwin-x86_64" @@ -483,6 +503,7 @@ def test_ccache_prepend_for_cc(): lheaderpad + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths) @@ -495,6 +516,7 @@ def test_no_ccache_prepend_for_fc(): [real_cc] + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths) os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=darwin-x86_64" @@ -505,5 +527,27 @@ def test_no_ccache_prepend_for_fc(): lheaderpad + test_include_paths + test_library_paths + + ['-Wl,--disable-new-dtags'] + test_wl_rpaths + test_args_without_paths) + + +@pytest.mark.regression('9160') +def test_disable_new_dtags(wrapper_flags): + with set_env(SPACK_TEST_COMMAND='dump-args'): + result = ld(*test_args, output=str).strip().split('\n') + assert '--disable-new-dtags' in result + result = cc(*test_args, output=str).strip().split('\n') + assert '-Wl,--disable-new-dtags' in result + + +@pytest.mark.regression('9160') +def test_filter_enable_new_dtags(wrapper_flags): + with set_env(SPACK_TEST_COMMAND='dump-args'): + result = ld(*(test_args + ['--enable-new-dtags']), output=str) + result = result.strip().split('\n') + assert '--enable-new-dtags' not in result + + result = cc(*(test_args + ['-Wl,--enable-new-dtags']), output=str) + result = result.strip().split('\n') + assert '-Wl,--enable-new-dtags' not in result From 685946b1f1d9195c4916abf547d8aba008dd7207 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Wed, 23 Oct 2019 14:24:14 -0700 Subject: [PATCH 405/499] syaml.dump now allows representing all syaml_ objects (originally this was only available for syaml.dump_config) (#13403) --- lib/spack/spack/util/spack_yaml.py | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py index c4910be8bda..264d5414de7 100644 --- a/lib/spack/spack/util/spack_yaml.py +++ b/lib/spack/spack/util/spack_yaml.py @@ -183,13 +183,6 @@ def represent_str(self, data): return super(OrderedLineDumper, self).represent_str(data) -# Make our special objects look like normal YAML ones. -OrderedLineDumper.add_representer(syaml_dict, OrderedLineDumper.represent_dict) -OrderedLineDumper.add_representer(syaml_list, OrderedLineDumper.represent_list) -OrderedLineDumper.add_representer(syaml_str, OrderedLineDumper.represent_str) -OrderedLineDumper.add_representer(syaml_int, OrderedLineDumper.represent_int) - - class SafeDumper(RoundTripDumper): def ignore_aliases(self, _data): @@ -197,10 +190,12 @@ def ignore_aliases(self, _data): return True -# Allow syaml_dict objects to be represented by ruamel.yaml.dump. With this, -# syaml_dict allows a user to provide an ordered dictionary to yaml.dump when -# the RoundTripDumper is used. +# Make our special objects look like normal YAML ones. RoundTripDumper.add_representer(syaml_dict, RoundTripDumper.represent_dict) +RoundTripDumper.add_representer(syaml_list, RoundTripDumper.represent_list) +RoundTripDumper.add_representer(syaml_int, RoundTripDumper.represent_int) +RoundTripDumper.add_representer(syaml_str, RoundTripDumper.represent_str) +OrderedLineDumper.add_representer(syaml_str, OrderedLineDumper.represent_str) #: Max integer helps avoid passing too large a value to cyaml. From bd7265ed5226078fd13d2fe55164a5e53f3193e3 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 23 Oct 2019 23:49:18 +0200 Subject: [PATCH 406/499] bison: Fix parallel build (#13402) --- .../repos/builtin/packages/bison/package.py | 7 +- .../builtin/packages/bison/parallel.patch | 85 +++++++++++++++++++ 2 files changed, 88 insertions(+), 4 deletions(-) create mode 100644 var/spack/repos/builtin/packages/bison/parallel.patch diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index 7444400d00b..167171c54cf 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -21,6 +21,9 @@ class Bison(AutotoolsPackage): version('3.0.4', sha256='b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e') version('2.7', sha256='19bbe7374fd602f7a6654c131c21a15aebdc06cc89493e8ff250cb7f9ed0a831') + # https://lists.gnu.org/archive/html/bug-bison/2019-08/msg00008.html + patch('parallel.patch', when='@3.4.2') + depends_on('diffutils', type='build') depends_on('m4', type=('build', 'run')) depends_on('perl', type='build') @@ -32,7 +35,3 @@ class Bison(AutotoolsPackage): patch('secure_snprintf.patch', level=0, when='@3.0.4') build_directory = 'spack-build' - - @property - def parallel(self): - return not self.spec.satisfies('@3.4.2') diff --git a/var/spack/repos/builtin/packages/bison/parallel.patch b/var/spack/repos/builtin/packages/bison/parallel.patch new file mode 100644 index 00000000000..7dec92ab19c --- /dev/null +++ b/var/spack/repos/builtin/packages/bison/parallel.patch @@ -0,0 +1,85 @@ +--- a/examples/c/reccalc/local.mk 2019-09-12 09:05:52.000000000 +0200 ++++ b/examples/c/reccalc/local.mk 2019-10-23 21:34:45.754643942 +0200 +@@ -36,16 +36,40 @@ + # additional dependency. + DASH = - + %D%/reccalc$(DASH)parse.o: %D%/scan.h ++# Tell Make scan.o depends on parse.h, except that Make sees only ++# parse.c, not parse.h. We can't use BUILT_SOURCES to this end, since ++# we use the built bison. ++%D%/reccalc$(DASH)scan.o: %D%/parse.c + ++# Likewise, but for Automake before 1.16. ++%D%/examples_c_reccalc_reccalc$(DASH)parse.o: %D%/scan.h ++%D%/examples_c_reccalc_reccalc$(DASH)scan.o: %D%/parse.c ++ ++## See "info automake 'Multiple Outputs'" for this rule. + %D%/scan.c %D%/scan.h: %D%/scan.stamp +- @test -f $@ || rm -f %D%/scan.stamp +- @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) %D%/scan.stamp ++## Recover from the removal of $@ ++ @if test -f $@; then :; else \ ++ trap 'rm -rf %D%/scan.lock %D%/scan.stamp' 1 2 13 15; \ ++## mkdir is a portable test-and-set ++ if mkdir %D%/scan.lock 2>/dev/null; then \ ++## This code is being executed by the first process. ++ rm -f %D%/scan.stamp; \ ++ $(MAKE) $(AM_MAKEFLAGS) %D%/scan.stamp; \ ++ result=$$?; rm -rf %D%/scan.lock; exit $$result; \ ++ else \ ++## This code is being executed by the follower processes. ++## Wait until the first process is done. ++ while test -d %D%/scan.lock; do sleep 1; done; \ ++## Succeed if and only if the first process succeeded. ++ test -f %D%/scan.stamp; \ ++ fi; \ ++ fi + + %D%/scan.stamp: %D%/scan.l + $(AM_V_LEX)rm -f $@ $@.tmp + $(AM_V_at)$(MKDIR_P) %D% + $(AM_V_at)touch $@.tmp +- $(AM_V_at)$(LEX) -o%D%/scan.c --header-file=%D%/scan.h $(srcdir)/%D%/scan.l ++ $(AM_V_at)$(LEX) $(AM_LFLAGS) $(LFLAGS) -o%D%/scan.c --header-file=%D%/scan.h $(srcdir)/%D%/scan.l + $(AM_V_at)mv $@.tmp $@ + + +--- a/Makefile.in 2019-09-12 17:41:48.000000000 +0200 ++++ b/Makefile.in 2019-10-23 21:34:56.899729446 +0200 +@@ -9314,16 +9314,33 @@ + + examples/c/reccalc/parse.c: $(dependencies) + examples/c/reccalc/reccalc$(DASH)parse.o: examples/c/reccalc/scan.h ++# Tell Make scan.o depends on parse.h, except that Make sees only ++# parse.c, not parse.h. We can't use BUILT_SOURCES to this end, since ++# we use the built bison. ++examples/c/reccalc/reccalc$(DASH)scan.o: examples/c/reccalc/parse.c ++ ++# Likewise, but for Automake before 1.16. ++examples/c/reccalc/examples_c_reccalc_reccalc$(DASH)parse.o: examples/c/reccalc/scan.h ++examples/c/reccalc/examples_c_reccalc_reccalc$(DASH)scan.o: examples/c/reccalc/parse.c + + examples/c/reccalc/scan.c examples/c/reccalc/scan.h: examples/c/reccalc/scan.stamp +- @test -f $@ || rm -f examples/c/reccalc/scan.stamp +- @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) examples/c/reccalc/scan.stamp ++ @if test -f $@; then :; else \ ++ trap 'rm -rf examples/c/reccalc/scan.lock examples/c/reccalc/scan.stamp' 1 2 13 15; \ ++ if mkdir examples/c/reccalc/scan.lock 2>/dev/null; then \ ++ rm -f examples/c/reccalc/scan.stamp; \ ++ $(MAKE) $(AM_MAKEFLAGS) examples/c/reccalc/scan.stamp; \ ++ result=$$?; rm -rf examples/c/reccalc/scan.lock; exit $$result; \ ++ else \ ++ while test -d examples/c/reccalc/scan.lock; do sleep 1; done; \ ++ test -f examples/c/reccalc/scan.stamp; \ ++ fi; \ ++ fi + + examples/c/reccalc/scan.stamp: examples/c/reccalc/scan.l + $(AM_V_LEX)rm -f $@ $@.tmp + $(AM_V_at)$(MKDIR_P) examples/c/reccalc + $(AM_V_at)touch $@.tmp +- $(AM_V_at)$(LEX) -oexamples/c/reccalc/scan.c --header-file=examples/c/reccalc/scan.h $(srcdir)/examples/c/reccalc/scan.l ++ $(AM_V_at)$(LEX) $(AM_LFLAGS) $(LFLAGS) -oexamples/c/reccalc/scan.c --header-file=examples/c/reccalc/scan.h $(srcdir)/examples/c/reccalc/scan.l + $(AM_V_at)mv $@.tmp $@ + examples/c/rpcalc/rpcalc.c: $(dependencies) + From f2ddffb8400934d6b2e975d359be22c1997d6863 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Wed, 23 Oct 2019 16:50:51 -0700 Subject: [PATCH 407/499] bugfix: web.push_to_url should not format the local path that is passed to it (#13408) fd58c98 formats the `Stage`'s `archive_path` in `Stage.archive` (as part of `web.push_to_url`). This is not needed and if the formatted differs from the original path (for example if the archive file name contains a URL query suffix), then the copy fails. This removes the formatting that occurs in `web.push_to_url`. We should figure out a way to handle bad cases like this *and* to have nicer filenames for downloaded files. One option that would work in this particular case would be to also pass `-J` / `--remote-header-name` to `curl`. We'll need to do follow-up work to determine if we can use `-J` everywhere. See also: https://github.com/spack/spack/pull/11117#discussion_r338301058 --- lib/spack/spack/util/web.py | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py index e0a23fb444a..abf549cc893 100644 --- a/lib/spack/spack/util/web.py +++ b/lib/spack/spack/util/web.py @@ -203,14 +203,9 @@ def warn_no_ssl_cert_checking(): "your Python to enable certificate verification.") -def push_to_url(local_path, remote_path, **kwargs): +def push_to_url(local_file_path, remote_path, **kwargs): keep_original = kwargs.get('keep_original', True) - local_url = url_util.parse(local_path) - local_file_path = url_util.local_file_path(local_url) - if local_file_path is None: - raise ValueError('local path must be a file:// url') - remote_url = url_util.parse(remote_path) verify_ssl = spack.config.get('config:verify_ssl') From 8c7a3e55dda6a8f6a671805a76f2513f21f9d1cc Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Wed, 23 Oct 2019 19:08:15 -0500 Subject: [PATCH 408/499] add `spack dev-build` command; deprecate `spack diy` (#13374) Rename the `spack diy` command to `spack dev-build` to make the use case clearer. The `spack diy` command has some useful functionality for developers using Spack to build their dependencies and configure/build/install the code they are developing. Developers do not notice it, partly because of the obscure name. The `spack dev-build` command has a `-u/--until PHASE` option to stop after a given phase of the build. This can be used to configure your project, run cmake on your project, or similarly stop after any stage of the build the user wants. These options are analogous to the existing `spack configure` and `spack build` commands, but for developer builds. To unify the syntax, we have deprecated the `spack configure` and `spack build` commands, and added a `-u/--until PHASE` option to the `spack install` command as well. The functionality in `spack dev-build` (specifically `spack dev-build -u cmake`) may be able to supersede the `spack setup` command, but this PR does not deprecate that command as that will require slightly more thought. --- lib/spack/spack/cmd/build.py | 6 +- lib/spack/spack/cmd/configure.py | 5 +- lib/spack/spack/cmd/dev_build.py | 97 +++++++++++++++++++ lib/spack/spack/cmd/diy.py | 89 ++--------------- lib/spack/spack/cmd/install.py | 6 +- lib/spack/spack/test/cmd/dev_build.py | 72 ++++++++++++++ .../dev-build-test-install/package.py | 27 ++++++ 7 files changed, 216 insertions(+), 86 deletions(-) create mode 100644 lib/spack/spack/cmd/dev_build.py create mode 100644 lib/spack/spack/test/cmd/dev_build.py create mode 100644 var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py diff --git a/lib/spack/spack/cmd/build.py b/lib/spack/spack/cmd/build.py index 84d82210902..8687e9a741e 100644 --- a/lib/spack/spack/cmd/build.py +++ b/lib/spack/spack/cmd/build.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import spack.cmd.configure as cfg +import llnl.util.tty as tty from spack.build_systems.autotools import AutotoolsPackage from spack.build_systems.cmake import CMakePackage @@ -15,7 +16,7 @@ from spack.build_systems.meson import MesonPackage from spack.build_systems.sip import SIPPackage -description = 'stops at build stage when installing a package, if possible' +description = 'DEPRECATED: stops at build stage when installing a package' section = "build" level = "long" @@ -38,4 +39,7 @@ def setup_parser(subparser): def build(parser, args): + tty.warn("This command is deprecated. Use `spack install --until` to" + " select an end phase instead. The `spack build` command will be" + " removed in a future version of Spack") cfg._stop_at_phase_during_install(args, build, build_system_to_phase) diff --git a/lib/spack/spack/cmd/configure.py b/lib/spack/spack/cmd/configure.py index b06d4edf1cf..10a1294a413 100644 --- a/lib/spack/spack/cmd/configure.py +++ b/lib/spack/spack/cmd/configure.py @@ -18,7 +18,7 @@ from spack.build_systems.meson import MesonPackage from spack.build_systems.sip import SIPPackage -description = 'stage and configure a package but do not install' +description = 'DEPRECATED: stage and configure a package but do not install' section = "build" level = "long" @@ -82,4 +82,7 @@ def _stop_at_phase_during_install(args, calling_fn, phase_mapping): def configure(parser, args): + tty.warn("This command is deprecated. Use `spack install --until` to" + " select an end phase instead. The `spack configure` command will" + " be removed in a future version of Spack.") _stop_at_phase_during_install(args, configure, build_system_to_phase) diff --git a/lib/spack/spack/cmd/dev_build.py b/lib/spack/spack/cmd/dev_build.py new file mode 100644 index 00000000000..7c92b004ca1 --- /dev/null +++ b/lib/spack/spack/cmd/dev_build.py @@ -0,0 +1,97 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import sys +import os +import argparse + +import llnl.util.tty as tty + +import spack.config +import spack.cmd +import spack.repo +import spack.cmd.common.arguments as arguments +from spack.stage import DIYStage + +description = "developer build: build from code in current working directory" +section = "build" +level = "long" + + +def setup_parser(subparser): + arguments.add_common_arguments(subparser, ['jobs']) + subparser.add_argument( + '-d', '--source-path', dest='source_path', default=None, + help="path to source directory. defaults to the current directory") + subparser.add_argument( + '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps', + help="don't try to install dependencies of requested packages") + arguments.add_common_arguments(subparser, ['no_checksum']) + subparser.add_argument( + '--keep-prefix', action='store_true', + help="do not remove the install prefix if installation fails") + subparser.add_argument( + '--skip-patch', action='store_true', + help="skip patching for the developer build") + subparser.add_argument( + '-q', '--quiet', action='store_true', dest='quiet', + help="do not display verbose build output while installing") + subparser.add_argument( + '-u', '--until', type=str, dest='until', default=None, + help="phase to stop after when installing (default None)") + subparser.add_argument( + 'spec', nargs=argparse.REMAINDER, + help="specs to use for install. must contain package AND version") + + cd_group = subparser.add_mutually_exclusive_group() + arguments.add_common_arguments(cd_group, ['clean', 'dirty']) + + +def dev_build(self, args): + if not args.spec: + tty.die("spack dev-build requires a package spec argument.") + + specs = spack.cmd.parse_specs(args.spec) + if len(specs) > 1: + tty.die("spack dev-build only takes one spec.") + + spec = specs[0] + if not spack.repo.path.exists(spec.name): + tty.die("No package for '{0}' was found.".format(spec.name), + " Use `spack create` to create a new package") + + if not spec.versions.concrete: + tty.die( + "spack dev-build spec must have a single, concrete version. " + "Did you forget a package version number?") + + spec.concretize() + package = spack.repo.get(spec) + + if package.installed: + tty.error("Already installed in %s" % package.prefix) + tty.msg("Uninstall or try adding a version suffix for this dev build.") + sys.exit(1) + + source_path = args.source_path + if source_path is None: + source_path = os.getcwd() + source_path = os.path.abspath(source_path) + + # Forces the build to run out of the current directory. + package.stage = DIYStage(source_path) + + # disable checksumming if requested + if args.no_checksum: + spack.config.set('config:checksum', False, scope='command_line') + + package.do_install( + make_jobs=args.jobs, + keep_prefix=args.keep_prefix, + install_deps=not args.ignore_deps, + verbose=not args.quiet, + keep_stage=True, # don't remove source dir for dev build. + dirty=args.dirty, + stop_at=args.until) diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py index 20e22066573..127a6bbed1a 100644 --- a/lib/spack/spack/cmd/diy.py +++ b/lib/spack/spack/cmd/diy.py @@ -2,96 +2,19 @@ # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - -import sys -import os -import argparse - +import spack.cmd.dev_build import llnl.util.tty as tty -import spack.config -import spack.cmd -import spack.repo -import spack.cmd.common.arguments as arguments -from spack.stage import DIYStage - -description = "do-it-yourself: build from an existing source directory" +description = "DEPRECATED: do-it-yourself: build from local source directory" section = "build" level = "long" def setup_parser(subparser): - arguments.add_common_arguments(subparser, ['jobs']) - subparser.add_argument( - '-d', '--source-path', dest='source_path', default=None, - help="path to source directory. defaults to the current directory") - subparser.add_argument( - '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps', - help="don't try to install dependencies of requested packages") - arguments.add_common_arguments(subparser, ['no_checksum']) - subparser.add_argument( - '--keep-prefix', action='store_true', - help="do not remove the install prefix if installation fails") - subparser.add_argument( - '--skip-patch', action='store_true', - help="skip patching for the DIY build") - subparser.add_argument( - '-q', '--quiet', action='store_true', dest='quiet', - help="do not display verbose build output while installing") - subparser.add_argument( - '-u', '--until', type=str, dest='until', default=None, - help="phase to stop after when installing (default None)") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help="specs to use for install. must contain package AND version") - - cd_group = subparser.add_mutually_exclusive_group() - arguments.add_common_arguments(cd_group, ['clean', 'dirty']) + spack.cmd.dev_build.setup_parser(subparser) def diy(self, args): - if not args.spec: - tty.die("spack diy requires a package spec argument.") - - specs = spack.cmd.parse_specs(args.spec) - if len(specs) > 1: - tty.die("spack diy only takes one spec.") - - spec = specs[0] - if not spack.repo.path.exists(spec.name): - tty.die("No package for '{0}' was found.".format(spec.name), - " Use `spack create` to create a new package") - - if not spec.versions.concrete: - tty.die( - "spack diy spec must have a single, concrete version. " - "Did you forget a package version number?") - - spec.concretize() - package = spack.repo.get(spec) - - if package.installed: - tty.error("Already installed in %s" % package.prefix) - tty.msg("Uninstall or try adding a version suffix for this DIY build.") - sys.exit(1) - - source_path = args.source_path - if source_path is None: - source_path = os.getcwd() - source_path = os.path.abspath(source_path) - - # Forces the build to run out of the current directory. - package.stage = DIYStage(source_path) - - # disable checksumming if requested - if args.no_checksum: - spack.config.set('config:checksum', False, scope='command_line') - - package.do_install( - make_jobs=args.jobs, - keep_prefix=args.keep_prefix, - install_deps=not args.ignore_deps, - verbose=not args.quiet, - keep_stage=True, # don't remove source dir for DIY. - dirty=args.dirty, - stop_at=args.until) + tty.warn("`spack diy` has been renamed to `spack dev-build`." + "The `diy` command will be removed in a future version of Spack") + spack.cmd.dev_build.dev_build(self, args) diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py index 876fb58f512..8fd63beeded 100644 --- a/lib/spack/spack/cmd/install.py +++ b/lib/spack/spack/cmd/install.py @@ -40,7 +40,8 @@ def update_kwargs_from_args(args, kwargs): 'dirty': args.dirty, 'use_cache': args.use_cache, 'cache_only': args.cache_only, - 'explicit': True # Always true for install command + 'explicit': True, # Always true for install command + 'stop_at': args.until }) kwargs.update({ @@ -68,6 +69,9 @@ def setup_parser(subparser): alternatively one can decide to install only the package or only the dependencies""" ) + subparser.add_argument( + '-u', '--until', type=str, dest='until', default=None, + help="phase to stop after when installing (default None)") arguments.add_common_arguments(subparser, ['jobs', 'install_status']) subparser.add_argument( '--overwrite', action='store_true', diff --git a/lib/spack/spack/test/cmd/dev_build.py b/lib/spack/spack/test/cmd/dev_build.py new file mode 100644 index 00000000000..835edac1386 --- /dev/null +++ b/lib/spack/spack/test/cmd/dev_build.py @@ -0,0 +1,72 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os +import spack.spec +from spack.main import SpackCommand + +dev_build = SpackCommand('dev-build') + + +def test_dev_build_basics(tmpdir, mock_packages, install_mockery): + spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized() + + with tmpdir.as_cwd(): + with open(spec.package.filename, 'w') as f: + f.write(spec.package.original_string) + + dev_build('dev-build-test-install@0.0.0') + + assert spec.package.filename in os.listdir(spec.prefix) + with open(os.path.join(spec.prefix, spec.package.filename), 'r') as f: + assert f.read() == spec.package.replacement_string + + +def test_dev_build_until(tmpdir, mock_packages, install_mockery): + spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized() + + with tmpdir.as_cwd(): + with open(spec.package.filename, 'w') as f: + f.write(spec.package.original_string) + + dev_build('-u', 'edit', 'dev-build-test-install@0.0.0') + + assert spec.package.filename in os.listdir(os.getcwd()) + with open(spec.package.filename, 'r') as f: + assert f.read() == spec.package.replacement_string + + assert not os.path.exists(spec.prefix) + + +def test_dev_build_fails_already_installed(tmpdir, mock_packages, + install_mockery): + spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized() + + with tmpdir.as_cwd(): + with open(spec.package.filename, 'w') as f: + f.write(spec.package.original_string) + + dev_build('dev-build-test-install@0.0.0') + output = dev_build('dev-build-test-install@0.0.0', fail_on_error=False) + assert 'Already installed in %s' % spec.prefix in output + + +def test_dev_build_fails_no_spec(): + output = dev_build(fail_on_error=False) + assert 'requires a package spec argument' in output + + +def test_dev_build_fails_multiple_specs(mock_packages): + output = dev_build('libelf', 'libdwarf', fail_on_error=False) + assert 'only takes one spec' in output + + +def test_dev_build_fails_nonexistent_package_name(mock_packages): + output = dev_build('no_such_package', fail_on_error=False) + assert "No package for 'no_such_package' was found" in output + + +def test_dev_build_fails_no_version(mock_packages): + output = dev_build('dev-build-test-install', fail_on_error=False) + assert 'dev-build spec must have a single, concrete version' in output diff --git a/var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py b/var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py new file mode 100644 index 00000000000..0eb96489415 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class DevBuildTestInstall(Package): + homepage = "example.com" + url = "fake.com" + + version('0.0.0', sha256='0123456789abcdefgh') + + phases = ['edit', 'install'] + + filename = 'dev-build-test-file.txt' + original_string = "This file should be edited" + replacement_string = "This file has been edited" + + def edit(self, spec, prefix): + with open(self.filename, 'r+') as f: + assert f.read() == self.original_string + f.seek(0) + f.truncate() + f.write(self.replacement_string) + + def install(self, spec, prefix): + install(self.filename, prefix) From d0d0456fa7e51acd04d4622788a921cc64945793 Mon Sep 17 00:00:00 2001 From: Eric Martin Date: Wed, 23 Oct 2019 23:05:27 -0500 Subject: [PATCH 409/499] vt: add version 0.5772 (#13367) --- var/spack/repos/builtin/packages/vt/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/vt/package.py b/var/spack/repos/builtin/packages/vt/package.py index 99d36b987b3..69dfc2ed6b2 100644 --- a/var/spack/repos/builtin/packages/vt/package.py +++ b/var/spack/repos/builtin/packages/vt/package.py @@ -12,6 +12,7 @@ class Vt(MakefilePackage): homepage = "http://genome.sph.umich.edu/wiki/vt" url = "https://github.com/atks/vt/archive/0.577.tar.gz" + version('0.5772', sha256='b147520478a2f7c536524511e48133d0360e88282c7159821813738ccbda97e7') version('0.577', sha256='009e2592e787ab37e471b4e8a66520141bb2791ca78142ca1767d27036f460d0') depends_on('zlib') From 177f661bb3bde9c6ca2989214069ef27cdc3e8ec Mon Sep 17 00:00:00 2001 From: Cody Balos Date: Wed, 23 Oct 2019 21:06:20 -0700 Subject: [PATCH 410/499] sundials: add version 5.0.0 and new variant (#13375) * sundials: add version 5.0.0 and new variant plus some cleanup * sundiaks: fix formatting * sundials: fix dependencies --- .../builtin/packages/sundials/package.py | 174 +++++++++++------- 1 file changed, 107 insertions(+), 67 deletions(-) diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py index e025c912cba..632bde8634a 100644 --- a/var/spack/repos/builtin/packages/sundials/package.py +++ b/var/spack/repos/builtin/packages/sundials/package.py @@ -14,11 +14,14 @@ class Sundials(CMakePackage): homepage = "https://computing.llnl.gov/projects/sundials" url = "https://computing.llnl.gov/projects/sundials/download/sundials-2.7.0.tar.gz" + git = "https://github.com/llnl/sundials.git" maintainers = ['cswoodward', 'gardner48', 'balos1'] # ========================================================================== # Versions # ========================================================================== + version('develop', branch='develop') + version('5.0.0', sha256='345141ec01c641d0bdfb3476c478b7e74fd6a7192a478a27cafe75d9da2d7dd3') version('4.1.0', sha256='280de1c27b2360170a6f46cb3799b2aee9dff3bddbafc8b08c291a47ab258aa5') version('4.0.1', sha256='29e409c8620e803990edbda1ebf49e03a38c08b9187b90658d86bddae913aed4') version('3.2.1', sha256='47d94d977ab2382cdcdd02f72a25ebd4ba8ca2634bbb2f191fe1636e71c86808') @@ -67,16 +70,18 @@ class Sundials(CMakePackage): description='Enable RAJA parallel vector') # External libraries - variant('lapack', default=False, - description='Enable LAPACK direct solvers') - variant('klu', default=False, - description='Enable KLU sparse, direct solver') - variant('superlu-mt', default=False, - description='Enable SuperLU_MT sparse, direct solver') - variant('hypre', default=False, + variant('hypre', default=False, description='Enable Hypre MPI parallel vector') - variant('petsc', default=False, + variant('lapack', default=False, + description='Enable LAPACK direct solvers') + variant('klu', default=False, + description='Enable KLU sparse, direct solver') + variant('petsc', default=False, description='Enable PETSc MPI parallel vector') + variant('superlu-mt', default=False, + description='Enable SuperLU_MT sparse, direct solver') + variant('superlu-dist', default=False, + description='Enable SuperLU_DIST sparse, direct solver') # Library type variant('shared', default=True, @@ -84,9 +89,11 @@ class Sundials(CMakePackage): variant('static', default=True, description='Build static libraries') - # Fortran interface + # Fortran interfaces variant('fcmix', default=False, - description='Enable Fortran interface') + description='Enable Fortran 77 interface') + variant('f2003', default=False, + description='Enable Fortran 2003 interface') # Examples variant('examples-c', default=True, @@ -97,10 +104,10 @@ class Sundials(CMakePackage): description='Enable Fortran 77 examples') variant('examples-f90', default=False, description='Enable Fortran 90 examples') + variant('examples-f2003', default=False, + description='Enable Fortran 2003 examples') variant('examples-cuda', default=False, description='Enable CUDA examples') - variant('examples-raja', default=False, - description='Enable RAJA examples') variant('examples-install', default=True, description='Install examples') @@ -121,25 +128,24 @@ class Sundials(CMakePackage): conflicts('+raja', when='@:2.7.0') conflicts('~int64', when='@:2.7.0') conflicts('+examples-cuda', when='@:2.7.0') - conflicts('+examples-raja', when='@:2.7.0') + conflicts('+superlu-dist', when='@:4.1.0') + conflicts('+f2003', when='@:4.1.0') # External libraries incompatible with 64-bit indices conflicts('+lapack', when='@3.0.0: +int64') conflicts('+hypre', when='+hypre@:2.6.1a +int64') # External libraries incompatible with single precision - conflicts('+klu', when='precision=single') - conflicts('+hypre', when='+hypre@:2.12.0 precision=single') + conflicts('+klu', when='precision=single') + conflicts('+hypre', when='+hypre@:2.12.0 precision=single') + conflicts('+superlu-dist', when='precision=single') # External libraries incompatible with extended (quad) precision - conflicts('+lapack', when='precision=extended') - conflicts('+superlu-mt', when='precision=extended') - conflicts('+klu', when='precision=extended') - conflicts('+hypre', when='+hypre@:2.12.0 precision=extended') - - # External libraries that need to be built with MPI - conflicts('+hypre', when='~mpi') - conflicts('+petsc', when='~mpi') + conflicts('+lapack', when='precision=extended') + conflicts('+superlu-mt', when='precision=extended') + conflicts('+superlu-dist', when='precision=extended') + conflicts('+klu', when='precision=extended') + conflicts('+hypre', when='+hypre@:2.12.0 precision=extended') # SuperLU_MT interface requires lapack for external blas (before v3.0.0) conflicts('+superlu-mt', when='@:2.7.0 ~lapack') @@ -149,39 +155,35 @@ class Sundials(CMakePackage): # ========================================================================== # Build dependencies - depends_on('cmake@2.8.1:', type='build') - depends_on('cmake@2.8.12:', type='build', when='@3.1.2') - depends_on('cmake@3.0.2:', type='build', when='@4.0.0-dev.1') - depends_on('cmake@3.1.3:', type='build', when='@3.2.0,4.0.0-dev.2') + depends_on('cmake@3.5:', type='build') # MPI related dependencies depends_on('mpi', when='+mpi') depends_on('mpi', when='+hypre') depends_on('mpi', when='+petsc') + depends_on('mpi', when='+superlu-dist') # Other parallelism dependencies depends_on('cuda', when='+cuda') - depends_on('raja', when='+raja') + depends_on('raja +cuda ~openmp', when='+raja') # External libraries - depends_on('blas', when='+lapack') - depends_on('lapack', when='+lapack') - depends_on('suite-sparse', when='+klu') + depends_on('lapack', when='+lapack') + depends_on('suite-sparse', when='+klu') + depends_on('petsc +mpi', when='+petsc') + depends_on('hypre +mpi', when='+hypre') + depends_on('superlu-dist@6.1.1:', when='+superlu-dist') # Require that external libraries built with the same precision depends_on('petsc~double~complex', when='+petsc precision=single') depends_on('petsc+double~complex', when='+petsc precision=double') # Require that external libraries built with the same index type - depends_on('hypre', when='+hypre') depends_on('hypre~int64', when='+hypre ~int64') depends_on('hypre+int64', when='+hypre +int64') - depends_on('petsc', when='+petsc') depends_on('petsc~int64', when='+petsc ~int64') depends_on('petsc+int64', when='+petsc +int64') - - # Require that PETSc is built with MPI - depends_on('petsc+mpi', when='+petsc') + depends_on('superlu-dist+int64', when='+superlu-dist +int64') # Require that SuperLU_MT built with external blas depends_on('superlu-mt+blas', when='+superlu-mt') @@ -231,7 +233,8 @@ def on_off(varstr): args.extend(['-DSUNDIALS_INDEX_TYPE=int32_t']) # Fortran interface - args.extend(['-DFCMIX_ENABLE=%s' % on_off('+fcmix')]) + args.extend(['-DF77_INTERFACE_ENABLE=%s' % on_off('+fcmix')]) + args.extend(['-DF2003_INTERFACE_ENABLE=%s' % on_off('+f2003')]) # library type args.extend([ @@ -263,12 +266,12 @@ def on_off(varstr): if ('+fcmix' in spec) and ('+examples-f90' in spec): args.extend(['-DMPI_MPIF90=%s' % spec['mpi'].mpifc]) - # Building with LAPACK and BLAS - if '+lapack' in spec: + # Building with Hypre + if '+hypre' in spec: args.extend([ - '-DLAPACK_ENABLE=ON', - '-DLAPACK_LIBRARIES=%s' - % (spec['lapack'].libs + spec['blas'].libs).joined(';') + '-DHYPRE_ENABLE=ON', + '-DHYPRE_INCLUDE_DIR=%s' % spec['hypre'].prefix.include, + '-DHYPRE_LIBRARY_DIR=%s' % spec['hypre'].prefix.lib ]) # Building with KLU @@ -279,6 +282,32 @@ def on_off(varstr): '-DKLU_LIBRARY_DIR=%s' % spec['suite-sparse'].prefix.lib ]) + # Building with LAPACK + if '+lapack' in spec: + args.extend([ + '-DLAPACK_ENABLE=ON', + '-DLAPACK_LIBRARIES=%s' + % (spec['lapack'].libs + spec['blas'].libs).joined(';') + ]) + + # Building with PETSc + if '+petsc' in spec: + args.extend([ + '-DPETSC_ENABLE=ON', + # PETSC_DIR was added in 5.0.0 + '-DPETSC_DIR=%s' % spec['petsc'].prefix, + # The following options were removed 5.0.0, but we keep + # them here for versions < 5.0.0. + '-DPETSC_INCLUDE_DIR=%s' % spec['petsc'].prefix.include, + '-DPETSC_LIBRARY_DIR=%s' % spec['petsc'].prefix.lib + ]) + + # Building with RAJA + if '+raja' in spec: + args.extend([ + '-DRAJA_DIR=%s' % spec['raja'].prefix.share.raja.cmake + ]) + # Building with SuperLU_MT if '+superlu-mt' in spec: if spec.satisfies('@3.0.0:'): @@ -298,37 +327,31 @@ def on_off(varstr): else: args.append('-DSUPERLUMT_THREAD_TYPE=Pthread') - # Building with Hypre - if '+hypre' in spec: + # Building with SuperLU_DIST + if '+superlu-dist' in spec: args.extend([ - '-DHYPRE_ENABLE=ON', - '-DHYPRE_INCLUDE_DIR=%s' % spec['hypre'].prefix.include, - '-DHYPRE_LIBRARY_DIR=%s' % spec['hypre'].prefix.lib - ]) - - # Building with PETSc - if '+petsc' in spec: - args.extend([ - '-DPETSC_ENABLE=ON', - '-DPETSC_INCLUDE_DIR=%s' % spec['petsc'].prefix.include, - '-DPETSC_LIBRARY_DIR=%s' % spec['petsc'].prefix.lib - ]) - - # Building with RAJA - if '+raja' in spec: - args.extend([ - '-DRAJA_DIR=%s' % spec['raja'].prefix.share.raja.cmake + '-DSUPERLUDIST_ENABLE=ON', + '-DSUPERLUDIST_INCLUDE_DIR=%s' + % spec['superlu-dist'].prefix.include, + '-DSUPERLUDIST_LIBRARY_DIR=%s' + % spec['superlu-dist'].prefix.lib, + '-DSUPERLUDIST_LIBRARIES=%s' + % spec['blas'].libs, + '-DSUPERLUDIST_OpenMP=%s' + % on_off('^superlu-dist+openmp') ]) # Examples if spec.satisfies('@3.0.0:'): args.extend([ - '-DEXAMPLES_ENABLE_C=%s' % on_off('+examples-c'), - '-DEXAMPLES_ENABLE_CXX=%s' % on_off('+examples-cxx'), - '-DEXAMPLES_ENABLE_F77=%s' % on_off('+examples-f77'), - '-DEXAMPLES_ENABLE_F90=%s' % on_off('+examples-f90'), - '-DEXAMPLES_ENABLE_CUDA=%s' % on_off('+examples-cuda'), - '-DEXAMPLES_ENABLE_RAJA=%s' % on_off('+examples-raja') + '-DEXAMPLES_ENABLE_C=%s' % on_off('+examples-c'), + '-DEXAMPLES_ENABLE_CXX=%s' % on_off('+examples-cxx'), + '-DEXAMPLES_ENABLE_F77=%s' % on_off('+examples-f77'), + '-DEXAMPLES_ENABLE_F90=%s' % on_off('+examples-f90'), + '-DEXAMPLES_ENABLE_F2003=%s' % on_off('+examples-f2003'), + '-DEXAMPLES_ENABLE_CUDA=%s' % on_off('+examples-cuda'), + # option removed in 5.0.0 + '-DEXAMPLES_ENABLE_RAJA=%s' % on_off('+raja') ]) else: args.extend([ @@ -378,10 +401,12 @@ def filter_compilers(self): 'arkode/C_openmp/Makefile', 'arkode/C_parallel/Makefile', 'arkode/C_parhyp/Makefile', + 'arkode/C_petsc/Makefile', 'arkode/C_serial/Makefile', 'cvode/C_openmp/Makefile', 'cvode/parallel/Makefile', 'cvode/parhyp/Makefile', + 'cvode/petsc/Makefile', 'cvode/serial/Makefile', 'cvodes/C_openmp/Makefile', 'cvodes/parallel/Makefile', @@ -418,6 +443,7 @@ def filter_compilers(self): 'sunlinsol/sptfqmr/parallel/Makefile', 'sunlinsol/sptfqmr/serial/Makefile', 'sunlinsol/superlumt/Makefile', + 'sunlinsol/superludist/Makefile', 'sunmatrix/band/Makefile', 'sunmatrix/dense/Makefile', 'sunmatrix/sparse/Makefile' @@ -450,6 +476,15 @@ def filter_compilers(self): 'arkode/F90_serial/Makefile' ] + f2003_files = [ + 'arkode/F2003_serial/Makefile', + 'cvode/F2003_serial/Makefile', + 'cvodes/F2003_serial/Makefike', + 'ida/F2003_serial/Makefile', + 'idas/F2003_serial/Makefile', + 'kinsol/F2003_serial/Makefile' + ] + for filename in cc_files: filter_file(os.environ['CC'], self.compiler.cc, os.path.join(dirname, filename), **kwargs) @@ -476,6 +511,11 @@ def filter_compilers(self): filter_file(os.environ['FC'], self.compiler.fc, os.path.join(dirname, filename), **kwargs) + if ('+f2003' in spec) and ('+examples-f2003' in spec): + for filename in f2003_files: + filter_file(os.environ['FC'], self.compiler.fc, + os.path.join(dirname, filename), **kwargs) + @property def headers(self): """Export the headers and defines of SUNDIALS. From 944ffe44a715898ff15c217c75060d3f4c4a3b54 Mon Sep 17 00:00:00 2001 From: Eric Martin Date: Wed, 23 Oct 2019 23:07:11 -0500 Subject: [PATCH 411/499] subread: add version 2.0.0 (#13368) --- var/spack/repos/builtin/packages/subread/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/subread/package.py b/var/spack/repos/builtin/packages/subread/package.py index f286d03b52e..5124d75d892 100644 --- a/var/spack/repos/builtin/packages/subread/package.py +++ b/var/spack/repos/builtin/packages/subread/package.py @@ -14,6 +14,7 @@ class Subread(MakefilePackage): homepage = "http://subread.sourceforge.net/" url = "https://downloads.sourceforge.net/project/subread/subread-1.5.2/subread-1.5.2-source.tar.gz" + version('2.0.0', sha256='bd7b45f7d8872b0f5db5d23a385059f21d18b49e432bcb6e3e4a879fe51b41a8') version('1.6.4', sha256='b7bd0ee3b0942d791aecce6454d2f3271c95a010beeeff2daf1ff71162e43969') version('1.6.2', sha256='77b4896c1c242967c5883a06c0a5576a5ff220008a12aa60af9669d2f9a87d7a') version('1.6.0', sha256='31251ec4c134e3965d25ca3097890fb37e2c7a4163f6234515534fd325b1002a') From 44485c56b602db48567290c6d0abddfee392e617 Mon Sep 17 00:00:00 2001 From: Eric Martin Date: Wed, 23 Oct 2019 23:16:22 -0500 Subject: [PATCH 412/499] blast-legacy: fix build issues (#13370) --- var/spack/repos/builtin/packages/blast-legacy/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/blast-legacy/package.py b/var/spack/repos/builtin/packages/blast-legacy/package.py index ed4d10e15d5..9bd9d486371 100644 --- a/var/spack/repos/builtin/packages/blast-legacy/package.py +++ b/var/spack/repos/builtin/packages/blast-legacy/package.py @@ -19,9 +19,10 @@ class BlastLegacy(Package): depends_on('tcsh', type='build') def install(self, spec, prefix): - filter_file('/bin/csh -f', '/bin/env tcsh', 'make/ln-if-absent', + filter_file('/bin/csh -f', '/usr/bin/env tcsh', 'make/ln-if-absent', string=True) + symlink(self.stage.source_path, '../ncbi') tcsh = which('tcsh') with working_dir('..'): tcsh('./ncbi/make/makedis.csh') From 845df79ac6ff886fdfae7dc72c3d29fb6a496521 Mon Sep 17 00:00:00 2001 From: Nick Forrington Date: Thu, 24 Oct 2019 10:51:00 -0400 Subject: [PATCH 413/499] Patch libtool when using the Arm compiler (#12004) * Patch libtool when using the arm, clang, and fujitsu compilers If libtool does not have values for linker/pic flags, patch them in --- lib/spack/spack/build_systems/autotools.py | 24 ++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py index eb237bcc4e6..ce0e40b34c2 100644 --- a/lib/spack/spack/build_systems/autotools.py +++ b/lib/spack/spack/build_systems/autotools.py @@ -5,10 +5,12 @@ import inspect +import fileinput import os import os.path import shutil import stat +import sys from subprocess import PIPE from subprocess import check_call @@ -56,6 +58,9 @@ class AutotoolsPackage(PackageBase): build_system_class = 'AutotoolsPackage' #: Whether or not to update ``config.guess`` on old architectures patch_config_guess = True + #: Whether or not to update ``libtool`` + #: (currently only for Arm/Clang/Fujitsu compilers) + patch_libtool = True #: Targets for ``make`` during the :py:meth:`~.AutotoolsPackage.build` #: phase @@ -148,6 +153,25 @@ def _do_patch_config_guess(self): raise RuntimeError('Failed to find suitable config.guess') + @run_after('configure') + def _do_patch_libtool(self): + """If configure generates a "libtool" script that does not correctly + detect the compiler (and patch_libtool is set), patch in the correct + flags for the Arm, Clang/Flang, and Fujitsu compilers.""" + + libtool = os.path.join(self.build_directory, "libtool") + if self.patch_libtool and os.path.exists(libtool): + if self.spec.satisfies('%arm') or self.spec.satisfies('%clang') \ + or self.spec.satisfies('%fj'): + for line in fileinput.input(libtool, inplace=True): + # Replace missing flags with those for Arm/Clang + if line == 'wl=""\n': + line = 'wl="-Wl,"\n' + if line == 'pic_flag=""\n': + line = 'pic_flag="{0}"\n'\ + .format(self.compiler.pic_flag) + sys.stdout.write(line) + @property def configure_directory(self): """Returns the directory where 'configure' resides. From f65f2450df583702b3305ad5fe9ae1d72a7588be Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Thu, 24 Oct 2019 12:43:49 -0500 Subject: [PATCH 414/499] database: update DB version and change to integer database versions (#13410) Update on version format: change to an integer database format version for simplicity, instead of tracking the Spack version. --- lib/spack/spack/database.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 5110e66c7a0..0ada7faa4cb 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -50,7 +50,9 @@ _db_dirname = '.spack-db' # DB version. This is stuck in the DB file to track changes in format. -_db_version = Version('0.9.3') +# Increment by one when the database format changes. +# versions before 5 were not integers +_db_version = Version('5') # Timeout for spack database locks in seconds _db_lock_timeout = 120 From 09133288128a4968bf211b603883dae7a23fac6a Mon Sep 17 00:00:00 2001 From: Chris Green Date: Thu, 24 Oct 2019 12:44:58 -0500 Subject: [PATCH 415/499] Correctly identify Skylake CPUs on Darwin. (#13377) * Correctly identify Skylake CPUs on Darwin. * Add a test for haswell on Mojave. --- lib/spack/llnl/util/cpu/detect.py | 4 ++++ lib/spack/spack/test/data/targets/darwin-mojave-haswell | 5 +++++ .../{darwin-mojave-broadwell => darwin-mojave-skylake} | 0 lib/spack/spack/test/llnl/util/cpu.py | 4 +++- 4 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 lib/spack/spack/test/data/targets/darwin-mojave-haswell rename lib/spack/spack/test/data/targets/{darwin-mojave-broadwell => darwin-mojave-skylake} (100%) diff --git a/lib/spack/llnl/util/cpu/detect.py b/lib/spack/llnl/util/cpu/detect.py index 92b75e9653b..c89f67c852c 100644 --- a/lib/spack/llnl/util/cpu/detect.py +++ b/lib/spack/llnl/util/cpu/detect.py @@ -117,6 +117,10 @@ def sysctl(*args): info['flags'] += ' sse4_2' if 'avx1.0' in info['flags']: info['flags'] += ' avx' + if 'clfsopt' in info['flags']: + info['flags'] += ' clflushopt' + if 'xsave' in info['flags']: + info['flags'] += ' xsavec xsaveopt' return info diff --git a/lib/spack/spack/test/data/targets/darwin-mojave-haswell b/lib/spack/spack/test/data/targets/darwin-mojave-haswell new file mode 100644 index 00000000000..45054c56763 --- /dev/null +++ b/lib/spack/spack/test/data/targets/darwin-mojave-haswell @@ -0,0 +1,5 @@ +machdep.cpu.vendor: GenuineIntel +machdep.cpu.model: 70 +machdep.cpu.brand_string: Intel(R) Core(TM) i7-4980HQ CPU @ 2.80GHz +machdep.cpu.features: FPU VME DE PSE TSC MSR PAE MCE CX8 APIC SEP MTRR PGE MCA CMOV PAT PSE36 CLFSH DS ACPI MMX FXSR SSE SSE2 SS HTT TM PBE SSE3 PCLMULQDQ DTES64 MON DSCPL VMX SMX EST TM2 SSSE3 FMA CX16 TPR PDCM SSE4.1 SSE4.2 x2APIC MOVBE POPCNT AES PCID XSAVE OSXSAVE SEGLIM64 TSCTMR AVX1.0 RDRAND F16C +machdep.cpu.leaf7_features: RDWRFSGS TSC_THREAD_OFFSET BMI1 AVX2 SMEP BMI2 ERMS INVPCID FPU_CSDS MDCLEAR IBRS STIBP L1DF SSBD diff --git a/lib/spack/spack/test/data/targets/darwin-mojave-broadwell b/lib/spack/spack/test/data/targets/darwin-mojave-skylake similarity index 100% rename from lib/spack/spack/test/data/targets/darwin-mojave-broadwell rename to lib/spack/spack/test/data/targets/darwin-mojave-skylake diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 2e03772d193..7e32dda71ad 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -29,7 +29,8 @@ 'linux-rhel6-piledriver', 'linux-centos7-power8le', 'darwin-mojave-ivybridge', - 'darwin-mojave-broadwell', + 'darwin-mojave-haswell', + 'darwin-mojave-skylake', 'bgq-rhel6-power7' ]) def expected_target(request, monkeypatch): @@ -156,6 +157,7 @@ def test_architecture_family(target_name, expected_family): ('skylake', 'sse3'), ('power8', 'altivec'), ('broadwell', 'sse4.1'), + ('skylake', 'clflushopt'), ('aarch64', 'neon') ]) def test_features_query(target_name, feature): From 2dd83523e20c98eea5bec11dab335947af93d7a5 Mon Sep 17 00:00:00 2001 From: Geoffrey Oxberry Date: Thu, 24 Oct 2019 11:08:51 -0700 Subject: [PATCH 416/499] mfem: add version 4.0 (without cuda) (#11880) * mfem: add version 4.0.0 (without cuda, raja, etc) * mfem@4.0.0: add occa variant * mfem@4.0.0: add raja variant * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py --- .../mfem/mfem-4.0.0-makefile-syntax-fix.patch | 27 ++++++++ .../repos/builtin/packages/mfem/package.py | 64 +++++++++++++++++-- 2 files changed, 84 insertions(+), 7 deletions(-) create mode 100644 var/spack/repos/builtin/packages/mfem/mfem-4.0.0-makefile-syntax-fix.patch diff --git a/var/spack/repos/builtin/packages/mfem/mfem-4.0.0-makefile-syntax-fix.patch b/var/spack/repos/builtin/packages/mfem/mfem-4.0.0-makefile-syntax-fix.patch new file mode 100644 index 00000000000..c10b24272cc --- /dev/null +++ b/var/spack/repos/builtin/packages/mfem/mfem-4.0.0-makefile-syntax-fix.patch @@ -0,0 +1,27 @@ +From e2147e51e2bff8907207036557bb9f45d45baaf8 Mon Sep 17 00:00:00 2001 +From: Geoffrey M Oxberry +Date: Sun, 25 Aug 2019 00:30:15 -0700 +Subject: [PATCH] makefile: add missing parenthesis to conditional + +This commit adds a missing parenthesis to a conditional in the MFEM +makefile that checks if PREFIX is set when MFEM_USE_OCCA equals YES. +--- + makefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/makefile b/makefile +index 98a29f3c9..22a9b5bac 100644 +--- a/makefile ++++ b/makefile +@@ -346,7 +346,7 @@ ifneq (,$(filter install,$(MAKECMDGOALS))) + @MFEM_EXT_LIBS@ + MFEM_LIB_FILE = @MFEM_LIB_DIR@/libmfem.$(if $(shared),$(SO_VER),a) + ifeq ($(MFEM_USE_OCCA),YES) +- ifneq ($(MFEM_INSTALL_DIR),$(abspath $(PREFIX)) ++ ifneq ($(MFEM_INSTALL_DIR),$(abspath $(PREFIX))) + $(error OCCA is enabled: PREFIX must be set during configuration!) + endif + endif +-- +2.23.0 + diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index bb27e6927f2..d8ff47d0b45 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -45,13 +45,20 @@ class Mfem(Package): # other version. version('develop', branch='master') + # Tagged development version used by xSDK + version('4.0.1-xsdk', commit='c55c80d17b82d80de04b849dd526e17044f8c99a') + + version('4.0.0', + 'df5bdac798ea84a263979f6fbf79de9013e1c55562f95f98644c3edcacfbc727', + url='https://bit.ly/mfem-4-0', extension='.tar.gz', + preferred=True) + # Tagged development version used by the laghos package: version('3.4.1-laghos-v2.0', tag='laghos-v2.0') version('3.4.0', sha256='4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05', - url='https://bit.ly/mfem-3-4', extension='.tar.gz', - preferred=True) + url='https://bit.ly/mfem-3-4', extension='.tar.gz') version('3.3.2', sha256='b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce', @@ -89,6 +96,9 @@ class Mfem(Package): description='Required for MPI parallelism') variant('openmp', default=False, description='Enable OpenMP parallelism') + variant('occa', default=False, description='Enable OCCA backend') + variant('raja', default=False, description='Enable RAJA backend') + variant('threadsafe', default=False, description=('Enable thread safe features.' ' Required for OpenMP.' @@ -161,12 +171,13 @@ class Mfem(Package): depends_on('metis', when='+metis') depends_on('blas', when='+lapack') - depends_on('lapack', when='+lapack') + depends_on('lapack@3.0:', when='+lapack') depends_on('sundials@2.7.0', when='@:3.3.0+sundials~mpi') depends_on('sundials@2.7.0+mpi+hypre', when='@:3.3.0+sundials+mpi') depends_on('sundials@2.7.0:', when='@3.3.2:+sundials~mpi') depends_on('sundials@2.7.0:+mpi+hypre', when='@3.3.2:+sundials+mpi') + depends_on('sundials@5.0.0', when='@4.0.1-xsdk:+sundials~mpi') depends_on('pumi', when='+pumi') depends_on('suite-sparse', when='+suite-sparse') depends_on('superlu-dist', when='+superlu-dist') @@ -178,23 +189,41 @@ class Mfem(Package): # depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps', # when='+petsc') depends_on('mpfr', when='+mpfr') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf@4.1.3:', when='+netcdf') depends_on('unwind', when='+libunwind') depends_on('zlib', when='+gzstream') depends_on('gnutls', when='+gnutls') depends_on('conduit@0.3.1:,master:', when='+conduit') depends_on('conduit+mpi', when='+conduit+mpi') + # The MFEM 4.0.0 SuperLU interface fails when using hypre@2.16.0 and + # superlu-dist@6.1.1. See https://github.com/mfem/mfem/issues/983. + conflicts('+hypre+superlu-dist', + when='mfem@4.0.0 ^hypre@2.16.0 ^superlu-dist@6.1.1') + + # The OCCA backend is first available in MFEM 4.0.0 + depends_on('occa', when='mfem@4.0.0:+occa') + conflicts('+occa', when='mfem@:3.99.999') + + # The RAJA backend is first available in MFEM 4.0.0 + depends_on('raja', when='mfem@4.0.0:+raja') + conflicts('+raja', when='mfem@:3.99.999') + patch('mfem_ppc_build.patch', when='@3.2:3.3.0 arch=ppc64le') patch('mfem-3.4.patch', when='@3.4.0') patch('mfem-3.3-3.4-petsc-3.9.patch', when='@3.3.0:3.4.0 +petsc ^petsc@3.9.0:') + # Patch to fix MFEM makefile syntax error. See + # https://github.com/mfem/mfem/issues/1042 for the bug report and + # https://github.com/mfem/mfem/pull/1043 for the bugfix contributed + # upstream. + patch('mfem-4.0.0-makefile-syntax-fix.patch', when='@4.0.0') phases = ['configure', 'build', 'install'] - def setup_environment(self, spack_env, run_env): - spack_env.unset('MFEM_DIR') - spack_env.unset('MFEM_BUILD_DIR') + def setup_build_environment(self, env): + env.unset('MFEM_DIR') + env.unset('MFEM_BUILD_DIR') # # Note: Although MFEM does support CMake configuration, MFEM @@ -261,7 +290,14 @@ def find_optional_library(name, prefix): 'MFEM_USE_OPENMP=%s' % yes_no('+openmp'), 'MFEM_USE_CONDUIT=%s' % yes_no('+conduit')] + if spec.satisfies('@4.0.0:'): + options += ['MFEM_USE_OCCA=%s' % yes_no('+occa'), + 'MFEM_USE_RAJA=%s' % yes_no('+raja')] + cxxflags = spec.compiler_flags['cxxflags'] + if self.spec.satisfies('@4.0:'): + cxxflags.append(self.compiler.cxx11_flag) + if cxxflags: # The cxxflags are set by the spack c++ compiler wrapper. We also # set CXXFLAGS explicitly, for clarity, and to properly export the @@ -371,6 +407,20 @@ def find_optional_library(name, prefix): if '+openmp' in spec: options += ['OPENMP_OPT=%s' % self.compiler.openmp_flag] + if '+occa' in spec: + options += ['OCCA_DIR=%s' % spec['occa'].prefix, + 'OCCA_OPT=-I%s' % spec['occa'].prefix.include, + 'OCCA_LIB=%s' % + ld_flags_from_dirs([spec['occa'].prefix.lib], + ['occa'])] + + if '+raja' in spec: + options += ['RAJA_DIR=%s' % spec['raja'].prefix, + 'RAJA_OPT=-I%s' % spec['raja'].prefix.include, + 'RAJA_LIB=%s' % + ld_flags_from_dirs([spec['raja'].prefix.lib], + ['RAJA'])] + timer_ids = {'std': '0', 'posix': '2', 'mac': '4', 'mpi': '6'} timer = spec.variants['timer'].value if timer != 'auto': From 5004b20f5cf427f47ae5a0c21445c4d421d7744f Mon Sep 17 00:00:00 2001 From: Jannek Squar Date: Thu, 24 Oct 2019 20:30:21 +0200 Subject: [PATCH 417/499] New package: py-cdsapi (#13363) * New package py-cdsapi to access Climate Data Store for downloading climate and weather reanalysis data * Improvements --- .../builtin/packages/py-cdsapi/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-cdsapi/package.py diff --git a/var/spack/repos/builtin/packages/py-cdsapi/package.py b/var/spack/repos/builtin/packages/py-cdsapi/package.py new file mode 100644 index 00000000000..aa0d412de52 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cdsapi/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCdsapi(PythonPackage): + """The Climate Data Store Application Program Interface is a service providing programmatic access to CDS data. Get your UID and API key from the CDS portal at the address https://cds.climate.copernicus.eu/user and write it into the configuration file. Look at https://pypi.org/project/cdsapi/ for an example""" + + homepage = "https://cds.climate.copernicus.eu" + url = "https://pypi.io/packages/source/c/cdsapi/cdsapi-0.2.3.tar.gz" + + version('0.2.3', sha256='333b31ec263224399635db9b21a2e1a50cd73451f5179f8d967437e7c9161d9b') + + depends_on('py-setuptools', type='build') + depends_on('py-requests@2.5.0:', type=('build', 'run')) + depends_on('py-tqdm', type=('build', 'run')) From 83016e96fdfaef34ee653e7f8c0fb6929aa70e89 Mon Sep 17 00:00:00 2001 From: Mikael Simberg Date: Thu, 24 Oct 2019 22:19:25 +0200 Subject: [PATCH 418/499] Extend HPX package (#13219) * Add master branch as version to HPX package * Remove C++98 option from HPX package * Add option to turn off examples in HPX package * Add MPI variant to HPX package --- .../repos/builtin/packages/hpx/package.py | 30 +++++++++++++++---- 1 file changed, 24 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/hpx/package.py b/var/spack/repos/builtin/packages/hpx/package.py index e5f6cf75cf4..6863689f231 100644 --- a/var/spack/repos/builtin/packages/hpx/package.py +++ b/var/spack/repos/builtin/packages/hpx/package.py @@ -13,6 +13,7 @@ class Hpx(CMakePackage, CudaPackage): homepage = "http://stellar.cct.lsu.edu/tag/hpx/" url = "https://github.com/STEllAR-GROUP/hpx/archive/1.2.1.tar.gz" + version('master', git='https://github.com/STEllAR-GROUP/hpx.git', branch='master') version('1.3.0', sha256='cd34da674064c4cc4a331402edbd65c5a1f8058fb46003314ca18fa08423c5ad') version('1.2.1', sha256='8cba9b48e919035176d3b7bbfc2c110df6f07803256626f1dad8d9dde16ab77a') version('1.2.0', sha256='20942314bd90064d9775f63b0e58a8ea146af5260a4c84d0854f9f968077c170') @@ -20,7 +21,7 @@ class Hpx(CMakePackage, CudaPackage): variant('cxxstd', default='17', - values=('98', '11', '14', '17'), + values=('11', '14', '17'), description='Use the specified C++ standard when building.') variant( @@ -33,9 +34,14 @@ class Hpx(CMakePackage, CudaPackage): 'apex', 'google_perftools', 'papi', 'valgrind' ), description='Add support for various kind of instrumentation') - variant('networking', default=True, - description='Support for networking and multi=node runs') + variant( + "networking", + values=any_combination_of("tcp", "mpi").with_default("tcp"), + description="Support for networking through parcelports", + ) + variant('tools', default=False, description='Build HPX tools') + variant('examples', default=False, description='Build examples') depends_on('boost') depends_on('hwloc') @@ -53,7 +59,6 @@ class Hpx(CMakePackage, CudaPackage): depends_on('hwloc@1.6:', when='@:1.1.0') # CXX Standard - depends_on('boost cxxstd=98', when='cxxstd=98') depends_on('boost cxxstd=11', when='cxxstd=11') depends_on('boost cxxstd=14', when='cxxstd=14') depends_on('boost cxxstd=17', when='cxxstd=17') @@ -63,6 +68,9 @@ class Hpx(CMakePackage, CudaPackage): depends_on('jemalloc', when='malloc=jemalloc') depends_on('tbb', when='malloc=tbbmalloc') + # MPI + depends_on('mpi', when='networking=mpi') + # Instrumentation depends_on('apex', when='instrumentation=apex') depends_on('gperftools', when='instrumentation=google_perftools') @@ -76,7 +84,6 @@ class Hpx(CMakePackage, CudaPackage): def cxx_standard(self): value = self.spec.variants['cxxstd'].value - value = '0X' if value == '98' else value return '-DHPX_WITH_CXX{0}=ON'.format(value) def instrumentation_args(self): @@ -104,7 +111,13 @@ def cmake_args(self): # Networking args.append('-DHPX_WITH_NETWORKING={0}'.format( - 'ON' if '+networking' in spec else 'OFF' + 'OFF' if 'networking=none' in spec else 'ON' + )) + args.append('-DHPX_WITH_PARCELPORT_TCP={0}'.format( + 'ON' if 'networking=tcp' in spec else 'OFF' + )) + args.append('-DHPX_WITH_PARCELPORT_MPI={0}'.format( + 'ON' if 'networking=mpi' in spec else 'OFF' )) # Cuda support @@ -117,6 +130,11 @@ def cmake_args(self): 'ON' if '+tools' in spec else 'OFF' )) + # Examples + args.append('-DHPX_WITH_EXAMPLES={0}'.format( + 'ON' if '+examples' in spec else 'OFF' + )) + args.extend([ '-DBOOST_ROOT={0}'.format(spec['boost'].prefix), '-DHWLOC_ROOT={0}'.format(spec['hwloc'].prefix), From 0f22e528f37525ed42e7eb9d4369879956677fef Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 24 Oct 2019 15:21:13 -0500 Subject: [PATCH 419/499] Add latest version of NetCDF libraries (#13416) --- var/spack/repos/builtin/packages/netcdf-cxx4/package.py | 5 +++-- var/spack/repos/builtin/packages/netcdf-fortran/package.py | 5 +++-- var/spack/repos/builtin/packages/netcdf/package.py | 4 +++- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index 6788f7dae1d..938d74d6aa5 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -9,9 +9,10 @@ class NetcdfCxx4(AutotoolsPackage): """C++ interface for NetCDF4""" - homepage = "http://www.unidata.ucar.edu/software/netcdf" - url = "https://www.github.com/unidata/netcdf-cxx4/tarball/v4.3.0" + homepage = "https://www.unidata.ucar.edu/software/netcdf" + url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.3.1.tar.gz" + version('4.3.1', sha256='6a1189a181eed043b5859e15d5c080c30d0e107406fbb212c8fb9814e90f3445') version('4.3.0', sha256='f4766d5a19c91093be80ddd2eaf1fbbd8d203854cc69fc73d2ad293b099ac799') # Usually the configure automatically inserts the pic flags, but we can diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py index ddfa2295f8e..d698ff1e8bb 100644 --- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -9,9 +9,10 @@ class NetcdfFortran(AutotoolsPackage): """Fortran interface for NetCDF4""" - homepage = "http://www.unidata.ucar.edu/software/netcdf" - url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz" + homepage = "https://www.unidata.ucar.edu/software/netcdf" + url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.2.tar.gz" + version('4.5.2', sha256='b959937d7d9045184e9d2040a915d94a7f4d0185f4a9dceb8f08c94b0c3304aa') version('4.4.5', sha256='2467536ce29daea348c736476aa8e684c075d2f6cab12f3361885cb6905717b8') version('4.4.4', sha256='b2d395175f8d283e68c8be516e231a96b191ade67ad0caafaf7fa01b1e6b5d75') version('4.4.3', sha256='330373aa163d5931e475b5e83da5c1ad041e855185f24e6a8b85d73b48d6cda9') diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index 09bdbbd17f2..46a5695c582 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -23,7 +23,7 @@ class Netcdf(AutotoolsPackage): homepage = "http://www.unidata.ucar.edu/software/netcdf" git = "https://github.com/Unidata/netcdf-c" - url = "https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.6.3.tar.gz" + url = "https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.2.tar.gz" def url_for_version(self, version): if version >= Version('4.6.2'): @@ -34,6 +34,8 @@ def url_for_version(self, version): return url.format(version.dotted) version('master', branch='master') + version('4.7.2', sha256='b751cc1f314ac8357df2e0a1bacf35a624df26fe90981d3ad3fa85a5bbd8989a') + version('4.7.1', sha256='5c537c585773e575a16b28c3973b9608a98fdc4cf7c42893aa5223024e0001fc') version('4.7.0', sha256='a512d2b4828c6177dd4b96791c4163e4e06e6bfc7123bebfbfe01762d777d1cb') version('4.6.3', sha256='335fdf16d7531f430ad75e732ed1a9a3fc83ad3ef91fb33a70119a555dd5415c') version('4.6.2', sha256='c37525981167b3cd82d32e1afa3022afb94e59287db5f116c57f5ed4d9c6a638') From a6ea0bbbaea533bc024fcc326fece709fe5b24a6 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Thu, 24 Oct 2019 16:27:21 -0500 Subject: [PATCH 420/499] Views: fix python in views when python prefix is under a symlink (#12575) * Fix python in views when python prefix is under a symlink * Add todo for future generalization --- var/spack/repos/builtin/packages/python/package.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 6087ff5be8d..15901872e9d 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -870,7 +870,18 @@ def add_files_to_view(self, view, merge_map): backup=False ) else: - orig_link_target = os.path.realpath(src) + # orig_link_target = os.path.realpath(src) is insufficient when + # the spack install tree is located at a symlink or a + # descendent of a symlink. What we need here is the real + # relative path from the python prefix to src + # TODO: generalize this logic in the link_tree object + # add a method to resolve a link relative to the link_tree + # object root. + realpath_src = os.path.realpath(src) + realpath_prefix = os.path.realpath(self.spec.prefix) + realpath_rel = os.path.relpath(realpath_src, realpath_prefix) + orig_link_target = os.path.join(self.spec.prefix, realpath_rel) + new_link_target = os.path.abspath(merge_map[orig_link_target]) view.link(new_link_target, dst) From 77af4684aa2986ae3860962d7007b790e0a97f50 Mon Sep 17 00:00:00 2001 From: Chris Green Date: Thu, 24 Oct 2019 17:48:54 -0500 Subject: [PATCH 421/499] Improvements to detection of AMD architectures. (#13407) New entry for K10 microarchitecture. Reorder Zen* microarchitectures to avoid triggering as k10. Remove some desktop-specific flags that were preventing Opteron Bulldozer/Piledriver/Steamroller/Excavator CPUs from being recognized as such. Remove one or two flags which weren't produced in /proc/cpuinfo on older OS (RHEL6 and friends). --- .../llnl/util/cpu/microarchitectures.json | 40 +++++++++++++++++-- .../test/data/targets/linux-scientific7-k10 | 26 ++++++++++++ .../data/targets/linux-scientific7-piledriver | 26 ++++++++++++ .../targets/linux-scientificfermi6-bulldozer | 25 ++++++++++++ .../targets/linux-scientificfermi6-piledriver | 25 ++++++++++++ lib/spack/spack/test/llnl/util/cpu.py | 4 ++ 6 files changed, 142 insertions(+), 4 deletions(-) create mode 100644 lib/spack/spack/test/data/targets/linux-scientific7-k10 create mode 100644 lib/spack/spack/test/data/targets/linux-scientific7-piledriver create mode 100644 lib/spack/spack/test/data/targets/linux-scientificfermi6-bulldozer create mode 100644 lib/spack/spack/test/data/targets/linux-scientificfermi6-piledriver diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 6873fc9676a..23cff4bf9af 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -694,6 +694,38 @@ } } }, + "k10": { + "from": "x86_64", + "vendor": "AuthenticAMD", + "features": [ + "mmx", + "sse", + "sse2", + "sse4a", + "abm", + "cx16", + "3dnow", + "3dnowext" + ], + "compilers": { + "gcc": { + "name": "amdfam10", + "versions": "4.3:", + "flags": "-march={name} -mtune={name}" + }, + "clang": { + "versions": "3.9:", + "name": "amdfam10", + "family": "x86-64", + "flags": "-march={family} -mcpu={name}" + }, + "intel": { + "versions": "16.0:", + "warnings": "Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors", + "flags": "-msse2" + } + } + }, "bulldozer": { "from": "x86_64", "vendor": "AuthenticAMD", @@ -705,7 +737,7 @@ "abm", "avx", "xop", - "lwp", + "fma4", "aes", "pclmulqdq", "cx16", @@ -743,7 +775,7 @@ "abm", "avx", "xop", - "lwp", + "fma4", "aes", "pclmulqdq", "cx16", @@ -785,7 +817,7 @@ "abm", "avx", "xop", - "lwp", + "fma4", "aes", "pclmulqdq", "cx16", @@ -828,7 +860,7 @@ "abm", "avx", "xop", - "lwp", + "fma4", "aes", "pclmulqdq", "cx16", diff --git a/lib/spack/spack/test/data/targets/linux-scientific7-k10 b/lib/spack/spack/test/data/targets/linux-scientific7-k10 new file mode 100644 index 00000000000..1522b17480e --- /dev/null +++ b/lib/spack/spack/test/data/targets/linux-scientific7-k10 @@ -0,0 +1,26 @@ +processor : 0 +vendor_id : AuthenticAMD +cpu family : 16 +model : 9 +model name : AMD Opteron(tm) Processor 6136 +stepping : 1 +microcode : 0x10000d9 +cpu MHz : 800.000 +cache size : 512 KB +physical id : 0 +siblings : 8 +core id : 0 +cpu cores : 8 +apicid : 16 +initial apicid : 0 +fpu : yes +fpu_exception : yes +cpuid level : 5 +wp : yes +flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc art rep_good nopl nonstop_tsc extd_apicid amd_dcm pni monitor cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt nodeid_msr hw_pstate retpoline_amd ibp_disable vmmcall npt lbrv svm_lock nrip_save pausefilter +bogomips : 4800.19 +TLB size : 1024 4K pages +clflush size : 64 +cache_alignment : 64 +address sizes : 48 bits physical, 48 bits virtual +power management: ts ttp tm stc 100mhzsteps hwpstate diff --git a/lib/spack/spack/test/data/targets/linux-scientific7-piledriver b/lib/spack/spack/test/data/targets/linux-scientific7-piledriver new file mode 100644 index 00000000000..4c823f6e46b --- /dev/null +++ b/lib/spack/spack/test/data/targets/linux-scientific7-piledriver @@ -0,0 +1,26 @@ +processor : 0 +vendor_id : AuthenticAMD +cpu family : 21 +model : 2 +model name : AMD Opteron(tm) Processor 6320 +stepping : 0 +microcode : 0x6000852 +cpu MHz : 1400.000 +cache size : 2048 KB +physical id : 0 +siblings : 8 +core id : 0 +cpu cores : 4 +apicid : 32 +initial apicid : 0 +fpu : yes +fpu_exception : yes +cpuid level : 13 +wp : yes +flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc art rep_good nopl nonstop_tsc extd_apicid amd_dcm aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 popcnt aes xsave avx f16c lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs xop skinit wdt fma4 tce nodeid_msr tbm topoext perfctr_core perfctr_nb cpb hw_pstate retpoline_amd ssbd ibpb vmmcall bmi1 arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold +bogomips : 5600.11 +TLB size : 1536 4K pages +clflush size : 64 +cache_alignment : 64 +address sizes : 48 bits physical, 48 bits virtual +power management: ts ttp tm 100mhzsteps hwpstate cpb eff_freq_ro diff --git a/lib/spack/spack/test/data/targets/linux-scientificfermi6-bulldozer b/lib/spack/spack/test/data/targets/linux-scientificfermi6-bulldozer new file mode 100644 index 00000000000..c240cfc6ce9 --- /dev/null +++ b/lib/spack/spack/test/data/targets/linux-scientificfermi6-bulldozer @@ -0,0 +1,25 @@ +processor : 0 +vendor_id : AuthenticAMD +cpu family : 21 +model : 1 +model name : AMD Opteron(TM) Processor 6212 +stepping : 2 +cpu MHz : 2600.188 +cache size : 2048 KB +physical id : 0 +siblings : 8 +core id : 0 +cpu cores : 4 +apicid : 32 +initial apicid : 0 +fpu : yes +fpu_exception : yes +cpuid level : 13 +wp : yes +flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nonstop_tsc extd_apicid amd_dcm aperfmperf pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 popcnt aes xsave avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 nodeid_msr topoext perfctr_core perfctr_nb cpb ssbd retpoline ibpb npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold +bogomips : 5200.37 +TLB size : 1536 4K pages +clflush size : 64 +cache_alignment : 64 +address sizes : 48 bits physical, 48 bits virtual +power management: ts ttp tm 100mhzsteps hwpstate cpb diff --git a/lib/spack/spack/test/data/targets/linux-scientificfermi6-piledriver b/lib/spack/spack/test/data/targets/linux-scientificfermi6-piledriver new file mode 100644 index 00000000000..a87afeee612 --- /dev/null +++ b/lib/spack/spack/test/data/targets/linux-scientificfermi6-piledriver @@ -0,0 +1,25 @@ +processor : 31 +vendor_id : AuthenticAMD +cpu family : 21 +model : 2 +model name : AMD Opteron(tm) Processor 6320 +stepping : 0 +cpu MHz : 2800.154 +cache size : 2048 KB +physical id : 3 +siblings : 8 +core id : 3 +cpu cores : 4 +apicid : 135 +initial apicid : 103 +fpu : yes +fpu_exception : yes +cpuid level : 13 +wp : yes +flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nonstop_tsc extd_apicid amd_dcm aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 popcnt aes xsave avx f16c lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 tce nodeid_msr tbm topoext perfctr_core perfctr_nb cpb ssbd retpoline ibpb npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold bmi1 +bogomips : 5599.22 +TLB size : 1536 4K pages +clflush size : 64 +cache_alignment : 64 +address sizes : 48 bits physical, 48 bits virtual +power management: ts ttp tm 100mhzsteps hwpstate cpb eff_freq_ro diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index 7e32dda71ad..f75c02f4b09 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -26,6 +26,10 @@ 'linux-rhel7-ivybridge', 'linux-rhel7-haswell', 'linux-rhel7-zen', + 'linux-scientific7-k10', + 'linux-scientificfermi6-bulldozer', + 'linux-scientificfermi6-piledriver', + 'linux-scientific7-piledriver', 'linux-rhel6-piledriver', 'linux-centos7-power8le', 'darwin-mojave-ivybridge', From 757387dc2a43a0add5a6d49ccc8bbc6a73352720 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Thu, 24 Oct 2019 16:01:31 -0700 Subject: [PATCH 422/499] commands: Add `--json` argument to `spack spec` (#13431) We've had `spack spec --yaml` for a while, and we've had methods for JSON for a while as well. We just haven't has a `--json` argument for `spack spec`. - [x] Add a `--json` argument to `spack spec`, just like `--yaml` --- lib/spack/spack/cmd/spec.py | 16 +++++++++++----- lib/spack/spack/test/cmd/spec.py | 12 ++++++++++++ 2 files changed, 23 insertions(+), 5 deletions(-) diff --git a/lib/spack/spack/cmd/spec.py b/lib/spack/spack/cmd/spec.py index f1a2a081190..f63ac638c4d 100644 --- a/lib/spack/spack/cmd/spec.py +++ b/lib/spack/spack/cmd/spec.py @@ -25,8 +25,11 @@ def setup_parser(subparser): arguments.add_common_arguments( subparser, ['long', 'very_long', 'install_status']) subparser.add_argument( - '-y', '--yaml', action='store_true', default=False, - help='print concrete spec as YAML') + '-y', '--yaml', action='store_const', dest='format', default=None, + const='yaml', help='print concrete spec as YAML') + subparser.add_argument( + '-j', '--json', action='store_const', dest='format', default=None, + const='json', help='print concrete spec as YAML') subparser.add_argument( '-c', '--cover', action='store', default='nodes', choices=['nodes', 'edges', 'paths'], @@ -59,12 +62,15 @@ def spec(parser, args): for spec in spack.cmd.parse_specs(args.specs): # With -y, just print YAML to output. - if args.yaml: + if args.format: if spec.name in spack.repo.path or spec.virtual: spec.concretize() - # use write because to_yaml already has a newline. - sys.stdout.write(spec.to_yaml(hash=ht.build_hash)) + if args.format == 'yaml': + # use write because to_yaml already has a newline. + sys.stdout.write(spec.to_yaml(hash=ht.build_hash)) + else: + print(spec.to_json(hash=ht.build_hash)) continue kwargs['hashes'] = False # Always False for input spec diff --git a/lib/spack/spack/test/cmd/spec.py b/lib/spack/spack/test/cmd/spec.py index 3038f4d9e44..4637e14a1f8 100644 --- a/lib/spack/spack/test/cmd/spec.py +++ b/lib/spack/spack/test/cmd/spec.py @@ -37,6 +37,18 @@ def test_spec_yaml(): assert 'mpich' in mpileaks +def test_spec_json(): + output = spec('--json', 'mpileaks') + + mpileaks = spack.spec.Spec.from_json(output) + assert 'mpileaks' in mpileaks + assert 'callpath' in mpileaks + assert 'dyninst' in mpileaks + assert 'libdwarf' in mpileaks + assert 'libelf' in mpileaks + assert 'mpich' in mpileaks + + def _parse_types(string): """Parse deptypes for specs from `spack spec -t` output.""" lines = string.strip().split('\n') From dbee91f7f1616113e21ebc5e186f0f66bfc21a9c Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Thu, 24 Oct 2019 16:02:28 -0700 Subject: [PATCH 423/499] bugfix: allow fetching no-code packages (#13429) Previously, spack would error out if we tried to fetch something with no code, but that would prevent fetching dependencies. In particular, this would fail: spack fetch --dependencies xsdk - [x] Instead of raising an error, just print a message that there is nothing to be fetched for packages like xsdk that do not have code. - [x] Make BundleFetchStrategy a bit more quiet about doing nothing. --- lib/spack/spack/fetch_strategy.py | 18 +++--------------- lib/spack/spack/package.py | 4 +++- lib/spack/spack/test/install.py | 12 ++++++------ 3 files changed, 12 insertions(+), 22 deletions(-) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 48122118127..8105402f99b 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -201,28 +201,16 @@ class BundleFetchStrategy(FetchStrategy): url_attr = '' def fetch(self): - tty.msg("No code to fetch.") + """Simply report success -- there is no code to fetch.""" return True - def check(self): - tty.msg("No code to check.") - - def expand(self): - tty.msg("No archive to expand.") - - def reset(self): - tty.msg("No code to reset.") - - def archive(self, destination): - tty.msg("No code to archive.") - @property def cachable(self): - tty.msg("No code to cache.") + """Report False as there is no code to cache.""" return False def source_id(self): - tty.msg("No code to be uniquely identified.") + """BundlePackages don't have a source id.""" return '' diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index b49c8c1a231..8a65d7b7335 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1046,7 +1046,9 @@ def do_fetch(self, mirror_only=False): raise ValueError("Can only fetch concrete packages.") if not self.has_code: - raise InvalidPackageOpError("Can only fetch a package with a URL.") + tty.msg( + "No fetch required for %s: package has no code." % self.name + ) start_time = time.time() checksum = spack.config.get('config:checksum') diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index e0a83f20b2d..571e9fcd584 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -9,8 +9,7 @@ from llnl.util.filesystem import mkdirp, touch, working_dir -from spack.package import \ - InstallError, InvalidPackageOpError, PackageBase, PackageStillNeededError +from spack.package import InstallError, PackageBase, PackageStillNeededError import spack.patch import spack.repo import spack.store @@ -327,7 +326,9 @@ def test_uninstall_by_spec_errors(mutable_database): PackageBase.uninstall_by_spec(rec.spec) -def test_nosource_pkg_install(install_mockery, mock_fetch, mock_packages): +@pytest.mark.disable_clean_stage_check +def test_nosource_pkg_install( + install_mockery, mock_fetch, mock_packages, capfd): """Test install phases with the nosource package.""" spec = Spec('nosource').concretized() pkg = spec.package @@ -336,9 +337,8 @@ def test_nosource_pkg_install(install_mockery, mock_fetch, mock_packages): pkg.do_install() # Also make sure an error is raised if `do_fetch` is called. - with pytest.raises(InvalidPackageOpError, - match="fetch a package with a URL"): - pkg.do_fetch() + pkg.do_fetch() + assert "No fetch required for nosource" in capfd.readouterr()[0] def test_nosource_pkg_install_post_install( From ebeb1ed62f8ac2a765213d872811eac7bac101c1 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 25 Oct 2019 07:10:03 -0700 Subject: [PATCH 424/499] bugfix: reindexing is not necessary for DB v0.9.3 to v5 upgrade (#13434) reindexing takes a significant amount of time, and there's no reason to do it from DB version 0.9.3 to version 5. The only difference is that v5 can contain "deprecated_for" fields. - [x] Add a `_skip_reindex` list at the start of `database.py` - [x] Skip the reindex for upgrades in this list. The new version will just be written to the file the first time we actually have to write the DB out (e.g., after an install), and reads will still work fine. --- lib/spack/spack/database.py | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 0ada7faa4cb..022a2d3871f 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -51,9 +51,20 @@ # DB version. This is stuck in the DB file to track changes in format. # Increment by one when the database format changes. -# versions before 5 were not integers +# Versions before 5 were not integers. _db_version = Version('5') +# For any version combinations here, skip reindex when upgrading. +# Reindexing can take considerable time and is not always necessary. +_skip_reindex = [ + # reindexing takes a significant amount of time, and there's + # no reason to do it from DB version 0.9.3 to version 5. The + # only difference is that v5 can contain "deprecated_for" + # fields. So, skip the reindex for this transition. The new + # version is saved to disk the first time the DB is written. + (Version('0.9.3'), Version('5')), +] + # Timeout for spack database locks in seconds _db_lock_timeout = 120 @@ -486,8 +497,19 @@ def check(cond, msg): if version > _db_version: raise InvalidDatabaseVersionError(_db_version, version) elif version < _db_version: - self.reindex(spack.store.layout) - installs = dict((k, v.to_dict()) for k, v in self._data.items()) + if not any( + old == version and new == _db_version + for old, new in _skip_reindex + ): + tty.warn( + "Spack database version changed from %s to %s. Upgrading." + % (version, _db_version) + ) + + self.reindex(spack.store.layout) + installs = dict( + (k, v.to_dict()) for k, v in self._data.items() + ) def invalid_record(hash_key, error): msg = ("Invalid record in Spack database: " From ab55890ba85fe03f649a6173a996bf3c9435b011 Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Fri, 25 Oct 2019 19:24:41 +0200 Subject: [PATCH 425/499] Make error msg of test_api_for_build_and_run_environment more informative (#13435) --- lib/spack/spack/test/package_sanity.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py index 290d21b85f8..bbf63881a7c 100644 --- a/lib/spack/spack/test/package_sanity.py +++ b/lib/spack/spack/test/package_sanity.py @@ -154,7 +154,8 @@ def test_api_for_build_and_run_environment(): failing.append(pkg) msg = ('there are {0} packages using the old API to set build ' - 'and run environment [{1}]') + 'and run environment [{1}], for further information see' + 'https://github.com/spack/spack/pull/11115') assert not failing, msg.format( len(failing), ','.join(x.name for x in failing) ) From e0b94dba14dcc3e5baa43cb2738fa32b3859c100 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 25 Oct 2019 11:02:52 -0700 Subject: [PATCH 426/499] completion: add bash completion for `spack spec --json` (#13433) --- share/spack/spack-completion.bash | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash index 935092aedb9..5e8936125f8 100755 --- a/share/spack/spack-completion.bash +++ b/share/spack/spack-completion.bash @@ -1051,7 +1051,8 @@ function _spack_spec { if $list_options then compgen -W "-h --help -l --long -L --very-long -I --install-status - -y --yaml -c --cover -N --namespaces -t --types" -- "$cur" + -j --json -y --yaml -c --cover -N --namespaces + -t --types" -- "$cur" else compgen -W "$(_all_packages)" -- "$cur" fi From 1b6ba9366815c6ecdf48c884c9fbd662d7dfafae Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Fri, 25 Oct 2019 16:43:54 -0500 Subject: [PATCH 427/499] py-gensim: new package at 3.8.0 (#13136) * py-gensim: new package at 3.8.0 * py-gensim: add 3.8.1 --- .../builtin/packages/py-gensim/package.py | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-gensim/package.py diff --git a/var/spack/repos/builtin/packages/py-gensim/package.py b/var/spack/repos/builtin/packages/py-gensim/package.py new file mode 100644 index 00000000000..48e0f09efc5 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-gensim/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyGensim(PythonPackage): + """Gensim is a Python library for topic modelling, document indexing and + similarity retrieval with large corpora. Target audience is the natural + language processing (NLP) and information retrieval (IR) community.""" + + homepage = "https://pypi.org/project/gensim/" + url = "https://files.pythonhosted.org/packages/3a/bc/1415be59292a23ff123298b4b46ec4be80b3bfe72c8d188b58ab2653dee4/gensim-3.8.0.tar.gz" + + version('3.8.1', sha256='33277fc0a8d7b0c7ce70fcc74bb82ad39f944c009b334856c6e86bf552b1dfdc', + url='https://files.pythonhosted.org/packages/73/f2/e9af000df6419bf1a63ffed3e6033a1b1d8fcf2f971fcdac15296619aff8/gensim-3.8.1.tar.gz') + version('3.8.0', sha256='ec5de7ff2bfa8692fa96a846bb5aae52f267fc322fbbe303c1f042d258af5766') + + depends_on('python@3.5:', type=('build', 'run')) + + depends_on('py-setuptools', type='build') + + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-scipy', type=('build', 'run')) + depends_on('py-smart-open', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) From 2f752d48802bc0891c1db7615e054b77a8aa6579 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sat, 26 Oct 2019 00:33:47 +0200 Subject: [PATCH 428/499] sqlite package: add version 3.30.1 (#13438) --- var/spack/repos/builtin/packages/sqlite/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py index 6cec0162d0f..2621678b1bf 100644 --- a/var/spack/repos/builtin/packages/sqlite/package.py +++ b/var/spack/repos/builtin/packages/sqlite/package.py @@ -14,6 +14,7 @@ class Sqlite(AutotoolsPackage): """ homepage = "https://www.sqlite.org" + version('3.30.1', sha256='8c5a50db089bd2a1b08dbc5b00d2027602ca7ff238ba7658fabca454d4298e60') version('3.30.0', sha256='e0a8cf4c7a87455e55e10413d16f358ca121ccec687fe1301eac95e2d340fc58') version('3.29.0', sha256='8e7c1e2950b5b04c5944a981cb31fffbf9d2ddda939d536838ebc854481afd5b') version('3.28.0', sha256='d61b5286f062adfce5125eaf544d495300656908e61fca143517afcc0a89b7c3') From d4ce124b65937a3d0d8e2f92eda509d77b598396 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sat, 26 Oct 2019 00:34:13 +0200 Subject: [PATCH 429/499] lmdb package: add version 0.9.24 (#13437) --- var/spack/repos/builtin/packages/lmdb/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/lmdb/package.py b/var/spack/repos/builtin/packages/lmdb/package.py index 3d45b223707..34dd4cbd206 100644 --- a/var/spack/repos/builtin/packages/lmdb/package.py +++ b/var/spack/repos/builtin/packages/lmdb/package.py @@ -15,6 +15,7 @@ class Lmdb(MakefilePackage): homepage = "https://lmdb.tech/" url = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.21.tar.gz" + version('0.9.24', sha256='44602436c52c29d4f301f55f6fd8115f945469b868348e3cddaf91ab2473ea26') version('0.9.22', sha256='f3927859882eb608868c8c31586bb7eb84562a40a6bf5cc3e13b6b564641ea28') version('0.9.21', sha256='1187b635a4cc415bb6972bba346121f81edd996e99b8f0816151d4090f90b559') version('0.9.16', sha256='49d7b40949f2ced9bc8b23ea6a89e75471a1c9126537a8b268c318a00b84322b') From 92e27588377e15a71cf48dd0e29c04cd2453d5bb Mon Sep 17 00:00:00 2001 From: Hans Pabst Date: Sat, 26 Oct 2019 00:34:54 +0200 Subject: [PATCH 430/499] LIBXSMM package: add version 1.14 (#13436) --- var/spack/repos/builtin/packages/libxsmm/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py index a6cd5ccc680..fd0c78afd95 100644 --- a/var/spack/repos/builtin/packages/libxsmm/package.py +++ b/var/spack/repos/builtin/packages/libxsmm/package.py @@ -14,10 +14,11 @@ class Libxsmm(MakefilePackage): and deep learning primitives.""" homepage = 'https://github.com/hfp/libxsmm' - url = 'https://github.com/hfp/libxsmm/archive/1.13.tar.gz' + url = 'https://github.com/hfp/libxsmm/archive/1.14.tar.gz' git = 'https://github.com/hfp/libxsmm.git' version('develop', branch='master') + version('1.14', sha256='9c0af4509ea341d1ee2c6c19fc6f19289318c3bd4b17844efeb9e7f9691abf76') version('1.13', sha256='47c034e169820a9633770eece0e0fdd8d4a744e09b81da2af8c2608a4625811e') version('1.12.1', sha256='3687fb98da00ba92cd50b5f0d18b39912c7886dad3856843573aee0cb34e9791') version('1.12', sha256='37432fae4404ca12d8c5a205bfec7f9326c2d607d9ec37680f42dae60b52382a') From ca917cfcccec9123cfc35274dc128fbbc8b6bd8e Mon Sep 17 00:00:00 2001 From: Sinan Date: Fri, 25 Oct 2019 15:36:28 -0700 Subject: [PATCH 431/499] New package: OSQP (#13432) --- .../repos/builtin/packages/osqp/package.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 var/spack/repos/builtin/packages/osqp/package.py diff --git a/var/spack/repos/builtin/packages/osqp/package.py b/var/spack/repos/builtin/packages/osqp/package.py new file mode 100644 index 00000000000..bed4d87d11e --- /dev/null +++ b/var/spack/repos/builtin/packages/osqp/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Osqp(CMakePackage): + """ + The OSQP (Operator Splitting Quadratic Program) solver is a numerical + optimization package for solving problems in the form: + minimize 0.5 x' P x + q' x, subject to l <= A x <= u, + where "x in R^n" is the optimization variable. + """ + + homepage = "https://osqp.org" + git = "https://github.com/oxfordcontrol/osqp.git" + + version('master', branch='master', submodules=True) + version('0.6.0', commit='0baddd36bd57ec1cace0a52c6dd9663e8f16df0a', submodules=True) + version('0.5.0', commit='97050184aa2cbebe446ae02d1f8b811243e180d6', submodules=True) From 32c0ef5ebdc08e0deec6cfcfb66ccd1709076df1 Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Sat, 26 Oct 2019 00:40:59 +0200 Subject: [PATCH 432/499] New package: py-defusedxml (#13419) --- .../builtin/packages/py-defusedxml/package.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-defusedxml/package.py diff --git a/var/spack/repos/builtin/packages/py-defusedxml/package.py b/var/spack/repos/builtin/packages/py-defusedxml/package.py new file mode 100644 index 00000000000..972c45e6272 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-defusedxml/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyDefusedxml(PythonPackage): + """defusing XML bombs and other exploits""" + + homepage = "https://github.com/tiran/defusedxml" + url = "https://pypi.io/packages/source/d/defusedxml/defusedxml-0.5.0.tar.gz" + + version('0.5.0', sha256='24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4') + + depends_on('py-setuptools', type='build') From 24ccc112421a2b623109c5163673ce2f4e16b1c0 Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Sat, 26 Oct 2019 00:42:49 +0200 Subject: [PATCH 433/499] py-nbformat package: add version 4.4.0 (#13421) --- var/spack/repos/builtin/packages/py-nbformat/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-nbformat/package.py b/var/spack/repos/builtin/packages/py-nbformat/package.py index aa58e035583..4bb931e6af8 100644 --- a/var/spack/repos/builtin/packages/py-nbformat/package.py +++ b/var/spack/repos/builtin/packages/py-nbformat/package.py @@ -12,6 +12,7 @@ class PyNbformat(PythonPackage): homepage = "https://github.com/jupyter/nbformat" url = "https://github.com/jupyter/nbformat/archive/4.1.0.tar.gz" + version('4.4.0', sha256='cfa7b2dbb81ab7a64492f09f2cb65d69a1d009fe5d6e18ee7bb94446b114ede3') version('4.1.0', sha256='751e77b58b66319be3977f86cc23a459763bded466a0113bbe39f137ec747872') version('4.0.1', sha256='5c46c21349f29379fa55bf19e4359afcd605fd4b5693a56807355874a2e87f78') version('4.0.0', sha256='f0dc6c6b47b9b0dcda1dfb02dd99c0818eb709571690a688d4e38a3129d2e95b') From cfbac14cba4ddc18a1addc2f02f8ff09947716b0 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Fri, 25 Oct 2019 16:01:45 -0700 Subject: [PATCH 434/499] bugfix: restore upstream lock safety; update tests Restore upstream lock safety; avoid calling methods directly on upstream DB in test. --- lib/spack/spack/database.py | 13 ++++---- lib/spack/spack/test/database.py | 54 +++++++++++++++++++++++++------- 2 files changed, 48 insertions(+), 19 deletions(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 022a2d3871f..a1748fc5852 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -257,11 +257,6 @@ def __init__(self, root, db_dir=None, upstream_dbs=None, self.is_upstream = is_upstream - if self.is_upstream: - self.lock = ForbiddenLock() - else: - self.lock = Lock(self._lock_path) - # initialize rest of state. self.db_lock_timeout = ( spack.config.get('config:db_lock_timeout') or _db_lock_timeout) @@ -273,8 +268,12 @@ def __init__(self, root, db_dir=None, upstream_dbs=None, if self.package_lock_timeout else 'No timeout') tty.debug('PACKAGE LOCK TIMEOUT: {0}'.format( str(timeout_format_str))) - self.lock = Lock(self._lock_path, - default_timeout=self.db_lock_timeout) + + if self.is_upstream: + self.lock = ForbiddenLock() + else: + self.lock = Lock(self._lock_path, + default_timeout=self.db_lock_timeout) self._data = {} self.upstream_dbs = list(upstream_dbs) if upstream_dbs else [] diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py index 099894e0d21..06ddc83a47e 100644 --- a/lib/spack/spack/test/database.py +++ b/lib/spack/spack/test/database.py @@ -159,6 +159,31 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db): spack.store.db = orig_db +@pytest.mark.usefixtures('config') +def test_cannot_write_upstream(tmpdir_factory, test_store, gen_mock_layout): + roots = [str(tmpdir_factory.mktemp(x)) for x in ['a', 'b']] + layouts = [gen_mock_layout(x) for x in ['/ra/', '/rb/']] + + x = MockPackage('x', [], []) + mock_repo = MockPackageMultiRepo([x]) + + # Instantiate the database that will be used as the upstream DB and make + # sure it has an index file + upstream_db_independent = spack.database.Database(roots[1]) + with upstream_db_independent.write_transaction(): + pass + + upstream_dbs = spack.store._construct_upstream_dbs_from_install_roots( + [roots[1]], _test=True) + + with spack.repo.swap(mock_repo): + spec = spack.spec.Spec('x') + spec.concretize() + + with pytest.raises(spack.database.ForbiddenLockError): + upstream_dbs[0].add(spec, layouts[1]) + + @pytest.mark.usefixtures('config') def test_recursive_upstream_dbs(tmpdir_factory, test_store, gen_mock_layout): roots = [str(tmpdir_factory.mktemp(x)) for x in ['a', 'b', 'c']] @@ -183,22 +208,27 @@ def test_recursive_upstream_dbs(tmpdir_factory, test_store, gen_mock_layout): db_a = spack.database.Database(roots[0], upstream_dbs=[db_b, db_c]) db_a.add(spec['x'], layouts[0]) - dbs = spack.store._construct_upstream_dbs_from_install_roots( - roots, _test=True) + upstream_dbs_from_scratch = ( + spack.store._construct_upstream_dbs_from_install_roots( + [roots[1], roots[2]], _test=True)) + db_a_from_scratch = spack.database.Database( + roots[0], upstream_dbs=upstream_dbs_from_scratch) - assert dbs[0].db_for_spec_hash(spec.dag_hash()) == dbs[0] - assert dbs[0].db_for_spec_hash(spec['y'].dag_hash()) == dbs[1] - assert dbs[0].db_for_spec_hash(spec['z'].dag_hash()) == dbs[2] + assert db_a_from_scratch.db_for_spec_hash(spec.dag_hash()) == ( + db_a_from_scratch) + assert db_a_from_scratch.db_for_spec_hash(spec['y'].dag_hash()) == ( + upstream_dbs_from_scratch[0]) + assert db_a_from_scratch.db_for_spec_hash(spec['z'].dag_hash()) == ( + upstream_dbs_from_scratch[1]) - dbs[0]._check_ref_counts() - dbs[1]._check_ref_counts() - dbs[2]._check_ref_counts() + db_a_from_scratch._check_ref_counts() + upstream_dbs_from_scratch[0]._check_ref_counts() + upstream_dbs_from_scratch[1]._check_ref_counts() - assert (dbs[0].installed_relatives(spec) == + assert (db_a_from_scratch.installed_relatives(spec) == set(spec.traverse(root=False))) - assert (dbs[0].installed_relatives(spec['z'], direction='parents') == - set([spec, spec['y']])) - assert not dbs[2].installed_relatives(spec['z'], direction='parents') + assert (db_a_from_scratch.installed_relatives( + spec['z'], direction='parents') == set([spec, spec['y']])) @pytest.fixture() From c566a610c9319098511f7ed645e1bb9e49927db3 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Fri, 25 Oct 2019 19:14:52 -0500 Subject: [PATCH 435/499] New package: gpu-burn (#13108) --- .../builtin/packages/gpu-burn/Makefile.patch | 18 ++++++ .../builtin/packages/gpu-burn/package.py | 55 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gpu-burn/Makefile.patch create mode 100644 var/spack/repos/builtin/packages/gpu-burn/package.py diff --git a/var/spack/repos/builtin/packages/gpu-burn/Makefile.patch b/var/spack/repos/builtin/packages/gpu-burn/Makefile.patch new file mode 100644 index 00000000000..57378a68762 --- /dev/null +++ b/var/spack/repos/builtin/packages/gpu-burn/Makefile.patch @@ -0,0 +1,18 @@ +--- a/Makefile 2018-12-08 05:36:48.000000000 -0600 ++++ b/Makefile 2019-10-04 13:08:37.095337704 -0500 +@@ -1,12 +1,6 @@ +-CUDAPATH=/usr/local/cuda +- +-# Have this point to an old enough gcc (for nvcc) +-GCCPATH=/usr +- + NVCC=nvcc +-CCPATH=${GCCPATH}/bin + + drv: +- PATH=${PATH}:.:${CCPATH}:${PATH} ${NVCC} -I${CUDAPATH}/include -arch=compute_30 -ptx compare.cu -o compare.ptx +- g++ -O3 -Wno-unused-result -I${CUDAPATH}/include -c gpu_burn-drv.cpp +- g++ -o gpu_burn gpu_burn-drv.o -O3 -lcuda -L${CUDAPATH}/lib64 -L${CUDAPATH}/lib -Wl,-rpath=${CUDAPATH}/lib64 -Wl,-rpath=${CUDAPATH}/lib -lcublas -lcudart -o gpu_burn ++ ${NVCC} -arch=compute_30 -ptx compare.cu -o compare.ptx ++ g++ -O3 -Wno-unused-result -c gpu_burn-drv.cpp ++ g++ -o gpu_burn gpu_burn-drv.o -O3 -lcuda -lcublas -lcudart -o gpu_burn diff --git a/var/spack/repos/builtin/packages/gpu-burn/package.py b/var/spack/repos/builtin/packages/gpu-burn/package.py new file mode 100644 index 00000000000..fd11176baa4 --- /dev/null +++ b/var/spack/repos/builtin/packages/gpu-burn/package.py @@ -0,0 +1,55 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class GpuBurn(MakefilePackage, CudaPackage): + """Multi-GPU CUDA stress test. Note that the file pointed to by COMPARE_PTX + needs to be copied or linked to the current working directory before + running gpu_burn.""" + + homepage = "http://wili.cc/blog/gpu-burn.html" + url = "http://wili.cc/blog/entries/gpu-burn/gpu_burn-1.0.tar.gz" + + version('1.0', sha256='d55994f0bee8dabf021966dbe574ef52be1e43386faeee91318dd4ebb36aa74a') + + patch('Makefile.patch') + + # This package uses CudaPackage to pick up the cuda_arch variant. A side + # effect is that it also picks up the cuda variant, but cuda is required + # for gpu-burn so is not really a variant. + variant('cuda', 'True', description='Use CUDA; must be true') + + conflicts('~cuda', msg='gpu-burn requires cuda') + + def edit(self, spec, prefix): + # update cuda architecture if necessary + if '+cuda' in self.spec: + cuda_arch = self.spec.variants['cuda_arch'].value + archflag = '' + + if cuda_arch != 'none': + if len(cuda_arch) > 1: + raise InstallError( + 'gpu-burn only supports compilation for a single GPU' + 'type.' + ) + archflag = '-arch=compute_{0}'.format(cuda_arch[0]) + + filter_file('-arch=compute_30', archflag, + 'Makefile', string=True) + + def install(self, spec, prefix): + mkdir(prefix.bin) + mkdir(prefix.share) + install('gpu_burn', prefix.bin) + install('compare.ptx', prefix.share) + + # The gpu_burn program looks for the compare.ptx file in the current + # working directory. Create an environment variable that can be pointed to + # so that it can be copied or linked. + def setup_environment(self, spack_env, run_env): + run_env.set('COMPARE_PTX', join_path(self.prefix.share, 'compare.ptx')) From 3dda714477259a2afb574fadef967461458f3d4b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 25 Oct 2019 21:26:29 -0500 Subject: [PATCH 436/499] Add latest version of py-readme-renderer (#13444) --- .../repos/builtin/packages/py-readme-renderer/package.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-readme-renderer/package.py b/var/spack/repos/builtin/packages/py-readme-renderer/package.py index b604ff787ba..925cf964022 100644 --- a/var/spack/repos/builtin/packages/py-readme-renderer/package.py +++ b/var/spack/repos/builtin/packages/py-readme-renderer/package.py @@ -11,13 +11,15 @@ class PyReadmeRenderer(PythonPackage): for Warehouse.""" homepage = "https://github.com/pypa/readme_renderer" - url = "https://pypi.io/packages/source/r/readme_renderer/readme_renderer-16.0.tar.gz" + url = "https://pypi.io/packages/source/r/readme_renderer/readme_renderer-24.0.tar.gz" + version('24.0', sha256='bb16f55b259f27f75f640acf5e00cf897845a8b3e4731b5c1a436e4b8529202f') version('16.0', sha256='c46b3418ddef3c3c3f819a4a9cfd56ede15c03d12197962a7e7a89edf1823dd5') - depends_on('python@2.6:2.8,3.2:3.3') depends_on('py-setuptools', type='build') - depends_on('py-bleach', type=('build', 'run')) + depends_on('py-bleach@2.1.0:', type=('build', 'run')) depends_on('py-docutils@0.13.1:', type=('build', 'run')) depends_on('py-pygments', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) + depends_on('py-pytest', type='test') + depends_on('py-mock', type='test') From 46ae845b6b39a0205fa6add0b3ef0eb3cdc980e6 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 25 Oct 2019 21:26:48 -0500 Subject: [PATCH 437/499] Add latest version of py-requests-toolbelt (#13445) --- .../repos/builtin/packages/py-requests-toolbelt/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py index 5645ab4e00f..c6e25d373e7 100644 --- a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py +++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py @@ -11,9 +11,10 @@ class PyRequestsToolbelt(PythonPackage): python-requests""" homepage = "https://toolbelt.readthedocs.org/" - url = "https://github.com/requests/toolbelt/archive/0.8.0.tar.gz" + url = "https://github.com/requests/toolbelt/archive/0.9.1.tar.gz" + version('0.9.1', sha256='c8e68e537e87ae088e3a0eb6d80ed5b7cf5d6df503d0e843e0a5e47283db487b') version('0.8.0', sha256='f151c07e88148dc05b6f31cc75dfb7a6770968e4a5c8e6690325eed4e79160a1') depends_on('py-setuptools', type='build') - depends_on('py-requests@2.0.1:3.0.0', type=('build', 'run')) + depends_on('py-requests@2.0.1:2.999', type=('build', 'run')) From d6735aa5cd6e3de5768f7d2885c274ea72c79f76 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 25 Oct 2019 21:27:12 -0500 Subject: [PATCH 438/499] Add latest version of py-tqdm (#13446) --- var/spack/repos/builtin/packages/py-tqdm/package.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-tqdm/package.py b/var/spack/repos/builtin/packages/py-tqdm/package.py index a10b078ea7d..fd3ac93510e 100644 --- a/var/spack/repos/builtin/packages/py-tqdm/package.py +++ b/var/spack/repos/builtin/packages/py-tqdm/package.py @@ -10,8 +10,13 @@ class PyTqdm(PythonPackage): """A Fast, Extensible Progress Meter""" homepage = "https://github.com/tqdm/tqdm" - url = "https://pypi.io/packages/source/t/tqdm/tqdm-4.8.4.tar.gz" + url = "https://pypi.io/packages/source/t/tqdm/tqdm-4.36.1.tar.gz" - version('4.8.4', sha256='bab05f8bb6efd2702ab6c532e5e6a758a66c0d2f443e09784b73e4066e6b3a37') + version('4.36.1', sha256='abc25d0ce2397d070ef07d8c7e706aede7920da163c64997585d42d3537ece3d') + version('4.8.4', sha256='bab05f8bb6efd2702ab6c532e5e6a758a66c0d2f443e09784b73e4066e6b3a37') + depends_on('python@2.6:2.8,3.2:', type=('build', 'run')) depends_on('py-setuptools', type='build') + depends_on('py-nose', type='test') + depends_on('py-flake8', type='test') + depends_on('py-coverage', type='test') From 85597be4d7f8772aefdf570058348183eb2d814c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 25 Oct 2019 21:27:29 -0500 Subject: [PATCH 439/499] Add py-pkginfo package (#13448) --- .../builtin/packages/py-pkginfo/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pkginfo/package.py diff --git a/var/spack/repos/builtin/packages/py-pkginfo/package.py b/var/spack/repos/builtin/packages/py-pkginfo/package.py new file mode 100644 index 00000000000..bca33619dd4 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pkginfo/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPkginfo(PythonPackage): + """Query metadatdata from sdists / bdists / installed packages.""" + + homepage = "https://code.launchpad.net/~tseaver/pkginfo/trunk" + url = "https://pypi.io/packages/source/p/pkginfo/pkginfo-1.5.0.1.tar.gz" + + version('1.5.0.1', sha256='7424f2c8511c186cd5424bbf31045b77435b37a8d604990b79d4e70d741148bb') + + depends_on('py-setuptools', type='build') + depends_on('py-nose', type='test') + depends_on('py-coverage', type='test') From 5582de837ef126ad736d44565a8d4231225b29da Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 25 Oct 2019 21:27:44 -0500 Subject: [PATCH 440/499] Add py-twine package (#13449) --- .../builtin/packages/py-twine/package.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-twine/package.py diff --git a/var/spack/repos/builtin/packages/py-twine/package.py b/var/spack/repos/builtin/packages/py-twine/package.py new file mode 100644 index 00000000000..d7ddcebd16b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-twine/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTwine(PythonPackage): + """Twine is a utility for publishing Python packages on PyPI.""" + + homepage = "https://twine.readthedocs.io/" + url = "https://pypi.io/packages/source/t/twine/twine-2.0.0.tar.gz" + + version('2.0.0', sha256='9fe7091715c7576df166df8ef6654e61bada39571783f2fd415bdcba867c6993') + + depends_on('python@3.6:', type=('build', 'run')) + depends_on('py-pkginfo@1.4.2:', type=('build', 'run')) + depends_on('py-readme-renderer@21.0:', type=('build', 'run')) + depends_on('py-requests-toolbelt@0.8.0:0.8.999,0.9.1:', type=('build', 'run')) + depends_on('py-setuptools@0.7.0:', type=('build', 'run')) + depends_on('py-tqdm@4.14:', type=('build', 'run')) From 4af448724f4f933b5306c4cdd2f7522d64dc8719 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Fri, 25 Oct 2019 21:47:28 -0700 Subject: [PATCH 441/499] `mirror create --all` can mirror everything (#12940) Support mirroring all packages with `spack mirror create --all`. In this mode there is no concretization: * Spack pulls every version of every package into the created mirror. * It also makes multiple attempts for each package/version combination (if there is a temporary connection failure). * Continues if all attempts fail. i.e., this makes its best effort to fetch evrerything, even if all attempts to fetch one package fail. This also changes mirroring logic to prefer storing sources by their hash or by a unique name derived from the source. For example: * Archives with checksums are named by the sha256 sum, i.e., `archive/f6/f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8.tar.gz` vs the previous `-package-version>.tar.gz` * VCS repositories are stored by a path derived from their URL, e.g. `git/google/leveldb.git/master.tar.gz`. The new mirror layout allows different packages to refer to the same resource or source without duplicating that download in the mirror/cache. This change is not essential to mirroring everything but is expected to save space when mirroring packages that all use the same resource. The new structure of the mirror is: ``` / _source-cache/ <-- the _source-cache directory is new archive/ <-- archives/resources/patches stored by hash 00/ <-- 2-letter sha256 prefix 002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056.tar.gz 01/ 0154c25c45b5506b6d618ca8e18d0ef093dac47946ac0df464fb21e77b504118.tar.gz 0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea.tar.gz ... git/ OpenFAST/ openfast.git/ master.tar.gz <-- repo by branch name PHASTA/ phasta.git/ 11f431f2d1a53a529dab4b0f079ab8aab7ca1109.tar.gz <-- repo by commit ... svn/ <-- each fetch strategy has its own subdirectory ... openmpi/ <-- the remaining package directories have the old format openmpi-1.10.1.tar.gz <-- human-readable name is symlink to _source-cache ``` In addition to the archive names as described above, `mirror create` now also creates symlinks with the old format to help users understand which package each mirrored archive is associated with, and to allow mirrors to work with old spack versions. The symlinks are relative so the mirror directory can still itself be archived. Other improvements: * `spack mirror create` will not re-download resources that have already been placed in it. * When creating a mirror, the resources downloaded to the mirror will not be cached (things are not stored twice). --- lib/spack/spack/caches.py | 29 ++-- lib/spack/spack/cmd/mirror.py | 117 +++++++++----- lib/spack/spack/fetch_strategy.py | 40 +++++ lib/spack/spack/mirror.py | 236 +++++++++++++++++++---------- lib/spack/spack/package.py | 68 +++++++-- lib/spack/spack/patch.py | 22 ++- lib/spack/spack/stage.py | 69 ++++++--- lib/spack/spack/test/cmd/mirror.py | 2 +- lib/spack/spack/test/install.py | 6 +- lib/spack/spack/test/mirror.py | 72 +++++---- lib/spack/spack/test/packaging.py | 4 +- 11 files changed, 451 insertions(+), 214 deletions(-) diff --git a/lib/spack/spack/caches.py b/lib/spack/spack/caches.py index e2352b2fcc0..bdece504214 100644 --- a/lib/spack/spack/caches.py +++ b/lib/spack/spack/caches.py @@ -15,7 +15,6 @@ import spack.fetch_strategy import spack.util.file_cache import spack.util.path -import spack.util.url as url_util def _misc_cache(): @@ -52,25 +51,25 @@ def _fetch_cache(): class MirrorCache(object): def __init__(self, root): - self.root = url_util.local_file_path(root) - if not self.root: - raise spack.error.SpackError( - 'MirrorCaches only work with file:// URLs') + self.root = os.path.abspath(root) - self.new_resources = set() - self.existing_resources = set() - - def store(self, fetcher, relative_dest): + def store(self, fetcher, relative_dest, cosmetic_path=None): # Note this will archive package sources even if they would not # normally be cached (e.g. the current tip of an hg/git branch) dst = os.path.join(self.root, relative_dest) + mkdirp(os.path.dirname(dst)) + fetcher.archive(dst) - if os.path.exists(dst): - self.existing_resources.add(relative_dest) - else: - self.new_resources.add(relative_dest) - mkdirp(os.path.dirname(dst)) - fetcher.archive(dst) + # Add a symlink path that a human can read to understand what resource + # the archive path refers to + if not cosmetic_path: + return + cosmetic_path = os.path.join(self.root, cosmetic_path) + relative_dst = os.path.relpath( + dst, start=os.path.dirname(cosmetic_path)) + if not os.path.exists(cosmetic_path): + mkdirp(os.path.dirname(cosmetic_path)) + os.symlink(relative_dst, cosmetic_path) #: Spack's local cache for downloaded source archives diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py index 91ed40a4c58..21723e49659 100644 --- a/lib/spack/spack/cmd/mirror.py +++ b/lib/spack/spack/cmd/mirror.py @@ -38,18 +38,25 @@ def setup_parser(subparser): create_parser = sp.add_parser('create', help=mirror_create.__doc__) create_parser.add_argument('-d', '--directory', default=None, help="directory in which to create mirror") + create_parser.add_argument( 'specs', nargs=argparse.REMAINDER, help="specs of packages to put in mirror") + create_parser.add_argument( + '-a', '--all', action='store_true', + help="mirror all versions of all packages in Spack, or all packages" + " in the current environment if there is an active environment" + " (this requires significant time and space)") create_parser.add_argument( '-f', '--file', help="file with specs of packages to put in mirror") + create_parser.add_argument( '-D', '--dependencies', action='store_true', help="also fetch all dependencies") create_parser.add_argument( - '-n', '--versions-per-spec', type=int, - default=1, - help="the number of versions to fetch for each spec") + '-n', '--versions-per-spec', + help="the number of versions to fetch for each spec, choose 'all' to" + " retrieve all versions of each package") # used to construct scope arguments below scopes = spack.config.scopes() @@ -225,6 +232,25 @@ def _read_specs_from_file(filename): def mirror_create(args): """Create a directory to be used as a spack mirror, and fill it with package archives.""" + if args.specs and args.all: + raise SpackError("Cannot specify specs on command line if you" + " chose to mirror all specs with '--all'") + elif args.file and args.all: + raise SpackError("Cannot specify specs with a file ('-f') if you" + " chose to mirror all specs with '--all'") + + if not args.versions_per_spec: + num_versions = 1 + elif args.versions_per_spec == 'all': + num_versions = 'all' + else: + try: + num_versions = int(args.versions_per_spec) + except ValueError: + raise SpackError( + "'--versions-per-spec' must be a number or 'all'," + " got '{0}'".format(args.versions_per_spec)) + # try to parse specs from the command line first. with spack.concretize.disable_compiler_existence_check(): specs = spack.cmd.parse_specs(args.specs, concretize=True) @@ -235,56 +261,67 @@ def mirror_create(args): tty.die("Cannot pass specs on the command line with --file.") specs = _read_specs_from_file(args.file) - # If nothing is passed, use environment or all if no active env if not specs: + # If nothing is passed, use environment or all if no active env + if not args.all: + tty.die("No packages were specified.", + "To mirror all packages, use the '--all' option" + " (this will require significant time and space).") + env = ev.get_env(args, 'mirror') if env: - specs = env.specs_by_hash.values() + mirror_specs = env.specs_by_hash.values() else: specs = [Spec(n) for n in spack.repo.all_package_names()] - specs.sort(key=lambda s: s.format("{name}{@version}").lower()) + mirror_specs = spack.mirror.get_all_versions(specs) + mirror_specs.sort( + key=lambda s: (s.name, s.version)) + else: + # If the user asked for dependencies, traverse spec DAG get them. + if args.dependencies: + new_specs = set() + for spec in specs: + spec.concretize() + for s in spec.traverse(): + new_specs.add(s) + specs = list(new_specs) - # If the user asked for dependencies, traverse spec DAG get them. - if args.dependencies: - new_specs = set() - for spec in specs: - spec.concretize() - for s in spec.traverse(): - new_specs.add(s) - specs = list(new_specs) + # Skip external specs, as they are already installed + external_specs = [s for s in specs if s.external] + specs = [s for s in specs if not s.external] - # Skip external specs, as they are already installed - external_specs = [s for s in specs if s.external] - specs = [s for s in specs if not s.external] + for spec in external_specs: + msg = 'Skipping {0} as it is an external spec.' + tty.msg(msg.format(spec.cshort_spec)) - for spec in external_specs: - msg = 'Skipping {0} as it is an external spec.' - tty.msg(msg.format(spec.cshort_spec)) + if num_versions == 'all': + mirror_specs = spack.mirror.get_all_versions(specs) + else: + mirror_specs = spack.mirror.get_matching_versions( + specs, num_versions=num_versions) - mirror = spack.mirror.Mirror( - args.directory or spack.config.get('config:source_cache')) + mirror = spack.mirror.Mirror( + args.directory or spack.config.get('config:source_cache')) - directory = url_util.format(mirror.push_url) + directory = url_util.format(mirror.push_url) - # Make sure nothing is in the way. - existed = web_util.url_exists(directory) + existed = web_util.url_exists(directory) - # Actually do the work to create the mirror - present, mirrored, error = spack.mirror.create( - directory, specs, num_versions=args.versions_per_spec) - p, m, e = len(present), len(mirrored), len(error) + # Actually do the work to create the mirror + present, mirrored, error = spack.mirror.create(directory, mirror_specs) + p, m, e = len(present), len(mirrored), len(error) - verb = "updated" if existed else "created" - tty.msg( - "Successfully %s mirror in %s" % (verb, directory), - "Archive stats:", - " %-4d already present" % p, - " %-4d added" % m, - " %-4d failed to fetch." % e) - if error: - tty.error("Failed downloads:") - colify(s.cformat("{name}{@version}") for s in error) - sys.exit(1) + verb = "updated" if existed else "created" + tty.msg( + "Successfully %s mirror in %s" % (verb, directory), + "Archive stats:", + " %-4d already present" % p, + " %-4d added" % m, + " %-4d failed to fetch." % e) + if error: + tty.error("Failed downloads:") + colify(s.cformat("{name}{@version}") for s in error) + sys.exit(1) def mirror(parser, args): diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 8105402f99b..393e3af9d12 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -166,11 +166,23 @@ def cachable(self): def source_id(self): """A unique ID for the source. + It is intended that a human could easily generate this themselves using + the information available to them in the Spack package. + The returned value is added to the content which determines the full hash for a package using `str()`. """ raise NotImplementedError + def mirror_id(self): + """This is a unique ID for a source that is intended to help identify + reuse of resources across packages. + + It is unique like source-id, but it does not include the package name + and is not necessarily easy for a human to create themselves. + """ + raise NotImplementedError + def __str__(self): # Should be human readable URL. return "FetchStrategy.__str___" @@ -273,6 +285,15 @@ def curl(self): def source_id(self): return self.digest + def mirror_id(self): + if not self.digest: + return None + # The filename is the digest. A directory is also created based on + # truncating the digest to avoid creating a directory with too many + # entries + return os.path.sep.join( + ['archive', self.digest[:2], self.digest]) + @_needs_stage def fetch(self): if self.archive_file: @@ -727,6 +748,13 @@ def cachable(self): def source_id(self): return self.commit or self.tag + def mirror_id(self): + repo_ref = self.commit or self.tag or self.branch + if repo_ref: + repo_path = url_util.parse(self.url).path + result = os.path.sep.join(['git', repo_path, repo_ref]) + return result + def get_source_id(self): if not self.branch: return @@ -908,6 +936,12 @@ def get_source_id(self): info = xml.etree.ElementTree.fromstring(output) return info.find('entry/commit').get('revision') + def mirror_id(self): + if self.revision: + repo_path = url_util.parse(self.url).path + result = os.path.sep.join(['svn', repo_path, self.revision]) + return result + @_needs_stage def fetch(self): if self.stage.expanded: @@ -1011,6 +1045,12 @@ def cachable(self): def source_id(self): return self.revision + def mirror_id(self): + if self.revision: + repo_path = url_util.parse(self.url).path + result = os.path.sep.join(['hg', repo_path, self.revision]) + return result + def get_source_id(self): output = self.hg('id', self.url, output=str) if output: diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py index e2329b68615..0c5e2a9cc26 100644 --- a/lib/spack/spack/mirror.py +++ b/lib/spack/spack/mirror.py @@ -13,6 +13,7 @@ """ import sys import os +import traceback import os.path import operator @@ -37,7 +38,6 @@ import spack.util.url as url_util import spack.spec from spack.version import VersionList -from spack.util.compression import allowed_archive from spack.util.spack_yaml import syaml_dict @@ -233,27 +233,16 @@ def __len__(self): return len(self._mirrors) -def mirror_archive_filename(spec, fetcher, resource_id=None): - """Get the name of the spec's archive in the mirror.""" - if not spec.version.concrete: - raise ValueError("mirror.path requires spec with concrete version.") - +def _determine_extension(fetcher): if isinstance(fetcher, fs.URLFetchStrategy): if fetcher.expand_archive: # If we fetch with a URLFetchStrategy, use URL's archive type ext = url.determine_url_file_extension(fetcher.url) - # If the filename does not end with a normal suffix, - # see if the package explicitly declares the extension - if not ext: - ext = spec.package.versions[spec.package.version].get( - 'extension', None) - if ext: # Remove any leading dots ext = ext.lstrip('.') - - if not ext: + else: msg = """\ Unable to parse extension from {0}. @@ -276,21 +265,92 @@ def mirror_archive_filename(spec, fetcher, resource_id=None): # Otherwise we'll make a .tar.gz ourselves ext = 'tar.gz' - if resource_id: - filename = "%s-%s" % (resource_id, spec.version) + ".%s" % ext - else: - filename = "%s-%s" % (spec.package.name, spec.version) + ".%s" % ext - - return filename + return ext -def mirror_archive_path(spec, fetcher, resource_id=None): - """Get the relative path to the spec's archive within a mirror.""" - return os.path.join( - spec.name, mirror_archive_filename(spec, fetcher, resource_id)) +class MirrorReference(object): + """A ``MirrorReference`` stores the relative paths where you can store a + package/resource in a mirror directory. + + The appropriate storage location is given by ``storage_path``. The + ``cosmetic_path`` property provides a reference that a human could generate + themselves based on reading the details of the package. + + A user can iterate over a ``MirrorReference`` object to get all the + possible names that might be used to refer to the resource in a mirror; + this includes names generated by previous naming schemes that are no-longer + reported by ``storage_path`` or ``cosmetic_path``. + """ + def __init__(self, cosmetic_path, global_path=None): + self.global_path = global_path + self.cosmetic_path = cosmetic_path + + @property + def storage_path(self): + if self.global_path: + return self.global_path + else: + return self.cosmetic_path + + def __iter__(self): + if self.global_path: + yield self.global_path + yield self.cosmetic_path -def get_matching_versions(specs, **kwargs): +def mirror_archive_paths(fetcher, per_package_ref, spec=None): + """Returns a ``MirrorReference`` object which keeps track of the relative + storage path of the resource associated with the specified ``fetcher``.""" + ext = None + if spec: + ext = spec.package.versions[spec.package.version].get( + 'extension', None) + # If the spec does not explicitly specify an extension (the default case), + # then try to determine it automatically. An extension can only be + # specified for the primary source of the package (e.g. the source code + # identified in the 'version' declaration). Resources/patches don't have + # an option to specify an extension, so it must be inferred for those. + ext = ext or _determine_extension(fetcher) + + if ext: + per_package_ref += ".%s" % ext + + global_ref = fetcher.mirror_id() + if global_ref: + global_ref = os.path.join('_source-cache', global_ref) + if global_ref and ext: + global_ref += ".%s" % ext + + return MirrorReference(per_package_ref, global_ref) + + +def get_all_versions(specs): + """Given a set of initial specs, return a new set of specs that includes + each version of each package in the original set. + + Note that if any spec in the original set specifies properties other than + version, this information will be omitted in the new set; for example; the + new set of specs will not include variant settings. + """ + + version_specs = [] + for spec in specs: + pkg = spec.package + + # Skip any package that has no known versions. + if not pkg.versions: + tty.msg("No safe (checksummed) versions for package %s" % pkg.name) + continue + + for version in pkg.versions: + version_spec = spack.spec.Spec(pkg.name) + version_spec.versions = VersionList([version]) + version_specs.append(version_spec) + + return version_specs + + +def get_matching_versions(specs, num_versions=1): """Get a spec for EACH known version matching any spec in the list. For concrete specs, this retrieves the concrete version and, if more than one version per spec is requested, retrieves the latest versions @@ -305,7 +365,7 @@ def get_matching_versions(specs, **kwargs): tty.msg("No safe (checksummed) versions for package %s" % pkg.name) continue - pkg_versions = kwargs.get('num_versions', 1) + pkg_versions = num_versions version_order = list(reversed(sorted(pkg.versions))) matching_spec = [] @@ -338,19 +398,7 @@ def get_matching_versions(specs, **kwargs): return matching -def suggest_archive_basename(resource): - """Return a tentative basename for an archive. - - Raises: - RuntimeError: if the name is not an allowed archive type. - """ - basename = os.path.basename(resource.fetcher.url) - if not allowed_archive(basename): - raise RuntimeError("%s is not an allowed archive tye" % basename) - return basename - - -def create(path, specs, **kwargs): +def create(path, specs): """Create a directory to be used as a spack mirror, and fill it with package archives. @@ -359,10 +407,6 @@ def create(path, specs, **kwargs): specs: Any package versions matching these specs will be added \ to the mirror. - Keyword args: - num_versions: Max number of versions to fetch per spec, \ - (default is 1 each spec) - Return Value: Returns a tuple of lists: (present, mirrored, error) @@ -376,69 +420,107 @@ def create(path, specs, **kwargs): """ parsed = url_util.parse(path) mirror_root = url_util.local_file_path(parsed) - - # Make sure nothing is in the way. - if mirror_root and os.path.isfile(mirror_root): - raise MirrorError("%s already exists and is a file." % mirror_root) + if not mirror_root: + raise spack.error.SpackError( + 'MirrorCaches only work with file:// URLs') # automatically spec-ify anything in the specs array. specs = [ s if isinstance(s, spack.spec.Spec) else spack.spec.Spec(s) for s in specs] - # Get concrete specs for each matching version of these specs. - version_specs = get_matching_versions( - specs, num_versions=kwargs.get('num_versions', 1)) - for s in version_specs: - s.concretize() - # Get the absolute path of the root before we start jumping around. - if mirror_root and not os.path.isdir(mirror_root): + if not os.path.isdir(mirror_root): try: mkdirp(mirror_root) except OSError as e: raise MirrorError( "Cannot create directory '%s':" % mirror_root, str(e)) - # Things to keep track of while parsing specs. - categories = { - 'present': [], - 'mirrored': [], - 'error': [] - } - - mirror_cache = spack.caches.MirrorCache(parsed) + mirror_cache = spack.caches.MirrorCache(mirror_root) + mirror_stats = MirrorStats() try: spack.caches.mirror_cache = mirror_cache # Iterate through packages and download all safe tarballs for each - for spec in version_specs: - add_single_spec(spec, parsed, categories, **kwargs) + for spec in specs: + mirror_stats.next_spec(spec) + add_single_spec(spec, mirror_root, mirror_stats) finally: spack.caches.mirror_cache = None - categories['mirrored'] = list(mirror_cache.new_resources) - categories['present'] = list(mirror_cache.existing_resources) - - return categories['present'], categories['mirrored'], categories['error'] + return mirror_stats.stats() -def add_single_spec(spec, mirror_root, categories, **kwargs): +class MirrorStats(object): + def __init__(self): + self.present = {} + self.new = {} + self.errors = set() + + self.current_spec = None + self.added_resources = set() + self.existing_resources = set() + + def next_spec(self, spec): + self._tally_current_spec() + self.current_spec = spec + + def _tally_current_spec(self): + if self.current_spec: + if self.added_resources: + self.new[self.current_spec] = len(self.added_resources) + if self.existing_resources: + self.present[self.current_spec] = len(self.existing_resources) + self.added_resources = set() + self.existing_resources = set() + self.current_spec = None + + def stats(self): + self._tally_current_spec() + return list(self.present), list(self.new), list(self.errors) + + def already_existed(self, resource): + # If an error occurred after caching a subset of a spec's + # resources, a secondary attempt may consider them already added + if resource not in self.added_resources: + self.existing_resources.add(resource) + + def added(self, resource): + self.added_resources.add(resource) + + def error(self): + self.errors.add(self.current_spec) + + +def add_single_spec(spec, mirror_root, mirror_stats): tty.msg("Adding package {pkg} to mirror".format( pkg=spec.format("{name}{@version}") )) - try: - spec.package.do_fetch() - spec.package.do_clean() + num_retries = 3 + while num_retries > 0: + try: + with spec.package.stage as pkg_stage: + pkg_stage.cache_mirror(mirror_stats) + for patch in spec.package.all_patches(): + patch.fetch(pkg_stage) + if patch.cache(): + patch.cache().cache_mirror(mirror_stats) + patch.clean() + exception = None + break + except Exception as e: + exc_tuple = sys.exc_info() + exception = e + num_retries -= 1 - except Exception as e: - tty.debug(e) + if exception: if spack.config.get('config:debug'): - sys.excepthook(*sys.exc_info()) + traceback.print_exception(file=sys.stderr, *exc_tuple) else: tty.warn( "Error while fetching %s" % spec.cformat('{name}{@version}'), - e.message) - categories['error'].append(spec) + exception.message) + mirror_stats.error() class MirrorError(spack.error.SpackError): diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 8a65d7b7335..38631c7a0e2 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -663,7 +663,8 @@ def global_license_file(self): @property def version(self): if not self.spec.versions.concrete: - raise ValueError("Can only get of package with concrete version.") + raise ValueError("Version requested for a package that" + " does not have a concrete version.") return self.spec.versions[0] @memoized @@ -741,19 +742,23 @@ def url_for_version(self, version): def _make_resource_stage(self, root_stage, fetcher, resource): resource_stage_folder = self._resource_stage(resource) - resource_mirror = spack.mirror.mirror_archive_path( - self.spec, fetcher, resource.name) + mirror_paths = spack.mirror.mirror_archive_paths( + fetcher, + os.path.join(self.name, "%s-%s" % (resource.name, self.version))) stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource, name=resource_stage_folder, - mirror_path=resource_mirror, + mirror_paths=mirror_paths, path=self.path) return stage def _make_root_stage(self, fetcher): # Construct a mirror path (TODO: get this out of package.py) - mp = spack.mirror.mirror_archive_path(self.spec, fetcher) + mirror_paths = spack.mirror.mirror_archive_paths( + fetcher, + os.path.join(self.name, "%s-%s" % (self.name, self.version)), + self.spec) # Construct a path where the stage should build.. s = self.spec stage_name = "{0}{1}-{2}-{3}".format(stage_prefix, s.name, s.version, @@ -763,8 +768,8 @@ def download_search(): dynamic_fetcher = fs.from_list_url(self) return [dynamic_fetcher] if dynamic_fetcher else [] - stage = Stage(fetcher, mirror_path=mp, name=stage_name, path=self.path, - search_fn=download_search) + stage = Stage(fetcher, mirror_paths=mirror_paths, name=stage_name, + path=self.path, search_fn=download_search) return stage def _make_stage(self): @@ -794,8 +799,9 @@ def stage(self): doesn't have one yet, but it does not create the Stage directory on the filesystem. """ - if not self.spec.concrete: - raise ValueError("Can only get a stage for a concrete package.") + if not self.spec.versions.concrete: + raise ValueError( + "Cannot retrieve stage for package without concrete version.") if self._stage is None: self._stage = self._make_stage() return self._stage @@ -873,8 +879,8 @@ def _make_fetcher(self): @property def fetcher(self): if not self.spec.versions.concrete: - raise ValueError( - "Can only get a fetcher for a package with concrete versions.") + raise ValueError("Cannot retrieve fetcher for" + " package without concrete version.") if not self._fetcher: self._fetcher = self._make_fetcher() return self._fetcher @@ -1081,6 +1087,8 @@ def do_fetch(self, mirror_only=False): for patch in self.spec.patches: patch.fetch(self.stage) + if patch.cache(): + patch.cache().cache_local() def do_stage(self, mirror_only=False): """Unpacks and expands the fetched tarball.""" @@ -1193,6 +1201,26 @@ def do_patch(self): else: touch(no_patches_file) + @classmethod + def all_patches(cls): + """Retrieve all patches associated with the package. + + Retrieves patches on the package itself as well as patches on the + dependencies of the package.""" + patches = [] + for _, patch_list in cls.patches.items(): + for patch in patch_list: + patches.append(patch) + + pkg_deps = cls.dependencies + for dep_name in pkg_deps: + for _, dependency in pkg_deps[dep_name].items(): + for _, patch_list in dependency.patches.items(): + for patch in patch_list: + patches.append(patch) + + return patches + def content_hash(self, content=None): """Create a hash based on the sources and logic used to build the package. This includes the contents of all applied patches and the @@ -1366,9 +1394,21 @@ def _if_ninja_target_execute(self, target, *args, **kwargs): def _get_needed_resources(self): resources = [] # Select the resources that are needed for this build - for when_spec, resource_list in self.resources.items(): - if when_spec in self.spec: - resources.extend(resource_list) + if self.spec.concrete: + for when_spec, resource_list in self.resources.items(): + if when_spec in self.spec: + resources.extend(resource_list) + else: + for when_spec, resource_list in self.resources.items(): + # Note that variant checking is always strict for specs where + # the name is not specified. But with strict variant checking, + # only variants mentioned in 'other' are checked. Here we only + # want to make sure that no constraints in when_spec + # conflict with the spec, so we need to invoke + # when_spec.satisfies(self.spec) vs. + # self.spec.satisfies(when_spec) + if when_spec.satisfies(self.spec, strict=False): + resources.extend(resource_list) # Sorts the resources by the length of the string representing their # destination. Since any nested resource must contain another # resource's name in its path, it seems that should work diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py index cb012af7ff4..79550538db5 100644 --- a/lib/spack/spack/patch.py +++ b/lib/spack/spack/patch.py @@ -16,6 +16,7 @@ import spack.repo import spack.stage import spack.util.spack_json as sjson +import spack from spack.util.compression import allowed_archive from spack.util.crypto import checksum, Checker @@ -87,6 +88,9 @@ def apply(self, stage): apply_patch(stage, self.path, self.level, self.working_dir) + def cache(self): + return None + def to_dict(self): """Partial dictionary -- subclases should add to this.""" return { @@ -180,6 +184,7 @@ def __init__(self, pkg, url, level=1, working_dir='.', ordering_key=None, if not self.sha256: raise PatchDirectiveError("URL patches require a sha256 checksum") + # TODO: this function doesn't use the stage arg def fetch(self, stage): """Retrieve the patch in a temporary stage and compute self.path @@ -191,15 +196,19 @@ def fetch(self, stage): if self.archive_sha256: fetch_digest = self.archive_sha256 - fetcher = fs.URLFetchStrategy(self.url, fetch_digest) - mirror = os.path.join(os.path.dirname(stage.mirror_path), - os.path.basename(self.url)) + fetcher = fs.URLFetchStrategy(self.url, fetch_digest, + expand=bool(self.archive_sha256)) - self.stage = spack.stage.Stage(fetcher, mirror_path=mirror) + per_package_ref = os.path.join( + self.owner.split('.')[-1], os.path.basename(self.url)) + # Reference starting with "spack." is required to avoid cyclic imports + mirror_ref = spack.mirror.mirror_archive_paths( + fetcher, per_package_ref) + + self.stage = spack.stage.Stage(fetcher, mirror_paths=mirror_ref) self.stage.create() self.stage.fetch() self.stage.check() - self.stage.cache_local() root = self.stage.path if self.archive_sha256: @@ -230,6 +239,9 @@ def fetch(self, stage): "sha256 checksum failed for %s" % self.path, "Expected %s but got %s" % (self.sha256, checker.sum)) + def cache(self): + return self.stage + def clean(self): self.stage.destroy() diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index 9621938bcd1..7869c5f863b 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -166,6 +166,14 @@ def get_stage_root(): return _stage_root +def _mirror_roots(): + mirrors = spack.config.get('mirrors') + return [ + sup.substitute_path_variables(root) if root.endswith(os.sep) + else sup.substitute_path_variables(root) + os.sep + for root in mirrors.values()] + + class Stage(object): """Manages a temporary stage directory for building. @@ -216,7 +224,7 @@ class Stage(object): def __init__( self, url_or_fetch_strategy, - name=None, mirror_path=None, keep=False, path=None, lock=True, + name=None, mirror_paths=None, keep=False, path=None, lock=True, search_fn=None): """Create a stage object. Parameters: @@ -230,10 +238,10 @@ def __init__( stage object later). If name is not provided, then this stage will be given a unique name automatically. - mirror_path + mirror_paths If provided, Stage will search Spack's mirrors for - this archive at the mirror_path, before using the - default fetch strategy. + this archive at each of the provided relative mirror paths + before using the default fetch strategy. keep By default, when used as a context manager, the Stage @@ -276,7 +284,7 @@ def __init__( self.name = name if name is None: self.name = stage_prefix + next(tempfile._get_candidate_names()) - self.mirror_path = mirror_path + self.mirror_paths = mirror_paths # Use the provided path or construct an optionally named stage path. if path is not None: @@ -350,8 +358,8 @@ def expected_archive_files(self): expanded = self.default_fetcher.expand_archive fnames.append(os.path.basename(self.default_fetcher.url)) - if self.mirror_path: - fnames.append(os.path.basename(self.mirror_path)) + if self.mirror_paths: + fnames.extend(os.path.basename(x) for x in self.mirror_paths) paths.extend(os.path.join(self.path, f) for f in fnames) if not expanded: @@ -399,10 +407,14 @@ def fetch(self, mirror_only=False): # TODO: Or @alalazo may have some ideas about how to use a # TODO: CompositeFetchStrategy here. self.skip_checksum_for_mirror = True - if self.mirror_path: - urls = [ - url_util.join(mirror.fetch_url, self.mirror_path) - for mirror in spack.mirror.MirrorCollection().values()] + if self.mirror_paths: + # Join URLs of mirror roots with mirror paths. Because + # urljoin() will strip everything past the final '/' in + # the root, so we add a '/' if it is not present. + urls = [] + for mirror in spack.mirror.MirrorCollection().values(): + for rel_path in self.mirror_paths: + urls.append(url_util.join(mirror.fetch_url, rel_path)) # If this archive is normally fetched from a tarball URL, # then use the same digest. `spack mirror` ensures that @@ -428,10 +440,11 @@ def fetch(self, mirror_only=False): # url, digest, expand=expand, extension=extension)) if self.default_fetcher.cachable: - fetchers.insert( - 0, spack.caches.fetch_cache.fetcher( - self.mirror_path, digest, expand=expand, - extension=extension)) + for rel_path in reversed(list(self.mirror_paths)): + cache_fetcher = spack.caches.fetch_cache.fetcher( + rel_path, digest, expand=expand, + extension=extension) + fetchers.insert(0, cache_fetcher) def generate_fetchers(): for fetcher in fetchers: @@ -476,10 +489,24 @@ def check(self): self.fetcher.check() def cache_local(self): - spack.caches.fetch_cache.store(self.fetcher, self.mirror_path) + spack.caches.fetch_cache.store( + self.fetcher, self.mirror_paths.storage_path) - if spack.caches.mirror_cache: - spack.caches.mirror_cache.store(self.fetcher, self.mirror_path) + def cache_mirror(self, stats): + """Perform a fetch if the resource is not already cached""" + dst_root = spack.caches.mirror_cache.root + absolute_storage_path = os.path.join( + dst_root, self.mirror_paths.storage_path) + + if os.path.exists(absolute_storage_path): + stats.already_existed(absolute_storage_path) + return + + self.fetch() + spack.caches.mirror_cache.store( + self.fetcher, self.mirror_paths.storage_path, + self.mirror_paths.cosmetic_path) + stats.added(absolute_storage_path) def expand_archive(self): """Changes to the stage directory and attempt to expand the downloaded @@ -591,7 +618,7 @@ def _add_to_root_stage(self): @pattern.composite(method_list=[ 'fetch', 'create', 'created', 'check', 'expand_archive', 'restage', - 'destroy', 'cache_local', 'managed_by_spack']) + 'destroy', 'cache_local', 'cache_mirror', 'managed_by_spack']) class StageComposite: """Composite for Stage type objects. The first item in this composite is considered to be the root package, and operations that return a value are @@ -629,10 +656,6 @@ def path(self): def archive_file(self): return self[0].archive_file - @property - def mirror_path(self): - return self[0].mirror_path - class DIYStage(object): """ diff --git a/lib/spack/spack/test/cmd/mirror.py b/lib/spack/spack/test/cmd/mirror.py index 266aa36a4b5..889d81f98b7 100644 --- a/lib/spack/spack/test/cmd/mirror.py +++ b/lib/spack/spack/test/cmd/mirror.py @@ -37,7 +37,7 @@ def test_mirror_from_env(tmpdir, mock_packages, mock_fetch, config, add('git-test') concretize() with spack.config.override('config:checksum', False): - mirror('create', '-d', mirror_dir) + mirror('create', '-d', mirror_dir, '--all') e = ev.read(env_name) assert set(os.listdir(mirror_dir)) == set([s.name for s in e.user_specs]) diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index 571e9fcd584..4bed12456af 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -460,11 +460,11 @@ def test_unconcretized_install(install_mockery, mock_fetch, mock_packages): with pytest.raises(ValueError, match="only install concrete packages"): spec.package.do_install() - with pytest.raises(ValueError, match="fetch concrete packages"): + with pytest.raises(ValueError, match="only fetch concrete packages"): spec.package.do_fetch() - with pytest.raises(ValueError, match="stage concrete packages"): + with pytest.raises(ValueError, match="only stage concrete packages"): spec.package.do_stage() - with pytest.raises(ValueError, match="patch concrete packages"): + with pytest.raises(ValueError, match="only patch concrete packages"): spec.package.do_patch() diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py index 2f80bae4081..da40cfac372 100644 --- a/lib/spack/spack/test/mirror.py +++ b/lib/spack/spack/test/mirror.py @@ -52,46 +52,50 @@ def check_mirror(): mirrors = {'spack-mirror-test': 'file://' + mirror_root} spack.config.set('mirrors', mirrors) with spack.config.override('config:checksum', False): - spack.mirror.create(mirror_root, repos) + specs = [Spec(x).concretized() for x in repos] + spack.mirror.create(mirror_root, specs) # Stage directory exists assert os.path.isdir(mirror_root) - # check that there are subdirs for each package - for name in repos: - subdir = os.path.join(mirror_root, name) - assert os.path.isdir(subdir) + for spec in specs: + fetcher = spec.package.fetcher[0] + per_package_ref = os.path.join( + spec.name, '-'.join([spec.name, str(spec.version)])) + mirror_paths = spack.mirror.mirror_archive_paths( + fetcher, + per_package_ref) + expected_path = os.path.join( + mirror_root, mirror_paths.storage_path) + assert os.path.exists(expected_path) - files = os.listdir(subdir) - assert len(files) == 1 + # Now try to fetch each package. + for name, mock_repo in repos.items(): + spec = Spec(name).concretized() + pkg = spec.package - # Now try to fetch each package. - for name, mock_repo in repos.items(): - spec = Spec(name).concretized() - pkg = spec.package + with spack.config.override('config:checksum', False): + with pkg.stage: + pkg.do_stage(mirror_only=True) - with spack.config.override('config:checksum', False): - with pkg.stage: - pkg.do_stage(mirror_only=True) + # Compare the original repo with the expanded archive + original_path = mock_repo.path + if 'svn' in name: + # have to check out the svn repo to compare. + original_path = os.path.join( + mock_repo.path, 'checked_out') - # Compare the original repo with the expanded archive - original_path = mock_repo.path - if 'svn' in name: - # have to check out the svn repo to compare. - original_path = os.path.join( - mock_repo.path, 'checked_out') + svn = which('svn', required=True) + svn('checkout', mock_repo.url, original_path) - svn = which('svn', required=True) - svn('checkout', mock_repo.url, original_path) + dcmp = filecmp.dircmp( + original_path, pkg.stage.source_path) - dcmp = filecmp.dircmp( - original_path, pkg.stage.source_path) - - # make sure there are no new files in the expanded - # tarball - assert not dcmp.right_only - # and that all original files are present. - assert all(l in exclude for l in dcmp.left_only) + # make sure there are no new files in the expanded + # tarball + assert not dcmp.right_only + # and that all original files are present. + assert all(l in exclude for l in dcmp.left_only) def test_url_mirror(mock_archive): @@ -148,7 +152,7 @@ def test_mirror_with_url_patches(mock_packages, config, monkeypatch): files_cached_in_mirror = set() - def record_store(_class, fetcher, relative_dst): + def record_store(_class, fetcher, relative_dst, cosmetic_path=None): files_cached_in_mirror.add(os.path.basename(relative_dst)) def successful_fetch(_class): @@ -178,5 +182,7 @@ def successful_apply(*args, **kwargs): with spack.config.override('config:checksum', False): spack.mirror.create(mirror_root, list(spec.traverse())) - assert not (set(['urlpatch.patch', 'urlpatch2.patch.gz']) - - files_cached_in_mirror) + assert not (set([ + 'abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234', + 'abcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcd.gz' # NOQA: ignore=E501 + ]) - files_cached_in_mirror) diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py index e865cac32ef..9c0396ef5ee 100644 --- a/lib/spack/spack/test/packaging.py +++ b/lib/spack/spack/test/packaging.py @@ -92,9 +92,7 @@ def test_buildcache(mock_archive, tmpdir): # Create the build cache and # put it directly into the mirror mirror_path = os.path.join(str(tmpdir), 'test-mirror') - spack.mirror.create( - mirror_path, specs=[], no_checksum=True - ) + spack.mirror.create(mirror_path, specs=[]) # register mirror with spack config mirrors = {'spack-mirror-test': 'file://' + mirror_path} From 847703c13d0fd69be0b06d355308c47f4a060e66 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 25 Oct 2019 21:49:27 -0700 Subject: [PATCH 442/499] tutorial: move tutorial to standalone site (#13450) * docs: add a spack environment for building the docs * docs: remove tutorial and link to spack-tutorial.readthedocs.io The tutorial now has its own standalone website, versioned by instances of the tutorial. Link to that instead of versioning it directly with Spack. --- lib/spack/docs/.gitignore | 2 + lib/spack/docs/build_systems/intelpackage.rst | 10 +- lib/spack/docs/conf.py | 2 +- lib/spack/docs/index.rst | 2 +- lib/spack/docs/spack.yaml | 19 + lib/spack/docs/tutorial.rst | 75 - lib/spack/docs/tutorial/examples/0.package.py | 39 - lib/spack/docs/tutorial/examples/1.package.py | 24 - lib/spack/docs/tutorial/examples/2.package.py | 25 - lib/spack/docs/tutorial/examples/3.package.py | 25 - lib/spack/docs/tutorial/examples/4.package.py | 27 - lib/spack/docs/tutorial/examples/5.package.py | 42 - .../tutorial/examples/Autotools/0.package.py | 27 - .../tutorial/examples/Autotools/1.package.py | 32 - .../docs/tutorial/examples/Cmake/0.package.py | 41 - .../docs/tutorial/examples/Cmake/1.package.py | 23 - .../docs/tutorial/examples/Cmake/2.package.py | 33 - .../tutorial/examples/Makefile/0.package.py | 26 - .../tutorial/examples/Makefile/1.package.py | 27 - .../tutorial/examples/Makefile/2.package.py | 25 - .../tutorial/examples/Makefile/3.package.py | 36 - .../tutorial/examples/PyPackage/0.package.py | 41 - .../tutorial/examples/PyPackage/1.package.py | 32 - .../tutorial/sc16-tutorial-slide-preview.png | Bin 71641 -> 0 bytes .../docs/tutorial_advanced_packaging.rst | 515 ----- lib/spack/docs/tutorial_basics.rst | 1736 ----------------- lib/spack/docs/tutorial_buildsystems.rst | 807 -------- lib/spack/docs/tutorial_configuration.rst | 951 --------- lib/spack/docs/tutorial_environments.rst | 815 -------- lib/spack/docs/tutorial_modules.rst | 1575 --------------- lib/spack/docs/tutorial_packaging.rst | 559 ------ 31 files changed, 28 insertions(+), 7565 deletions(-) create mode 100644 lib/spack/docs/spack.yaml delete mode 100644 lib/spack/docs/tutorial.rst delete mode 100644 lib/spack/docs/tutorial/examples/0.package.py delete mode 100644 lib/spack/docs/tutorial/examples/1.package.py delete mode 100644 lib/spack/docs/tutorial/examples/2.package.py delete mode 100644 lib/spack/docs/tutorial/examples/3.package.py delete mode 100644 lib/spack/docs/tutorial/examples/4.package.py delete mode 100644 lib/spack/docs/tutorial/examples/5.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Autotools/0.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Autotools/1.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Cmake/0.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Cmake/1.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Cmake/2.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Makefile/0.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Makefile/1.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Makefile/2.package.py delete mode 100644 lib/spack/docs/tutorial/examples/Makefile/3.package.py delete mode 100644 lib/spack/docs/tutorial/examples/PyPackage/0.package.py delete mode 100644 lib/spack/docs/tutorial/examples/PyPackage/1.package.py delete mode 100644 lib/spack/docs/tutorial/sc16-tutorial-slide-preview.png delete mode 100644 lib/spack/docs/tutorial_advanced_packaging.rst delete mode 100644 lib/spack/docs/tutorial_basics.rst delete mode 100644 lib/spack/docs/tutorial_buildsystems.rst delete mode 100644 lib/spack/docs/tutorial_configuration.rst delete mode 100644 lib/spack/docs/tutorial_environments.rst delete mode 100644 lib/spack/docs/tutorial_modules.rst delete mode 100644 lib/spack/docs/tutorial_packaging.rst diff --git a/lib/spack/docs/.gitignore b/lib/spack/docs/.gitignore index 0b6258af509..1624dfeaeab 100644 --- a/lib/spack/docs/.gitignore +++ b/lib/spack/docs/.gitignore @@ -3,3 +3,5 @@ command_index.rst spack*.rst llnl*.rst _build +.spack-env +spack.lock diff --git a/lib/spack/docs/build_systems/intelpackage.rst b/lib/spack/docs/build_systems/intelpackage.rst index 30c567373e0..f7d975899e9 100644 --- a/lib/spack/docs/build_systems/intelpackage.rst +++ b/lib/spack/docs/build_systems/intelpackage.rst @@ -120,7 +120,7 @@ version numbers seen with most other Spack packages. For example, we have: ... Preferred version: professional.2018.3 http:... - + Safe versions: professional.2018.3 http:... ... @@ -728,7 +728,7 @@ For packages that contain a compiler, follow `the previous section .. code-block:: console - $ spack install intel-mpi@2018.3.199 + $ spack install intel-mpi@2018.3.199 $ spack install intel-mpi@2018.3.199 %intel@18 4. To prepare the new packages for use with client packages, @@ -802,7 +802,7 @@ by one of the following means: Configure the order of compilers in the appropriate ``packages.yaml`` file, under either an ``all:`` or client-package-specific entry, in a ``compiler:`` list. Consult the Spack documentation for - :ref:`Configuring Package Preferences ` + `Configuring Package Preferences `_ and :ref:`Concretization Preferences `. @@ -851,7 +851,7 @@ client packages, edit the ``packages.yaml`` file. Customize, either in the the virtual packages and whose values are the Spack specs that satisfy the virtual package, in order of decreasing preference. To learn more about the ``providers:`` settings, see the Spack tutorial for -:ref:`Configuring Package Preferences ` +`Configuring Package Preferences `_ and the section :ref:`Concretization Preferences `. @@ -972,7 +972,7 @@ a *virtual* ``mkl`` package is declared in Spack. .. code-block:: python self.spec['blas'].headers.include_flags - + and to generate linker options (``-L -llibname ...``), use the same as above, .. code-block:: python diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py index cacbbb3a412..e5305a93175 100644 --- a/lib/spack/docs/conf.py +++ b/lib/spack/docs/conf.py @@ -159,7 +159,7 @@ def setup(sphinx): # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build', '_spack_root'] +exclude_patterns = ['_build', '_spack_root', '.spack-env'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst index 5c93285cbbf..48af67982aa 100644 --- a/lib/spack/docs/index.rst +++ b/lib/spack/docs/index.rst @@ -55,7 +55,7 @@ or refer to the full manual below. getting_started basic_usage workflows - tutorial + Tutorial: Spack 101 known_issues .. toctree:: diff --git a/lib/spack/docs/spack.yaml b/lib/spack/docs/spack.yaml new file mode 100644 index 00000000000..bade961fce4 --- /dev/null +++ b/lib/spack/docs/spack.yaml @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# +# These are requirements for building the documentation. You can run +# these commands in this directory to install Sphinx and its plugins, +# then build the docs: +# +# spack install +# spack env activate . +# make +# +spack: + specs: + - py-sphinx + - py-sphinxcontrib-programoutput + - py-sphinx-rtd-theme diff --git a/lib/spack/docs/tutorial.rst b/lib/spack/docs/tutorial.rst deleted file mode 100644 index 4ece87ade00..00000000000 --- a/lib/spack/docs/tutorial.rst +++ /dev/null @@ -1,75 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _spack-101: - -============================= -Tutorial: Spack 101 -============================= - -This is a full-day introduction to Spack with lectures and live demos. -It was last presented at the `Practice and Experience in Advanced -Research Computing Conference (PEARC19) -`_ on July 31, 2019. - -You can use these materials to teach a course on Spack at your own site, -or you can just skip ahead and read the live demo scripts to see how -Spack is used in practice. - -.. _sc16-slides: - -.. rubric:: Slides - -.. figure:: tutorial/sc16-tutorial-slide-preview.png - :target: https://spack.io/slides/spack-pearc19-tutorial-slides.pdf - :height: 72px - :align: left - :alt: Slide Preview - -`Download Slides `_. - -**Full citation:** Levi Baber, Gregory Becker, Adam J. Stewart, and Todd -Gamblin. Managing HPC Software Complexity with Spack. Tutorial presented -at the Practice and Experience in Advanced Research Computing Conference -(PEARC19). July 31, 2019. Chicago, IL, USA. - -.. _sc16-live-demos: - -.. rubric:: Live Demos - -We provide scripts that take you step-by-step through basic Spack tasks. -They correspond to sections in the slides above. You can use one of the -following methods to run through the scripts: - - 1. We provide the `spack/tutorial - `_ container image on - Docker Hub that you can use to do the tutorial on your local - machine. You can invoke ``docker run -it spack/tutorial`` to start - using the container. - - 2. When we host the tutorial, we also provision VM instances in `AWS - `_, so that users who are unfamiliar with - Docker can simply log into a VPM to do the demo exercises. - -You should now be ready to run through our demo scripts: - - 1. :ref:`basics-tutorial` - 2. :ref:`configs-tutorial` - 3. :ref:`packaging-tutorial` - 4. :ref:`environments-tutorial` - 5. :ref:`modules-tutorial` - 6. :ref:`build-systems-tutorial` - 7. :ref:`advanced-packaging-tutorial` - -Full contents: - -.. toctree:: - tutorial_basics - tutorial_configuration - tutorial_packaging - tutorial_environments - tutorial_modules - tutorial_buildsystems - tutorial_advanced_packaging diff --git a/lib/spack/docs/tutorial/examples/0.package.py b/lib/spack/docs/tutorial/examples/0.package.py deleted file mode 100644 index 990ba7d3d87..00000000000 --- a/lib/spack/docs/tutorial/examples/0.package.py +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -# -# This is a template package file for Spack. We've put "FIXME" -# next to all the things you'll want to change. Once you've handled -# them, you can save this file and test your package like this: -# -# spack install mpileaks -# -# You can edit this file again by typing: -# -# spack edit mpileaks -# -# See the Spack documentation for more information on packaging. -# If you submit this package back to Spack as a pull request, -# please first remove this boilerplate and all FIXME comments. -# -from spack import * - - -class Mpileaks(Package): - """FIXME: Put a proper description of your package here.""" - - # FIXME: Add a proper url for your package's homepage here. - homepage = "http://www.example.com" - url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825') - - # FIXME: Add dependencies if required. - # depends_on('foo') - - def install(self, spec, prefix): - # FIXME: Unknown build system - make() - make('install') diff --git a/lib/spack/docs/tutorial/examples/1.package.py b/lib/spack/docs/tutorial/examples/1.package.py deleted file mode 100644 index f2d515fa4a4..00000000000 --- a/lib/spack/docs/tutorial/examples/1.package.py +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpileaks(Package): - """Tool to detect and report MPI objects like MPI_Requests and - MPI_Datatypes.""" - - homepage = "https://github.com/LLNL/mpileaks" - url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825') - - # FIXME: Add dependencies if required. - # depends_on('foo') - - def install(self, spec, prefix): - # FIXME: Unknown build system - make() - make('install') diff --git a/lib/spack/docs/tutorial/examples/2.package.py b/lib/spack/docs/tutorial/examples/2.package.py deleted file mode 100644 index d0f1e6d0626..00000000000 --- a/lib/spack/docs/tutorial/examples/2.package.py +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpileaks(Package): - """Tool to detect and report MPI objects like MPI_Requests and - MPI_Datatypes.""" - - homepage = "https://github.com/LLNL/mpileaks" - url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825') - - depends_on('mpi') - depends_on('adept-utils') - depends_on('callpath') - - def install(self, spec, prefix): - # FIXME: Unknown build system - make() - make('install') diff --git a/lib/spack/docs/tutorial/examples/3.package.py b/lib/spack/docs/tutorial/examples/3.package.py deleted file mode 100644 index 05fd7aa00a2..00000000000 --- a/lib/spack/docs/tutorial/examples/3.package.py +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpileaks(Package): - """Tool to detect and report MPI objects like MPI_Requests and - MPI_Datatypes.""" - - homepage = "https://github.com/LLNL/mpileaks" - url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825') - - depends_on('mpi') - depends_on('adept-utils') - depends_on('callpath') - - def install(self, spec, prefix): - configure() - make() - make('install') diff --git a/lib/spack/docs/tutorial/examples/4.package.py b/lib/spack/docs/tutorial/examples/4.package.py deleted file mode 100644 index 626e7d3fec1..00000000000 --- a/lib/spack/docs/tutorial/examples/4.package.py +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpileaks(Package): - """Tool to detect and report MPI objects like MPI_Requests and - MPI_Datatypes.""" - - homepage = "https://github.com/LLNL/mpileaks" - url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825') - - depends_on('mpi') - depends_on('adept-utils') - depends_on('callpath') - - def install(self, spec, prefix): - configure('--prefix={0}'.format(prefix), - '--with-adept-utils={0}'.format(spec['adept-utils'].prefix), - '--with-callpath={0}'.format(spec['callpath'].prefix)) - make() - make('install') diff --git a/lib/spack/docs/tutorial/examples/5.package.py b/lib/spack/docs/tutorial/examples/5.package.py deleted file mode 100644 index 9a1dec20792..00000000000 --- a/lib/spack/docs/tutorial/examples/5.package.py +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpileaks(Package): - """Tool to detect and report MPI objects like MPI_Requests and - MPI_Datatypes.""" - - homepage = "https://github.com/LLNL/mpileaks" - url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825') - - variant('stackstart', values=int, default=0, - description='Specify the number of stack frames to truncate') - - depends_on('mpi') - depends_on('adept-utils') - depends_on('callpath') - - def install(self, spec, prefix): - stackstart = int(spec.variants['stackstart'].value) - - args = [ - '--prefix={0}'.format(prefix), - '--with-adept-utils={0}'.format(spec['adept-utils'].prefix), - '--with-callpath={0}'.format(spec['callpath'].prefix), - ] - - if stackstart: - args.extend([ - '--with-stack-start-c={0}'.format(stackstart), - '--with-stack-start-fortran={0}'.format(stackstart) - ]) - - configure(*args) - make() - make('install') diff --git a/lib/spack/docs/tutorial/examples/Autotools/0.package.py b/lib/spack/docs/tutorial/examples/Autotools/0.package.py deleted file mode 100644 index 213965e5c63..00000000000 --- a/lib/spack/docs/tutorial/examples/Autotools/0.package.py +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpileaks(AutotoolsPackage): - """Tool to detect and report leaked MPI objects like MPI_Requests and - MPI_Datatypes.""" - - homepage = "https://github.com/hpc/mpileaks" - url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', '8838c574b39202a57d7c2d68692718aa') - - depends_on("mpi") - depends_on("adept-utils") - depends_on("callpath") - - def install(self, spec, prefix): - configure("--prefix=" + prefix, - "--with-adept-utils=" + spec['adept-utils'].prefix, - "--with-callpath=" + spec['callpath'].prefix) - make() - make("install") diff --git a/lib/spack/docs/tutorial/examples/Autotools/1.package.py b/lib/spack/docs/tutorial/examples/Autotools/1.package.py deleted file mode 100644 index 639f1305960..00000000000 --- a/lib/spack/docs/tutorial/examples/Autotools/1.package.py +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpileaks(AutotoolsPackage): - """Tool to detect and report leaked MPI objects like MPI_Requests and - MPI_Datatypes.""" - - homepage = "https://github.com/hpc/mpileaks" - url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - - version('1.0', '8838c574b39202a57d7c2d68692718aa') - - variant("stackstart", values=int, default=0, - description="Specify the number of stack frames to truncate") - - depends_on("mpi") - depends_on("adept-utils") - depends_on("callpath") - - def configure_args(self): - stackstart = int(self.spec.variants['stackstart'].value) - args = ["--with-adept-utils=" + spec['adept-utils'].prefix, - "--with-callpath=" + spec['callpath'].prefix] - if stackstart: - args.extend(['--with-stack-start-c=%s' % stackstart, - '--with-stack-start-fortran=%s' % stackstart]) - return args diff --git a/lib/spack/docs/tutorial/examples/Cmake/0.package.py b/lib/spack/docs/tutorial/examples/Cmake/0.package.py deleted file mode 100644 index b8c96a19293..00000000000 --- a/lib/spack/docs/tutorial/examples/Cmake/0.package.py +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -# -# This is a template package file for Spack. We've put "FIXME" -# next to all the things you'll want to change. Once you've handled -# them, you can save this file and test your package like this: -# -# spack install callpath -# -# You can edit this file again by typing: -# -# spack edit callpath -# -# See the Spack documentation for more information on packaging. -# If you submit this package back to Spack as a pull request, -# please first remove this boilerplate and all FIXME comments. -# -from spack import * - - -class Callpath(CMakePackage): - """FIXME: Put a proper description of your package here.""" - - # FIXME: Add a proper url for your package's homepage here. - homepage = "http://www.example.com" - url = "https://github.com/llnl/callpath/archive/v1.0.1.tar.gz" - - version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a') - - # FIXME: Add dependencies if required. - # depends_on('foo') - - def cmake_args(self): - # FIXME: Add arguments other than - # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE - # FIXME: If not needed delete this function - args = [] - return args diff --git a/lib/spack/docs/tutorial/examples/Cmake/1.package.py b/lib/spack/docs/tutorial/examples/Cmake/1.package.py deleted file mode 100644 index 8a0d9d0e822..00000000000 --- a/lib/spack/docs/tutorial/examples/Cmake/1.package.py +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Callpath(CMakePackage): - """Library for representing callpaths consistently in - distributed-memory performance tools.""" - - homepage = "https://github.com/llnl/callpath" - url = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz" - - version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a') - - depends_on("elf", type="link") - depends_on("libdwarf") - depends_on("dyninst") - depends_on("adept-utils") - depends_on("mpi") - depends_on("cmake@2.8:", type="build") diff --git a/lib/spack/docs/tutorial/examples/Cmake/2.package.py b/lib/spack/docs/tutorial/examples/Cmake/2.package.py deleted file mode 100644 index 2b4faca90dd..00000000000 --- a/lib/spack/docs/tutorial/examples/Cmake/2.package.py +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Callpath(CMakePackage): - """Library for representing callpaths consistently in - distributed-memory performance tools.""" - - homepage = "https://github.com/llnl/callpath" - url = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz" - - version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a') - - depends_on("elf", type="link") - depends_on("libdwarf") - depends_on("dyninst") - depends_on("adept-utils") - depends_on("mpi") - depends_on("cmake@2.8:", type="build") - - def cmake_args(self): - args = ["-DCALLPATH_WALKER=dyninst"] - - if self.spec.satisfies("^dyninst@9.3.0:"): - std.flag = self.compiler.cxx_flag - args.append("-DCMAKE_CXX_FLAGS='{0}' -fpermissive'".format( - std_flag)) - - return args diff --git a/lib/spack/docs/tutorial/examples/Makefile/0.package.py b/lib/spack/docs/tutorial/examples/Makefile/0.package.py deleted file mode 100644 index 8ad252f5b39..00000000000 --- a/lib/spack/docs/tutorial/examples/Makefile/0.package.py +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Bowtie(MakefilePackage): - """FIXME: Put a proper description of your package here.""" - - # FIXME: Add a proper url for your package's homepage here. - homepage = "http://www.example.com" - url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" - - version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') - - # FIXME: Add dependencies if required. - # depends_on('foo') - - def edit(self, spec, prefix): - # FIXME: Edit the Makefile if necessary - # FIXME: If not needed delete this function - # makefile = FileFilter('Makefile') - # makefile.filter('CC = .*', 'CC = cc') - return diff --git a/lib/spack/docs/tutorial/examples/Makefile/1.package.py b/lib/spack/docs/tutorial/examples/Makefile/1.package.py deleted file mode 100644 index 16988dc1b04..00000000000 --- a/lib/spack/docs/tutorial/examples/Makefile/1.package.py +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Bowtie(MakefilePackage): - """Bowtie is an ultrafast, memory efficient short read aligner - for short DNA sequences (reads) from next-gen sequencers.""" - - homepage = "https://sourceforge.net/projects/bowtie-bio/" - url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" - - version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') - - variant("tbb", default=False, description="Use Intel thread building block") - - depends_on("tbb", when="+tbb") - - def edit(self, spec, prefix): - # FIXME: Edit the Makefile if necessary - # FIXME: If not needed delete this function - # makefile = FileFilter('Makefile') - # makefile.filter('CC = .*', 'CC = cc') - return diff --git a/lib/spack/docs/tutorial/examples/Makefile/2.package.py b/lib/spack/docs/tutorial/examples/Makefile/2.package.py deleted file mode 100644 index 0973b2028e7..00000000000 --- a/lib/spack/docs/tutorial/examples/Makefile/2.package.py +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Bowtie(MakefilePackage): - """Bowtie is an ultrafast, memory efficient short read aligner - for short DNA sequences (reads) from next-gen sequencers.""" - - homepage = "https://sourceforge.net/projects/bowtie-bio/" - url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" - - version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') - - variant("tbb", default=False, description="Use Intel thread building block") - - depends_on("tbb", when="+tbb") - - def edit(self, spec, prefix): - makefile = FileFilter("Makefile") - makefile.filter('CC= .*', 'CC = ' + env['CC']) - makefile.filter('CXX = .*', 'CXX = ' + env['CXX']) diff --git a/lib/spack/docs/tutorial/examples/Makefile/3.package.py b/lib/spack/docs/tutorial/examples/Makefile/3.package.py deleted file mode 100644 index 6a1942e627f..00000000000 --- a/lib/spack/docs/tutorial/examples/Makefile/3.package.py +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Bowtie(MakefilePackage): - """Bowtie is an ultrafast, memory efficient short read aligner - for short DNA sequences (reads) from next-gen sequencers.""" - - homepage = "https://sourceforge.net/projects/bowtie-bio/" - url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" - - version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') - - variant("tbb", default=False, description="Use Intel thread building block") - - depends_on("tbb", when="+tbb") - - def edit(self, spec, prefix): - makefile = FileFilter("Makefile") - makefile.filter('CC= .*', 'CC = ' + env['CC']) - makefile.filter('CXX = .*', 'CXX = ' + env['CXX']) - - @property - def build_targets(self): - if "+tbb" in spec: - return [] - else: - return ["NO_TBB=1"] - - @property - def install_targets(self): - return ['prefix={0}'.format(self.prefix), 'install'] diff --git a/lib/spack/docs/tutorial/examples/PyPackage/0.package.py b/lib/spack/docs/tutorial/examples/PyPackage/0.package.py deleted file mode 100644 index 9ad94189d92..00000000000 --- a/lib/spack/docs/tutorial/examples/PyPackage/0.package.py +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -# -# This is a template package file for Spack. We've put "FIXME" -# next to all the things you'll want to change. Once you've handled -# them, you can save this file and test your package like this: -# -# spack install py-pandas -# -# You can edit this file again by typing: -# -# spack edit py-pandas -# -# See the Spack documentation for more information on packaging. -# If you submit this package back to Spack as a pull request, -# please first remove this boilerplate and all FIXME comments. -# -from spack import * - - -class PyPandas(PythonPackage): - """FIXME: Put a proper description of your package here.""" - - # FIXME: Add a proper url for your package's homepage here. - homepage = "http://www.example.com" - url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz" - - version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3') - - # FIXME: Add dependencies if required. - # depends_on('py-setuptools', type='build') - # depends_on('py-foo', type=('build', 'run')) - - def build_args(self, spec, prefix): - # FIXME: Add arguments other than --prefix - # FIXME: If not needed delete this function - args = [] - return args diff --git a/lib/spack/docs/tutorial/examples/PyPackage/1.package.py b/lib/spack/docs/tutorial/examples/PyPackage/1.package.py deleted file mode 100644 index 8ac335d4a6e..00000000000 --- a/lib/spack/docs/tutorial/examples/PyPackage/1.package.py +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PyPandas(PythonPackage): - """pandas is a Python package providing fast, flexible, and expressive - data structures designed to make working with relational or - labeled data both easy and intuitive. It aims to be the - fundamental high-level building block for doing practical, real - world data analysis in Python. Additionally, it has the broader - goal of becoming the most powerful and flexible open source data - analysis / manipulation tool available in any language. - """ - homepage = "http://pandas.pydata.org/" - url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz" - - version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3') - version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') - version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') - version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73') - - depends_on('py-dateutil', type=('build', 'run')) - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-setuptools', type='build') - depends_on('py-cython', type='build') - depends_on('py-pytz', type=('build', 'run')) - depends_on('py-numexpr', type=('build', 'run')) - depends_on('py-bottleneck', type=('build', 'run')) diff --git a/lib/spack/docs/tutorial/sc16-tutorial-slide-preview.png b/lib/spack/docs/tutorial/sc16-tutorial-slide-preview.png deleted file mode 100644 index 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Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _advanced-packaging-tutorial: - -============================ -Advanced Topics in Packaging -============================ - -Spack tries to automatically configure packages with information from -dependencies such that all you need to do is to list the dependencies -(i.e., with the ``depends_on`` directive) and the build system (for example -by deriving from :code:`CmakePackage`). - -However, there are many special cases. Often you need to retrieve details -about dependencies to set package-specific configuration options, or to -define package-specific environment variables used by the package's build -system. This tutorial covers how to retrieve build information from -dependencies, and how you can automatically provide important information to -dependents in your package. - ----------------------- -Setup for the tutorial ----------------------- - -.. note:: - - We do not recommend doing this section of the tutorial in a - production Spack instance. - -The tutorial uses custom package definitions with missing sections that -will be filled in during the tutorial. These package definitions are stored -in a separate package repository, which can be enabled with: - -.. code-block:: console - - $ spack repo add --scope=site var/spack/repos/tutorial - -This section of the tutorial may also require a newer version of -gcc. If you have not already installed gcc@7.2.0 and added it to your -configuration, you can do so with: - -.. code-block:: console - - $ spack install gcc@7.2.0 %gcc@5.4.0 - $ spack compiler add --scope=site `spack location -i gcc@7.2.0 %gcc@5.4.0` - -If you are using the tutorial docker image, all dependency packages -will have been installed. Otherwise, to install these packages you can use -the following commands: - -.. code-block:: console - - $ spack install openblas - $ spack install netlib-lapack - $ spack install mpich - -Now, you are ready to set your preferred ``EDITOR`` and continue with -the rest of the tutorial. - -.. note:: - - Several of these packages depend on an MPI implementation. You can use - OpenMPI if you install it from scratch, but this is slow (>10 min.). - A binary cache of MPICH may be provided, in which case you can force - the package to use it and install quickly. All tutorial examples with - packages that depend on MPICH include the spec syntax for building with it - -.. _adv_pkg_tutorial_start: - ---------------------------------------- -Modifying a package's build environment ---------------------------------------- - -Spack sets up several environment variables like ``PATH`` by default to aid in -building a package, but many packages make use of environment variables which -convey specific information about their dependencies (e.g., ``MPICC``). -This section covers how to update your Spack packages so that package-specific -environment variables are defined at build-time. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Set environment variables in dependent packages at build-time -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Dependencies can set environment variables that are required when their -dependents build. For example, when a package depends on a python extension -like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH`` -so it is available at build time; this is required because the default setup -that spack does is not sufficient for python to import modules. - -Any package can override the -:py:func:`setup_dependent_build_environment ` -method to setup the build environment for a dependent. -This method takes as an argument a :py:class:`EnvironmentModifications ` -object which includes convenience methods to update the environment. For -example, an MPI implementation can set ``MPICC`` for packages that depend on it: - -.. code-block:: python - - def setup_dependent_build_environment(self, env, dependent_spec): - env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - -In this case packages that depend on ``mpi`` will have ``MPICC`` defined in -their environment when they build. This section is focused on setting up the -build-time environment but it's worth noting that a similar method called -:py:func:`setup_dependent_run_environment ` -can be used to code modifications that will be included in Spack's automatically-generated -module files. - -We can practice by editing the ``mpich`` package to set the ``MPICC`` -environment variable in the build-time environment of dependent packages. - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit mpich - -Once you're finished, the method should look like this: - -.. code-block:: python - - def setup_dependent_build_environment(self, env, dependent_spec): - env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) - env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) - - env.set('MPICH_CC', spack_cc) - env.set('MPICH_CXX', spack_cxx) - env.set('MPICH_F77', spack_f77) - env.set('MPICH_F90', spack_fc) - env.set('MPICH_FC', spack_fc) - -At this point we can, for instance, install ``netlib-scalapack`` with -``mpich``: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich - ... - ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z - ==> No patches needed for netlib-scalapack - ==> Building netlib-scalapack [CMakePackage] - ==> Executing phase: 'cmake' - ==> Executing phase: 'build' - ==> Executing phase: 'install' - ==> Successfully installed netlib-scalapack - Fetch: 0.01s. Build: 3m 59.86s. Total: 3m 59.87s. - [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z - - -and double check the environment logs to verify that every variable was -set to the correct value. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Set environment variables in your own package -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Packages can override the -:py:func:`setup_build_environment ` -or the -:py:func:`setup_run_environment ` -methods to modify their own build-time or run-time environment respectively. -An example of a package that overrides both methods is ``qt``: - -.. code-block:: python - - def setup_build_environment(self, env): - env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) - - def setup_run_environment(self, env): - env.set('QTDIR', self.prefix) - -When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment. Likewise, when a -module file is created for ``qt`` it will contain commands to define ``QTDIR`` appropriately. - -To contrast with ``qt``'s -:py:func:`setup_dependent_build_environment ` -function: - -.. code-block:: python - - def setup_dependent_build_environment(self, env, dependent_spec): - env.set('QTDIR', self.prefix) - -Let's see how it works by completing the ``elpa`` package: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit elpa - -In the end your method should look like: - -.. code-block:: python - - def setup_build_environment(self, env): - spec = self.spec - - env.set('CC', spec['mpi'].mpicc) - env.set('FC', spec['mpi'].mpifc) - env.set('CXX', spec['mpi'].mpicxx) - env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) - - env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) - env.append_flags('LIBS', spec['lapack'].libs.link_flags) - -At this point it's possible to proceed with the installation of ``elpa ^mpich`` - ------------------------------- -Retrieving library information ------------------------------- - -Although Spack attempts to help packages locate their dependency libraries -automatically (e.g. by setting ``PKG_CONFIG_PATH`` and ``CMAKE_PREFIX_PATH``), -a package may have unique configuration options that are required to locate -libraries. When a package needs information about dependency libraries, the -general approach in Spack is to query the dependencies for the locations of -their libraries and set configuration options accordingly. By default most -Spack packages know how to automatically locate their libraries. This section -covers how to retrieve library information from dependencies and how to locate -libraries when the default logic doesn't work. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Accessing dependency libraries -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -If you need to access the libraries of a dependency, you can do so -via the ``libs`` property of the spec, for example in the ``arpack-ng`` -package: - -.. code-block:: python - - def install(self, spec, prefix): - lapack_libs = spec['lapack'].libs.joined(';') - blas_libs = spec['blas'].libs.joined(';') - - cmake(*[ - '-DLAPACK_LIBRARIES={0}'.format(lapack_libs), - '-DBLAS_LIBRARIES={0}'.format(blas_libs) - ], '.') - -Note that ``arpack-ng`` is querying virtual dependencies, which Spack -automatically resolves to the installed implementation (e.g. ``openblas`` -for ``blas``). - -We've started work on a package for ``armadillo``. You should open it, -read through the comment that starts with ``# TUTORIAL:`` and complete -the ``cmake_args`` section: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit armadillo - -If you followed the instructions in the package, when you are finished your -``cmake_args`` method should look like: - -.. code-block:: python - - def cmake_args(self): - spec = self.spec - - return [ - # ARPACK support - '-DARPACK_LIBRARY={0}'.format(spec['arpack-ng'].libs.joined(";")), - # BLAS support - '-DBLAS_LIBRARY={0}'.format(spec['blas'].libs.joined(";")), - # LAPACK support - '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].libs.joined(";")), - # SuperLU support - '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include), - '-DSuperLU_LIBRARY={0}'.format(spec['superlu'].libs.joined(";")), - # HDF5 support - '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF') - ] - -As you can see, getting the list of libraries that your dependencies provide -is as easy as accessing the their ``libs`` attribute. Furthermore, the interface -remains the same whether you are querying regular or virtual dependencies. - -At this point you can complete the installation of ``armadillo`` using ``openblas`` -as a LAPACK provider (``armadillo ^openblas ^mpich``): - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install armadillo ^openblas ^mpich - ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj - ... - ==> superlu is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-5.2.1-q2mbtw2wo4kpzis2e2n227ip2fquxrno - ==> Installing armadillo - ==> Using cached archive: /usr/local/var/spack/cache/armadillo/armadillo-8.100.1.tar.xz - ==> Staging archive: /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4/armadillo-8.100.1.tar.xz - ==> Created stage in /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4 - ==> Applied patch undef_linux.patch - ==> Building armadillo [CMakePackage] - ==> Executing phase: 'cmake' - ==> Executing phase: 'build' - ==> Executing phase: 'install' - ==> Successfully installed armadillo - Fetch: 0.01s. Build: 3.96s. Total: 3.98s. - [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4 - -Hopefully the installation went fine and the code we added expanded to the right list -of semicolon separated libraries (you are encouraged to open ``armadillo``'s -build logs to double check). - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Providing libraries to dependents -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Spack provides a default implementation for ``libs`` which often works -out of the box. A user can write a package definition without having to -implement a ``libs`` property and dependents can retrieve its libraries -as shown in the above section. However, the default implementation assumes that -libraries follow the naming scheme ``lib.so`` (or e.g. -``lib.a`` for static libraries). Packages which don't -follow this naming scheme must implement this function themselves, e.g. -``opencv``: - -.. code-block:: python - - @property - def libs(self): - shared = "+shared" in self.spec - return find_libraries( - "libopencv_*", root=self.prefix, shared=shared, recurse=True - ) - -This issue is common for packages which implement an interface (i.e. -virtual package providers in Spack). If we try to build another version of -``armadillo`` tied to ``netlib-lapack`` (``armadillo ^netlib-lapack ^mpich``) -we'll notice that this time the installation won't complete: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack ^mpich - ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj - ... - ==> openmpi is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f - ==> Installing arpack-ng - ==> Using cached archive: /usr/local/var/spack/cache/arpack-ng/arpack-ng-3.5.0.tar.gz - ==> Already staged arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un in /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un - ==> No patches needed for arpack-ng - ==> Building arpack-ng [Package] - ==> Executing phase: 'install' - ==> Error: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z - RuntimeError: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z - - /usr/local/var/spack/repos/builtin/packages/arpack-ng/package.py:105, in install: - 5 options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) - 6 - 7 # Make sure we use Spack's blas/lapack: - >> 8 lapack_libs = spec['lapack'].libs.joined(';') - 9 blas_libs = spec['blas'].libs.joined(';') - 10 - 11 options.extend([ - - See build log for details: - /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un/arpack-ng-3.5.0/spack-build-out.txt - -Unlike ``openblas`` which provides a library named ``libopenblas.so``, -``netlib-lapack`` provides ``liblapack.so``, so it needs to implement -customized library search logic. Let's edit it: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit netlib-lapack - -and follow the instructions in the ``# TUTORIAL:`` comment as before. -What we need to implement is: - -.. code-block:: python - - @property - def lapack_libs(self): - shared = True if '+shared' in self.spec else False - return find_libraries( - 'liblapack', root=self.prefix, shared=shared, recursive=True - ) - -i.e., a property that returns the correct list of libraries for the LAPACK interface. - -We use the name ``lapack_libs`` rather than ``libs`` because -``netlib-lapack`` can also provide ``blas``, and when it does it is provided -as a separate library file. Using this name ensures that when -dependents ask for ``lapack`` libraries, ``netlib-lapack`` will retrieve only -the libraries associated with the ``lapack`` interface. Now we can finally -install ``armadillo ^netlib-lapack ^mpich``: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack ^mpich - ... - - ==> Building armadillo [CMakePackage] - ==> Executing phase: 'cmake' - ==> Executing phase: 'build' - ==> Executing phase: 'install' - ==> Successfully installed armadillo - Fetch: 0.01s. Build: 3.75s. Total: 3.76s. - [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-sxmpu5an4dshnhickh6ykchyfda7jpyn - -Since each implementation of a virtual package is responsible for locating the -libraries associated with the interfaces it provides, dependents do not need -to include special-case logic for different implementations and for example -need only ask for :code:`spec['blas'].libs`. - ----------------------- -Other Packaging Topics ----------------------- - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Attach attributes to other packages -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Build tools usually also provide a set of executables that can be used -when another package is being installed. Spack gives you the opportunity -to monkey-patch dependent modules and attach attributes to them. This -helps make the packager experience as similar as possible to what would -have been the manual installation of the same package. - -An example here is the ``automake`` package, which overrides -:py:func:`setup_dependent_package `: - -.. code-block:: python - - def setup_dependent_package(self, module, dependent_spec): - # Automake is very likely to be a build dependency, - # so we add the tools it provides to the dependent module - executables = ['aclocal', 'automake'] - for name in executables: - setattr(module, name, self._make_executable(name)) - -so that every other package that depends on it can use directly ``aclocal`` -and ``automake`` with the usual function call syntax of :py:class:`Executable `: - -.. code-block:: python - - aclocal('--force') - -^^^^^^^^^^^^^^^^^^^^^^^ -Extra query parameters -^^^^^^^^^^^^^^^^^^^^^^^ - -An advanced feature of the Spec's build-interface protocol is the support -for extra parameters after the subscript key. In fact, any of the keys used in the query -can be followed by a comma-separated list of extra parameters which can be -inspected by the package receiving the request to fine-tune a response. - -Let's look at an example and try to install ``netcdf ^mpich``: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install netcdf ^mpich - ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a - ... - ==> Error: AttributeError: 'list' object has no attribute 'search_flags' - AttributeError: AttributeError: 'list' object has no attribute 'search_flags' - - /usr/local/var/spack/repos/builtin/packages/netcdf/package.py:207, in configure_args: - 50 # used instead. - 51 hdf5_hl = self.spec['hdf5:hl'] - 52 CPPFLAGS.append(hdf5_hl.headers.cpp_flags) - >> 53 LDFLAGS.append(hdf5_hl.libs.search_flags) - 54 - 55 if '+parallel-netcdf' in self.spec: - 56 config_args.append('--enable-pnetcdf') - - See build log for details: - /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj/netcdf-4.4.1.1/spack-build-out.txt - -We can see from the error that ``netcdf`` needs to know how to link the *high-level interface* -of ``hdf5``, and thus passes the extra parameter ``hl`` after the request to retrieve it. -Clearly the implementation in the ``hdf5`` package is not complete, and we need to fix it: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack edit hdf5 - -If you followed the instructions correctly, the code added to the -``lib`` property should be similar to: - -.. code-block:: python - :emphasize-lines: 1 - - query_parameters = self.spec.last_query.extra_parameters - key = tuple(sorted(query_parameters)) - libraries = query2libraries[key] - shared = '+shared' in self.spec - return find_libraries( - libraries, root=self.prefix, shared=shared, recurse=True - ) - -where we highlighted the line retrieving the extra parameters. Now we can successfully -complete the installation of ``netcdf ^mpich``: - -.. code-block:: console - - root@advanced-packaging-tutorial:/# spack install netcdf ^mpich - ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a - ... - ==> Installing netcdf - ==> Using cached archive: /usr/local/var/spack/cache/netcdf/netcdf-4.4.1.1.tar.gz - ==> Already staged netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj in /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj - ==> Already patched netcdf - ==> Building netcdf [AutotoolsPackage] - ==> Executing phase: 'autoreconf' - ==> Executing phase: 'configure' - ==> Executing phase: 'build' - ==> Executing phase: 'install' - ==> Successfully installed netcdf - Fetch: 0.01s. Build: 24.61s. Total: 24.62s. - [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj diff --git a/lib/spack/docs/tutorial_basics.rst b/lib/spack/docs/tutorial_basics.rst deleted file mode 100644 index 9a6a2074b3c..00000000000 --- a/lib/spack/docs/tutorial_basics.rst +++ /dev/null @@ -1,1736 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _basics-tutorial: - -========================================= -Basic Installation Tutorial -========================================= - -This tutorial will guide you through the process of installing -software using Spack. We will first cover the `spack install` command, -focusing on the power of the spec syntax and the flexibility it gives -to users. We will also cover the `spack find` command for viewing -installed packages and the `spack uninstall` command. Finally, we will -touch on how Spack manages compilers, especially as it relates to -using Spack-built compilers within Spack. We will include full output -from all of the commands demonstrated, although we will frequently -call attention to only small portions of that output (or merely to the -fact that it succeeded). The provided output is all from an AWS -instance running Ubuntu 16.04 - -.. _basics-tutorial-install: - ----------------- -Installing Spack ----------------- - -Spack works out of the box. Simply clone spack and get going. We will -clone Spack and immediately checkout the most recent release, v0.12. - -.. code-block:: console - - $ git clone https://github.com/spack/spack - git clone https://github.com/spack/spack - Cloning into 'spack'... - remote: Enumerating objects: 68, done. - remote: Counting objects: 100% (68/68), done. - remote: Compressing objects: 100% (56/56), done. - remote: Total 135389 (delta 40), reused 16 (delta 9), pack-reused 135321 - Receiving objects: 100% (135389/135389), 47.31 MiB | 1.01 MiB/s, done. - Resolving deltas: 100% (64414/64414), done. - Checking connectivity... done. - $ cd spack - $ git checkout releases/v0.12 - Branch releases/v0.12 set up to track remote branch releases/v0.12 from origin. - Switched to a new branch 'releases/v0.12' - -Next add Spack to your path. Spack has some nice command line -integration tools, so instead of simply appending to your ``PATH`` -variable, source the spack setup script. Then add Spack to your path. - -.. code-block:: console - - $ . share/spack/setup-env.sh - -You're good to go! - ------------------ -What is in Spack? ------------------ - -The ``spack list`` command shows available packages. - -.. code-block:: console - - $ spack list - ==> 2907 packages. - abinit libgpuarray py-espresso r-mlrmbo - abyss libgridxc py-espressopp r-mmwrweek - accfft libgtextutils py-et-xmlfile r-mnormt - ... - -The ``spack list`` command can also take a query string. Spack -automatically adds wildcards to both ends of the string. For example, -we can view all available python packages. - -.. code-block:: console - - $ spack list py- - ==> 479 packages. - lumpy-sv py-funcsigs py-numpydoc py-utililib - perl-file-copy-recursive py-functools32 py-olefile py-pywavelets - py-3to2 py-future py-ont-fast5-api py-pyyaml - ... - -------------------- -Installing Packages -------------------- - -Installing a package with Spack is very simple. To install a piece of -software, simply type ``spack install ``. - -.. code-block:: console - - $ spack install zlib - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Warning: No Spack mirrors are currently configured - ==> No binary for zlib found: installing from source - ==> Fetching http://zlib.net/fossils/zlib-1.2.11.tar.gz - ######################################################################## 100.0% - ==> Staging archive: /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz - ==> Created stage in /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> No patches needed for zlib - ==> Building zlib [Package] - ==> Executing phase: 'install' - ==> Successfully installed zlib - Fetch: 3.27s. Build: 2.18s. Total: 5.44s. - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - -Spack can install software either from source or from a binary -cache. Packages in the binary cache are signed with GPG for -security. For the tutorial we have prepared a binary cache so you -don't have to wait on slow compilation from source. To be able to -install from the binary cache, we will need to configure Spack with -the location of the binary cache and trust the GPG key that the binary -cache was signed with. - -.. code-block:: console - - $ spack mirror add tutorial /mirror - $ spack gpg trust /mirror/public.key - gpg: keybox '/home/spack1/spack/opt/spack/gpg/pubring.kbx' created - gpg: /home/spack1/spack/opt/spack/gpg/trustdb.gpg: trustdb created - gpg: key 3B7C69B2: public key "sc-tutorial (GPG created for Spack) " imported - gpg: Total number processed: 1 - gpg: imported: 1 - -You'll learn more about configuring Spack later in the tutorial, but -for now you will be able to install the rest of the packages in the -tutorial from a binary cache using the same ``spack install`` -command. By default this will install the binary cached version if it -exists and fall back on installing from source. - -Spack's spec syntax is the interface by which we can request specific -configurations of the package. The ``%`` sigil is used to specify -compilers. - -.. code-block:: console - - $ spack install zlib %clang - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-texinfo-6.5-cuqnfgfhhmudqp5f7upmld6ax7pratzw.spec.yaml - ######################################################################## 100.0% - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spec.yaml - ######################################################################## 100.0% - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-dyninst-9.3.2-bu6s2jzievsjkwtcnrtimc5b625j5omf.spec.yaml - ######################################################################## 100.0% - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4.spec.yaml - ... - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul - -Note that this installation is located separately from the previous -one. We will discuss this in more detail later, but this is part of what -allows Spack to support arbitrarily versioned software. - -You can check for particular versions before requesting them. We will -use the ``spack versions`` command to see the available versions, and then -install a different version of ``zlib``. - -.. code-block:: console - - $ spack versions zlib - ==> Safe versions (already checksummed): - 1.2.11 1.2.8 1.2.3 - ==> Remote versions (not yet checksummed): - 1.2.10 1.2.7 1.2.5.1 1.2.4.2 1.2.3.7 - ... - -The ``@`` sigil is used to specify versions, both of packages and of -compilers. - -.. code-block:: console - - $ spack install zlib@1.2.8 - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:30 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc - - $ spack install zlib %gcc@4.7 - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 04:55:30 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r - -The spec syntax also includes compiler flags. Spack accepts -``cppflags``, ``cflags``, ``cxxflags``, ``fflags``, ``ldflags``, and -``ldlibs`` parameters. The values of these fields must be quoted on -the command line if they include spaces. These values are injected -into the compile line automatically by the Spack compiler wrappers. - -.. code-block:: console - - $ spack install zlib @1.2.8 cppflags=-O3 - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu - -The ``spack find`` command is used to query installed packages. Note that -some packages appear identical with the default output. The ``-l`` flag -shows the hash of each package, and the ``-f`` flag shows any non-empty -compiler flags of those packages. - -.. code-block:: console - - $ spack find - ==> 5 installed packages. - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - zlib@1.2.8 zlib@1.2.8 zlib@1.2.11 - - - $ spack find -lf - ==> 5 installed packages. - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - bkyl5bh zlib@1.2.8%gcc - - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - - 5nus6kn zlib@1.2.11%gcc - -Spack generates a hash for each spec. This hash is a function of the full -provenance of the package, so any change to the spec affects the -hash. Spack uses this value to compare specs and to generate unique -installation directories for every combinatorial version. As we move into -more complicated packages with software dependencies, we can see that -Spack reuses existing packages to satisfy a dependency only when the -existing package's hash matches the desired spec. - -.. code-block:: console - - $ spack install tcl - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing tcl - ==> Searching for binary cache of tcl - ==> Finding buildcaches in /mirror/build_cache - ==> Installing tcl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:15 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed tcl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt - -Dependencies can be explicitly requested using the ``^`` sigil. Note that -the spec syntax is recursive. Anything we could specify about the -top-level package, we can also specify about a dependency using ``^``. - -.. code-block:: console - - $ spack install tcl ^zlib @1.2.8 %clang - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:09:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5 - ==> Installing tcl - ==> Searching for binary cache of tcl - ==> Installing tcl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:10:21 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed tcl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc - -Packages can also be referred to from the command line by their package -hash. Using the ``spack find -lf`` command earlier we saw that the hash -of our optimized installation of zlib (``cppflags="-O3"``) began with -``64mns5m``. We can now explicitly build with that package without typing -the entire spec, by using the ``/`` sigil to refer to it by hash. As with -other tools like git, you do not need to specify an *entire* hash on the -command line. You can specify just enough digits to identify a hash -uniquely. If a hash prefix is ambiguous (i.e., two or more installed -packages share the prefix) then spack will report an error. - -.. code-block:: console - - $ spack install tcl ^/64mn - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu - ==> Installing tcl - ==> Searching for binary cache of tcl - ==> Finding buildcaches in /mirror/build_cache - ==> Installing tcl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:11:53 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed tcl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2 - -The ``spack find`` command can also take a ``-d`` flag, which can show -dependency information. Note that each package has a top-level entry, -even if it also appears as a dependency. - -.. code-block:: console - - $ spack find -ldf - ==> 9 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - i426yu3 ^zlib@1.2.8%clang - - i426yu3 zlib@1.2.8%clang - - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - am4pbat tcl@8.6.8%gcc - 64mns5m ^zlib@1.2.8%gcc cppflags="-O3" - - qhwyccy tcl@8.6.8%gcc - 5nus6kn ^zlib@1.2.11%gcc - - bkyl5bh zlib@1.2.8%gcc - - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - - 5nus6kn zlib@1.2.11%gcc - - -Let's move on to slightly more complicated packages. ``HDF5`` is a -good example of a more complicated package, with an MPI dependency. If -we install it "out of the box," it will build with ``openmpi``. - -.. code-block:: console - - $ spack install hdf5 - ==> Installing libsigsegv - ==> Searching for binary cache of libsigsegv - ==> Finding buildcaches in /mirror/build_cache - ==> Installing libsigsegv from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libsigsegv from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> Installing m4 - ==> Searching for binary cache of m4 - ==> Installing m4 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:11 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed m4 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> Installing libtool - ==> Searching for binary cache of libtool - ==> Installing libtool from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:47 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libtool from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> Installing pkgconf - ==> Searching for binary cache of pkgconf - ==> Installing pkgconf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:00:47 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed pkgconf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> Installing util-macros - ==> Searching for binary cache of util-macros - ==> Installing util-macros from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed util-macros from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr - ==> Installing libpciaccess - ==> Searching for binary cache of libpciaccess - ==> Installing libpciaccess from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:09:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libpciaccess from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc - ==> Installing xz - ==> Searching for binary cache of xz - ==> Installing xz from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:05:03 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed xz from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing libxml2 - ==> Searching for binary cache of libxml2 - ==> Installing libxml2 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 04:56:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libxml2 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7 - ==> Installing ncurses - ==> Searching for binary cache of ncurses - ==> Installing ncurses from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:04:49 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed ncurses from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> Installing readline - ==> Searching for binary cache of readline - ==> Installing readline from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:04:56 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed readline from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> Installing gdbm - ==> Searching for binary cache of gdbm - ==> Installing gdbm from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed gdbm from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> Installing perl - ==> Searching for binary cache of perl - ==> Installing perl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:45 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed perl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> Installing autoconf - ==> Searching for binary cache of autoconf - ==> Installing autoconf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69/linux-ubuntu16.04-x86_64-gcc-5.4.0-autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:03 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed autoconf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> Installing automake - ==> Searching for binary cache of automake - ==> Installing automake from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:03 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed automake from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> Installing numactl - ==> Searching for binary cache of numactl - ==> Installing numactl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed numactl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc - ==> Installing hwloc - ==> Searching for binary cache of hwloc - ==> Installing hwloc from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:08:00 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hwloc from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava - ==> Installing openmpi - ==> Searching for binary cache of openmpi - ==> Installing openmpi from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:01:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed openmpi from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:23:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw - -Spack packages can also have build options, called variants. Boolean -variants can be specified using the ``+`` and ``~`` or ``-`` -sigils. There are two sigils for ``False`` to avoid conflicts with -shell parsing in different situations. Variants (boolean or otherwise) -can also be specified using the same syntax as compiler flags. Here -we can install HDF5 without MPI support. - -.. code-block:: console - - $ spack install hdf5~mpi - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Finding buildcaches in /mirror/build_cache - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:23:24 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja - -We might also want to install HDF5 with a different MPI -implementation. While MPI is not a package itself, packages can depend on -abstract interfaces like MPI. Spack handles these through "virtual -dependencies." A package, such as HDF5, can depend on the MPI -interface. Other packages (``openmpi``, ``mpich``, ``mvapich``, etc.) -provide the MPI interface. Any of these providers can be requested for -an MPI dependency. For example, we can build HDF5 with MPI support -provided by mpich by specifying a dependency on ``mpich``. Spack also -supports versioning of virtual dependencies. A package can depend on the -MPI interface at version 3, and provider packages specify what version of -the interface *they* provide. The partial spec ``^mpi@3`` can be safisfied -by any of several providers. - -.. code-block:: console - - $ spack install hdf5+hl+mpi ^mpich - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> Installing texinfo - ==> Searching for binary cache of texinfo - ==> Finding buildcaches in /mirror/build_cache - ==> Installing texinfo from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:29 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed texinfo from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn - ==> Installing findutils - ==> Searching for binary cache of findutils - ==> Installing findutils from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:17 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed findutils from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v - ==> Installing mpich - ==> Searching for binary cache of mpich - ==> Installing mpich from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:23:57 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mpich from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:32 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob - -We'll do a quick check in on what we have installed so far. - -.. code-block:: console - - $ spack find -ldf - ==> 32 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - i426yu3 ^zlib@1.2.8%clang - - i426yu3 zlib@1.2.8%clang - - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - 3sx2gxe autoconf@2.69%gcc - suf5jtc ^m4@1.4.18%gcc - fypapcp ^libsigsegv@2.11%gcc - ic2kyoa ^perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - rymw7im automake@1.16.1%gcc - ic2kyoa ^perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - d4iajxs findutils@4.6.0%gcc - - q4fpyuo gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - 5vcv5r6 hdf5@1.10.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - - ozyvmhz hdf5@1.10.4%gcc - 3njc4q5 ^openmpi@3.1.3%gcc - 43tkw5m ^hwloc@1.11.9%gcc - 5urc6tc ^libpciaccess@0.13.5%gcc - wpexsph ^libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - ft463od ^numactl@2.0.11%gcc - - xxd7syh hdf5@1.10.4%gcc - p3f7p2r ^mpich@3.2.1%gcc - 5nus6kn ^zlib@1.2.11%gcc - - 43tkw5m hwloc@1.11.9%gcc - 5urc6tc ^libpciaccess@0.13.5%gcc - wpexsph ^libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - ft463od ^numactl@2.0.11%gcc - - 5urc6tc libpciaccess@0.13.5%gcc - - fypapcp libsigsegv@2.11%gcc - - o2pfwjf libtool@2.4.6%gcc - - wpexsph libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - - suf5jtc m4@1.4.18%gcc - fypapcp ^libsigsegv@2.11%gcc - - p3f7p2r mpich@3.2.1%gcc - - 3o765ou ncurses@6.1%gcc - - ft463od numactl@2.0.11%gcc - - 3njc4q5 openmpi@3.1.3%gcc - 43tkw5m ^hwloc@1.11.9%gcc - 5urc6tc ^libpciaccess@0.13.5%gcc - wpexsph ^libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - ft463od ^numactl@2.0.11%gcc - - ic2kyoa perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - fovrh7a pkgconf@1.4.2%gcc - - nxhwrg7 readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - am4pbat tcl@8.6.8%gcc - 64mns5m ^zlib@1.2.8%gcc cppflags="-O3" - - qhwyccy tcl@8.6.8%gcc - 5nus6kn ^zlib@1.2.11%gcc - - zs7a2pc texinfo@6.5%gcc - ic2kyoa ^perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - milz7fm util-macros@1.19.1%gcc - - teneqii xz@5.2.4%gcc - - bkyl5bh zlib@1.2.8%gcc - - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - - 5nus6kn zlib@1.2.11%gcc - - -Spack models the dependencies of packages as a directed acyclic graph -(DAG). The ``spack find -d`` command shows the tree representation of -that graph. We can also use the ``spack graph`` command to view the entire -DAG as a graph. - -.. code-block:: console - - $ spack graph hdf5+hl+mpi ^mpich - o hdf5 - |\ - o | zlib - / - o mpich - o findutils - |\ - | |\ - | | |\ - | | | |\ - o | | | | texinfo - | | | o | automake - | |_|/| | - |/| | | | - | | | |/ - | | | o autoconf - | |_|/| - |/| |/ - | |/| - o | | perl - o | | gdbm - o | | readline - o | | ncurses - o | | pkgconf - / / - | o libtool - |/ - o m4 - o libsigsegv - -You may also have noticed that there are some packages shown in the -``spack find -d`` output that we didn't install explicitly. These are -dependencies that were installed implicitly. A few packages installed -implicitly are not shown as dependencies in the ``spack find -d`` -output. These are build dependencies. For example, ``libpciaccess`` is a -dependency of openmpi and requires ``m4`` to build. Spack will build ``m4`` as -part of the installation of ``openmpi``, but it does not become a part of -the DAG because it is not linked in at run time. Spack handles build -dependencies differently because of their different (less strict) -consistency requirements. It is entirely possible to have two packages -using different versions of a dependency to build, which obviously cannot -be done with linked dependencies. - -``HDF5`` is more complicated than our basic example of zlib and -openssl, but it's still within the realm of software that an experienced -HPC user could reasonably expect to install given a bit of time. Now -let's look at an even more complicated package. - -.. code-block:: console - - $ spack install trilinos - ==> Installing diffutils - ==> Searching for binary cache of diffutils - ==> Finding buildcaches in /mirror/build_cache - ==> Installing diffutils from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:17 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed diffutils from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34 - ==> Installing bzip2 - ==> Searching for binary cache of bzip2 - ==> Installing bzip2 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:34:37 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed bzip2 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing boost - ==> Searching for binary cache of boost - ==> Installing boost from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 04:58:55 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed boost from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> Installing openssl - ==> Searching for binary cache of openssl - ==> Installing openssl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:10 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed openssl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha - ==> Installing cmake - ==> Searching for binary cache of cmake - ==> Installing cmake from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:33:15 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed cmake from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx - ==> Installing glm - ==> Searching for binary cache of glm - ==> Installing glm from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:33 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed glm from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> util-macros is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr - ==> libpciaccess is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc - ==> xz is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz - ==> libxml2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7 - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> numactl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc - ==> hwloc is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava - ==> openmpi is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:09:10 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y - ==> Installing openblas - ==> Searching for binary cache of openblas - ==> Installing openblas from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:32:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed openblas from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn - ==> Installing hypre - ==> Searching for binary cache of hypre - ==> Installing hypre from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hypre from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju - ==> Installing matio - ==> Searching for binary cache of matio - ==> Installing matio from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:05:13 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed matio from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h - ==> Installing metis - ==> Searching for binary cache of metis - ==> Installing metis from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:31:42 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed metis from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc - ==> Installing netlib-scalapack - ==> Searching for binary cache of netlib-scalapack - ==> Installing netlib-scalapack from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:22 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netlib-scalapack from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b - ==> Installing mumps - ==> Searching for binary cache of mumps - ==> Installing mumps from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:32 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mumps from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q - ==> Installing netcdf - ==> Searching for binary cache of netcdf - ==> Installing netcdf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:11:57 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netcdf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g - ==> Installing parmetis - ==> Searching for binary cache of parmetis - ==> Installing parmetis from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed parmetis from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7 - ==> Installing suite-sparse - ==> Searching for binary cache of suite-sparse - ==> Installing suite-sparse from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:22:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed suite-sparse from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon - ==> Installing trilinos - ==> Searching for binary cache of trilinos - ==> Installing trilinos from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:10 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed trilinos from binary cache - -Now we're starting to see the power of Spack. Trilinos in its default -configuration has 23 top level dependecies, many of which have -dependencies of their own. Installing more complex packages can take -days or weeks even for an experienced user. Although we've done a -binary installation for the tutorial, a source installation of -trilinos using Spack takes about 3 hours (depending on the system), -but only 20 seconds of programmer time. - -Spack manages constistency of the entire DAG. Every MPI dependency will -be satisfied by the same configuration of MPI, etc. If we install -``trilinos`` again specifying a dependency on our previous HDF5 built -with ``mpich``: - -.. code-block:: console - - $ spack install trilinos +hdf5 ^hdf5+hl+mpi ^mpich - ==> diffutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34 - ==> bzip2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> boost is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> openssl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha - ==> cmake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx - ==> glm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> texinfo is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn - ==> findutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v - ==> mpich is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5 - ==> hdf5 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob - ==> openblas is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn - ==> Installing hypre - ==> Searching for binary cache of hypre - ==> Finding buildcaches in /mirror/build_cache - ==> Installing hypre from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:34:36 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hypre from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb - ==> Installing matio - ==> Searching for binary cache of matio - ==> Installing matio from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:25:11 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed matio from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh - ==> metis is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc - ==> Installing netlib-scalapack - ==> Searching for binary cache of netlib-scalapack - ==> Installing netlib-scalapack from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:32:20 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netlib-scalapack from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r - ==> Installing mumps - ==> Searching for binary cache of mumps - ==> Installing mumps from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:33:18 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mumps from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur - ==> Installing netcdf - ==> Searching for binary cache of netcdf - ==> Installing netcdf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netcdf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd - ==> Installing parmetis - ==> Searching for binary cache of parmetis - ==> Installing parmetis from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:41 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed parmetis from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz - ==> suite-sparse is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon - ==> Installing trilinos - ==> Searching for binary cache of trilinos - ==> Installing trilinos from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:15 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed trilinos from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w - - -We see that every package in the trilinos DAG that depends on MPI now -uses ``mpich``. - -.. code-block:: console - - $ spack find -d trilinos - ==> 2 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - trilinos@12.12.1 - ^boost@1.68.0 - ^bzip2@1.0.6 - ^zlib@1.2.11 - ^glm@0.9.7.1 - ^hdf5@1.10.4 - ^openmpi@3.1.3 - ^hwloc@1.11.9 - ^libpciaccess@0.13.5 - ^libxml2@2.9.8 - ^xz@5.2.4 - ^numactl@2.0.11 - ^hypre@2.15.1 - ^openblas@0.3.3 - ^matio@1.5.9 - ^metis@5.1.0 - ^mumps@5.1.1 - ^netlib-scalapack@2.0.2 - ^netcdf@4.6.1 - ^parmetis@4.0.3 - ^suite-sparse@5.3.0 - - trilinos@12.12.1 - ^boost@1.68.0 - ^bzip2@1.0.6 - ^zlib@1.2.11 - ^glm@0.9.7.1 - ^hdf5@1.10.4 - ^mpich@3.2.1 - ^hypre@2.15.1 - ^openblas@0.3.3 - ^matio@1.5.9 - ^metis@5.1.0 - ^mumps@5.1.1 - ^netlib-scalapack@2.0.2 - ^netcdf@4.6.1 - ^parmetis@4.0.3 - ^suite-sparse@5.3.0 - - -As we discussed before, the ``spack find -d`` command shows the -dependency information as a tree. While that is often sufficient, many -complicated packages, including trilinos, have dependencies that -cannot be fully represented as a tree. Again, the ``spack graph`` -command shows the full DAG of the dependency information. - -.. code-block:: console - - $ spack graph trilinos - o trilinos - |\ - | |\ - | | |\ - | | | |\ - | | | | |\ - | | | | | |\ - | | | | | | |\ - | | | | | | | |\ - | | | | | | | | |\ - | | | | | | | | | |\ - | | | | | | | | | | |\ - | | | | | | | | | | | |\ - | | | | | | | | | | | | |\ - o | | | | | | | | | | | | | suite-sparse - |\ \ \ \ \ \ \ \ \ \ \ \ \ \ - | |_|_|/ / / / / / / / / / / - |/| | | | | | | | | | | | | - | |\ \ \ \ \ \ \ \ \ \ \ \ \ - | | |_|_|_|_|_|/ / / / / / / - | |/| | | | | | | | | | | | - | | | |_|_|_|_|_|_|_|/ / / - | | |/| | | | | | | | | | - | | | o | | | | | | | | | parmetis - | | |/| | | | | | | | | | - | |/|/| | | | | | | | | | - | | | |/ / / / / / / / / - | | | | | | o | | | | | mumps - | |_|_|_|_|/| | | | | | - |/| | | |_|/| | | | | | - | | | |/| |/ / / / / / - | | | | |/| | | | | | - | | | | o | | | | | | netlib-scalapack - | |_|_|/| | | | | | | - |/| | |/| | | | | | | - | | |/|/ / / / / / / - | o | | | | | | | | metis - | |/ / / / / / / / - | | | | | | | o | glm - | | |_|_|_|_|/ / - | |/| | | | | | - | o | | | | | | cmake - | |\ \ \ \ \ \ \ - | o | | | | | | | openssl - | |\ \ \ \ \ \ \ \ - | | | | | o | | | | netcdf - | | |_|_|/| | | | | - | |/| | |/| | | | | - | | | | | |\ \ \ \ \ - | | | | | | | |_|/ / - | | | | | | |/| | | - | | | | | | | o | | matio - | | |_|_|_|_|/| | | - | |/| | | | |/ / / - | | | | | | | o | hypre - | |_|_|_|_|_|/| | - |/| | | | |_|/ / - | | | | |/| | | - | | | | | | o | hdf5 - | | |_|_|_|/| | - | |/| | | |/ / - | | | | |/| | - | | | | o | | openmpi - | | |_|/| | | - | |/| | | | | - | | | | |\ \ \ - | | | | | o | | hwloc - | | | | |/| | | - | | | | | |\ \ \ - | | | | | | |\ \ \ - | | | | | | o | | | libxml2 - | | |_|_|_|/| | | | - | |/| | | |/| | | | - | | | | | | | | | o boost - | | |_|_|_|_|_|_|/| - | |/| | | | | | | | - | o | | | | | | | | zlib - | / / / / / / / / - | | | | | o | | | xz - | | | | | / / / - | | | | | o | | libpciaccess - | | | | |/| | | - | | | | | |\ \ \ - | | | | | o | | | util-macros - | | | | | / / / - | | | o | | | | numactl - | | | |\ \ \ \ \ - | | | | |_|_|/ / - | | | |/| | | | - | | | | |\ \ \ \ - | | | | | |_|/ / - | | | | |/| | | - | | | | | |\ \ \ - | | | | | o | | | automake - | | |_|_|/| | | | - | |/| | | | | | | - | | | | | |/ / / - | | | | | o | | autoconf - | | |_|_|/| | | - | |/| | |/ / / - | | | |/| | | - | o | | | | | perl - | o | | | | | gdbm - | o | | | | | readline - | |/ / / / / - | o | | | | ncurses - | | |_|/ / - | |/| | | - | o | | | pkgconf - | / / / - o | | | openblas - / / / - | o | libtool - |/ / - o | m4 - o | libsigsegv - / - o bzip2 - o diffutils - -You can control how the output is displayed with a number of options. - -The ASCII output from ``spack graph`` can be difficult to parse for -complicated packages. The output can be changed to the ``graphviz`` -``.dot`` format using the ``--dot`` flag. - -.. code-block:: console - - $ spack graph --dot trilinos | dot -Tpdf trilinos_graph.pdf - -.. _basics-tutorial-uninstall: - ---------------------- -Uninstalling Packages ---------------------- - -Earlier we installed many configurations each of zlib and tcl. Now we -will go through and uninstall some of those packages that we didn't -really need. - -.. code-block:: console - - $ spack find -d tcl - ==> 3 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - tcl@8.6.8 - ^zlib@1.2.8 - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - tcl@8.6.8 - ^zlib@1.2.8 - - tcl@8.6.8 - ^zlib@1.2.11 - - - $ spack find zlib - ==> 6 installed packages. - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - zlib@1.2.8 zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - zlib@1.2.8 zlib@1.2.8 zlib@1.2.11 - -We can uninstall packages by spec using the same syntax as install. - -.. code-block:: console - - $ spack uninstall zlib %gcc@4.7 - ==> The following packages will be uninstalled: - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc+optimize+pic+shared - - ==> Do you want to proceed? [y/N] y - ==> Successfully uninstalled zlib@1.2.11%gcc@4.7+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 /bq2wtdx - - $ spack find -lf zlib - ==> 5 installed packages. - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - i426yu3 zlib@1.2.8%clang - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - bkyl5bh zlib@1.2.8%gcc - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - 5nus6kn zlib@1.2.11%gcc - -We can also uninstall packages by referring only to their hash. - -We can use either ``-f`` (force) or ``-R`` (remove dependents as well) to -remove packages that are required by another installed package. - -.. code-block:: console - - $ spack uninstall zlib/i426 - ==> Error: Will not uninstall zlib@1.2.8%clang@3.8.0-2ubuntu4/i426yu3 - - The following packages depend on it: - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - - ==> Error: Use \`spack uninstall --dependents\` to uninstall these dependencies as well. - - $ spack uninstall -R zlib/i426 - ==> The following packages will be uninstalled: - - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - i426yu3 zlib@1.2.8%clang+optimize+pic+shared - ==> Do you want to proceed? [y/N] y - ==> Successfully uninstalled tcl@8.6.8%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 /6wc66et - ==> Successfully uninstalled zlib@1.2.8%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 /i426yu3 - -Spack will not uninstall packages that are not sufficiently -specified. The ``-a`` (all) flag can be used to uninstall multiple -packages at once. - -.. code-block:: console - - $ spack uninstall trilinos - ==> Error: trilinos matches multiple packages: - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 - kqc52mo trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 - - ==> Error: You can either: - a) use a more specific spec, or - b) use `spack uninstall --all` to uninstall ALL matching specs. - - - $ spack uninstall /rlsr - ==> The following packages will be uninstalled: - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 - ==> Do you want to proceed? [y/N] y - ==> Successfully uninstalled trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64 /rlsruav - ------------------------------ -Advanced ``spack find`` Usage ------------------------------ - -We will go over some additional uses for the ``spack find`` command not -already covered in the :ref:`basics-tutorial-install` and -:ref:`basics-tutorial-uninstall` sections. - -The ``spack find`` command can accept what we call "anonymous specs." -These are expressions in spec syntax that do not contain a package -name. For example, ``spack find ^mpich`` will return every installed -package that depends on mpich, and ``spack find cppflags="-O3"`` will -return every package which was built with ``cppflags="-O3"``. - -.. code-block:: console - - $ spack find ^mpich - ==> 8 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - hdf5@1.10.4 matio@1.5.9 netcdf@4.6.1 parmetis@4.0.3 - hypre@2.15.1 mumps@5.1.1 netlib-scalapack@2.0.2 trilinos@12.12.1 - - $ spack find cppflags=-O3 - ==> 1 installed packages. - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - zlib@1.2.8 - -The ``find`` command can also show which packages were installed -explicitly (rather than pulled in as a dependency) using the ``-x`` -flag. The ``-X`` flag shows implicit installs only. The ``find`` command can -also show the path to which a spack package was installed using the ``-p`` -command. - -.. code-block:: console - - $ spack find -px - ==> 10 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - zlib@1.2.11 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja - hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw - hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob - tcl@8.6.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2 - tcl@8.6.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt - trilinos@12.12.1 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w - zlib@1.2.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc - zlib@1.2.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu - zlib@1.2.11 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ---------------------- -Customizing Compilers ---------------------- - - -Spack manages a list of available compilers on the system, detected -automatically from from the user's ``PATH`` variable. The ``spack -compilers`` command is an alias for the command ``spack compiler list``. - -.. code-block:: console - - $ spack compilers - ==> Available compilers - -- clang ubuntu16.04-x86_64 ------------------------------------- - clang@3.8.0-2ubuntu4 clang@3.7.1-2ubuntu2 - - -- gcc ubuntu16.04-x86_64 --------------------------------------- - gcc@5.4.0 gcc@4.7 - -The compilers are maintained in a YAML file. Later in the tutorial you -will learn how to configure compilers by hand for special cases. Spack -also has tools to add compilers, and compilers built with Spack can be -added to the configuration. - -.. code-block:: console - - $ spack install gcc @7.2.0 - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> Installing gmp - ==> Searching for binary cache of gmp - ==> Finding buildcaches in /mirror/build_cache - ==> Installing gmp from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:16 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed gmp from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw - ==> Installing isl - ==> Searching for binary cache of isl - ==> Installing isl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:05:19 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed isl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax - ==> Installing mpfr - ==> Searching for binary cache of mpfr - ==> Installing mpfr from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:32:07 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mpfr from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv - ==> Installing mpc - ==> Searching for binary cache of mpc - ==> Installing mpc from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:35 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mpc from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - Installing gcc - ==> Searching for binary cache of gcc - ==> Finding buildcaches in /mirror/build_cache - ==> Installing gcc from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:22:47 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) " [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed gcc from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs - - $ spack find -p gcc - spack find -p gcc - ==> 1 installed package - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - gcc@7.2.0 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs - -We can add gcc to Spack as an available compiler using the ``spack -compiler add`` command. This will allow future packages to build with -gcc@7.2.0. - -.. code-block:: console - - $ spack compiler add `spack location -i gcc@7.2.0` - ==> Added 1 new compiler to /home/ubuntu/.spack/linux/compilers.yaml - gcc@7.2.0 - ==> Compilers are defined in the following files: - /home/ubuntu/.spack/linux/compilers.yaml - -We can also remove compilers from our configuration using ``spack compiler remove `` - -.. code-block:: console - - $ spack compiler remove gcc@7.2.0 - ==> Removed compiler gcc@7.2.0 diff --git a/lib/spack/docs/tutorial_buildsystems.rst b/lib/spack/docs/tutorial_buildsystems.rst deleted file mode 100644 index 9f3785e7ee7..00000000000 --- a/lib/spack/docs/tutorial_buildsystems.rst +++ /dev/null @@ -1,807 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _build-systems-tutorial: - -============================== -Spack Package Build Systems -============================== - -You may begin to notice after writing a couple of package template files a -pattern emerge for some packages. For example, you may find yourself writing -an :code:`install()` method that invokes: :code:`configure`, :code:`cmake`, -:code:`make`, :code:`make install`. You may also find yourself writing -:code:`"prefix=" + prefix` as an argument to :code:`configure` or :code:`cmake`. -Rather than having you repeat these lines for all packages, Spack has -classes that can take care of these patterns. In addition, -these package files allow for finer grained control of these build systems. -In this section, we will describe each build system and give examples on -how these can be manipulated to install a package. - ------------------------ -Package Class Hierarchy ------------------------ - -.. graphviz:: - - digraph G { - - node [ - shape = "record" - ] - edge [ - arrowhead = "empty" - ] - - PackageBase -> Package [dir=back] - PackageBase -> MakefilePackage [dir=back] - PackageBase -> AutotoolsPackage [dir=back] - PackageBase -> CMakePackage [dir=back] - PackageBase -> PythonPackage [dir=back] - } - -The above diagram gives a high level view of the class hierarchy and how each -package relates. Each subclass inherits from the :code:`PackageBaseClass` -super class. The bulk of the work is done in this super class which includes -fetching, extracting to a staging directory and installing. Each subclass -then adds additional build-system-specific functionality. In the following -sections, we will go over examples of how to utilize each subclass and to see -how powerful these abstractions are when packaging. - ------------------ -Package ------------------ - -We've already seen examples of a :code:`Package` class in our walkthrough for writing -package files, so we won't be spending much time with them here. Briefly, -the Package class allows for abitrary control over the build process, whereas -subclasses rely on certain patterns (e.g. :code:`configure` :code:`make` -:code:`make install`) to be useful. :code:`Package` classes are particularly useful -for packages that have a non-conventional way of being built since the packager -can utilize some of Spack's helper functions to customize the building and -installing of a package. - -------------------- -Autotools -------------------- - -As we have seen earlier, packages using :code:`Autotools` use :code:`configure`, -:code:`make` and :code:`make install` commands to execute the build and -install process. In our :code:`Package` class, your typical build incantation will -consist of the following: - -.. code-block:: python - - def install(self, spec, prefix): - configure("--prefix=" + prefix) - make() - make("install") - -You'll see that this looks similar to what we wrote in our packaging tutorial. - -The :code:`Autotools` subclass aims to simplify writing package files and provides -convenience methods to manipulate each of the different phases for a :code:`Autotools` -build system. - -:code:`Autotools` packages consist of four phases: - -1. :code:`autoreconf()` -2. :code:`configure()` -3. :code:`build()` -4. :code:`install()` - - -Each of these phases have sensible defaults. Let's take a quick look at some -the internals of the :code:`Autotools` class: - -.. code-block:: console - - $ spack edit --build-system autotools - - -This will open the :code:`AutotoolsPackage` file in your text editor. - -.. note:: - The examples showing code for these classes is abridged to avoid having - long examples. We only show what is relevant to the packager. - - -.. literalinclude:: _spack_root/lib/spack/spack/build_systems/autotools.py - :language: python - :emphasize-lines: 33,36,54 - :lines: 30-76,240-248 - :linenos: - - -Important to note are the highlighted lines. These properties allow the -packager to set what build targets and install targets they want for their -package. If, for example, we wanted to add as our build target :code:`foo` -then we can append to our :code:`build_targets` property: - -.. code-block:: python - - build_targets = ["foo"] - -Which is similiar to invoking make in our Package - -.. code-block:: python - - make("foo") - -This is useful if we have packages that ignore environment variables and need -a command-line argument. - -Another thing to take note of is in the :code:`configure()` method. -Here we see that the :code:`prefix` argument is already included since it is a -common pattern amongst packages using :code:`Autotools`. We then only have to -override :code:`configure_args()`, which will then return it's output to -to :code:`configure()`. Then, :code:`configure()` will append the common -arguments - -Packagers also have the option to run :code:`autoreconf` in case a package -needs to update the build system and generate a new :code:`configure`. Though, -for the most part this will be unnecessary. - -Let's look at the :code:`mpileaks` package.py file that we worked on earlier: - -.. code-block:: console - - $ spack edit mpileaks - -Notice that mpileaks is a :code:`Package` class but uses the :code:`Autotools` -build system. Although this package is acceptable let's make this into an -:code:`AutotoolsPackage` class and simplify it further. - -.. literalinclude:: tutorial/examples/Autotools/0.package.py - :language: python - :emphasize-lines: 9 - :linenos: - -We first inherit from the :code:`AutotoolsPackage` class. - - -Although we could keep the :code:`install()` method, most of it can be handled -by the :code:`AutotoolsPackage` base class. In fact, the only thing that needs -to be overridden is :code:`configure_args()`. - -.. literalinclude:: tutorial/examples/Autotools/1.package.py - :language: python - :emphasize-lines: 25,26,27,28,29,30,31,32 - :linenos: - -Since Spack takes care of setting the prefix for us we can exclude that as -an argument to :code:`configure`. Our packages look simpler, and the packager -does not need to worry about whether they have properly included :code:`configure` -and :code:`make`. - -This version of the :code:`mpileaks` package installs the same as the previous, -but the :code:`AutotoolsPackage` class lets us do it with a cleaner looking -package file. - ------------------ -Makefile ------------------ - -Packages that utilize :code:`Make` or a :code:`Makefile` usually require you -to edit a :code:`Makefile` to set up platform and compiler specific variables. -These packages are handled by the :code:`Makefile` subclass which provides -convenience methods to help write these types of packages. - -A :code:`MakefilePackage` class has three phases that can be overridden. These include: - - 1. :code:`edit()` - 2. :code:`build()` - 3. :code:`install()` - -Packagers then have the ability to control how a :code:`Makefile` is edited, and -what targets to include for the build phase or install phase. - -Let's also take a look inside the :code:`MakefilePackage` class: - -.. code-block:: console - - $ spack edit --build-system makefile - -Take note of the following: - - -.. literalinclude:: _spack_root/lib/spack/spack/build_systems/makefile.py - :language: python - :lines: 14,43-61,70-88 - :emphasize-lines: 21,27,34 - :linenos: - -Similar to :code:`Autotools`, :code:`MakefilePackage` class has properties -that can be set by the packager. We can also override the different -methods highlighted. - - -Let's try to recreate the Bowtie_ package: - -.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml - - -.. code-block:: console - - $ spack create -f https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip - ==> This looks like a URL for bowtie - ==> Found 1 version of bowtie: - - 1.2.1.1 https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip - - ==> How many would you like to checksum? (default is 1, q to abort) 1 - ==> Downloading... - ==> Fetching https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip - ######################################################################## 100.0% - ==> Checksummed 1 version of bowtie - ==> This package looks like it uses the makefile build system - ==> Created template for bowtie package - ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/bowtie/package.py - -Once the fetching is completed, Spack will open up your text editor in the -usual fashion and create a template of a :code:`MakefilePackage` package.py. - -.. literalinclude:: tutorial/examples/Makefile/0.package.py - :language: python - :linenos: - -Spack was successfully able to detect that :code:`Bowtie` uses :code:`Make`. -Let's add in the rest of our details for our package: - -.. literalinclude:: tutorial/examples/Makefile/1.package.py - :language: python - :emphasize-lines: 10,11,13,14,18,20 - :linenos: - -As we mentioned earlier, most packages using a :code:`Makefile` have hard-coded -variables that must be edited. These variables are fine if you happen to not -care about setup or types of compilers used but Spack is designed to work with -any compiler. The :code:`MakefilePackage` subclass makes it easy to edit -these :code:`Makefiles` by having an :code:`edit()` method that -can be overridden. - -Let's take a look at the default :code:`Makefile` that :code:`Bowtie` provides. -If we look inside, we see that :code:`CC` and :code:`CXX` point to our GNU -compiler: - -.. code-block:: console - - $ spack stage bowtie - -.. note:: - As usual make sure you have shell support activated with spack: - :code:`source /path/to/spack_root/spack/share/spack/setup-env.sh` - -.. code-block:: console - - $ spack cd -s bowtie - $ cd bowtie-1.2 - $ vim Makefile - - -.. code-block:: make - - CPP = g++ -w - CXX = $(CPP) - CC = gcc - LIBS = $(LDFLAGS) -lz - HEADERS = $(wildcard *.h) - -To fix this, we need to use the :code:`edit()` method to write our custom -:code:`Makefile`. - -.. literalinclude:: tutorial/examples/Makefile/2.package.py - :language: python - :emphasize-lines: 23,24,25 - :linenos: - -Here we use a :code:`FileFilter` object to edit our :code:`Makefile`. It takes -in a regular expression and then replaces :code:`CC` and :code:`CXX` to whatever -Spack sets :code:`CC` and :code:`CXX` environment variables to. This allows us to -build :code:`Bowtie` with whatever compiler we specify through Spack's -:code:`spec` syntax. - -Let's change the build and install phases of our package: - -.. literalinclude:: tutorial/examples/Makefile/3.package.py - :language: python - :emphasize-lines: 28,29,30,31,32,35,36 - :linenos: - -Here demonstrate another strategy that we can use to manipulate our package -We can provide command-line arguments to :code:`make()`. Since :code:`Bowtie` -can use :code:`tbb` we can either add :code:`NO_TBB=1` as a argument to prevent -:code:`tbb` support or we can just invoke :code:`make` with no arguments. - -:code:`Bowtie` requires our :code:`install_target` to provide a path to -the install directory. We can do this by providing :code:`prefix=` as a command -line argument to :code:`make()`. - -Let's look at a couple of other examples and go through them: - -.. code-block:: console - - $ spack edit esmf - -Some packages allow environment variables to be set and will honor them. -Packages that use :code:`?=` for assignment in their :code:`Makefile` -can be set using environment variables. In our :code:`esmf` example we -set two environment variables in our :code:`edit()` method: - -.. code-block:: python - - def edit(self, spec, prefix): - for var in os.environ: - if var.startswith('ESMF_'): - os.environ.pop(var) - - # More code ... - - if self.compiler.name == 'gcc': - os.environ['ESMF_COMPILER'] = 'gfortran' - elif self.compiler.name == 'intel': - os.environ['ESMF_COMPILER'] = 'intel' - elif self.compiler.name == 'clang': - os.environ['ESMF_COMPILER'] = 'gfortranclang' - elif self.compiler.name == 'nag': - os.environ['ESMF_COMPILER'] = 'nag' - elif self.compiler.name == 'pgi': - os.environ['ESMF_COMPILER'] = 'pgi' - else: - msg = "The compiler you are building with, " - msg += "'{0}', is not supported by ESMF." - raise InstallError(msg.format(self.compiler.name)) - -As you may have noticed, we didn't really write anything to the :code:`Makefile` -but rather we set environment variables that will override variables set in -the :code:`Makefile`. - -Some packages include a configuration file that sets certain compiler variables, -platform specific variables, and the location of dependencies or libraries. -If the file is simple and only requires a couple of changes, we can overwrite -those entries with our :code:`FileFilter` object. If the configuration involves -complex changes, we can write a new configuration file from scratch. - -Let's look at an example of this in the :code:`elk` package: - -.. code-block:: console - - $ spack edit elk - -.. code-block:: python - - def edit(self, spec, prefix): - # Dictionary of configuration options - config = { - 'MAKE': 'make', - 'AR': 'ar' - } - - # Compiler-specific flags - flags = '' - if self.compiler.name == 'intel': - flags = '-O3 -ip -unroll -no-prec-div' - elif self.compiler.name == 'gcc': - flags = '-O3 -ffast-math -funroll-loops' - elif self.compiler.name == 'pgi': - flags = '-O3 -lpthread' - elif self.compiler.name == 'g95': - flags = '-O3 -fno-second-underscore' - elif self.compiler.name == 'nag': - flags = '-O4 -kind=byte -dusty -dcfuns' - elif self.compiler.name == 'xl': - flags = '-O3' - config['F90_OPTS'] = flags - config['F77_OPTS'] = flags - - # BLAS/LAPACK support - # Note: BLAS/LAPACK must be compiled with OpenMP support - # if the +openmp variant is chosen - blas = 'blas.a' - lapack = 'lapack.a' - if '+blas' in spec: - blas = spec['blas'].libs.joined() - if '+lapack' in spec: - lapack = spec['lapack'].libs.joined() - # lapack must come before blas - config['LIB_LPK'] = ' '.join([lapack, blas]) - - # FFT support - if '+fft' in spec: - config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib, - 'libfftw3.so') - config['SRC_FFT'] = 'zfftifc_fftw.f90' - else: - config['LIB_FFT'] = 'fftlib.a' - config['SRC_FFT'] = 'zfftifc.f90' - - # MPI support - if '+mpi' in spec: - config['F90'] = spec['mpi'].mpifc - config['F77'] = spec['mpi'].mpif77 - else: - config['F90'] = spack_fc - config['F77'] = spack_f77 - config['SRC_MPI'] = 'mpi_stub.f90' - - # OpenMP support - if '+openmp' in spec: - config['F90_OPTS'] += ' ' + self.compiler.openmp_flag - config['F77_OPTS'] += ' ' + self.compiler.openmp_flag - else: - config['SRC_OMP'] = 'omp_stub.f90' - - # Libxc support - if '+libxc' in spec: - config['LIB_libxc'] = ' '.join([ - join_path(spec['libxc'].prefix.lib, 'libxcf90.so'), - join_path(spec['libxc'].prefix.lib, 'libxc.so') - ]) - config['SRC_libxc'] = ' '.join([ - 'libxc_funcs.f90', - 'libxc.f90', - 'libxcifc.f90' - ]) - else: - config['SRC_libxc'] = 'libxcifc_stub.f90' - - # Write configuration options to include file - with open('make.inc', 'w') as inc: - for key in config: - inc.write('{0} = {1}\n'.format(key, config[key])) - -:code:`config` is just a dictionary that we can add key-value pairs to. By the -end of the :code:`edit()` method we write the contents of our dictionary to -:code:`make.inc`. - ---------------- -CMake ---------------- - -CMake_ is another common build system that has been gaining popularity. It works -in a similar manner to :code:`Autotools` but with differences in variable names, -the number of configuration options available, and the handling of shared libraries. -Typical build incantations look like this: - -.. _CMake: https://cmake.org - -.. code-block:: python - - def install(self, spec, prefix): - cmake("-DCMAKE_INSTALL_PREFIX:PATH=/path/to/install_dir ..") - make() - make("install") - -As you can see from the example above, it's very similar to invoking -:code:`configure` and :code:`make` in an :code:`Autotools` build system. However, -the variable names and options differ. Most options in CMake are prefixed -with a :code:`'-D'` flag to indicate a configuration setting. - -In the :code:`CMakePackage` class we can override the following phases: - -1. :code:`cmake()` -2. :code:`build()` -3. :code:`install()` - -The :code:`CMakePackage` class also provides sensible defaults so we only need to -override :code:`cmake_args()`. - -Let's look at these defaults in the :code:`CMakePackage` class in the :code:`_std_args()` method: - -.. code-block:: console - - $ spack edit --build-system cmake - -.. literalinclude:: _spack_root/lib/spack/spack/build_systems/cmake.py - :language: python - :lines: 102-147 - :emphasize-lines: 10,18,24,36,37,38,44 - :linenos: - -Some :code:`CMake` packages use different generators. Spack is able to support -Unix-Makefile_ generators as well as Ninja_ generators. - -.. _Unix-Makefile: https://cmake.org/cmake/help/v3.4/generator/Unix%20Makefiles.html -.. _Ninja: https://cmake.org/cmake/help/v3.4/generator/Ninja.html - -If no generator is specified Spack will default to :code:`Unix Makefiles`. - -Next we setup the build type. In :code:`CMake` you can specify the build type -that you want. Options include: - -1. :code:`empty` -2. :code:`Debug` -3. :code:`Release` -4. :code:`RelWithDebInfo` -5. :code:`MinSizeRel` - -With these options you can specify whether you want your executable to have -the debug version only, release version or the release with debug information. -Release executables tend to be more optimized than Debug. In Spack, we set -the default as RelWithDebInfo unless otherwise specified through a variant. - -Spack then automatically sets up the :code:`-DCMAKE_INSTALL_PREFIX` path, -appends the build type (:code:`RelWithDebInfo` default), and then specifies a verbose -:code:`Makefile`. - -Next we add the :code:`rpaths` to :code:`-DCMAKE_INSTALL_RPATH:STRING`. - - -Finally we add to :code:`-DCMAKE_PREFIX_PATH:STRING` the locations of all our -dependencies so that :code:`CMake` can find them. - -In the end our :code:`cmake` line will look like this (example is :code:`xrootd`): - -.. code-block:: console - - $ cmake $HOME/spack/var/spack/stage/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/xrootd-4.6.0 -G Unix Makefiles -DCMAKE_INSTALL_PREFIX:PATH=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_FIND_FRAMEWORK:STRING=LAST -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE -DCMAKE_INSTALL_RPATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib:$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib64 -DCMAKE_PREFIX_PATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/cmake-3.9.4-hally3vnbzydiwl3skxcxcbzsscaasx5 - -We can see now how :code:`CMake` takes care of a lot of the boilerplate code -that would have to be otherwise typed in. - -Let's try to recreate callpath_: - -.. _callpath: https://github.com/LLNL/callpath.git - -.. code-block:: console - - $ spack create -f https://github.com/llnl/callpath/archive/v1.0.3.tar.gz - ==> This looks like a URL for callpath - ==> Found 4 versions of callpath: - - 1.0.3 https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz - 1.0.2 https://github.com/LLNL/callpath/archive/v1.0.2.tar.gz - 1.0.1 https://github.com/LLNL/callpath/archive/v1.0.1.tar.gz - 1.0 https://github.com/LLNL/callpath/archive/v1.0.tar.gz - - ==> How many would you like to checksum? (default is 1, q to abort) 1 - ==> Downloading... - ==> Fetching https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz - ######################################################################## 100.0% - ==> Checksummed 1 version of callpath - ==> This package looks like it uses the cmake build system - ==> Created template for callpath package - ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/callpath/package.py - - -which then produces the following template: - -.. literalinclude:: tutorial/examples/Cmake/0.package.py - :language: python - :linenos: - -Again we fill in the details: - -.. literalinclude:: tutorial/examples/Cmake/1.package.py - :language: python - :linenos: - :emphasize-lines: 9,13,14,18,19,20,21,22,23 - -As mentioned earlier, Spack will use sensible defaults to prevent repeated code -and to make writing :code:`CMake` package files simpler. - -In callpath, we want to add options to :code:`CALLPATH_WALKER` as well as add -compiler flags. We add the following options like so: - -.. literalinclude:: tutorial/examples/Cmake/2.package.py - :language: python - :linenos: - :emphasize-lines: 26,30,31 - -Now we can control our build options using :code:`cmake_args()`. If defaults are -sufficient enough for the package, we can leave this method out. - -:code:`CMakePackage` classes allow for control of other features in the -build system. For example, you can specify the path to the "out of source" -build directory and also point to the root of the :code:`CMakeLists.txt` file if it -is placed in a non-standard location. - -A good example of a package that has its :code:`CMakeLists.txt` file located at a -different location is found in :code:`spades`. - -.. code-block:: console - - $ spack edit spades - -.. code-block:: python - - root_cmakelists_dir = "src" - -Here :code:`root_cmakelists_dir` will tell Spack where to find the location -of :code:`CMakeLists.txt`. In this example, it is located a directory level below in -the :code:`src` directory. - -Some :code:`CMake` packages also require the :code:`install` phase to be -overridden. For example, let's take a look at :code:`sniffles`. - -.. code-block:: console - - $ spack edit sniffles - -In the :code:`install()` method, we have to manually install our targets -so we override the :code:`install()` method to do it for us: - -.. code-block:: python - - # the build process doesn't actually install anything, do it by hand - def install(self, spec, prefix): - mkdir(prefix.bin) - src = "bin/sniffles-core-{0}".format(spec.version.dotted) - binaries = ['sniffles', 'sniffles-debug'] - for b in binaries: - install(join_path(src, b), join_path(prefix.bin, b)) - - --------------- -PythonPackage --------------- - -Python extensions and modules are built differently from source than most -applications. Python uses a :code:`setup.py` script to install Python modules. -The script consists of a call to :code:`setup()` which provides the information -required to build a module to Distutils. If you're familiar with pip or -easy_install, setup.py does the same thing. - -These modules are usually installed using the following line: - -.. code-block:: console - - $ python setup.py install - -There are also a list of commands and phases that you can call. To see the full -list you can run: - -.. code-block:: console - - $ python setup.py --help-commands - Standard commands: - build build everything needed to install - build_py "build" pure Python modules (copy to build directory) - build_ext build C/C++ extensions (compile/link to build directory) - build_clib build C/C++ libraries used by Python extensions - build_scripts "build" scripts (copy and fixup #! line) - clean (no description available) - install install everything from build directory - install_lib install all Python modules (extensions and pure Python) - install_headers install C/C++ header files - install_scripts install scripts (Python or otherwise) - install_data install data files - sdist create a source distribution (tarball, zip file, etc.) - register register the distribution with the Python package index - bdist create a built (binary) distribution - bdist_dumb create a "dumb" built distribution - bdist_rpm create an RPM distribution - bdist_wininst create an executable installer for MS Windows - upload upload binary package to PyPI - check perform some checks on the package - - -We can write package files for Python packages using the :code:`Package` class, -but the class brings with it a lot of methods that are useless for Python packages. -Instead, Spack has a :code:`PythonPackage` subclass that allows packagers -of Python modules to be able to invoke :code:`setup.py` and use :code:`Distutils`, -which is much more familiar to a typical python user. - -To see the defaults that Spack has for each a methods, we will take a look -at the :code:`PythonPackage` class: - -.. code-block:: console - - $ spack edit --build-system python - -We see the following: - - -.. literalinclude:: _spack_root/lib/spack/spack/build_systems/python.py - :language: python - :lines: 19,146-357 - :linenos: - -Each of these methods have sensible defaults or they can be overridden. - -We will write a package file for Pandas_: - -.. _pandas: https://pandas.pydata.org - -.. code-block:: console - - $ spack create -f https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz - ==> This looks like a URL for pandas - ==> Warning: Spack was unable to fetch url list due to a certificate verification problem. You can try running spack -k, which will not check SSL certificates. Use this at your own risk. - ==> Found 1 version of pandas: - - 0.19.0 https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz - - ==> How many would you like to checksum? (default is 1, q to abort) 1 - ==> Downloading... - ==> Fetching https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz - ######################################################################## 100.0% - ==> Checksummed 1 version of pandas - ==> This package looks like it uses the python build system - ==> Changing package name from pandas to py-pandas - ==> Created template for py-pandas package - ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/py-pandas/package.py - -And we are left with the following template: - -.. literalinclude:: tutorial/examples/PyPackage/0.package.py - :language: python - :linenos: - -As you can see this is not any different than any package template that we have -written. We have the choice of providing build options or using the sensible -defaults - -Luckily for us, there is no need to provide build args. - -Next we need to find the dependencies of a package. Dependencies are usually -listed in :code:`setup.py`. You can find the dependencies by searching for -:code:`install_requires` keyword in that file. Here it is for :code:`Pandas`: - -.. code-block:: python - - # ... code - if sys.version_info[0] >= 3: - - setuptools_kwargs = { - 'zip_safe': False, - 'install_requires': ['python-dateutil >= 2', - 'pytz >= 2011k', - 'numpy >= %s' % min_numpy_ver], - 'setup_requires': ['numpy >= %s' % min_numpy_ver], - } - if not _have_setuptools: - sys.exit("need setuptools/distribute for Py3k" - "\n$ pip install distribute") - - # ... more code - -You can find a more comprehensive list at the Pandas documentation_. - -.. _documentation: https://pandas.pydata.org/pandas-docs/stable/install.html - - -By reading the documentation and :code:`setup.py` we found that :code:`Pandas` -depends on :code:`python-dateutil`, :code:`pytz`, and :code:`numpy`, :code:`numexpr`, -and finally :code:`bottleneck`. - -Here is the completed :code:`Pandas` script: - -.. literalinclude:: tutorial/examples/PyPackage/1.package.py - :language: python - :linenos: - -It is quite important to declare all the dependencies of a Python package. -Spack can "activate" Python packages to prevent the user from having to -load each dependency module explictly. If a dependency is missed, Spack will -be unable to properly activate the package and it will cause an issue. To -learn more about extensions go to :ref:`cmd-spack-extensions`. - -From this example, you can see that building Python modules is made easy -through the :code:`PythonPackage` class. - -------------------- -Other Build Systems -------------------- - -Although we won't get in depth with any of the other build systems that Spack -supports, it is worth mentioning that Spack does provide subclasses -for the following build systems: - -1. :code:`IntelPackage` -2. :code:`SconsPackage` -3. :code:`WafPackage` -4. :code:`RPackage` -5. :code:`PerlPackage` -6. :code:`QMakePackage` - - -Each of these classes have their own abstractions to help assist in writing -package files. For whatever doesn't fit nicely into the other build-systems, -you can use the :code:`Package` class. - -Hopefully by now you can see how we aim to make packaging simple and -robust through these classes. If you want to learn more about these build -systems, check out :ref:`installation_procedure` in the Packaging Guide. diff --git a/lib/spack/docs/tutorial_configuration.rst b/lib/spack/docs/tutorial_configuration.rst deleted file mode 100644 index 879bb949670..00000000000 --- a/lib/spack/docs/tutorial_configuration.rst +++ /dev/null @@ -1,951 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _configs-tutorial: - -====================== -Configuration Tutorial -====================== - -This tutorial will guide you through various configuration options -that allow you to customize Spack's behavior with respect to -software installation. We will first cover the configuration file -hierarchy. Then, we will cover configuration options for compilers, -focusing on how they can be used to extend Spack's compiler auto-detection. -Next, we will cover the packages configuration file, focusing on -how it can be used to override default build options as well as -specify external package installations to use. Finally, we will -briefly touch on the config configuration file, which manages more -high-level Spack configuration options. - -For all of these features, we will demonstrate how we build up a full -configuration file. For some, we will then demonstrate how the -configuration affects the install command, and for others we will use -the ``spack spec`` command to demonstrate how the configuration -changes have affected Spack's concretization algorithm. The provided -output is all from a server running Ubuntu version 16.04. - -.. _configs-tutorial-scopes: - --------------------- -Configuration Scopes --------------------- - -Depending on your use case, you may want to provide configuration -settings common to everyone on your team, or you may want to set -default behaviors specific to a single user account. Spack provides -six configuration *scopes* to handle this customization. These scopes, -in order of decreasing priority, are: - -============ =================================================== -Scope Directory -============ =================================================== -Command-line N/A -Custom Custom directory, specified with ``--config-scope`` -User ``~/.spack/`` -Site ``$SPACK_ROOT/etc/spack/`` -System ``/etc/spack/`` -Defaults ``$SPACK_ROOT/etc/spack/defaults/`` -============ =================================================== - -Spack's default configuration settings reside in -``$SPACK_ROOT/etc/spack/defaults``. These are useful for reference, -but should never be directly edited. To override these settings, -create new configuration files in any of the higher-priority -configuration scopes. - -A particular cluster may have multiple Spack installations associated -with different projects. To provide settings common to all Spack -installations, put your configuration files in ``/etc/spack``. -To provide settings specific to a particular Spack installation, -you can use the ``$SPACK_ROOT/etc/spack`` directory. - -For settings specific to a particular user, you will want to add -configuration files to the ``~/.spack`` directory. When Spack first -checked for compilers on your system, you may have noticed that it -placed your compiler configuration in this directory. - -Configuration settings can also be placed in a custom location, -which is then specified on the command line via ``--config-scope``. -An example use case is managing two sets of configurations, one for -development and another for production preferences. - -Settings specified on the command line have precedence over all -other configuration scopes. - -You can also use ``spack config blame `` for displaying -the effective configuration. Spack will show from which scopes -the configuration has been assembled. - -^^^^^^^^^^^^^^^^^^^^^^^^ -Platform-specific Scopes -^^^^^^^^^^^^^^^^^^^^^^^^ - -Some facilities manage multiple platforms from a single shared -file system. In order to handle this, each of the configuration -scopes listed above has two *sub-scopes*: platform-specific and -platform-independent. For example, compiler settings can be stored -in ``compilers.yaml`` configuration files in the following locations: - -#. ``~/.spack//compilers.yaml`` -#. ``~/.spack/compilers.yaml`` -#. ``$SPACK_ROOT/etc/spack//compilers.yaml`` -#. ``$SPACK_ROOT/etc/spack/compilers.yaml`` -#. ``/etc/spack//compilers.yaml`` -#. ``/etc/spack/compilers.yaml`` -#. ``$SPACK_ROOT/etc/defaults//compilers.yaml`` -#. ``$SPACK_ROOT/etc/defaults/compilers.yaml`` - -These files are listed in decreasing order of precedence, so files in -``~/.spack/`` will override settings in ``~/.spack``. - ------------ -YAML Format ------------ - -Spack configurations are YAML dictionaries. Every configuration file -begins with a top-level dictionary that tells Spack which -configuration set it modifies. When Spack checks its configuration, -the configuration scopes are updated as dictionaries in increasing -order of precedence, allowing higher precedence files to override -lower. YAML dictionaries use a colon ":" to specify key-value -pairs. Spack extends YAML syntax slightly to allow a double-colon -"::" to specify a key-value pair. When a double-colon is used to -specify a key-value pair, instead of adding that section, Spack -replaces what was in that section with the new value. For example, -consider a user's compilers configuration file as follows: - -.. code-block:: yaml - - compilers:: - - compiler: - environment: {} - extra_rpaths: [] - flags: {} - modules: [] - operating_system: ubuntu16.04 - paths: - cc: /usr/bin/gcc - cxx: /usr/bin/g++ - f77: /usr/bin/gfortran - fc: /usr/bin/gfortran - spec: gcc@5.4.0 - target: x86_64 - - -This ensures that no other compilers are used, as the user configuration -scope is the last scope searched and the ``compilers::`` line replaces -all previous configuration files information. If the same -configuration file had a single colon instead of the double colon, it -would add the GCC version 5.4.0 compiler to whatever other compilers -were listed in other configuration files. - -.. _configs-tutorial-compilers: - ----------------------- -Compiler Configuration ----------------------- - -For most tasks, we can use Spack with the compilers auto-detected the -first time Spack runs on a system. As discussed in the basic -installation tutorial, we can also tell Spack where compilers are -located using the ``spack compiler add`` command. However, in some -circumstances we want even more fine-grained control over the -compilers available. This section will teach you how to exercise that -control using the compilers configuration file. - -We will start by opening the compilers configuration file: - -.. code-block:: console - - $ spack config edit compilers - - -.. code-block:: yaml - - compilers: - - compiler: - environment: {} - extra_rpaths: [] - flags: {} - modules: [] - operating_system: ubuntu16.04 - paths: - cc: /usr/bin/clang-3.7 - cxx: /usr/bin/clang++-3.7 - f77: null - fc: null - spec: clang@3.7.1-2ubuntu2 - target: x86_64 - - compiler: - environment: {} - extra_rpaths: [] - flags: {} - modules: [] - operating_system: ubuntu16.04 - paths: - cc: /usr/bin/clang - cxx: /usr/bin/clang++ - f77: null - fc: null - spec: clang@3.8.0-2ubuntu4 - target: x86_64 - - compiler: - environment: {} - extra_rpaths: [] - flags: {} - modules: [] - operating_system: ubuntu16.04 - paths: - cc: /usr/bin/gcc-4.7 - cxx: /usr/bin/g++-4.7 - f77: /usr/bin/gfortran-4.7 - fc: /usr/bin/gfortran-4.7 - spec: gcc@4.7 - target: x86_64 - - compiler: - environment: {} - extra_rpaths: [] - flags: {} - modules: [] - operating_system: ubuntu16.04 - paths: - cc: /usr/bin/gcc - cxx: /usr/bin/g++ - f77: /usr/bin/gfortran - fc: /usr/bin/gfortran - spec: gcc@5.4.0 - target: x86_64 - - -This specifies two versions of the GCC compiler and two versions of the -Clang compiler with no Flang compiler. Now suppose we have a code that -we want to compile with the Clang compiler for C/C++ code, but with -gfortran for Fortran components. We can do this by adding another entry -to the ``compilers.yaml`` file. - -.. code-block:: yaml - - - compiler: - environment: {} - extra_rpaths: [] - flags: {} - modules: [] - operating_system: ubuntu16.04 - paths: - cc: /usr/bin/clang - cxx: /usr/bin/clang++ - f77: /usr/bin/gfortran - fc: /usr/bin/gfortran - spec: clang@3.8.0-gfortran - target: x86_64 - - -Let's talk about the sections of this compiler entry that we've changed. -The biggest change we've made is to the ``paths`` section. This lists -the paths to the compilers to use for each language/specification. -In this case, we point to the Clang compiler for C/C++ and the gfortran -compiler for both specifications of Fortran. We've also changed the -``spec`` entry for this compiler. The ``spec`` entry is effectively the -name of the compiler for Spack. It consists of a name and a version -number, separated by the ``@`` sigil. The name must be one of the supported -compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce, arm). -The version number can be an arbitrary string of alphanumeric characters, -as well as ``-``, ``.``, and ``_``. The ``target`` and ``operating_system`` -sections we leave unchanged. These sections specify when Spack can use -different compilers, and are primarily useful for configuration files that -will be used across multiple systems. - -We can verify that our new compiler works by invoking it now: - -.. code-block:: console - - $ spack install --no-cache zlib %clang@3.8.0-gfortran - ... - - -This new compiler also works on Fortran codes: - -.. code-block:: console - - $ spack install --no-cache cfitsio~bzip2 %clang@3.8.0-gfortran - ... - - -^^^^^^^^^^^^^^ -Compiler Flags -^^^^^^^^^^^^^^ - -Some compilers may require specific compiler flags to work properly in -a particular computing environment. Spack provides configuration -options for setting compiler flags every time a specific compiler is -invoked. These flags become part of the package spec and therefore of -the build provenance. As on the command line, the flags are set -through the implicit build variables ``cflags``, ``cxxflags``, ``cppflags``, -``fflags``, ``ldflags``, and ``ldlibs``. - -Let's open our compilers configuration file again and add a compiler flag: - -.. code-block:: yaml - - - compiler: - environment: {} - extra_rpaths: [] - flags: - cppflags: -g - modules: [] - operating_system: ubuntu16.04 - paths: - cc: /usr/bin/clang - cxx: /usr/bin/clang++ - f77: /usr/bin/gfortran - fc: /usr/bin/gfortran - spec: clang@3.8.0-gfortran - target: x86_64 - - -We can test this out using the ``spack spec`` command to show how the -spec is concretized: - -.. code-block:: console - - $ spack spec cfitsio %clang@3.8.0-gfortran - Input spec - -------------------------------- - cfitsio%clang@3.8.0-gfortran - - Normalized - -------------------------------- - cfitsio%clang@3.8.0-gfortran - - Concretized - -------------------------------- - cfitsio@3.410%clang@3.8.0-gfortran cppflags="-g" +bzip2+shared arch=linux-ubuntu16.04-x86_64 - ^bzip2@1.0.6%clang@3.8.0-gfortran cppflags="-g" +shared arch=linux-ubuntu16.04-x86_64 - - -We can see that ``cppflags="-g"`` has been added to every node in the DAG. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Advanced Compiler Configuration -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -There are three fields of the compiler configuration entry that we -have not yet talked about. - -The ``modules`` field of the compiler is used primarily on Cray systems, -but can be useful on any system that has compilers that are only -useful when a particular module is loaded. Any modules in the -``modules`` field of the compiler configuration will be loaded as part -of the build environment for packages using that compiler. - -The ``extra_rpaths`` field of the compiler configuration is used for -compilers that do not rpath all of their dependencies by -default. Since compilers are often installed externally to Spack, -Spack is unable to manage compiler dependencies and enforce -rpath usage. This can lead to packages not finding link dependencies -imposed by the compiler properly. For compilers that impose link -dependencies on the resulting executables that are not rpath'ed into -the executable automatically, the ``extra_rpaths`` field of the compiler -configuration tells Spack which dependencies to rpath into every -executable created by that compiler. The executables will then be able -to find the link dependencies imposed by the compiler. As an example, -this field can be set by: - -.. code-block:: yaml - - - compiler: - ... - extra_rpaths: - - /apps/intel/ComposerXE2017/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin - ... - - -The ``environment`` field of the compiler configuration is used for -compilers that require environment variables to be set during build -time. For example, if your Intel compiler suite requires the -``INTEL_LICENSE_FILE`` environment variable to point to the proper -license server, you can set this in ``compilers.yaml`` as follows: - -.. code-block:: yaml - - - compiler: - environment: - set: - INTEL_LICENSE_FILE: 1713@license4 - ... - - -In addition to ``set``, ``environment`` also supports ``unset``, -``prepend-path``, and ``append-path``. - -.. _configs-tutorial-package-prefs: - -------------------------------- -Configuring Package Preferences -------------------------------- - -Package preferences in Spack are managed through the ``packages.yaml`` -configuration file. First, we will look at the default -``packages.yaml`` file. - -.. code-block:: console - - $ spack config --scope defaults edit packages - - -.. literalinclude:: _spack_root/etc/spack/defaults/packages.yaml - :language: yaml - - -This sets the default preferences for compilers and for providers of -virtual packages. To illustrate how this works, suppose we want to -change the preferences to prefer the Clang compiler and to prefer -MPICH over OpenMPI. Currently, we prefer GCC and OpenMPI. - -.. code-block:: console - - $ spack spec hdf5 - Input spec - -------------------------------- - hdf5 - - Concretized - -------------------------------- - hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64 - ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64 - ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64 - ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64 - ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - - -Now we will open the packages configuration file and update our -preferences. - -.. code-block:: console - - $ spack config edit packages - - -.. code-block:: yaml - - packages: - all: - compiler: [clang, gcc, intel, pgi, xl, nag] - providers: - mpi: [mpich, openmpi] - - -Because of the configuration scoping we discussed earlier, this -overrides the default settings just for these two items. - -.. code-block:: console - - $ spack spec hdf5 - Input spec - -------------------------------- - hdf5 - - Concretized - -------------------------------- - hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64 - ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64 - ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - - -^^^^^^^^^^^^^^^^^^^ -Variant Preferences -^^^^^^^^^^^^^^^^^^^ - -The packages configuration file can also set variant preferences for -package variants. For example, let's change our preferences to build all -packages without shared libraries. We will accomplish this by turning -off the ``shared`` variant on all packages that have one. - -.. code-block:: yaml - - packages: - all: - compiler: [clang, gcc, intel, pgi, xl, nag] - providers: - mpi: [mpich, openmpi] - variants: ~shared - - -We can check the effect of this command with ``spack spec hdf5`` again. - -.. code-block:: console - - $ spack spec hdf5 - Input spec - -------------------------------- - hdf5 - - Concretized - -------------------------------- - hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64 - ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64 - ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64 - ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64 - - -So far we have only made global changes to the package preferences. As -we've seen throughout this tutorial, HDF5 builds with MPI enabled by -default in Spack. If we were working on a project that would routinely -need serial HDF5, that might get annoying quickly, having to type -``hdf5~mpi`` all the time. Instead, we'll update our preferences for -HDF5. - -.. code-block:: yaml - - packages: - all: - compiler: [clang, gcc, intel, pgi, xl, nag] - providers: - mpi: [mpich, openmpi] - variants: ~shared - hdf5: - variants: ~mpi - - -Now hdf5 will concretize without an MPI dependency by default. - -.. code-block:: console - - $ spack spec hdf5 - Input spec - -------------------------------- - hdf5 - - Concretized - -------------------------------- - hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64 - - -In general, every attribute that we can set for all packages we can -set separately for an individual package. - -^^^^^^^^^^^^^^^^^ -External Packages -^^^^^^^^^^^^^^^^^ - -The packages configuration file also controls when Spack will build -against an externally installed package. On these systems we have a -pre-installed zlib. - -.. code-block:: yaml - - packages: - all: - compiler: [clang, gcc, intel, pgi, xl, nag] - providers: - mpi: [mpich, openmpi] - variants: ~shared - hdf5: - variants: ~mpi - zlib: - paths: - zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr - - -Here, we've told Spack that zlib 1.2.8 is installed on our system. -We've also told it the installation prefix where zlib can be found. -We don't know exactly which variants it was built with, but that's -okay. - -.. code-block:: console - - $ spack spec hdf5 - Input spec - -------------------------------- - hdf5 - - Concretized - -------------------------------- - hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64 - - -You'll notice that Spack is now using the external zlib installation, -but the compiler used to build zlib is now overriding our compiler -preference of clang. If we explicitly specify Clang: - -.. code-block:: console - - $ spack spec hdf5 %clang - Input spec - -------------------------------- - hdf5%clang - - Concretized - -------------------------------- - hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64 - - -Spack concretizes to both HDF5 and zlib being built with Clang. -This has a side-effect of rebuilding zlib. If we want to force -Spack to use the system zlib, we have two choices. We can either -specify it on the command line, or we can tell Spack that it's -not allowed to build its own zlib. We'll go with the latter. - -.. code-block:: yaml - - packages: - all: - compiler: [clang, gcc, intel, pgi, xl, nag] - providers: - mpi: [mpich, openmpi] - variants: ~shared - hdf5: - variants: ~mpi - zlib: - paths: - zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr - buildable: False - - -Now Spack will be forced to choose the external zlib. - -.. code-block:: console - - $ spack spec hdf5 %clang - Input spec - -------------------------------- - hdf5%clang - - Concretized - -------------------------------- - hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64 - - -This gets slightly more complicated with virtual dependencies. Suppose -we don't want to build our own MPI, but we now want a parallel version -of HDF5? Well, fortunately we have MPICH installed on these systems. - -.. code-block:: yaml - - packages: - all: - compiler: [clang, gcc, intel, pgi, xl, nag] - providers: - mpi: [mpich, openmpi] - variants: ~shared - hdf5: - variants: ~mpi - zlib: - paths: - zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr - buildable: False - mpich: - paths: - mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr - buildable: False - - -If we concretize ``hdf5+mpi`` with this configuration file, we will just -build with an alternate MPI implementation. - -.. code-block:: console - - $ spack spec hdf5+mpi %clang - Input spec - -------------------------------- - hdf5%clang+mpi - - Concretized - -------------------------------- - hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^openmpi@3.1.3%clang@3.8.0-2ubuntu4~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64 - ^hwloc@1.11.9%clang@3.8.0-2ubuntu4~cairo~cuda+libxml2+pci~shared arch=linux-ubuntu16.04-x86_64 - ^libpciaccess@0.13.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^util-macros@1.19.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^libxml2@2.9.8%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64 - ^xz@5.2.4%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64 - ^numactl@2.0.11%clang@3.8.0-2ubuntu4 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64 - ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64 - ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 - - -We have only expressed a preference for MPICH over other MPI -implementations, and Spack will happily build with one we haven't -forbid it from building. We could resolve this by requesting -``hdf5+mpi%clang^mpich`` explicitly, or we can configure Spack not to -use any other MPI implementation. Since we're focused on -configurations here and the former can get tedious, we'll need to -modify our ``packages.yaml`` file again. - -While we're at it, we can configure HDF5 to build with MPI by default -again. - -.. code-block:: yaml - - packages: - all: - compiler: [clang, gcc, intel, pgi, xl, nag] - providers: - mpi: [mpich, openmpi] - variants: ~shared - zlib: - paths: - zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr - buildable: False - mpich: - paths: - mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr - buildable: False - openmpi: - buildable: False - mvapich2: - buildable: False - intel-mpi: - buildable: False - intel-parallel-studio: - buildable: False - spectrum-mpi: - buildable: False - mpilander: - buildable: False - charm: - buildable: False - charmpp: - buildable: False - - -Now that we have configured Spack not to build any of the possible -providers for MPI, we can try again. - -.. code-block:: console - - $ spack spec hdf5 %clang - Input spec - -------------------------------- - hdf5%clang - - Concretized - -------------------------------- - hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - ^mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64 - - -By configuring most of our package preferences in ``packages.yaml``, -we can cut down on the amount of work we need to do when specifying -a spec on the command line. In addition to compiler and variant -preferences, we can specify version preferences as well. Except for -selecting providers via `^`, anything that you can specify on the -command line can be specified in ``packages.yaml`` with the exact -same spec syntax. - -^^^^^^^^^^^^^^^^^^^^^^^^ -Installation Permissions -^^^^^^^^^^^^^^^^^^^^^^^^ - -The ``packages.yaml`` file also controls the default permissions -to use when installing a package. You'll notice that by default, -the installation prefix will be world readable but only user writable. - -Let's say we need to install ``converge``, a licensed software package. -Since a specific research group, ``fluid_dynamics``, pays for this -license, we want to ensure that only members of this group can access -the software. We can do this like so: - -.. code-block:: yaml - - packages: - converge: - permissions: - read: group - group: fluid_dynamics - - -Now, only members of the ``fluid_dynamics`` group can use any -``converge`` installations. - -.. warning:: - - Make sure to delete or move the ``packages.yaml`` you have been - editing up to this point. Otherwise, it will change the hashes - of your packages, leading to differences in the output of later - tutorial sections. - - ------------------ -High-level Config ------------------ - -In addition to compiler and package settings, Spack allows customization -of several high-level settings. These settings are stored in the generic -``config.yaml`` configuration file. You can see the default settings by -running: - -.. code-block:: console - - $ spack config --scope defaults edit config - - -.. literalinclude:: _spack_root/etc/spack/defaults/config.yaml - :language: yaml - - -As you can see, many of the directories Spack uses can be customized. -For example, you can tell Spack to install packages to a prefix -outside of the ``$SPACK_ROOT`` hierarchy. Module files can be -written to a central location if you are using multiple Spack -instances. If you have a fast scratch file system, you can run builds -from this file system with the following ``config.yaml``: - -.. code-block:: yaml - - config: - build_stage: - - /scratch/$user/spack-stage - - -.. note:: - - It is important to distinguish the build stage directory from other - directories in your scratch space to ensure ``spack clean`` does not - inadvertently remove unrelated files. Spack prepends ``spack-stage-`` - to temporary staging directory names to reduce this risk. Using a - combination of ``spack`` and or ``stage`` in each specified path, as - shown in the default settings and documented examples, will add - another layer of protection. See :ref:`config-yaml` for details. - - -On systems with compilers that absolutely *require* environment variables -like ``LD_LIBRARY_PATH``, it is possible to prevent Spack from cleaning -the build environment with the ``dirty`` setting: - -.. code-block:: yaml - - config: - dirty: true - - -However, this is strongly discouraged, as it can pull unwanted libraries -into the build. - -One last setting that may be of interest to many users is the ability -to customize the parallelism of Spack builds. By default, Spack -installs all packages in parallel with the number of jobs equal to the -number of cores on the node (up to a maximum of 16). For example, on a -node with 16 cores, this will look like: - -.. code-block:: console - - $ spack install --no-cache --verbose --overwrite zlib - ==> Installing zlib - ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz - ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz - ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> No patches needed for zlib - ==> Building zlib [Package] - ==> Executing phase: 'install' - ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb' - ... - ==> 'make' '-j16' - ... - ==> 'make' '-j16' 'install' - ... - ==> Successfully installed zlib - Fetch: 0.00s. Build: 1.03s. Total: 1.03s. - [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - - -As you can see, we are building with all 16 cores on the node. If you are -on a shared login node, this can slow down the system for other users. If -you have a strict ulimit or restriction on the number of available licenses, -you may not be able to build at all with this many cores. On nodes with 64+ -cores, you may not see a significant speedup of the build anyway. To limit -the number of cores our build uses, set ``build_jobs`` like so: - -.. code-block:: yaml - - config: - build_jobs: 2 - - -If we uninstall and reinstall zlib, we see that it now uses only 2 cores: - -.. code-block:: console - - $ spack install --no-cache --verbose --overwrite zlib - ==> Installing zlib - ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz - ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz - ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> No patches needed for zlib - ==> Building zlib [Package] - ==> Executing phase: 'install' - ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb' - ... - ==> 'make' '-j2' - ... - ==> 'make' '-j2' 'install' - ... - ==> Successfully installed zlib - Fetch: 0.00s. Build: 1.03s. Total: 1.03s. - [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - - -Obviously, if you want to build everything in serial for whatever reason, -you would set ``build_jobs`` to 1. - --------- -Examples --------- - -For examples of how other sites configure Spack, see -https://github.com/spack/spack-configs. If you use Spack at your site -and want to share your config files, feel free to submit a pull request! diff --git a/lib/spack/docs/tutorial_environments.rst b/lib/spack/docs/tutorial_environments.rst deleted file mode 100644 index 4b86dbd5aca..00000000000 --- a/lib/spack/docs/tutorial_environments.rst +++ /dev/null @@ -1,815 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _environments-tutorial: - -===================== -Environments Tutorial -===================== - -We've shown you how to install and remove packages with Spack. You can -use :ref:`cmd-spack-install` to install packages, -:ref:`cmd-spack-uninstall` to remove them, and :ref:`cmd-spack-find` to -look at and query what is installed. We've also shown you how to -customize Spack's installation with configuration files like -:ref:`packages.yaml `. - -If you build a lot of software, or if you work on multiple projects, -managing everything in one place can be overwhelming. The default ``spack -find`` output may contain many packages, but you may want to *just* focus -on packages for a particular project. Moreover, you may want to include -special configuration with your package groups, e.g., to build all the -packages in the same group the same way. - -Spack **environments** provide a way to handle these problems. - -------------------- -Environment basics -------------------- - -Let's look at the output of ``spack find`` at this point in the tutorial. - -.. code-block:: console - - $ spack find - ==> 70 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - tcl@8.6.8 zlib@1.2.8 zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - adept-utils@1.0.1 hdf5@1.10.4 mpc@1.1.0 perl@5.26.2 - autoconf@2.69 hdf5@1.10.4 mpfr@3.1.6 pkgconf@1.4.2 - automake@1.16.1 hdf5@1.10.4 mpich@3.2.1 readline@7.0 - boost@1.68.0 hwloc@1.11.9 mpileaks@1.0 suite-sparse@5.3.0 - bzip2@1.0.6 hypre@2.15.1 mumps@5.1.1 tar@1.30 - callpath@1.0.4 hypre@2.15.1 mumps@5.1.1 tcl@8.6.8 - cmake@3.12.3 isl@0.18 ncurses@6.1 tcl@8.6.8 - diffutils@3.6 libdwarf@20180129 netcdf@4.6.1 texinfo@6.5 - dyninst@9.3.2 libiberty@2.31.1 netcdf@4.6.1 trilinos@12.12.1 - elfutils@0.173 libpciaccess@0.13.5 netlib-scalapack@2.0.2 trilinos@12.12.1 - findutils@4.6.0 libsigsegv@2.11 netlib-scalapack@2.0.2 util-macros@1.19.1 - gcc@7.2.0 libtool@2.4.6 numactl@2.0.11 xz@5.2.4 - gdbm@1.14.1 libxml2@2.9.8 openblas@0.3.3 zlib@1.2.8 - gettext@0.19.8.1 m4@1.4.18 openmpi@3.1.3 zlib@1.2.8 - glm@0.9.7.1 matio@1.5.9 openssl@1.0.2o zlib@1.2.11 - gmp@6.1.2 matio@1.5.9 parmetis@4.0.3 - hdf5@1.10.4 metis@5.1.0 parmetis@4.0.3 - - -This is a complete, but cluttered view. There are packages built with -both ``openmpi`` and ``mpich``, as well as multiple variants of other -packages, like ``zlib``. The query mechanism we learned about in ``spack -find`` can help, but it would be nice if we could start from a clean -slate without losing what we've already done. - - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Creating and activating environments -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -The ``spack env`` command can help. Let's create a new environment: - -.. code-block:: console - - $ spack env create myproject - ==> Created environment 'myproject' in ~/spack/var/spack/environments/myproject - -An environment is a virtualized ``spack`` instance that you can use for a -specific purpose. You can see the environments we've created so far like this: - -.. code-block:: console - - $ spack env list - ==> 1 environments - myproject - -And you can **activate** an environment with ``spack env activate``: - -.. code-block:: console - - $ spack env activate myproject - -Once you enter an environment, ``spack find`` shows only what is in the -current environment. That's nothing, so far: - -.. code-block:: console - - $ spack find - ==> In environment myproject - ==> No root specs - - ==> 0 installed packages - -The ``spack find`` output is still *slightly* different. It tells you -that you're in the ``myproject`` environment, so that you don't panic -when you see that there is nothing installed. It also says that there -are *no root specs*. We'll get back to what that means later. - -If you *only* want to check what environment you are in, you can use -``spack env status``: - -.. code-block:: console - - $ spack env status - ==> In environment myproject - -And, if you want to leave this environment and go back to normal Spack, -you can use ``spack env deactivate``. We like to use the -``despacktivate`` alias (which Spack sets up automatically) for short: - -.. code-block:: console - - $ despacktivate # short alias for `spack env deactivate` - $ spack env status - ==> No active environment - $ spack find - netcdf@4.6.1 readline@7.0 zlib@1.2.11 - diffutils@3.6 hdf5@1.10.4 m4@1.4.18 netcdf@4.6.1 suite-sparse@5.3.0 - dyninst@10.0.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 tar@1.30 - elfutils@0.173 hypre@2.15.1 matio@1.5.9 netlib-scalapack@2.0.2 tcl@8.6.8 - findutils@4.6.0 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 tcl@8.6.8 - gcc@7.2.0 intel-tbb@2019 mpc@1.1.0 openblas@0.3.3 texinfo@6.5~ - - -^^^^^^^^^^^^^^^^^^^ -Installing packages -^^^^^^^^^^^^^^^^^^^ - -Ok, now that we understand how creation and activation work, let's go -back to ``myproject`` and *install* a few packages: - -.. code-block:: console - - $ spack env activate myproject - $ spack install tcl - ==> tcl is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt - $ spack install trilinos - ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r - $ spack find - ==> In environment myproject - ==> Root specs - tcl trilinos - - ==> 22 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - boost@1.68.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4 - bzip2@1.0.6 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11 - glm@0.9.7.1 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8 - hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1 - -We've installed ``tcl`` and ``trilinos`` in our environment, along with -all of their dependencies. We call ``tcl`` and ``trilinos`` the -**roots** because we asked for them explicitly. The other 20 packages -listed under "installed packages" are present because they were needed as -dependencies. So, these are the roots of the packages' dependency graph. - -The " is already installed" messages above are generated because -we already installed these packages in previous steps of the tutorial, -and we don't have to rebuild them to put them in an environment. - -Now let's create *another* project. We'll call this one ``myproject2``: - -.. code-block:: console - - $ spack env create myproject2 - ==> Created environment 'myproject2' in ~/spack/var/spack/environments/myproject2 - $ spack env activate myproject2 - $ spack install hdf5 - ==> hdf5 is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw - $ spack install trilinos - ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r - $ spack find - ==> In environment myproject2 - ==> Root specs - hdf5 trilinos - - ==> 22 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - boost@1.68.0 hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 xz@5.2.4 - bzip2@1.0.6 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 zlib@1.2.11 - glm@0.9.7.1 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 - hdf5@1.10.4 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 trilinos@12.12.1 - -Now we have two environments: one with ``tcl`` and ``trilinos``, and -another with ``hdf5`` and ``trilinos``. - -We can uninstall trilinos from ``myproject2`` as you would expect: - -.. code-block:: console - - $ spack uninstall trilinos - ==> The following packages will be uninstalled: - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 - ==> Do you want to proceed? [y/N] y - $ spack find - ==> In environment myproject2 - ==> Root specs - hdf5 - - ==> 8 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - hdf5@1.10.4 libpciaccess@0.13.5 numactl@2.0.11 xz@5.2.4 - hwloc@1.11.9 libxml2@2.9.8 openmpi@3.1.3 zlib@1.2.11 - -Now there is only one root spec, ``hdf5``, which requires fewer -additional dependencies. - -However, we still needed ``trilinos`` for the ``myproject`` environment! -What happened to it? Let's switch back and see. - -.. code-block:: console - - $ despacktivate - $ spack env activate myproject - $ spack find - ==> In environment myproject - ==> Root specs - tcl trilinos - - ==> 22 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - boost@1.68.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4 - bzip2@1.0.6 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11 - glm@0.9.7.1 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8 - hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1 - - -Spack is smart enough to realize that ``trilinos`` is still present in -the other environment. Trilinos won't *actually* be uninstalled unless -it is no longer needed by any environments or packages. If it is still -needed, it is only removed from the environment. - -------------------------------- -Dealing with many specs at once -------------------------------- - -In the above examples, we just used ``install`` and ``uninstall``. There -are other ways to deal with groups of packages, as well. - -^^^^^^^^^^^^^ -Adding specs -^^^^^^^^^^^^^ - -Let's go back to our first ``myproject`` environment and *add* a few specs instead of installing them: - -.. code-block:: console - - $ spack add hdf5 - ==> Adding hdf5 to environment myproject - $ spack add gmp - ==> Adding mumps to environment myproject - $ spack find - ==> In environment myproject - ==> Root specs - gmp hdf5 tcl trilinos - - ==> 22 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - boost@1.68.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4 - bzip2@1.0.6 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11 - glm@0.9.7.1 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8 - hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1 - -Let's take a close look at what happened. The two packages we added, -``hdf5`` and ``gmp``, are present, but they're not installed in the -environment yet. ``spack add`` just adds *roots* to the environment, but -it does not automatically install them. - -We can install *all* the as-yet uninstalled packages in an environment by -simply running ``spack install`` with no arguments: - -.. code-block:: console - - $ spack install - ==> Concretizing hdf5 - [+] ozyvmhz hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - [+] 3njc4q5 ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64 - [+] 43tkw5m ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64 - [+] 5urc6tc ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] milz7fm ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] wpexsph ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64 - [+] teneqii ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - [+] ft463od ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64 - [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ==> Concretizing gmp - [+] qc4qcfz gmp@6.1.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ==> Installing environment myproject - ==> tcl is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt - ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r - ==> hdf5 is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw - ==> gmp is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw - -Spack will concretize the new roots, and install everything you added to -the environment. Now we can see the installed roots in the output of -``spack find``: - -.. code-block:: console - - $ spack find - ==> In environment myproject - ==> Root specs - gmp hdf5 tcl trilinos - - ==> 24 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - boost@1.68.0 hdf5@1.10.4 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8 - bzip2@1.0.6 hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1 - glm@0.9.7.1 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4 - gmp@6.1.2 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11 - -We can build whole environments this way, by adding specs and installing -all at once, or we can install them with the usual ``install`` and -``uninstall`` portions. The advantage to doing them all at once is that -we don't have to write a script outside of Spack to automate this, and we -can kick off a large build of many packages easily. - -^^^^^^^^^^^^^^^^^^^^^ -Configuration -^^^^^^^^^^^^^^^^^^^^^ - -So far, ``myproject`` does not have any special configuration associated -with it. The specs concretize using Spack's defaults: - -.. code-block:: console - - $ spack spec hypre - Input spec - -------------------------------- - hypre - - Concretized - -------------------------------- - hypre@2.15.1%gcc@5.4.0~debug~int64+internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64 - ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64 - ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64 - ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64 - ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64 - ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64 - ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - -You may want to add extra configuration to your environment. You can see -how your environment is configured using ``spack config get``: - -.. code-block:: console - - $ spack config get - # This is a Spack Environment file. - # - # It describes a set of packages to be installed, along with - # configuration settings. - spack: - # add package specs to the `specs` list - specs: [tcl, trilinos, hdf5, gmp] - -It turns out that this is a special configuration format where Spack -stores the state for the environment. Currently, the file is just a -``spack:`` header and a list of ``specs``. These are the roots. - -You can edit this file to add your own custom configuration. Spack -provides a shortcut to do that: - -.. code-block:: console - - spack config edit - -You should now see the same file, and edit it to look like this: - -.. code-block:: yaml - - # This is a Spack Environment file. - # - # It describes a set of packages to be installed, along with - # configuration settings. - spack: - packages: - all: - providers: - mpi: [mpich] - - # add package specs to the `specs` list - specs: [tcl, trilinos, hdf5, gmp] - -Now if we run ``spack spec`` again in the environment, specs will concretize with ``mpich`` as the MPI implementation: - -.. code-block:: console - - $ spack spec hypre - Input spec - -------------------------------- - hypre - - Concretized - -------------------------------- - hypre@2.15.1%gcc@5.4.0~debug~int64+internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64 - ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64 - ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64 - ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64 - -In addition to the ``specs`` section, an environment's configuration can -contain any of the configuration options from Spack's various config -sections. You can add custom repositories, a custom install location, -custom compilers, or custom external packages, in addition to the ``package`` -preferences we show here. - -But now we have a problem. We already installed part of this environment -with openmpi, but now we want to install it with ``mpich``. - -You can run ``spack concretize`` inside of an environment to concretize -all of its specs. We can run it here: - -.. code-block:: console - - $ spack concretize -f - ==> Concretizing tcl - [+] qhwyccy tcl@8.6.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - ==> Concretizing trilinos - [+] kqc52mo trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64 - [+] zbgfxap ^boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64 - [+] ufczdvs ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64 - [+] 2rhuivg ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - [+] otafqzh ^cmake@3.12.3%gcc@5.4.0~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-ubuntu16.04-x86_64 - [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] b4y3w3b ^openssl@1.0.2o%gcc@5.4.0+systemcerts arch=linux-ubuntu16.04-x86_64 - [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] jnw622j ^glm@0.9.7.1%gcc@5.4.0 build_type=RelWithDebInfo arch=linux-ubuntu16.04-x86_64 - [+] xxd7syh ^hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - [+] p3f7p2r ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64 - [+] d4iajxs ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64 - [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] zs7a2pc ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] obewuoz ^hypre@2.15.1%gcc@5.4.0~debug~int64~internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64 - [+] cyeg2yi ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64 - [+] gvyqldh ^matio@1.5.9%gcc@5.4.0+hdf5+shared+zlib arch=linux-ubuntu16.04-x86_64 - [+] 3wnvp4j ^metis@5.1.0%gcc@5.4.0 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 ~real64+shared arch=linux-ubuntu16.04-x86_64 - [+] cumcj5a ^mumps@5.1.1%gcc@5.4.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-ubuntu16.04-x86_64 - [+] p7iln2p ^netlib-scalapack@2.0.2%gcc@5.4.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64 - [+] wmmx5sg ^netcdf@4.6.1%gcc@5.4.0~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=linux-ubuntu16.04-x86_64 - [+] jehtata ^parmetis@4.0.3%gcc@5.4.0 build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=linux-ubuntu16.04-x86_64 - [+] zaau4ki ^suite-sparse@5.3.0%gcc@5.4.0~cuda~openmp+pic~tbb arch=linux-ubuntu16.04-x86_64 - ==> Concretizing hdf5 - - zjgyn3w hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - [+] p3f7p2r ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64 - [+] d4iajxs ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64 - [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] zs7a2pc ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - ==> Concretizing gmp - [+] qc4qcfz gmp@6.1.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - -Now, all the specs in the environment are concrete and ready to be -installed with ``mpich`` as the MPI implementation. - -Normally, we could just run ``spack config edit``, edit the environment -configuration, ``spack add`` some specs, and ``spack install``. - -But, when we already have installed packages in the environment, we have -to force everything in the environment to be re-concretized using ``spack -concretize -f``. *Then* we can re-run ``spack install``. - - ------------------------------------ -``spack.yaml`` and ``spack.lock`` ------------------------------------ - -So far we've shown you how to interact with environments from the command -line, but they also have a file-based interface that can be used by -developers and admins to manage workflows for projects. - -In this section we'll dive a little deeper to see how environments are -implemented, and how you could use this in your day-to-day development. - -^^^^^^^^^^^^^^ -``spack.yaml`` -^^^^^^^^^^^^^^ - -Earlier, we changed an environment's configuration using ``spack config -edit``. We were actually editing a special file called ``spack.yaml``. -Let's take a look. - -We can get directly to the current environment's location using ``spack cd``: - -.. code-block:: console - - $ spack cd -e myproject - $ pwd - ~/spack/var/spack/environments/myproject - $ ls - spack.lock spack.yaml - -We notice two things here. First, the environment is just a directory -inside of ``var/spack/environments`` within the Spack installation. -Second, it contains two important files: ``spack.yaml`` and -``spack.lock``. - -``spack.yaml`` is the configuration file for environments that we've -already seen, but it does not *have* to live inside Spack. If you create -an environment using ``spack env create``, it is *managed* by -Spack in the ``var/spack/environments`` directory, and you can refer to -it by name. - -You can actually put a ``spack.yaml`` file *anywhere*, and you can use it -to bundle an environment, or a list of dependencies to install, with your -project. Let's make a simple project: - -.. code-block:: console - - $ cd - $ mkdir code - $ cd code - $ spack env create -d . - ==> Created environment in ~/code - -Here, we made a new directory called *code*, and we used the ``-d`` -option to create an environment in it. - -What really happened? - -.. code-block:: console - - $ ls - spack.yaml - $ cat spack.yaml - # This is a Spack Environment file. - # - # It describes a set of packages to be installed, along with - # configuration settings. - spack: - # add package specs to the `specs` list - specs: [] - -Spack just created a ``spack.yaml`` file in the code directory, with an -empty list of root specs. Now we have a Spack environment, *in a -directory*, that we can use to manage dependencies. Suppose your project -depends on ``boost``, ``trilinos``, and ``openmpi``. You can add these -to your spec list: - -.. code-block:: yaml - - # This is a Spack Environment file. - # - # It describes a set of packages to be installed, along with - # configuration settings. - spack: - # add package specs to the `specs` list - specs: - - boost - - trilinos - - openmpi - -And now *anyone* who uses the *code* repository can use this format to -install the project's dependencies. They need only clone the repository, -``cd`` into it, and type ``spack install``: - -.. code-block:: console - - $ spack install - ==> Concretizing boost - [+] zbgfxap boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64 - [+] ufczdvs ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64 - [+] 2rhuivg ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - ==> Concretizing trilinos - [+] rlsruav trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64 - [+] zbgfxap ^boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64 - [+] ufczdvs ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64 - [+] 2rhuivg ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - [+] otafqzh ^cmake@3.12.3%gcc@5.4.0~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-ubuntu16.04-x86_64 - [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] b4y3w3b ^openssl@1.0.2o%gcc@5.4.0+systemcerts arch=linux-ubuntu16.04-x86_64 - [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] jnw622j ^glm@0.9.7.1%gcc@5.4.0 build_type=RelWithDebInfo arch=linux-ubuntu16.04-x86_64 - [+] oqwnui7 ^hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 - [+] 3njc4q5 ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64 - [+] 43tkw5m ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64 - [+] 5urc6tc ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] milz7fm ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] wpexsph ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64 - [+] teneqii ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] ft463od ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64 - [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] fshksdp ^hypre@2.15.1%gcc@5.4.0~debug~int64~internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64 - [+] cyeg2yi ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64 - [+] lmzdgss ^matio@1.5.9%gcc@5.4.0+hdf5+shared+zlib arch=linux-ubuntu16.04-x86_64 - [+] 3wnvp4j ^metis@5.1.0%gcc@5.4.0 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 ~real64+shared arch=linux-ubuntu16.04-x86_64 - [+] acsg2dz ^mumps@5.1.1%gcc@5.4.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-ubuntu16.04-x86_64 - [+] wotpfwf ^netlib-scalapack@2.0.2%gcc@5.4.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64 - [+] mhm4izp ^netcdf@4.6.1%gcc@5.4.0~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=linux-ubuntu16.04-x86_64 - [+] uv6h3sq ^parmetis@4.0.3%gcc@5.4.0 build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=linux-ubuntu16.04-x86_64 - [+] zaau4ki ^suite-sparse@5.3.0%gcc@5.4.0~cuda~openmp+pic~tbb arch=linux-ubuntu16.04-x86_64 - ==> Concretizing openmpi - [+] 3njc4q5 openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64 - [+] 43tkw5m ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64 - [+] 5urc6tc ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 - [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] milz7fm ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] wpexsph ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64 - [+] teneqii ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 - [+] ft463od ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64 - [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 - [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64 - [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64 - ==> Installing environment ~/code - ==> boost is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt - ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r - ==> openmpi is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx - - -Spack concretizes the specs in the ``spack.yaml`` file and installs them. - -What happened here? If you ``cd`` into a directory that has a -``spack.yaml`` file in it, Spack considers this directory's environment -to be activated. The directory does not have to live within Spack; it -can be anywhere. - -So, from ``~/code``, we can actually manipulate ``spack.yaml`` using -``spack add`` and ``spack remove`` (just like managed environments): - -.. code-block:: console - - $ spack add hdf5@5.5.1 - ==> Adding hdf5 to environment ~/code - $ cat spack.yaml - # This is a Spack Environment file. - # - # It describes a set of packages to be installed, along with - # configuration settings. - spack: - # add package specs to the `specs` list - specs: - - boost - - trilinos - - openmpi - - hdf5@5.5.1 - - $ spack remove hdf5 - ==> Removing hdf5 from environment ~/code - $ cat spack.yaml - # This is a Spack Environment file. - # - # It describes a set of packages to be installed, along with - # configuration settings. - spack: - # add package specs to the `specs` list - specs: - - boost - - trilinos - - openmpi - - -^^^^^^^^^^^^^^ -``spack.lock`` -^^^^^^^^^^^^^^ - -Okay, we've covered managed environments, environments in directories, and -the last thing we'll cover is ``spack.lock``. You may remember that when -we ran ``spack install``, Spack concretized all the specs in the -``spack.yaml`` file and installed them. - -Whenever we concretize Specs in an environment, all concrete specs in the -environment are written out to a ``spack.lock`` file *alongside* -``spack.yaml``. The ``spack.lock`` file is not really human-readable -like the ``spack.yaml`` file. It is a ``json`` format that contains all -the information that we need to *reproduce* the build of an -environment: - -.. code-block:: console - - $ head spack.lock - { - "concrete_specs": { - "teneqii2xv5u6zl5r6qi3pwurc6pmypz": { - "xz": { - "version": "5.2.4", - "arch": { - "platform": "linux", - "platform_os": "ubuntu16.04", - "target": "x86_64" - }, - ... - -``spack.yaml`` and ``spack.lock`` correspond to two fundamental concepts -in Spack, but for environments: - - * ``spack.yaml`` is the set of *abstract* specs and configuration that - you want to install. - * ``spack.lock`` is the set of all fully *concretized* specs generated - from concretizing ``spack.yaml`` - -Using either of these, you can recreate an environment that someone else -built. ``spack env create`` takes an extra optional argument, which can -be either a ``spack.yaml`` or a ``spack.lock`` file: - -.. code-block:: console - - $ spack env create my-project spack.yaml - - $ spack env create my-project spack.lock - -Both of these create a new environment called ``my-project``, but which -one you choose to use depends on your needs: - -#. copying the yaml file allows someone else to build your *requirements*, - potentially a different way. - -#. copying the lock file allows someone else to rebuild your - *installation* exactly as you built it. - -The first use case can *re-concretize* the same specs on new platforms in -order to build, but it will preserve the abstract requirements. The -second use case (currently) requires you to be on the same machine, but -it retains all decisions made during concretization and is faithful to a -prior install. diff --git a/lib/spack/docs/tutorial_modules.rst b/lib/spack/docs/tutorial_modules.rst deleted file mode 100644 index 686da9f26e7..00000000000 --- a/lib/spack/docs/tutorial_modules.rst +++ /dev/null @@ -1,1575 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _modules-tutorial: - -============ -Module Files -============ - -In this tutorial, we'll introduce a few concepts that are fundamental -to the generation of module files with Spack, and we'll guide you through -the customization of both module files content and their layout on disk. In the end you -should have a clear understanding of: - - * What are module files and how they work - * How Spack generates them - * Which commands are available to ease their maintenance - * How it is possible to customize them in all aspects - -.. _module_file_tutorial_overview: - -------------------- -Modules at a glance -------------------- - -Let's start by summarizing what module files are and how you can use -them to modify your environment. The idea is to give enough information so that -people without any previous exposure to them will be able to follow the tutorial -later on. We'll also give a high-level view of how module files are generated -in Spack. If you are already familiar with these topics you can quickly skim -through this section or move directly to :ref:`module_file_tutorial_prerequisites`. - -.. _module_file_tutorial_what_are_modules: - -^^^^^^^^^^^^^^^^^^^^^^ -What are module files? -^^^^^^^^^^^^^^^^^^^^^^ - -Module files are an easy way to modify your environment in a controlled manner -during a shell session. In general, they contain the information needed to run an -application or use a library, and they work in conjunction with a tool that -interprets them. -Typical module files instruct this tool to modify the environment variables when a -module file is loaded: - - .. code-block:: console - - $ module show zlib - ------------------------------------------------------------------- - /home/mculpo/PycharmProjects/spack/share/spack/modules/linux-ubuntu14.04-x86_64/zlib/1.2.11-gcc-7.2.0-linux-ubuntu14.04-x86_64-co2px3k: - - module-whatis A free, general-purpose, legally unencumbered lossless data-compression library. - prepend-path MANPATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/share/man - prepend-path LIBRARY_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib - prepend-path LD_LIBRARY_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib - prepend-path CPATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/include - prepend-path PKG_CONFIG_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib/pkgconfig - prepend-path CMAKE_PREFIX_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/ - ------------------------------------------------------------------- - - $ echo $LD_LIBRARY_PATH - - $ module load zlib - $ echo $LD_LIBRARY_PATH - /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib - -and to undo the modifications when the same module file is unloaded: - - .. code-block:: console - - $ module unload zlib - $ echo $LD_LIBRARY_PATH - - $ - -Different formats exist for module files, and different tools -provide various levels of support for them. Spack can natively generate: - -1. Non-hierarchical module files written in TCL -2. Hierarchical module files written in Lua - -and can build `environment-modules `_ -and `lmod `_ as support tools. -Which of the formats or tools best suits one's needs depends on each particular -use-case. For the sake of illustration, we'll be working on -both formats using ``lmod``. - -.. seealso:: - Environment modules - This is the original tool that provided modules support. Its first - version was coded in C in the early '90s and was later substituted by a version - completely coded in TCL - the one Spack is distributing. More details on - its features are given in the `homepage of the project `_ - or in its `github page `_. The tool is able to - interpret the non-hierarchical TCL modulefiles written by Spack. - - Lmod - Lmod is a module system written in Lua, designed to easily handle hierarchies of - module files. It's a drop-in replacement of Environment Modules and works with - both of the module file formats generated by Spack. - Despite being fully compatible with Environment Modules there are many features that - are unique to Lmod. These features are either - `targeted towards safety `_ - or meant to - `extend the module system functionality `_. - - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -How do we generate module files? -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Before we dive into the hands-on sections it's worth spending a couple of words to explain how -module files are generated by Spack. The following diagram provides a high-level view -of the process: - - -.. image:: module_file_generation.* - -The red dashed line above represents Spack's boundaries, the blue one Spack's dependencies [#f1]_. -Module files are generated by combining: - - * the configuration details in ``config.yaml`` and ``modules.yaml`` - * the information contained in Spack packages (and processed by the module subpackage) - * a set of template files - -with `Jinja2 `_, an external template engine -that stamps out each particular module file. As Spack serves very diverse needs -this process has many points of customization, and we'll explore most of -them in the next sections. - -.. [#f1] Spack vendors its dependencies! This means that Spack comes with a copy of - each one of its dependencies, including ``Jinja2``, and is already configured to use them. - -.. _module_file_tutorial_prerequisites: - ----------------------- -Setup for the tutorial ----------------------- - -In order to showcase the capabilities of Spack's module file generation, we need -a representative set of software to work with. This set must include different -flavors of the same packages installed alongside each other and some -:ref:`external packages `. - -The purpose of this setup is not to make our life harder but to demonstrate -how Spack can help with similar situations, as they will happen on real HPC clusters. -For instance, it's often preferable for Spack to use vendor-provided MPI -implementations than to build one itself. - -To keep the set of software we're dealing with manageable, we're going -to uninstall everything from earlier in the tutorial. - -.. code-block: console - - $ spack uninstall -ay - -^^^^^^^^^^^^^^^^^^^ -Build a module tool -^^^^^^^^^^^^^^^^^^^ - -The first thing that we need is the module tool. In this case we -choose ``lmod`` as it can work with both hierarchical and non-hierarchical -module file layouts. - -.. code-block:: console - - $ bin/spack install lmod - -Once the module tool is installed we need to have it available in the -current shell. As the installation directories are definitely not easy -to remember, we'll employ the command ``spack location`` to retrieve the -``lmod`` prefix directly from Spack: - -.. code-block:: console - - $ . $(spack location -i lmod)/lmod/lmod/init/bash - -Now we can re-source the setup file and Spack modules will be put in -our module path. - -.. code-block:: console - - $ . share/spack/setup-env.sh - -.. FIXME: this needs bootstrap support for ``lmod`` - -.. FIXME: check the docs here, update them if necessary - If you need to install Lmod or Environment module you can refer - to the documentation :ref:`here `. - - -^^^^^^^^^^^^^^^^^^ -Add a new compiler -^^^^^^^^^^^^^^^^^^ - -The second step is to build a recent compiler. On first use, Spack -scans the environment and automatically locates the compiler(s) -already available on the system. For this tutorial, however, we want -to use ``gcc@7.2.0``. - - -.. code-block:: console - - $ spack install gcc@7.2.0 - ... - Wait a long time - ... - -Once ``gcc`` is installed we can use shell support to load it and make -it readily available: - -.. code-block:: console - - $ spack load gcc@7.2.0 - -It may not be apparent, but the last command employed the module files -generated automatically by Spack. What happens under the hood when you use -the ``spack load`` command is: - -1. the spec passed as argument is translated into a module file name -2. the current module tool is used to load that module file - -You can use this command to double check: - -.. code-block:: console - - $ module list - Currently Loaded Modules: - 1) gcc-7.2.0-gcc-5.4.0-b7smjjc - -Note that the 7-digit hash at the end of the generated module may vary depending -on architecture or package version. Now that we have ``gcc@7.2.0`` in ``PATH`` we -can finally add it to the list of compilers known to Spack: - -.. code-block:: console - - $ spack compiler add - ==> Added 1 new compiler to /home/spack1/.spack/linux/compilers.yaml - gcc@7.2.0 - ==> Compilers are defined in the following files: - /home/spack1/.spack/linux/compilers.yaml - - $ spack compiler list - ==> Available compilers - -- clang ubuntu16.04-x86_64 ------------------------------------- - clang@3.8.0-2ubuntu4 clang@3.7.1-2ubuntu2 - - -- gcc ubuntu16.04-x86_64 --------------------------------------- - gcc@7.2.0 gcc@5.4.0 gcc@4.7 - - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Build the software that will be used in the tutorial -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Finally, we should use Spack to install the packages used in the examples: - -.. code-block:: console - - $ spack install netlib-scalapack ^openmpi ^openblas - $ spack install netlib-scalapack ^mpich ^openblas - $ spack install netlib-scalapack ^openmpi ^netlib-lapack - $ spack install netlib-scalapack ^mpich ^netlib-lapack - $ spack install py-scipy ^openblas - - -.. _module_file_tutorial_non_hierarchical: - ------------------------------ -Non-hierarchical module files ------------------------------ - -If you arrived to this point you should have an environment that looks similar to: - -.. code-block:: console - - $ module avail - - ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ----------------------------------------------- - autoconf-2.69-gcc-5.4.0-3sx2gxe libsigsegv-2.11-gcc-7.2.0-g67xpfd openssl-1.0.2o-gcc-5.4.0-b4y3w3b - autoconf-2.69-gcc-7.2.0-yb2makb libtool-2.4.6-gcc-5.4.0-o2pfwjf openssl-1.0.2o-gcc-7.2.0-cvldq3v - automake-1.16.1-gcc-5.4.0-rymw7im libtool-2.4.6-gcc-7.2.0-kt2udm6 pcre-8.42-gcc-5.4.0-gt5lgzi - automake-1.16.1-gcc-7.2.0-qoowd5q libxml2-2.9.8-gcc-5.4.0-wpexsph perl-5.26.2-gcc-5.4.0-ic2kyoa - bzip2-1.0.6-gcc-5.4.0-ufczdvs libxml2-2.9.8-gcc-7.2.0-47gf5kk perl-5.26.2-gcc-7.2.0-fdwz5yu - bzip2-1.0.6-gcc-7.2.0-mwamumj lmod-7.8-gcc-5.4.0-kmhks3p pkgconf-1.4.2-gcc-5.4.0-fovrh7a - cmake-3.12.3-gcc-7.2.0-obqgn2v lua-5.3.4-gcc-5.4.0-cpfeo2w pkgconf-1.4.2-gcc-7.2.0-yoxwmgb - curl-7.60.0-gcc-5.4.0-vzqreb2 lua-luafilesystem-1_6_3-gcc-5.4.0-alakjim py-numpy-1.15.2-gcc-7.2.0-wbwtcxf - diffutils-3.6-gcc-5.4.0-2rhuivg lua-luaposix-33.4.0-gcc-5.4.0-7wqhwoc py-scipy-1.1.0-gcc-7.2.0-d5n3cph - diffutils-3.6-gcc-7.2.0-eauxwi7 m4-1.4.18-gcc-5.4.0-suf5jtc py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn - expat-2.2.5-gcc-5.4.0-emyv67q m4-1.4.18-gcc-7.2.0-wdzvagl python-2.7.15-gcc-7.2.0-ucmr2mn - findutils-4.6.0-gcc-7.2.0-ca4b7zq mpc-1.1.0-gcc-5.4.0-iuf3gc3 readline-7.0-gcc-5.4.0-nxhwrg7 - gcc-7.2.0-gcc-5.4.0-b7smjjc (L) mpfr-3.1.6-gcc-5.4.0-jnt2nnp readline-7.0-gcc-7.2.0-ccruj2i - gdbm-1.14.1-gcc-5.4.0-q4fpyuo mpich-3.2.1-gcc-7.2.0-vt5xcat sqlite-3.23.1-gcc-7.2.0-5ltus3a - gdbm-1.14.1-gcc-7.2.0-zk5lhob ncurses-6.1-gcc-5.4.0-3o765ou tar-1.30-gcc-5.4.0-dk7lrpo - gettext-0.19.8.1-gcc-5.4.0-tawgous ncurses-6.1-gcc-7.2.0-xcgzqdv tcl-8.6.8-gcc-5.4.0-qhwyccy - git-2.19.1-gcc-5.4.0-p3gjnfa netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd texinfo-6.5-gcc-7.2.0-cuqnfgf - gmp-6.1.2-gcc-5.4.0-qc4qcfz netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g unzip-6.0-gcc-5.4.0-ba23fbg - hwloc-1.11.9-gcc-7.2.0-gbyc65s netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg util-macros-1.19.1-gcc-7.2.0-t62kozq - isl-0.18-gcc-5.4.0-vttqout netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d xz-5.2.4-gcc-5.4.0-teneqii - libbsd-0.8.6-gcc-5.4.0-f4qkkwm netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252 xz-5.2.4-gcc-7.2.0-rql5kog - libiconv-1.15-gcc-5.4.0-u2x3umv numactl-2.0.11-gcc-7.2.0-rifwktk zlib-1.2.11-gcc-5.4.0-5nus6kn - libpciaccess-0.13.5-gcc-7.2.0-riipwi2 openblas-0.3.3-gcc-7.2.0-xxoxfh4 zlib-1.2.11-gcc-7.2.0-ezuwp4p - libsigsegv-2.11-gcc-5.4.0-fypapcp openmpi-3.1.3-gcc-7.2.0-do5xfer - - Where: - L: Module is loaded - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -The non-hierarchical module files that have been generated so far -follow :ref:`the default rules for module generation `. -Taking a look at the ``gcc`` module you'll see, for example: - -.. code-block:: console - - $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc: - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ") - prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin") - prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib") - prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64") - prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64") - prepend_path("CPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/include") - prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/") - setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc") - setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++") - setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C, - Fortran, Ada, and Go, as well as libraries for these languages. - ]]) - -As expected, a few environment variables representing paths will be modified -by the module file according to the default prefix inspection rules. - - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Filter unwanted modifications to the environment -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Now consider the case that your site has decided that ``CPATH`` and -``LIBRARY_PATH`` modifications should not be present in module files. What you can -do to abide by the rules is to create a configuration file ``~/.spack/modules.yaml`` -with the following content: - -.. code-block:: yaml - - modules: - tcl: - all: - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - -Next you should regenerate all the module files: - -.. code-block:: console - - $ spack module tcl refresh - ==> You are about to regenerate tcl module files for: - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - 3sx2gxe autoconf@2.69 b7smjjc gcc@7.2.0 f4qkkwm libbsd@0.8.6 cpfeo2w lua@5.3.4 3o765ou ncurses@6.1 dk7lrpo tar@1.30 - rymw7im automake@1.16.1 q4fpyuo gdbm@1.14.1 u2x3umv libiconv@1.15 alakjim lua-luafilesystem@1_6_3 b4y3w3b openssl@1.0.2o qhwyccy tcl@8.6.8 - ufczdvs bzip2@1.0.6 tawgous gettext@0.19.8.1 fypapcp libsigsegv@2.11 7wqhwoc lua-luaposix@33.4.0 gt5lgzi pcre@8.42 ba23fbg unzip@6.0 - vzqreb2 curl@7.60.0 p3gjnfa git@2.19.1 o2pfwjf libtool@2.4.6 suf5jtc m4@1.4.18 ic2kyoa perl@5.26.2 teneqii xz@5.2.4 - 2rhuivg diffutils@3.6 qc4qcfz gmp@6.1.2 wpexsph libxml2@2.9.8 iuf3gc3 mpc@1.1.0 fovrh7a pkgconf@1.4.2 5nus6kn zlib@1.2.11 - emyv67q expat@2.2.5 vttqout isl@0.18 kmhks3p lmod@7.8 jnt2nnp mpfr@3.1.6 nxhwrg7 readline@7.0 - - -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 ------------------------- - yb2makb autoconf@2.69 riipwi2 libpciaccess@0.13.5 6jgjbyg netlib-scalapack@2.0.2 fdwz5yu perl@5.26.2 cuqnfgf texinfo@6.5 - qoowd5q automake@1.16.1 g67xpfd libsigsegv@2.11 zxpt252 netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 t62kozq util-macros@1.19.1 - mwamumj bzip2@1.0.6 kt2udm6 libtool@2.4.6 67nmj7g netlib-scalapack@2.0.2 wbwtcxf py-numpy@1.15.2 rql5kog xz@5.2.4 - obqgn2v cmake@3.12.3 47gf5kk libxml2@2.9.8 prgo67d netlib-scalapack@2.0.2 d5n3cph py-scipy@1.1.0 ezuwp4p zlib@1.2.11 - eauxwi7 diffutils@3.6 wdzvagl m4@1.4.18 rifwktk numactl@2.0.11 5dbwfwn py-setuptools@40.4.3 - ca4b7zq findutils@4.6.0 vt5xcat mpich@3.2.1 xxoxfh4 openblas@0.3.3 ucmr2mn python@2.7.15 - zk5lhob gdbm@1.14.1 xcgzqdv ncurses@6.1 do5xfer openmpi@3.1.3 ccruj2i readline@7.0 - gbyc65s hwloc@1.11.9 fj7nayd netlib-lapack@3.8.0 cvldq3v openssl@1.0.2o 5ltus3a sqlite@3.23.1 - - ==> Do you want to proceed? [y/n] y - ==> Regenerating tcl module files - -If you take a look now at the module for ``gcc`` you'll see that the unwanted -paths have disappeared: - -.. code-block:: console - - $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc: - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ") - prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin") - prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64") - prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/") - setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc") - setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++") - setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C, - Fortran, Ada, and Go, as well as libraries for these languages. - ]]) - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Prevent some module files from being generated -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Another common request at many sites is to avoid exposing software that -is only needed as an intermediate step when building a newer stack. -Let's try to prevent the generation of -module files for anything that is compiled with ``gcc@5.4.0`` (the OS provided compiler). - -To do this you should add a ``blacklist`` keyword to ``~/.spack/modules.yaml``: - -.. code-block:: yaml - :emphasize-lines: 3,4 - - modules: - tcl: - blacklist: - - '%gcc@5.4.0' - all: - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - -and regenerate the module files: - -This time it is convenient to pass the option ``--delete-tree`` to the command that -regenerates the module files to instruct it to delete the existing tree and regenerate -a new one instead of overwriting the files in the existing directory. - -.. code-block:: console - - $ spack module tcl refresh --delete-tree - ==> You are about to regenerate tcl module files for: - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - 3sx2gxe autoconf@2.69 b7smjjc gcc@7.2.0 f4qkkwm libbsd@0.8.6 cpfeo2w lua@5.3.4 3o765ou ncurses@6.1 dk7lrpo tar@1.30 - rymw7im automake@1.16.1 q4fpyuo gdbm@1.14.1 u2x3umv libiconv@1.15 alakjim lua-luafilesystem@1_6_3 b4y3w3b openssl@1.0.2o qhwyccy tcl@8.6.8 - ufczdvs bzip2@1.0.6 tawgous gettext@0.19.8.1 fypapcp libsigsegv@2.11 7wqhwoc lua-luaposix@33.4.0 gt5lgzi pcre@8.42 ba23fbg unzip@6.0 - vzqreb2 curl@7.60.0 p3gjnfa git@2.19.1 o2pfwjf libtool@2.4.6 suf5jtc m4@1.4.18 ic2kyoa perl@5.26.2 teneqii xz@5.2.4 - 2rhuivg diffutils@3.6 qc4qcfz gmp@6.1.2 wpexsph libxml2@2.9.8 iuf3gc3 mpc@1.1.0 fovrh7a pkgconf@1.4.2 5nus6kn zlib@1.2.11 - emyv67q expat@2.2.5 vttqout isl@0.18 kmhks3p lmod@7.8 jnt2nnp mpfr@3.1.6 nxhwrg7 readline@7.0 - - -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 ------------------------- - yb2makb autoconf@2.69 riipwi2 libpciaccess@0.13.5 6jgjbyg netlib-scalapack@2.0.2 fdwz5yu perl@5.26.2 cuqnfgf texinfo@6.5 - qoowd5q automake@1.16.1 g67xpfd libsigsegv@2.11 zxpt252 netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 t62kozq util-macros@1.19.1 - mwamumj bzip2@1.0.6 kt2udm6 libtool@2.4.6 67nmj7g netlib-scalapack@2.0.2 wbwtcxf py-numpy@1.15.2 rql5kog xz@5.2.4 - obqgn2v cmake@3.12.3 47gf5kk libxml2@2.9.8 prgo67d netlib-scalapack@2.0.2 d5n3cph py-scipy@1.1.0 ezuwp4p zlib@1.2.11 - eauxwi7 diffutils@3.6 wdzvagl m4@1.4.18 rifwktk numactl@2.0.11 5dbwfwn py-setuptools@40.4.3 - ca4b7zq findutils@4.6.0 vt5xcat mpich@3.2.1 xxoxfh4 openblas@0.3.3 ucmr2mn python@2.7.15 - zk5lhob gdbm@1.14.1 xcgzqdv ncurses@6.1 do5xfer openmpi@3.1.3 ccruj2i readline@7.0 - gbyc65s hwloc@1.11.9 fj7nayd netlib-lapack@3.8.0 cvldq3v openssl@1.0.2o 5ltus3a sqlite@3.23.1 - - ==> Do you want to proceed? [y/n] y - ==> Regenerating tcl module files - - $ module avail - - ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ----------------------------------------------- - autoconf-2.69-gcc-7.2.0-yb2makb m4-1.4.18-gcc-7.2.0-wdzvagl perl-5.26.2-gcc-7.2.0-fdwz5yu - automake-1.16.1-gcc-7.2.0-qoowd5q mpich-3.2.1-gcc-7.2.0-vt5xcat pkgconf-1.4.2-gcc-7.2.0-yoxwmgb - bzip2-1.0.6-gcc-7.2.0-mwamumj ncurses-6.1-gcc-7.2.0-xcgzqdv py-numpy-1.15.2-gcc-7.2.0-wbwtcxf - cmake-3.12.3-gcc-7.2.0-obqgn2v netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd py-scipy-1.1.0-gcc-7.2.0-d5n3cph - diffutils-3.6-gcc-7.2.0-eauxwi7 netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn - findutils-4.6.0-gcc-7.2.0-ca4b7zq netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg python-2.7.15-gcc-7.2.0-ucmr2mn - gdbm-1.14.1-gcc-7.2.0-zk5lhob netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d readline-7.0-gcc-7.2.0-ccruj2i - hwloc-1.11.9-gcc-7.2.0-gbyc65s netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252 sqlite-3.23.1-gcc-7.2.0-5ltus3a - libpciaccess-0.13.5-gcc-7.2.0-riipwi2 numactl-2.0.11-gcc-7.2.0-rifwktk texinfo-6.5-gcc-7.2.0-cuqnfgf - libsigsegv-2.11-gcc-7.2.0-g67xpfd openblas-0.3.3-gcc-7.2.0-xxoxfh4 util-macros-1.19.1-gcc-7.2.0-t62kozq - libtool-2.4.6-gcc-7.2.0-kt2udm6 openmpi-3.1.3-gcc-7.2.0-do5xfer xz-5.2.4-gcc-7.2.0-rql5kog - libxml2-2.9.8-gcc-7.2.0-47gf5kk openssl-1.0.2o-gcc-7.2.0-cvldq3v zlib-1.2.11-gcc-7.2.0-ezuwp4p - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -If you look closely you'll see though that we went too far in blacklisting modules: -the module for ``gcc@7.2.0`` disappeared as it was bootstrapped with ``gcc@5.4.0``. To specify -exceptions to the blacklist rules you can use ``whitelist``: - -.. code-block:: yaml - :emphasize-lines: 3,4 - - modules: - tcl: - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - -``whitelist`` rules always have precedence over ``blacklist`` rules. If you regenerate the modules again: - -.. code-block:: console - - $ spack module tcl refresh -y - ==> Regenerating tcl module files - - -you'll see that now the module for ``gcc@7.2.0`` has reappeared: - -.. code-block:: console - - $ module avail gcc-7.2.0-gcc-5.4.0-b7smjjc - - -------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 --------------------------------------------- - gcc-7.2.0-gcc-5.4.0-b7smjjc - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -An additional possibility that you can leverage to unclutter the environment -is that of preventing the generation of module files for implicitly installed -packages. In this case all one needs to do is to add the following line: - -.. code-block:: yaml - :emphasize-lines: 3 - - modules: - tcl: - blacklist_implicits: true - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - -to ``modules.yaml`` and regenerate the module file tree as above. - -^^^^^^^^^^^^^^^^^^^^^^^^^ -Change module file naming -^^^^^^^^^^^^^^^^^^^^^^^^^ - -The next step in making module files more user-friendly is to -improve their naming scheme. -To reduce the length of the hash or remove it altogether you can -use the ``hash_length`` keyword in the configuration file: - -.. code-block:: yaml - :emphasize-lines: 3 - - modules: - tcl: - hash_length: 0 - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - -If you try to regenerate the module files now you will get an error: - -.. code-block:: console - - $ spack module tcl refresh --delete-tree -y - ==> Error: Name clashes detected in module files: - - file: /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/netlib-scalapack-2.0.2-gcc-7.2.0 - spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64 - spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64 - spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64 - spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64 - - ==> Error: Operation aborted - -.. note:: - We try to check for errors upfront! - In Spack we check for errors upfront whenever possible, so don't worry about your module files: - as a name clash was detected nothing has been changed on disk. - -The problem here is that without -the hashes the four different flavors of ``netlib-scalapack`` map to the same module file -name. We can add suffixes to differentiate them: - -.. code-block:: yaml - :emphasize-lines: 9-11,14-17 - - modules: - tcl: - hash_length: 0 - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - suffixes: - '^openblas': openblas - '^netlib-lapack': netlib - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - netlib-scalapack: - suffixes: - '^openmpi': openmpi - '^mpich': mpich - -As you can see it is possible to specify rules that apply only to a -restricted set of packages using :ref:`anonymous specs `. -Regenerating module files now we obtain: - -.. code-block:: console - - $ spack module tcl refresh --delete-tree -y - ==> Regenerating tcl module files - $ module avail - - ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ----------------------------------------------- - autoconf-2.69-gcc-7.2.0 m4-1.4.18-gcc-7.2.0 pkgconf-1.4.2-gcc-7.2.0 - automake-1.16.1-gcc-7.2.0 mpich-3.2.1-gcc-7.2.0 py-numpy-1.15.2-gcc-7.2.0-openblas - bzip2-1.0.6-gcc-7.2.0 ncurses-6.1-gcc-7.2.0 py-scipy-1.1.0-gcc-7.2.0-openblas - cmake-3.12.3-gcc-7.2.0 netlib-lapack-3.8.0-gcc-7.2.0 py-setuptools-40.4.3-gcc-7.2.0 - diffutils-3.6-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich python-2.7.15-gcc-7.2.0 - findutils-4.6.0-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-openmpi readline-7.0-gcc-7.2.0 - gcc-7.2.0-gcc-5.4.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-mpich sqlite-3.23.1-gcc-7.2.0 - gdbm-1.14.1-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-openmpi texinfo-6.5-gcc-7.2.0 - hwloc-1.11.9-gcc-7.2.0 numactl-2.0.11-gcc-7.2.0 util-macros-1.19.1-gcc-7.2.0 - libpciaccess-0.13.5-gcc-7.2.0 openblas-0.3.3-gcc-7.2.0 xz-5.2.4-gcc-7.2.0 - libsigsegv-2.11-gcc-7.2.0 openmpi-3.1.3-gcc-7.2.0 zlib-1.2.11-gcc-7.2.0 - libtool-2.4.6-gcc-7.2.0 openssl-1.0.2o-gcc-7.2.0 - libxml2-2.9.8-gcc-7.2.0 perl-5.26.2-gcc-7.2.0 - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -Finally we can set a ``naming_scheme`` to prevent users from loading -modules that refer to different flavors of the same library/application: - -.. code-block:: yaml - :emphasize-lines: 4,10,11 - - modules: - tcl: - hash_length: 0 - naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}' - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - conflict: - - '{name}' - suffixes: - '^openblas': openblas - '^netlib-lapack': netlib - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - netlib-scalapack: - suffixes: - '^openmpi': openmpi - '^mpich': mpich - -The final result should look like: - -.. code-block:: console - - $ spack module tcl refresh --delete-tree -y - ==> Regenerating tcl module files - $ module avail - - ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ----------------------------------------------- - autoconf/2.69-gcc-7.2.0 m4/1.4.18-gcc-7.2.0 pkgconf/1.4.2-gcc-7.2.0 - automake/1.16.1-gcc-7.2.0 mpich/3.2.1-gcc-7.2.0 py-numpy/1.15.2-gcc-7.2.0-openblas - bzip2/1.0.6-gcc-7.2.0 ncurses/6.1-gcc-7.2.0 py-scipy/1.1.0-gcc-7.2.0-openblas - cmake/3.12.3-gcc-7.2.0 netlib-lapack/3.8.0-gcc-7.2.0 py-setuptools/40.4.3-gcc-7.2.0 - diffutils/3.6-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich python/2.7.15-gcc-7.2.0 - findutils/4.6.0-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi readline/7.0-gcc-7.2.0 - gcc/7.2.0-gcc-5.4.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich sqlite/3.23.1-gcc-7.2.0 - gdbm/1.14.1-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D) texinfo/6.5-gcc-7.2.0 - hwloc/1.11.9-gcc-7.2.0 numactl/2.0.11-gcc-7.2.0 util-macros/1.19.1-gcc-7.2.0 - libpciaccess/0.13.5-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0 xz/5.2.4-gcc-7.2.0 - libsigsegv/2.11-gcc-7.2.0 openmpi/3.1.3-gcc-7.2.0 zlib/1.2.11-gcc-7.2.0 - libtool/2.4.6-gcc-7.2.0 openssl/1.0.2o-gcc-7.2.0 - libxml2/2.9.8-gcc-7.2.0 perl/5.26.2-gcc-7.2.0 - - Where: - D: Default Module - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -.. note:: - TCL specific directive - The directives ``naming_scheme`` and ``conflict`` are TCL specific and - can't be used in the ``lmod`` section of the configuration file. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Add custom environment modifications -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At many sites it is customary to set an environment variable in a -package's module file that points to the folder in which the package -is installed. You can achieve this with Spack by adding an -``environment`` directive to the configuration file: - -.. code-block:: yaml - :emphasize-lines: 17-19 - - modules: - tcl: - hash_length: 0 - naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}' - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - conflict: - - '{name}' - suffixes: - '^openblas': openblas - '^netlib-lapack': netlib - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - environment: - set: - '{name}_ROOT': '{prefix}' - netlib-scalapack: - suffixes: - '^openmpi': openmpi - '^mpich': mpich - -Under the hood Spack uses the :meth:`~spack.spec.Spec.format` API to substitute -tokens in either environment variable names or values. There are two caveats though: - -- The set of allowed tokens in variable names is restricted to - ``name``, ``version``, ``compiler``, ``compiler.name``, - ``compiler.version``, ``architecture`` -- Any token expanded in a variable name is made uppercase, but other than that - case sensitivity is preserved - -Regenerating the module files results in something like: - -.. code-block:: console - :emphasize-lines: 15 - - $ spack module tcl refresh -y - ==> Regenerating tcl module files - - $ module show gcc - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0: - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ") - conflict("gcc") - prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin") - prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64") - prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/") - setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc") - setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++") - setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs") - help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C, - Fortran, Ada, and Go, as well as libraries for these languages. - ]]) - -As you can see, the ``gcc`` module has the environment variable ``GCC_ROOT`` set. - -Sometimes it's also useful to apply environment modifications selectively and target -only certain packages. You can, for instance set the common variables ``CC``, ``CXX``, -etc. in the ``gcc`` module file and apply other custom modifications to the -``openmpi`` modules as follows: - -.. code-block:: yaml - :emphasize-lines: 20-32 - - modules: - tcl: - hash_length: 0 - naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}' - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - conflict: - - '{name}' - suffixes: - '^openblas': openblas - '^netlib-lapack': netlib - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - environment: - set: - '{name}_ROOT': '{prefix}' - gcc: - environment: - set: - CC: gcc - CXX: g++ - FC: gfortran - F90: gfortran - F77: gfortran - openmpi: - environment: - set: - SLURM_MPI_TYPE: pmi2 - OMPI_MCA_btl_openib_warn_default_gid_prefix: '0' - netlib-scalapack: - suffixes: - '^openmpi': openmpi - '^mpich': mpich - -This time we will be more selective and regenerate only the ``gcc`` and -``openmpi`` module files: - -.. code-block:: console - - $ spack module tcl refresh -y gcc - ==> Regenerating tcl module files - - $ spack module tcl refresh -y openmpi - ==> Regenerating tcl module files - - $ module show gcc - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0: - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ") - conflict("gcc") - prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin") - prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64") - prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/") - setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc") - setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++") - setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran") - setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs") - setenv("CC","gcc") - setenv("CXX","g++'") - setenv("FC","gfortran") - setenv("F77","gfortran") - setenv("F90","gfortran") - help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C, - Fortran, Ada, and Go, as well as libraries for these languages. - ]]) - - $ module show openmpi - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/openmpi/3.1.3-gcc-7.2.0: - ------------------------------------------------------------------------------------------------------------------------------------------------------------------- - whatis("An open source Message Passing Interface implementation. ") - conflict("openmpi") - prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/bin") - prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/share/man") - prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib") - prepend_path("PKG_CONFIG_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib/pkgconfig") - prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/") - setenv("OPENMPI_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4") - setenv("SLURM_MPI_TYPE","pmi2") - setenv("OMPI_MCA_btl_openib_warn_default_gid_prefix","0") - help([[An open source Message Passing Interface implementation. The Open MPI - Project is an open source Message Passing Interface implementation that - is developed and maintained by a consortium of academic, research, and - industry partners. Open MPI is therefore able to combine the expertise, - technologies, and resources from all across the High Performance - Computing community in order to build the best MPI library available. - Open MPI offers advantages for system and software vendors, application - developers and computer science researchers. - ]]) - - -^^^^^^^^^^^^^^^^^^^^^ -Autoload dependencies -^^^^^^^^^^^^^^^^^^^^^ - -Spack can also generate module files that contain code to load the -dependencies automatically. You can, for instance generate python -modules that load their dependencies by adding the ``autoload`` -directive and assigning it the value ``direct``: - -.. code-block:: yaml - :emphasize-lines: 3,38,39 - - modules: - tcl: - verbose: True - hash_length: 0 - naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}' - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - conflict: - - '{name}' - suffixes: - '^openblas': openblas - '^netlib-lapack': netlib - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - environment: - set: - '{name}_ROOT': '{prefix}' - gcc: - environment: - set: - CC: gcc - CXX: g++ - FC: gfortran - F90: gfortran - F77: gfortran - openmpi: - environment: - set: - SLURM_MPI_TYPE: pmi2 - OMPI_MCA_btl_openib_warn_default_gid_prefix: '0' - netlib-scalapack: - suffixes: - '^openmpi': openmpi - '^mpich': mpich - ^python: - autoload: 'direct' - -and regenerating the module files for every package that depends on ``python``: - -.. code-block:: console - - root@module-file-tutorial:/# spack module tcl refresh -y ^python - ==> Regenerating tcl module files - -Now the ``py-scipy`` module will be: - -.. code-block:: tcl - - #%Module1.0 - ## Module file created by spack (https://github.com/spack/spack) on 2018-11-11 22:10:48.834221 - ## - ## py-scipy@1.1.0%gcc@7.2.0 arch=linux-ubuntu16.04-x86_64 /d5n3cph - ## - - - module-whatis "SciPy (pronounced 'Sigh Pie') is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization." - - proc ModulesHelp { } { - puts stderr "SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It" - puts stderr "provides many user-friendly and efficient numerical routines such as" - puts stderr "routines for numerical integration and optimization." - } - - if { [ module-info mode load ] && ![ is-loaded python/2.7.15-gcc-7.2.0 ] } { - puts stderr "Autoloading python/2.7.15-gcc-7.2.0" - module load python/2.7.15-gcc-7.2.0 - } - if { [ module-info mode load ] && ![ is-loaded openblas/0.3.3-gcc-7.2.0 ] } { - puts stderr "Autoloading openblas/0.3.3-gcc-7.2.0" - module load openblas/0.3.3-gcc-7.2.0 - } - if { [ module-info mode load ] && ![ is-loaded py-numpy/1.15.2-gcc-7.2.0-openblas ] } { - puts stderr "Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas" - module load py-numpy/1.15.2-gcc-7.2.0-openblas - } - conflict py-scipy - - prepend-path LD_LIBRARY_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib" - prepend-path CMAKE_PREFIX_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/" - prepend-path PYTHONPATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib/python2.7/site-packages" - setenv PY_SCIPY_ROOT "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn" - -and will contain code to autoload all the dependencies: - -.. code-block:: console - - $ module load py-scipy - Autoloading python/2.7.15-gcc-7.2.0 - Autoloading openblas/0.3.3-gcc-7.2.0 - Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas - -In case messages are unwanted during the autoload procedure, it will be -sufficient to omit the line setting ``verbose: True`` in the configuration file above. - -------------------------- -Hierarchical module files -------------------------- - -So far we worked with non-hierarchical module files, i.e. with module files -that are all generated in the same root directory and don't attempt to -dynamically modify the ``MODULEPATH``. This results in a flat module structure where -all the software is visible at the same time: - -.. code-block:: console - - $ module avail - - ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ----------------------------------------------- - autoconf/2.69-gcc-7.2.0 m4/1.4.18-gcc-7.2.0 pkgconf/1.4.2-gcc-7.2.0 - automake/1.16.1-gcc-7.2.0 mpich/3.2.1-gcc-7.2.0 py-numpy/1.15.2-gcc-7.2.0-openblas (L) - bzip2/1.0.6-gcc-7.2.0 ncurses/6.1-gcc-7.2.0 py-scipy/1.1.0-gcc-7.2.0-openblas (L) - cmake/3.12.3-gcc-7.2.0 netlib-lapack/3.8.0-gcc-7.2.0 py-setuptools/40.4.3-gcc-7.2.0 - diffutils/3.6-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich python/2.7.15-gcc-7.2.0 (L) - findutils/4.6.0-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi readline/7.0-gcc-7.2.0 - gcc/7.2.0-gcc-5.4.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich sqlite/3.23.1-gcc-7.2.0 - gdbm/1.14.1-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D) texinfo/6.5-gcc-7.2.0 - hwloc/1.11.9-gcc-7.2.0 numactl/2.0.11-gcc-7.2.0 util-macros/1.19.1-gcc-7.2.0 - libpciaccess/0.13.5-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0 (L) xz/5.2.4-gcc-7.2.0 - libsigsegv/2.11-gcc-7.2.0 openmpi/3.1.3-gcc-7.2.0 zlib/1.2.11-gcc-7.2.0 - libtool/2.4.6-gcc-7.2.0 openssl/1.0.2o-gcc-7.2.0 - libxml2/2.9.8-gcc-7.2.0 perl/5.26.2-gcc-7.2.0 - - Where: - L: Module is loaded - D: Default Module - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -This layout is quite simple to deploy, but you can see from the above snippet -that nothing prevents users from loading incompatible sets of modules: - -.. code-block:: console - - $ module purge - $ module load netlib-lapack/3.8.0-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0 - $ module list - - Currently Loaded Modules: - 1) netlib-lapack/3.8.0-gcc-7.2.0 2) openblas/0.3.3-gcc-7.2.0 - -Even if ``conflicts`` directives are carefully placed in module files, they: - - - won't enforce a consistent environment, but will just report an error - - need constant updates, for instance as soon as a new compiler or MPI library is installed - -`Hierarchical module files `_ try to -overcome these shortcomings by showing at start-up only a restricted view of what is -available on the system: more specifically only the software that has been installed with -OS provided compilers. Among this software there will be other - usually more recent - compilers -that, once loaded, will prepend new directories to ``MODULEPATH`` unlocking all the software -that was compiled with them. This "unlocking" idea can then be extended arbitrarily to -virtual dependencies, as we'll see in the following section. - -^^^^^^^^^^^^^^^^^ -Core/Compiler/MPI -^^^^^^^^^^^^^^^^^ - -The most widely used hierarchy is the so called ``Core/Compiler/MPI`` where, on top -of the compilers, different MPI libraries also unlock software linked to them. -There are just a few steps needed to adapt the ``modules.yaml`` file we used previously: - - #. enable the ``lmod`` file generator - #. change the ``tcl`` tag to ``lmod`` - #. remove ``tcl`` specific directives (``naming_scheme`` and ``conflict``) - #. declare which compilers are considered ``core_compilers`` - #. remove the ``mpi`` related suffixes (as they will be substituted by hierarchies) - -After these modifications your configuration file should look like: - -.. code-block:: yaml - :emphasize-lines: 2-8 - - modules: - enable:: - - lmod - lmod: - core_compilers: - - 'gcc@5.4.0' - hierarchy: - - mpi - hash_length: 0 - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - suffixes: - '^openblas': openblas - '^netlib-lapack': netlib - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - environment: - set: - '{name}_ROOT': '{prefix}' - gcc: - environment: - set: - CC: gcc - CXX: g++ - FC: gfortran - F90: gfortran - F77: gfortran - openmpi: - environment: - set: - SLURM_MPI_TYPE: pmi2 - OMPI_MCA_btl_openib_warn_default_gid_prefix: '0' - - -.. note:: - Double colon in configuration files - The double colon after ``enable`` is intentional and it serves the - purpose of overriding the default list of enabled generators so - that only ``lmod`` will be active (see :ref:`config-overrides` for more - details). - -The directive ``core_compilers`` accepts a list of compilers. Everything built -using these compilers will create a module in the ``Core`` part of the hierarchy, -which is the entry point for hierarchical module files. It is -common practice to put the OS provided compilers in the list and only build common utilities -and other compilers with them. - -If we now regenerate the module files: - -.. code-block:: console - - $ spack module lmod refresh --delete-tree -y - ==> Regenerating lmod module files - -and update ``MODULEPATH`` to point to the ``Core``: - -.. code-block:: console - - $ module purge - $ module unuse $HOME/spack/share/spack/modules/linux-ubuntu16.04-x86_64 - $ module use $HOME/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core - -asking for the available modules will return: - -.. code-block:: console - - $ module avail - - ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------ - gcc/7.2.0 - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -Unsurprisingly, the only visible module is ``gcc``. Loading that we'll unlock -the ``Compiler`` part of the hierarchy: - -.. code-block:: console - - $ module load gcc - $ module avail - - ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -------------------------------------------- - autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 python/2.7.15 xz/5.2.4 - automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 readline/7.0 zlib/1.2.11 - bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 py-numpy/1.15.2-openblas sqlite/3.23.1 - cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 openmpi/3.1.3 py-scipy/1.1.0-openblas texinfo/6.5 - diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o py-setuptools/40.4.3 util-macros/1.19.1 - - ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------ - gcc/7.2.0 (L) - - Where: - L: Module is loaded - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -The same holds true also for the ``MPI`` part, that you can enable by loading -either ``mpich`` or ``openmpi``. Let's start by loading ``mpich``: - -.. code-block:: console - - $ module load mpich - $ module avail - - --------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/mpich/3.2.1-vt5xcat/gcc/7.2.0 ---------------------------------- - netlib-scalapack/2.0.2-netlib netlib-scalapack/2.0.2-openblas (D) - - ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -------------------------------------------- - autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 python/2.7.15 xz/5.2.4 - automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 readline/7.0 zlib/1.2.11 - bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 py-numpy/1.15.2-openblas sqlite/3.23.1 - cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 (L) openmpi/3.1.3 py-scipy/1.1.0-openblas texinfo/6.5 - diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o py-setuptools/40.4.3 util-macros/1.19.1 - - ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------ - gcc/7.2.0 (L) - - Where: - L: Module is loaded - D: Default Module - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - - - root@module-file-tutorial:/# module load openblas netlib-scalapack/2.0.2-openblas - root@module-file-tutorial:/# module list - - Currently Loaded Modules: - 1) gcc/7.2.0 2) mpich/3.2.1 3) openblas/0.3.3 4) netlib-scalapack/2.0.2-openblas - -At this point we can showcase the improved consistency that a hierarchical layout provides -over a non-hierarchical one: - -.. code-block:: console - - $ module load openmpi - - Lmod is automatically replacing "mpich/3.2.1" with "openmpi/3.1.3". - - - Due to MODULEPATH changes, the following have been reloaded: - 1) netlib-scalapack/2.0.2-openblas - -``Lmod`` took care of swapping the MPI provider for us, and it also substituted the -``netlib-scalapack`` module to conform to the change in the MPI. -In this way we can't accidentally pull-in two different MPI providers at the -same time or load a module file for a package linked to ``openmpi`` when ``mpich`` is also loaded. -Consistency for compilers and MPI is ensured by the tool. - - -^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Add LAPACK to the hierarchy -^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -The hierarchy just shown is already a great improvement over non-hierarchical layouts, -but it still has an asymmetry: ``LAPACK`` providers cover the same semantic role -as ``MPI`` providers, but yet they are not part of the hierarchy. - -To be more practical, this means that although we have gained an improved consistency in -our environment when it comes to ``MPI``, we still have the same problems as we had before -for ``LAPACK`` implementations: - -.. code-block:: console - - root@module-file-tutorial:/# module list - - Currently Loaded Modules: - 1) gcc/7.2.0 2) openblas/0.3.3 3) openmpi/3.1.3 4) netlib-scalapack/2.0.2-openblas - - root@module-file-tutorial:/# module load netlib-scalapack/2.0.2-netlib - - The following have been reloaded with a version change: - 1) netlib-scalapack/2.0.2-openblas => netlib-scalapack/2.0.2-netlib - - root@module-file-tutorial:/# module list - - Currently Loaded Modules: - 1) gcc/7.2.0 2) openblas/0.3.3 3) openmpi/3.1.3 4) netlib-scalapack/2.0.2-netlib - -Hierarchies that are deeper than ``Core``/``Compiler``/``MPI`` are -probably still considered "unusual" or "impractical" at many sites, mainly because -module files are written manually and keeping track of the combinations -among multiple providers quickly becomes quite involved. - -For instance, having both ``MPI`` and ``LAPACK`` in the hierarchy -means we must classify software into one of four categories: - - #. Software that doesn't depend on ``MPI`` or ``LAPACK`` - #. Software that depends only on ``MPI`` - #. Software that depends only on ``LAPACK`` - #. Software that depends on both - -to decide when to show it to the user. The situation becomes more involved as the number of virtual -dependencies in the hierarchy increases. - -We can take advantage of the DAG that Spack maintains for the installed software and solve -this combinatorial problem in a clean and automated way. -In some sense Spack's ability to manage this combinatorial complexity makes deeper -hierarchies feasible. - -Coming back to our example, let's add ``lapack`` to the hierarchy and remove any remaining suffix: - -.. code-block:: yaml - :emphasize-lines: 9 - - modules: - enable:: - - lmod - lmod: - core_compilers: - - 'gcc@5.4.0' - hierarchy: - - mpi - - lapack - hash_length: 0 - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - all: - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - environment: - set: - '{name}_ROOT': '{prefix}' - gcc: - environment: - set: - CC: gcc - CXX: g++ - FC: gfortran - F90: gfortran - F77: gfortran - openmpi: - environment: - set: - SLURM_MPI_TYPE: pmi2 - OMPI_MCA_btl_openib_warn_default_gid_prefix: '0' - -After module files have been regenerated as usual: - -.. code-block:: console - - root@module-file-tutorial:/# module purge - - root@module-file-tutorial:/# spack module lmod refresh --delete-tree -y - ==> Regenerating lmod module files - -we can see that now we have additional components in the hierarchy: - -.. code-block:: console - - $ module load gcc - $ module load openblas - $ module avail - - -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 -------------------------------- - py-numpy/1.15.2 py-scipy/1.1.0 - - ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -------------------------------------------- - autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 sqlite/3.23.1 - automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 texinfo/6.5 - bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 (L) py-setuptools/40.4.3 util-macros/1.19.1 - cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 openmpi/3.1.3 python/2.7.15 xz/5.2.4 - diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o readline/7.0 zlib/1.2.11 - - ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------ - gcc/7.2.0 (L) - - Where: - L: Module is loaded - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - - - $ module load openmpi - $ module avail - - --------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/3.1.3-do5xfer/openblas/0.3.3-xxoxfh4/gcc/7.2.0 --------------------- - netlib-scalapack/2.0.2 - - -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 -------------------------------- - py-numpy/1.15.2 py-scipy/1.1.0 - - ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 -------------------------------------------- - autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 sqlite/3.23.1 - automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 texinfo/6.5 - bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 (L) py-setuptools/40.4.3 util-macros/1.19.1 - cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 openmpi/3.1.3 (L) python/2.7.15 xz/5.2.4 - diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o readline/7.0 zlib/1.2.11 - - ---------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ---------------------------------------------- - gcc/7.2.0 (L) - - Where: - L: Module is loaded - - Use "module spider" to find all possible modules. - Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". - -Both ``MPI`` and ``LAPACK`` providers will now benefit from the same safety features: - -.. code-block:: console - - $ module load py-numpy netlib-scalapack - $ module load mpich - - Lmod is automatically replacing "openmpi/3.1.3" with "mpich/3.2.1". - - - Due to MODULEPATH changes, the following have been reloaded: - 1) netlib-scalapack/2.0.2 - - $ module load netlib-lapack - - Lmod is automatically replacing "openblas/0.3.3" with "netlib-lapack/3.8.0". - - - Inactive Modules: - 1) py-numpy - - Due to MODULEPATH changes, the following have been reloaded: - 1) netlib-scalapack/2.0.2 - -Because we only compiled ``py-numpy`` with ``openblas`` the module -is made inactive when we switch the ``LAPACK`` provider. The user -environment is now consistent by design! - ----------------------- -Working with templates ----------------------- - -As briefly mentioned in the introduction, Spack uses `Jinja2 `_ -to generate each individual module file. -This means that you have all of its flexibility and power when it comes to -customizing what gets generated! - -^^^^^^^^^^^^^^^^^^^^^ -Module file templates -^^^^^^^^^^^^^^^^^^^^^ - -The templates that Spack uses to generate module files are stored in the -``share/spack/templates/module`` directory within the Spack prefix, and -they all share the same common structure. Usually, they start with a -header that identifies the type of module being generated. In the case of -hierarchical module files it's: - -.. literalinclude:: _spack_root/share/spack/templates/modules/modulefile.lua - :language: jinja - :lines: 1-6 - -The statements within double curly brackets ``{{ ... }}`` denote -`expressions `_ -that will be evaluated and substituted at module generation time. -The rest of the file is then divided into -`blocks `_ -that can be overridden or extended by users, if need be. -`Control structures `_ -, delimited by ``{% ... %}``, -are also permitted in the template language: - -.. literalinclude:: _spack_root/share/spack/templates/modules/modulefile.lua - :language: jinja - :lines: 73-88 - -The locations where Spack looks for templates are specified -in ``config.yaml``: - -.. literalinclude:: _spack_root/etc/spack/defaults/config.yaml - :language: yaml - :lines: 21-24 - -and can be extended by users to employ custom templates, as we'll see next. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Extend the default templates -^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Let's assume one of our software is protected by group membership: -allowed users belong to the same linux group, and access is granted at group level. -Wouldn't it be nice if people that are not -yet entitled to use it could receive a helpful message at module load time -that tells them who to contact in your organization to be inserted in the group? - -To automate the generation of module files with such site-specific behavior -we'll start by extending the list of locations where Spack looks for module -files. Let's create the file ``~/.spack/config.yaml`` with the content: - -.. code-block:: yaml - - config: - template_dirs: - - $HOME/.spack/templates - -This tells Spack to also search another location when looking for template files. -Next, we need to create our custom template extension in the folder listed above: - -.. code-block:: jinja - - {% extends "modules/modulefile.lua" %} - {% block footer %} - -- Access is granted only to specific groups - if not isDir("{{ spec.prefix }}") then - LmodError ( - "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n", - "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n" - ) - end - {% endblock %} - -Let's name this file ``group-restricted.lua``. The line: - -.. code-block:: jinja - - {% extends "modules/modulefile.lua" %} - -tells Jinja2 that we are reusing the standard template for hierarchical module files. -The section: - -.. code-block:: jinja - - {% block footer %} - -- Access is granted only to specific groups - if not isDir("{{ spec.prefix }}") then - LmodError ( - "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n", - "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n" - ) - end - {% endblock %} - -overrides the ``footer`` block. -Finally, we need to add a couple of lines in ``modules.yaml`` to tell Spack which specs -need to use the new custom template. For the sake of illustration let's assume -it's ``netlib-scalapack``: - -.. code-block:: yaml - :emphasize-lines: 35-36 - - modules: - enable:: - - lmod - lmod: - core_compilers: - - 'gcc@5.4.0' - hierarchy: - - mpi - - lapack - hash_length: 0 - whitelist: - - gcc - blacklist: - - '%gcc@5.4.0' - - readline - all: - filter: - environment_blacklist: ['CPATH', 'LIBRARY_PATH'] - environment: - set: - '{name}_ROOT': '{prefix}' - gcc: - environment: - set: - CC: gcc - CXX: g++ - FC: gfortran - F90: gfortran - F77: gfortran - openmpi: - environment: - set: - SLURM_MPI_TYPE: pmi2 - OMPI_MCA_btl_openib_warn_default_gid_prefix: '0' - netlib-scalapack: - template: 'group-restricted.lua' - -If we regenerate the module files one last time: - -.. code-block:: console - - root@module-file-tutorial:/# spack module lmod refresh -y netlib-scalapack - ==> Regenerating lmod module files - -we'll find the following at the end of each ``netlib-scalapack`` module file: - -.. code-block:: lua - - -- Access is granted only to specific groups - if not isDir("/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/netlib-scalapack-2.0.2-d3lertflood3twaor44eam2kcr4l72ag") then - LmodError ( - "You don't have the necessary rights to run \"netlib-scalapack\".\n\n", - "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n" - ) - end - -and every user that doesn't have access to the software will now be redirected to -the right e-mail address where to ask for it! diff --git a/lib/spack/docs/tutorial_packaging.rst b/lib/spack/docs/tutorial_packaging.rst deleted file mode 100644 index ca693ba14f7..00000000000 --- a/lib/spack/docs/tutorial_packaging.rst +++ /dev/null @@ -1,559 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _packaging-tutorial: - -========================= -Package Creation Tutorial -========================= - -This tutorial will walk you through the steps behind building a simple -package installation script. We'll focus on writing a package for -mpileaks, an MPI debugging tool. By creating a package file we're -essentially giving Spack a recipe for how to build a particular piece of -software. We're describing some of the software's dependencies, where to -find the package, what commands and options are used to build the package -from source, and more. Once we've specified a package's recipe, we can -ask Spack to build that package in many different ways. - -This tutorial assumes you have a basic familiarity with some of the Spack -commands, and that you have a working version of Spack installed. If -not, we suggest looking at Spack's :ref:`getting_started` guide. This -tutorial also assumes you have at least a beginner's-level familiarity -with Python. - -Also note that this document is a tutorial. It can help you get started -with packaging, but is not intended to be complete. See Spack's -:ref:`packaging-guide` for more complete documentation on this topic. - ---------------- -Getting Started ---------------- - -A few things before we get started: - -- We'll refer to the Spack installation location via the environment - variable ``SPACK_ROOT``. You should point ``SPACK_ROOT`` at wherever - you have Spack installed. -- Add ``$SPACK_ROOT/bin`` to your ``PATH`` before you start. -- Make sure your ``EDITOR`` environment variable is set to your - preferred text editor. -- We'll be writing Python code as part of this tutorial. You can find - successive versions of the Python code in - ``$SPACK_ROOT/lib/spack/docs/tutorial/examples``. - -------------------------- -Creating the Package File -------------------------- - -We will use a separate package repository for the tutorial. Package -repositories allow you to separate sets of packages that take -precedence over one another. We will use the tutorial repo that ships -with Spack to avoid breaking the builtin Spack packages. - -.. code-block:: console - - $ spack repo add $SPACK_ROOT/var/spack/repos/tutorial/ - ==> Added repo with namespace 'tutorial'. - -Spack comes with a handy command to create a new package: ``spack create``. - -This command is given the location of a package's source code, downloads -the code, and sets up some basic packaging infrastructure for you. The -mpileaks source code can be found on GitHub, and here's what happens when -we run ``spack create`` on it: - -.. code-block:: console - - $ spack create -t generic https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz - ==> This looks like a URL for mpileaks - ==> Found 1 version of mpileaks: - - 1.0 https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz - - ==> How many would you like to checksum? (default is 1, q to abort) 1 - ==> Downloading... - ==> Fetching https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz - ############################################################################# 100.0% - ==> Checksummed 1 version of mpileaks - ==> Using specified package template: 'generic' - ==> Created template for mpileaks package - ==> Created package file: ~/spack/var/spack/repos/tutorial/packages/mpileaks/package.py - -Spack should spawn a text editor with this file: - -.. literalinclude:: tutorial/examples/0.package.py - :language: python - -Spack has created this file in -``$SPACK_ROOT/var/spack/repos/tutorial/packages/mpileaks/package.py``. Take a -moment to look over the file. There's a few placeholders that Spack has -created, which we'll fill in as part of this tutorial: - -- We'll document some information about this package in the comments. -- We'll fill in the dependency list for this package. -- We'll fill in some of the configuration arguments needed to build this - package. - -For the moment, exit your editor and let's see what happens when we try -to build this package: - -.. code-block:: console - - $ spack install mpileaks - ==> Installing mpileaks - ==> Searching for binary cache of mpileaks - ==> Warning: No Spack mirrors are currently configured - ==> No binary for mpileaks found: installing from source - ==> Fetching https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz - ############################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu/mpileaks-1.0.tar.gz - ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu - ==> No patches needed for mpileaks - ==> Building mpileaks [Package] - ==> Executing phase: 'install' - ==> Error: ProcessError: Command exited with status 2: - 'make' '-j16' - - 1 error found in build log: - 1 ==> Executing phase: 'install' - 2 ==> 'make' '-j16' - >> 3 make: *** No targets specified and no makefile found. Stop. - - See build log for details: - ~/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu/spack-build-out.txt - -This obviously didn't work; we need to fill in the package-specific -information. Specifically, Spack didn't try to build any of mpileaks' -dependencies, nor did it use the proper configure arguments. Let's start -fixing things. - ---------------------- -Package Documentation ---------------------- - -We can bring the ``package.py`` file back into our ``EDITOR`` with the -``spack edit`` command: - -.. code-block:: console - - $ spack edit mpileaks - -Let's remove some of the ``FIXME`` comments, add links to the mpileaks -homepage, and document what mpileaks does. I'm also going to cut out the -Copyright clause at this point to keep this tutorial document shorter, -but you shouldn't do that normally. The results of these changes can be -found in ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/1.package.py`` -and are displayed below. Make these changes to your ``package.py``: - -.. literalinclude:: tutorial/examples/1.package.py - :lines: 6- - :language: python - -We've filled in the comment that describes what this package does and -added a link to its website. That won't help us build yet, but it will -allow Spack to provide some documentation on this package to other users: - -.. code-block:: console - - $ spack info mpileaks - Package: mpileaks - - Description: - Tool to detect and report MPI objects like MPI_Requests and - MPI_Datatypes. - - Homepage: https://github.com/LLNL/mpileaks - - Tags: - None - - Preferred version: - 1.0 https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz - - Safe versions: - 1.0 https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz - - Variants: - None - - Installation Phases: - install - - Build Dependencies: - None - - Link Dependencies: - None - - Run Dependencies: - None - - Virtual Packages: - None - -As we fill in more information about this package the ``spack info`` command -will become more informative. Now let's start making this package build. - ------------- -Dependencies ------------- - -The mpileaks package depends on three other packages: ``mpi``, -``adept-utils``, and ``callpath``. Let's add those via the -``depends_on`` command in our ``package.py`` (this version is in -``$SPACK_ROOT/lib/spack/docs/tutorial/examples/2.package.py``): - -.. literalinclude:: tutorial/examples/2.package.py - :lines: 6- - :language: python - -Now when we go to build mpileaks, Spack will fetch and build these -dependencies before building mpileaks. Note that the mpi dependency is a -different kind of beast than the adept-utils and callpath dependencies; -there is no mpi package available in Spack. Instead mpi is a *virtual -dependency*. Spack may satisfy that dependency by installing packages -such as ``openmpi`` or ``mvapich2``. See the :ref:`packaging-guide` for more -information on virtual dependencies. - -Now when we try to install this package, a lot more happens: - -.. code-block:: console - - $ spack install mpileaks - ... - ==> Successfully installed libdwarf from binary cache - [+] ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libdwarf-20180129-p4jeflorwlnkoq2vpuyocwrbcht2ayak - ==> Installing callpath - ==> Searching for binary cache of callpath - ==> Installing callpath from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x.spack - ######################################################################## 100.0% - ==> Successfully installed callpath from binary cache - [+] ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x - ==> Installing mpileaks - ==> Searching for binary cache of mpileaks - ==> No binary for mpileaks found: installing from source - ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz - ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz - ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb - ==> No patches needed for mpileaks - ==> Building mpileaks [Package] - ==> Executing phase: 'install' - ==> Error: ProcessError: Command exited with status 2: - 'make' '-j16' - - 1 error found in build log: - 1 ==> Executing phase: 'install' - 2 ==> 'make' '-j16' - >> 3 make: *** No targets specified and no makefile found. Stop. - - See build log for details: - ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0/spack-build-out.txt - -Note that this command may take a while to run and produce more output if -you don't have an MPI already installed or configured in Spack. - -Now Spack has identified and made sure all of our dependencies have been -built. It found the ``openmpi`` package that will satisfy our ``mpi`` -dependency, and the ``callpath`` and ``adept-utils`` package to satisfy our -concrete dependencies. - ------------------------- -Debugging Package Builds ------------------------- - -Our ``mpileaks`` package is still not building. It may be obvious to -many of you that we never ran the configure script. Let's add a -call to ``configure()`` to the top of the install routine. The resulting -``package.py`` is in ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/3.package.py``: - -.. literalinclude:: tutorial/examples/3.package.py - :lines: 6- - :language: python - -If we re-run we still get errors: - -.. code-block:: console - - $ spack install mpileaks - ... - ==> Installing mpileaks - ==> Searching for binary cache of mpileaks - ==> Finding buildcaches in /mirror/build_cache - ==> No binary for mpileaks found: installing from source - ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz - ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz - ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb - ==> No patches needed for mpileaks - ==> Building mpileaks [Package] - ==> Executing phase: 'install' - ==> Error: ProcessError: Command exited with status 1: - './configure' - - 1 error found in build log: - 25 checking for ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3 - njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc... ~/spack/opt/spack/linux-ubuntu16.04- - x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc - 26 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1 - .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-showme:compile'... no - 27 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1 - .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-showme'... no - 28 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1 - .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-compile-info'... no - 29 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1 - .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-show'... no - 30 ./configure: line 4809: Echo: command not found - >> 31 configure: error: unable to locate adept-utils installation - - See build log for details: - ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0/spack-build-out.txt - -Again, the problem may be obvious. But let's pretend we're not -all experienced Autotools developers and use this opportunity to spend some -time debugging. We have a few options that can tell us about -what's going wrong: - -As per the error message, Spack has given us a ``spack-build-out.txt`` debug -log: - -.. code-block:: console - - ==> Executing phase: 'install' - ==> './configure' - checking metadata... no - checking installation directory variables... yes - checking for a BSD-compatible install... /usr/bin/install -c - checking whether build environment is sane... yes - checking for a thread-safe mkdir -p... /bin/mkdir -p - checking for gawk... gawk - checking whether make sets $(MAKE)... yes - checking for gcc... /home/spack1/spack/lib/spack/env/gcc/gcc - checking for C compiler default output file name... a.out - checking whether the C compiler works... yes - checking whether we are cross compiling... no - checking for suffix of executables... - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether /home/spack1/spack/lib/spack/env/gcc/gcc accepts -g... yes - checking for /home/spack1/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed - checking for style of include used by make... GNU - checking dependency style of /home/spack1/spack/lib/spack/env/gcc/gcc... gcc3 - checking whether /home/spack1/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes - checking whether we are using the GNU C++ compiler... yes - checking whether /home/spack1/spack/lib/spack/env/gcc/g++ accepts -g... yes - checking dependency style of /home/spack1/spack/lib/spack/env/gcc/g++... gcc3 - checking for /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc - Checking whether /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes - configure: error: unable to locate adept-utils installation - -This gives us the output from the build, and mpileaks isn't -finding its ``adept-utils`` package. Spack has -automatically added the include and library directories of -``adept-utils`` to the compiler's search path, but some packages like -mpileaks can sometimes be picky and still want things spelled out on -their command line. But let's continue to pretend we're not experienced -developers, and explore some other debugging paths: - -We can also enter the build area and try to manually run the build: - -.. code-block:: console - - $ spack build-env mpileaks bash - $ spack cd mpileaks - -The ``spack build-env`` command spawned a new shell that contains the same -environment that Spack used to build the mpileaks package (you can -substitute bash for your favorite shell). The ``spack cd`` command -changed our working dirctory to the last attempted build for mpileaks. -From here we can manually re-run the build: - -.. code-block:: console - - $ ./configure - checking metadata... no - checking installation directory variables... yes - checking for a BSD-compatible install... /usr/bin/install -c - checking whether build environment is sane... yes - checking for a thread-safe mkdir -p... /bin/mkdir -p - checking for gawk... gawk - checking whether make sets $(MAKE)... yes - checking for gcc... /home/spack1/spack/lib/spack/env/gcc/gcc - checking for C compiler default output file name... a.out - checking whether the C compiler works... yes - checking whether we are cross compiling... no - checking for suffix of executables... - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether /home/spack1/spack/lib/spack/env/gcc/gcc accepts -g... yes - checking for /home/spack1/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed - checking for style of include used by make... GNU - checking dependency style of /home/spack1/spack/lib/spack/env/gcc/gcc... gcc3 - checking whether /home/spack1/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes - checking whether we are using the GNU C++ compiler... yes - checking whether /home/spack1/spack/lib/spack/env/gcc/g++ accepts -g... yes - checking dependency style of /home/spack1/spack/lib/spack/env/gcc/g++... gcc3 - checking for /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc - Checking whether /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes - configure: error: unable to locate adept-utils installation - -We're seeing the same error, but now we're in a shell where we can run -the command ourselves and debug as needed. We could, for example, run -``./configure --help`` to see what options we can use to specify -dependencies. - -We can use the ``exit`` command to leave the shell spawned by ``spack -build-env``. - ------------------------------- -Specifying Configure Arguments ------------------------------- - -Let's add the configure arguments to the mpileaks' ``package.py``. This -version can be found in -``$SPACK_ROOT/lib/spack/docs/tutorial/examples/4.package.py``: - -.. literalinclude:: tutorial/examples/4.package.py - :lines: 6- - :language: python - -This is all we need for a working mpileaks package! If we install now we'll see: - -.. code-block:: console - - $ spack install mpileaks - ... - ==> Installing mpileaks - ==> Searching for binary cache of mpileaks - ==> Finding buildcaches in /mirror/build_cache - ==> No binary for mpileaks found: installing from source - ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz - ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz - ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb - ==> No patches needed for mpileaks - ==> Building mpileaks [Package] - ==> Executing phase: 'install' - ==> Successfully installed mpileaks - Fetch: 0.00s. Build: 9.41s. Total: 9.41s. - [+] ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb - -There are some special circumstances in this package that are worth highlighting. -Normally, Spack would have automatically detected that mpileaks was an -Autotools-based package when we ran ``spack create`` and made it an ``AutoToolsPackage`` -class (except we added the ``-t generic`` option to skip this). Instead of -a full install routine we would have just written: - -.. code-block:: python - - def configure_args(self): - return [ - '--with-adept-utils={0}'.format(self.spec['adept-utils'].prefix), - '--with-callpath={0}'.format(self.spec['callpath'].prefix) - ] - -Similarly, if this had been a CMake-based package we -would have been filling in a ``cmake_args`` function instead of -``configure_args``. There are similar default package types for -many build environments that will be discussed later in the tutorial. - --------- -Variants --------- - -We have a successful mpileaks build, but let's take some time to improve -it. ``mpileaks`` has a build-time option to truncate parts of the stack -that it walks. Let's add a variant to allow users to set this when they -build mpileaks with Spack. - -To do this, we'll add a variant to our package, as per the following (see -``$SPACK_ROOT/lib/spack/docs/tutorial/examples/5.package.py``): - -.. literalinclude:: tutorial/examples/5.package.py - :lines: 6- - :language: python - -We've added the variant ``stackstart``, and given it a default value of -``0``. If we install now we can see the stackstart variant added to the -configure line (output truncated for length): - -.. code-block:: console - - $ spack install --verbose mpileaks stackstart=4 - ... - ==> Installing mpileaks - ==> Searching for binary cache of mpileaks - ==> Finding buildcaches in /mirror/build_cache - ==> No binary for mpileaks found: installing from source - ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz - ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto/mpileaks-1.0.tar.gz - ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto - ==> No patches needed for mpileaks - ==> Building mpileaks [Package] - ==> Executing phase: 'install' - ==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto' '--with-adept-utils=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/adept-utils-1.0.1-7tippnvo5g76wpijk7x5kwfpr3iqiaen' '--with-callpath=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x' '--with-stack-start-c=4' '--with-stack-start-fortran=4' - ---------------- -The Spec Object ---------------- - -This tutorial has glossed over a few important features, which weren't -too relevant for mpileaks but may be useful for other packages. There -were several places we reference the ``self.spec`` object. This is a -powerful class for querying information about what we're building. For -example, you could use the spec to query information about how a -package's dependencies were built, or what compiler was being used, or -what version of a package is being installed. Full documentation can be -found in the :ref:`packaging-guide`, but here's some quick snippets with -common queries: - -- Am I building ``mpileaks`` version ``1.1`` or greater? - -.. code-block:: python - - if self.spec.satisfies('@1.1:'): - # Do things needed for 1.1+ - -- Is ``openmpi`` the MPI I'm building with? - -.. code-block:: python - - if self.spec['mpi'].name == 'openmpi': - # Do openmpi things - -- Am I building with ``gcc`` version less than ``5.0.0``: - -.. code-block:: python - - if self.spec.satisfies('%gcc@:5.0.0'): - # Add arguments specific to gcc's earlier than 5.0.0 - -- Am I building with the ``debug`` variant: - -.. code-block:: python - - if self.spec.satisfies('+debug'): - # Add -g option to configure flags - -- Is my ``dyninst`` dependency greater than version ``8.0``? - -.. code-block:: python - - if self.spec['dyninst'].satisfies('@8.0:'): - # Use newest dyninst options - -More examples can be found in the thousands of packages already added to -Spack in ``$SPACK_ROOT/var/spack/repos/builtin/packages``. - -Good Luck! - -To ensure that future sections of the tutorial run properly, please -uninstall mpileaks and remove the tutorial repo from your -configuration. - -.. code-block:: console - - $ spack uninstall -ay mpileaks - $ spack repo remove tutorial - $ rm -rf $SPACK_ROOT/var/spack/repos/tutorial/packages/mpileaks From 8eeb64096c98b8a43d1c587f13ece743c864fba9 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 25 Oct 2019 21:53:38 -0700 Subject: [PATCH 443/499] version bump: 0.13.0 --- lib/spack/spack/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 71473ae4cc4..3c2e9226803 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -5,7 +5,7 @@ #: major, minor, patch version for Spack, in a tuple -spack_version_info = (0, 12, 1) +spack_version_info = (0, 13, 0) #: String containing Spack version joined with .'s spack_version = '.'.join(str(v) for v in spack_version_info) From f7de8942b893bfde640c66a833122e65dd59687a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 25 Oct 2019 23:19:36 -0700 Subject: [PATCH 444/499] Add top-level `CHANGELOG.md` with release notes. --- CHANGELOG.md | 262 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 262 insertions(+) create mode 100644 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000000..69781d8290e --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,262 @@ +# v0.13.0 (2019-10-25) + +`v0.13.0` is our biggest Spack release yet, with *many* new major features. +From facility deployment to improved environments, microarchitecture +support, and auto-generated build farms, this release has features for all of +our users. + +Spack grew by over 700 packages in the past year, and the project now has +over 450 contributors. Thanks to all of you for making this release possible. + +## Major new core features +- Chaining: use dependencies from external "upstream" Spack instances +- Environments now behave more like virtualenv/conda + - Each env has a *view*: a directory with all packages symlinked in + - Activating an environment sets `PATH`, `LD_LIBRARY_PATH`, `CPATH`, + `CMAKE_PREFIX_PATH`, `PKG_CONFIG_PATH`, etc. to point to this view. +- Spack detects and builds specifically for your microarchitecture + - named, understandable targets like `skylake`, `broadwell`, `power9`, `zen2` + - Spack knows which compilers can build for which architectures + - Packages can easily query support for features like `avx512` and `sse3` + - You can pick a target with, e.g. `spack install foo target=icelake` +- Spack stacks: combinatorial environments for facility deployment + - Environments can now build cartesian products of specs (with `matrix:`) + - Conditional syntax support to exclude certain builds from the stack +- Projections: ability to build easily navigable symlink trees environments +- Support no-source packages (BundlePackage) to aggregate related packages +- Extensions: users can write custom commands that live outside of Spack repo +- Support ARM and Fujitsu compilers + +## CI/build farm support +- `spack release-jobs` can detect `package.py` changes and generate + `.gitlab-ci.yml` to create binaries for an environment or stack + in parallel (initial support -- will change in future release). +- Results of build pipelines can be uploaded to a CDash server. +- Spack can now upload/fetch from package mirrors in Amazon S3 + +## New commands/options +- `spack mirror create --all` downloads *all* package sources/resources/patches +- `spack dev-build` runs phases of the install pipeline on the working directory +- `spack deprecate` permanently symlinks an old, unwanted package to a new one +- `spack verify` chcecks that packages' files match what was originally installed +- `spack find --json` prints `JSON` that is easy to parse with, e.g. `jq` +- `spack find --format FORMAT` allows you to flexibly print package metadata +- `spack spec --json` prints JSON version of `spec.yaml` + +## Selected improvements +- Auto-build requested compilers if they do not exist +- Spack automatically adds `RPATHs` needed to make executables find compiler + runtime libraries (e.g., path to newer `libstdc++` in `icpc` or `g++`) +- setup-env.sh is now compatible with Bash, Dash, and Zsh +- Spack now caps build jobs at min(16, ncores) by default +- `spack compiler find` now also throttles number of spawned processes +- Spack now writes stage directories directly to `$TMPDIR` instead of + symlinking stages within `$spack/var/spack/cache`. +- Improved and more powerful `spec` format strings +- You can pass a `spec.yaml` file anywhere in the CLI you can type a spec. +- Many improvements to binary caching +- Gradually supporting new features from Environment Modules v4 +- `spack edit` respects `VISUAL` environment variable +- Simplified package syntax for specifying build/run environment modifications +- Numerous improvements to support for environments across Spack commands +- Concretization improvements + +## Documentation +- Multi-lingual documentation (Started a Japanese translation) +- Tutorial now has its own site at spack-tutorial.readthedocs.io + - This enables us to keep multiple versions of the tutorial around + +## Deprecations +- Spack no longer supports dotkit (LLNL's homegrown, now deprecated module tool) +- `spack build`, `spack configure`, `spack diy` deprecated in favor of + `spack dev-build` and `spack install` + +## Important package changes +- 3,563 total packages (718 added since 0.12.1) +- Spack now defaults to Python 3 (previously preferred 2.7 by default) +- Much improved ARM support thanks to Fugaku (RIKEN) and SNL teams +- Support new special versions: master, trunk, and head (in addition to develop) +- Better finding logic for libraries and headers + + +# v0.12.1 (2018-11-13) + +This is a minor bugfix release, with a minor fix in the tutorial and a `flake8` fix. + +Bugfixes +* Add `r` back to regex strings in binary distribution +* Fix gcc install version in the tutorial + + +# v0.12.0 (2018-11-13) + +## Major new features +- Spack environments +- `spack.yaml` and `spack.lock` files for tracking dependencies +- Custom configurations via command line +- Better support for linking Python packages into view directories +- Packages have more control over compiler flags via flag handlers +- Better support for module file generation +- Better support for Intel compilers, Intel MPI, etc. +- Many performance improvements, improved startup time + +## License +- As of this release, all of Spack is permissively licensed under Apache-2.0 or MIT, at the user's option. +- Consents from over 300 contributors were obtained to make this relicense possible. +- Previous versions were distributed under the LGPL license, version 2.1. + +## New packages +Over 2,900 packages (800 added since last year) + +Spack would not be possible without our community. Thanks to all of our +[contributors](https://github.com/spack/spack/graphs/contributors) for the +new features and packages in this release! + + +# v0.11.2 (2018-02-07) + +This release contains the following fixes: + +* Fixes for `gfortran` 7 compiler detection (#7017) +* Fixes for exceptions thrown during module generation (#7173) + + +# v0.11.1 (2018-01-19) + +This release contains bugfixes for compiler flag handling. There were issues in `v0.11.0` that caused some packages to be built without proper optimization. + +Fixes: +* Issue #6999: FFTW installed with Spack 0.11.0 gets built without optimisations + +Includes: +* PR #6415: Fixes for flag handling behavior +* PR #6960: Fix type issues with setting flag handlers +* 880e319: Upstream fixes to `list_url` in various R packages + + +# v0.11.0 (2018-01-17) + +Spack v0.11.0 contains many improvements since v0.10.0. +Below is a summary of the major features, broken down by category. + +## New packages +- Spack now has 2,178 packages (from 1,114 in v0.10.0) +- Many more Python packages (356) and R packages (471) +- 48 Exascale Proxy Apps (try `spack list -t proxy-app`) + + +## Core features for users +- Relocatable binary packages (`spack buildcache`, #4854) +- Spack now fully supports Python 3 (#3395) +- Packages can be tagged and searched by tags (#4786) +- Custom module file templates using Jinja (#3183) +- `spack bootstrap` command now sets up a basic module environment (#3057) +- Simplified and better organized help output (#3033) +- Improved, less redundant `spack install` output (#5714, #5950) +- Reworked `spack dependents` and `spack dependencies` commands (#4478) + + +## Major new features for packagers +- Multi-valued variants (#2386) +- New `conflicts()` directive (#3125) +- New dependency type: `test` dependencies (#5132) +- Packages can require their own patches on dependencies (#5476) + - `depends_on(..., patches=)` +- Build interface for passing linker information through Specs (#1875) + - Major packages that use blas/lapack now use this interface +- Flag handlers allow packages more control over compiler flags (#6415) +- Package subclasses support many more build systems: + - autotools, perl, qmake, scons, cmake, makefile, python, R, WAF + - package-level support for installing Intel HPC products (#4300) +- `spack blame` command shows contributors to packages (#5522) +- `spack create` now guesses many more build systems (#2707) +- Better URL parsing to guess package version URLs (#2972) +- Much improved `PythonPackage` support (#3367) + + +## Core +- Much faster concretization (#5716, #5783) +- Improved output redirection (redirecting build output works properly #5084) +- Numerous improvements to internal structure and APIs + + +## Tutorials & Documentation +- Many updates to documentation +- [New tutorial material from SC17](https://spack.readthedocs.io/en/latest/tutorial.html) + - configuration + - build systems + - build interface + - working with module generation +- Documentation on docker workflows and best practices + + +## Selected improvements and bug fixes +- No longer build Python eggs -- installations are plain directories (#3587) +- Improved filtering of system paths from build PATHs and RPATHs (#2083, #3910) +- Git submodules are properly handled on fetch (#3956) +- Can now set default number of parallel build jobs in `config.yaml` +- Improvements to `setup-env.csh` (#4044) +- Better default compiler discovery on Mac OS X (#3427) + - clang will automatically mix with gfortran +- Improved compiler detection on Cray machines (#3075) +- Better support for IBM XL compilers +- Better tab completion +- Resume gracefully after prematurely terminated partial installs (#4331) +- Better mesa support (#5170) + + +Spack would not be possible without our community. Thanks to all of our +[contributors](https://github.com/spack/spack/graphs/contributors) for the +new features and packages in this release! + + +# v0.10.0 (2017-01-17) + +This is Spack `v0.10.0`. With this release, we will start to push Spack +releases more regularly. This is the last Spack release without +automated package testing. With the next release, we will begin to run +package tests in addition to unit tests. + +Spack has grown rapidly from 422 to +[1,114 packages](https://spack.readthedocs.io/en/v0.10.0/package_list.html), +thanks to the hard work of over 100 contributors. Below is a condensed +version of all the changes since `v0.9.1`. + +### Packages +- Grew from 422 to 1,114 packages + - Includes major updates like X11, Qt + - Expanded HPC, R, and Python ecosystems + +### Core +- Major speed improvements for spack find and concretization +- Completely reworked architecture support + - Platforms can have front-end and back-end OS/target combinations + - Much better support for Cray and BG/Q cross-compiled environments +- Downloads are now cached locally +- Support installations in deeply nested directories: patch long shebangs using `sbang` + +### Basic usage +- Easier global configuration via config.yaml + - customize install, stage, and cache locations +- Hierarchical configuration scopes: default, site, user + - Platform-specific scopes allow better per-platform defaults +- Ability to set `cflags`, `cxxflags`, `fflags` on the command line +- YAML-configurable support for both Lmod and tcl modules in mainline +- `spack install` supports --dirty option for emergencies + +### For developers +- Support multiple dependency types: `build`, `link`, and `run` +- Added `Package` base classes for custom build systems + - `AutotoolsPackage`, `CMakePackage`, `PythonPackage`, etc. + - `spack create` now guesses many more build systems +- Development environment integration with `spack setup` +- New interface to pass linking information via `spec` objects + - Currently used for `BLAS`/`LAPACK`/`SCALAPACK` libraries + - Polymorphic virtual dependency attributes: `spec['blas'].blas_libs` + +### Testing & Documentation +- Unit tests run continuously on Travis CI for Mac and Linux +- Switched from `nose` to `pytest` for unit tests. + - Unit tests take 1 minute now instead of 8 +- Massively expanded documentation +- Docs are now hosted on [spack.readthedocs.io](http://spack.readthedocs.io) From d68b554cd3e00cb19d02c5c166cbc7997b486c68 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 26 Oct 2019 11:06:37 -0500 Subject: [PATCH 445/499] Add latest version of py-fiscalyear (#13451) --- var/spack/repos/builtin/packages/py-fiscalyear/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-fiscalyear/package.py b/var/spack/repos/builtin/packages/py-fiscalyear/package.py index c4ffdbdbe64..8e03b2457b4 100644 --- a/var/spack/repos/builtin/packages/py-fiscalyear/package.py +++ b/var/spack/repos/builtin/packages/py-fiscalyear/package.py @@ -13,17 +13,19 @@ class PyFiscalyear(PythonPackage): the fiscal year and fiscal quarter of a date or datetime object.""" homepage = "https://github.com/adamjstewart/fiscalyear" - url = "https://pypi.io/packages/source/f/fiscalyear/fiscalyear-0.1.0.tar.gz" + url = "https://pypi.io/packages/source/f/fiscalyear/fiscalyear-0.2.0.tar.gz" git = "https://github.com/adamjstewart/fiscalyear.git" maintainers = ['adamjstewart'] import_modules = ['fiscalyear'] version('master', branch='master') + version('0.2.0', sha256='f513616aeb03046406c56d7c69cd9e26f6a12963c71c1410cc3d4532a5bfee71') version('0.1.0', sha256='3fde4a12eeb72da446beb487e078adf1223a92d130520e589b82d7d1509701a2') - depends_on('python@2.5:') + depends_on('python@2.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-pytest', type='test') depends_on('py-pytest-runner', type='test') + depends_on('py-pytest-mock', type='test') From c107b7531c0ce2ec3fca9033a7aef0d381179335 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Sat, 26 Oct 2019 22:03:39 -0400 Subject: [PATCH 446/499] MPICH: Fix Slurm Find Issue (#13263) Set include and library path to slurm explicitly. --- var/spack/repos/builtin/packages/mpich/package.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 5d7a74cb59b..231dc884bf1 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -180,6 +180,15 @@ def configure_args(self): spec else 'yes') ] + if '+slurm' in spec: + config_args.append('--with-slurm=yes') + config_args.append('--with-slurm-include={0}'.format( + spec['slurm'].prefix.include)) + config_args.append('--with-slurm-lib={0}'.format( + spec['slurm'].prefix.lib)) + else: + config_args.append('--with-slurm=no') + if 'pmi=off' in spec: config_args.append('--with-pmi=no') elif 'pmi=pmi' in spec: From 59a6226f746614b09570c6a37213b3f8bb649f38 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 27 Oct 2019 19:21:06 -0500 Subject: [PATCH 447/499] Update PyTorch variable name (#13461) --- var/spack/repos/builtin/packages/py-torch/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py index 9325b2504cb..451c71d7432 100644 --- a/var/spack/repos/builtin/packages/py-torch/package.py +++ b/var/spack/repos/builtin/packages/py-torch/package.py @@ -207,7 +207,7 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False): enable_or_disable('caffe2', keyword='BUILD', var='CAFFE2_OPS') enable_or_disable('gloo', newer=True) - enable_or_disable('gloo', var='GLOO_IBVERBS', newer=True) + enable_or_disable('gloo', var='IBVERBS', newer=True) enable_or_disable('opencv', newer=True) enable_or_disable('openmp', newer=True) enable_or_disable('ffmpeg', newer=True) From 57f040753daec48f7252d966f83f0b8d8df97035 Mon Sep 17 00:00:00 2001 From: Sinan Date: Sun, 27 Oct 2019 19:53:38 -0700 Subject: [PATCH 448/499] new package: ecos (#13453) --- .../repos/builtin/packages/ecos/package.py | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ecos/package.py diff --git a/var/spack/repos/builtin/packages/ecos/package.py b/var/spack/repos/builtin/packages/ecos/package.py new file mode 100644 index 00000000000..61facbfffe6 --- /dev/null +++ b/var/spack/repos/builtin/packages/ecos/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Ecos(MakefilePackage): + """A lightweight conic solver for second-order cone programming.""" + + homepage = "https://github.com/embotech/ecos" + url = "https://github.com/embotech/ecos/archive/2.0.7.tar.gz" + + version('2.0.7', sha256='bdb6a84f7d150820459bd0a796cb64ffbb019afb95dc456d22acc2dafb2e70e0') + + build_targets = ['all', 'shared'] + + def install(self, spec, prefix): + install_tree('include', prefix.include) + + mkdir(prefix.lib) + install('libecos.a', prefix.lib) + install('libecos_bb.a', prefix.lib) + install('libecos.so', prefix.lib) + + mkdir(prefix.bin) + install('runecos', prefix.bin) + install('runecosexp', prefix.bin) From 929ec39a6303f8828ef60bf624bf0c410969441e Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Mon, 28 Oct 2019 03:54:04 +0100 Subject: [PATCH 449/499] mariadb-c-client: Add 3.1.4 (#13447) --- var/spack/repos/builtin/packages/mariadb-c-client/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/mariadb-c-client/package.py b/var/spack/repos/builtin/packages/mariadb-c-client/package.py index e64a34303a3..54f6f405e32 100644 --- a/var/spack/repos/builtin/packages/mariadb-c-client/package.py +++ b/var/spack/repos/builtin/packages/mariadb-c-client/package.py @@ -22,6 +22,7 @@ class MariadbCClient(CMakePackage): list_url = "https://downloads.mariadb.com/Connectors/c/" list_depth = 1 + version('3.1.4', sha256='7a1a72fee00e4c28060f96c3efbbf38aabcbbab17903e82fce85a85002565316') version('3.0.9', sha256='7277c0caba6f50b1d07e1d682baf0b962a63e2e6af9e00e09b8dcf36a7858641') version('3.0.8', sha256='2ca368fd79e87e80497a5c9fd18922d8316af8584d87cecb35bd5897cb1efd05') version('3.0.7', sha256='f63883c9360675d111646fba5c97feb0d08e0def5873dd189d78bafbb75fa004') From 82428133d692a8274b2365ed58f0130953539234 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Mon, 28 Oct 2019 03:55:06 +0100 Subject: [PATCH 450/499] mariadb: Fix openssl dependencies (#13443) --- var/spack/repos/builtin/packages/mariadb/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py index 42019809c7e..5990660d5de 100644 --- a/var/spack/repos/builtin/packages/mariadb/package.py +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -47,5 +47,7 @@ class Mariadb(CMakePackage): depends_on('lz4') depends_on('zeromq') depends_on('msgpack-c') + depends_on('openssl') + depends_on('openssl@:1.0', when='@:10.1') conflicts('%gcc@9.1.0:', when='@:5.5') From ea6e279bbc4c5973d1030013f1c8b21b15fc745b Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Mon, 28 Oct 2019 03:59:13 +0100 Subject: [PATCH 451/499] LLVM code-signing on OSX: link to the offical documentation (#13428) * LLVM code-signing on OSX: link to the offical documentation * LLVM: update setup_environment method --- var/spack/repos/builtin/packages/llvm/package.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index b79798eb534..1e146a88d68 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -619,17 +619,18 @@ def check_darwin_lldb_codesign_requirement(self): except ProcessError: explanation = ('The "lldb_codesign" identity must be available' - ' to build LLVM with LLDB. See https://github.com/' - 'jevinskie/llvm-lldb/blob/master/docs/code-signing' - '.txt for details on how to create this identity.') + ' to build LLVM with LLDB. See https://lldb.llvm' + '.org/resources/build.html#code-signing-on-macos' + 'for details on how to create this identity.') raise RuntimeError(explanation) - def setup_environment(self, spack_env, run_env): - spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + def setup_build_environment(self, env): + env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + def setup_run_environment(self, env): if '+clang' in self.spec: - run_env.set('CC', join_path(self.spec.prefix.bin, 'clang')) - run_env.set('CXX', join_path(self.spec.prefix.bin, 'clang++')) + env.set('CC', join_path(self.spec.prefix.bin, 'clang')) + env.set('CXX', join_path(self.spec.prefix.bin, 'clang++')) def cmake_args(self): spec = self.spec From c0a2e8651b53e5053f4a4e6e6bc49972c45b456c Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Mon, 28 Oct 2019 04:22:25 +0100 Subject: [PATCH 452/499] new package: py-pandocfilters (#13418) dependency of py-nbconvert --- .../builtin/packages/py-pandocfilters/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pandocfilters/package.py diff --git a/var/spack/repos/builtin/packages/py-pandocfilters/package.py b/var/spack/repos/builtin/packages/py-pandocfilters/package.py new file mode 100644 index 00000000000..df5ab976cde --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pandocfilters/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPandocfilters(PythonPackage): + """A python module for writing pandoc filters""" + + homepage = "https://github.com/jgm/pandocfilters" + url = "https://pypi.io/packages/source/p/pandocfilters/pandocfilters-1.4.2.tar.gz" + + version('1.4.2', sha256='b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9') From 1d760e79a63eed01e6cdb2ecaf8f9f3bc8e4aa4e Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Sun, 27 Oct 2019 22:24:06 -0500 Subject: [PATCH 453/499] Libbeagle fixes (#13463) * Fixes for libbeagle This PR fixes a couple of issues with the libbeagle package. - Use args.append('--with-cuda=%s' % self.spec['cuda'].prefix) - Disable the default of compiling with -march=native as Spack now inserts architecture specific flags - Set BEAST_LIB in the beast1 package not in libbeagle. * Use new setup_run_environment method --- var/spack/repos/builtin/packages/beast1/package.py | 5 +++-- .../repos/builtin/packages/libbeagle/package.py | 12 ++++++------ 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/beast1/package.py b/var/spack/repos/builtin/packages/beast1/package.py index 2361dd95c09..e5d528b60f3 100644 --- a/var/spack/repos/builtin/packages/beast1/package.py +++ b/var/spack/repos/builtin/packages/beast1/package.py @@ -24,8 +24,9 @@ def url_for_version(self, ver): base = 'https://github.com/beast-dev/beast-mcmc/releases/download' return '{0}/v{1}/BEASTv{1}.tgz'.format(base, ver.dotted) - def setup_environment(self, spack_env, run_env): - run_env.set('BEAST1', self.prefix) + def setup_run_environment(self, env): + env.set('BEAST1', self.prefix) + env.set('BEAST_LIB', self.prefix.lib) def install(self, spec, prefix): install_tree('bin', prefix.bin) diff --git a/var/spack/repos/builtin/packages/libbeagle/package.py b/var/spack/repos/builtin/packages/libbeagle/package.py index 0c21905a0a0..edae048df5d 100644 --- a/var/spack/repos/builtin/packages/libbeagle/package.py +++ b/var/spack/repos/builtin/packages/libbeagle/package.py @@ -44,15 +44,15 @@ def patch(self): 'configure.ac', string=True) def configure_args(self): - args = [] + args = [ + # Since spack will inject architecture flags turn off -march=native + # when building libbeagle. + '--disable-march-native', + ] if '+cuda' in self.spec: - args.append('--with-cuda=%s' % spec['cuda'].prefix) + args.append('--with-cuda=%s' % self.spec['cuda'].prefix) else: args.append('--without-cuda') return args - - def setup_environment(self, spack_env, run_env): - prefix = self.prefix - run_env.prepend_path('BEAST_LIB', prefix.lib) From 7b86251bef63980508ca9fd73eb9457a8de6ced7 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Sun, 27 Oct 2019 20:24:27 -0700 Subject: [PATCH 454/499] Add Lizard (LZ5) (#13456) * Add Lizard (LZ5) Add a new package for Lizard, formerly LZ5, a very fast compressor and decompressor library. * c-blosc2: use external lizard Use an external Lizard (LZ5) dependency and add missing "when="s for other compressor dependents. --- .../builtin/packages/c-blosc2/package.py | 14 ++-- .../lizard/fix-install-decompress.patch | 76 +++++++++++++++++++ .../repos/builtin/packages/lizard/package.py | 27 +++++++ 3 files changed, 109 insertions(+), 8 deletions(-) create mode 100644 var/spack/repos/builtin/packages/lizard/fix-install-decompress.patch create mode 100644 var/spack/repos/builtin/packages/lizard/package.py diff --git a/var/spack/repos/builtin/packages/c-blosc2/package.py b/var/spack/repos/builtin/packages/c-blosc2/package.py index d9bcdde290d..1596a9c1d5b 100644 --- a/var/spack/repos/builtin/packages/c-blosc2/package.py +++ b/var/spack/repos/builtin/packages/c-blosc2/package.py @@ -32,12 +32,11 @@ class CBlosc2(CMakePackage): description='support for ZSTD') depends_on('cmake@2.8.10:', type='build') - # TODO https://github.com/inikep/lizard/issues/21 - # depends_on('lizard') - depends_on('lz4') - depends_on('snappy') - depends_on('zlib') - depends_on('zstd') + depends_on('lizard', when='+lizard') + depends_on('lz4', when='+lz4') + depends_on('snappy', when='+snappy') + depends_on('zlib', when='+zlib') + depends_on('zstd', when='+zstd') def cmake_args(self): spec = self.spec @@ -53,8 +52,7 @@ def cmake_args(self): 'ON' if '~zlib' in spec else 'OFF'), '-DDEACTIVATE_ZSTD={0}'.format( 'ON' if '~zstd' in spec else 'OFF'), - # TODO https://github.com/inikep/lizard/issues/21 - '-DPREFER_EXTERNAL_LIZARD=OFF', + '-DPREFER_EXTERNAL_LIZARD=ON', '-DPREFER_EXTERNAL_LZ4=ON', # snappy is supported via external install only '-DPREFER_EXTERNAL_ZLIB=ON', diff --git a/var/spack/repos/builtin/packages/lizard/fix-install-decompress.patch b/var/spack/repos/builtin/packages/lizard/fix-install-decompress.patch new file mode 100644 index 00000000000..d5a8242a234 --- /dev/null +++ b/var/spack/repos/builtin/packages/lizard/fix-install-decompress.patch @@ -0,0 +1,76 @@ +From 02c35c25e565a090ec6b49fbc6210f6593519b44 Mon Sep 17 00:00:00 2001 +From: Przemyslaw Skibinski +Date: Fri, 25 Oct 2019 10:03:39 +0200 +Subject: [PATCH] Fix missing `lizard_decompress.h` after `make install`. + +--- + lib/Makefile | 2 ++ + lib/lizard_common.h | 7 +++++++ + lib/lizard_decompress.h | 9 +-------- + 3 files changed, 10 insertions(+), 8 deletions(-) + +diff --git a/lib/Makefile b/lib/Makefile +index 64c07dd..9484056 100644 +--- a/lib/Makefile ++++ b/lib/Makefile +@@ -143,6 +143,7 @@ endif + @ln -sf liblizard.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)/liblizard.$(SHARED_EXT) + @echo Installing includes + @$(INSTALL_DATA) lizard_compress.h $(DESTDIR)$(INCLUDEDIR)/lizard_compress.h ++ @$(INSTALL_DATA) lizard_decompress.h $(DESTDIR)$(INCLUDEDIR)/lizard_decompress.h + @$(INSTALL_DATA) lizard_common.h $(DESTDIR)$(INCLUDEDIR)/lizard_common.h + @$(INSTALL_DATA) lizard_frame.h $(DESTDIR)$(INCLUDEDIR)/lizard_frame.h + @echo lizard static and shared libraries installed +@@ -154,6 +155,7 @@ uninstall: + @$(RM) $(DESTDIR)$(LIBDIR)/liblizard.$(SHARED_EXT_VER) + @$(RM) $(DESTDIR)$(LIBDIR)/liblizard.a + @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_compress.h ++ @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_decompress.h + @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_common.h + @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_frame.h + @echo lizard libraries successfully uninstalled +diff --git a/lib/lizard_common.h b/lib/lizard_common.h +index 1677abb..45730cf 100644 +--- a/lib/lizard_common.h ++++ b/lib/lizard_common.h +@@ -192,6 +192,13 @@ struct Lizard_stream_s + const BYTE* destBase; + }; + ++struct Lizard_streamDecode_s { ++ const BYTE* externalDict; ++ size_t extDictSize; ++ const BYTE* prefixEnd; ++ size_t prefixSize; ++}; ++ + struct Lizard_dstream_s + { + const BYTE* offset16Ptr; +diff --git a/lib/lizard_decompress.h b/lib/lizard_decompress.h +index 5453b4d..ad9fc8e 100644 +--- a/lib/lizard_decompress.h ++++ b/lib/lizard_decompress.h +@@ -39,8 +39,6 @@ + extern "C" { + #endif + +-#include "entropy/mem.h" /* U32 */ +- + + /*^*************************************************************** + * Export parameters +@@ -95,12 +93,7 @@ LIZARDDLIB_API int Lizard_decompress_safe_partial (const char* source, char* des + /*-********************************************** + * Streaming Decompression Functions + ************************************************/ +-typedef struct { +- const BYTE* externalDict; +- size_t extDictSize; +- const BYTE* prefixEnd; +- size_t prefixSize; +-} Lizard_streamDecode_t; ++typedef struct Lizard_streamDecode_s Lizard_streamDecode_t; + + /* + * Lizard_streamDecode_t diff --git a/var/spack/repos/builtin/packages/lizard/package.py b/var/spack/repos/builtin/packages/lizard/package.py new file mode 100644 index 00000000000..d2b2b23c0a0 --- /dev/null +++ b/var/spack/repos/builtin/packages/lizard/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Lizard(MakefilePackage): + """Lizard (formerly LZ5) is an efficient compressor with very + fast decompression. It achieves compression ratio that is + comparable to zip/zlib and zstd/brotli (at low and medium + compression levels) at decompression speed of 1000 MB/s and + faster.""" + + homepage = "https://github.com/inikep/lizard" + url = "https://github.com/inikep/lizard/archive/v1.0.tar.gz" + git = "https://github.com/inikep/lizard.git" + + version('develop', branch='lizard') + version('1.0', + sha256='6f666ed699fc15dc7fdaabfaa55787b40ac251681b50c0d8df017c671a9457e6') + + patch('fix-install-decompress.patch', when='@1.0') + + def install(self, spec, prefix): + make("PREFIX=%s" % prefix, "install") From c11c3f27103ba4734bd50116fc6b611a932c2f91 Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Sun, 27 Oct 2019 22:27:55 -0500 Subject: [PATCH 455/499] QE Update Oct 2019 (#13406) * This filter_file was difficult to maintain and is no longer needed. * Clarify lack of support for HDF5 in serial QE. * Update QE and HDF5 conflicts based on user feedback. --- .../packages/quantum-espresso/package.py | 49 +++++++------------ 1 file changed, 18 insertions(+), 31 deletions(-) diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py index 2c68a6fbf50..ea43a617313 100644 --- a/var/spack/repos/builtin/packages/quantum-espresso/package.py +++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py @@ -86,10 +86,22 @@ class QuantumEspresso(Package): msg='elpa is a parallel library and needs MPI support' ) - # HDF5 support introduced in 6.1 - hdf5_warning = 'HDF5 support only in QE 6.1 and later' - conflicts('hdf5=parallel', when='@:6.0', msg=hdf5_warning) - conflicts('hdf5=serial', when='@:6.0', msg=hdf5_warning) + # HDF5 support introduced in 6.1.0, but the configure had some limitations. + # In recent tests (Oct 2019), GCC and Intel work with the HDF5 Spack + # package for the default variant. This is only for hdf5=parallel variant. + # Support, for hdf5=serial was introduced later with some limitation. See + # the last conflict. + conflicts( + 'hdf5=parallel', + when='@:6.0', + msg='parallel HDF5 support only in QE 6.1.0 and later' + ) + + conflicts( + 'hdf5=serial', + when='@:6.4.0', + msg='serial HDF5 support only in QE 6.4.1 and later' + ) conflicts( 'hdf5=parallel', @@ -99,8 +111,8 @@ class QuantumEspresso(Package): conflicts( 'hdf5=serial', - when='~mpi @6.1:6.3', - msg='serial HDF5 in serial QE only works in develop version' + when='~mpi', + msg='serial HDF5 detection with serial QE is broken' ) # Elpa is formally supported by @:5.4.0, but QE configure searches @@ -236,31 +248,6 @@ def install(self, spec, prefix): configure(*options) - # Apparently the build system of QE is so broken that - # make_inc needs to be modified manually: - # - # 1. The variable reported on stdout as HDF5_LIBS is actually - # called HDF5_LIB (singular) - # 2. The link flags omit a few `-L` from the line, and this - # causes the linker to break - # 3. Serial HDF5 case is supported both with and without MPI. - # - # Below we try to match the entire HDF5_LIB line and substitute - # with the list of libraries that needs to be linked. - if spec.variants['hdf5'].value != 'none': - make_inc = join_path(self.stage.source_path, 'make.inc') - hdf5_libs = ' '.join(spec['hdf5:hl,fortran'].libs) - filter_file(r'HDF5_LIB([\s]*)=([\s\w\-\/.,]*)', - 'HDF5_LIB = {0}'.format(hdf5_libs), - make_inc) - if spec.variants['hdf5'].value == 'serial': - # Note that there is a benign side effect with this filter - # file statement. It replaces an instance of MANUAL_DFLAGS - # that is a comment in make.inc. - filter_file(r'MANUAL_DFLAGS([\s]*)=([\s]*)', - 'MANUAL_DFLAGS = -D__HDF5_SERIAL', - make_inc) - if '+epw' in spec: make('all', 'epw') else: From ba69ebc5f7831562f0fb83fac6ea68e023bb907f Mon Sep 17 00:00:00 2001 From: wenlibin02 Date: Mon, 28 Oct 2019 11:31:10 +0800 Subject: [PATCH 456/499] Add dependency and patch for perl-dbfile (#13261) * Add dependency and patch perl-dbfile There are two problems for the building of `perl-dbfile`: 1) this package depends on the package `berkeley-db` 2) fix the building using a patch, which locates the position of `berkeley-db` and modify the configuration file for the building * Update and reformat the script package.py * Simplify the patch * Update package.py * Update package.py --- var/spack/repos/builtin/packages/perl-dbfile/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-dbfile/package.py index c56d98f8426..19cc9410c17 100644 --- a/var/spack/repos/builtin/packages/perl-dbfile/package.py +++ b/var/spack/repos/builtin/packages/perl-dbfile/package.py @@ -20,3 +20,8 @@ class PerlDbfile(PerlPackage): version('1.840', sha256='b7864707fad0f2d1488c748c4fa08f1fb8bcfd3da247c36909fd42f20bfab2c4') depends_on('perl-extutils-makemaker', type='build') + depends_on('berkeley-db', type='build') + + def patch(self): + filter_file('/usr/local/BerkeleyDB', + self.spec['berkeley-db'].prefix, 'config.in') From cacd0fb139280ef326775c267cdf60a532eea2c1 Mon Sep 17 00:00:00 2001 From: Mark Olesen Date: Mon, 28 Oct 2019 15:58:25 +0100 Subject: [PATCH 457/499] scotch: added version 6.0.8 (#13467) --- var/spack/repos/builtin/packages/scotch/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index 935de81075a..8e1b18d474d 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -14,6 +14,7 @@ class Scotch(Package): url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.4.tar.gz" list_url = "http://gforge.inria.fr/frs/?group_id=248" + version('6.0.8', sha256='0ba3f145026174304f910c8770a3cbb034f213c91d939573751cfbb4fd46d45e') version('6.0.6', sha256='686f0cad88d033fe71c8b781735ff742b73a1d82a65b8b1586526d69729ac4cf') version('6.0.5a', sha256='5b21b95e33acd5409d682fa7253cefbdffa8db82875549476c006d8cbe7c556f') version('6.0.4', sha256='f53f4d71a8345ba15e2dd4e102a35fd83915abf50ea73e1bf6efe1bc2b4220c7') From 283b3e601ce17eff8b88bc63053dbc31ebb92e58 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 28 Oct 2019 11:46:27 -0500 Subject: [PATCH 458/499] Update emacs to version 26.3 (#13469) --- var/spack/repos/builtin/packages/emacs/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py index c556c446ce4..ecf3c0c5729 100644 --- a/var/spack/repos/builtin/packages/emacs/package.py +++ b/var/spack/repos/builtin/packages/emacs/package.py @@ -14,6 +14,7 @@ class Emacs(AutotoolsPackage): homepage = "https://www.gnu.org/software/emacs" url = "https://ftpmirror.gnu.org/emacs/emacs-24.5.tar.gz" + version('26.3', sha256='09c747e048137c99ed35747b012910b704e0974dde4db6696fde7054ce387591') version('26.2', sha256='4f99e52a38a737556932cc57479e85c305a37a8038aaceb5156625caf102b4eb') version('26.1', sha256='760382d5e8cdc5d0d079e8f754bce1136fbe1473be24bb885669b0e38fc56aa3') version('25.3', sha256='f72c6a1b48b6fbaca2b991eed801964a208a2f8686c70940013db26cd37983c9') From b4e027e91888f09badfa20de0d346b983406872f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 28 Oct 2019 11:46:59 -0500 Subject: [PATCH 459/499] Output directory Spack is looking in for MKL libs (#13465) --- lib/spack/spack/build_systems/intel.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/build_systems/intel.py b/lib/spack/spack/build_systems/intel.py index 858b4e37fb8..524f3d89469 100644 --- a/lib/spack/spack/build_systems/intel.py +++ b/lib/spack/spack/build_systems/intel.py @@ -786,7 +786,8 @@ def blas_libs(self): debug_print(mkl_libs) if len(mkl_libs) < 3: - raise_lib_error('Cannot locate core MKL libraries:', mkl_libnames) + raise_lib_error('Cannot locate core MKL libraries:', mkl_libnames, + 'in:', self.component_lib_dir('mkl')) # The Intel MKL link line advisor recommends these system libraries system_libs = find_system_libraries( From 33a34f9619a1eff866a1ae3b673f92d4ce5936a5 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 28 Oct 2019 11:47:21 -0500 Subject: [PATCH 460/499] Fix PyTorch build with Intel MKL (#13464) --- var/spack/repos/builtin/packages/py-torch/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py index 451c71d7432..8fec773e3d5 100644 --- a/var/spack/repos/builtin/packages/py-torch/package.py +++ b/var/spack/repos/builtin/packages/py-torch/package.py @@ -169,6 +169,11 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False): else: env.set('NO_' + var, 'ON') + # Build system has problems locating MKL libraries + # See https://github.com/pytorch/pytorch/issues/24334 + if 'mkl' in self.spec: + env.prepend_path('CMAKE_PREFIX_PATH', self.spec['mkl'].prefix.mkl) + env.set('MAX_JOBS', make_jobs) enable_or_disable('cuda') From f4e6f28e6dc0f1b16ed81fe0e14b2ce653ff63a0 Mon Sep 17 00:00:00 2001 From: Paul Date: Mon, 28 Oct 2019 14:19:14 -0600 Subject: [PATCH 461/499] Go package: add versions (including 1.13.3) and update environment setup (#13254) * Add versinos 1.13.3, 1.13.2, 1.12.12, and 1.12.11 * Replace setup_environment/setup_dependent_environment with setup_build_environment and setup_dependent_{build, run}_environment according to 9ddc98e --- .../repos/builtin/packages/go/package.py | 27 ++++++++++++------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 1090718ea33..2d1d51ccac3 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -35,8 +35,12 @@ class Go(Package): extendable = True + version('1.13.3', sha256='4f7123044375d5c404280737fbd2d0b17064b66182a65919ffe20ffe8620e3df') + version('1.13.2', sha256='1ea68e01472e4276526902b8817abd65cf84ed921977266f0c11968d5e915f44') version('1.13.1', sha256='81f154e69544b9fa92b1475ff5f11e64270260d46e7e36c34aafc8bc96209358') version('1.13', sha256='3fc0b8b6101d42efd7da1da3029c0a13f22079c0c37ef9730209d8ec665bf122') + version('1.12.12', sha256='fcb33b5290fa9bcc52be3211501540df7483d7276b031fc77528672a3c705b99') + version('1.12.11', sha256='fcf58935236802929f5726e96cd1d900853b377bec2c51b2e37219c658a4950f') version('1.12.10', sha256='f56e48fce80646d3c94dcf36d3e3f490f6d541a92070ad409b87b6bbb9da3954') version('1.12.9', sha256='ab0e56ed9c4732a653ed22e232652709afbf573e710f56a07f7fdeca578d62fc') version('1.12.8', sha256='11ad2e2e31ff63fcf8a2bdffbe9bfa2e1845653358daed593c8c2d03453c9898') @@ -104,12 +108,12 @@ def install(self, spec, prefix): install_tree(wd, prefix) - def setup_environment(self, spack_env, run_env): - spack_env.set('GOROOT_FINAL', self.spec.prefix) + def setup_build_environment(self, env): + env.set('GOROOT_FINAL', self.spec.prefix) # We need to set CC/CXX_FOR_TARGET, otherwise cgo will use the # internal Spack wrappers and fail. - spack_env.set('CC_FOR_TARGET', self.compiler.cc) - spack_env.set('CXX_FOR_TARGET', self.compiler.cxx) + env.set('CC_FOR_TARGET', self.compiler.cc) + env.set('CXX_FOR_TARGET', self.compiler.cxx) def setup_dependent_package(self, module, dependent_spec): """Called before go modules' install() methods. @@ -123,19 +127,24 @@ def setup_dependent_package(self, module, dependent_spec): # Add a go command/compiler for extensions module.go = self.spec['go'].command - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def generate_path_components(self, dependent_spec): if os.environ.get('GOROOT', False): tty.warn('GOROOT is set, this is not recommended') + # Set to include paths of dependencies path_components = [] - # Set GOPATH to include paths of dependencies for d in dependent_spec.traverse(): if d.package.extends(self.spec): path_components.append(d.prefix) + return path_components + def setup_dependent_build_environment(self, env, dependent_spec): # This *MUST* be first, this is where new code is installed - spack_env.set('GOPATH', ':'.join(path_components)) + env.set('GOPATH', ':'.join(self.generate_path_components( + dependent_spec))) + def setup_dependent_run_environment(self, env, dependent_spec): # Allow packages to find this when using module files - run_env.prepend_path('GOPATH', ':'.join( - [dependent_spec.prefix] + path_components)) + env.prepend_path('GOPATH', ':'.join( + [dependent_spec.prefix] + self.generate_path_components( + dependent_spec))) From 802c3c0c5133c44bd037cac2f798b0fe3ea444fb Mon Sep 17 00:00:00 2001 From: Brian Van Essen Date: Mon, 28 Oct 2019 13:24:50 -0700 Subject: [PATCH 462/499] Packages: Add cuDNN versions; update LBANN dependencies (#13412) * Add cuDNN version 7.6.3-10.1 (for x86_64 and ppc64le) * Add py-pytest and py-protobuf depenencies to LBANN --- var/spack/repos/builtin/packages/cudnn/package.py | 6 +++++- var/spack/repos/builtin/packages/lbann/package.py | 2 ++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py index b56aacab4fe..8a872ce949d 100644 --- a/var/spack/repos/builtin/packages/cudnn/package.py +++ b/var/spack/repos/builtin/packages/cudnn/package.py @@ -13,6 +13,10 @@ class Cudnn(Package): homepage = "https://developer.nvidia.com/cudnn" + version('7.6.3-10.1-x86_64', sha256='352557346d8111e2f954c494be1a90207103d316b8777c33e62b3a7f7b708961', + url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.6.3/cudnn-10.1-linux-x64-v7.6.3.30.tgz') + version('7.6.3-10.1-ppc64le', sha256='f274735a8fc31923d3623b1c3d2b1d0d35bb176687077c6a4d4353c6b900d8ee', + url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.6.3/cudnn-10.1-linux-ppc64le-v7.6.3.30.tgz') version('7.5.1-10.1-x86_64', sha256='2c833f43c9147d9a25a20947a4c5a5f5c33b2443240fd767f63b330c482e68e0', url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.1-linux-x64-v7.5.1.10.tgz') version('7.5.1-10.1-ppc64le', sha256='a9e23bc83c970daec20874ccd1d8d80b648adf15440ecd0164818b330b1e2663', @@ -41,7 +45,7 @@ class Cudnn(Package): depends_on('cuda@8:', when='@5.1:@7') depends_on('cuda@9:', when='@7.2:@7.4') depends_on('cuda@10:', when='@7.5.0-10.0-ppc64le,7.5.0-10.0-x86_64,7.5.1-10.0-ppc64le,7.5.1-10.0-x86_64') - depends_on('cuda@10.1:', when='@7.5.0-10.1-ppc64le,7.5.0-10.1-x86_64,7.5.1-10.1-ppc64le,7.5.1-10.1-x86_64') + depends_on('cuda@10.1:', when='@7.5.0-10.1-ppc64le,7.5.0-10.1-x86_64,7.5.1-10.1-ppc64le,7.5.1-10.1-x86_64,7.6.3-10.1-ppc64le,7.6.3-10.1-x86_64') def install(self, spec, prefix): install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py index cf39b3e5c1a..79fd5f0035e 100644 --- a/var/spack/repos/builtin/packages/lbann/package.py +++ b/var/spack/repos/builtin/packages/lbann/package.py @@ -112,6 +112,8 @@ class Lbann(CMakePackage): depends_on('py-onnx@1.3.0:', type='run', when='@:0.90,0.99:') depends_on('py-pandas@0.24.1:', type='run', when='@:0.90,0.99:') depends_on('py-texttable@1.4.0:', type='run', when='@:0.90,0.99:') + depends_on('py-pytest', type='test', when='@:0.90,0.99:') + depends_on('py-protobuf+cpp', type='run', when='@:0.90,0.99:') depends_on('py-breathe', type='build', when='+docs') depends_on('py-m2r', type='build', when='+docs') From 8786cb468a357edcb94905eb70e155885e641c9a Mon Sep 17 00:00:00 2001 From: Jon Rood Date: Mon, 28 Oct 2019 15:55:08 -0600 Subject: [PATCH 463/499] Paraview package: add version 5.7.0 and update environment setup (#13255) Replace setup_environment/setup_dependent_environment with setup__dependent_build_environment and setup_run_environment according to 9ddc98e --- .../builtin/packages/paraview/package.py | 33 ++++++++++--------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 938004b97c7..e19039caa5b 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -12,7 +12,7 @@ class Paraview(CMakePackage, CudaPackage): visualization application.""" homepage = 'https://www.paraview.org' - url = "https://www.paraview.org/files/v5.6/ParaView-v5.6.2.tar.xz" + url = "https://www.paraview.org/files/v5.7/ParaView-v5.7.0.tar.xz" list_url = "https://www.paraview.org/files" list_depth = 1 git = "https://gitlab.kitware.com/paraview/paraview.git" @@ -20,6 +20,7 @@ class Paraview(CMakePackage, CudaPackage): maintainers = ['chuckatkins', 'danlipsa'] version('develop', branch='master', submodules=True) + version('5.7.0', sha256='e41e597e1be462974a03031380d9e5ba9a7efcdb22e4ca2f3fec50361f310874') version('5.6.2', sha256='1f3710b77c58a46891808dbe23dc59a1259d9c6b7bb123aaaeaa6ddf2be882ea') version('5.6.0', sha256='cb8c4d752ad9805c74b4a08f8ae6e83402c3f11e38b274dba171b99bb6ac2460') version('5.5.2', sha256='64561f34c4402b88f3cb20a956842394dde5838efd7ebb301157a837114a0e2d') @@ -126,16 +127,16 @@ def paraview_subdir(self): """The paraview subdirectory name as paraview-major.minor""" return 'paraview-{0}'.format(self.spec.version.up_to(2)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env): if os.path.isdir(self.prefix.lib64): lib_dir = self.prefix.lib64 else: lib_dir = self.prefix.lib - spack_env.set('ParaView_DIR', self.prefix) - spack_env.set('PARAVIEW_VTK_DIR', - join_path(lib_dir, 'cmake', self.paraview_subdir)) + env.set('ParaView_DIR', self.prefix) + env.set('PARAVIEW_VTK_DIR', + join_path(lib_dir, 'cmake', self.paraview_subdir)) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # paraview 5.5 and later # - cmake under lib/cmake/paraview-5.5 # - libs under lib @@ -145,31 +146,31 @@ def setup_environment(self, spack_env, run_env): else: lib_dir = self.prefix.lib - run_env.set('ParaView_DIR', self.prefix) - run_env.set('PARAVIEW_VTK_DIR', - join_path(lib_dir, 'cmake', self.paraview_subdir)) + env.set('ParaView_DIR', self.prefix) + env.set('PARAVIEW_VTK_DIR', + join_path(lib_dir, 'cmake', self.paraview_subdir)) if self.spec.version <= Version('5.4.1'): lib_dir = join_path(lib_dir, self.paraview_subdir) - run_env.prepend_path('LIBRARY_PATH', lib_dir) - run_env.prepend_path('LD_LIBRARY_PATH', lib_dir) + env.prepend_path('LIBRARY_PATH', lib_dir) + env.prepend_path('LD_LIBRARY_PATH', lib_dir) if '+python' in self.spec or '+python3' in self.spec: if self.spec.version <= Version('5.4.1'): pv_pydir = join_path(lib_dir, 'site-packages') - run_env.prepend_path('PYTHONPATH', pv_pydir) - run_env.prepend_path('PYTHONPATH', join_path(pv_pydir, 'vtk')) + env.prepend_path('PYTHONPATH', pv_pydir) + env.prepend_path('PYTHONPATH', join_path(pv_pydir, 'vtk')) else: python_version = self.spec['python'].version.up_to(2) pv_pydir = join_path(lib_dir, 'python{0}'.format(python_version), 'site-packages') - run_env.prepend_path('PYTHONPATH', pv_pydir) + env.prepend_path('PYTHONPATH', pv_pydir) # The Trilinos Catalyst adapter requires # the vtkmodules directory in PYTHONPATH - run_env.prepend_path('PYTHONPATH', join_path(pv_pydir, - 'vtkmodules')) + env.prepend_path('PYTHONPATH', join_path(pv_pydir, + 'vtkmodules')) def cmake_args(self): """Populate cmake arguments for ParaView.""" From ffb4e02a53760dff03cccadd27f1f199c8303a2a Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Mon, 28 Oct 2019 16:31:23 -0600 Subject: [PATCH 464/499] Fix gcc recipe for RHEL7. (#13460) * Fix gcc recipe for RHEL7. + It appears that macOS related changes to the gcc recipe broke gcc on RHEL7. This bug manifests as `libstdc++.so: undefined reference to libiconv` when gcc is used. + Fixes #13452 by moving `--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix)` into the darwin OS section of the configuration. + Change qualification of `depends_on(libiconv)` to limit dependency to macOS. * Replace deprecated 'setup_environment' with 'setup_run_environment'. * Fix cut and paste error. * Rename 'run_env' to just 'env'. --- var/spack/repos/builtin/packages/gcc/package.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 836c018604b..e42d977698e 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -100,7 +100,7 @@ class Gcc(AutotoolsPackage): depends_on('isl@0.15:0.18', when='@6:8.9') depends_on('isl@0.15:0.20', when='@9:') depends_on('zlib', when='@6:') - depends_on('libiconv') + depends_on('libiconv', when='platform=darwin') depends_on('gnat', when='languages=ada') depends_on('binutils~libiberty', when='+binutils') depends_on('zip', type='build', when='languages=java') @@ -279,7 +279,6 @@ def configure_args(self): ','.join(spec.variants['languages'].value)), # Drop gettext dependency '--disable-nls', - '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix), '--with-mpfr={0}'.format(spec['mpfr'].prefix), '--with-gmp={0}'.format(spec['gmp'].prefix), ] @@ -328,7 +327,8 @@ def configure_args(self): if sys.platform == 'darwin': options.extend([ '--with-native-system-header-dir=/usr/include', - '--with-sysroot={0}'.format(macos_sdk_path()) + '--with-sysroot={0}'.format(macos_sdk_path()), + '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix) ]) return options @@ -424,7 +424,7 @@ def write_rpath_specs(self): self.prefix.lib, self.prefix.lib64)) set_install_permissions(specs_file) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # Search prefix directory for possibly modified compiler names from spack.compilers.gcc import Gcc as Compiler @@ -450,6 +450,6 @@ def setup_environment(self, spack_env, run_env): continue # Set the proper environment variable - run_env.set(lang.upper(), abspath) + env.set(lang.upper(), abspath) # Stop searching filename/regex combos for this language break From 1b3f546ba459735ea91c73494b1fd5a93653917e Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Mon, 28 Oct 2019 15:32:16 -0700 Subject: [PATCH 465/499] update conduit for 0.5.0 release (#13455) * add support for static (via ~shared) and use vtk-m 1.2 * updating vtkh package to output cmake configure file and pinning it to vtkm 1.2 * trying a different cmake for vtkh * removing problematic b * making conduit respect ~python * fixing ascent python logic * update ascent package * consistant cmake usage * conditionally add tbb in ascent if vtkh * applying becker fix * adding vtkh tag * fixing vtkh tagged version * updating ascent and conduit for static builds * enabling openmp * reverting files that should not have been changed * ascent updates * more robust handling of variants * fixing ascent package typo * ascent: add optional support for mfem * enable mfem conduit support for ascent * add optional adios dep to conduit * remove ver req from conduit * ascent: remove confusing comment * tweaks to conduit and ascent pkg recipes * fix typo in conduit package * pref conduit master * fixing mfem typo for ascent * reverting files * adding mirror for bzip * changing mfem to depend on conduit@master to get updated relay * restore use of conduit 0.3.1 or greater for mfem * set master as prefered conduit version * allow mfem to use conduit master * adding rover package and editing ascent * updating vtkm cmake dep * updates from axom * guard ascent python support on +shared * removing rover to simply ascent package * add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified * fix fortran compiler check so it can work on cray systems * working towards cuda fix for vtkm lagrange filter * update ascent package with more variants, and patch to avoid nvcc issue * hdf5 flags fix for BGQ * flake8 * extra guards for cuda patch * conduit and ascent fortran fix * fix patch for non cuda case * add test variant to conduit, tweak ascent pkg * change min ver of cmake used for ascent * h5z-zfp package: unset FC when ~fortran * conform to expected upstream solution * pinning vtkm * going back to vtkm master * add back vtk-m variant for shared libs * update ascent and vtkh packages * wire up option to run tests during install * add post install test * add testing to ascent * tweak for blueos xl * add ctest output on error for run_tests * enable ctest output on error for run_tests * add testing of the using-with-make example * update using-with-make examples * typo in ascent using-with-cmake test * fix ascent using test exe names * more fixes, less sleep * more fixes, less sleep ... * remove unwired up version * improvments suggested on review * adding new cmake * Update package.py * Update package.py * changes post cori os update * fix cray hack * Update package.py Fixing 'fix'. Inconsistent variable names in conduit package * type in spack recipes * add zfp support to conduit * fix indent error in conduit pkg * move to use build phases, add sphinx rtd as dep, fix ex names in tests * add conduit 0.5.0 release * flake8 * remove old cray hack * incorp feedback from review * fix to use proper build env sig --- .../repos/builtin/packages/ascent/package.py | 25 +++-- .../repos/builtin/packages/conduit/package.py | 92 +++++++++++++++---- 2 files changed, 92 insertions(+), 25 deletions(-) diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py index d837e51010f..8d8210edd12 100644 --- a/var/spack/repos/builtin/packages/ascent/package.py +++ b/var/spack/repos/builtin/packages/ascent/package.py @@ -72,7 +72,7 @@ class Ascent(Package): # package dependencies ########################################################################### - depends_on("cmake@3.9.2:3.9.999", type='build') + depends_on("cmake@3.14:", type='build') depends_on("conduit~python", when="~python") depends_on("conduit+python", when="+python+shared") depends_on("conduit~shared~python", when="~shared") @@ -120,8 +120,8 @@ class Ascent(Package): ####################### depends_on("py-sphinx", when="+python+doc", type='build') - def setup_environment(self, spack_env, run_env): - spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1') + def setup_build_environment(self, env): + env.set('CTEST_OUTPUT_ON_FAILURE', '1') def install(self, spec, prefix): """ @@ -353,12 +353,21 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): cfg.write("# MPI Support\n") if "+mpi" in spec: + mpicc_path = spec['mpi'].mpicc + mpicxx_path = spec['mpi'].mpicxx + mpifc_path = spec['mpi'].mpifc + # if we are using compiler wrappers on cray systems + # use those for mpi wrappers, b/c spec['mpi'].mpicxx + # etc make return the spack compiler wrappers + # which can trip up mpi detection in CMake 3.14 + if cpp_compiler == "CC": + mpicc_path = "cc" + mpicxx_path = "CC" + mpifc_path = "ftn" cfg.write(cmake_cache_entry("ENABLE_MPI", "ON")) - cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc)) - cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", - spec['mpi'].mpicxx)) - cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", - spec['mpi'].mpifc)) + cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path)) + cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path)) + cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path)) mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py index af1cc70c85a..acc1498b70f 100644 --- a/var/spack/repos/builtin/packages/conduit/package.py +++ b/var/spack/repos/builtin/packages/conduit/package.py @@ -38,6 +38,7 @@ class Conduit(Package): git = "https://github.com/LLNL/conduit.git" version('master', branch='master', submodules=True, preferred=True) + version('0.5.0', sha256='7efac668763d02bd0a2c0c1b134d9f5ee27e99008183905bb0512e5502b8b4fe') version('0.4.0', sha256='c228e6f0ce5a9c0ffb98e0b3d886f2758ace1a4b40d00f3f118542c0747c1f52') version('0.3.1', sha256='7b358ca03bb179876291d4a55d6a1c944b7407a80a588795b9e47940b1990521') version('0.3.0', sha256='52e9cf5720560e5f7492876c39ef2ea20ae73187338361d2744bdf67567da155') @@ -66,6 +67,9 @@ class Conduit(Package): variant("silo", default=False, description="Build Conduit Silo support") variant("adios", default=False, description="Build Conduit ADIOS support") + # zfp compression + variant("zfp", default=True, description="Build Conduit ZFP support") + # variants for dev-tools (docs, etc) variant("doc", default=False, description="Build Conduit's documentation") # doxygen support is wip, since doxygen has several dependencies @@ -94,6 +98,10 @@ class Conduit(Package): ####################### # I/O Packages ####################### + + ############### + # HDF5 + ############### # TODO: cxx variant is disabled due to build issue Cyrus # experienced on BGQ. When on, the static build tries # to link against shared libs. @@ -105,15 +113,26 @@ class Conduit(Package): depends_on("hdf5~cxx~mpi~fortran", when="+hdf5~hdf5_compat+shared") depends_on("hdf5~shared~cxx~mpi~fortran", when="+hdf5~hdf5_compat~shared") + ############### + # Silo + ############### # we are not using silo's fortran features depends_on("silo~fortran", when="+silo+shared") depends_on("silo~shared~fortran", when="+silo~shared") + ############### + # ADIOS + ############### depends_on("adios+mpi~hdf5+shared", when="+adios+mpi+shared") depends_on("adios+mpi~hdf5~shared~blosc", when="+adios+mpi~shared") depends_on("adios~mpi~hdf5+shared", when="+adios~mpi+shared") depends_on("adios~mpi~hdf5~shared~blosc", when="+adios~mpi~shared") + ####################### + # ZFP + ####################### + depends_on("zfp", when="+zfp") + ####################### # MPI ####################### @@ -123,10 +142,14 @@ class Conduit(Package): # Documentation related ####################### depends_on("py-sphinx", when="+python+doc", type='build') + depends_on("py-sphinx-rtd-theme", when="+python+doc", type='build') depends_on("doxygen", when="+doc+doxygen") - def setup_environment(self, spack_env, run_env): - spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1') + # build phases used by this package + phases = ["configure", "build", "install"] + + def setup_build_environment(self, env): + env.set('CTEST_OUTPUT_ON_FAILURE', '1') def url_for_version(self, version): """ @@ -145,9 +168,9 @@ def url_for_version(self, version): return "https://github.com/LLNL/conduit/releases/download/v{0}/conduit-v{1}-src-with-blt.tar.gz".format(v, v) return url - def install(self, spec, prefix): + def configure(self, spec, prefix): """ - Build and install Conduit. + Configure Conduit. """ with working_dir('spack-build', create=True): py_site_pkgs_dir = None @@ -157,6 +180,9 @@ def install(self, spec, prefix): host_cfg_fname = self.create_host_config(spec, prefix, py_site_pkgs_dir) + # save this filename for + # other package recipe steps to access + self.host_cfg_fname = host_cfg_fname cmake_args = [] # if we have a static build, we need to avoid any of # spack's default cmake settings related to rpaths @@ -170,17 +196,31 @@ def install(self, spec, prefix): cmake_args.extend(["-C", host_cfg_fname, "../src"]) print("Configuring Conduit...") cmake(*cmake_args) + + def build(self, spec, prefix): + """ + Build Conduit. + """ + with working_dir('spack-build'): print("Building Conduit...") make() - # run unit tests if requested - if "+test" in spec and self.run_tests: - print("Running Conduit Unit Tests...") - make("test") - print("Installing Conduit...") + + @run_after('build') + @on_package_attributes(run_tests=True) + def test(self): + with working_dir('spack-build'): + print("Running Conduit Unit Tests...") + make("test") + + def install(self, spec, prefix): + """ + Install Conduit. + """ + with working_dir('spack-build'): make("install") # install copy of host config for provenance print("Installing Conduit CMake Host Config File...") - install(host_cfg_fname, prefix) + install(self.host_cfg_fname, prefix) @run_after('install') @on_package_attributes(run_tests=True) @@ -203,7 +243,7 @@ def check_install(self): example_src_dir] cmake(*cmake_args) make() - example = Executable('./example') + example = Executable('./conduit_example') example() print("Checking using-with-make example...") example_src_dir = join_path(install_prefix, @@ -216,7 +256,7 @@ def check_install(self): for example_file in example_files: shutil.copy(example_file, ".") make("CONDUIT_DIR={0}".format(install_prefix)) - example = Executable('./example') + example = Executable('./conduit_example') example() def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): @@ -366,12 +406,21 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): cfg.write("# MPI Support\n") if "+mpi" in spec: + mpicc_path = spec['mpi'].mpicc + mpicxx_path = spec['mpi'].mpicxx + mpifc_path = spec['mpi'].mpifc + # if we are using compiler wrappers on cray systems + # use those for mpi wrappers, b/c spec['mpi'].mpicxx + # etc make return the spack compiler wrappers + # which can trip up mpi detection in CMake 3.14 + if cpp_compiler == "CC": + mpicc_path = "cc" + mpicxx_path = "CC" + mpifc_path = "ftn" cfg.write(cmake_cache_entry("ENABLE_MPI", "ON")) - cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc)) - cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", - spec['mpi'].mpicxx)) - cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", - spec['mpi'].mpifc)) + cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path)) + cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path)) + cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path)) mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE @@ -385,6 +434,15 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): else: cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF")) + ####################### + # ZFP + ####################### + cfg.write("# zfp from spack \n") + if "+zfp" in spec: + cfg.write(cmake_cache_entry("ZFP_DIR", spec['zfp'].prefix)) + else: + cfg.write("# zfp not built by spack \n") + ####################################################################### # I/O Packages ####################################################################### From e5b1dbf4b43a7aad027f616bf06c1d3aac87d920 Mon Sep 17 00:00:00 2001 From: Sinan Date: Mon, 28 Oct 2019 15:33:33 -0700 Subject: [PATCH 466/499] new Package/scs (#13454) * new package: SCS * make flake8 happy * add missing patch, improve style * fix typo * Update var/spack/repos/builtin/packages/scs/package.py Co-Authored-By: Adam J. Stewart * move filefilter to edit phase --- .../repos/builtin/packages/scs/make_gpu.patch | 14 +++++++ .../repos/builtin/packages/scs/package.py | 41 +++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 var/spack/repos/builtin/packages/scs/make_gpu.patch create mode 100644 var/spack/repos/builtin/packages/scs/package.py diff --git a/var/spack/repos/builtin/packages/scs/make_gpu.patch b/var/spack/repos/builtin/packages/scs/make_gpu.patch new file mode 100644 index 00000000000..3e38d832ccd --- /dev/null +++ b/var/spack/repos/builtin/packages/scs/make_gpu.patch @@ -0,0 +1,14 @@ +diff --git a/Makefile.orig b/Makefile +index b4f2bc9..8a28fc4 100644 +--- a/Makefile.orig ++++ b/Makefile +@@ -129,7 +129,8 @@ install: $(INSTALL_INC_FILES) $(INSTALL_TARGETS) + $(INSTALL) -d $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR) + $(INSTALL) -m 644 $(INSTALL_INC_FILES) $(INSTALL_INC_DIR) + $(INSTALL) -m 644 $(INSTALL_TARGETS) $(INSTALL_LIB_DIR) +-install_gpu: $(INSTALL_INC_FILES) $(INSTALL_GPU_TARGETS) ++install_gpu: $(INSTALL_INC_FILES) $(INSTALL_GPU_TARGETS) $(INSTALL_TARGETS) + $(INSTALL) -d $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR) + $(INSTALL) -m 644 $(INSTALL_INC_FILES) $(INSTALL_INC_DIR) + $(INSTALL) -m 644 $(INSTALL_GPU_TARGETS) $(INSTALL_LIB_DIR) ++ $(INSTALL) -m 644 $(INSTALL_TARGETS) $(INSTALL_LIB_DIR) diff --git a/var/spack/repos/builtin/packages/scs/package.py b/var/spack/repos/builtin/packages/scs/package.py new file mode 100644 index 00000000000..db086a99d1d --- /dev/null +++ b/var/spack/repos/builtin/packages/scs/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Scs(MakefilePackage): + """A C package that solves convex cone problems via operator splitting""" + + homepage = "https://github.com/cvxgrp/scs" + url = "https://github.com/cvxgrp/scs/archive/2.1.1.tar.gz" + + version('2.1.1', sha256='0e20b91e8caf744b84aa985ba4e98cc7235ee33612b2bad2bf31ea5ad4e07d93') + + variant('cuda', default=False, description='Build with Cuda support') + + depends_on('blas') + depends_on('lapack') + depends_on('cuda', when='+cuda') + + # make sure install_gpu target installs all libs not only the gpu ones + patch('make_gpu.patch') + + def edit(self, spec, prefix): + filter_file(r'-lblas', spec['blas'].libs.ld_flags, 'scs.mk') + filter_file(r'-llapack', spec['lapack'].libs.ld_flags, 'scs.mk') + + def build(self, spec, prefix): + if '+cuda' in spec: + make('default', 'gpu') + else: + make() + + def install(self, spec, prefix): + if '+cuda' in spec: + make('PREFIX=' + prefix, 'install_gpu') + else: + make('PREFIX=' + prefix, 'install') From 4367e16740ccd39515ad75e86cce9f65ac46ca69 Mon Sep 17 00:00:00 2001 From: Jim Galarowicz Date: Mon, 28 Oct 2019 17:36:12 -0500 Subject: [PATCH 467/499] Update the module files for cbtf-krell and openspeedshop (#13400) * Update the module files for cbtf-krell and openspeedshop adding man paths and needed papi and libmonitor paths. * Update module files for new API. * Use the same python for both develop and release branches. --- .../packages/cbtf-argonavis-gui/package.py | 33 +++++++------ .../packages/cbtf-argonavis/package.py | 46 ++++++++++--------- .../builtin/packages/cbtf-krell/package.py | 30 ++++++------ .../packages/openspeedshop-utils/package.py | 31 ++++++------- .../builtin/packages/openspeedshop/package.py | 41 +++++++++-------- 5 files changed, 96 insertions(+), 85 deletions(-) diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py index 58d699b7da1..8c3338f164c 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py @@ -52,19 +52,22 @@ class CbtfArgonavisGui(QMakePackage): parallel = False - def setup_environment(self, spack_env, run_env): - """Set up the compile and runtime environments for a package.""" - spack_env.set('BOOSTROOT', self.spec['boost'].prefix) - spack_env.set('CBTF_ROOT', self.spec['cbtf'].prefix) - spack_env.set('CBTF_KRELL_ROOT', self.spec['cbtf-krell'].prefix) - spack_env.set('CBTF_ARGONAVIS_ROOT', - self.spec['cbtf-argonavis'].prefix) - spack_env.set('OSS_CBTF_ROOT', self.spec['openspeedshop-utils'].prefix) - spack_env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix) - spack_env.set('QTGRAPHLIB_ROOT', self.spec['qtgraph'].prefix) - spack_env.set('KRELL_ROOT_MRNET', self.spec['mrnet'].prefix) - spack_env.set('KRELL_ROOT_XERCES', self.spec['xerces-c'].prefix) - spack_env.set('INSTALL_ROOT', self.spec.prefix) + def setup_build_environment(self, env): + """Set up the build environment for this package.""" + env.set('BOOSTROOT', self.spec['boost'].prefix) + env.set('CBTF_ROOT', self.spec['cbtf'].prefix) + env.set('CBTF_KRELL_ROOT', self.spec['cbtf-krell'].prefix) + env.set('CBTF_ARGONAVIS_ROOT', + self.spec['cbtf-argonavis'].prefix) + env.set('OSS_CBTF_ROOT', self.spec['openspeedshop-utils'].prefix) + env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix) + env.set('QTGRAPHLIB_ROOT', self.spec['qtgraph'].prefix) + env.set('KRELL_ROOT_MRNET', self.spec['mrnet'].prefix) + env.set('KRELL_ROOT_XERCES', self.spec['xerces-c'].prefix) + env.set('INSTALL_ROOT', self.spec.prefix) + + def setup_run_environment(self, env): + """Set up the runtime environment for this package.""" # The implementor of qtgraph has set up the library and include # paths in a non-conventional way. We reflect that here. @@ -74,14 +77,14 @@ def setup_environment(self, spack_env, run_env): else: qtgraph_lib_dir = self.spec['qtgraph'].prefix.lib - run_env.prepend_path( + env.prepend_path( 'LD_LIBRARY_PATH', join_path( qtgraph_lib_dir, '{0}'.format(self.spec['qt'].version.up_to(3)))) # The openspeedshop libraries are needed to actually load the # performance information into the GUI. - run_env.prepend_path( + env.prepend_path( 'LD_LIBRARY_PATH', self.spec['openspeedshop-utils'].prefix.lib64) def qmake_args(self): diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py index 93fcfe204f4..7905a3b0bc4 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py @@ -41,38 +41,38 @@ class CbtfArgonavis(CMakePackage): depends_on("boost@1.66.0:1.69.0") # For MRNet - depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti') - depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop~cti') - depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti') - depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999~cti') + depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run')) + depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop~cti', type=('build', 'link', 'run')) + depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run')) + depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999~cti', type=('build', 'link', 'run')) # For CBTF - depends_on("cbtf@develop", when='@develop') - depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999') + depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run')) + depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999', type=('build', 'link', 'run')) # For CBTF with cti - depends_on("cbtf@develop+cti", when='@develop+cti') - depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti') + depends_on("cbtf@develop+cti", when='@develop+cti', type=('build', 'link', 'run')) + depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run')) # For CBTF with runtime - depends_on("cbtf@develop+runtime", when='@develop+runtime') - depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime') + depends_on("cbtf@develop+runtime", when='@develop+runtime', type=('build', 'link', 'run')) + depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run')) # For libmonitor - depends_on("libmonitor@2013.02.18+krellpatch") + depends_on("libmonitor@2013.02.18+krellpatch", type=('build', 'link', 'run')) # For PAPI - depends_on("papi@5.4.1:") + depends_on("papi@5.4.1:", type=('build', 'link', 'run')) # For CBTF-KRELL - depends_on("cbtf-krell@develop", when='@develop') - depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999') + depends_on("cbtf-krell@develop", when='@develop', type=('build', 'link', 'run')) + depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999', type=('build', 'link', 'run')) - depends_on('cbtf-krell@develop+cti', when='@develop+cti') - depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti') + depends_on('cbtf-krell@develop+cti', when='@develop+cti', type=('build', 'link', 'run')) + depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti', type=('build', 'link', 'run')) - depends_on('cbtf-krell@develop+runtime', when='@develop+runtime') - depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime') + depends_on('cbtf-krell@develop+runtime', when='@develop+runtime', type=('build', 'link', 'run')) + depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run')) # For CUDA depends_on("cuda") @@ -105,12 +105,16 @@ def cmake_args(self): return cmake_args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" - run_env.prepend_path( + env.prepend_path( 'LD_LIBRARY_PATH', self.spec['cuda'].prefix + '/extras/CUPTI/lib64') - spack_env.prepend_path( + + def setup_build_environment(self, env): + """Set up the compile and runtime environments for a package.""" + + env.prepend_path( 'LD_LIBRARY_PATH', self.spec['cuda'].prefix + '/extras/CUPTI/lib64') diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py index 194367060ce..8e8bbdea48e 100644 --- a/var/spack/repos/builtin/packages/cbtf-krell/package.py +++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py @@ -83,12 +83,12 @@ class CbtfKrell(CMakePackage): depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run')) # for services and collectors - depends_on("libmonitor@2013.02.18+krellpatch") + depends_on("libmonitor@2013.02.18+krellpatch", type=('build', 'link', 'run')) depends_on("libunwind", when='@develop') depends_on("libunwind@1.2.1", when='@1.9.1.0:9999') - depends_on("papi@5.4.1:") + depends_on("papi@5.4.1:", type=('build', 'link', 'run')) depends_on("llvm-openmp-ompt@tr6_forwards+standalone") @@ -229,15 +229,15 @@ def cmake_args(self): return cmake_args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" # Environment settings for cbtf-krell, bin is automatically # added to the path in the module file - run_env.prepend_path('PATH', self.prefix.sbin) + env.prepend_path('PATH', self.prefix.sbin) - run_env.set('XPLAT_RSH', 'ssh') - run_env.set('MRNET_COMM_PATH', self.prefix.sbin.cbtf_mrnet_commnode) + env.set('XPLAT_RSH', 'ssh') + env.set('MRNET_COMM_PATH', self.prefix.sbin.cbtf_mrnet_commnode) # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation # This is needed by CBTF tools to deploy the correct @@ -246,19 +246,23 @@ def setup_environment(self, spack_env, run_env): # manually if multiple mpi's are specified in the build if self.spec.satisfies('+mpich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich") + env.set('CBTF_MPI_IMPLEMENTATION', "mpich") if self.spec.satisfies('+mvapich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") if self.spec.satisfies('+mvapich2'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") if self.spec.satisfies('+mpt'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt") + env.set('CBTF_MPI_IMPLEMENTATION', "mpt") if self.spec.satisfies('+openmpi'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") + env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") - run_env.set('CBTF_MRNET_BACKEND_PATH', - self.prefix.sbin.cbtf_libcbtf_mrnet_backend) + env.set('CBTF_MRNET_BACKEND_PATH', + self.prefix.sbin.cbtf_libcbtf_mrnet_backend) + + env.prepend_path('PATH', self.spec['libmonitor'].prefix.bin) + env.prepend_path('PATH', self.spec['papi'].prefix.bin) + env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) diff --git a/var/spack/repos/builtin/packages/openspeedshop-utils/package.py b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py index b4e1fe97bd7..ffa5a106f39 100644 --- a/var/spack/repos/builtin/packages/openspeedshop-utils/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py @@ -96,8 +96,7 @@ class OpenspeedshopUtils(CMakePackage): depends_on("dyninst@develop", when='@develop') depends_on("dyninst@10:", when='@2.3.1.3:9999') - depends_on("python", when='@develop', type=('build', 'run')) - depends_on("python@2.7.14:2.7.99", when='@2.3.1.3:9999', type=('build', 'run')) + depends_on("python@2.7.14:2.7.99", type=('build', 'run')) depends_on("libxml2") @@ -269,7 +268,7 @@ def set_mpi_cmake_options(self, spec, cmake_options): cmake_options.extend(mpi_options) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" # Find Dyninst library path, this is needed to @@ -281,26 +280,26 @@ def setup_environment(self, spack_env, run_env): shared=True, recursive=True) # Set Dyninst RT library path to support OSS loop resolution code - run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) + env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) # Find openspeedshop library path oss_libdir = find_libraries( 'libopenss-framework', root=self.spec['openspeedshop-utils'].prefix, shared=True, recursive=True) - run_env.prepend_path('LD_LIBRARY_PATH', - os.path.dirname(oss_libdir.joined())) + env.prepend_path('LD_LIBRARY_PATH', + os.path.dirname(oss_libdir.joined())) - run_env.set('OPENSS_RAWDATA_DIR', '.') + env.set('OPENSS_RAWDATA_DIR', '.') cbtf_mc = '/sbin/cbtf_mrnet_commnode' cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend' - run_env.set('XPLAT_RSH', 'ssh') - run_env.set('MRNET_COMM_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) - run_env.set('CBTF_MRNET_BACKEND_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) - run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) - run_env.prepend_path('PATH', self.spec['python'].prefix.bin) + env.set('XPLAT_RSH', 'ssh') + env.set('MRNET_COMM_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) + env.set('CBTF_MRNET_BACKEND_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) + env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) + env.prepend_path('PATH', self.spec['python'].prefix.bin) diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index 349ddee0526..c580be12298 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -92,8 +92,7 @@ class Openspeedshop(CMakePackage): depends_on("dyninst@develop", when='@develop') depends_on("dyninst@10:", when='@2.3.1.3:9999') - depends_on("python", when='@develop', type=('build', 'run')) - depends_on("python@2.7.14:2.7.99", when='@2.3.1.3:9999', type=('build', 'run')) + depends_on("python@2.7.14:2.7.99", type=('build', 'run')) depends_on("libxml2") @@ -278,7 +277,7 @@ def set_mpi_cmake_options(self, spec, cmake_options): cmake_options.extend(mpi_options) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" # Find Dyninst library path, this is needed to @@ -290,9 +289,9 @@ def setup_environment(self, spack_env, run_env): shared=True, recursive=True) # Set Dyninst RT library path to support OSS loop resolution code - run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) + env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) - run_env.set('OPENSS_RAWDATA_DIR', '.') + env.set('OPENSS_RAWDATA_DIR', '.') # Set the openspeedshop plugin path if os.path.isdir(self.prefix.lib64): @@ -301,13 +300,13 @@ def setup_environment(self, spack_env, run_env): lib_dir = self.prefix.lib plugin_path = '/openspeedshop' oss_plugin_path = lib_dir + plugin_path - run_env.set('OPENSS_PLUGIN_PATH', oss_plugin_path) + env.set('OPENSS_PLUGIN_PATH', oss_plugin_path) cbtf_mc = '/sbin/cbtf_mrnet_commnode' cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend' - run_env.set('XPLAT_RSH', 'ssh') - run_env.set('MRNET_COMM_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) + env.set('XPLAT_RSH', 'ssh') + env.set('MRNET_COMM_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation # This is needed by O|SS and CBTF tools to deploy the correct @@ -315,23 +314,25 @@ def setup_environment(self, spack_env, run_env): # Users may have to set the CBTF_MPI_IMPLEMENTATION variable # manually if multiple mpi's are specified in the build if self.spec.satisfies('+mpich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich") + env.set('CBTF_MPI_IMPLEMENTATION', "mpich") if self.spec.satisfies('+mvapich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") if self.spec.satisfies('+mvapich2'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") if self.spec.satisfies('+mpt'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt") + env.set('CBTF_MPI_IMPLEMENTATION', "mpt") if self.spec.satisfies('+openmpi'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") + env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") - run_env.set('CBTF_MRNET_BACKEND_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) - run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) - run_env.prepend_path('PATH', self.spec['python'].prefix.bin) + env.set('CBTF_MRNET_BACKEND_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) + env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) + mpath = '/share/man' + env.prepend_path('MANPATH', self.spec['cbtf-krell'].prefix + mpath) + env.prepend_path('PATH', self.spec['python'].prefix.bin) From 2264e30d99d8b9fbdec8fa69b594e53d8ced15a1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 28 Oct 2019 20:27:54 -0500 Subject: [PATCH 468/499] Update URL parsing regexes and tests (#13411) * Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta --- lib/spack/docs/getting_started.rst | 2 +- lib/spack/spack/cmd/url.py | 41 ++++-- lib/spack/spack/test/url_parse.py | 138 ++++++++++++++---- lib/spack/spack/url.py | 76 +++++++--- .../repos/builtin/packages/adios/package.py | 2 +- .../repos/builtin/packages/adios2/package.py | 4 +- .../repos/builtin/packages/adlbx/package.py | 10 +- .../repos/builtin/packages/alglib/package.py | 3 - .../builtin/packages/allpaths-lg/package.py | 2 +- .../repos/builtin/packages/amp/package.py | 2 +- .../repos/builtin/packages/aria2/package.py | 2 +- .../builtin/packages/arm-forge/package.py | 42 +++--- .../builtin/packages/armadillo/package.py | 2 +- .../repos/builtin/packages/asagi/package.py | 4 +- .../repos/builtin/packages/ascent/package.py | 26 ++-- .../builtin/packages/augustus/package.py | 8 +- .../builtin/packages/autofact/package.py | 10 +- .../repos/builtin/packages/axl/package.py | 2 +- .../builtin/packages/biopieces/package.py | 12 +- .../builtin/packages/breakdancer/package.py | 6 +- .../builtin/packages/bsseeker2/package.py | 2 +- .../packages/{cares => c-ares}/package.py | 2 +- .../builtin/packages/c-blosc2/package.py | 1 - .../packages/candle-benchmarks/package.py | 2 +- .../packages/{catch => catch2}/package.py | 7 +- .../repos/builtin/packages/cdo/package.py | 4 +- .../repos/builtin/packages/ceed/README.md | 3 - .../repos/builtin/packages/ceed/package.py | 13 +- .../builtin/packages/channelflow/package.py | 14 +- .../repos/builtin/packages/check/package.py | 4 +- .../{clustalo => clustal-omega}/package.py | 2 +- .../repos/builtin/packages/cmor/package.py | 4 +- .../repos/builtin/packages/cppzmq/package.py | 4 +- .../repos/builtin/packages/cquery/package.py | 6 +- .../repos/builtin/packages/cub/package.py | 2 +- .../repos/builtin/packages/czmq/package.py | 4 +- .../repos/builtin/packages/damaris/package.py | 6 +- .../repos/builtin/packages/davix/package.py | 2 +- .../repos/builtin/packages/dbcsr/package.py | 4 +- .../repos/builtin/packages/dealii/package.py | 10 +- .../repos/builtin/packages/dislin/package.py | 22 +-- .../packages/dotnet-core-sdk/package.py | 8 +- .../repos/builtin/packages/eccodes/package.py | 4 +- .../builtin/packages/ecp-viz-sdk/package.py | 2 +- .../{elmer-fem => elmerfem}/package.py | 6 +- .../builtin/packages/{eqr => eq-r}/package.py | 22 +-- .../repos/builtin/packages/er/package.py | 2 +- .../packages/{es => es-shell}/package.py | 3 +- .../repos/builtin/packages/esmf/package.py | 4 +- .../builtin/packages/exmcutils/package.py | 2 +- .../builtin/packages/exodusii/package.py | 6 +- .../builtin/packages/fastmath/package.py | 19 +-- .../builtin/packages/fastq-screen/package.py | 2 +- .../repos/builtin/packages/ferret/package.py | 4 +- .../repos/builtin/packages/flibcpp/package.py | 2 +- .../builtin/packages/flux-core/package.py | 17 ++- .../repos/builtin/packages/fpocket/package.py | 6 +- .../repos/builtin/packages/fstrack/package.py | 22 +-- .../repos/builtin/packages/funhpc/package.py | 2 +- .../repos/builtin/packages/gdal/package.py | 10 +- .../repos/builtin/packages/gdl/package.py | 2 +- .../repos/builtin/packages/ginkgo/package.py | 1 - .../repos/builtin/packages/gmsh/package.py | 2 +- .../repos/builtin/packages/gmt/package.py | 4 +- .../{gnu-prolog => gprolog}/package.py | 2 +- .../repos/builtin/packages/grass/package.py | 4 +- .../builtin/packages/grib-api/package.py | 4 +- .../repos/builtin/packages/grpc/package.py | 2 +- .../builtin/packages/guidance/package.py | 6 +- .../repos/builtin/packages/hc/package.py | 12 +- .../repos/builtin/packages/henson/package.py | 3 +- .../repos/builtin/packages/hisea/package.py | 1 - .../repos/builtin/packages/homer/package.py | 2 +- .../repos/builtin/packages/hpgmg/package.py | 2 +- .../repos/builtin/packages/hub/package.py | 4 +- .../repos/builtin/packages/ibmisc/package.py | 2 +- .../{image-magick => imagemagick}/package.py | 2 +- .../repos/builtin/packages/ioapi/package.py | 2 +- .../repos/builtin/packages/julia/package.py | 2 +- .../repos/builtin/packages/kvtree/package.py | 2 +- .../repos/builtin/packages/lammps/package.py | 2 +- .../builtin/packages/libcheck/package.py | 17 --- .../repos/builtin/packages/libgit2/package.py | 2 +- .../builtin/packages/libgpuarray/package.py | 2 +- .../repos/builtin/packages/libnrm/package.py | 2 +- .../packages/{zeromq => libzmq}/package.py | 2 +- .../repos/builtin/packages/likwid/package.py | 2 +- .../repos/builtin/packages/lsf/package.py | 1 - .../builtin/packages/lua-bitlib/package.py | 3 +- .../builtin/packages/lua-lpeg/package.py | 3 +- .../{lua-jit => lua-luajit}/package.py | 2 +- .../builtin/packages/lua-mpack/package.py | 3 +- .../repos/builtin/packages/macsio/package.py | 2 +- .../repos/builtin/packages/maker/package.py | 2 +- .../repos/builtin/packages/mariadb/package.py | 2 +- .../repos/builtin/packages/meme/package.py | 2 +- .../repos/builtin/packages/mfem/package.py | 6 +- .../repos/builtin/packages/moab/package.py | 6 +- .../{libmongoc => mongo-c-driver}/package.py | 2 +- .../packages/mongo-cxx-driver/package.py | 2 +- .../{mpibash => mpi-bash}/mpibash-4.3.patch | 0 .../packages/{mpibash => mpi-bash}/package.py | 2 +- .../repos/builtin/packages/mxnet/package.py | 5 +- .../repos/builtin/packages/nauty/package.py | 4 +- .../repos/builtin/packages/nccmp/package.py | 2 +- .../repos/builtin/packages/ncl/package.py | 12 +- .../repos/builtin/packages/nco/package.py | 14 +- .../repos/builtin/packages/ncview/package.py | 4 +- .../packages/{netcdf => netcdf-c}/package.py | 27 ++-- .../builtin/packages/netcdf-cxx/package.py | 4 +- .../builtin/packages/netcdf-cxx4/package.py | 8 +- .../packages/netcdf-fortran/package.py | 11 +- .../repos/builtin/packages/nrm/package.py | 2 +- .../repos/builtin/packages/ntpoly/package.py | 2 +- .../repos/builtin/packages/nut/package.py | 8 +- .../repos/builtin/packages/octave/package.py | 4 +- .../repos/builtin/packages/omega-h/package.py | 2 +- .../builtin/packages/openldap/package.py | 2 +- .../builtin/packages/openpmd-api/package.py | 25 ++-- .../repos/builtin/packages/pagit/package.py | 35 ++--- .../builtin/packages/paraview/package.py | 4 +- .../{parquet => parquet-cpp}/package.py | 2 +- .../packages/perl-alien-libxml2/package.py | 2 +- .../package.py | 5 +- .../{perl-dbfile => perl-db-file}/package.py | 2 +- .../packages/perl-devel-symdump/package.py | 2 +- .../packages/perl-file-chdir/package.py | 2 +- .../package.py | 4 +- .../package.py | 2 +- .../packages/perl-io-prompt/package.py | 2 +- .../builtin/packages/perl-io-tty/package.py | 2 +- .../packages/perl-libwww-perl/package.py | 1 + .../packages/perl-log-log4perl/package.py | 4 +- .../perl-lwp-protocol-https/package.py | 2 +- .../builtin/packages/perl-lwp/package.py | 26 ---- .../package.py | 2 +- .../package.py | 2 +- .../packages/perl-star-fusion/package.py | 4 +- .../package.py | 2 +- .../perl-xml-namespacesupport/package.py | 2 +- .../repos/builtin/packages/pism/package.py | 8 +- .../repos/builtin/packages/prank/package.py | 2 +- .../repos/builtin/packages/ps-lite/package.py | 2 +- .../py-avro-json-serializer/package.py | 4 +- .../builtin/packages/py-brian2/package.py | 2 +- .../builtin/packages/py-cdat-lite/package.py | 2 +- .../builtin/packages/py-cf-units/package.py | 2 +- .../builtin/packages/py-espressopp/package.py | 2 +- .../package.py | 2 +- .../builtin/packages/py-filelock/package.py | 21 ++- .../packages/{py-fn => py-fn-py}/package.py | 2 +- .../builtin/packages/py-fsspec/package.py | 4 +- .../builtin/packages/py-hpccm/package.py | 4 +- .../{py-jpype => py-jpype1}/package.py | 2 +- .../builtin/packages/py-jsonpatch/package.py | 4 +- .../packages/py-jsonpointer/package.py | 4 +- .../packages/py-jupyter-client/package.py | 2 +- .../builtin/packages/py-jupyterhub/package.py | 2 +- .../{py-lrudict => py-lru-dict}/package.py | 6 +- .../builtin/packages/py-macholib/package.py | 2 +- .../builtin/packages/py-matplotlib/package.py | 2 +- .../builtin/packages/py-methylcode/package.py | 10 +- .../builtin/packages/py-mongo/package.py | 20 --- .../package.py | 2 +- .../single-version.patch | 0 .../builtin/packages/py-netcdf4/package.py | 14 +- .../package.py | 2 +- .../builtin/packages/py-opentuner/package.py | 2 +- .../packages/py-performance/package.py | 2 +- .../builtin/packages/py-plotly/package.py | 4 +- .../{py-cpuinfo => py-py-cpuinfo}/package.py | 2 +- .../{py-git2 => py-pygit2}/package.py | 8 +- .../builtin/packages/py-pygpu/package.py | 2 +- .../repos/builtin/packages/py-pyke/package.py | 6 +- .../builtin/packages/py-pymongo/package.py | 2 + .../builtin/packages/py-pynio/package.py | 22 +-- .../{py-perf => py-pyperf}/package.py | 2 +- .../package.py | 2 +- .../{py-meep => py-python-meep}/package.py | 2 +- .../builtin/packages/py-pyyaml/package.py | 3 +- .../packages/{py-zmq => py-pyzmq}/package.py | 4 +- .../packages/py-requests-toolbelt/package.py | 6 +- .../builtin/packages/py-scoop/package.py | 2 +- .../packages/py-sphinxautomodapi/package.py | 4 +- .../builtin/packages/py-spyder/package.py | 2 +- .../builtin/packages/py-symengine/package.py | 6 +- .../builtin/packages/py-tables/package.py | 13 +- .../{py-tappy => py-tap-py}/package.py | 4 +- .../builtin/packages/py-udunits/package.py | 50 ------- .../repos/builtin/packages/py-wand/package.py | 2 +- .../packages/py-widgetsnbextension/package.py | 2 +- .../repos/builtin/packages/py-xdot/package.py | 34 ++--- .../builtin/packages/qt-creator/package.py | 6 +- .../builtin/packages/r-animation/package.py | 2 +- .../builtin/packages/r-checkpoint/package.py | 2 +- .../builtin/packages/r-magick/package.py | 2 +- .../repos/builtin/packages/r-mzr/package.py | 2 +- .../repos/builtin/packages/r-ncdf4/package.py | 2 +- .../repos/builtin/packages/r-nmf/package.py | 2 +- .../builtin/packages/r-pbdzmq/package.py | 2 +- .../builtin/packages/r-pkgmaker/package.py | 2 +- .../packages/r-randomfieldsutils/package.py | 2 +- .../builtin/packages/r-rngtools/package.py | 2 +- .../repos/builtin/packages/r-rzmq/package.py | 2 +- .../builtin/packages/r-udunits2/package.py | 2 +- .../repos/builtin/packages/r-units/package.py | 2 +- .../repos/builtin/packages/r-wgcna/package.py | 2 +- .../repos/builtin/packages/r-xlsx/package.py | 2 +- .../repos/builtin/packages/r3d/package.py | 8 +- .../repos/builtin/packages/rankstr/package.py | 2 +- .../repos/builtin/packages/redset/package.py | 2 +- .../repos/builtin/packages/regcm/package.py | 4 +- .../builtin/packages/repeatmodeler/package.py | 2 +- .../repos/builtin/packages/rose/package.py | 7 +- .../repos/builtin/packages/seacas/package.py | 8 +- .../builtin/packages/shuffile/package.py | 2 +- .../repos/builtin/packages/siesta/package.py | 4 +- .../builtin/packages/simulationio/package.py | 2 +- .../repos/builtin/packages/squid/package.py | 3 +- .../{sra-toolkit => sratoolkit}/package.py | 6 +- .../repos/builtin/packages/stc/package.py | 2 +- .../builtin/packages/subversion/package.py | 2 +- .../repos/builtin/packages/thrift/package.py | 8 +- .../builtin/packages/transabyss/package.py | 2 +- .../trilinos-catalyst-ioss-adapter/package.py | 11 +- .../builtin/packages/trilinos/package.py | 6 +- .../repos/builtin/packages/trinity/package.py | 12 +- .../repos/builtin/packages/turbine/package.py | 10 +- .../packages/{udunits2 => udunits}/package.py | 2 +- .../repos/builtin/packages/vmatch/package.py | 4 - .../packages/{vtkh => vtk-h}/package.py | 30 ++-- .../vtkm_lagrange_cuda_fix.patch | 0 .../packages/{vtkm => vtk-m}/package.py | 11 +- .../repos/builtin/packages/vtk/package.py | 10 +- .../repos/builtin/packages/warpx/package.py | 12 +- .../builtin/packages/wireshark/package.py | 2 +- .../repos/builtin/packages/xdmf3/package.py | 1 - .../repos/builtin/packages/xeus/package.py | 2 +- .../repos/builtin/packages/xios/package.py | 8 +- .../repos/builtin/packages/yambo/package.py | 12 +- 240 files changed, 773 insertions(+), 805 deletions(-) rename var/spack/repos/builtin/packages/{cares => c-ares}/package.py (96%) rename var/spack/repos/builtin/packages/{catch => catch2}/package.py (96%) delete mode 100644 var/spack/repos/builtin/packages/ceed/README.md rename var/spack/repos/builtin/packages/{clustalo => clustal-omega}/package.py (93%) rename var/spack/repos/builtin/packages/{elmer-fem => elmerfem}/package.py (95%) rename var/spack/repos/builtin/packages/{eqr => eq-r}/package.py (81%) rename var/spack/repos/builtin/packages/{es => es-shell}/package.py (96%) rename var/spack/repos/builtin/packages/{gnu-prolog => gprolog}/package.py (96%) rename var/spack/repos/builtin/packages/{image-magick => imagemagick}/package.py (97%) delete mode 100644 var/spack/repos/builtin/packages/libcheck/package.py rename var/spack/repos/builtin/packages/{zeromq => libzmq}/package.py (98%) rename var/spack/repos/builtin/packages/{lua-jit => lua-luajit}/package.py (96%) rename var/spack/repos/builtin/packages/{libmongoc => mongo-c-driver}/package.py (98%) rename var/spack/repos/builtin/packages/{mpibash => mpi-bash}/mpibash-4.3.patch (100%) rename var/spack/repos/builtin/packages/{mpibash => mpi-bash}/package.py (96%) rename var/spack/repos/builtin/packages/{netcdf => netcdf-c}/package.py (94%) rename var/spack/repos/builtin/packages/{parquet => parquet-cpp}/package.py (97%) rename var/spack/repos/builtin/packages/{perl-bio-perl => perl-bioperl}/package.py (96%) rename var/spack/repos/builtin/packages/{perl-dbfile => perl-db-file}/package.py (97%) rename var/spack/repos/builtin/packages/{perl-gd-graph => perl-gdgraph}/package.py (88%) rename var/spack/repos/builtin/packages/{perl-gd-text => perl-gdtextutil}/package.py (94%) delete mode 100644 var/spack/repos/builtin/packages/perl-lwp/package.py rename var/spack/repos/builtin/packages/{perl-version => perl-perl-version}/package.py (94%) rename var/spack/repos/builtin/packages/{perl-intervaltree => perl-set-intervaltree}/package.py (94%) rename var/spack/repos/builtin/packages/{perl-term-readkey => perl-termreadkey}/package.py (96%) rename var/spack/repos/builtin/packages/{py-exodus => py-exodus-bundler}/package.py (95%) rename var/spack/repos/builtin/packages/{py-fn => py-fn-py}/package.py (95%) rename var/spack/repos/builtin/packages/{py-jpype => py-jpype1}/package.py (96%) rename var/spack/repos/builtin/packages/{py-lrudict => py-lru-dict}/package.py (81%) delete mode 100644 var/spack/repos/builtin/packages/py-mongo/package.py rename var/spack/repos/builtin/packages/{py-mysql-connector => py-mysql-connector-python}/package.py (95%) rename var/spack/repos/builtin/packages/{py-mysql-connector => py-mysql-connector-python}/single-version.patch (100%) rename var/spack/repos/builtin/packages/{py-jupyter-notebook => py-notebook}/package.py (98%) rename var/spack/repos/builtin/packages/{py-cpuinfo => py-py-cpuinfo}/package.py (94%) rename var/spack/repos/builtin/packages/{py-git2 => py-pygit2}/package.py (81%) rename var/spack/repos/builtin/packages/{py-perf => py-pyperf}/package.py (95%) rename var/spack/repos/builtin/packages/{py-igraph => py-python-igraph}/package.py (94%) rename var/spack/repos/builtin/packages/{py-meep => py-python-meep}/package.py (98%) rename var/spack/repos/builtin/packages/{py-zmq => py-pyzmq}/package.py (93%) rename var/spack/repos/builtin/packages/{py-tappy => py-tap-py}/package.py (90%) delete mode 100644 var/spack/repos/builtin/packages/py-udunits/package.py rename var/spack/repos/builtin/packages/{sra-toolkit => sratoolkit}/package.py (83%) rename var/spack/repos/builtin/packages/{udunits2 => udunits}/package.py (95%) rename var/spack/repos/builtin/packages/{vtkh => vtk-h}/package.py (90%) rename var/spack/repos/builtin/packages/{vtkh => vtk-h}/vtkm_lagrange_cuda_fix.patch (100%) rename var/spack/repos/builtin/packages/{vtkm => vtk-m}/package.py (94%) diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst index b7ba386bb29..319d7f3c880 100644 --- a/lib/spack/docs/getting_started.rst +++ b/lib/spack/docs/getting_started.rst @@ -97,7 +97,7 @@ Check Installation With Spack installed, you should be able to run some basic Spack commands. For example: -.. command-output:: spack spec netcdf +.. command-output:: spack spec netcdf-c ^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/lib/spack/spack/cmd/url.py b/lib/spack/spack/cmd/url.py index a24fcc575c6..3101f28f08e 100644 --- a/lib/spack/spack/cmd/url.py +++ b/lib/spack/spack/cmd/url.py @@ -434,23 +434,10 @@ def name_parsed_correctly(pkg, name): Returns: bool: True if the name was correctly parsed, else False """ - pkg_name = pkg.name + pkg_name = remove_prefix(pkg.name) name = simplify_name(name) - # After determining a name, `spack create` determines a build system. - # Some build systems prepend a special string to the front of the name. - # Since this can't be guessed from the URL, it would be unfair to say - # that these names are incorrectly parsed, so we remove them. - if pkg_name.startswith('r-'): - pkg_name = pkg_name[2:] - elif pkg_name.startswith('py-'): - pkg_name = pkg_name[3:] - elif pkg_name.startswith('perl-'): - pkg_name = pkg_name[5:] - elif pkg_name.startswith('octave-'): - pkg_name = pkg_name[7:] - return name == pkg_name @@ -475,8 +462,32 @@ def version_parsed_correctly(pkg, version): return False +def remove_prefix(pkg_name): + """Remove build system prefix ('py-', 'perl-', etc.) from a package name. + + After determining a name, `spack create` determines a build system. + Some build systems prepend a special string to the front of the name. + Since this can't be guessed from the URL, it would be unfair to say + that these names are incorrectly parsed, so we remove them. + + Args: + pkg_name (str): the name of the package + + Returns: + str: the name of the package with any build system prefix removed + """ + prefixes = [ + 'r-', 'py-', 'tcl-', 'lua-', 'perl-', 'ruby-', 'llvm-', + 'intel-', 'votca-', 'octave-', 'gtkorvo-' + ] + + prefix = next((p for p in prefixes if pkg_name.startswith(p)), '') + + return pkg_name[len(prefix):] + + def remove_separators(version): - """Removes separator characters ('.', '_', and '-') from a version. + """Remove separator characters ('.', '_', and '-') from a version. A version like 1.2.3 may be displayed as 1_2_3 in the URL. Make sure 1.2.3, 1-2-3, 1_2_3, and 123 are considered equal. diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py index c557f78405e..7c292938d2a 100644 --- a/lib/spack/spack/test/url_parse.py +++ b/lib/spack/spack/test/url_parse.py @@ -60,6 +60,8 @@ ('cppad-20170114.gpl', 'cppad-20170114'), # Arch ('pcraster-4.1.0_x86-64', 'pcraster-4.1.0'), + ('dislin-11.0.linux.i586_64', 'dislin-11.0'), + ('PAGIT.V1.01.64bit', 'PAGIT.V1.01'), # OS - linux ('astyle_2.04_linux', 'astyle_2.04'), # OS - unix @@ -85,20 +87,31 @@ # Combinations of multiple patterns - darwin ('ghc-7.0.4-x86_64-apple-darwin', 'ghc-7.0.4'), ('ghc-7.0.4-i386-apple-darwin', 'ghc-7.0.4'), + # Combinations of multiple patterns - centos + ('sratoolkit.2.8.2-1-centos_linux64', 'sratoolkit.2.8.2-1'), # Combinations of multiple patterns - arch ('VizGlow_v2.2alpha17-R21November2016-Linux-x86_64-Install', 'VizGlow_v2.2alpha17-R21November2016'), ('jdk-8u92-linux-x64', 'jdk-8u92'), ('cuda_6.5.14_linux_64.run', 'cuda_6.5.14'), + ('Mathematica_12.0.0_LINUX.sh', 'Mathematica_12.0.0'), + ('trf407b.linux64', 'trf407b'), # Combinations of multiple patterns - with ('mafft-7.221-with-extensions-src', 'mafft-7.221'), ('spark-2.0.0-bin-without-hadoop', 'spark-2.0.0'), + ('conduit-v0.3.0-src-with-blt', 'conduit-v0.3.0'), + # Combinations of multiple patterns - rock + ('bitlib-23-2.src.rock', 'bitlib-23-2'), # Combinations of multiple patterns - public ('dakota-6.3-public.src', 'dakota-6.3'), # Combinations of multiple patterns - universal ('synergy-1.3.6p2-MacOSX-Universal', 'synergy-1.3.6p2'), # Combinations of multiple patterns - dynamic ('snptest_v2.5.2_linux_x86_64_dynamic', 'snptest_v2.5.2'), + # Combinations of multiple patterns - other + ('alglib-3.11.0.cpp.gpl', 'alglib-3.11.0'), + ('hpcviewer-2019.08-linux.gtk.x86_64', 'hpcviewer-2019.08'), + ('apache-mxnet-src-1.3.0-incubating', 'apache-mxnet-src-1.3.0'), ]) def test_url_strip_version_suffixes(url, expected): stripped = strip_version_suffixes(url) @@ -109,24 +122,40 @@ def test_url_strip_version_suffixes(url, expected): # No suffix ('rgb-1.0.6', '1.0.6', 'rgb'), ('nauty26r7', '26r7', 'nauty'), + ('PAGIT.V1.01', '1.01', 'PAGIT'), + ('AmpliconNoiseV1.29', '1.29', 'AmpliconNoise'), # Download type - install ('converge_install_2.3.16', '2.3.16', 'converge'), # Download type - src ('jpegsrc.v9b', '9b', 'jpeg'), + ('blatSrc35', '35', 'blat'), + # Download type - open + ('RepeatMasker-open-4-0-7', '4-0-7', 'RepeatMasker'), # Download type - archive ('coinhsl-archive-2014.01.17', '2014.01.17', 'coinhsl'), # Download type - std ('ghostscript-fonts-std-8.11', '8.11', 'ghostscript-fonts'), + # Download type - bin + ('GapCloser-bin-v1.12-r6', '1.12-r6', 'GapCloser'), + # Download type - software + ('orthomclSoftware-v2.0.9', '2.0.9', 'orthomcl'), # Download version - release ('cbench_release_1.3.0.tar.gz', '1.3.0', 'cbench'), # Download version - snapshot ('gts-snapshot-121130', '121130', 'gts'), # Download version - distrib ('zoltan_distrib_v3.83', '3.83', 'zoltan'), + # Download version - latest + ('Platypus-latest', 'N/A', 'Platypus'), + # Download version - complex + ('qt-everywhere-opensource-src-5.7.0', '5.7.0', 'qt'), + # Arch + ('VESTA-x86_64', '3.4.6', 'VESTA'), # VCS - bazaar ('libvterm-0+bzr681', '681', 'libvterm'), # License - gpl - ('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt-x11') + ('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt'), + ('PyQt4_gpl_x11-4.12.3', '4.12.3', 'PyQt4'), ]) def test_url_strip_name_suffixes(url, version, expected): stripped = strip_name_suffixes(url, version) @@ -182,6 +211,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): @pytest.mark.parametrize('name,version,url', [ # Common Repositories - github downloads + # name/archive/ver.ver ('nco', '4.6.2', 'https://github.com/nco/nco/archive/4.6.2.tar.gz'), # name/archive/vver.ver ('vim', '8.0.0134', 'https://github.com/vim/vim/archive/v8.0.0134.tar.gz'), @@ -257,6 +287,15 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # Common Tarball Formats + # 1st Pass: Simplest case + # Assume name contains no digits and version contains no letters + + # name-ver.ver + ('libpng', '1.6.37', 'http://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz'), + + # 2nd Pass: Version only + # Assume version contains no letters + # ver.ver ('eigen', '3.2.7', 'https://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2'), # ver.ver-ver @@ -266,10 +305,17 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # vver_ver ('luafilesystem', '1_6_3', 'https://github.com/keplerproject/luafilesystem/archive/v1_6_3.tar.gz'), - # No separators + # 3rd Pass: No separator characters are used + # Assume name contains no digits + + # namever ('turbolinux', '702', 'file://{0}/turbolinux702.tar.gz'.format(os.getcwd())), ('nauty', '26r7', 'http://pallini.di.uniroma1.it/nauty26r7.tar.gz'), - # Dashes only + + # 4th Pass: A single separator character is used + # Assume name contains no digits + + # name-name-ver-ver ('Trilinos', '12-10-1', 'https://github.com/trilinos/Trilinos/archive/trilinos-release-12-10-1.tar.gz'), ('panda', '2016-03-07', @@ -278,7 +324,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): 'http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz'), ('cdd', '061a', 'http://www.cs.mcgill.ca/~fukuda/download/cdd/cdd-061a.tar.gz'), - # Only underscores + # name_name_ver_ver ('tinyxml', '2_6_2', 'https://sourceforge.net/projects/tinyxml/files/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz'), ('boost', '1_55_0', @@ -287,9 +333,6 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): 'https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz'), ('tbb', '44_20160413', 'https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz'), - - # Only dots - # name.name.ver.ver ('prank', '150803', 'http://wasabiapp.org/download/prank/prank.source.150803.tgz'), ('jpeg', '9b', 'http://www.ijg.org/files/jpegsrc.v9b.tar.gz'), @@ -302,61 +345,51 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): ('geant', '4.10.01.p03', 'http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz'), ('tcl', '8.6.5', 'http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz'), - # Dash and dots + # 5th Pass: Two separator characters are used + # Name may contain digits, version may contain letters # name-name-ver.ver - # digit in name ('m4', '1.4.17', 'https://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz'), - # letter in version ('gmp', '6.0.0a', 'https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2'), - # version starts with 'v' ('LaunchMON', '1.0.2', 'https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz'), # name-ver-ver.ver ('libedit', '20150325-3.1', 'http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz'), - - # Dash and unserscores - # name-name-ver_ver ('icu4c', '57_1', 'http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz'), - - # Underscores and dots - # name_name_ver.ver ('superlu_dist', '4.1', 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz'), ('pexsi', '0.9.0', 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz'), # name_name.ver.ver ('fer', '696', 'ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.v696.tar.gz'), - - # Dash dot dah dot - + # name_name_ver-ver + ('Bridger', '2014-12-01', + 'https://downloads.sourceforge.net/project/rnaseqassembly/Bridger_r2014-12-01.tar.gz'), # name-name-ver.ver-ver.ver ('sowing', '1.1.23-p1', 'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz'), ('bib2xhtml', '3.0-15-gf506', 'http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'), # namever.ver-ver.ver ('go', '1.4-bootstrap-20161024', 'https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz'), - # Underscore dash dot + # 6th Pass: All three separator characters are used + # Name may contain digits, version may contain letters # name_name-ver.ver ('the_silver_searcher', '0.32.0', 'http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz'), ('sphinx_rtd_theme', '0.1.10a0', 'https://pypi.python.org/packages/source/s/sphinx_rtd_theme/sphinx_rtd_theme-0.1.10a0.tar.gz'), - - # Dot underscore dot dash dot - # name.name_ver.ver-ver.ver ('TH.data', '1.0-8', 'https://cran.r-project.org/src/contrib/TH.data_1.0-8.tar.gz'), ('XML', '3.98-1.4', 'https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz'), - - # Dash dot underscore dot - # name-name-ver.ver_ver.ver ('pypar', '2.1.5_108', 'https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pypar/pypar-2.1.5_108.tgz'), # name-namever.ver_ver.ver ('STAR-CCM+', '11.06.010_02', 'file://{0}/STAR-CCM+11.06.010_02_linux-x86_64.tar.gz'.format(os.getcwd())), + # name-name_name-ver.ver + ('PerlIO-utf8_strict', '0.002', + 'http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/PerlIO-utf8_strict-0.002.tar.gz'), # Various extensions # .tar.gz @@ -399,18 +432,61 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # .txz ('kim-api', '2.1.0', 'https://s3.openkim.org/kim-api/kim-api-2.1.0.txz'), - # Weird URLS + # 8th Pass: Query strings - # github.com/repo/name/releases/download/name-vver/name - ('nextflow', '0.20.1', 'https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow'), # suffix queries ('swiftsim', '0.3.0', 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'), - ('swiftsim', '0.3.0', 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'), + ('swiftsim', '0.3.0', + 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'), ('sionlib', '1.7.1', 'http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1'), + ('jube2', '2.2.2', 'https://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=2.2.2'), + ('archive', '1.0.0', 'https://code.ornl.gov/eck/papyrus/repository/archive.tar.bz2?ref=v1.0.0'), + ('VecGeom', '0.3.rc', + 'https://gitlab.cern.ch/api/v4/projects/VecGeom%2FVecGeom/repository/archive.tar.gz?sha=v0.3.rc'), + ('parsplice', '1.1', + 'https://gitlab.com/api/v4/projects/exaalt%2Fparsplice/repository/archive.tar.gz?sha=v1.1'), + ('busco', '2.0.1', 'https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1'), + ('libaec', '1.0.2', + 'https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2'), + ('icet', '2.1.1', + 'https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-2.1.1'), + ('vtk-m', '1.3.0', + 'https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.3.0'), + ('GATK', '3.8-1-0-gf15c1c3ef', + 'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef'), # stem queries ('slepc', '3.6.2', 'http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz'), ('otf', '1.12.5salmon', 'http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz'), + ('eospac', '6.4.0beta.1', + 'http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz'), + ('vampirtrace', '5.14.4', + 'http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz'), + # (we don't actually look for these, they are picked up + # during the preliminary stem parsing) + ('octopus', '6.0', 'http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz'), + ('cloog', '0.18.1', 'http://www.bastoul.net/cloog/pages/download/count.php3?url=./cloog-0.18.1.tar.gz'), + ('libxc', '2.2.2', 'http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz'), + ('cistem', '1.0.0-beta', + 'https://cistem.org/system/tdf/upload3/cistem-1.0.0-beta-source-code.tar.gz?file=1&type=cistem_details&id=37&force=0'), + ('Magics', '4.1.0', + 'https://confluence.ecmwf.int/download/attachments/3473464/Magics-4.1.0-Source.tar.gz?api=v2'), + ('grib_api', '1.17.0', + 'https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2'), + ('eccodes', '2.2.0', + 'https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.2.0-Source.tar.gz?api=v2'), + ('SWFFT', '1.0', + 'https://xgitlab.cels.anl.gov/api/v4/projects/hacc%2FSWFFT/repository/archive.tar.gz?sha=v1.0'), + + # 9th Pass: Version in path + + # github.com/repo/name/releases/download/name-vver/name + ('nextflow', '0.20.1', 'https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow'), + # ver/name + ('ncbi', '2.2.26', 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz'), + + # Other tests for corner cases + # single character name ('R', '3.3.2', 'https://cloud.r-project.org/src/base/R-3/R-3.3.2.tar.gz'), # name starts with digit diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py index 11b289a0b1f..a298d44ea24 100644 --- a/lib/spack/spack/url.py +++ b/lib/spack/spack/url.py @@ -153,13 +153,14 @@ def strip_version_suffixes(path): r'[Ii]nstall', r'all', r'code', - r'src(_0)?', r'[Ss]ources?', r'file', r'full', r'single', - r'public', r'with[a-zA-Z_-]+', + r'rock', + r'src(_0)?', + r'public', r'bin', r'binary', r'run', @@ -189,15 +190,24 @@ def strip_version_suffixes(path): r'ia32', r'intel', r'amd64', + r'linux64', r'x64', + r'64bit', r'x86[_-]64', + r'i586_64', r'x86', r'i[36]86', r'ppc64(le)?', r'armv?(7l|6l|64)', + # Other + r'cpp', + r'gtk', + r'incubating', + # OS r'[Ll]inux(_64)?', + r'LINUX', r'[Uu]ni?x', r'[Ss]un[Oo][Ss]', r'[Mm]ac[Oo][Ss][Xx]?', @@ -208,14 +218,18 @@ def strip_version_suffixes(path): r'[Ww]in(64|32)?', r'[Cc]ygwin(64|32)?', r'[Mm]ingw', + r'centos', # Arch # Needs to come before and after OS, appears in both orders r'ia32', r'intel', r'amd64', + r'linux64', r'x64', + r'64bit', r'x86[_-]64', + r'i586_64', r'x86', r'i[36]86', r'ppc64(le)?', @@ -270,31 +284,41 @@ def strip_name_suffixes(path, version): # name-ver # name_ver # name.ver - r'[._-]v?' + str(version) + '.*', + r'[._-][rvV]?' + str(version) + '.*', # namever - str(version) + '.*', + r'V?' + str(version) + '.*', # Download type r'install', - r'src', + r'[Ss]rc', r'(open)?[Ss]ources?', + r'[._-]open', r'[._-]archive', r'[._-]std', + r'[._-]bin', + r'Software', # Download version r'release', r'snapshot', r'distrib', + r'everywhere', + r'latest', # Arch - r'Linux64', + r'Linux(64)?', + r'x86_64', # VCS r'0\+bzr', # License r'gpl', + + # Needs to come before and after gpl, appears in both orders + r'[._-]x11', + r'gpl', ] for regex in suffix_regexes: @@ -407,7 +431,7 @@ def parse_version_offset(path): # 3. names can contain A-Z, a-z, 0-9, '+', separators # 4. versions can contain A-Z, a-z, 0-9, separators # 5. versions always start with a digit - # 6. versions are often prefixed by a 'v' character + # 6. versions are often prefixed by a 'v' or 'r' character # 7. separators are most reliable to determine name/version boundaries # List of the following format: @@ -450,7 +474,7 @@ def parse_version_offset(path): (r'^[a-zA-Z+-]*(\d[\da-zA-Z-]*)$', stem), # name_name_ver_ver - # e.g. tinyxml_2_6_2, boost_1_55_0, tbb2017_20161128, v1_6_3 + # e.g. tinyxml_2_6_2, boost_1_55_0, tbb2017_20161128 (r'^[a-zA-Z+_]*(\d[\da-zA-Z_]*)$', stem), # name.name.ver.ver @@ -476,6 +500,10 @@ def parse_version_offset(path): # e.g. fer_source.v696 (r'^[a-zA-Z\d+_]+\.v?(\d[\da-zA-Z.]*)$', stem), + # name_ver-ver + # e.g. Bridger_r2014-12-01 + (r'^[a-zA-Z\d+]+_r?(\d[\da-zA-Z-]*)$', stem), + # name-name-ver.ver-ver.ver # e.g. sowing-1.1.23-p1, bib2xhtml-v3.0-15-gf506, 4.6.3-alpha04 (r'^(?:[a-zA-Z\d+-]+-)?v?(\d[\da-zA-Z.-]*)$', stem), @@ -507,19 +535,17 @@ def parse_version_offset(path): # e.g. STAR-CCM+11.06.010_02 (r'^[a-zA-Z+-]+(\d[\da-zA-Z._]*)$', stem), + # name-name_name-ver.ver + # e.g. PerlIO-utf8_strict-0.002 + (r'^[a-zA-Z\d+_-]+-v?(\d[\da-zA-Z.]*)$', stem), + # 7th Pass: Specific VCS # bazaar # e.g. libvterm-0+bzr681 (r'bzr(\d[\da-zA-Z._-]*)$', stem), - # 8th Pass: Version in path - - # github.com/repo/name/releases/download/vver/name - # e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow - (r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path), # noqa - - # 9th Pass: Query strings + # 8th Pass: Query strings # e.g. https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0 (r'\?sha=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix), @@ -528,13 +554,24 @@ def parse_version_offset(path): (r'\?ref=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix), # e.g. http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1 - (r'\?version=v?(\d[\da-zA-Z._-]*)$', suffix), + # e.g. https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef + (r'[?&]version=v?(\d[\da-zA-Z._-]*)$', suffix), # e.g. http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz - (r'\?filename=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), + # e.g. http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz + (r'[?&]filename=[a-zA-Z\d+-]+[_-]v?(\d[\da-zA-Z.]*)', stem), # e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz - (r'\?package=[a-zA-Z\d+-]+&get=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), # noqa + (r'&get=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), # noqa + + # 9th Pass: Version in path + + # github.com/repo/name/releases/download/vver/name + # e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow + (r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path), # noqa + + # e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz + (r'(\d[\da-zA-Z._-]*)/[^/]+$', path), ] for i, version_regex in enumerate(version_regexes): @@ -662,6 +699,9 @@ def parse_name_offset(path, v=None): # e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz (r'\?package=([A-Za-z\d+-]+)', stem), + # ?package=name-version + (r'\?package=([A-Za-z\d]+)', suffix), + # download.php # e.g. http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1 (r'([^/]+)/download.php$', path), diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index 4b8e417a11b..939ec797ab8 100644 --- a/var/spack/repos/builtin/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -84,7 +84,7 @@ class Adios(AutotoolsPackage): depends_on('c-blosc@1.12.0:', when='+blosc') # optional transports & file converters depends_on('hdf5@1.8:+hl+mpi', when='+hdf5') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('libevpath', when='staging=flexpath') depends_on('dataspaces+mpi', when='staging=dataspaces') diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index e5e10db9966..29adcddaae3 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -85,8 +85,8 @@ class Adios2(CMakePackage): # depends_on('flex', when='+sst') # optional in FFS, depends on BISON depends_on('mpi', when='+mpi') - depends_on('zeromq', when='+dataman') - depends_on('zeromq', when='@2.4: +ssc') + depends_on('libzmq', when='+dataman') + depends_on('libzmq', when='@2.4: +ssc') depends_on('dataspaces@1.8.0:', when='+dataspaces') depends_on('hdf5', when='+hdf5') diff --git a/var/spack/repos/builtin/packages/adlbx/package.py b/var/spack/repos/builtin/packages/adlbx/package.py index e4e7c178f9c..096a2cedd9a 100644 --- a/var/spack/repos/builtin/packages/adlbx/package.py +++ b/var/spack/repos/builtin/packages/adlbx/package.py @@ -11,7 +11,7 @@ class Adlbx(AutotoolsPackage): """ADLB/X: Master-worker library + work stealing and data dependencies""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.9.2.tar.gz' git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') @@ -27,11 +27,11 @@ class Adlbx(AutotoolsPackage): depends_on('m4', type='build', when='@master') depends_on('mpi') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('CXXLD', spec['mpi'].mpicxx) + env.set('CC', spec['mpi'].mpicc) + env.set('CXX', spec['mpi'].mpicxx) + env.set('CXXLD', spec['mpi'].mpicxx) @property def configure_directory(self): diff --git a/var/spack/repos/builtin/packages/alglib/package.py b/var/spack/repos/builtin/packages/alglib/package.py index 30a1c0b2c40..1f01fcc3f59 100644 --- a/var/spack/repos/builtin/packages/alglib/package.py +++ b/var/spack/repos/builtin/packages/alglib/package.py @@ -18,9 +18,6 @@ class Alglib(MakefilePackage): version('3.11.0', sha256='34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0') - def url_for_version(self, version): - return 'http://www.alglib.net/translator/re/alglib-{0}.cpp.gpl.tgz'.format(version.dotted) - build_directory = 'src' def edit(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/allpaths-lg/package.py b/var/spack/repos/builtin/packages/allpaths-lg/package.py index c8d580d08e6..dc2099948dc 100644 --- a/var/spack/repos/builtin/packages/allpaths-lg/package.py +++ b/var/spack/repos/builtin/packages/allpaths-lg/package.py @@ -11,7 +11,7 @@ class AllpathsLg(AutotoolsPackage): small and large (mammalian size) genomes.""" homepage = "http://www.broadinstitute.org/software/allpaths-lg/blog/" - url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz" + url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-52488.tar.gz" version('52488', sha256='035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542') diff --git a/var/spack/repos/builtin/packages/amp/package.py b/var/spack/repos/builtin/packages/amp/package.py index 5410db48492..27bc465ffda 100644 --- a/var/spack/repos/builtin/packages/amp/package.py +++ b/var/spack/repos/builtin/packages/amp/package.py @@ -110,7 +110,7 @@ def cmake_args(self): if '+netcdf' in spec: tpl_list = tpl_list + ";NETCDF" options.extend(['-DTPL_NETCDF_INSTALL_DIR=%s' % - spec['netcdf'].prefix, ]) + spec['netcdf-c'].prefix, ]) if '+hypre' in spec: tpl_list = tpl_list + ";HYPRE" options.extend(['-DTPL_HYPRE_INSTALL_DIR=%s' % diff --git a/var/spack/repos/builtin/packages/aria2/package.py b/var/spack/repos/builtin/packages/aria2/package.py index 7cb7e3cfae8..7518d3b488f 100644 --- a/var/spack/repos/builtin/packages/aria2/package.py +++ b/var/spack/repos/builtin/packages/aria2/package.py @@ -19,5 +19,5 @@ class Aria2(AutotoolsPackage): depends_on('libssh2') depends_on('libgcrypt') depends_on('zlib') - depends_on('cares') + depends_on('c-ares') depends_on('sqlite') diff --git a/var/spack/repos/builtin/packages/arm-forge/package.py b/var/spack/repos/builtin/packages/arm-forge/package.py index 94f853fef62..2434222796b 100644 --- a/var/spack/repos/builtin/packages/arm-forge/package.py +++ b/var/spack/repos/builtin/packages/arm-forge/package.py @@ -19,107 +19,107 @@ class ArmForge(Package): # versions (and checksums) based on the target platform shows up version( - "19.0.4-linux-rhel6-x86_64", + "19.0.4-Redhat-6.0-x86_64", sha256="0b0b6ed5c3d6833bad46d5ea84346cd46f0e4b3020c31f2fd4318b75ddaf01aa", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-6.0-x86_64.tar", ) version( - "19.0.4-linux-rhel7-x86_64", + "19.0.4-Redhat-7.0-x86_64", sha256="de3c669f7cb4daf274aae603294c416a953fb558e101eb03bcccf0ef4291e079", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.0-x86_64.tar", ) version( - "19.0.4-linux-sles11-x86_64", + "19.0.4-Suse-11-x86_64", sha256="24a2c7761c2163f128e4f4b60e963c53774196809ddfa880131c5dde5eb454c2", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-11-x86_64.tar", ) version( - "19.0.4-linux-sles12-x86_64", + "19.0.4-Suse-12-x86_64", sha256="6688192291fe9696922a34371d07ea66f89bff9b976fd99796e5f9a6651f86e6", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-12-x86_64.tar", ) version( - "19.0.4-linux-sles15-x86_64", + "19.0.4-Suse-15-x86_64", sha256="dea60d93a157ab6952fd6887f40123ab9d633d5589ffe7824d53fb269294cf35", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-15-x86_64.tar", ) version( - "19.0.4-linux-ubuntu16.04-x86_64", + "19.0.4-19.0.4-Ubuntu-16.04-x86_64", sha256="240741beff96f6a0b3976bc98d90863fe475366d5c093af9b96b877a230d479c", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-16.04-x86_64.tar", ) version( - "19.0.4-linux-ubuntu14.04-x86_64", + "19.0.4-Ubuntu-14.04-x86_64", sha256="135903906111b61045ddd3e98f1d8e8fd02b5b6ef554a68dfbe6760c76ec65a2", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-14.04-x86_64.tar", ) version( - "19.0.4-linux-rhel7-ppc64le", + "19.0.4-Redhat-7.2-ppc64le", sha256="73cb9f4005278e8dd2106a871dcbb53edb8855faeeda75c7abd7936f85fcce56", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.2-ppc64le.tar", ) version( - "19.0.4-linux-rhel7-aarch64", + "19.0.4-Redhat-7.4-aarch64", sha256="8d168e5665a158f65b72d7b996fd283f7f538efbff15648eff44cfb7371ecad7", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.4-aarch64.tar", ) version( - "19.0.4-linux-sles12-aarch64", + "19.0.4-Suse-12-aarch64", sha256="de3aa62c5b5d5181a7947dcd1dfa66df5d06fd482394044100147210c8182d75", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-12-aarch64.tar", ) version( - "19.0.4-linux-ubuntu16.04-aarch64", + "19.0.4-Ubuntu-16.04-aarch64", sha256="3910e320c635dd5c09af7f5696909c7c0ae25406910d2e592e522ed0233e0451", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-16.04-aarch64.tar", ) version( - "19.0.3-linux-rhel6-x86_64", + "19.0.3-Redhat-6.0-x86_64", sha256="0ace88a1847d8f622f077cd38fa9dddf7f2d6dd6aad086be0e0a66e10fb8b64b", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-6.0-x86_64.tar", ) version( - "19.0.3-linux-rhel7-x86_64", + "19.0.3-Redhat-7.0-x86_64", sha256="35c7a9532aa19251343c37b8f5eb51ef04f7b6e8b42bea2bd932f4d83a1e8375", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.0-x86_64.tar", ) version( - "19.0.3-linux-sles11-x86_64", + "19.0.3-Suse-11-x86_64", sha256="48fe2b1b81a824909fedf5e02cd08d8a62033cce80440eca6efbea0ae8023e75", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-11-x86_64.tar", ) version( - "19.0.3-linux-sles12-x86_64", + "19.0.3-Suse-12-x86_64", sha256="b4d0f91780dc43544ea946f5117a50ba18750fd50ef811cae5b6b6771b4ebb77", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-12-x86_64.tar", ) version( - "19.0.3-linux-ubuntu16.04-x86_64", + "19.0.3-Ubuntu-16.04-x86_64", sha256="ed6726434a6d24d413ed6183756433d63438936dc671cb6a3567b407c8e233e1", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-16.04-x86_64.tar", ) version( - "19.0.3-linux-ubuntu14.04-x86_64", + "19.0.3-Ubuntu-14.04-x86_64", sha256="22350d068c4ef60d1aad330636d443f00269c0cc49bed4c05b80f93b9d9a9c66", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-14.04-x86_64.tar", ) version( - "19.0.3-linux-rhel7-ppc64le", + "19.0.3-Redhat-7.2-ppc64le", sha256="dc6ea53eead78f0d9ffd8fa74ffddb80e8bd3b4ab8a1edd6f8505ffbea9cea15", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.2-ppc64le.tar", ) version( - "19.0.3-linux-rhel7-aarch64", + "19.0.3-Redhat-7.4-aarch64", sha256="4e19d4200e2936d542bf2b9dc79c7f8b00ccfb37b9191dfc90ac0787680a8b0c", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.4-aarch64.tar", ) version( - "19.0.3-linux-sles12-aarch64", + "19.0.3-Suse-12-aarch64", sha256="9b27b678d0228b4e51fd517ef0acd1df65b780a3a0b226caa6b6f1b7dccf31e6", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-12-aarch64.tar", ) version( - "19.0.3-linux-ubuntu16.04-aarch64", + "19.0.3-Ubuntu-16.04-aarch64", sha256="4470f7067d4a4e0369df8af28b6ca95f58fa0062bf8dffc49f0b7415112c0332", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-16.04-aarch64.tar", ) diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index de4c92c3852..dd2576bb552 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -12,7 +12,7 @@ class Armadillo(CMakePackage): ease of use.""" homepage = "http://arma.sourceforge.net/" - url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" + url = "http://sourceforge.net/projects/arma/files/armadillo-8.100.1.tar.xz" version('8.100.1', sha256='54773f7d828bd3885c598f90122b530ded65d9b195c9034e082baea737cd138d') version('7.950.1', sha256='a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b') diff --git a/var/spack/repos/builtin/packages/asagi/package.py b/var/spack/repos/builtin/packages/asagi/package.py index f24c83a68da..f99bad2f7e2 100644 --- a/var/spack/repos/builtin/packages/asagi/package.py +++ b/var/spack/repos/builtin/packages/asagi/package.py @@ -46,8 +46,8 @@ class Asagi(CMakePackage): depends_on('mpi', when="+mpi") depends_on('mpi@3:', when="+mpi3") - depends_on('netcdf +mpi', when="+mpi") - depends_on('netcdf ~mpi', when="~mpi") + depends_on('netcdf-c +mpi', when="+mpi") + depends_on('netcdf-c ~mpi', when="~mpi") depends_on('numactl', when="+numa") conflicts('%gcc@5:', when='@:1.0.0') diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py index 8d8210edd12..4e31fa051eb 100644 --- a/var/spack/repos/builtin/packages/ascent/package.py +++ b/var/spack/repos/builtin/packages/ascent/package.py @@ -96,15 +96,17 @@ class Ascent(Package): # TPLs for Runtime Features ############################# - depends_on("vtkh@develop", when="+vtkh") - depends_on("vtkh@develop~openmp", when="+vtkh~openmp") - depends_on("vtkh@develop+cuda+openmp", when="+vtkh+cuda+openmp") - depends_on("vtkh@develop+cuda~openmp", when="+vtkh+cuda~openmp") + depends_on("vtk-m", when="+vtkh") - depends_on("vtkh@develop~shared", when="~shared+vtkh") - depends_on("vtkh@develop~shared~openmp", when="~shared+vtkh~openmp") - depends_on("vtkh@develop~shared+cuda", when="~shared+vtkh+cuda") - depends_on("vtkh@develop~shared+cuda~openmp", when="~shared+vtkh+cuda~openmp") + depends_on("vtk-h@develop", when="+vtkh") + depends_on("vtk-h@develop~openmp", when="+vtkh~openmp") + depends_on("vtk-h@develop+cuda+openmp", when="+vtkh+cuda+openmp") + depends_on("vtk-h@develop+cuda~openmp", when="+vtkh+cuda~openmp") + + depends_on("vtk-h@develop~shared", when="~shared+vtkh") + depends_on("vtk-h@develop~shared~openmp", when="~shared+vtkh~openmp") + depends_on("vtk-h@develop~shared+cuda", when="~shared+vtkh+cuda") + depends_on("vtk-h@develop~shared+cuda~openmp", when="~shared+vtkh+cuda~openmp") # mfem depends_on("mfem+shared+mpi+conduit", when="+shared+mfem+mpi") @@ -178,8 +180,8 @@ def check_install(self): create=True): cmake_args = ["-DASCENT_DIR={0}".format(install_prefix), "-DCONDUIT_DIR={0}".format(spec['conduit'].prefix), - "-DVTKM_DIR={0}".format(spec['vtkm'].prefix), - "-DVTKH_DIR={0}".format(spec['vtkh'].prefix), + "-DVTKM_DIR={0}".format(spec['vtk-m'].prefix), + "-DVTKH_DIR={0}".format(spec['vtk-h'].prefix), example_src_dir] cmake(*cmake_args) make() @@ -405,10 +407,10 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): if "+vtkh" in spec: cfg.write("# vtk-m from spack\n") - cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtkm'].prefix)) + cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtk-m'].prefix)) cfg.write("# vtk-h from spack\n") - cfg.write(cmake_cache_entry("VTKH_DIR", spec['vtkh'].prefix)) + cfg.write(cmake_cache_entry("VTKH_DIR", spec['vtk-h'].prefix)) else: cfg.write("# vtk-h not built by spack \n") diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index 18b30d29d40..c909ce102ae 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -16,7 +16,7 @@ class Augustus(MakefilePackage): # Releases have moved to github version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2') - version('3.3.1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab', + version('3.3.1-tag1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab', url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz') version('3.3', sha256='b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee', url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz') @@ -98,7 +98,7 @@ def filter_sbang(self): for file in files: filter_file(pattern, repl, *files, backup=False) - def setup_environment(self, spack_env, run_env): - run_env.set('AUGUSTUS_CONFIG_PATH', join_path( + def setup_run_environment(self, env): + env.set('AUGUSTUS_CONFIG_PATH', join_path( self.prefix, 'config')) - run_env.prepend_path('PATH', join_path(self.prefix, 'scripts')) + env.prepend_path('PATH', join_path(self.prefix, 'scripts')) diff --git a/var/spack/repos/builtin/packages/autofact/package.py b/var/spack/repos/builtin/packages/autofact/package.py index a22af26671e..44bb89bff18 100644 --- a/var/spack/repos/builtin/packages/autofact/package.py +++ b/var/spack/repos/builtin/packages/autofact/package.py @@ -16,9 +16,9 @@ class Autofact(Package): version('3_4', sha256='1465d263b19adb42f01f6e636ac40ef1c2e3dbd63461f977b89da9493fe9c6f4') depends_on('perl', type='run') - depends_on('perl-bio-perl', type='run') + depends_on('perl-bioperl', type='run') depends_on('perl-io-string', type='run') - depends_on('perl-lwp', type='run') + depends_on('perl-libwww-perl', type='run') depends_on('blast-legacy', type='run') def patch(self): @@ -31,6 +31,6 @@ def patch(self): def install(self, spec, prefix): install_tree(self.stage.source_path, prefix) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix.scripts) - run_env.set('PATH2AUTOFACT', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix.scripts) + env.set('PATH2AUTOFACT', self.prefix) diff --git a/var/spack/repos/builtin/packages/axl/package.py b/var/spack/repos/builtin/packages/axl/package.py index a524ca06430..85b5e0873da 100644 --- a/var/spack/repos/builtin/packages/axl/package.py +++ b/var/spack/repos/builtin/packages/axl/package.py @@ -20,7 +20,7 @@ class Axl(CMakePackage): """Asynchronous transfer library""" homepage = "https://github.com/ECP-VeloC/AXL" - url = "https://github.com/ECP-VeloC/AXL/archive/v0.1.0.zip" + url = "https://github.com/ECP-VeloC/AXL/archive/v0.1.1.zip" git = "https://github.com/ecp-veloc/axl.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/biopieces/package.py b/var/spack/repos/builtin/packages/biopieces/package.py index 2091f8508f9..888ef18ccb0 100644 --- a/var/spack/repos/builtin/packages/biopieces/package.py +++ b/var/spack/repos/builtin/packages/biopieces/package.py @@ -21,21 +21,21 @@ class Biopieces(Package): depends_on('perl-module-build', type=('build', 'run')) depends_on('perl-bit-vector', type=('build', 'run')) depends_on('perl-svg', type=('build', 'run')) - depends_on('perl-term-readkey', type=('build', 'run')) + depends_on('perl-termreadkey', type=('build', 'run')) depends_on('perl-time-hires', type=('build', 'run')) depends_on('perl-dbi', type=('build', 'run')) depends_on('perl-xml-parser', type=('build', 'run')) depends_on('perl-carp-clan', type=('build', 'run')) depends_on('perl-class-inspector', type=('build', 'run')) depends_on('perl-html-parser', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) depends_on('perl-soap-lite', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) depends_on('perl-inline', type=('build', 'run')) depends_on('perl-inline-c', type=('build', 'run')) depends_on('perl-parse-recdescent', type=('build', 'run')) - depends_on('perl-version', type=('build', 'run')) - depends_on('perl-dbfile', type=('build', 'run')) + depends_on('perl-perl-version', type=('build', 'run')) + depends_on('perl-db-file', type=('build', 'run')) depends_on('perl-dbd-mysql', type=('build', 'run')) depends_on('ruby@1.9:') @@ -61,10 +61,10 @@ class Biopieces(Package): def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # Note: user will need to set environment variables on their own, # dependent on where they will want data to be located: # BP_DATA - Contains genomic data etc. # BP_TMP - Required temporary directory # BP_LOG - Required log directory - run_env.prepend_path('BP_DIR', prefix) + env.prepend_path('BP_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py index 3ad2cdfc01a..c943e885021 100644 --- a/var/spack/repos/builtin/packages/breakdancer/package.py +++ b/var/spack/repos/builtin/packages/breakdancer/package.py @@ -32,7 +32,7 @@ class Breakdancer(CMakePackage): depends_on('perl-statistics-descriptive', type='run') depends_on('perl-math-cdf', type='run') - depends_on('perl-gd-graph', type='run') + depends_on('perl-gdgraph', type='run') depends_on('perl-gdgraph-histogram', type='run') depends_on('perl-list-moreutils', type='run') depends_on('perl-exporter-tiny', type='run') @@ -41,9 +41,9 @@ class Breakdancer(CMakePackage): parallel = False - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # get the perl tools in the path - run_env.prepend_path('PATH', self.prefix.lib) + env.prepend_path('PATH', self.prefix.lib) def edit(self, spec, prefix): # perl tools end up in a silly lib subdirectory, fixing that diff --git a/var/spack/repos/builtin/packages/bsseeker2/package.py b/var/spack/repos/builtin/packages/bsseeker2/package.py index 73fd8ca24bb..5b782942505 100644 --- a/var/spack/repos/builtin/packages/bsseeker2/package.py +++ b/var/spack/repos/builtin/packages/bsseeker2/package.py @@ -13,7 +13,7 @@ class Bsseeker2(Package): url = "https://github.com/BSSeeker/BSseeker2/archive/BSseeker2-v2.1.8.tar.gz" version('2.1.8', sha256='34ebedce36a0fca9e22405d4c2c20bc978439d4a34d1d543657fbc53ff847934') - version('2.1.5', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a', + version('2.1.7', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a', url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.7.tar.gz') version('2.1.2', sha256='08055dd314f85a9b74c259c2cb894ea2affdab2c7a120af3589c649e1900c5c6', url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz') diff --git a/var/spack/repos/builtin/packages/cares/package.py b/var/spack/repos/builtin/packages/c-ares/package.py similarity index 96% rename from var/spack/repos/builtin/packages/cares/package.py rename to var/spack/repos/builtin/packages/c-ares/package.py index f3b35ee6103..2311e4ac91b 100644 --- a/var/spack/repos/builtin/packages/cares/package.py +++ b/var/spack/repos/builtin/packages/c-ares/package.py @@ -6,7 +6,7 @@ from spack import * -class Cares(CMakePackage): +class CAres(CMakePackage): """c-ares: A C library for asynchronous DNS requests""" homepage = "https://c-ares.haxx.se" diff --git a/var/spack/repos/builtin/packages/c-blosc2/package.py b/var/spack/repos/builtin/packages/c-blosc2/package.py index 1596a9c1d5b..450e93ed2c2 100644 --- a/var/spack/repos/builtin/packages/c-blosc2/package.py +++ b/var/spack/repos/builtin/packages/c-blosc2/package.py @@ -11,7 +11,6 @@ class CBlosc2(CMakePackage): other bells and whistles""" homepage = "http://www.blosc.org" - url = "https://github.com/Blosc/c-blosc2/archive/v2.0.0-beta.1.tar.gz" git = "https://github.com/Blosc/c-blosc2.git" maintainers = ['ax3l'] diff --git a/var/spack/repos/builtin/packages/candle-benchmarks/package.py b/var/spack/repos/builtin/packages/candle-benchmarks/package.py index fb8401108d1..5fcee8deeba 100644 --- a/var/spack/repos/builtin/packages/candle-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/candle-benchmarks/package.py @@ -10,7 +10,7 @@ class CandleBenchmarks(Package): """ECP-CANDLE Benchmarks""" homepage = "https://github.com/ECP-CANDLE/Benchmarks" - url = "https://github.com/ECP-CANDLE/Benchmarks/archive/v1.0.tar.gz" + url = "https://github.com/ECP-CANDLE/Benchmarks/archive/v0.1.tar.gz" tags = ['proxy-app', 'ecp-proxy-app'] diff --git a/var/spack/repos/builtin/packages/catch/package.py b/var/spack/repos/builtin/packages/catch2/package.py similarity index 96% rename from var/spack/repos/builtin/packages/catch/package.py rename to var/spack/repos/builtin/packages/catch2/package.py index a9d8cb412b5..939706c823b 100644 --- a/var/spack/repos/builtin/packages/catch/package.py +++ b/var/spack/repos/builtin/packages/catch2/package.py @@ -6,11 +6,12 @@ from spack import * -class Catch(CMakePackage): - """Catch tests""" +class Catch2(CMakePackage): + """Catch2 is a multi-paradigm test framework for C++, which also + supports Objective-C (and maybe C).""" homepage = "https://github.com/catchorg/Catch2" - url = "https://github.com/catchorg/Catch2/archive/v1.3.0.tar.gz" + url = "https://github.com/catchorg/Catch2/archive/v2.9.1.tar.gz" variant('single_header', default=True, description='Install a single header only.') diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py index 77111281865..0c0692852a7 100644 --- a/var/spack/repos/builtin/packages/cdo/package.py +++ b/var/spack/repos/builtin/packages/cdo/package.py @@ -51,7 +51,7 @@ class Cdo(AutotoolsPackage): depends_on('pkgconfig', type='build') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') # In this case CDO does not depend on hdf5 directly but we need the backend # of netcdf to be thread safe. depends_on('hdf5+threadsafe', when='+netcdf') @@ -63,7 +63,7 @@ class Cdo(AutotoolsPackage): depends_on('hdf5+threadsafe', when='+hdf5') - depends_on('udunits2', when='+udunits2') + depends_on('udunits', when='+udunits2') depends_on('libxml2', when='+libxml2') depends_on('proj@:5', when='+proj') depends_on('curl', when='+curl') diff --git a/var/spack/repos/builtin/packages/ceed/README.md b/var/spack/repos/builtin/packages/ceed/README.md deleted file mode 100644 index 74bcae1d171..00000000000 --- a/var/spack/repos/builtin/packages/ceed/README.md +++ /dev/null @@ -1,3 +0,0 @@ -This is a bundle for the CEED software suite. - -See https://ceed.exascaleproject.org for details. diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py index 4d598c03db4..d594ac5544c 100644 --- a/var/spack/repos/builtin/packages/ceed/package.py +++ b/var/spack/repos/builtin/packages/ceed/package.py @@ -4,10 +4,9 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import os -class Ceed(Package): +class Ceed(BundlePackage): """Ceed is a collection of benchmarks, miniapps, software libraries and APIs for efficient high-order finite element and spectral element discretizations for exascale applications developed in the Department of @@ -17,12 +16,6 @@ class Ceed(Package): homepage = "https://ceed.exascaleproject.org" - url = 'file://' + os.path.dirname(__file__) + '/README.md' - sha256 = '418c4b6b6a098648e25befdc28cdf9c351ecea9deaa660c0d9a674f8c6917122' - - version('2.0.0', sha256, expand=False) - version('1.0.0', sha256, expand=False) - variant('cuda', default=False, description='Build MAGMA; enable CUDA support in libCEED and OCCA') variant('mfem', default=True, description='Build MFEM and Laghos') @@ -139,7 +132,3 @@ class Ceed(Package): # If using gcc version <= 4.8 build suite-sparse version <= 5.1.0 depends_on('suite-sparse@:5.1.0', when='@1.0.0%gcc@:4.8+mfem+petsc') - - # Dummy install - def install(self, spec, prefix): - install('README.md', prefix) diff --git a/var/spack/repos/builtin/packages/channelflow/package.py b/var/spack/repos/builtin/packages/channelflow/package.py index 4a22819678e..fad8a1d0181 100644 --- a/var/spack/repos/builtin/packages/channelflow/package.py +++ b/var/spack/repos/builtin/packages/channelflow/package.py @@ -12,13 +12,9 @@ class Channelflow(CMakePackage): """ homepage = 'https://github.com/epfl-ecps/channelflow' - url = 'https://github.com/epfl-ecps/channelflow.git' + git = 'https://github.com/epfl-ecps/channelflow.git' - version( - 'develop', - git='https://github.com/epfl-ecps/channelflow.git', - branch='master' - ) + version('master', branch='master') variant('shared', default=True, description='Build shared libs') variant('mpi', default=True, description='Enable MPI parallelism') @@ -38,8 +34,8 @@ class Channelflow(CMakePackage): # Support for different I/O formats depends_on('hdf5+cxx', when='+hdf5') - depends_on('netcdf', when='netcdf=serial') - depends_on('netcdf+mpi', when='netcdf=parallel') + depends_on('netcdf-c', when='netcdf=serial') + depends_on('netcdf-c+mpi', when='netcdf=parallel') # Python bindings depends_on('boost+python', when='+python') @@ -73,7 +69,7 @@ def cmake_args(self): } args.append('-DWITH_NETCDF:STRING={0}'.format( - netcdf_str[spec.variants['netcdf'].value] + netcdf_str[spec.variants['netcdf-c'].value] )) # Set an MPI compiler for parallel builds diff --git a/var/spack/repos/builtin/packages/check/package.py b/var/spack/repos/builtin/packages/check/package.py index ed7e933bc8a..95076fdfc14 100644 --- a/var/spack/repos/builtin/packages/check/package.py +++ b/var/spack/repos/builtin/packages/check/package.py @@ -15,6 +15,8 @@ class Check(AutotoolsPackage): logging format.""" homepage = "https://libcheck.github.io/check/index.html" - url = "https://downloads.sourceforge.net/project/check/check/0.10.0/check-0.10.0.tar.gz" + url = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz" + version('0.12.0', sha256='464201098bee00e90f5c4bdfa94a5d3ead8d641f9025b560a27755a83b824234') + version('0.11.0', sha256='24f7a48aae6b74755bcbe964ce8bc7240f6ced2141f8d9cf480bc3b3de0d5616') version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052') diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustal-omega/package.py similarity index 93% rename from var/spack/repos/builtin/packages/clustalo/package.py rename to var/spack/repos/builtin/packages/clustal-omega/package.py index 59b7606e6ce..7c32f1f0968 100644 --- a/var/spack/repos/builtin/packages/clustalo/package.py +++ b/var/spack/repos/builtin/packages/clustal-omega/package.py @@ -6,7 +6,7 @@ from spack import * -class Clustalo(AutotoolsPackage): +class ClustalOmega(AutotoolsPackage): """Clustal Omega: the last alignment program you'll ever need.""" homepage = "http://www.clustal.org/omega/" diff --git a/var/spack/repos/builtin/packages/cmor/package.py b/var/spack/repos/builtin/packages/cmor/package.py index 31460e1645a..ef8dd2f94b3 100644 --- a/var/spack/repos/builtin/packages/cmor/package.py +++ b/var/spack/repos/builtin/packages/cmor/package.py @@ -24,8 +24,8 @@ class Cmor(AutotoolsPackage): variant('python', default=False, description='Enable PYTHON support') depends_on('uuid') - depends_on('netcdf') - depends_on('udunits2') + depends_on('netcdf-c') + depends_on('udunits') depends_on('hdf5@:1.8.19') extends('python', when='+python') diff --git a/var/spack/repos/builtin/packages/cppzmq/package.py b/var/spack/repos/builtin/packages/cppzmq/package.py index 0adaebf9c3c..0a29b1b194e 100644 --- a/var/spack/repos/builtin/packages/cppzmq/package.py +++ b/var/spack/repos/builtin/packages/cppzmq/package.py @@ -18,5 +18,5 @@ class Cppzmq(CMakePackage): version('4.2.2', sha256='3ef50070ac5877c06c6bb25091028465020e181bbfd08f110294ed6bc419737d') depends_on('cmake@3.0.0:', type='build') - depends_on('zeromq@4.2.5', when='@4.3.0') - depends_on('zeromq@4.2.2', when='@4.2.2') + depends_on('libzmq@4.2.5', when='@4.3.0') + depends_on('libzmq@4.2.2', when='@4.2.2') diff --git a/var/spack/repos/builtin/packages/cquery/package.py b/var/spack/repos/builtin/packages/cquery/package.py index 40edd13ce23..86ad88db711 100644 --- a/var/spack/repos/builtin/packages/cquery/package.py +++ b/var/spack/repos/builtin/packages/cquery/package.py @@ -11,10 +11,10 @@ class Cquery(CMakePackage): """ homepage = "https://github.com/cquery-project/cquery" - url = "https://github.com/cquery-project/cquery/archive/v20180718.tar.gz" + git = "https://github.com/cquery-project/cquery.git" - version('v20180823', commit='70c755b2e390d3edfb594a84a7531beb26b2bc07', - submodules=True, git='https://github.com/cquery-project/cquery') + version('2018-08-23', commit='70c755b2e390d3edfb594a84a7531beb26b2bc07', + submodules=True) depends_on('llvm') diff --git a/var/spack/repos/builtin/packages/cub/package.py b/var/spack/repos/builtin/packages/cub/package.py index 9076ac78b11..17411dcddb0 100644 --- a/var/spack/repos/builtin/packages/cub/package.py +++ b/var/spack/repos/builtin/packages/cub/package.py @@ -11,7 +11,7 @@ class Cub(Package): and other utilities for CUDA kernel programming.""" homepage = "https://nvlabs.github.com/cub" - url = "https://github.com/NVlabs/cub/archive/1.6.4.zip" + url = "https://github.com/NVlabs/cub/archive/1.7.1.zip" version('1.7.1', sha256='50b8777b83093fdfdab429a61fccdbfbbb991b3bbc08385118e5ad58e8f62e1d') diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index b92de9106ad..053d72aa2f8 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -19,8 +19,8 @@ class Czmq(AutotoolsPackage): depends_on('automake', type='build') depends_on('autoconf', type='build') depends_on('pkgconfig', type='build') - depends_on("libuuid") - depends_on('zeromq') + depends_on('libuuid') + depends_on('libzmq') def autoreconf(self, spec, prefix): autogen = Executable('./autogen.sh') diff --git a/var/spack/repos/builtin/packages/damaris/package.py b/var/spack/repos/builtin/packages/damaris/package.py index 6c3ec891bd2..6988973a7bc 100644 --- a/var/spack/repos/builtin/packages/damaris/package.py +++ b/var/spack/repos/builtin/packages/damaris/package.py @@ -12,10 +12,10 @@ class Damaris(CMakePackage): targeting large-scale, MPI-based HPC simulations.""" homepage = "https://project.inria.fr/damaris/" - url = "https://gitlab.inria.fr/Damaris/damaris" + git = "https://gitlab.inria.fr/Damaris/damaris.git" - version('master', git='https://gitlab.inria.fr/Damaris/damaris.git') - version('1.3.1', git='https://gitlab.inria.fr/Damaris/damaris.git', tag='v1.3.1', preferred=True) + version('master', branch='master') + version('1.3.1', tag='v1.3.1') variant('fortran', default=True, description='Enables Fortran support') variant('hdf5', default=False, description='Enables the HDF5 storage plugin') diff --git a/var/spack/repos/builtin/packages/davix/package.py b/var/spack/repos/builtin/packages/davix/package.py index 381251a62dd..e1b66e6d395 100644 --- a/var/spack/repos/builtin/packages/davix/package.py +++ b/var/spack/repos/builtin/packages/davix/package.py @@ -10,7 +10,7 @@ class Davix(CMakePackage): """High-performance file management over WebDAV/HTTP.""" homepage = "https://dmc.web.cern.ch/projects/davix" - url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.7/davix-0.6.7.tar.gz" + url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.8/davix-0.6.8.tar.gz" list_url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/" list_depth = 1 diff --git a/var/spack/repos/builtin/packages/dbcsr/package.py b/var/spack/repos/builtin/packages/dbcsr/package.py index 0fef73b8fa4..82a1cca300c 100644 --- a/var/spack/repos/builtin/packages/dbcsr/package.py +++ b/var/spack/repos/builtin/packages/dbcsr/package.py @@ -10,9 +10,9 @@ class Dbcsr(CMakePackage): """Distributed Block Compressed Sparse Row matrix library.""" homepage = "https://github.com/cp2k/dbcsr" - url = "https://github.com/cp2k/dbcsr/archive/v1.0.0-rc.0.tar.gz" + git = "https://github.com/cp2k/dbcsr.git" - version('develop', git='https://github.com/cp2k/dbcsr.git', branch='develop') + version('develop', branch='develop') variant('mpi', default=True, description='Compile with MPI') variant('openmp', default=False, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 109b67da2da..9f1796f5b4b 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -137,7 +137,7 @@ class Dealii(CMakePackage, CudaPackage): depends_on('metis@5:~int64', when='+metis~int64') depends_on('muparser', when='+muparser') depends_on('nanoflann', when='@9.0:+nanoflann') - depends_on('netcdf+mpi', when='+netcdf+mpi') + depends_on('netcdf-c+mpi', when='+netcdf+mpi') depends_on('netcdf-cxx', when='+netcdf+mpi') depends_on('oce', when='+oce') depends_on('p4est', when='+p4est+mpi') @@ -393,13 +393,13 @@ def cmake_args(self): # since Netcdf is spread among two, need to do it by hand: if '+netcdf' in spec and '+mpi' in spec: - netcdf = spec['netcdf-cxx'].libs + spec['netcdf'].libs + netcdf = spec['netcdf-cxx'].libs + spec['netcdf-c'].libs options.extend([ '-DNETCDF_FOUND=true', '-DNETCDF_LIBRARIES=%s' % netcdf.joined(';'), '-DNETCDF_INCLUDE_DIRS=%s;%s' % ( spec['netcdf-cxx'].prefix.include, - spec['netcdf'].prefix.include), + spec['netcdf-c'].prefix.include), ]) else: options.extend([ @@ -447,5 +447,5 @@ def cmake_args(self): return options - def setup_environment(self, spack_env, run_env): - run_env.set('DEAL_II_DIR', self.prefix) + def setup_run_environment(self, env): + env.set('DEAL_II_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py index cfdffeb9ba2..ca380ebb7ad 100644 --- a/var/spack/repos/builtin/packages/dislin/package.py +++ b/var/spack/repos/builtin/packages/dislin/package.py @@ -14,7 +14,7 @@ class Dislin(Package): homepage = "http://www.mps.mpg.de/dislin" url = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz" - version('11.2.linux.i586_64', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10') + version('11.0', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10') depends_on('motif') depends_on('gl') @@ -39,16 +39,18 @@ def libs(self): libraries, root=self.prefix, shared=True, recursive=True ) - def setup_environment(self, spack_env, run_env): - spack_env.set('DISLIN', self.prefix) - run_env.set('DISLIN', self.prefix) - run_env.prepend_path('PATH', self.prefix) - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix) - run_env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib) - run_env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib) + def setup_build_environment(self, env): + env.set('DISLIN', self.prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix) + def setup_run_environment(self, env): + env.set('DISLIN', self.prefix) + env.prepend_path('PATH', self.prefix) + env.prepend_path('LD_LIBRARY_PATH', self.prefix) + env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib) + env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('LD_LIBRARY_PATH', self.prefix) def install(self, spec, prefix): install = Executable('./INSTALL') diff --git a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py index 5d9a3ef014a..3a1b623ca0f 100644 --- a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py +++ b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py @@ -12,19 +12,17 @@ class DotnetCoreSdk(Package): applications for all types of infrastructure.""" homepage = "https://www.microsoft.com/net/" - url = "https://github.com/dotnet/core/" version('2.1.300', - url='https://download.microsoft.com/download/8/8/5/88544F33-836A' - '-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz', + url='https://download.microsoft.com/download/8/8/5/88544F33-836A-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz', sha256='fabca4c8825182ff18e5a2f82dfe75aecd10260ee9e7c85a8c4b3d108e5d8e1b') variant('telemetry', default=False, description='allow collection of telemetry data') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '-telemetry' in self.spec: - spack_env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1) + env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1) def install(self, spec, prefix): mkdirp('bin') diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py index 5bbc02f96b2..8b8a4eceb7f 100644 --- a/var/spack/repos/builtin/packages/eccodes/package.py +++ b/var/spack/repos/builtin/packages/eccodes/package.py @@ -49,7 +49,7 @@ class Eccodes(CMakePackage): # tests are enabled but the testing scripts don't use it. # depends_on('valgrind', type='test', when='+test') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('openjpeg@1.5.0:1.5.999,2.1.0:2.1.999', when='jp2k=openjpeg') depends_on('jasper', when='jp2k=jasper') depends_on('libpng', when='+png') @@ -100,7 +100,7 @@ def cmake_args(self): '-DHDF5_ROOT=' + self.spec['hdf5'].prefix, # Prevent possible overriding by environment variables # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH. - '-DNETCDF_PATH=' + self.spec['netcdf'].prefix]) + '-DNETCDF_PATH=' + self.spec['netcdf-c'].prefix]) else: args.append('-DENABLE_NETCDF=OFF') diff --git a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py index f86330613c4..e099e2f1b10 100644 --- a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py +++ b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py @@ -37,7 +37,7 @@ class EcpVizSdk(CMakePackage): depends_on('paraview', when='+paraview') depends_on('sz', when='+sz') depends_on('visit', when='+visit') - depends_on('vtkm', when='+vtkm') + depends_on('vtk-m', when='+vtkm') depends_on('zfp', when='+zfp') def cmake_args(self): diff --git a/var/spack/repos/builtin/packages/elmer-fem/package.py b/var/spack/repos/builtin/packages/elmerfem/package.py similarity index 95% rename from var/spack/repos/builtin/packages/elmer-fem/package.py rename to var/spack/repos/builtin/packages/elmerfem/package.py index a22c1226f2b..0fff28e8173 100644 --- a/var/spack/repos/builtin/packages/elmer-fem/package.py +++ b/var/spack/repos/builtin/packages/elmerfem/package.py @@ -6,7 +6,7 @@ from spack import * -class ElmerFem(CMakePackage): +class Elmerfem(CMakePackage): """Elmer is an open source multiphysical simulation software. It includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics.""" @@ -83,5 +83,5 @@ def cmake_args(self): return args - def setup_environment(self, spack_env, run_env): - run_env.set('ELMER_HOME', self.prefix) + def setup_run_environment(self, env): + env.set('ELMER_HOME', self.prefix) diff --git a/var/spack/repos/builtin/packages/eqr/package.py b/var/spack/repos/builtin/packages/eq-r/package.py similarity index 81% rename from var/spack/repos/builtin/packages/eqr/package.py rename to var/spack/repos/builtin/packages/eq-r/package.py index e31f88bb39c..76c10c82c5e 100644 --- a/var/spack/repos/builtin/packages/eqr/package.py +++ b/var/spack/repos/builtin/packages/eq-r/package.py @@ -7,20 +7,18 @@ import os -class Eqr(AutotoolsPackage): +class EqR(AutotoolsPackage): """ EMEWS Queues for R (EQ/R) Installs EQ/R. """ - git = "https://github.com/emews/EQ-R" - - version('develop', branch='master') - - configure_directory = 'src' - homepage = "http://emews.org" url = "https://github.com/emews/EQ-R/archive/1.0.tar.gz" + git = "https://github.com/emews/EQ-R.git" + + version('master', branch='master') + version('1.0', sha256='68047cb0edf088eaaefc5e36cefda9818292e5c832593e10a1dd9c73c27661b6') depends_on('autoconf', type='build') @@ -34,11 +32,13 @@ class Eqr(AutotoolsPackage): depends_on('tcl') depends_on('swig') - def setup_environment(self, spack_env, run_env): + configure_directory = 'src' + + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('CXXLD', spec['mpi'].mpicxx) + env.set('CC', spec['mpi'].mpicc) + env.set('CXX', spec['mpi'].mpicxx) + env.set('CXXLD', spec['mpi'].mpicxx) def configure_args(self): args = ['--with-tcl=' + self.spec['tcl'].prefix] diff --git a/var/spack/repos/builtin/packages/er/package.py b/var/spack/repos/builtin/packages/er/package.py index 2edc201b97d..0664b391e0a 100644 --- a/var/spack/repos/builtin/packages/er/package.py +++ b/var/spack/repos/builtin/packages/er/package.py @@ -10,7 +10,7 @@ class Er(CMakePackage): """Encoding and redundancy on a file set""" homepage = "https://github.com/ECP-VeloC/er" - url = "https://github.com/ECP-VeloC/er/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/er/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/er.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/es/package.py b/var/spack/repos/builtin/packages/es-shell/package.py similarity index 96% rename from var/spack/repos/builtin/packages/es/package.py rename to var/spack/repos/builtin/packages/es-shell/package.py index 99b846e96f4..f8f745f4888 100644 --- a/var/spack/repos/builtin/packages/es/package.py +++ b/var/spack/repos/builtin/packages/es-shell/package.py @@ -6,8 +6,7 @@ from spack import * -class Es(AutotoolsPackage): - +class EsShell(AutotoolsPackage): """Es is an extensible shell. The language was derived from the Plan 9 shell, rc, and was influenced by functional programming languages, such as Scheme, and the Tcl embeddable programming language. This diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py index bfe35d9f198..1f93eb372ac 100644 --- a/var/spack/repos/builtin/packages/esmf/package.py +++ b/var/spack/repos/builtin/packages/esmf/package.py @@ -34,7 +34,7 @@ class Esmf(MakefilePackage): # Optional dependencies depends_on('mpi', when='+mpi') depends_on('lapack@3:', when='+lapack') - depends_on('netcdf@3.6:', when='+netcdf') + depends_on('netcdf-c@3.6:', when='+netcdf') depends_on('netcdf-fortran@3.6:', when='+netcdf') depends_on('parallel-netcdf@1.2.0:', when='+pnetcdf') depends_on('xerces-c@3.1.0:', when='+xerces') @@ -200,7 +200,7 @@ def edit(self, spec, prefix): if '+netcdf' in spec: # ESMF provides the ability to read Grid and Mesh data in # NetCDF format. - if spec.satisfies('^netcdf@4.2:'): + if spec.satisfies('^netcdf-c@4.2:'): # ESMF_NETCDF_LIBS will be set to "-lnetcdff -lnetcdf". # This option is useful for systems which have the Fortran # and C bindings archived in seperate library files. diff --git a/var/spack/repos/builtin/packages/exmcutils/package.py b/var/spack/repos/builtin/packages/exmcutils/package.py index 8d53b7a71a8..bbd90d0ed00 100644 --- a/var/spack/repos/builtin/packages/exmcutils/package.py +++ b/var/spack/repos/builtin/packages/exmcutils/package.py @@ -11,7 +11,7 @@ class Exmcutils(AutotoolsPackage): """ExM C-Utils: Generic C utility library for ADLB/X and Swift/T""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.5.7.tar.gz' git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py index 6472b7b9970..d4b38b19a62 100644 --- a/var/spack/repos/builtin/packages/exodusii/package.py +++ b/var/spack/repos/builtin/packages/exodusii/package.py @@ -30,8 +30,8 @@ class Exodusii(CMakePackage): depends_on('mpi', when='+mpi') # https://github.com/gsjaardema/seacas/blob/master/NetCDF-Mapping.md - depends_on('netcdf@4.6.1:+mpi', when='+mpi') - depends_on('netcdf@4.6.1:~mpi', when='~mpi') + depends_on('netcdf-c@4.6.1:+mpi', when='+mpi') + depends_on('netcdf-c@4.6.1:~mpi', when='~mpi') def cmake_args(self): spec = self.spec @@ -49,7 +49,7 @@ def cmake_args(self): '-DSEACASProj_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=ON', '-DSEACASProj_ENABLE_CXX11:BOOL=OFF', '-DSEACASProj_ENABLE_Zoltan:BOOL=OFF', - '-DNetCDF_DIR:PATH={0}'.format(spec['netcdf'].prefix), + '-DNetCDF_DIR:PATH={0}'.format(spec['netcdf-c'].prefix), # MPI Flags # '-DTPL_ENABLE_MPI={0}'.format('ON' if '+mpi' in spec else 'OFF'), diff --git a/var/spack/repos/builtin/packages/fastmath/package.py b/var/spack/repos/builtin/packages/fastmath/package.py index bc04da72378..463197cd970 100644 --- a/var/spack/repos/builtin/packages/fastmath/package.py +++ b/var/spack/repos/builtin/packages/fastmath/package.py @@ -6,7 +6,7 @@ from spack import * -class Fastmath(Package): +class Fastmath(BundlePackage): """FASTMath is a suite of ~15 numerical libraries frequently used together in various SciDAC and CSE applications. The suite includes discretization libraries for structured, AMR and unstructured grids as well as solver @@ -14,16 +14,12 @@ class Fastmath(Package): Solvers.""" homepage = "www.fastmath-scidac.org/" - url = "https://github.com/citibeth/dummy/tarball/v1.0" - version('1.0', sha256='402a2198e40b7e9022a99ab88ba6f0ee1c04b103fc15589b22c892859f14b60a') - - # BundlePackage depends_on('amrex') # default is 3 dimensions depends_on('chombo@3.2') depends_on('hypre~internal-superlu') -# depends_on('ml-trilinos') # hoping for stripped down install of just ml -# depends_on('nox-trilinos') # hoping for stripped down install of just nox + # depends_on('ml-trilinos') # hoping for stripped down install of just ml + # depends_on('nox-trilinos') # hoping for stripped down install of just nox depends_on('mpi') depends_on('arpack-ng') depends_on('petsc') @@ -33,12 +29,3 @@ class Fastmath(Package): depends_on('superlu-dist') depends_on('trilinos') depends_on('zoltan') - - # Dummy install for now, will be removed when metapackage is available - def install(self, spec, prefix): - # Prevent the error message - # ==> Error: Install failed for fastmath. Nothing was installed! - # ==> Error: Installation process had nonzero exit code : 256 - with open(join_path(spec.prefix, 'bundle-package.txt'), 'w') as out: - out.write('This is a bundle\n') - out.close() diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py index ef651a4c9da..7898ee31b43 100644 --- a/var/spack/repos/builtin/packages/fastq-screen/package.py +++ b/var/spack/repos/builtin/packages/fastq-screen/package.py @@ -17,7 +17,7 @@ class FastqScreen(Package): version('0.11.2', sha256='a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207') depends_on('perl', type='run') - depends_on('perl-gd-graph', type='run') + depends_on('perl-gdgraph', type='run') depends_on('bowtie') depends_on('bowtie2') depends_on('bwa') diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py index 0113dfba3a9..47aff3cbf5a 100644 --- a/var/spack/repos/builtin/packages/ferret/package.py +++ b/var/spack/repos/builtin/packages/ferret/package.py @@ -19,7 +19,7 @@ class Ferret(Package): version('6.96', sha256='7eb87156aa586cfe838ab83f08b2102598f9ab62062d540a5da8c9123816331a') depends_on("hdf5+hl") - depends_on("netcdf") + depends_on("netcdf-c") depends_on("netcdf-fortran") depends_on("readline") depends_on("zlib") @@ -63,7 +63,7 @@ def patch(self): "-L%s -lnetcdff" % self.spec['netcdf-fortran'].prefix.lib, 'FERRET/platform_specific.mk.x86_64-linux') filter_file(r'\$\(NETCDF4_DIR\)/lib64/libnetcdf.a', - "-L%s -lnetcdf" % self.spec['netcdf'].prefix.lib, + "-L%s -lnetcdf" % self.spec['netcdf-c'].prefix.lib, 'FERRET/platform_specific.mk.x86_64-linux') filter_file(r'\$\(HDF5_DIR\)/lib64/libhdf5_hl.a', "-L%s -lhdf5_hl" % self.spec['hdf5'].prefix.lib, diff --git a/var/spack/repos/builtin/packages/flibcpp/package.py b/var/spack/repos/builtin/packages/flibcpp/package.py index b03fa79cbb4..81d30b15682 100644 --- a/var/spack/repos/builtin/packages/flibcpp/package.py +++ b/var/spack/repos/builtin/packages/flibcpp/package.py @@ -12,7 +12,7 @@ class Flibcpp(CMakePackage): homepage = "https://flibcpp.readthedocs.io/en/latest" git = "https://github.com/swig-fortran/flibcpp.git" - url = "https://github.com/swig-fortran/flibcpp/archive/v0.3.0.tar.gz" + url = "https://github.com/swig-fortran/flibcpp/archive/v0.3.1.tar.gz" version('master', branch='master') version('0.3.1', sha256='871570124122c18018478275d5040b4b787d1966e50ee95b634b0b5e0cd27e91') diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py index 11cb14d23c1..e2b52f741ce 100644 --- a/var/spack/repos/builtin/packages/flux-core/package.py +++ b/var/spack/repos/builtin/packages/flux-core/package.py @@ -27,7 +27,7 @@ class FluxCore(AutotoolsPackage): variant('docs', default=False, description='Build flux manpages') variant('cuda', default=False, description='Build dependencies with support for CUDA') - depends_on("zeromq@4.0.4:") + depends_on("libzmq@4.0.4:") depends_on("czmq") depends_on("czmq@2.2:3.99", when="@0.1:0.6.99") depends_on("czmq@3.0.1:", when="@0.7:,master") @@ -95,28 +95,29 @@ def lua_share_dir(self): def lua_lib_dir(self): return os.path.join('lib', 'lua', str(self.lua_version)) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Ensure ./fluxometer.lua can be found during flux's make check spack_env.append_path('LUA_PATH', './?.lua', separator=';') - run_env.prepend_path( + def setup_run_environment(self, env): + env.prepend_path( 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'), separator=';') - run_env.prepend_path( + env.prepend_path( 'LUA_CPATH', os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'), separator=';') - run_env.prepend_path( + env.prepend_path( 'PYTHONPATH', os.path.join( self.spec.prefix.lib, "python{0}".format(self.spec['python'].version.up_to(2)), "site-packages"), ) - run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules) - run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd) - run_env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux) + env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules) + env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd) + env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux) def configure_args(self): args = ['--enable-pylint=no'] diff --git a/var/spack/repos/builtin/packages/fpocket/package.py b/var/spack/repos/builtin/packages/fpocket/package.py index 5d5e92dc4db..a4516f0b107 100644 --- a/var/spack/repos/builtin/packages/fpocket/package.py +++ b/var/spack/repos/builtin/packages/fpocket/package.py @@ -14,11 +14,11 @@ class Fpocket(MakefilePackage): version('master', branch='master', git='https://github.com/Discngine/fpocket.git') - depends_on("netcdf") + depends_on("netcdf-c") - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if self.compiler.name == 'gcc': - spack_env.set('CXX', 'g++') + env.set('CXX', 'g++') def edit(self): makefile = FileFilter('makefile') diff --git a/var/spack/repos/builtin/packages/fstrack/package.py b/var/spack/repos/builtin/packages/fstrack/package.py index 297af6dbac7..ffbb1714f52 100644 --- a/var/spack/repos/builtin/packages/fstrack/package.py +++ b/var/spack/repos/builtin/packages/fstrack/package.py @@ -20,25 +20,25 @@ class Fstrack(MakefilePackage): variant('flow', default=True, description='Build the flow tracker') depends_on('gmt@4.0:4.999', when='+flow') - depends_on('netcdf', when='+flow') + depends_on('netcdf-c', when='+flow') parallel = False - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Compilers - spack_env.set('F90', spack_fc) + env.set('F90', spack_fc) # Compiler flags (assumes GCC) - spack_env.set('CFLAGS', '-O2') - spack_env.set('FFLAGS', '-ffixed-line-length-132 -x f77-cpp-input -O2') - spack_env.set('FFLAGS_DEBUG', '-g -x f77-cpp-input') - spack_env.set('F90FLAGS', '-O2 -x f95-cpp-input') - spack_env.set('F90FLAGS_DEBUG', '-g -x f95-cpp-input') - spack_env.set('LDFLAGS', '-lm') + env.set('CFLAGS', '-O2') + env.set('FFLAGS', '-ffixed-line-length-132 -x f77-cpp-input -O2') + env.set('FFLAGS_DEBUG', '-g -x f77-cpp-input') + env.set('F90FLAGS', '-O2 -x f95-cpp-input') + env.set('F90FLAGS_DEBUG', '-g -x f95-cpp-input') + env.set('LDFLAGS', '-lm') if '+flow' in self.spec: - spack_env.set('GMTHOME', self.spec['gmt'].prefix) - spack_env.set('NETCDFDIR', self.spec['netcdf'].prefix) + env.set('GMTHOME', self.spec['gmt'].prefix) + env.set('NETCDFDIR', self.spec['netcdf-c'].prefix) def build(self, spec, prefix): with working_dir('eispack'): diff --git a/var/spack/repos/builtin/packages/funhpc/package.py b/var/spack/repos/builtin/packages/funhpc/package.py index ed69e4f88ee..fe8adba18c4 100644 --- a/var/spack/repos/builtin/packages/funhpc/package.py +++ b/var/spack/repos/builtin/packages/funhpc/package.py @@ -11,7 +11,7 @@ class Funhpc(CMakePackage): """FunHPC: Functional HPC Programming""" homepage = "https://github.com/eschnett/FunHPC.cxx" - url = "https://github.com/eschnett/FunHPC.cxx/archive/version/0.1.0.tar.gz" + url = "https://github.com/eschnett/FunHPC.cxx/archive/version/1.3.0.tar.gz" git = "https://github.com/eschnett/FunHPC.cxx.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py index 32e746472d3..7e3fb6d8a03 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -114,7 +114,7 @@ class Gdal(AutotoolsPackage): depends_on('hdf', when='+hdf4') depends_on('hdf5', when='+hdf5') depends_on('kealib', when='+kea @2:') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('jasper@1.900.1', patches='uuid.patch', when='+jasper') depends_on('openjpeg', when='+openjpeg') depends_on('xerces-c', when='+xerces') @@ -157,12 +157,12 @@ class Gdal(AutotoolsPackage): conflicts('+mdb', when='~java', msg='MDB driver requires Java') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Needed to install Python bindings to GDAL installation # prefix instead of Python installation prefix. # See swig/python/GNUmakefile for more details. - spack_env.set('PREFIX', self.prefix) - spack_env.set('DESTDIR', '/') + env.set('PREFIX', self.prefix) + env.set('DESTDIR', '/') # https://trac.osgeo.org/gdal/wiki/BuildHints def configure_args(self): @@ -299,7 +299,7 @@ def configure_args(self): # https://trac.osgeo.org/gdal/wiki/NetCDF if '+netcdf' in spec: - args.append('--with-netcdf={0}'.format(spec['netcdf'].prefix)) + args.append('--with-netcdf={0}'.format(spec['netcdf-c'].prefix)) else: args.append('--with-netcdf=no') diff --git a/var/spack/repos/builtin/packages/gdl/package.py b/var/spack/repos/builtin/packages/gdl/package.py index eef7ada1c01..ab7a79c3520 100644 --- a/var/spack/repos/builtin/packages/gdl/package.py +++ b/var/spack/repos/builtin/packages/gdl/package.py @@ -57,7 +57,7 @@ class Gdl(CMakePackage): depends_on('libsm') depends_on('libxinerama') depends_on('libxxf86vm') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('pslib') depends_on('readline') diff --git a/var/spack/repos/builtin/packages/ginkgo/package.py b/var/spack/repos/builtin/packages/ginkgo/package.py index 23d2b53495f..bd94dbcab6d 100644 --- a/var/spack/repos/builtin/packages/ginkgo/package.py +++ b/var/spack/repos/builtin/packages/ginkgo/package.py @@ -12,7 +12,6 @@ class Ginkgo(CMakePackage, CudaPackage): with a focus on sparse solution of linear systems.""" homepage = "https://ginkgo-project.github.io/" - url = "https://github.com/ginkgo-project/ginkgo.git" git = "https://github.com/ginkgo-project/ginkgo.git" maintainers = ['tcojean', 'hartwiganzt'] diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 1e1d1972958..3d3e3e4e535 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -17,7 +17,7 @@ class Gmsh(CMakePackage): """ homepage = 'http://gmsh.info' - url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz' + url = 'http://gmsh.info/src/gmsh-4.4.1-source.tgz' version('4.4.1', sha256='853c6438fc4e4b765206e66a514b09182c56377bb4b73f1d0d26eda7eb8af0dc') version('4.2.2', sha256='e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc') diff --git a/var/spack/repos/builtin/packages/gmt/package.py b/var/spack/repos/builtin/packages/gmt/package.py index 045f4e11f68..c3dbbfc8e51 100644 --- a/var/spack/repos/builtin/packages/gmt/package.py +++ b/var/spack/repos/builtin/packages/gmt/package.py @@ -33,7 +33,7 @@ class Gmt(Package): depends_on('ghostscript') depends_on('subversion') depends_on('cmake@2.8.5:', type='build', when='@5:') - depends_on('netcdf@4:') + depends_on('netcdf-c@4:') depends_on('curl', when='@5.4:') # Optional dependencies @@ -58,7 +58,7 @@ def install(self, spec, prefix): def install(self, spec, prefix): args = [ '--prefix={0}'.format(prefix), - '--enable-netcdf={0}'.format(spec['netcdf'].prefix), + '--enable-netcdf={0}'.format(spec['netcdf-c'].prefix), '--enable-shared', '--without-x' ] diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gprolog/package.py similarity index 96% rename from var/spack/repos/builtin/packages/gnu-prolog/package.py rename to var/spack/repos/builtin/packages/gprolog/package.py index d3327110777..aa923deea86 100644 --- a/var/spack/repos/builtin/packages/gnu-prolog/package.py +++ b/var/spack/repos/builtin/packages/gprolog/package.py @@ -6,7 +6,7 @@ from spack import * -class GnuProlog(Package): +class Gprolog(Package): """A free Prolog compiler with constraint solving over finite domains.""" homepage = "http://www.gprolog.org/" url = "http://www.gprolog.org/gprolog-1.4.5.tar.gz" diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py index f480d95fe3e..ca070112a0b 100644 --- a/var/spack/repos/builtin/packages/grass/package.py +++ b/var/spack/repos/builtin/packages/grass/package.py @@ -69,7 +69,7 @@ class Grass(AutotoolsPackage): depends_on('readline', when='+readline') depends_on('opencl', when='+opencl') depends_on('bzip2', when='+bzlib') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('geos', when='+geos') def url_for_version(self, version): @@ -184,7 +184,7 @@ def configure_args(self): if '+netcdf' in spec: args.append('--with-netcdf={0}/bin/nc-config'.format( - spec['netcdf'].prefix)) + spec['netcdf-c'].prefix)) else: args.append('--without-netcdf') diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py index b54e9093673..12978a4b754 100644 --- a/var/spack/repos/builtin/packages/grib-api/package.py +++ b/var/spack/repos/builtin/packages/grib-api/package.py @@ -50,7 +50,7 @@ class GribApi(CMakePackage): # tests are enabled but the testing scripts don't use it. # depends_on('valgrind', type='test', when='+test') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('openjpeg@1.5.0:1.5.999', when='jp2k=openjpeg') depends_on('jasper', when='jp2k=jasper') depends_on('libpng', when='+png') @@ -100,7 +100,7 @@ def cmake_args(self): '-DHDF5_ROOT=' + self.spec['hdf5'].prefix, # Prevent possible overriding by environment variables # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH. - '-DNETCDF_PATH=' + self.spec['netcdf'].prefix]) + '-DNETCDF_PATH=' + self.spec['netcdf-c'].prefix]) else: args.append('-DENABLE_NETCDF=OFF') diff --git a/var/spack/repos/builtin/packages/grpc/package.py b/var/spack/repos/builtin/packages/grpc/package.py index 20d09541ff2..5c207d33588 100644 --- a/var/spack/repos/builtin/packages/grpc/package.py +++ b/var/spack/repos/builtin/packages/grpc/package.py @@ -20,7 +20,7 @@ class Grpc(CMakePackage): depends_on('protobuf') depends_on('openssl') depends_on('zlib') - depends_on('cares') + depends_on('c-ares') def cmake_args(self): args = [ diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py index ef4de4596cb..32c75afeff2 100644 --- a/var/spack/repos/builtin/packages/guidance/package.py +++ b/var/spack/repos/builtin/packages/guidance/package.py @@ -17,7 +17,7 @@ class Guidance(MakefilePackage): version('2.02', sha256='825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844') depends_on('perl', type=('build', 'run')) - depends_on('perl-bio-perl', type=('build', 'run')) + depends_on('perl-bioperl', type=('build', 'run')) depends_on('ruby') depends_on('prank') depends_on('clustalw') @@ -43,5 +43,5 @@ def install(self, spac, prefix): install('guidance.pl', join_path(prefix.bin.www.Guidance, 'guidance')) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', prefix.bin.www.Guidance) + def setup_run_environment(self, env): + env.prepend_path('PATH', prefix.bin.www.Guidance) diff --git a/var/spack/repos/builtin/packages/hc/package.py b/var/spack/repos/builtin/packages/hc/package.py index 19fd4c6b4fb..157b3ee6c7e 100644 --- a/var/spack/repos/builtin/packages/hc/package.py +++ b/var/spack/repos/builtin/packages/hc/package.py @@ -17,7 +17,7 @@ class Hc(MakefilePackage): version('1.0.7', sha256='7499ea76ac4739a9c0941bd57d124fb681fd387c8d716ebb358e6af3395103ed') depends_on('gmt@4.2.1:4.999') - depends_on('netcdf') + depends_on('netcdf-c') # Build phase fails in parallel with the following error messages: # /usr/bin/ld: cannot find -lrick @@ -25,11 +25,11 @@ class Hc(MakefilePackage): # /usr/bin/ld: cannot find -lggrd parallel = False - def setup_environment(self, spack_env, run_env): - spack_env.set('GMTHOME', self.spec['gmt'].prefix) - spack_env.set('NETCDFHOME', self.spec['netcdf'].prefix) - spack_env.set('HC_HOME', self.prefix) - spack_env.unset('ARCH') + def setup_build_environment(self, env): + env.set('GMTHOME', self.spec['gmt'].prefix) + env.set('NETCDFHOME', self.spec['netcdf-c'].prefix) + env.set('HC_HOME', self.prefix) + env.unset('ARCH') def install(self, spec, prefix): # Most files are installed during the build stage. diff --git a/var/spack/repos/builtin/packages/henson/package.py b/var/spack/repos/builtin/packages/henson/package.py index 11701e62d47..9e0b8d0ad79 100644 --- a/var/spack/repos/builtin/packages/henson/package.py +++ b/var/spack/repos/builtin/packages/henson/package.py @@ -10,10 +10,9 @@ class Henson(CMakePackage): """Cooperative multitasking for in situ processing.""" homepage = "https://github.com/henson-insitu/henson" - url = "https://github.com/henson-insitu/henson" git = "https://github.com/henson-insitu/henson.git" - version('develop', branch='master') + version('master', branch='master') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/hisea/package.py b/var/spack/repos/builtin/packages/hisea/package.py index f934edbee5b..68584523190 100644 --- a/var/spack/repos/builtin/packages/hisea/package.py +++ b/var/spack/repos/builtin/packages/hisea/package.py @@ -12,7 +12,6 @@ class Hisea(MakefilePackage): among others.""" homepage = "https://doi.org/10.1186/s12859-017-1953-9" - url = "https://github.com/lucian-ilie/HISEA" version('2017.12.26', sha256='3c6ddfb8490a327cc5f9e45f64cd4312abc6ef5719661ce8892db8a20a1e9c5e', url='https://github.com/lucian-ilie/HISEA/tarball/39e01e98caa0f2101da806ca59306296effe789c') diff --git a/var/spack/repos/builtin/packages/homer/package.py b/var/spack/repos/builtin/packages/homer/package.py index bf190eb0558..48063ce0888 100644 --- a/var/spack/repos/builtin/packages/homer/package.py +++ b/var/spack/repos/builtin/packages/homer/package.py @@ -11,7 +11,7 @@ class Homer(Package): """Software for motif discovery and next generation sequencing analysis""" homepage = "http://homer.ucsd.edu/homer" - url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.zip" + url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.1.zip" version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9') diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py index 18053151301..9979fc4c6ff 100644 --- a/var/spack/repos/builtin/packages/hpgmg/package.py +++ b/var/spack/repos/builtin/packages/hpgmg/package.py @@ -17,7 +17,7 @@ class Hpgmg(Package): """ homepage = "https://bitbucket.org/hpgmg/hpgmg" - url = "https://hpgmg.org/static/hpgmg-0.tar.gz" + url = "https://hpgmg.org/static/hpgmg-0.4.tar.gz" git = "https://bitbucket.org/hpgmg/hpgmg.git" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/hub/package.py b/var/spack/repos/builtin/packages/hub/package.py index 068e7b4a35a..437c8b62a36 100644 --- a/var/spack/repos/builtin/packages/hub/package.py +++ b/var/spack/repos/builtin/packages/hub/package.py @@ -11,10 +11,10 @@ class Hub(Package): """The github git wrapper""" homepage = "https://github.com/github/hub" - url = "https://github.com/github/hub/archive/v2.2.3.tar.gz" + url = "https://github.com/github/hub/archive/v2.2.2.tar.gz" git = "https://github.com/github/hub.git" - version('head', branch='master') + version('master', branch='master') version('2.2.2', sha256='610572ee903aea1fa8622c16ab7ddef2bd1bfec9f4854447ab8e0fbdbe6a0cae') version('2.2.1', sha256='9350aba6a8e3da9d26b7258a4020bf84491af69595f7484f922d75fc8b86dc10') version('2.2.0', sha256='2da1351197eb5696c207f22c69a5422af052d74277b73d0b8661efb9ec1d0eb1') diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index 1e901220a35..3281301abf7 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -40,7 +40,7 @@ class Ibmisc(CMakePackage): depends_on('proj@:4', when='+proj') depends_on('blitz', when='+blitz') depends_on('netcdf-cxx4', when='+netcdf') - depends_on('udunits2', when='+udunits2') + depends_on('udunits', when='+udunits2') depends_on('googletest', when='+googletest', type='build') depends_on('py-cython', when='+python', type=('build', 'run')) depends_on('py-numpy', when='+python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/imagemagick/package.py similarity index 97% rename from var/spack/repos/builtin/packages/image-magick/package.py rename to var/spack/repos/builtin/packages/imagemagick/package.py index 2f9229c496d..bbdc11213cf 100644 --- a/var/spack/repos/builtin/packages/image-magick/package.py +++ b/var/spack/repos/builtin/packages/imagemagick/package.py @@ -6,7 +6,7 @@ from spack import * -class ImageMagick(AutotoolsPackage): +class Imagemagick(AutotoolsPackage): """ImageMagick is a software suite to create, edit, compose, or convert bitmap images.""" diff --git a/var/spack/repos/builtin/packages/ioapi/package.py b/var/spack/repos/builtin/packages/ioapi/package.py index 2081d707547..0c66f4c51a4 100644 --- a/var/spack/repos/builtin/packages/ioapi/package.py +++ b/var/spack/repos/builtin/packages/ioapi/package.py @@ -15,7 +15,7 @@ class Ioapi(MakefilePackage): homepage = "https://www.cmascenter.org/ioapi/" url = "https://www.cmascenter.org/ioapi/download/ioapi-3.2.tar.gz" version('3.2', sha256='56771ff0053d47f2445e00ff369bca7bfc484325a2816b2c648744e523134fe9') - depends_on('netcdf@4:') + depends_on('netcdf-c@4:') depends_on('netcdf-fortran@4:') depends_on('sed', type='build') diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 7191faf2345..655e5f4fee0 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -237,7 +237,7 @@ def install(self, spec, prefix): if "+plot" in spec: julia("-e", pkgstart + 'Pkg.add("PyPlot"); using PyPlot') julia("-e", pkgstart + 'Pkg.add("Colors"); using Colors') - # These require maybe gtk and image-magick + # These require maybe gtk and imagemagick julia("-e", pkgstart + 'Pkg.add("Plots"); using Plots') julia("-e", pkgstart + 'Pkg.add("PlotRecipes"); using PlotRecipes') julia( diff --git a/var/spack/repos/builtin/packages/kvtree/package.py b/var/spack/repos/builtin/packages/kvtree/package.py index 6f164b12d64..a9e2630ee33 100644 --- a/var/spack/repos/builtin/packages/kvtree/package.py +++ b/var/spack/repos/builtin/packages/kvtree/package.py @@ -11,7 +11,7 @@ class Kvtree(CMakePackage): hashes.""" homepage = "https://github.com/ECP-VeloC/KVTree" - url = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.1.zip" + url = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.2.zip" git = "https://github.com/ecp-veloc/kvtree.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py index 1b9e4c1fd82..413b8a924de 100644 --- a/var/spack/repos/builtin/packages/lammps/package.py +++ b/var/spack/repos/builtin/packages/lammps/package.py @@ -74,7 +74,7 @@ def url_for_version(self, version): depends_on('mpi', when='+mpiio') depends_on('fftw', when='+kspace') depends_on('voropp+pic', when='+voronoi') - depends_on('netcdf+mpi', when='+user-netcdf') + depends_on('netcdf-c+mpi', when='+user-netcdf') depends_on('blas', when='+user-atc') depends_on('lapack', when='+user-atc') depends_on('latte@1.0.1', when='@:20180222+latte') diff --git a/var/spack/repos/builtin/packages/libcheck/package.py b/var/spack/repos/builtin/packages/libcheck/package.py deleted file mode 100644 index 86886037f36..00000000000 --- a/var/spack/repos/builtin/packages/libcheck/package.py +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Libcheck(CMakePackage): - """A unit testing framework for C.""" - - homepage = "https://libcheck.github.io/check/index.html" - url = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz" - - version('0.12.0', sha256='464201098bee00e90f5c4bdfa94a5d3ead8d641f9025b560a27755a83b824234') - version('0.11.0', sha256='24f7a48aae6b74755bcbe964ce8bc7240f6ced2141f8d9cf480bc3b3de0d5616') - version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052') diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py index 5ada427806b..165ed6840aa 100644 --- a/var/spack/repos/builtin/packages/libgit2/package.py +++ b/var/spack/repos/builtin/packages/libgit2/package.py @@ -14,7 +14,7 @@ class Libgit2(CMakePackage): """ homepage = "https://libgit2.github.com/" - url = "https://github.com/libgit2/libgit2/archive/v0.24.2.tar.gz" + url = "https://github.com/libgit2/libgit2/archive/v0.26.0.tar.gz" version('0.26.0', sha256='6a62393e0ceb37d02fe0d5707713f504e7acac9006ef33da1e88960bd78b6eac') diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py index 1f26b756280..9ab2beba2b5 100644 --- a/var/spack/repos/builtin/packages/libgpuarray/package.py +++ b/var/spack/repos/builtin/packages/libgpuarray/package.py @@ -25,4 +25,4 @@ class Libgpuarray(CMakePackage): depends_on('cuda') depends_on('cmake@3:', type='build') - depends_on('libcheck') + depends_on('check') diff --git a/var/spack/repos/builtin/packages/libnrm/package.py b/var/spack/repos/builtin/packages/libnrm/package.py index ad79170f9e2..178e4e7d344 100644 --- a/var/spack/repos/builtin/packages/libnrm/package.py +++ b/var/spack/repos/builtin/packages/libnrm/package.py @@ -19,5 +19,5 @@ class Libnrm(AutotoolsPackage): depends_on('automake', type='build') depends_on('libtool', type='build') - depends_on('zeromq') + depends_on('libzmq') depends_on('mpich') diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/libzmq/package.py similarity index 98% rename from var/spack/repos/builtin/packages/zeromq/package.py rename to var/spack/repos/builtin/packages/libzmq/package.py index 7612bf5695d..531d268f03b 100644 --- a/var/spack/repos/builtin/packages/zeromq/package.py +++ b/var/spack/repos/builtin/packages/libzmq/package.py @@ -6,7 +6,7 @@ from spack import * -class Zeromq(AutotoolsPackage): +class Libzmq(AutotoolsPackage): """The ZMQ networking/concurrency library and core API""" homepage = "http://zguide.zeromq.org/" diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py index 411a6f8fe66..6e7c44ad991 100644 --- a/var/spack/repos/builtin/packages/likwid/package.py +++ b/var/spack/repos/builtin/packages/likwid/package.py @@ -17,7 +17,7 @@ class Likwid(Package): for information.""" homepage = "https://github.com/RRZE-HPC/likwid" - url = "https://github.com/RRZE-HPC/likwid/archive/4.1.2.tar.gz" + url = "https://github.com/RRZE-HPC/likwid/archive/4.3.4.tar.gz" version('4.3.4', sha256='5c0d1c66b25dac8292a02232f06454067f031a238f010c62f40ef913c6609a83') version('4.3.3', sha256='a681378cd66c1679ca840fb5fac3136bfec93c01b3d78cc1d00a641db325a9a3') diff --git a/var/spack/repos/builtin/packages/lsf/package.py b/var/spack/repos/builtin/packages/lsf/package.py index 7c8827c0bf6..b257274c3a3 100644 --- a/var/spack/repos/builtin/packages/lsf/package.py +++ b/var/spack/repos/builtin/packages/lsf/package.py @@ -11,7 +11,6 @@ class Lsf(Package): """IBM Platform LSF is a batch scheduler for HPC environments""" homepage = "https://www.ibm.com/marketplace/hpc-workload-management" - url = "https://www.ibm.com/marketplace/hpc-workload-management" # LSF needs to be added as an external package to SPACK. For this, the # config file packages.yaml needs to be adjusted: diff --git a/var/spack/repos/builtin/packages/lua-bitlib/package.py b/var/spack/repos/builtin/packages/lua-bitlib/package.py index ca5d20764f0..cf05980704e 100644 --- a/var/spack/repos/builtin/packages/lua-bitlib/package.py +++ b/var/spack/repos/builtin/packages/lua-bitlib/package.py @@ -14,8 +14,7 @@ class LuaBitlib(Package): homepage = "http://luaforge.net/projects/bitlib" url = "https://luarocks.org/bitlib-23-2.src.rock" - version('23', sha256='fe226edc2808162e67418e6b2c98befc0ed25a489ecffc6974fa153f951c0c34', - url="https://luarocks.org/bitlib-23-2.src.rock", + version('23-2', sha256='fe226edc2808162e67418e6b2c98befc0ed25a489ecffc6974fa153f951c0c34', expand=False) extends('lua') diff --git a/var/spack/repos/builtin/packages/lua-lpeg/package.py b/var/spack/repos/builtin/packages/lua-lpeg/package.py index 8d6d35d1ff4..73f9d2e4c66 100644 --- a/var/spack/repos/builtin/packages/lua-lpeg/package.py +++ b/var/spack/repos/builtin/packages/lua-lpeg/package.py @@ -13,8 +13,7 @@ class LuaLpeg(Package): homepage = "http://www.inf.puc-rio.br/~roberto/lpeg/" url = "https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock" - version('0.12.1', sha256='3962e8d695d0f9095c9453f2a42f9f1a89fb94db9b0c3bf22934c1e8a3b0ef5a', - url='https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock', + version('0.12-1', sha256='3962e8d695d0f9095c9453f2a42f9f1a89fb94db9b0c3bf22934c1e8a3b0ef5a', expand=False) extends("lua") diff --git a/var/spack/repos/builtin/packages/lua-jit/package.py b/var/spack/repos/builtin/packages/lua-luajit/package.py similarity index 96% rename from var/spack/repos/builtin/packages/lua-jit/package.py rename to var/spack/repos/builtin/packages/lua-luajit/package.py index a0f8e2b88d0..552096d7167 100644 --- a/var/spack/repos/builtin/packages/lua-jit/package.py +++ b/var/spack/repos/builtin/packages/lua-luajit/package.py @@ -7,7 +7,7 @@ from spack import * -class LuaJit(Package): +class LuaLuajit(Package): """Flast flexible JITed lua""" homepage = "http://www.luajit.org" url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz" diff --git a/var/spack/repos/builtin/packages/lua-mpack/package.py b/var/spack/repos/builtin/packages/lua-mpack/package.py index 777ff19e18a..f332aba1e1b 100644 --- a/var/spack/repos/builtin/packages/lua-mpack/package.py +++ b/var/spack/repos/builtin/packages/lua-mpack/package.py @@ -15,8 +15,7 @@ class LuaMpack(Package): depends_on('msgpack-c') - version('1.0.0-0', sha256='9068d9d3f407c72a7ea18bc270b0fa90aad60a2f3099fa23d5902dd71ea4cd5f', - url='https://luarocks.org/manifests/tarruda/mpack-1.0.6-0.src.rock', + version('1.0.6-0', sha256='9068d9d3f407c72a7ea18bc270b0fa90aad60a2f3099fa23d5902dd71ea4cd5f', expand=False) extends('lua') diff --git a/var/spack/repos/builtin/packages/macsio/package.py b/var/spack/repos/builtin/packages/macsio/package.py index d90aad340dd..264e41590d7 100644 --- a/var/spack/repos/builtin/packages/macsio/package.py +++ b/var/spack/repos/builtin/packages/macsio/package.py @@ -93,6 +93,6 @@ def cmake_args(self): .format(spec['exodusii'].prefix)) # exodus requires netcdf cmake_args.append("-DWITH_NETCDF_PREFIX={0}" - .format(spec['netcdf'].prefix)) + .format(spec['netcdf-c'].prefix)) return cmake_args diff --git a/var/spack/repos/builtin/packages/maker/package.py b/var/spack/repos/builtin/packages/maker/package.py index 41363ec0a1e..0528b3ed8fd 100644 --- a/var/spack/repos/builtin/packages/maker/package.py +++ b/var/spack/repos/builtin/packages/maker/package.py @@ -55,7 +55,7 @@ def url_for_version(self, version): depends_on('perl-inline-c', type=('build', 'run')) depends_on('perl-io-all', type=('build', 'run')) depends_on('perl-io-prompt', type=('build', 'run')) - depends_on('perl-bio-perl', type=('build', 'run')) + depends_on('perl-bioperl', type=('build', 'run')) depends_on('blast-plus') depends_on('snap-korf') depends_on('repeatmasker') diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py index 5990660d5de..774aeebf8c0 100644 --- a/var/spack/repos/builtin/packages/mariadb/package.py +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -45,7 +45,7 @@ class Mariadb(CMakePackage): depends_on('curl') depends_on('libxml2') depends_on('lz4') - depends_on('zeromq') + depends_on('libzmq') depends_on('msgpack-c') depends_on('openssl') depends_on('openssl@:1.0', when='@:10.1') diff --git a/var/spack/repos/builtin/packages/meme/package.py b/var/spack/repos/builtin/packages/meme/package.py index a045e6d1ee8..aeed3ed2390 100644 --- a/var/spack/repos/builtin/packages/meme/package.py +++ b/var/spack/repos/builtin/packages/meme/package.py @@ -25,7 +25,7 @@ class Meme(AutotoolsPackage): depends_on('perl', type=('build', 'run')) depends_on('python@2.7:', type=('build', 'run')) depends_on('mpi', when='+mpi') - depends_on('image-magick', type=('build', 'run'), when='+image-magick') + depends_on('imagemagick', type=('build', 'run'), when='+image-magick') depends_on('perl-xml-parser', type=('build', 'run')) def configure_args(self): diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index d8ff47d0b45..747fe707cd4 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -189,7 +189,7 @@ class Mfem(Package): # depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps', # when='+petsc') depends_on('mpfr', when='+mpfr') - depends_on('netcdf@4.1.3:', when='+netcdf') + depends_on('netcdf-c@4.1.3:', when='+netcdf') depends_on('unwind', when='+libunwind') depends_on('zlib', when='+gzstream') depends_on('gnutls', when='+gnutls') @@ -368,9 +368,9 @@ def find_optional_library(name, prefix): if '+netcdf' in spec: options += [ - 'NETCDF_OPT=-I%s' % spec['netcdf'].prefix.include, + 'NETCDF_OPT=-I%s' % spec['netcdf-c'].prefix.include, 'NETCDF_LIB=%s' % - ld_flags_from_dirs([spec['netcdf'].prefix.lib], ['netcdf'])] + ld_flags_from_dirs([spec['netcdf-c'].prefix.lib], ['netcdf'])] if '+gzstream' in spec: if "@:3.3.2" in spec: diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py index 6ab1311309c..b1b22cb2819 100644 --- a/var/spack/repos/builtin/packages/moab/package.py +++ b/var/spack/repos/builtin/packages/moab/package.py @@ -39,8 +39,6 @@ class Moab(AutotoolsPackage): description='Required to enable the ExodusII reader/writer.') variant('pnetcdf', default=False, description='Enable pnetcdf (AKA parallel-netcdf) support') - variant('netcdf', default=False, - description='Required to enable the ExodusII reader/writer.') variant('zoltan', default=False, description='Enable zoltan support') variant('cgm', default=False, description='Enable common geometric module') variant('metis', default=True, description='Enable metis link') @@ -77,7 +75,7 @@ class Moab(AutotoolsPackage): depends_on('mpi', when='+mpi') depends_on('hdf5', when='+hdf5') depends_on('hdf5+mpi', when='+hdf5+mpi') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('parallel-netcdf', when='+pnetcdf') depends_on('cgm', when='+cgm') depends_on('metis', when='+metis') @@ -129,7 +127,7 @@ def configure_args(self): options.append('--without-hdf5') if '+netcdf' in spec: - options.append('--with-netcdf=%s' % spec['netcdf'].prefix) + options.append('--with-netcdf=%s' % spec['netcdf-c'].prefix) else: options.append('--without-netcdf') diff --git a/var/spack/repos/builtin/packages/libmongoc/package.py b/var/spack/repos/builtin/packages/mongo-c-driver/package.py similarity index 98% rename from var/spack/repos/builtin/packages/libmongoc/package.py rename to var/spack/repos/builtin/packages/mongo-c-driver/package.py index 0d3110a803e..aeac6d31db1 100644 --- a/var/spack/repos/builtin/packages/libmongoc/package.py +++ b/var/spack/repos/builtin/packages/mongo-c-driver/package.py @@ -6,7 +6,7 @@ from spack import * -class Libmongoc(AutotoolsPackage): +class MongoCDriver(AutotoolsPackage): """libmongoc is a client library written in C for MongoDB.""" homepage = "https://github.com/mongodb/mongo-c-driver" diff --git a/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py b/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py index 0f36e6174e2..47732dcbb41 100644 --- a/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py +++ b/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py @@ -15,4 +15,4 @@ class MongoCxxDriver(CMakePackage): version('3.2.0', sha256='e26edd44cf20bd6be91907403b6d63a065ce95df4c61565770147a46716aad8c') - depends_on('libmongoc@1.9.2:') + depends_on('mongo-c-driver@1.9.2:') diff --git a/var/spack/repos/builtin/packages/mpibash/mpibash-4.3.patch b/var/spack/repos/builtin/packages/mpi-bash/mpibash-4.3.patch similarity index 100% rename from var/spack/repos/builtin/packages/mpibash/mpibash-4.3.patch rename to var/spack/repos/builtin/packages/mpi-bash/mpibash-4.3.patch diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpi-bash/package.py similarity index 96% rename from var/spack/repos/builtin/packages/mpibash/package.py rename to var/spack/repos/builtin/packages/mpi-bash/package.py index 174109f6d9d..5b3731fbbe1 100644 --- a/var/spack/repos/builtin/packages/mpibash/package.py +++ b/var/spack/repos/builtin/packages/mpi-bash/package.py @@ -6,7 +6,7 @@ from spack import * -class Mpibash(AutotoolsPackage): +class MpiBash(AutotoolsPackage): """Parallel scripting right from the Bourne-Again Shell (Bash)""" homepage = "https://github.com/lanl/MPI-Bash" diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py index 43796ab7d8f..d261f602470 100644 --- a/var/spack/repos/builtin/packages/mxnet/package.py +++ b/var/spack/repos/builtin/packages/mxnet/package.py @@ -11,10 +11,9 @@ class Mxnet(MakefilePackage): designed for both efficiency and flexibility.""" homepage = "http://mxnet.io" - url = "https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz" + url = "https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz" - version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2', - url='https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz') + version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2') variant('cuda', default=False, description='Enable CUDA support') variant('opencv', default=True, description='Enable OpenCV support') diff --git a/var/spack/repos/builtin/packages/nauty/package.py b/var/spack/repos/builtin/packages/nauty/package.py index 444629efd73..8e897c37d60 100644 --- a/var/spack/repos/builtin/packages/nauty/package.py +++ b/var/spack/repos/builtin/packages/nauty/package.py @@ -48,8 +48,8 @@ class Nauty(AutotoolsPackage): } # Iterate over patches for condition, urls in urls_for_patches.items(): - for url, sha256 in urls: - patch(url, when=condition, level=1, sha256=sha256) + for path, sha256 in urls: + patch(path, when=condition, level=1, sha256=sha256) depends_on('m4', type='build', when='@2.6r7') depends_on('autoconf', type='build', when='@2.6r7') diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py index 6bf5fdb1b40..575b72a6abd 100644 --- a/var/spack/repos/builtin/packages/nccmp/package.py +++ b/var/spack/repos/builtin/packages/nccmp/package.py @@ -13,7 +13,7 @@ class Nccmp(Package): version('1.8.2.0', sha256='7f5dad4e8670568a71f79d2bcebb08d95b875506d3d5faefafe1a8b3afa14f18') - depends_on('netcdf') + depends_on('netcdf-c') def install(self, spec, prefix): # Configure says: F90 and F90FLAGS are replaced by FC and diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py index c3940136c43..60e530bae9d 100644 --- a/var/spack/repos/builtin/packages/ncl/package.py +++ b/var/spack/repos/builtin/packages/ncl/package.py @@ -42,7 +42,7 @@ class Ncl(Package): # Non-optional dependencies according to the manual: depends_on('jpeg') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('cairo+X+pdf') # Extra dependencies that may be missing from build system: @@ -65,7 +65,7 @@ class Ncl(Package): depends_on('bzip2') depends_on('freetype') - # In Spack, we do not have an option to compile netcdf without netcdf-4 + # In Spack, we do not have an option to compile netcdf-c without netcdf-4 # support, so we will tell the ncl configuration script that we want # support for netcdf-4, but the script assumes that hdf5 is compiled with # szip support. We introduce this restriction with the following dependency @@ -76,13 +76,13 @@ class Ncl(Package): # ESMF is only required at runtime (for ESMF_regridding.ncl) depends_on('esmf', type='run') - # In Spack, we also do not have an option to compile netcdf without DAP + # In Spack, we also do not have an option to compile netcdf-c without DAP # support, so we will tell the ncl configuration script that we have it. # Some of the optional dependencies according to the manual: depends_on('hdf', when='+hdf4') depends_on('gdal+proj@:2.4', when='+gdal') - depends_on('udunits2', when='+udunits2') + depends_on('udunits', when='+udunits2') # We need src files of triangle to appear in ncl's src tree if we want # triangle's features. @@ -123,8 +123,8 @@ def install(self, spec, prefix): self.prepare_src_tree() make('Everything', parallel=False) - def setup_environment(self, spack_env, run_env): - run_env.set('NCARG_ROOT', self.spec.prefix) + def setup_run_environment(self, env): + env.set('NCARG_ROOT', self.spec.prefix) def prepare_site_config(self): fc_flags = [] diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py index 951d6f59741..2fb78fcda2a 100644 --- a/var/spack/repos/builtin/packages/nco/package.py +++ b/var/spack/repos/builtin/packages/nco/package.py @@ -30,10 +30,10 @@ class Nco(AutotoolsPackage): # See "Compilation Requirements" at: # http://nco.sourceforge.net/#bld - depends_on('netcdf') + depends_on('netcdf-c') depends_on('antlr@2.7.7+cxx') # required for ncap2 depends_on('gsl') # desirable for ncap2 - depends_on('udunits2') # allows dimensional unit transformations + depends_on('udunits') # allows dimensional unit transformations depends_on('flex', type='build') depends_on('bison', type='build') @@ -45,9 +45,9 @@ def configure_args(self): spec = self.spec return ['--{0}-doc'.format('enable' if '+doc' in spec else 'disable')] - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('NETCDF_INC', spec['netcdf'].prefix.include) - spack_env.set('NETCDF_LIB', spec['netcdf'].prefix.lib) - spack_env.set('ANTLR_ROOT', spec['antlr'].prefix) - spack_env.set('UDUNITS2_PATH', spec['udunits2'].prefix) + env.set('NETCDF_INC', spec['netcdf-c'].prefix.include) + env.set('NETCDF_LIB', spec['netcdf-c'].prefix.lib) + env.set('ANTLR_ROOT', spec['antlr'].prefix) + env.set('UDUNITS2_PATH', spec['udunits'].prefix) diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py index 3f1d6f4d8cc..96666a29be2 100644 --- a/var/spack/repos/builtin/packages/ncview/package.py +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -13,8 +13,8 @@ class Ncview(AutotoolsPackage): version('2.1.7', sha256='a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82') - depends_on('netcdf') - depends_on('udunits2') + depends_on('netcdf-c') + depends_on('udunits') depends_on('libpng') depends_on('libxaw') diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py similarity index 94% rename from var/spack/repos/builtin/packages/netcdf/package.py rename to var/spack/repos/builtin/packages/netcdf-c/package.py index 46a5695c582..e548848be03 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf-c/package.py @@ -16,13 +16,13 @@ def is_integral(x): return False -class Netcdf(AutotoolsPackage): - """NetCDF is a set of software libraries and self-describing, - machine-independent data formats that support the creation, access, - and sharing of array-oriented scientific data.""" +class NetcdfC(AutotoolsPackage): + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the C distribution.""" homepage = "http://www.unidata.ucar.edu/software/netcdf" - git = "https://github.com/Unidata/netcdf-c" + git = "https://github.com/Unidata/netcdf-c.git" url = "https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.2.tar.gz" def url_for_version(self, version): @@ -45,7 +45,7 @@ def url_for_version(self, version): # Version 4.4.1.1 is having problems in tests # https://github.com/Unidata/netcdf-c/issues/343 version('4.4.1.1', sha256='4d44c6f4d02a8faf10ea619bfe1ba8224cd993024f4da12988c7465f663c8cae') - # netcdf@4.4.1 can crash on you (in real life and in tests). See: + # Version 4.4.1 can crash on you (in real life and in tests). See: # https://github.com/Unidata/netcdf-c/issues/282 version('4.4.1', sha256='8915cc69817f7af6165fbe69a8d1dfe21d5929d7cca9d10b10f568669ec6b342') version('4.4.0', sha256='0d40cb7845abd03c363abcd5f57f16e3c0685a0faf8badb2c59867452f6bcf78') @@ -121,20 +121,20 @@ def url_for_version(self, version): # Starting version 4.4.0, it became possible to disable parallel I/O even # if HDF5 supports it. For previous versions of the library we need # HDF5 without mpi support to disable parallel I/O. - # The following doesn't work if hdf5+mpi by default and netcdf~mpi is + # The following doesn't work if hdf5+mpi by default and netcdf-c~mpi is # specified in packages.yaml # depends_on('hdf5~mpi', when='@:4.3~mpi') # Thus, we have to introduce a conflict conflicts('~mpi', when='@:4.3^hdf5+mpi', - msg='netcdf@:4.3~mpi requires hdf5~mpi') + msg='netcdf-c@:4.3~mpi requires hdf5~mpi') # We need HDF5 with mpi support to enable parallel I/O. - # The following doesn't work if hdf5~mpi by default and netcdf+mpi is + # The following doesn't work if hdf5~mpi by default and netcdf-c+mpi is # specified in packages.yaml # depends_on('hdf5+mpi', when='+mpi') # Thus, we have to introduce a conflict conflicts('+mpi', when='^hdf5~mpi', - msg='netcdf+mpi requires hdf5+mpi') + msg='netcdf-c+mpi requires hdf5+mpi') # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later # https://github.com/Unidata/netcdf-c/issues/250 @@ -264,3 +264,10 @@ def configure_args(self): def check(self): # h5_test fails when run in parallel make('check', parallel=False) + + @property + def libs(self): + shared = '+shared' in self.spec + return find_libraries( + 'libnetcdf', root=self.prefix, shared=shared, recursive=True + ) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py index 94bb28412f8..3c550e56692 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -17,7 +17,7 @@ class NetcdfCxx(AutotoolsPackage): version('4.2', sha256='95ed6ab49a0ee001255eac4e44aacb5ca4ea96ba850c08337a3e4c9a0872ccd1') - depends_on('netcdf') + depends_on('netcdf-c') variant( 'netcdf4', default=True, description='Compile with netCDF4 support') @@ -38,7 +38,7 @@ def configure_args(self): # Add these to LDFLAGS explicitly, so the linker doesn't accidentally # use system versions ldflags = [ - self.spec['netcdf'].libs.search_flags, + self.spec['netcdf-c'].libs.search_flags, self.spec['hdf5'].libs.search_flags, ] args.append('LDFLAGS=' + ' '.join(ldflags)) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index 938d74d6aa5..b80b38be9e0 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -7,7 +7,9 @@ class NetcdfCxx4(AutotoolsPackage): - """C++ interface for NetCDF4""" + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the C++ distribution.""" homepage = "https://www.unidata.ucar.edu/software/netcdf" url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.3.1.tar.gz" @@ -19,7 +21,7 @@ class NetcdfCxx4(AutotoolsPackage): # force its usage with this variant. variant('pic', default=True, description='Produce position-independent code (for shared libs)') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('automake', type='build') depends_on('autoconf', type='build') @@ -32,7 +34,7 @@ def flag_handler(self, name, flags): if name == 'cflags' and '+pic' in self.spec: flags.append(self.compiler.pic_flag) elif name == 'cppflags': - flags.append('-I' + self.spec['netcdf'].prefix.include) + flags.append('-I' + self.spec['netcdf-c'].prefix.include) return (None, None, flags) diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py index d698ff1e8bb..cfc4bc10183 100644 --- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -7,7 +7,10 @@ class NetcdfFortran(AutotoolsPackage): - """Fortran interface for NetCDF4""" + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the Fortran + distribution.""" homepage = "https://www.unidata.ucar.edu/software/netcdf" url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.2.tar.gz" @@ -20,7 +23,7 @@ class NetcdfFortran(AutotoolsPackage): variant('pic', default=True, description='Produce position-independent code (for shared libs)') - depends_on('netcdf') + depends_on('netcdf-c') # The default libtool.m4 is too old to handle NAG compiler properly: # https://github.com/Unidata/netcdf-fortran/issues/94 @@ -30,14 +33,14 @@ def flag_handler(self, name, flags): if name in ['cflags', 'fflags'] and '+pic' in self.spec: flags.append(self.compiler.pic_flag) elif name == 'cppflags': - flags.append(self.spec['netcdf'].headers.cpp_flags) + flags.append(self.spec['netcdf-c'].headers.cpp_flags) elif name == 'ldflags': # We need to specify LDFLAGS to get correct dependency_libs # in libnetcdff.la, so packages that use libtool for linking # could correctly link to all the dependencies even when the # building takes place outside of Spack environment, i.e. # without Spack's compiler wrappers. - flags.append(self.spec['netcdf'].libs.search_flags) + flags.append(self.spec['netcdf-c'].libs.search_flags) return None, None, flags diff --git a/var/spack/repos/builtin/packages/nrm/package.py b/var/spack/repos/builtin/packages/nrm/package.py index b15bc113231..fa0b88201eb 100644 --- a/var/spack/repos/builtin/packages/nrm/package.py +++ b/var/spack/repos/builtin/packages/nrm/package.py @@ -16,7 +16,7 @@ class Nrm(PythonPackage): depends_on('py-setuptools', type=('build')) depends_on('py-six', type=('build', 'run')) - depends_on('py-zmq@17.1.2', type=('build', 'run')) + depends_on('py-pyzmq@17.1.2', type=('build', 'run')) depends_on('py-pyyaml', type=('build', 'run')) depends_on('py-tornado@5.1.1', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/ntpoly/package.py b/var/spack/repos/builtin/packages/ntpoly/package.py index d390e19dba9..75ba5a6890a 100644 --- a/var/spack/repos/builtin/packages/ntpoly/package.py +++ b/var/spack/repos/builtin/packages/ntpoly/package.py @@ -16,7 +16,7 @@ class Ntpoly(CMakePackage): """ homepage = "https://william-dawson.github.io/NTPoly/" - url = "https://github.com/william-dawson/NTPoly/archive/ntpoly-v2.3.1-alpha.tar.gz" + url = "https://github.com/william-dawson/NTPoly/archive/ntpoly-v2.3.1.tar.gz" version('2.3.1', sha256='af8c7690321607fbdee9671b9cb3acbed945148014e0541435858cf82bfd887e') diff --git a/var/spack/repos/builtin/packages/nut/package.py b/var/spack/repos/builtin/packages/nut/package.py index f159838c639..d5649fdaec3 100644 --- a/var/spack/repos/builtin/packages/nut/package.py +++ b/var/spack/repos/builtin/packages/nut/package.py @@ -13,7 +13,7 @@ class Nut(CMakePackage): and performance issues.""" homepage = "https://github.com/lanl/NuT" - url = "https://github.com/lanl/NuT/archive/0.1.0.tar.gz" + url = "https://github.com/lanl/NuT/archive/0.1.1.tar.gz" git = "https://github.com/lanl/NuT.git" tags = ['proxy-app'] @@ -29,11 +29,11 @@ class Nut(CMakePackage): conflicts('%xl', when='@serial') conflicts('%nag', when='@serial') - def setup_environment(self, spack_env, run_env): - spack_env.set('RANDOM123_DIR', self.spec['random123'].prefix) - build_targets = ['VERBOSE=on'] + def setup_build_environment(self, env): + env.set('RANDOM123_DIR', self.spec['random123'].prefix) + def install(self, spec, prefix): install('README.md', prefix) mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index cdfa076c73b..f153ff839d0 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -75,7 +75,7 @@ class Octave(AutotoolsPackage): depends_on('glpk', when='+glpk') depends_on('gl2ps', when='+gl2ps') depends_on('gnuplot', when='+gnuplot') - depends_on('image-magick', when='+magick') + depends_on('imagemagick', when='+magick') depends_on('hdf5', when='+hdf5') depends_on('java', when='+jdk') # TODO: requires Java 6 ? depends_on('llvm', when='+llvm') @@ -156,7 +156,7 @@ def configure_args(self): if '+magick' in spec: config_args.append("--with-magick=%s" - % spec['image-magick'].prefix.lib) + % spec['imagemagick'].prefix.lib) else: config_args.append("--without-magick") diff --git a/var/spack/repos/builtin/packages/omega-h/package.py b/var/spack/repos/builtin/packages/omega-h/package.py index e4594061648..0c9c3236509 100644 --- a/var/spack/repos/builtin/packages/omega-h/package.py +++ b/var/spack/repos/builtin/packages/omega-h/package.py @@ -12,7 +12,7 @@ class OmegaH(CMakePackage): """ homepage = "https://github.com/SNLComputation/omega_h" - url = "https://github.com/SNLComputation/omega_h/archive/v9.13.4.tar.gz" + url = "https://github.com/SNLComputation/omega_h/archive/v9.29.0.tar.gz" git = "https://github.com/SNLComputation/omega_h.git" maintainers = ['ibaned'] diff --git a/var/spack/repos/builtin/packages/openldap/package.py b/var/spack/repos/builtin/packages/openldap/package.py index 3c8a9e453e5..2bd92a41f43 100644 --- a/var/spack/repos/builtin/packages/openldap/package.py +++ b/var/spack/repos/builtin/packages/openldap/package.py @@ -17,7 +17,7 @@ class Openldap(AutotoolsPackage): """ homepage = "https://www.openldap.org/" - url = "ftp://ftp.openldap.org/pub/OpenLDAP/openldap-release/openldap-2.4.9.tgz" + url = "ftp://ftp.openldap.org/pub/OpenLDAP/openldap-release/openldap-2.4.48.tgz" version('2.4.48', sha256='d9523ffcab5cd14b709fcf3cb4d04e8bc76bb8970113255f372bc74954c6074d') diff --git a/var/spack/repos/builtin/packages/openpmd-api/package.py b/var/spack/repos/builtin/packages/openpmd-api/package.py index fe9972776f2..6dc7c89d786 100644 --- a/var/spack/repos/builtin/packages/openpmd-api/package.py +++ b/var/spack/repos/builtin/packages/openpmd-api/package.py @@ -33,7 +33,7 @@ class OpenpmdApi(CMakePackage): depends_on('cmake@3.11.0:', type='build') depends_on('mpark-variant@1.4.0:') - depends_on('catch@2.6.1: ~single_header', type='test') + depends_on('catch2@2.6.1: ~single_header', type='test') depends_on('mpi@2.3:', when='+mpi') # might become MPI 3.0+ depends_on('hdf5@1.8.13:', when='+hdf5') depends_on('hdf5@1.8.13: ~mpi', when='~mpi +hdf5') @@ -93,25 +93,24 @@ def cmake_args(self): return args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): spec = self.spec # pre-load dependent CMake-PUBLIC header-only libs - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['mpark-variant'].prefix) - run_env.prepend_path('CPATH', spec['mpark-variant'].prefix.include) + env.prepend_path('CMAKE_PREFIX_PATH', spec['mpark-variant'].prefix) + env.prepend_path('CPATH', spec['mpark-variant'].prefix.include) # more deps searched in openPMDConfig.cmake if spec.satisfies("+mpi"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['mpi'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['mpi'].prefix) if spec.satisfies("+adios1"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['adios'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['adios'].prefix) if spec.satisfies("+adios2"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['adios2'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['adios2'].prefix) if spec.satisfies("+hdf5"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['hdf5'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['hdf5'].prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # pre-load dependent CMake-PUBLIC header-only libs - spack_env.prepend_path('CMAKE_PREFIX_PATH', - self.spec['mpark-variant'].prefix) - spack_env.prepend_path('CPATH', - self.spec['mpark-variant'].prefix.include) + env.prepend_path('CMAKE_PREFIX_PATH', + self.spec['mpark-variant'].prefix) + prepend_path('CPATH', self.spec['mpark-variant'].prefix.include) diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py index 7cc1496b53a..3bce58cd395 100644 --- a/var/spack/repos/builtin/packages/pagit/package.py +++ b/var/spack/repos/builtin/packages/pagit/package.py @@ -18,10 +18,6 @@ class Pagit(Package): depends_on('java', type=('build', 'run')) depends_on('perl', type=('build', 'run')) - def url_for_version(self, version): - url = 'ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V{0}.64bit.tgz' - return url.format(version) - def install(self, spec, prefix): with working_dir('PAGIT'): install_tree('ABACAS', prefix.ABACAS) @@ -31,19 +27,18 @@ def install(self, spec, prefix): install_tree('lib', prefix.lib) install_tree('RATT', prefix.RATT) - def setup_environment(self, spack_env, run_env): - run_env.set('PAGIT_HOME', self.prefix) - run_env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5')) - run_env.set('ICORN_HOME', self.prefix.icorn) - run_env.set('SNPOMATIC_HOME', self.prefix.bin) - run_env.set('RATT_HOME', self.prefix.RATT) - run_env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config')) - run_env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5', - 'ssaha2')) - run_env.prepend_path('PATH', join_path(self.prefix.bin, - 'pileup_v0.5')) - run_env.prepend_path('PATH', self.prefix.IMAGE) - run_env.prepend_path('PATH', self.prefix.ABACAS) - run_env.prepend_path('PATH', self.prefix.ICORN) - run_env.prepend_path('PATH', self.prefix.RATT) - run_env.prepend_path('PERL5LIB', self.prefix.lib) + def setup_run_environment(self, env): + env.set('PAGIT_HOME', self.prefix) + env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5')) + env.set('ICORN_HOME', self.prefix.icorn) + env.set('SNPOMATIC_HOME', self.prefix.bin) + env.set('RATT_HOME', self.prefix.RATT) + env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config')) + env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5', + 'ssaha2')) + env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5')) + env.prepend_path('PATH', self.prefix.IMAGE) + env.prepend_path('PATH', self.prefix.ABACAS) + env.prepend_path('PATH', self.prefix.ICORN) + env.prepend_path('PATH', self.prefix.RATT) + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index e19039caa5b..0ca4ef375f6 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -93,7 +93,7 @@ class Paraview(CMakePackage, CudaPackage): depends_on('libpng') depends_on('libtiff') depends_on('libxml2') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('expat') # depends_on('netcdf-cxx') # depends_on('protobuf') # version mismatches? @@ -127,7 +127,7 @@ def paraview_subdir(self): """The paraview subdirectory name as paraview-major.minor""" return 'paraview-{0}'.format(self.spec.version.up_to(2)) - def setup_dependent_build_environment(self, env): + def setup_dependent_build_environment(self, env, dependent_spec): if os.path.isdir(self.prefix.lib64): lib_dir = self.prefix.lib64 else: diff --git a/var/spack/repos/builtin/packages/parquet/package.py b/var/spack/repos/builtin/packages/parquet-cpp/package.py similarity index 97% rename from var/spack/repos/builtin/packages/parquet/package.py rename to var/spack/repos/builtin/packages/parquet-cpp/package.py index ac130b359fd..de6559dc5e2 100644 --- a/var/spack/repos/builtin/packages/parquet/package.py +++ b/var/spack/repos/builtin/packages/parquet-cpp/package.py @@ -6,7 +6,7 @@ from spack import * -class Parquet(CMakePackage): +class ParquetCpp(CMakePackage): """C++ bindings for the Apache Parquet columnar data format. """ diff --git a/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py index 98c0a488d93..0c299e06b41 100644 --- a/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py +++ b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py @@ -10,7 +10,7 @@ class PerlAlienLibxml2(PerlPackage): """This module provides libxml2 for other modules to use.""" homepage = "https://metacpan.org/pod/Alien::Libxml2" - url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.09.tar.gz" + url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.10_01.tar.gz" version('0.10_01', sha256='2f45b308b33503292f48bf46a75fe1e653d6b209ba5caf0628d8cc103f8d61ac') diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bioperl/package.py similarity index 96% rename from var/spack/repos/builtin/packages/perl-bio-perl/package.py rename to var/spack/repos/builtin/packages/perl-bioperl/package.py index a8680d8b2e9..8f585b376e1 100644 --- a/var/spack/repos/builtin/packages/perl-bio-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-bioperl/package.py @@ -7,7 +7,7 @@ import inspect -class PerlBioPerl(PerlPackage): +class PerlBioperl(PerlPackage): """BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are @@ -36,8 +36,7 @@ class PerlBioPerl(PerlPackage): url = "https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.6.tar.gz" version('1.7.6', sha256='df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d') - version('1.7.2', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1', - url="http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz") + version('1.007002', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1') # According to cpandeps.grinnz.com Module-Build is both a build and run # time dependency for BioPerl diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-db-file/package.py similarity index 97% rename from var/spack/repos/builtin/packages/perl-dbfile/package.py rename to var/spack/repos/builtin/packages/perl-db-file/package.py index 19cc9410c17..ff7263517fa 100644 --- a/var/spack/repos/builtin/packages/perl-dbfile/package.py +++ b/var/spack/repos/builtin/packages/perl-db-file/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlDbfile(PerlPackage): +class PerlDbFile(PerlPackage): """DB_File is a module which allows Perl programs to make use of the facilities provided by Berkeley DB version 1.x (if you have a newer version of DB, see "Using DB_File with Berkeley DB version 2 or greater"). diff --git a/var/spack/repos/builtin/packages/perl-devel-symdump/package.py b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py index 9dfdc5ae984..386add30e4c 100644 --- a/var/spack/repos/builtin/packages/perl-devel-symdump/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py @@ -10,6 +10,6 @@ class PerlDevelSymdump(PerlPackage): """Devel::Symdump - dump symbol names or the symbol table""" homepage = "https://metacpan.org/pod/Devel::Symdump" - url = "https://cpan.metacpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.18.tar.gz" + url = "https://cpan.metacpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.0604.tar.gz" version('2.0604', sha256='1f9eaa557733f775ccaa852e846566274c017e6fee380aeb8d08e425cfa86d3e') diff --git a/var/spack/repos/builtin/packages/perl-file-chdir/package.py b/var/spack/repos/builtin/packages/perl-file-chdir/package.py index b628ca12e54..e26adb298f0 100644 --- a/var/spack/repos/builtin/packages/perl-file-chdir/package.py +++ b/var/spack/repos/builtin/packages/perl-file-chdir/package.py @@ -18,6 +18,6 @@ class PerlFileChdir(PerlPackage): combine all the power of chdir(), File::Spec and Cwd.""" homepage = "https://metacpan.org/pod/File::chdir" - url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1010.tar.gz" + url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1011.tar.gz" version('0.1011', sha256='31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79') diff --git a/var/spack/repos/builtin/packages/perl-gd-graph/package.py b/var/spack/repos/builtin/packages/perl-gdgraph/package.py similarity index 88% rename from var/spack/repos/builtin/packages/perl-gd-graph/package.py rename to var/spack/repos/builtin/packages/perl-gdgraph/package.py index a4c83eefc4b..98f015db35c 100644 --- a/var/spack/repos/builtin/packages/perl-gd-graph/package.py +++ b/var/spack/repos/builtin/packages/perl-gdgraph/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlGdGraph(PerlPackage): +class PerlGdgraph(PerlPackage): """Graph Plotting Module for Perl 5""" homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm" @@ -16,5 +16,5 @@ class PerlGdGraph(PerlPackage): depends_on('perl-capture-tiny', type=('build', 'run')) depends_on('perl-test-exception', type=('build', 'run')) - depends_on('perl-gd-text', type=('build', 'run')) + depends_on('perl-gdtextutil', type=('build', 'run')) depends_on('perl-gd', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-gd-text/package.py b/var/spack/repos/builtin/packages/perl-gdtextutil/package.py similarity index 94% rename from var/spack/repos/builtin/packages/perl-gd-text/package.py rename to var/spack/repos/builtin/packages/perl-gdtextutil/package.py index 1988eeaf708..929ac0e34ec 100644 --- a/var/spack/repos/builtin/packages/perl-gd-text/package.py +++ b/var/spack/repos/builtin/packages/perl-gdtextutil/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlGdText(PerlPackage): +class PerlGdtextutil(PerlPackage): """Text utilities for use with GD""" homepage = "http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm" diff --git a/var/spack/repos/builtin/packages/perl-io-prompt/package.py b/var/spack/repos/builtin/packages/perl-io-prompt/package.py index 2bf41449906..4734a3bc550 100644 --- a/var/spack/repos/builtin/packages/perl-io-prompt/package.py +++ b/var/spack/repos/builtin/packages/perl-io-prompt/package.py @@ -31,5 +31,5 @@ class PerlIoPrompt(PerlPackage): depends_on('perl-module-build', type='build') - depends_on('perl-term-readkey', type=('build', 'run')) + depends_on('perl-termreadkey', type=('build', 'run')) depends_on('perl-want', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-io-tty/package.py b/var/spack/repos/builtin/packages/perl-io-tty/package.py index 217b4fb71bf..332a09e2f49 100644 --- a/var/spack/repos/builtin/packages/perl-io-tty/package.py +++ b/var/spack/repos/builtin/packages/perl-io-tty/package.py @@ -12,6 +12,6 @@ class PerlIoTty(PerlPackage): For a list of importable constants, see IO::Tty::Constant.""" homepage = "https://metacpan.org/pod/IO::Tty" - url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IO-Tty-1.12.tar.gz" + url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IO-Tty-1.13_01.tar.gz" version('1.13_01', sha256='89798eba7c31d9c169ef2f38ff49490aa769b1d9a68033de365595cfaf9cc258') diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py index 63a36a0e65e..b57ee53bbd8 100644 --- a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py @@ -16,6 +16,7 @@ class PerlLibwwwPerl(PerlPackage): url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz" version('6.33', sha256='97417386f11f007ae129fe155b82fd8969473ce396a971a664c8ae6850c69b99') + version('6.29', sha256='4c6f2697999d2d0e6436b584116b12b30dc39990ec0622751c1a6cec2c0e6662') depends_on('perl-encode-locale', type=('build', 'run')) depends_on('perl-file-listing', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py index ef7faad32c0..9b1db2e856e 100644 --- a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py +++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py @@ -10,6 +10,6 @@ class PerlLogLog4perl(PerlPackage): """Log4j implementation for Perl""" homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm" - url = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz" + url = "https://cpan.metacpan.org/authors/id/M/MS/MSCHILLI/Log-Log4perl-1.46.tar.gz" - version('146', sha256='a361e483095795753b97f8a506b40c24c753cf73828bb8697665499ef8596402') + version('1.46', sha256='31011a17c04e78016e73eaa4865d0481d2ffc3dc22813c61065d90ad73c64e6f') diff --git a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py index 0974a00bc7a..5567f6fbd22 100644 --- a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py +++ b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py @@ -18,4 +18,4 @@ class PerlLwpProtocolHttps(PerlPackage): depends_on('perl-io-socket-ssl', type=('build', 'run')) depends_on('perl-net-http', type=('build', 'run')) depends_on('perl-mozilla-ca', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-lwp/package.py b/var/spack/repos/builtin/packages/perl-lwp/package.py deleted file mode 100644 index 4cbe00854e0..00000000000 --- a/var/spack/repos/builtin/packages/perl-lwp/package.py +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PerlLwp(PerlPackage): - """The World-Wide Web library for Perl""" - - homepage = "http://search.cpan.org/~oalders/libwww-perl-6.29/lib/LWP.pm" - url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.29.tar.gz" - - version('6.29', sha256='4c6f2697999d2d0e6436b584116b12b30dc39990ec0622751c1a6cec2c0e6662') - - depends_on('perl-test-requiresinternet', type=('build', 'run')) - depends_on('perl-http-message', type=('build', 'run')) - depends_on('perl-file-listing', type=('build', 'run')) - depends_on('perl-http-daemon', type=('build', 'run')) - depends_on('perl-html-parser', type=('build', 'run')) - depends_on('perl-http-cookies', type=('build', 'run')) - depends_on('perl-www-robotrules', type=('build', 'run')) - depends_on('perl-test-fatal', type=('build', 'run')) - depends_on('perl-http-negotiate', type=('build', 'run')) - depends_on('perl-net-http', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-version/package.py b/var/spack/repos/builtin/packages/perl-perl-version/package.py similarity index 94% rename from var/spack/repos/builtin/packages/perl-version/package.py rename to var/spack/repos/builtin/packages/perl-perl-version/package.py index a1413c0c373..68155b87e8e 100644 --- a/var/spack/repos/builtin/packages/perl-version/package.py +++ b/var/spack/repos/builtin/packages/perl-perl-version/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlVersion(PerlPackage): +class PerlPerlVersion(PerlPackage): """Parse and manipulate Perl version strings""" homepage = "http://search.cpan.org/~bdfoy/Perl-Version-1.013/lib/Perl/Version.pm" diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-set-intervaltree/package.py similarity index 94% rename from var/spack/repos/builtin/packages/perl-intervaltree/package.py rename to var/spack/repos/builtin/packages/perl-set-intervaltree/package.py index 5f875cdd6ec..96ed744908d 100644 --- a/var/spack/repos/builtin/packages/perl-intervaltree/package.py +++ b/var/spack/repos/builtin/packages/perl-set-intervaltree/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlIntervaltree(PerlPackage): +class PerlSetIntervaltree(PerlPackage): """Set::IntervalTree uses Interval Trees to store and efficiently look up ranges using a range-based lookup.""" diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py index ccab3095ad5..625546c9c8c 100644 --- a/var/spack/repos/builtin/packages/perl-star-fusion/package.py +++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py @@ -23,9 +23,9 @@ class PerlStarFusion(Package): depends_on('star', type=('build', 'run')) depends_on('perl', type=('build', 'run')) - depends_on('perl-intervaltree', type=('build', 'run')) + depends_on('perl-set-intervaltree', type=('build', 'run')) depends_on('perl-dbi', type=('build', 'run')) - depends_on('perl-dbfile', type=('build', 'run')) + depends_on('perl-db-file', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/perl-term-readkey/package.py b/var/spack/repos/builtin/packages/perl-termreadkey/package.py similarity index 96% rename from var/spack/repos/builtin/packages/perl-term-readkey/package.py rename to var/spack/repos/builtin/packages/perl-termreadkey/package.py index 0e89420d336..f764964d293 100644 --- a/var/spack/repos/builtin/packages/perl-term-readkey/package.py +++ b/var/spack/repos/builtin/packages/perl-termreadkey/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlTermReadkey(PerlPackage): +class PerlTermreadkey(PerlPackage): """Term::ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized diff --git a/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py index cb7e58bcd11..ef816a95e82 100644 --- a/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py @@ -12,6 +12,6 @@ class PerlXmlNamespacesupport(PerlPackage): prefix to namespace URI map, and provides a number of basic checks.""" homepage = "https://metacpan.org/pod/XML::NamespaceSupport" - url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-NamespaceSupport-1.12.tar.gz" + url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-NamespaceSupport-1.12_9.tar.gz" version('1.12_9', sha256='2e84a057f0a8c845a612d212742cb94fca4fc8a433150b5721bd448f77d1e4a9') diff --git a/var/spack/repos/builtin/packages/pism/package.py b/var/spack/repos/builtin/packages/pism/package.py index 10bc658dff6..356b726cb4c 100644 --- a/var/spack/repos/builtin/packages/pism/package.py +++ b/var/spack/repos/builtin/packages/pism/package.py @@ -10,7 +10,7 @@ class Pism(CMakePackage): """Parallel Ice Sheet Model""" homepage = "http://pism-docs.org/wiki/doku.php:=" - url = "https://github.com/pism/pism/archive/v0.7.3.tar.gz" + url = "https://github.com/pism/pism/archive/v1.1.4.tar.gz" git = "https://github.com/pism/pism.git" maintainers = ['citibeth'] @@ -73,9 +73,9 @@ class Pism(CMakePackage): depends_on('fftw') depends_on('gsl') depends_on('mpi') - depends_on('netcdf') # Only the C interface is used, no netcdf-cxx4 + depends_on('netcdf-c') # Only the C interface is used, no netcdf-cxx4 depends_on('petsc') - depends_on('udunits2') + depends_on('udunits') depends_on('proj@:4') depends_on('everytrace', when='+everytrace') @@ -116,7 +116,7 @@ def cmake_args(self): '-DPism_USE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO')] - def setup_environment(self, spack_env, env): + def setup_run_environment(self, env): env.set('PISM_PREFIX', self.prefix) env.set('PISM_BIN', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py index 0eb0050d341..d45eadb0284 100644 --- a/var/spack/repos/builtin/packages/prank/package.py +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -10,7 +10,7 @@ class Prank(Package): """A powerful multiple sequence alignment browser.""" homepage = "http://wasabiapp.org/software/prank/" - url = "http://wasabiapp.org/download/prank/prank.source.150803.tgz" + url = "http://wasabiapp.org/download/prank/prank.source.170427.tgz" version('170427', sha256='623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859') diff --git a/var/spack/repos/builtin/packages/ps-lite/package.py b/var/spack/repos/builtin/packages/ps-lite/package.py index 92a0b7ff884..9d20d09d550 100644 --- a/var/spack/repos/builtin/packages/ps-lite/package.py +++ b/var/spack/repos/builtin/packages/ps-lite/package.py @@ -17,6 +17,6 @@ class PsLite(CMakePackage): version('20170328', commit='acdb698fa3bb80929ef83bb37c705f025e119b82') depends_on('protobuf@3:') - depends_on('zeromq') + depends_on('libzmq') patch('cmake.patch') diff --git a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py index 029745dec16..5d949c053a5 100644 --- a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py +++ b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py @@ -10,9 +10,9 @@ class PyAvroJsonSerializer(PythonPackage): """Serializes data into a JSON format using AVRO schema.""" homepage = "https://github.com/linkedin/python-avro-json-serializer" - url = "https://github.com/linkedin/python-avro-json-serializer/archive/0.4.tar.gz" + url = "https://pypi.io/packages/source/a/avro_json_serializer/avro_json_serializer-0.4.tar.gz" - version('0.4', sha256='58df57e6c85b1b453668eb0bff2b049efcfd83d6e5dfa72cee1df220f330820d') + version('0.4', sha256='f9dac2dac92036c5dd5aba8c716545fc0a0630cc365a51ab15bc2ac47eac28f1') depends_on('py-setuptools', type='build') depends_on('py-simplejson', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-brian2/package.py b/var/spack/repos/builtin/packages/py-brian2/package.py index 5ebb9f85bc9..0d79bb5c5e9 100644 --- a/var/spack/repos/builtin/packages/py-brian2/package.py +++ b/var/spack/repos/builtin/packages/py-brian2/package.py @@ -24,6 +24,6 @@ class PyBrian2(PythonPackage): depends_on('py-sympy@0.7.6:', type=('build', 'run')) depends_on('py-pyparsing', type=('build', 'run')) depends_on('py-jinja2@2.7:', type=('build', 'run')) - depends_on('py-cpuinfo@0.1.6:', type=('build', 'run')) + depends_on('py-py-cpuinfo@0.1.6:', type=('build', 'run')) depends_on('py-sphinx@1.4.2:', type=('build', 'run'), when='+docs') depends_on('py-nosetests@1.0:', type='test') diff --git a/var/spack/repos/builtin/packages/py-cdat-lite/package.py b/var/spack/repos/builtin/packages/py-cdat-lite/package.py index facb14a43f0..19614e5cbad 100644 --- a/var/spack/repos/builtin/packages/py-cdat-lite/package.py +++ b/var/spack/repos/builtin/packages/py-cdat-lite/package.py @@ -17,7 +17,7 @@ class PyCdatLite(PythonPackage): version('6.0.1', sha256='092ae4ff1fb03dee00096e8dd595b769b422759ce972d96525950adf8e1c9374') - depends_on("netcdf") + depends_on("netcdf-c") depends_on("python@2.5:2.8", type=('build', 'run')) depends_on("py-numpy", type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cf-units/package.py b/var/spack/repos/builtin/packages/py-cf-units/package.py index aaa2505d103..ea7634afbb8 100644 --- a/var/spack/repos/builtin/packages/py-cf-units/package.py +++ b/var/spack/repos/builtin/packages/py-cf-units/package.py @@ -26,4 +26,4 @@ class PyCfUnits(PythonPackage): depends_on('py-numpy', type=('build', 'run')) depends_on('py-antlr4-python3-runtime', type=('build', 'run')) depends_on('py-pytest-runner', type=('build')) - depends_on('udunits2') + depends_on('udunits') diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py index 95bf54a8e98..8111ba1e800 100644 --- a/var/spack/repos/builtin/packages/py-espressopp/package.py +++ b/var/spack/repos/builtin/packages/py-espressopp/package.py @@ -14,7 +14,7 @@ class PyEspressopp(CMakePackage): atomistic or bead-spring models as they are used in soft matter research """ homepage = "https://espressopp.github.io" - url = "https://github.com/espressopp/espressopp/tarball/v1.9.4.1" + url = "https://github.com/espressopp/espressopp/tarball/v2.0.2" git = "https://github.com/espressopp/espressopp.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/py-exodus/package.py b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py similarity index 95% rename from var/spack/repos/builtin/packages/py-exodus/package.py rename to var/spack/repos/builtin/packages/py-exodus-bundler/package.py index 5794a146a64..42cf282cdf9 100644 --- a/var/spack/repos/builtin/packages/py-exodus/package.py +++ b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py @@ -6,7 +6,7 @@ from spack import * -class PyExodus(PythonPackage): +class PyExodusBundler(PythonPackage): """Exodus is a tool that makes it easy to successfully relocate Linux ELF binaries from one system to another.""" diff --git a/var/spack/repos/builtin/packages/py-filelock/package.py b/var/spack/repos/builtin/packages/py-filelock/package.py index b82459a2568..89d0a7b37c3 100644 --- a/var/spack/repos/builtin/packages/py-filelock/package.py +++ b/var/spack/repos/builtin/packages/py-filelock/package.py @@ -12,15 +12,14 @@ class PyFilelock(PythonPackage): inter-process communication""" homepage = "https://github.com/benediktschmitt/py-filelock" - url = "https://github.com/benediktschmitt/py-filelock/archive/v3.0.4.tar.gz" + url = "https://pypi.io/packages/source/f/filelock/filelock-3.0.4.tar.gz" - version('3.0.4', sha256='8521523f3eafb7bbbdd0a5a7a15ddb8076ea6f106385bbfc4c9d055db2585214') - version('3.0.3', sha256='8e1b1ad91de70e091de381ab8705b37e41d240c211d8d888dcf1d0e31d6274bb') - version('3.0.1', sha256='533107ab60de691030b7e90105ab38c8b0d60d52de382fe5302819cba95561f8') - version('3.0.0', sha256='f41bed24b280b2fd11b2f12fecdfd2a21e5f9babc4e89929b316946288fa195c') - version('2.0.13', sha256='85e2a001693c2995854e42783a8c11994d143f8ba9c92d31f573476a22a5b3b3') - version('2.0.12', sha256='3b67cddd8c405c27b9118a1383d5257b5b6e066d3a9a30ab03d42b4dc6828cbb') - version('2.0.11', sha256='97c36de6e0c2eaed6638a9575a96d176e4ec2820b888f3da3194bbb852f86c5e') - version('2.0.10', sha256='f15d99cfa3e89072d7709bf3b5d354cf1c9096cffdb1127c4dbff1ca4a89cb84') - version('2.0.9', sha256='86d8e95afe77bc92a94c2e0db2b452c067b453b017fd78edfbb679b199dadbd5') - version('2.0.8', sha256='4f69474338ebf6ead2e0c2e91c5f94a25af8125d307f539db10886a19e2e2628') + version('3.0.4', sha256='011327d4ed939693a5b28c0fdf2fd9bda1f68614c1d6d0643a89382ce9843a71') + version('3.0.3', sha256='7d8a86350736aa0efea0730e6a7f774195cbb1c2d61134c15f6be576399e87ff') + version('3.0.0', sha256='b3ad481724adfb2280773edd95ce501e497e88fa4489c6e41e637ab3fd9a456c') + version('2.0.13', sha256='d05079e7d7cae7576e192749d3461999ca6b0843d35b0f79f1fa956b0f6fc7d8') + version('2.0.12', sha256='eb4314a9a032707a914b037433ce866d4ed363fce8605d45f0c9d2cd6ac52f98') + version('2.0.11', sha256='e9e370efe86c30b19a2c8c36dd9fcce8e5ce294ef4ed6ac86664b666eaf852ca') + version('2.0.10', sha256='c73bf706d8a0c5722de0b745495fed9cda0e46c0eabb44eb18ee3f00520fa85f') + version('2.0.9', sha256='0f91dce339c9f25d6f2e0733a17e4f9a47b139dffda52619a0e61e013e5c6782') + version('2.0.8', sha256='7e48e4906de3c9a5d64d8f235eb3ae1050dfefa63fd65eaf318cc915c935212b') diff --git a/var/spack/repos/builtin/packages/py-fn/package.py b/var/spack/repos/builtin/packages/py-fn-py/package.py similarity index 95% rename from var/spack/repos/builtin/packages/py-fn/package.py rename to var/spack/repos/builtin/packages/py-fn-py/package.py index 95cf3d4adfb..0d4888be3a2 100644 --- a/var/spack/repos/builtin/packages/py-fn/package.py +++ b/var/spack/repos/builtin/packages/py-fn-py/package.py @@ -6,7 +6,7 @@ from spack import * -class PyFn(PythonPackage): +class PyFnPy(PythonPackage): """Functional programming in Python: implementation of missing features to enjoy FP.""" diff --git a/var/spack/repos/builtin/packages/py-fsspec/package.py b/var/spack/repos/builtin/packages/py-fsspec/package.py index 7d7372f66a6..4e774360f0f 100644 --- a/var/spack/repos/builtin/packages/py-fsspec/package.py +++ b/var/spack/repos/builtin/packages/py-fsspec/package.py @@ -10,9 +10,9 @@ class PyFsspec(PythonPackage): """A specification for pythonic filesystems.""" homepage = "https://github.com/intake/filesystem_spec" - url = "https://github.com/intake/filesystem_spec/archive/0.4.4.tar.gz" + url = "https://pypi.io/packages/source/f/fsspec/fsspec-0.4.4.tar.gz" - version('0.4.4', sha256='27dfc3dab37d5c037683c7a3eaf7acd8b24ee56e4ce3edb14af54bdb43973d43') + version('0.4.4', sha256='97697a46e8bf8be34461c2520d6fc4bfca0ed749b22bb2b7c21939fd450a7d63') depends_on('python@3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-hpccm/package.py b/var/spack/repos/builtin/packages/py-hpccm/package.py index fee945d1ed1..31d80744705 100644 --- a/var/spack/repos/builtin/packages/py-hpccm/package.py +++ b/var/spack/repos/builtin/packages/py-hpccm/package.py @@ -11,9 +11,9 @@ class PyHpccm(PythonPackage): tool to make it easier to generate container specification files.""" homepage = "https://github.com/NVIDIA/hpc-container-maker" - url = "https://github.com/NVIDIA/hpc-container-maker/archive/v19.2.0.tar.gz" + url = "https://pypi.io/packages/source/h/hpccm/hpccm-19.2.0.tar.gz" - version('19.2.0', sha256='99eb0f48cfbdfb29815aed8bcd0fa8c5a857fd912a2bb9658b217b0712ca4af5') + version('19.2.0', sha256='c60eec914a802b0a76596cfd5fdf7122d3f8665fcef06ef928323f5dfb5219a6') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jpype/package.py b/var/spack/repos/builtin/packages/py-jpype1/package.py similarity index 96% rename from var/spack/repos/builtin/packages/py-jpype/package.py rename to var/spack/repos/builtin/packages/py-jpype1/package.py index f8292f41320..0d8ccd7e972 100644 --- a/var/spack/repos/builtin/packages/py-jpype/package.py +++ b/var/spack/repos/builtin/packages/py-jpype1/package.py @@ -6,7 +6,7 @@ from spack import * -class PyJpype(PythonPackage): +class PyJpype1(PythonPackage): """JPype is an effort to allow python programs full access to java class libraries.""" diff --git a/var/spack/repos/builtin/packages/py-jsonpatch/package.py b/var/spack/repos/builtin/packages/py-jsonpatch/package.py index b9e60c9a882..6c374ac1695 100644 --- a/var/spack/repos/builtin/packages/py-jsonpatch/package.py +++ b/var/spack/repos/builtin/packages/py-jsonpatch/package.py @@ -10,9 +10,9 @@ class PyJsonpatch(PythonPackage): """Library to apply JSON Patches according to RFC 6902""" homepage = "https://github.com/stefankoegl/python-json-patch" - url = "https://github.com/stefankoegl/python-json-patch/archive/v1.23.tar.gz" + url = "https://pypi.io/packages/source/j/jsonpatch/jsonpatch-1.23.tar.gz" - version('1.23', sha256='0af03651204ea3049bc4aedaa42b591e134a4ee16e421f9c5f3ac4e9092885ad') + version('1.23', sha256='49f29cab70e9068db3b1dc6b656cbe2ee4edf7dfe9bf5a0055f17a4b6804a4b9') depends_on('py-setuptools', type='build') depends_on('py-jsonpointer@1.9', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jsonpointer/package.py b/var/spack/repos/builtin/packages/py-jsonpointer/package.py index 9e33b53b0d8..99bd34913b9 100644 --- a/var/spack/repos/builtin/packages/py-jsonpointer/package.py +++ b/var/spack/repos/builtin/packages/py-jsonpointer/package.py @@ -10,8 +10,8 @@ class PyJsonpointer(PythonPackage): """Library to resolve JSON Pointers according to RFC 6901""" homepage = "https://github.com/stefankoegl/python-json-pointer" - url = "https://github.com/stefankoegl/python-json-pointer/archive/v2.0.tar.gz" + url = "https://pypi.io/packages/source/j/jsonpointer/jsonpointer-2.0.tar.gz" - version('2.0', sha256='9594b7574a3216c9994181e9db7566a5cafb4ab24956e554f2dba1bb39edecb2') + version('2.0', sha256='c192ba86648e05fdae4f08a17ec25180a9aef5008d973407b581798a83975362') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-jupyter-client/package.py b/var/spack/repos/builtin/packages/py-jupyter-client/package.py index 1b69aa1e4ee..ef66494661f 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-client/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-client/package.py @@ -24,4 +24,4 @@ class PyJupyterClient(PythonPackage): depends_on('python@2.7:2.8,3.3:') depends_on('py-traitlets', type=('build', 'run')) depends_on('py-jupyter-core', type=('build', 'run')) - depends_on('py-zmq@13:', type=('build', 'run')) + depends_on('py-pyzmq@13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jupyterhub/package.py b/var/spack/repos/builtin/packages/py-jupyterhub/package.py index 2b3e39a3891..0ada6193521 100644 --- a/var/spack/repos/builtin/packages/py-jupyterhub/package.py +++ b/var/spack/repos/builtin/packages/py-jupyterhub/package.py @@ -31,5 +31,5 @@ class PyJupyterhub(PythonPackage): depends_on('py-oauthlib@3.0:', when='@1.0.0:', type=('build', 'run')) depends_on('py-python-oauth2@1.0:', when='@:9.4', type=('build', 'run')) depends_on('py-pamela', type=('build', 'run')) - depends_on('py-jupyter-notebook', type=('build', 'run')) + depends_on('py-notebook', type=('build', 'run')) depends_on('py-prometheus-client@0.0.21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-lrudict/package.py b/var/spack/repos/builtin/packages/py-lru-dict/package.py similarity index 81% rename from var/spack/repos/builtin/packages/py-lrudict/package.py rename to var/spack/repos/builtin/packages/py-lru-dict/package.py index 79c35502192..a3bd6c023fe 100644 --- a/var/spack/repos/builtin/packages/py-lrudict/package.py +++ b/var/spack/repos/builtin/packages/py-lru-dict/package.py @@ -7,13 +7,13 @@ from spack import * -class PyLrudict(PythonPackage): - """ A fast LRU cache""" +class PyLruDict(PythonPackage): + """A fast LRU cache""" homepage = "https://github.com/amitdev/lru-dict" url = "https://pypi.io/packages/source/l/lru-dict/lru-dict-1.1.6.tar.gz" version('1.1.6', sha256='365457660e3d05b76f1aba3e0f7fedbfcd6528e97c5115a351ddd0db488354cc') - depends_on('python@2.7:') + depends_on('python@2.7:', type=('build', 'run')) depends_on('py-setuptools', type=('build')) diff --git a/var/spack/repos/builtin/packages/py-macholib/package.py b/var/spack/repos/builtin/packages/py-macholib/package.py index 4f730733c87..368aba2ec14 100644 --- a/var/spack/repos/builtin/packages/py-macholib/package.py +++ b/var/spack/repos/builtin/packages/py-macholib/package.py @@ -10,7 +10,7 @@ class PyMacholib(PythonPackage): """Python package for Mach-O header analysis and editing""" homepage = "https://pypi.python.org/pypi/macholib" - url = "https://pypi.io/packages/source/m/macholib/macholib-1.8.tar.gz" + url = "https://pypi.io/packages/source/m/macholib/macholib-1.11.tar.gz" version('1.11', 'c4180ffc6f909bf8db6cd81cff4b6f601d575568f4d5dee148c830e9851eb9db') diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index a53c2c892b1..dfefbf01757 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -113,7 +113,7 @@ class PyMatplotlib(PythonPackage): # Optional dependencies depends_on('ffmpeg', when='+movies') # depends_on('libav', when='+movies') - depends_on('image-magick', when='+animation') + depends_on('imagemagick', when='+animation') depends_on('py-pillow@3.4:', when='+image', type=('build', 'run')) depends_on('texlive', when='+latex', type='run') depends_on('ghostscript@0.9:', when='+latex', type='run') diff --git a/var/spack/repos/builtin/packages/py-methylcode/package.py b/var/spack/repos/builtin/packages/py-methylcode/package.py index 512d1f2d014..53b9292edf9 100644 --- a/var/spack/repos/builtin/packages/py-methylcode/package.py +++ b/var/spack/repos/builtin/packages/py-methylcode/package.py @@ -11,15 +11,13 @@ class PyMethylcode(PythonPackage): reads and outputs per-base methylation data. """ homepage = "https://github.com/brentp/methylcode" - url = "https://github.com/brentp/methylcode/archive/master.zip" + git = "https://github.com/brentp/methylcode.git" - version('1.0.0', sha256='30f707a690a887e3161c8debba3c322bd313865df40212275b02203c52a416ae') + version('master', branch='master') - depends_on('python@2.7.0:2.7.999') - depends_on('py-six') - depends_on('py-setuptools') + depends_on('python@2.6:2.8', type=('build', 'run')) + depends_on('py-setuptools', type='build') depends_on('py-numpy') - depends_on('py-pyparsing') depends_on('py-pyfasta') depends_on('py-bsddb3') depends_on('bowtie') diff --git a/var/spack/repos/builtin/packages/py-mongo/package.py b/var/spack/repos/builtin/packages/py-mongo/package.py deleted file mode 100644 index 117c59cf704..00000000000 --- a/var/spack/repos/builtin/packages/py-mongo/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PyMongo(PythonPackage): - """Python driver for MongoDB """ - - homepage = "http://github.com/mongodb/mongo-python-driver" - url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.6.0.tar.gz" - - version('3.6.0', sha256='c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8') - version('3.3.0', sha256='3d45302fc2622fabf34356ba274c69df41285bac71bbd229f1587283b851b91e') - - depends_on('python@2.6:2.8,3.3:') - - depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-mysql-connector/package.py b/var/spack/repos/builtin/packages/py-mysql-connector-python/package.py similarity index 95% rename from var/spack/repos/builtin/packages/py-mysql-connector/package.py rename to var/spack/repos/builtin/packages/py-mysql-connector-python/package.py index e3e04280c4c..07000af952a 100644 --- a/var/spack/repos/builtin/packages/py-mysql-connector/package.py +++ b/var/spack/repos/builtin/packages/py-mysql-connector-python/package.py @@ -6,7 +6,7 @@ from spack import * -class PyMysqlConnector(PythonPackage): +class PyMysqlConnectorPython(PythonPackage): """MySQL Connector/Python is implementing the MySQL Client/Server protocol completely in Python. No MySQL libraries are needed, and no compilation is necessary to run this Python DB API v2.0 diff --git a/var/spack/repos/builtin/packages/py-mysql-connector/single-version.patch b/var/spack/repos/builtin/packages/py-mysql-connector-python/single-version.patch similarity index 100% rename from var/spack/repos/builtin/packages/py-mysql-connector/single-version.patch rename to var/spack/repos/builtin/packages/py-mysql-connector-python/single-version.patch diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py index ef9bbafad14..f76b6067b67 100644 --- a/var/spack/repos/builtin/packages/py-netcdf4/package.py +++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py @@ -22,15 +22,15 @@ class PyNetcdf4(PythonPackage): depends_on('py-numpy@1.7:', type=('build', 'run')) depends_on('py-cftime', type=('build', 'run')) - depends_on('netcdf') + depends_on('netcdf-c') depends_on('hdf5@1.8.0:+hl') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): """Ensure installed netcdf and hdf5 libraries are used""" # Explicitly set these variables so setup.py won't erroneously pick up # system versions - spack_env.set('USE_SETUPCFG', '0') - spack_env.set('HDF5_INCDIR', self.spec['hdf5'].prefix.include) - spack_env.set('HDF5_LIBDIR', self.spec['hdf5'].prefix.lib) - spack_env.set('NETCDF4_INCDIR', self.spec['netcdf'].prefix.include) - spack_env.set('NETCDF4_LIBDIR', self.spec['netcdf'].prefix.lib) + env.set('USE_SETUPCFG', '0') + env.set('HDF5_INCDIR', self.spec['hdf5'].prefix.include) + env.set('HDF5_LIBDIR', self.spec['hdf5'].prefix.lib) + env.set('NETCDF4_INCDIR', self.spec['netcdf-c'].prefix.include) + env.set('NETCDF4_LIBDIR', self.spec['netcdf-c'].prefix.lib) diff --git a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py b/var/spack/repos/builtin/packages/py-notebook/package.py similarity index 98% rename from var/spack/repos/builtin/packages/py-jupyter-notebook/package.py rename to var/spack/repos/builtin/packages/py-notebook/package.py index 55c2f0f2565..4eb62b3ac8f 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py +++ b/var/spack/repos/builtin/packages/py-notebook/package.py @@ -6,7 +6,7 @@ from spack import * -class PyJupyterNotebook(PythonPackage): +class PyNotebook(PythonPackage): """Jupyter Interactive Notebook""" homepage = "https://github.com/jupyter/notebook" diff --git a/var/spack/repos/builtin/packages/py-opentuner/package.py b/var/spack/repos/builtin/packages/py-opentuner/package.py index 5c34fbfab72..f8f23476922 100644 --- a/var/spack/repos/builtin/packages/py-opentuner/package.py +++ b/var/spack/repos/builtin/packages/py-opentuner/package.py @@ -18,7 +18,7 @@ class PyOpentuner(PythonPackage): depends_on('python@2.7:2.8', type=('build', 'run')) depends_on('py-argparse@1.2.1:', type=('build', 'run')) - depends_on('py-fn@0.2.12:', type=('build', 'run')) + depends_on('py-fn-py@0.2.12:', type=('build', 'run')) depends_on('py-numpy@1.8.0:', type=('build', 'run')) depends_on('py-pysqlite@2.6.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-performance/package.py b/var/spack/repos/builtin/packages/py-performance/package.py index 9abc3c4d482..0be0b0b5bad 100644 --- a/var/spack/repos/builtin/packages/py-performance/package.py +++ b/var/spack/repos/builtin/packages/py-performance/package.py @@ -22,4 +22,4 @@ class PyPerformance(PythonPackage): depends_on('py-setuptools', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) - depends_on('py-perf', type=('build', 'run')) + depends_on('py-pyperf', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-plotly/package.py b/var/spack/repos/builtin/packages/py-plotly/package.py index cd315180ed3..6bf5ea9da0e 100644 --- a/var/spack/repos/builtin/packages/py-plotly/package.py +++ b/var/spack/repos/builtin/packages/py-plotly/package.py @@ -10,9 +10,9 @@ class PyPlotly(PythonPackage): """An interactive, browser-based graphing library for Python""" homepage = "https://plot.ly/python/" - url = "https://github.com/plotly/plotly.py/archive/v2.2.0.tar.gz" + url = "https://pypi.io/packages/source/p/plotly/plotly-2.2.0.tar.gz" - version('2.2.0', sha256='dad2a49fe355dddb6ae159e96c10ac22413a33cbac513b4dbf3791e63ec33c1f') + version('2.2.0', sha256='ca668911ffb4d11fed6d7fbb12236f8ecc6a7209db192326bcb64bdb41451a58') depends_on('py-setuptools', type='build') depends_on('py-requests@2.3.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cpuinfo/package.py b/var/spack/repos/builtin/packages/py-py-cpuinfo/package.py similarity index 94% rename from var/spack/repos/builtin/packages/py-cpuinfo/package.py rename to var/spack/repos/builtin/packages/py-py-cpuinfo/package.py index e9f4db31426..c4278bf6788 100644 --- a/var/spack/repos/builtin/packages/py-cpuinfo/package.py +++ b/var/spack/repos/builtin/packages/py-py-cpuinfo/package.py @@ -6,7 +6,7 @@ from spack import * -class PyCpuinfo(PythonPackage): +class PyPyCpuinfo(PythonPackage): """Get CPU info with pure Python 2 & 3""" homepage = "https://github.com/workhorsy/py-cpuinfo" diff --git a/var/spack/repos/builtin/packages/py-git2/package.py b/var/spack/repos/builtin/packages/py-pygit2/package.py similarity index 81% rename from var/spack/repos/builtin/packages/py-git2/package.py rename to var/spack/repos/builtin/packages/py-pygit2/package.py index a4c6404ef13..216c61a74f5 100644 --- a/var/spack/repos/builtin/packages/py-git2/package.py +++ b/var/spack/repos/builtin/packages/py-pygit2/package.py @@ -6,7 +6,7 @@ from spack import * -class PyGit2(PythonPackage): +class PyPygit2(PythonPackage): """Pygit2 is a set of Python bindings to the libgit2 shared library, libgit2 implements the core of Git. """ @@ -24,8 +24,8 @@ class PyGit2(PythonPackage): depends_on('py-six', type=('build', 'run')) depends_on('py-cffi', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec # http://www.pygit2.org/install.html - spack_env.set('LIBGIT2', spec['libgit2'].prefix) - spack_env.set('LIBGIT2_LIB', spec['libgit2'].prefix.lib) + env.set('LIBGIT2', spec['libgit2'].prefix) + env.set('LIBGIT2_LIB', spec['libgit2'].prefix.lib) diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py index 3675482b086..84182e5a430 100644 --- a/var/spack/repos/builtin/packages/py-pygpu/package.py +++ b/var/spack/repos/builtin/packages/py-pygpu/package.py @@ -28,4 +28,4 @@ class PyPygpu(PythonPackage): depends_on('py-nose', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) depends_on('py-mako', type=('build', 'run')) - depends_on('libcheck') + depends_on('check') diff --git a/var/spack/repos/builtin/packages/py-pyke/package.py b/var/spack/repos/builtin/packages/py-pyke/package.py index e003dbc981e..c2fdbe69f17 100644 --- a/var/spack/repos/builtin/packages/py-pyke/package.py +++ b/var/spack/repos/builtin/packages/py-pyke/package.py @@ -13,8 +13,8 @@ class PyPyke(PythonPackage): """ homepage = "http://sourceforge.net/projects/pyke" - url = "https://downloads.sourceforge.net/pyke/pyke3-1.1.1.zip" + url = "https://sourceforge.net/projects/pyke/files/pyke/1.1.1/pyke-1.1.1.zip" - version('1.1.1', sha256='b877b390e70a2eacc01d97c3a992fde947276afc2798ca3ac6c6f74c796cb6dc') + version('1.1.1', sha256='b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae') - depends_on('python@3:') + depends_on('python@3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pymongo/package.py b/var/spack/repos/builtin/packages/py-pymongo/package.py index 8e28001e4ce..3f52238dfdc 100644 --- a/var/spack/repos/builtin/packages/py-pymongo/package.py +++ b/var/spack/repos/builtin/packages/py-pymongo/package.py @@ -19,6 +19,8 @@ class PyPymongo(PythonPackage): url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.9.0.tar.gz" version('3.9.0', sha256='4249c6ba45587b959292a727532826c5032d59171f923f7f823788f413c2a5a3') + version('3.6.0', sha256='c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8') + version('3.3.0', sha256='3d45302fc2622fabf34356ba274c69df41285bac71bbd229f1587283b851b91e') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pynio/package.py b/var/spack/repos/builtin/packages/py-pynio/package.py index d6d40765548..d1d489a1ba9 100644 --- a/var/spack/repos/builtin/packages/py-pynio/package.py +++ b/var/spack/repos/builtin/packages/py-pynio/package.py @@ -27,7 +27,7 @@ class PyPynio(PythonPackage): # Spack does not currently have netcdf below 4.x, and 3.x is a # fundamentally different format. So, currently this is only providing # support for netcdf4. - depends_on('netcdf@3.6.0:') + depends_on('netcdf-c@3.6.0:') # Turning on the hdf (i.e. hdf4) dependency causes it not to build, with # compile errors that (weirdly) relate to the declarations of HDF5. @@ -50,22 +50,22 @@ class PyPynio(PythonPackage): depends_on('py-numpy', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): """ These environment variables are how the setup.py knows which options to turn on, and how to find them. """ - spack_env.set('F2CLIBS', 'gfortran') - spack_env.set('HAS_NETCDF4', '1') - spack_env.set('NETCDF4_PREFIX', self.spec['netcdf'].prefix) + env.set('F2CLIBS', 'gfortran') + env.set('HAS_NETCDF4', '1') + env.set('NETCDF4_PREFIX', self.spec['netcdf-c'].prefix) if '+hdf5' in self.spec: - spack_env.set('HAS_HDF5', '1') - spack_env.set('HDF5_PREFIX', self.spec['hdf5'].prefix) + env.set('HAS_HDF5', '1') + env.set('HDF5_PREFIX', self.spec['hdf5'].prefix) if '+gdal' in self.spec: - spack_env.set('HAS_GDAL', '1') - spack_env.set('GDAL_PREFIX', self.spec['gdal'].prefix) + env.set('HAS_GDAL', '1') + env.set('GDAL_PREFIX', self.spec['gdal'].prefix) # This one is trouble - see comments above. # if '+hdf4' in self.spec: -# spack_env.set('HAS_HDF4', '1') -# spack_env.set('HDF4_PREFIX', self.spec['hdf'].prefix) +# env.set('HAS_HDF4', '1') +# env.set('HDF4_PREFIX', self.spec['hdf'].prefix) diff --git a/var/spack/repos/builtin/packages/py-perf/package.py b/var/spack/repos/builtin/packages/py-pyperf/package.py similarity index 95% rename from var/spack/repos/builtin/packages/py-perf/package.py rename to var/spack/repos/builtin/packages/py-pyperf/package.py index 2d2c025691b..53106bb4685 100644 --- a/var/spack/repos/builtin/packages/py-perf/package.py +++ b/var/spack/repos/builtin/packages/py-pyperf/package.py @@ -6,7 +6,7 @@ from spack import * -class PyPerf(PythonPackage): +class PyPyperf(PythonPackage): """The Python perf module is a toolkit to write, run and analyze benchmarks. """ diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-python-igraph/package.py similarity index 94% rename from var/spack/repos/builtin/packages/py-igraph/package.py rename to var/spack/repos/builtin/packages/py-python-igraph/package.py index e6f6ccdf209..7812983c210 100644 --- a/var/spack/repos/builtin/packages/py-igraph/package.py +++ b/var/spack/repos/builtin/packages/py-python-igraph/package.py @@ -6,7 +6,7 @@ from spack import * -class PyIgraph(PythonPackage): +class PyPythonIgraph(PythonPackage): """igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use.""" diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-python-meep/package.py similarity index 98% rename from var/spack/repos/builtin/packages/py-meep/package.py rename to var/spack/repos/builtin/packages/py-python-meep/package.py index 81a219145f4..4eedd1ef176 100644 --- a/var/spack/repos/builtin/packages/py-meep/package.py +++ b/var/spack/repos/builtin/packages/py-python-meep/package.py @@ -6,7 +6,7 @@ from spack import * -class PyMeep(PythonPackage): +class PyPythonMeep(PythonPackage): """Python-meep is a wrapper around libmeep. It allows the scripting of Meep-simulations with Python""" diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py index 980d5fae516..39b5b7f5165 100644 --- a/var/spack/repos/builtin/packages/py-pyyaml/package.py +++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py @@ -8,8 +8,9 @@ class PyPyyaml(PythonPackage): """PyYAML is a YAML parser and emitter for Python.""" + homepage = "http://pyyaml.org/wiki/PyYAML" - url = "http://pyyaml.org/download/pyyaml/PyYAML-5.1.2.tar.gz" + url = "https://pypi.io/packages/source/P/PyYAML/PyYAML-5.1.2.tar.gz" version('5.1.2', sha256='01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4') version('3.13', sha256='3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf') diff --git a/var/spack/repos/builtin/packages/py-zmq/package.py b/var/spack/repos/builtin/packages/py-pyzmq/package.py similarity index 93% rename from var/spack/repos/builtin/packages/py-zmq/package.py rename to var/spack/repos/builtin/packages/py-pyzmq/package.py index 7d2d783a7ac..e3e3944e2d8 100644 --- a/var/spack/repos/builtin/packages/py-zmq/package.py +++ b/var/spack/repos/builtin/packages/py-pyzmq/package.py @@ -6,7 +6,7 @@ from spack import * -class PyZmq(PythonPackage): +class PyPyzmq(PythonPackage): """PyZMQ: Python bindings for zeromq.""" homepage = "https://github.com/zeromq/pyzmq" url = "https://github.com/zeromq/pyzmq/archive/v14.7.0.tar.gz" @@ -18,4 +18,4 @@ class PyZmq(PythonPackage): depends_on('py-cython@0.16:', type=('build', 'run')) depends_on('py-py', type=('build', 'run')) depends_on('py-cffi', type=('build', 'run')) - depends_on('zeromq') + depends_on('libzmq') diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py index c6e25d373e7..875563f260b 100644 --- a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py +++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py @@ -11,10 +11,10 @@ class PyRequestsToolbelt(PythonPackage): python-requests""" homepage = "https://toolbelt.readthedocs.org/" - url = "https://github.com/requests/toolbelt/archive/0.9.1.tar.gz" + url = "https://pypi.io/packages/source/r/requests-toolbelt/requests-toolbelt-0.9.1.tar.gz" - version('0.9.1', sha256='c8e68e537e87ae088e3a0eb6d80ed5b7cf5d6df503d0e843e0a5e47283db487b') - version('0.8.0', sha256='f151c07e88148dc05b6f31cc75dfb7a6770968e4a5c8e6690325eed4e79160a1') + version('0.9.1', sha256='968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0') + version('0.8.0', sha256='f6a531936c6fa4c6cfce1b9c10d5c4f498d16528d2a54a22ca00011205a187b5') depends_on('py-setuptools', type='build') depends_on('py-requests@2.0.1:2.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-scoop/package.py b/var/spack/repos/builtin/packages/py-scoop/package.py index b26140c3846..0c9cf81e3e0 100644 --- a/var/spack/repos/builtin/packages/py-scoop/package.py +++ b/var/spack/repos/builtin/packages/py-scoop/package.py @@ -19,4 +19,4 @@ class PyScoop(PythonPackage): depends_on('py-setuptools', type='build') depends_on('py-greenlet@0.3.4:', type=('build', 'run')) - depends_on('py-zmq@13.1.0:', type=('build', 'run')) + depends_on('py-pyzmq@13.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py index 0781ea59f3b..34100e15d6d 100644 --- a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py @@ -10,9 +10,9 @@ class PySphinxautomodapi(PythonPackage): """Provides Sphinx directives to autogenerate API documentation pages""" homepage = "https://sphinx-automodapi.readthedocs.io/en/latest/" - url = "https://github.com/astropy/sphinx-automodapi/archive/v0.9.tar.gz" + url = "https://pypi.io/packages/source/s/sphinx-automodapi/sphinx-automodapi-0.9.tar.gz" - version('0.9', sha256='017817812e9266319fdcfcc89ddfbe570935ca87a3bda62d61c8507cf1337aa8') + version('0.9', sha256='71a69e1a7ab8d849f416d7431db854d7b1925f749ba6345bc7d88f288892871d') depends_on('py-setuptools', type='build') depends_on('py-sphinx@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-spyder/package.py b/var/spack/repos/builtin/packages/py-spyder/package.py index 607a52393bf..c8e48ec2a73 100644 --- a/var/spack/repos/builtin/packages/py-spyder/package.py +++ b/var/spack/repos/builtin/packages/py-spyder/package.py @@ -39,6 +39,6 @@ class PySpyder(PythonPackage): # to pick up webkit, but this is the easier solution (see #9207) depends_on('qt+webkit', type=('build', 'run')) depends_on('py-pickleshare', type=('build', 'run')) - depends_on('py-zmq', type=('build', 'run')) + depends_on('py-pyzmq', type=('build', 'run')) depends_on('py-chardet@2.0.0:', type=('build', 'run')) depends_on('py-numpydoc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-symengine/package.py b/var/spack/repos/builtin/packages/py-symengine/package.py index 3e3664f0758..33953c4b9e7 100644 --- a/var/spack/repos/builtin/packages/py-symengine/package.py +++ b/var/spack/repos/builtin/packages/py-symengine/package.py @@ -10,14 +10,14 @@ class PySymengine(PythonPackage): """Python wrappers for SymEngine, a symbolic manipulation library.""" homepage = "https://github.com/symengine/symengine.py" - url = "https://github.com/symengine/symengine.py/archive/v0.2.0.tar.gz" + url = "https://pypi.io/packages/source/s/symengine/symengine-0.2.0.tar.gz" git = "https://github.com/symengine/symengine.py.git" version('develop', branch='master') - version('0.2.0', sha256='8f6468137baa7f799e047dd0b9149c4017d8d32e755f1e0329209680879c1f8f') + version('0.2.0', sha256='78a14aea7aad5e7cbfb5cabe141581f9bba30e3c319690e5db8ad99fdf2d8885') # Build dependencies - depends_on('python@2.7:2.8,3.3:') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-cython@0.19.1:', type='build') depends_on('cmake@2.8.7:', type='build') diff --git a/var/spack/repos/builtin/packages/py-tables/package.py b/var/spack/repos/builtin/packages/py-tables/package.py index 2fcb494c6ce..c6476692d82 100644 --- a/var/spack/repos/builtin/packages/py-tables/package.py +++ b/var/spack/repos/builtin/packages/py-tables/package.py @@ -11,18 +11,17 @@ class PyTables(PythonPackage): efficiently and easily cope with extremely large amounts of data.""" homepage = "http://www.pytables.org/" - url = "https://github.com/PyTables/PyTables/archive/v3.6.0.tar.gz" + url = "https://pypi.io/packages/source/t/tables/tables-3.6.0.tar.gz" import_modules = [ 'tables', 'tables.misc', 'tables.nodes', 'tables.scripts' ] - version('3.6.0', sha256='2dcd077f42b195f48aa00f5a720b79189ea92fba0d16ad35e2881e403ba6914e') - version('3.5.2', sha256='e4fc6f1194f02a8b10ff923e77364fb70710592f620d7de35f4d4e064dc70e91') - version('3.4.4', sha256='c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114') - version('3.3.0', sha256='dceb15fef556a2775121bcc695561df4ff0e09248e0ce3a2d58f5244a9f61421') - version('3.2.2', sha256='2626e874caa6b3fcf2bfc28b9dd6a40a3f859c72e19ce0764a60a6d77e350008', - url='https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz') + version('3.6.0', sha256='db3488214864fb313a611fca68bf1c9019afe4e7877be54d0e61c84416603d4d') + version('3.5.2', sha256='b220e32262bab320aa41d33125a7851ff898be97c0de30b456247508e2cc33c2') + version('3.4.4', sha256='bdc5c073712af2a43babd139c4855fc99496bb2c3f3f5d1b4770a985e6f9ce29') + version('3.3.0', sha256='8383ccf02e041a5d55494a09fc5514140b4653055a2732c981b5fd0f7408822c') + version('3.2.2', sha256='3564b351a71ec1737b503b001eb7ceae1f65d5d6e3ffe1ea75aafba10f37fa84') variant('zlib', default=True, description='Support for zlib compression') variant('bzip2', default=False, description='Support for bzip2 compression') diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tap-py/package.py similarity index 90% rename from var/spack/repos/builtin/packages/py-tappy/package.py rename to var/spack/repos/builtin/packages/py-tap-py/package.py index 1c97e7a763a..c0ece59fd6e 100644 --- a/var/spack/repos/builtin/packages/py-tappy/package.py +++ b/var/spack/repos/builtin/packages/py-tap-py/package.py @@ -6,10 +6,10 @@ from spack import * -class PyTappy(PythonPackage): +class PyTapPy(PythonPackage): """Python TAP interface module for unit tests""" + homepage = "https://github.com/mblayman/tappy" - # base https://pypi.python.org/pypi/cffi url = "https://pypi.io/packages/source/t/tap.py/tap.py-1.6.tar.gz" version('1.6', sha256='3ee315567cd1cf444501c405b7f7146ffdb2e630bac58d0840d378a3b9a0dbe4') diff --git a/var/spack/repos/builtin/packages/py-udunits/package.py b/var/spack/repos/builtin/packages/py-udunits/package.py deleted file mode 100644 index b7fb343439e..00000000000 --- a/var/spack/repos/builtin/packages/py-udunits/package.py +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * -import os - - -class PyUdunits(PythonPackage): - """The MetOffice cf_units Python interface to the UDUNITS-2 Library.""" - homepage = "https://github.com/SciTools/cf_units" - url = "https://github.com/SciTools/cf_units/archive/v1.1.3.tar.gz" - - version('1.1.3', sha256='cc27f4f06c99d242c36beb8dc5c517e1b1124a8c65ca3f76f372b9674aa320ba') - - maintainers = ['citibeth'] - - depends_on('py-setuptools', type='build') - depends_on('py-six', type=('build', 'run')) - depends_on('py-netcdf4', type=('build', 'run')) - depends_on('udunits2') - - # See: https://github.com/SciTools/cf_units/blob/master/cf_units/etc/site.cfg.template - # udunits2_path = /path/to/libudunits2.so - # udunits2_xml_path = /path/to/udunits2.xml - site_cfg_template = """[System] -udunits2_path = %s -udunits2_xml_path = %s -""" - - @run_after('install') - def configure_template(self): - spec = self.spec - - cfg_templates = find(spec.prefix, ['site.cfg.template']) - if len(cfg_templates) != 1: - tty.die( - 'Found %d instances of site.cfg.template, wanted 1' % - len(cfg_templates)) - cfg_template = cfg_templates[0] - - cfg = os.path.join(os.path.split(cfg_template)[0], 'site.cfg') - - udunits2_xml_path = os.path.join( - spec['udunits2'].prefix, 'share', 'udunits', 'udunits2.xml') - - with open(cfg, 'w') as fout: - fout.write(self.site_cfg_template % - (spec['udunits2'].libs, udunits2_xml_path)) diff --git a/var/spack/repos/builtin/packages/py-wand/package.py b/var/spack/repos/builtin/packages/py-wand/package.py index ac4f82fd5b3..fcecd5e663a 100644 --- a/var/spack/repos/builtin/packages/py-wand/package.py +++ b/var/spack/repos/builtin/packages/py-wand/package.py @@ -20,7 +20,7 @@ class PyWand(PythonPackage): depends_on('py-setuptools', type='build') # provides libmagickwand - depends_on('image-magick') + depends_on('imagemagick') depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-sphinx@1:', type='build', when='+docs') diff --git a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py index 589e733c77b..9ce05b1c35a 100644 --- a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py +++ b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py @@ -16,4 +16,4 @@ class PyWidgetsnbextension(PythonPackage): depends_on('py-setuptools', type='build') depends_on('python@2.7:2.8,3.3:') - depends_on('py-jupyter-notebook@4.2.0:', type=('build', 'run')) + depends_on('py-notebook@4.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-xdot/package.py b/var/spack/repos/builtin/packages/py-xdot/package.py index ecdc47e4941..3f09fc6b32c 100644 --- a/var/spack/repos/builtin/packages/py-xdot/package.py +++ b/var/spack/repos/builtin/packages/py-xdot/package.py @@ -11,12 +11,12 @@ class PyXdot(PythonPackage): dot language.""" homepage = "https://github.com/jrfonseca/xdot.py" - url = "https://github.com/jrfonseca/xdot.py/archive/0.9.tar.gz" + url = "https://pypi.io/packages/source/x/xdot/xdot-1.0.tar.gz" git = "https://github.com/jrfonseca/xdot.py.git" - version('master', branch="master") - version('1.0', sha256='a8594f94f43f938e01e42ff6015c7e00e3ee1a00c7f06d6287d8c939ffa94f76') - version('0.9', sha256='df7790db573d7a5512e6fa618d9051508c43cf64ca432d97c2207c87b6f20dbd') + version('master', branch='master') + version('1.0', sha256='7e067896d729af82f1fd0758e265f129944d469c30f550e3f15dbdb751cc42a1') + version('0.9', sha256='a33701664ecfefe7c7313a120a587e87334f3a566409bc451538fcde5edd6907') # setuptools is required at runtime to avoid: # No module named 'pkg_resources' @@ -46,17 +46,17 @@ def post_install(self): python3 = spec['python'].command python3('-m', 'compileall', dst) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): spec = self.spec - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['pango'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['atk'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['gdk-pixbuf'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['gtkplus'].prefix.lib, - 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['pango'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['atk'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['gdk-pixbuf'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['gtkplus'].prefix.lib, + 'girepository-1.0')) diff --git a/var/spack/repos/builtin/packages/qt-creator/package.py b/var/spack/repos/builtin/packages/qt-creator/package.py index 9b23300a655..1aae1353b6e 100644 --- a/var/spack/repos/builtin/packages/qt-creator/package.py +++ b/var/spack/repos/builtin/packages/qt-creator/package.py @@ -9,7 +9,7 @@ class QtCreator(QMakePackage): """The Qt Creator IDE.""" homepage = 'https://www.qt.io/ide/' - url = 'http://download.qt.io/official_releases/qtcreator/4.3/4.3.1/qt-creator-opensource-src-4.3.1.tar.gz' + url = 'http://download.qt.io/official_releases/qtcreator/4.8/4.8.0/qt-creator-opensource-src-4.8.0.tar.gz' list_url = 'http://download.qt.io/official_releases/qtcreator/' list_depth = 2 @@ -32,8 +32,8 @@ def url_for_version(self, version): url = 'http://download.qt.io/official_releases/qtcreator/{0}/{1}/qt-creator-opensource-src-{1}.tar.gz' return url.format(version.up_to(2), version) - def setup_environment(self, spack_env, run_env): - spack_env.set('INSTALL_ROOT', self.prefix) + def setup_build_environment(self, env): + env.set('INSTALL_ROOT', self.prefix) def qmake_args(self): return ['-r'] diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py index 69426a1cd7f..7883e4c8e35 100644 --- a/var/spack/repos/builtin/packages/r-animation/package.py +++ b/var/spack/repos/builtin/packages/r-animation/package.py @@ -22,7 +22,7 @@ class RAnimation(RPackage): depends_on('r@2.14:', type=('build', 'run')) depends_on('r-magick', when='@2.6:', type=('build', 'run')) - depends_on('image-magick') + depends_on('imagemagick') depends_on('ffmpeg') depends_on('swftools') depends_on('texlive') diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index c212794956b..08656458f40 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -13,7 +13,7 @@ class RCheckpoint(RPackage): date as if you had a CRAN time machine.""" homepage = "https://cloud.r-project.org/package=checkpoint" - url = "https://cloud.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz" + url = "https://cloud.r-project.org/src/contrib/checkpoint_0.4.6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint" version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') diff --git a/var/spack/repos/builtin/packages/r-magick/package.py b/var/spack/repos/builtin/packages/r-magick/package.py index 66ae0496151..858b92174fc 100644 --- a/var/spack/repos/builtin/packages/r-magick/package.py +++ b/var/spack/repos/builtin/packages/r-magick/package.py @@ -27,4 +27,4 @@ class RMagick(RPackage): depends_on('r-rcpp@0.12.12:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-curl', type=('build', 'run')) - depends_on('image-magick') + depends_on('imagemagick') diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py index 5ccf4dd6cd5..4ff0958eea1 100644 --- a/var/spack/repos/builtin/packages/r-mzr/package.py +++ b/var/spack/repos/builtin/packages/r-mzr/package.py @@ -24,5 +24,5 @@ class RMzr(RPackage): depends_on('r-protgenerics', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('netcdf') + depends_on('netcdf-c') depends_on('r@3.4.0:3.4.9', when='@2.10.0') diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index 14e12733811..1a837ded216 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -30,4 +30,4 @@ class RNcdf4(RPackage): version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253') version('1.15', sha256='d58298f4317c6c80a041a70216126492fd09ba8ecde9da09d5145ae26f324d4d') - depends_on('netcdf@4.1:') + depends_on('netcdf-c@4.1:') diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index 95346b8290d..d89d20ef029 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -15,7 +15,7 @@ class RNmf(RPackage): computations on multicore machines..""" homepage = "http://renozao.github.io/NMF" - url = "https://cloud.r-project.org/src/contrib/NMF_0.20.6.tar.gz" + url = "https://cloud.r-project.org/src/contrib/NMF_0.21.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index 4ec6ee90557..7e44f3b9e82 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -27,4 +27,4 @@ class RPbdzmq(RPackage): depends_on('r@3.0.0:', when='@:0.2-5', type=('build', 'run')) depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run')) depends_on('r-r6', when='@:0.2-6', type=('build', 'run')) - depends_on('zeromq@4.0.4:') + depends_on('libzmq@4.0.4:') diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index e400f1228fb..d2c2843f3a3 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -16,7 +16,7 @@ class RPkgmaker(RPackage): changes in the interface(s) are more than likely to happen.""" homepage = "https://renozao.github.io/pkgmaker" - url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" + url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.27.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index f8420eebb0a..f3d5e951f93 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -13,7 +13,7 @@ class RRandomfieldsutils(RPackage): Furthermore, it includes the Struve functions.""" homepage = "https://cloud.r-project.org/package=RandomFieldsUtils" - url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.3.25.tar.gz" + url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.5.3.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFieldsUtils" version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index c4b52c34371..30762d74642 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -14,7 +14,7 @@ class RRngtools(RPackage): the way current RNG settings can be changed.""" homepage = "https://renozao.github.io/rngtools" - url = "https://cloud.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + url = "https://cloud.r-project.org/src/contrib/rngtools_1.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rngtools" version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index aeaa990a459..862ebcf0663 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -19,4 +19,4 @@ class RRzmq(RPackage): version('0.7.7', sha256='bdbaf77a0e04c5b6d6ce79ab2747848a5044355eed2e2c4d39c4ba16f97dc83d') depends_on('r@3.1.0:', when='@0.9.0:', type=('build', 'run')) - depends_on('zeromq@3.0.0:') + depends_on('libzmq@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py index 551455471fe..120895ec77c 100644 --- a/var/spack/repos/builtin/packages/r-udunits2/package.py +++ b/var/spack/repos/builtin/packages/r-udunits2/package.py @@ -16,4 +16,4 @@ class RUdunits2(RPackage): version('0.13', sha256='d155d3c07f6202b65dec4075ffd1e1c3f4f35f5fdece8cfb319d39256a3e5b79') depends_on('r@2.10.0:', type=('build', 'run')) - depends_on('udunits2') + depends_on('udunits') diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py index c6b4ce8f193..936a4a695c5 100644 --- a/var/spack/repos/builtin/packages/r-units/package.py +++ b/var/spack/repos/builtin/packages/r-units/package.py @@ -25,4 +25,4 @@ class RUnits(RPackage): depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-udunits2@0.13:', when='@:0.5-1', type=('build', 'run')) depends_on('r-rcpp@0.12.10:', type=('build', 'run')) - depends_on('udunits2', when='@0.6-0:') + depends_on('udunits', when='@0.6-0:') diff --git a/var/spack/repos/builtin/packages/r-wgcna/package.py b/var/spack/repos/builtin/packages/r-wgcna/package.py index 7b21e756edd..426116c677a 100644 --- a/var/spack/repos/builtin/packages/r-wgcna/package.py +++ b/var/spack/repos/builtin/packages/r-wgcna/package.py @@ -10,7 +10,7 @@ class RWgcna(RPackage): """WGCNA: Weighted Correlation Network Analysis""" homepage = "https://cloud.r-project.org/package=WGCNA" - url = "https://cloud.r-project.org/src/contrib/WGCNA_1.66.tar.gz" + url = "https://cloud.r-project.org/src/contrib/WGCNA_1.68.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/WGCNA/" version('1.68', sha256='0a04f15a20817f9260ae1896eda3be83a7f4855a27a348df85c7f4d376f1efe8') diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index ee0f934447b..2f575b9cfa8 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -11,7 +11,7 @@ class RXlsx(RPackage): 97/2000/XP/2003 file formats.""" homepage = "http://code.google.com/p/rexcel/" - url = "https://cloud.r-project.org/src/contrib/xlsx_0.5.7.tar.gz" + url = "https://cloud.r-project.org/src/contrib/xlsx_0.6.1.tar.gz" listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') diff --git a/var/spack/repos/builtin/packages/r3d/package.py b/var/spack/repos/builtin/packages/r3d/package.py index 6e2984253c6..6704e054192 100644 --- a/var/spack/repos/builtin/packages/r3d/package.py +++ b/var/spack/repos/builtin/packages/r3d/package.py @@ -11,11 +11,11 @@ class R3d(MakefilePackage): conservative voxelization.""" homepage = "https://github.com/devonmpowell/r3d" - url = "https://github.com/devonmpowell/r3d.git" + git = "https://github.com/devonmpowell/r3d.git" - version('2019-04-24', git=url, commit='86cea79c124c6a8edd8c8cdea61e3e923acb0b22') - version('2018-12-19', git=url, commit='47308f68c782ed3227d3dab1eff24d41f6421f21') - version('2018-01-07', git=url, commit='d6799a582256a120ef3bd7e18959e96cba0e5495') + version('2019-04-24', commit='86cea79c124c6a8edd8c8cdea61e3e923acb0b22') + version('2018-12-19', commit='47308f68c782ed3227d3dab1eff24d41f6421f21') + version('2018-01-07', commit='d6799a582256a120ef3bd7e18959e96cba0e5495') variant("test", default=False, description="Build R3D regression tests") diff --git a/var/spack/repos/builtin/packages/rankstr/package.py b/var/spack/repos/builtin/packages/rankstr/package.py index c72c46b54a8..d56b9211ad0 100644 --- a/var/spack/repos/builtin/packages/rankstr/package.py +++ b/var/spack/repos/builtin/packages/rankstr/package.py @@ -10,7 +10,7 @@ class Rankstr(CMakePackage): """Assign one-to-one mapping of MPI ranks to strings""" homepage = "https://github.com/ECP-VeloC/rankstr" - url = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.1.zip" + url = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.2.zip" git = "https://github.com/ecp-veloc/rankstr.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/redset/package.py b/var/spack/repos/builtin/packages/redset/package.py index d875c1ddfc9..c439bdd10e1 100644 --- a/var/spack/repos/builtin/packages/redset/package.py +++ b/var/spack/repos/builtin/packages/redset/package.py @@ -10,7 +10,7 @@ class Redset(CMakePackage): """Create MPI communicators for disparate redundancy sets""" homepage = "https://github.com/ECP-VeloC/redset" - url = "https://github.com/ECP-VeloC/redset/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/redset/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/redset.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/regcm/package.py b/var/spack/repos/builtin/packages/regcm/package.py index fc80deb4d03..136c2703596 100644 --- a/var/spack/repos/builtin/packages/regcm/package.py +++ b/var/spack/repos/builtin/packages/regcm/package.py @@ -45,11 +45,11 @@ class Regcm(AutotoolsPackage): description='Build NetCDF using the high performance parallel ' 'NetCDF implementation.') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') depends_on('hdf5') depends_on('mpi') - depends_on('netcdf +parallel-netcdf', when='+pnetcdf') + depends_on('netcdf-c +parallel-netcdf', when='+pnetcdf') intel_msg = ('Intel compiler not working with this specific version of ' 'RegCM (generates a bug at runtime): please install a newer ' diff --git a/var/spack/repos/builtin/packages/repeatmodeler/package.py b/var/spack/repos/builtin/packages/repeatmodeler/package.py index fa395f4109a..f068fb26009 100644 --- a/var/spack/repos/builtin/packages/repeatmodeler/package.py +++ b/var/spack/repos/builtin/packages/repeatmodeler/package.py @@ -18,7 +18,7 @@ class Repeatmodeler(Package): depends_on('perl', type=('build', 'run')) depends_on('perl-json', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) depends_on('repeatmasker', type='run') depends_on('recon+repeatmasker', type='run') diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index 23b497a2e74..90b6d0d6dd6 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -16,8 +16,7 @@ class Rose(AutotoolsPackage): (Developed at Lawrence Livermore National Lab)""" homepage = "http://rosecompiler.org/" - # url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.7.0.tar.gz" - url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.9.104.zip" + url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.10.0.zip" git = "https://github.com/rose-compiler/rose-develop.git" # -------------------------------------------------------------------------- @@ -212,9 +211,9 @@ def configure_args(self): return args - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if "+codethorn" in self.spec: - spack_env.set("CXXFLAGS", "-std=c++11") + env.set("CXXFLAGS", "-std=c++11") def build(self, spec, prefix): # Spack will automatically pass ncpus as the number of make jobs. diff --git a/var/spack/repos/builtin/packages/seacas/package.py b/var/spack/repos/builtin/packages/seacas/package.py index f02cb9b09e0..f4c145d243e 100644 --- a/var/spack/repos/builtin/packages/seacas/package.py +++ b/var/spack/repos/builtin/packages/seacas/package.py @@ -71,8 +71,8 @@ class Seacas(CMakePackage): # Everything should be compiled position independent (-fpic) - depends_on('netcdf@4.6.2:+mpi+parallel-netcdf', when='+mpi') - depends_on('netcdf@4.6.2:~mpi', when='~mpi') + depends_on('netcdf-c@4.6.2:+mpi+parallel-netcdf', when='+mpi') + depends_on('netcdf-c@4.6.2:~mpi', when='~mpi') depends_on('cgns@develop+mpi+scoping', when='+cgns +mpi') depends_on('cgns@develop~mpi+scoping', when='+cgns ~mpi') depends_on('adios2@develop~mpi', when='+adios2 ~mpi') @@ -198,10 +198,10 @@ def cmake_args(self): ]) # ##################### Dependencies ########################## - # Always need NetCDF + # Always need NetCDF-C options.extend([ '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix, + '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix, ]) if '+metis' in spec: diff --git a/var/spack/repos/builtin/packages/shuffile/package.py b/var/spack/repos/builtin/packages/shuffile/package.py index 13ba8b96b4b..bfd6defb233 100644 --- a/var/spack/repos/builtin/packages/shuffile/package.py +++ b/var/spack/repos/builtin/packages/shuffile/package.py @@ -10,7 +10,7 @@ class Shuffile(CMakePackage): """Shuffle files between MPI ranks""" homepage = "https://github.com/ECP-VeloC/shuffile" - url = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/shuffile.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/siesta/package.py b/var/spack/repos/builtin/packages/siesta/package.py index 70d52a2607c..1733585274a 100644 --- a/var/spack/repos/builtin/packages/siesta/package.py +++ b/var/spack/repos/builtin/packages/siesta/package.py @@ -23,7 +23,7 @@ class Siesta(Package): depends_on('blas') depends_on('lapack') depends_on('scalapack') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') phases = ['configure', 'build', 'install'] @@ -40,7 +40,7 @@ def configure(self, spec, prefix): spec['blas'].libs), '--with-scalapack=%s' % spec['scalapack'].libs, '--with-netcdf=%s' % (spec['netcdf-fortran'].libs + - spec['netcdf'].libs), + spec['netcdf-c'].libs), # need to specify MPIFC explicitly below, otherwise # Intel's mpiifort is not found 'MPIFC=%s' % spec['mpi'].mpifc diff --git a/var/spack/repos/builtin/packages/simulationio/package.py b/var/spack/repos/builtin/packages/simulationio/package.py index 51b43719d89..d209f702f72 100644 --- a/var/spack/repos/builtin/packages/simulationio/package.py +++ b/var/spack/repos/builtin/packages/simulationio/package.py @@ -11,7 +11,7 @@ class Simulationio(CMakePackage): """SimulationIO: Efficient and convenient I/O for large PDE simulations""" homepage = "https://github.com/eschnett/SimulationIO" - url = "https://github.com/eschnett/SimulationIO/archive/version/0.1.0.tar.gz" + url = "https://github.com/eschnett/SimulationIO/archive/version/9.0.1.tar.gz" git = "https://github.com/eschnett/SimulationIO.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/squid/package.py b/var/spack/repos/builtin/packages/squid/package.py index a039bbedc5b..bce6f19590f 100644 --- a/var/spack/repos/builtin/packages/squid/package.py +++ b/var/spack/repos/builtin/packages/squid/package.py @@ -10,5 +10,6 @@ class Squid(AutotoolsPackage): """C function library for sequence analysis.""" homepage = "http://eddylab.org/software.html" + url = "http://eddylab.org/software/squid/squid-1.9g.tar.gz" - version('1.9g', sha256='302f42e8794aa4dbcfa0996c14fb7a70a7c4397fc45c2bbd2748055460d8dca7', url='http://eddylab.org/software/squid/squid.tar.gz') + version('1.9g', sha256='302f42e8794aa4dbcfa0996c14fb7a70a7c4397fc45c2bbd2748055460d8dca7') diff --git a/var/spack/repos/builtin/packages/sra-toolkit/package.py b/var/spack/repos/builtin/packages/sratoolkit/package.py similarity index 83% rename from var/spack/repos/builtin/packages/sra-toolkit/package.py rename to var/spack/repos/builtin/packages/sratoolkit/package.py index 972f4d8a70d..a8cf5d9b6cd 100644 --- a/var/spack/repos/builtin/packages/sra-toolkit/package.py +++ b/var/spack/repos/builtin/packages/sratoolkit/package.py @@ -6,7 +6,7 @@ from spack import * -class SraToolkit(Package): +class Sratoolkit(Package): """The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.""" @@ -18,10 +18,6 @@ class SraToolkit(Package): version('2.9.2', sha256='17dbe13aa1ed7955d31e1e76e8b62786e80a77e9ed9d396631162dc3ad8b716d') version('2.8.2-1', sha256='b053061aae7c6d00162fe0f514be4128a60365b4b2b5b36e7f4798b348b55cf5') - def url_for_version(self, version): - url = 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{0}/sratoolkit.{0}-centos_linux64.tar.gz' - return url.format(version) - def install(self, spec, prefix): install_tree('bin', prefix.bin, symlinks=True) install_tree('example', prefix.example) diff --git a/var/spack/repos/builtin/packages/stc/package.py b/var/spack/repos/builtin/packages/stc/package.py index ce52a418f26..631d7647e7b 100644 --- a/var/spack/repos/builtin/packages/stc/package.py +++ b/var/spack/repos/builtin/packages/stc/package.py @@ -11,7 +11,7 @@ class Stc(AutotoolsPackage): """STC: The Swift-Turbine Compiler""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.8.3.tar.gz' git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index de26e0decea..ba621061fdd 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -34,7 +34,7 @@ class Subversion(AutotoolsPackage): extends('perl', when='+perl') depends_on('swig@1.3.24:3.0.0', when='+perl') - depends_on('perl-term-readkey', when='+perl') + depends_on('perl-termreadkey', when='+perl') # Installation has race cases. parallel = False diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 0644ed1feaa..098de9bacd5 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -17,7 +17,7 @@ class Thrift(Package): """ homepage = "http://thrift.apache.org" - url = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz" + url = "http://apache.mirrors.ionfish.org/thrift/0.11.0/thrift-0.11.0.tar.gz" version('0.11.0', sha256='c4ad38b6cb4a3498310d405a91fef37b9a8e79a50cd0968148ee2524d2fa60c2') version('0.10.0', sha256='2289d02de6e8db04cbbabb921aeb62bfe3098c4c83f36eec6c31194301efa10b') @@ -47,10 +47,10 @@ class Thrift(Package): depends_on('zlib', when='+c') depends_on('libevent', when='+c') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '+pic' in self.spec: - spack_env.append_flags('CFLAGS', self.compiler.pic_flag) - spack_env.append_flags('CXXFLAGS', self.compiler.pic_flag) + env.append_flags('CFLAGS', self.compiler.pic_flag) + env.append_flags('CXXFLAGS', self.compiler.pic_flag) def install(self, spec, prefix): env['PY_PREFIX'] = prefix diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py index 85cf56bd858..a77fcbd621b 100644 --- a/var/spack/repos/builtin/packages/transabyss/package.py +++ b/var/spack/repos/builtin/packages/transabyss/package.py @@ -16,7 +16,7 @@ class Transabyss(Package): depends_on('abyss@1.5.2') depends_on('python@2.7.6:', type=('build', 'run')) - depends_on('py-igraph@0.7.0:', type=('build', 'run')) + depends_on('py-python-igraph@0.7.0:', type=('build', 'run')) depends_on('blat') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py b/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py index f1bc186dcf8..0826b8d00ce 100644 --- a/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py +++ b/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py @@ -10,7 +10,6 @@ class TrilinosCatalystIossAdapter(CMakePackage): """Adapter for Trilinos Seacas Ioss and Paraview Catalyst""" homepage = "https://trilinos.org/" - url = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-12-1.tar.gz" git = "https://github.com/trilinos/Trilinos.git" version('develop', branch='develop') @@ -20,17 +19,17 @@ class TrilinosCatalystIossAdapter(CMakePackage): depends_on('flex', type='build') depends_on('paraview+mpi+python+osmesa') depends_on('py-numpy', type=('build', 'run')) - # Here we avoid paraview trying to use netcdf~parallel-netcdf - # which is netcdf's default, even though paraview depends on 'netcdf' + # Here we avoid paraview trying to use netcdf-c~parallel-netcdf + # which is netcdf-c's default, even though paraview depends on 'netcdf-c' # without any variants. Concretizer bug? - depends_on('netcdf+parallel-netcdf') + depends_on('netcdf-c+parallel-netcdf') root_cmakelists_dir = join_path('packages', 'seacas', 'libraries', 'ioss', 'src', 'visualization', 'ParaViewCatalystIossAdapter') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PYTHONPATH', self.prefix.python) + def setup_run_environment(self, env): + env.prepend_path('PYTHONPATH', self.prefix.python) def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 47e1fb1936f..db6621ed6b9 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -297,8 +297,8 @@ class Trilinos(CMakePackage): # MPI related dependencies depends_on('mpi') - depends_on('netcdf+mpi', when="~pnetcdf") - depends_on('netcdf+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:") + depends_on('netcdf-c+mpi', when="~pnetcdf") + depends_on('netcdf-c+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:") depends_on('parallel-netcdf', when="+pnetcdf@master,12.12.1:") depends_on('parmetis', when='+metis') depends_on('cgns', when='+cgns') @@ -505,7 +505,7 @@ def cmake_args(self): '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names), '-DLAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories), '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix, + '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix, '-DTPL_ENABLE_X11:BOOL=%s' % ( 'ON' if '+x11' in spec else 'OFF'), '-DTrilinos_ENABLE_Gtest:BOOL=%s' % ( diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py index 997e36c0efd..68b8c7b98c2 100644 --- a/var/spack/repos/builtin/packages/trinity/package.py +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -52,7 +52,7 @@ class Trinity(MakefilePackage): depends_on("samtools", type="run") depends_on("py-numpy", type="run") depends_on("express", type="run") - depends_on("perl-dbfile", type="run") + depends_on("perl-db-file", type="run") depends_on("perl-uri", type="run") depends_on("r-fastcluster", type="run") depends_on("r-ctc", type="run") @@ -85,7 +85,9 @@ def install(self, spec, prefix): force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin', '.hidden')) - def setup_environment(self, spack_env, run_env): - run_env.set('TRINITY_HOME', self.prefix.bin) - run_env.prepend_path('PATH', self.prefix.bin.util) - spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag) + def setup_build_environment(self, env): + env.append_flags('CXXFLAGS', self.compiler.openmp_flag) + + def setup_run_environment(self, env): + env.set('TRINITY_HOME', self.prefix.bin) + env.prepend_path('PATH', self.prefix.bin.util) diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py index 4788efd070f..902cae7a946 100644 --- a/var/spack/repos/builtin/packages/turbine/package.py +++ b/var/spack/repos/builtin/packages/turbine/package.py @@ -13,7 +13,7 @@ class Turbine(AutotoolsPackage): """Turbine: The Swift/T runtime""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-1.2.3.tar.gz' git = "https://github.com/swift-lang/swift-t.git" configure_directory = 'turbine/code' @@ -44,12 +44,12 @@ class Turbine(AutotoolsPackage): depends_on('libtool', type='build', when='@master') depends_on('m4', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('CXXLD', spec['mpi'].mpicxx) + env.set('CC', spec['mpi'].mpicc) + env.set('CXX', spec['mpi'].mpicxx) + env.set('CXXLD', spec['mpi'].mpicxx) @property def configure_directory(self): diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits/package.py similarity index 95% rename from var/spack/repos/builtin/packages/udunits2/package.py rename to var/spack/repos/builtin/packages/udunits/package.py index c5704d6a5e1..e3e31bee5c9 100644 --- a/var/spack/repos/builtin/packages/udunits2/package.py +++ b/var/spack/repos/builtin/packages/udunits/package.py @@ -6,7 +6,7 @@ from spack import * -class Udunits2(AutotoolsPackage): +class Udunits(AutotoolsPackage): """Automated units conversion""" homepage = "http://www.unidata.ucar.edu/software/udunits" diff --git a/var/spack/repos/builtin/packages/vmatch/package.py b/var/spack/repos/builtin/packages/vmatch/package.py index 3cedce4ede6..b4433f6174e 100644 --- a/var/spack/repos/builtin/packages/vmatch/package.py +++ b/var/spack/repos/builtin/packages/vmatch/package.py @@ -15,9 +15,5 @@ class Vmatch(Package): version('2.3.0', sha256='5e18d0dddf04e86dad193fcdde6e48f3901365932634125602d8808f35acf979') - def url_for_version(self, version): - url = 'http://www.vmatch.de/distributions/vmatch-{0}-Linux_x86_64-64bit.tar.gz' - return url.format(version) - def install(self, spec, prefix): install_tree(self.stage.source_path, prefix.bin) diff --git a/var/spack/repos/builtin/packages/vtkh/package.py b/var/spack/repos/builtin/packages/vtk-h/package.py similarity index 90% rename from var/spack/repos/builtin/packages/vtkh/package.py rename to var/spack/repos/builtin/packages/vtk-h/package.py index 3d60ee9a504..e3c1bd4031b 100644 --- a/var/spack/repos/builtin/packages/vtkh/package.py +++ b/var/spack/repos/builtin/packages/vtk-h/package.py @@ -28,7 +28,7 @@ def cmake_cache_entry(name, value, vtype=None): return 'set({0} "{1}" CACHE {2} "")\n\n'.format(name, value, vtype) -class Vtkh(Package): +class VtkH(Package): """VTK-h is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-h brings together several projects like VTK-m and DIY2 to provide a toolkit with hybrid parallel capabilities.""" @@ -53,29 +53,29 @@ class Vtkh(Package): depends_on("intel-tbb", when="@0.1.0+tbb") depends_on("cuda", when="+cuda") - depends_on("vtkm@1.2.0", when="@0.1.0") - depends_on("vtkm@1.2.0+tbb", when="@0.1.0+tbb") - depends_on("vtkm@1.2.0+cuda", when="@0.1.0+cuda") - depends_on("vtkm@1.2.0~shared", when="@0.1.0~shared") + depends_on("vtk-m@1.2.0", when="@0.1.0") + depends_on("vtk-m@1.2.0+tbb", when="@0.1.0+tbb") + depends_on("vtk-m@1.2.0+cuda", when="@0.1.0+cuda") + depends_on("vtk-m@1.2.0~shared", when="@0.1.0~shared") - depends_on("vtkm@master~tbb+openmp", when="@develop+openmp") - depends_on("vtkm@master~tbb~openmp", when="@develop~openmp") + depends_on("vtk-m@master~tbb+openmp", when="@develop+openmp") + depends_on("vtk-m@master~tbb~openmp", when="@develop~openmp") - depends_on("vtkm@master+cuda~tbb+openmp", when="@develop+cuda+openmp") - depends_on("vtkm@master+cuda~tbb~openmp", when="@develop+cuda~openmp") + depends_on("vtk-m@master+cuda~tbb+openmp", when="@develop+cuda+openmp") + depends_on("vtk-m@master+cuda~tbb~openmp", when="@develop+cuda~openmp") - depends_on("vtkm@master~tbb+openmp~shared", when="@develop+openmp~shared") - depends_on("vtkm@master~tbb~openmp~shared", when="@develop~openmp~shared") + depends_on("vtk-m@master~tbb+openmp~shared", when="@develop+openmp~shared") + depends_on("vtk-m@master~tbb~openmp~shared", when="@develop~openmp~shared") - depends_on("vtkm@master+cuda~tbb+openmp~shared", when="@develop+cuda+openmp~shared") - depends_on("vtkm@master+cuda~tbb~openmp~shared", when="@develop+cuda~openmp~shared") + depends_on("vtk-m@master+cuda~tbb+openmp~shared", when="@develop+cuda+openmp~shared") + depends_on("vtk-m@master+cuda~tbb~openmp~shared", when="@develop+cuda~openmp~shared") patch('vtkm_lagrange_cuda_fix.patch') def install(self, spec, prefix): with working_dir('spack-build', create=True): cmake_args = ["../src", - "-DVTKM_DIR={0}".format(spec["vtkm"].prefix), + "-DVTKM_DIR={0}".format(spec["vtk-m"].prefix), "-DENABLE_TESTS=OFF", "-DBUILD_TESTING=OFF"] @@ -203,7 +203,7 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): cfg.write(cmake_cache_entry("ENABLE_OPENMP", "ON")) cfg.write("# vtk-m from spack\n") - cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtkm'].prefix)) + cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtk-m'].prefix)) ####################################################################### # Optional Dependencies diff --git a/var/spack/repos/builtin/packages/vtkh/vtkm_lagrange_cuda_fix.patch b/var/spack/repos/builtin/packages/vtk-h/vtkm_lagrange_cuda_fix.patch similarity index 100% rename from var/spack/repos/builtin/packages/vtkh/vtkm_lagrange_cuda_fix.patch rename to var/spack/repos/builtin/packages/vtk-h/vtkm_lagrange_cuda_fix.patch diff --git a/var/spack/repos/builtin/packages/vtkm/package.py b/var/spack/repos/builtin/packages/vtk-m/package.py similarity index 94% rename from var/spack/repos/builtin/packages/vtkm/package.py rename to var/spack/repos/builtin/packages/vtk-m/package.py index eee37bf9af1..317343bc82c 100644 --- a/var/spack/repos/builtin/packages/vtkm/package.py +++ b/var/spack/repos/builtin/packages/vtk-m/package.py @@ -9,7 +9,7 @@ import sys -class Vtkm(CMakePackage, CudaPackage): +class VtkM(CMakePackage, CudaPackage): """VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale @@ -90,8 +90,7 @@ def cmake_args(self): # logging support if "+logging" in spec: - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('logging is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_LOGGING:BOOL=ON") @@ -100,8 +99,7 @@ def cmake_args(self): # mpi support if "+mpi" in spec: - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('mpi is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_MPI:BOOL=ON") @@ -111,8 +109,7 @@ def cmake_args(self): # openmp support if "+openmp" in spec: # openmp is added since version 1.3.0 - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('OpenMP is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_OPENMP:BOOL=ON") diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 3d9d108ae44..8ed305c53f1 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -86,7 +86,7 @@ class Vtk(CMakePackage): depends_on('jsoncpp') depends_on('libxml2') depends_on('lz4') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-cxx') depends_on('libpng') depends_on('libtiff') @@ -96,10 +96,10 @@ def url_for_version(self, version): url = "http://www.vtk.org/files/release/{0}/VTK-{1}.tar.gz" return url.format(version.up_to(2), version) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # VTK has some trouble finding freetype unless it is set in # the environment - spack_env.set('FREETYPE_DIR', self.spec['freetype'].prefix) + env.set('FREETYPE_DIR', self.spec['freetype'].prefix) def cmake_args(self): spec = self.spec @@ -120,8 +120,8 @@ def cmake_args(self): '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF', '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF', - '-DNETCDF_DIR={0}'.format(spec['netcdf'].prefix), - '-DNETCDF_C_ROOT={0}'.format(spec['netcdf'].prefix), + '-DNETCDF_DIR={0}'.format(spec['netcdf-c'].prefix), + '-DNETCDF_C_ROOT={0}'.format(spec['netcdf-c'].prefix), '-DNETCDF_CXX_ROOT={0}'.format(spec['netcdf-cxx'].prefix), # Allow downstream codes (e.g. VisIt) to override VTK's classes diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py index 015c38406b6..89c0117d2e6 100644 --- a/var/spack/repos/builtin/packages/warpx/package.py +++ b/var/spack/repos/builtin/packages/warpx/package.py @@ -16,10 +16,10 @@ class Warpx(MakefilePackage): """ homepage = "https://ecp-warpx.github.io/index.html" - url = "https://github.com/ECP-WarpX/WarpX" + git = "https://github.com/ECP-WarpX/WarpX.git" - version('master', git='https://github.com/ECP-WarpX/WarpX.git', tag='master') - version('dev', git='https://github.com/ECP-WarpX/WarpX.git', tag='dev') + version('master', tag='master') + version('dev', tag='dev') depends_on('mpi') @@ -94,11 +94,11 @@ def torf(s): 'TINY_PROFILE = {0}'.format(torf('+tprof'))) makefile.filter('EBASE .*', 'EBASE = warpx') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # --- Fool the compiler into using the "unknown" configuration. # --- With this, it will use the spack provided mpi. - spack_env.set('HOSTNAME', 'unknown') - spack_env.set('NERSC_HOST', 'unknown') + env.set('HOSTNAME', 'unknown') + env.set('NERSC_HOST', 'unknown') def install(self, spec, prefix): make('WarpxBinDir = {0}'.format(prefix.bin), 'all') diff --git a/var/spack/repos/builtin/packages/wireshark/package.py b/var/spack/repos/builtin/packages/wireshark/package.py index 5df47d773b0..cd334ed76e6 100644 --- a/var/spack/repos/builtin/packages/wireshark/package.py +++ b/var/spack/repos/builtin/packages/wireshark/package.py @@ -24,7 +24,7 @@ class Wireshark(CMakePackage): variant('headers', default=True, description='Install headers') depends_on('bison', type='build') - depends_on('cares') + depends_on('c-ares') depends_on('doxygen', type='build') depends_on('flex', type='build') depends_on('git', type='build') diff --git a/var/spack/repos/builtin/packages/xdmf3/package.py b/var/spack/repos/builtin/packages/xdmf3/package.py index 772135846c4..8a245ddc2db 100644 --- a/var/spack/repos/builtin/packages/xdmf3/package.py +++ b/var/spack/repos/builtin/packages/xdmf3/package.py @@ -13,7 +13,6 @@ class Xdmf3(CMakePackage): """ homepage = "http://xdmf.org" - url = "https://gitlab.kitware.com/xdmf/xdmf/-/archive/master/xdmf-master.tar.bz2" git = "https://gitlab.kitware.com/xdmf/xdmf.git" # There is no official release of XDMF and development has largely ceased, diff --git a/var/spack/repos/builtin/packages/xeus/package.py b/var/spack/repos/builtin/packages/xeus/package.py index d67d32d1883..1cca2c2cf5d 100644 --- a/var/spack/repos/builtin/packages/xeus/package.py +++ b/var/spack/repos/builtin/packages/xeus/package.py @@ -23,7 +23,7 @@ class Xeus(CMakePackage): conflicts('%clang@:3.6') conflicts('%intel@:17') - depends_on('zeromq@4.2.5:-libsodium') + depends_on('libzmq@4.2.5:-libsodium') depends_on('cppzmq@4.3.0:') depends_on('cryptopp@7.0.0:') depends_on('xtl@0.4.0:') diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py index 799bdc03d7c..997e54ec57c 100644 --- a/var/spack/repos/builtin/packages/xios/package.py +++ b/var/spack/repos/builtin/packages/xios/package.py @@ -21,7 +21,7 @@ class Xios(Package): description='Build for debugging, development or production') # NOTE: oasis coupler could be supported with a variant - # Use spack versions of blitz and netcdf for compatibility + # Use spack versions of blitz and netcdf-c for compatibility # with recent compilers and optimised platform libraries: patch('bld_extern_1.0.patch', when='@:1.0') patch('bld_extern_1.x.patch', when='@1.1:') @@ -30,7 +30,7 @@ class Xios(Package): # followed by a character is broken (e.g. duration '1d'): patch('llvm_bug_17782.patch', when='@1.1: %clang') - depends_on('netcdf+mpi') + depends_on('netcdf-c+mpi') depends_on('netcdf-fortran') depends_on('hdf5+mpi') depends_on('mpi') @@ -60,8 +60,8 @@ def xios_env(self): def xios_path(self): file = join_path('arch', 'arch-SPACK.path') spec = self.spec - paths = {'NETCDF_INC_DIR': spec['netcdf'].prefix.include, - 'NETCDF_LIB_DIR': spec['netcdf'].prefix.lib, + paths = {'NETCDF_INC_DIR': spec['netcdf-c'].prefix.include, + 'NETCDF_LIB_DIR': spec['netcdf-c'].prefix.lib, 'HDF5_INC_DIR': spec['hdf5'].prefix.include, 'HDF5_LIB_DIR': spec['hdf5'].prefix.lib} text = r""" diff --git a/var/spack/repos/builtin/packages/yambo/package.py b/var/spack/repos/builtin/packages/yambo/package.py index 29d84a20b79..e4c07cf679e 100644 --- a/var/spack/repos/builtin/packages/yambo/package.py +++ b/var/spack/repos/builtin/packages/yambo/package.py @@ -45,20 +45,20 @@ class Yambo(AutotoolsPackage): # MPI dependencies are forced, until we have proper forwarding of variants # # Note that yambo is used as an application, and not linked as a library, - # thus there will be no case where another package pulls-in e.g. netcdf+mpi - # and wants to depend on yambo~mpi. + # thus there will be no case where another package pulls-in e.g. + # netcdf-c+mpi and wants to depend on yambo~mpi. depends_on('mpi', when='+mpi') - depends_on('netcdf+mpi', when='+mpi') + depends_on('netcdf-c+mpi', when='+mpi') depends_on('hdf5+mpi', when='+mpi') depends_on('fftw+mpi', when='+mpi') depends_on('scalapack', when='+mpi') - depends_on('netcdf~mpi', when='~mpi') + depends_on('netcdf-c~mpi', when='~mpi') depends_on('hdf5~mpi', when='~mpi') depends_on('fftw~mpi', when='~mpi') depends_on('hdf5+fortran') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') depends_on('libxc@2.0.3:') @@ -124,7 +124,7 @@ def configure_args(self): '--enable-netcdf-hdf5', '--enable-hdf5-compression', '--with-hdf5-libs={0}'.format(spec['hdf5'].libs), - '--with-netcdf-path={0}'.format(spec['netcdf'].prefix), + '--with-netcdf-path={0}'.format(spec['netcdf-c'].prefix), '--with-netcdff-path={0}'.format(spec['netcdf-fortran'].prefix) ]) From 330cd565177ade3357822aa7aa0e41094534c5d3 Mon Sep 17 00:00:00 2001 From: Sinan Date: Mon, 28 Oct 2019 18:28:42 -0700 Subject: [PATCH 469/499] new package: py-osqp (#13475) --- .../repos/builtin/packages/py-osqp/package.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-osqp/package.py diff --git a/var/spack/repos/builtin/packages/py-osqp/package.py b/var/spack/repos/builtin/packages/py-osqp/package.py new file mode 100644 index 00000000000..2e75e7600f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-osqp/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyOsqp(PythonPackage): + """OSQP: The Operator Splitting QP Solver""" + + homepage = "https://osqp.org/" + url = "https://pypi.io/packages/source/o/osqp/osqp-0.6.1.tar.gz" + + version('0.6.1', sha256='47b17996526d6ecdf35cfaead6e3e05d34bc2ad48bcb743153cefe555ecc0e8c') + + depends_on('cmake', type='build') + depends_on('py-setuptools', type='build') + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-scipy@0.13.2:', type=('build', 'run')) + depends_on('py-future', type=('build', 'run')) From 95e0d118be127e8a513ea82e5451750cd34bbd81 Mon Sep 17 00:00:00 2001 From: Sinan Date: Mon, 28 Oct 2019 18:30:40 -0700 Subject: [PATCH 470/499] new package: py-ecos (#13476) * new package: py-ecos * flake8 --- .../repos/builtin/packages/py-ecos/package.py | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-ecos/package.py diff --git a/var/spack/repos/builtin/packages/py-ecos/package.py b/var/spack/repos/builtin/packages/py-ecos/package.py new file mode 100644 index 00000000000..9c89efa90d0 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ecos/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyEcos(PythonPackage): + """This is the Python package for ECOS: Embedded Cone Solver.""" + + homepage = "https://github.com/embotech/ecos" + url = "https://www.pypi.io/packages/source/e/ecos/ecos-2.0.7.post1.tar.gz" + + version('2.0.7.post1', sha256='83e90f42b3f32e2a93f255c3cfad2da78dbd859119e93844c45d2fca20bdc758') + + depends_on('py-setuptools', type='build') + depends_on('py-nose', type='test') + depends_on('py-numpy@1.6:', type=('build', 'run')) + depends_on('py-scipy@0.9:', type=('build', 'run')) From bc930f310f0511955956b497bf96689b5f4f0ebe Mon Sep 17 00:00:00 2001 From: Sinan Date: Mon, 28 Oct 2019 20:55:08 -0700 Subject: [PATCH 471/499] new package: py-cvxpy (#13478) * new package: py-cvxpy * improve dependency specs --- .../builtin/packages/py-cvxpy/package.py | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-cvxpy/package.py diff --git a/var/spack/repos/builtin/packages/py-cvxpy/package.py b/var/spack/repos/builtin/packages/py-cvxpy/package.py new file mode 100644 index 00000000000..8fc146c3311 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cvxpy/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyCvxpy(PythonPackage): + """Convex optimization, for everyone.""" + + homepage = "https://www.cvxpy.org/index.html" + url = "https://www.pypi.io/packages/source/c/cvxpy/cvxpy-1.0.25.tar.gz" + + version('1.0.25', sha256='8535529ddb807067b0d59661dce1d9a6ddb2a218398a38ea7772328ad8a6ea13') + + depends_on('py-setuptools', type='build') + depends_on('py-nose', type='test') + + depends_on('py-numpy@1.15:', type=('build', 'run')) + depends_on('py-scipy@1.1.0:', type=('build', 'run')) + depends_on('py-ecos@2:', type=('build', 'run')) + depends_on('py-scs@1.1.3:', type=('build', 'run')) + depends_on('py-osqp@0.4.1', type=('build', 'run')) + + depends_on('py-multiprocess', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) From aad8ea172c404b533ab011e60c0e878cc48883f1 Mon Sep 17 00:00:00 2001 From: Simon Pintarelli <1237199+simonpintarelli@users.noreply.github.com> Date: Tue, 29 Oct 2019 04:57:07 +0100 Subject: [PATCH 472/499] Add SpFFT: sparse 3D FFT library (#13458) * Add SpFFT: sparse 3D FFT library SpFFT is required as a dependency for SIRIUS * cleanup * add missing dependency --- .../repos/builtin/packages/spfft/package.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/spfft/package.py diff --git a/var/spack/repos/builtin/packages/spfft/package.py b/var/spack/repos/builtin/packages/spfft/package.py new file mode 100644 index 00000000000..703a1a1674e --- /dev/null +++ b/var/spack/repos/builtin/packages/spfft/package.py @@ -0,0 +1,44 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Spfft(CMakePackage): + """Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.""" + + homepage = "https://github.com/eth-cscs/SpFFT" + url = "https://github.com/eth-cscs/SpFFT/archive/v0.9.8.zip" + + version('0.9.8', sha256='f49fa51316bbfa68309e951d2375e1f6904120c93868cbe13bc2974c0b801a3f') + + variant('openmp', default=True, description="Build with OpenMP support") + variant('mpi', default=True, description="enable MPI") + variant('single_precision', default=False, description="Sinlge precision") + variant('gpu_direct', default=False, description="GPU aware MPI") + variant('static', default=False, description="build static library") + variant('cuda', default=False, description="CUDA") + variant('build_type', default='Release', description='CMake build type', + values=('Debug', 'Release', 'RelWithDebInfo')) + depends_on('fftw') + depends_on('mpi', when='+mpi') + depends_on('cuda', when='+cuda') + + def cmake_args(self): + args = [] + if self.spec.satisfies('+openmp'): + args += ["-DSPFFT_OMP=On"] + if self.spec.satisfies('+mpi'): + args += ["-DSPFFT_MPI=On"] + if self.spec.satisfies('+single_precision'): + args += ["-DSPFFT_SINGLE_PRECISION=On"] + if self.spec.satisfies('+gpu_direct'): + args += ["-DSPFFT_GPU_DIRECT=On"] + if self.spec.satisfies('+cuda'): + args += ["-DSPFFT_BACKEND=CUDA"] + if self.spec.satisfies('+cuda'): + args += ["-DSPFFT_BACKEND=CUDA"] + return args From 3cf21e6edc14e8431a0a65867a45df35aef1911e Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Tue, 29 Oct 2019 00:25:59 -0700 Subject: [PATCH 473/499] bugfix: make `spack -d test test_changed_files` work (#13229) The `test_changed_files` in `test/cmd/flake8.py` was failing because it calls `ArgumentParser.parse_args()` without arguments. Normally that would just parse `sys.argv` but it seems to fail because of something in either `spack test` or `pytest`. Call it with an empty array so that it doesn't try to touch`sys.argv` at all. - [x] allow `-d` spack option for `test_changed_files` --- lib/spack/spack/test/cmd/flake8.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/test/cmd/flake8.py b/lib/spack/spack/test/cmd/flake8.py index b95db93364c..6cad6950ba3 100644 --- a/lib/spack/spack/test/cmd/flake8.py +++ b/lib/spack/spack/test/cmd/flake8.py @@ -45,7 +45,7 @@ def flake8_package(): def test_changed_files(parser, flake8_package): - args = parser.parse_args() + args = parser.parse_args([]) # changed_files returns file paths relative to the root # directory of Spack. Convert to absolute file paths. From 0a5c184a5dc76f0a85650e9f42cce94251d9791a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tiziano=20M=C3=BCller?= Date: Tue, 29 Oct 2019 14:08:58 +0100 Subject: [PATCH 474/499] CP2K: drop json-fortran dependency and add support for the Nvidia V100 (#13468) * cp2k: drop json-fortran dep since that's now handled in SIRIUS internally * cp2k: gained support for Nvidias V100 --- var/spack/repos/builtin/packages/cp2k/package.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index 36b94926dab..4bccecf8607 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -50,7 +50,7 @@ class Cp2k(MakefilePackage, CudaPackage): variant('cuda_arch', description='CUDA architecture', default='none', - values=('none', '35', '37', '60'), + values=('none', '35', '37', '60', '70'), multi=False) variant('cuda_arch_35_k20x', default=False, description=('CP2K (resp. DBCSR) has specific parameter sets for' @@ -121,8 +121,6 @@ class Cp2k(MakefilePackage, CudaPackage): # a consistent/compat. combination is pulled in to the dependency graph. depends_on('sirius+fortran+vdwxc+shared+openmp', when='+sirius+openmp') depends_on('sirius+fortran+vdwxc+shared~openmp', when='+sirius~openmp') - # to get JSON-based UPF format support used in combination with SIRIUS - depends_on('json-fortran', when='+sirius') # the bundled libcusmm uses numpy in the parameter prediction (v7+) depends_on('py-numpy', when='@7:+cuda', type='build') @@ -370,10 +368,6 @@ def edit(self, spec, prefix): fcflags += ['-I{0}'.format(os.path.join(sirius.prefix, 'fortran'))] libs += list(sirius.libs) - cppflags.append('-D__JSON') - fcflags += ['$(shell pkg-config --cflags json-fortran)'] - libs += ['$(shell pkg-config --libs json-fortran)'] - if self.spec.satisfies('+cuda'): cppflags += ['-D__ACC'] libs += ['-lcudart', '-lnvrtc', '-lcuda'] @@ -394,6 +388,7 @@ def edit(self, spec, prefix): '35': 'K40', '37': 'K80', '60': 'P100', + '70': 'V100', }[cuda_arch] if (cuda_arch == '35' From 944ef2f6906beac587a08f2ef1d822dd6b13dffe Mon Sep 17 00:00:00 2001 From: Sinan Date: Tue, 29 Oct 2019 11:11:31 -0700 Subject: [PATCH 475/499] new package: py-scs (#13477) * new package: py-scs * rename * flake8 * Update var/spack/repos/builtin/packages/py-scs/package.py Co-Authored-By: Adam J. Stewart --- .../repos/builtin/packages/py-scs/package.py | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-scs/package.py diff --git a/var/spack/repos/builtin/packages/py-scs/package.py b/var/spack/repos/builtin/packages/py-scs/package.py new file mode 100644 index 00000000000..88f251bd7d0 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-scs/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyScs(PythonPackage): + """SCS: splitting conic solver""" + + homepage = "https://github.com/cvxgrp/scs" + url = "https://www.pypi.io/packages/source/s/scs/scs-2.1.1-2.tar.gz" + + version('2.1.1-2', sha256='f816cfe3d4b4cff3ac2b8b96588c5960ddd2a3dc946bda6b09db04e7bc6577f2') + + variant('cuda', default=False, description="Also compile the GPU CUDA version of SCS") + variant('float32', default=False, description="Use 32 bit (single precision) floats, default is 64 bit") + variant('extra_verbose', default=False, description="Extra verbose SCS (for debugging)") + variant('int32', default=False, description="Use 32 bit ints") + variant('blas64', default=False, description="Use 64 bit ints for the blas/lapack libs") + + depends_on('py-setuptools', type='build') + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-scipy@0.13.2:', type=('build', 'run')) + + def build_args(self, spec, prefix): + args = [] + if '+cuda' in spec or '+float32' in spec or '+int32' in spec or\ + '+extra_verbose' in spec or '+blas64' in spec: + args = ['--scs'] + if '+cuda' in spec: + args.append('--gpu') + if '+float32' in spec: + args.append('--float') + if '+extra_verbose' in spec: + args.append('--extraverbose') + if '+int32' in spec: + args.append('--int') + if '+blas64' in spec: + args.append('--blas64') + return args From e29a6c532cee38662901404116bd2398ff31b885 Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Wed, 30 Oct 2019 03:32:36 +0900 Subject: [PATCH 476/499] mumps: Add '-DMAIN_COMP' when using Fujitsu compiler. (#13480) --- var/spack/repos/builtin/packages/mumps/package.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 48e8cca29e7..b44228bcb57 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -119,6 +119,7 @@ def write_makefile_inc(self): using_pgi = self.compiler.name == "pgi" using_intel = self.compiler.name == "intel" using_xl = self.compiler.name in ['xl', 'xl_r'] + using_fj = self.compiler.name == "fj" # The llvm compiler suite does not contain a Fortran compiler by # default. Its possible that a Spack user may have configured @@ -183,10 +184,11 @@ def write_makefile_inc(self): # TODO: change the value to the correct one according to the # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER - if using_intel or using_pgi: - # Intel & PGI Fortran compiler provides the main() function so - # C examples linked with the Fortran compiler require a - # hack defined by _DMAIN_COMP (see examples/c_example.c) + if using_intel or using_pgi or using_fj: + # Intel, PGI, and Fujitsu Fortran compiler provides + # the main() function so C examples linked with the Fortran + # compiler require a hack defined by _DMAIN_COMP + # (see examples/c_example.c) makefile_conf.append("CDEFS = -DAdd_ -DMAIN_COMP") else: if not using_xlf: From c99d367a11b14fc47da7bb607f532156923ad075 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Tue, 29 Oct 2019 13:51:48 -0700 Subject: [PATCH 477/499] syaml_int type should use int.__repr__ rather than str.__repr__ (#13487) --- lib/spack/spack/util/spack_yaml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py index 264d5414de7..1d92d59ad28 100644 --- a/lib/spack/spack/util/spack_yaml.py +++ b/lib/spack/spack/util/spack_yaml.py @@ -47,7 +47,7 @@ class syaml_str(str): class syaml_int(int): - __repr__ = str.__repr__ + __repr__ = int.__repr__ #: mapping from syaml type -> primitive type From d76ec7b2da8028bf9215e184450352e83e6aa88a Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Tue, 29 Oct 2019 18:08:51 -0500 Subject: [PATCH 478/499] r-dada2: new package at 1.14 (#13492) * r-dada2: new package at 1.14 * r-dada2: add gmake dependency * Update var/spack/repos/builtin/packages/r-dada2/package.py Co-Authored-By: Adam J. Stewart --- .../repos/builtin/packages/r-dada2/package.py | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-dada2/package.py diff --git a/var/spack/repos/builtin/packages/r-dada2/package.py b/var/spack/repos/builtin/packages/r-dada2/package.py new file mode 100644 index 00000000000..41354055fed --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dada2/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDada2(RPackage): + """Accurate sample inference from amplicon data with single nucleotide + resolution""" + + homepage = "http://benjjneb.github.io/dada2/" + url = "https://github.com/benjjneb/dada2/archive/v1.14.tar.gz" + + version('1.14', sha256='19980b9d7b0a0e80e86010357cae11d1fc07c2d02067c4445169143cf1f99906') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-rcpp@0.12.0:', type=('build', 'run')) + depends_on('r-biostrings@2.42.1:', type=('build', 'run')) + depends_on('r-ggplot2@2.1.0:', type=('build', 'run')) + depends_on('r-reshape2@1.4.1:', type=('build', 'run')) + depends_on('r-shortread@1.32.0:', type=('build', 'run')) + depends_on('r-rcppparallel@4.3.0:', type=('build', 'run')) + depends_on('r-iranges@2.6.0:', type=('build', 'run')) + depends_on('r-xvector@0.16.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.22.0:', type=('build', 'run')) + + depends_on('gmake', type='build') From 4d345429ab1ede205df47fbde4a008c5e4e388ed Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Tue, 29 Oct 2019 18:09:05 -0500 Subject: [PATCH 479/499] r-dotcall64: new package at 1.0-0 (#13493) * r-dotcall64: new package at 1.0-0 * r-dotcall64: break up long line --- .../builtin/packages/r-dotcall64/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-dotcall64/package.py diff --git a/var/spack/repos/builtin/packages/r-dotcall64/package.py b/var/spack/repos/builtin/packages/r-dotcall64/package.py new file mode 100644 index 00000000000..270eeccdf60 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dotcall64/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDotcall64(RPackage): + """dotCall64: Enhanced Foreign Function Interface Supporting Long + Vectors.""" + + homepage = "https://git.math.uzh.ch/reinhard.furrer/dotCall64" + url = "https://cloud.r-project.org/src/contrib/dotCall64_1.0-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dotCall64" + + version('1.0-0', sha256='69318dc6b8aecc54d4f789c8105e672198363b395f1a764ebaeb54c0473d17ad') + + depends_on('r@3.1:', type=('build', 'run')) From 9a0ab3a87ac4c7858b5bde95804ac9c4119b52bb Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Tue, 29 Oct 2019 18:09:16 -0500 Subject: [PATCH 480/499] r-spam: new package at 2.3-0.2 (#13494) --- .../repos/builtin/packages/r-spam/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-spam/package.py diff --git a/var/spack/repos/builtin/packages/r-spam/package.py b/var/spack/repos/builtin/packages/r-spam/package.py new file mode 100644 index 00000000000..860ce770022 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spam/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSpam(RPackage): + """spam: SPArse Matrix""" + + homepage = "https://www.math.uzh.ch/pages/spam/" + url = "https://cloud.r-project.org/src/contrib/spam_2.3-0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/spam" + + version('2.3-0.2', sha256='848fa95c0a71ac82af6344539af7b1c33563c687f06ead42851a68b621fff533') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-dotcall64', type=('build', 'run')) From ccd20c9973135e9bb0d08853cb2dd0875d7ba233 Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Tue, 29 Oct 2019 18:09:34 -0500 Subject: [PATCH 481/499] r-fields: new package at 9.9 (#13495) --- .../builtin/packages/r-fields/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-fields/package.py diff --git a/var/spack/repos/builtin/packages/r-fields/package.py b/var/spack/repos/builtin/packages/r-fields/package.py new file mode 100644 index 00000000000..989967c7994 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fields/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFields(RPackage): + """fields: Tools for Spatial Data""" + + homepage = "https://github.com/NCAR/Fields" + url = "https://cloud.r-project.org/src/contrib/fields_9.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fields" + + version('9.9', sha256='262f03c630773b580c7162ab2a031c894ca489fd83989fd8a2f67573306e78e1') + + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-maps', type=('build', 'run')) + depends_on('r-spam', type=('build', 'run')) From 7af668f4521d11d8bc58f9989c6b5d5f08693480 Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Tue, 29 Oct 2019 18:09:46 -0500 Subject: [PATCH 482/499] r-bio3d: new package at 2.3-4 (#13496) --- .../repos/builtin/packages/r-bio3d/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-bio3d/package.py diff --git a/var/spack/repos/builtin/packages/r-bio3d/package.py b/var/spack/repos/builtin/packages/r-bio3d/package.py new file mode 100644 index 00000000000..a01e1de40ce --- /dev/null +++ b/var/spack/repos/builtin/packages/r-bio3d/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBio3d(RPackage): + """bio3d: Biological Structure Analysis""" + + homepage = "http://thegrantlab.org/bio3d/" + url = "https://cloud.r-project.org/src/contrib/bio3d_2.3-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bio3d" + + version('2.3-4', sha256='f9b39ab242cbedafcd98c1732cb1f5c0dd9ef66e28be39695e3420dd93e2bafe') + + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) From ad6908e35d875c0386699360d52b746c3616e74c Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Wed, 30 Oct 2019 13:08:25 +0900 Subject: [PATCH 483/499] mumps: Fix compile commands. (#13497) --- var/spack/repos/builtin/packages/mumps/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index b44228bcb57..a793b307194 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -177,9 +177,9 @@ def write_makefile_inc(self): "MUMPS_TYPE = par"]) else: makefile_conf.extend( - ["CC = cc", - "FC = fc", - "FL = fc", + ["CC = {0}".format(spack_cc), + "FC = {0}".format(spack_fc), + "FL = {0}".format(spack_fc), "MUMPS_TYPE = seq"]) # TODO: change the value to the correct one according to the From 4626c28c2735a8b6243b39270e55b9cdfc26e0da Mon Sep 17 00:00:00 2001 From: Gregory Lee Date: Tue, 29 Oct 2019 21:09:21 -0700 Subject: [PATCH 484/499] fix openmpi wrappers with libfabric (#13439) * fix openmpi wrappers with libfabric * flake8 fix * flake8 fix * openmpi fix deprecated API * openmpi fix deprecated API --- .../repos/builtin/packages/openmpi/package.py | 26 ++++++++++++------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index b5ddba63556..fe625f97c74 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -311,16 +311,16 @@ def libs(self): libraries, root=self.prefix, shared=True, recursive=True ) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) - spack_env.set('OMPI_CC', spack_cc) - spack_env.set('OMPI_CXX', spack_cxx) - spack_env.set('OMPI_FC', spack_fc) - spack_env.set('OMPI_F77', spack_f77) + env.set('OMPI_CC', spack_cc) + env.set('OMPI_CXX', spack_cxx) + env.set('OMPI_FC', spack_fc) + env.set('OMPI_F77', spack_f77) def setup_dependent_package(self, module, dependent_spec): self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') @@ -430,6 +430,13 @@ def configure_args(self): # Fabrics if 'fabrics=auto' not in spec: config_args.extend(self.with_or_without('fabrics')) + # The wrappers fail to automatically link libfabric. This will cause + # undefined references unless we add the appropriate flags. + if 'fabrics=libfabric' in spec: + config_args.append('--with-wrapper-ldflags=-L{0} -Wl,-rpath={0}' + .format(spec['libfabric'].prefix.lib)) + config_args.append('--with-wrapper-libs=-lfabric') + # Schedulers if 'schedulers=auto' not in spec: config_args.extend(self.with_or_without('schedulers')) @@ -444,7 +451,6 @@ def configure_args(self): # Hwloc support if spec.satisfies('@1.5.2:'): config_args.append('--with-hwloc={0}'.format(spec['hwloc'].prefix)) - # Java support if spec.satisfies('@1.7.4:'): if '+java' in spec: From cf1c38162ebf546266a827badb41145a337e5489 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 30 Oct 2019 17:25:46 +0100 Subject: [PATCH 485/499] cuda: fix conflict statements for x86-64 targets (#13472) * cuda: fix conflict statements for x86-64 targets fixes #13462 This build system mixin was not updated after the support for specific targets has been merged. * Updated the version range of cuda that conflicts with gcc@8: * Updated the version range of cuda that conflicts with gcc@8: for ppc64le * Relaxed conflicts for version > 10.1 * Updated versions in conflicts Co-Authored-By: Axel Huebl --- lib/spack/spack/build_systems/cuda.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/lib/spack/spack/build_systems/cuda.py b/lib/spack/spack/build_systems/cuda.py index 436bc307293..b75807fd06b 100644 --- a/lib/spack/spack/build_systems/cuda.py +++ b/lib/spack/spack/build_systems/cuda.py @@ -56,11 +56,12 @@ def cuda_flags(arch_list): # Linux x86_64 compiler conflicts from here: # https://gist.github.com/ax3l/9489132 - arch_platform = ' arch=x86_64 platform=linux' + arch_platform = ' target=x86_64: platform=linux' conflicts('%gcc@5:', when='+cuda ^cuda@:7.5' + arch_platform) conflicts('%gcc@6:', when='+cuda ^cuda@:8' + arch_platform) conflicts('%gcc@7:', when='+cuda ^cuda@:9.1' + arch_platform) - conflicts('%gcc@8:', when='+cuda ^cuda@10.0.130' + arch_platform) + conflicts('%gcc@8:', when='+cuda ^cuda@:10.0.130' + arch_platform) + conflicts('%gcc@9:', when='+cuda ^cuda@:10.1.243' + arch_platform) conflicts('%pgi@:14.8', when='+cuda ^cuda@:7.0.27' + arch_platform) conflicts('%pgi@:15.3,15.5:', when='+cuda ^cuda@7.5' + arch_platform) conflicts('%pgi@:16.2,16.0:16.3', when='+cuda ^cuda@8' + arch_platform) @@ -82,10 +83,11 @@ def cuda_flags(arch_list): # https://docs.nvidia.com/cuda/archive/9.0/cuda-installation-guide-linux/index.html # https://docs.nvidia.com/cuda/archive/8.0/cuda-installation-guide-linux/index.html - arch_platform = ' arch=ppc64le platform=linux' + arch_platform = ' target=ppc64le: platform=linux' # information prior to CUDA 9 difficult to find conflicts('%gcc@6:', when='+cuda ^cuda@:9' + arch_platform) - conflicts('%gcc@8:', when='+cuda ^cuda@10.0.130' + arch_platform) + conflicts('%gcc@8:', when='+cuda ^cuda@:10.0.130' + arch_platform) + conflicts('%gcc@9:', when='+cuda ^cuda@:10.1.243' + arch_platform) conflicts('%pgi', when='+cuda ^cuda@:8' + arch_platform) conflicts('%pgi@:16', when='+cuda ^cuda@:9.1.185' + arch_platform) conflicts('%pgi@:17', when='+cuda ^cuda@:10' + arch_platform) From 230c6aa32625cd97a229f82082e4d91f813b696d Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Wed, 30 Oct 2019 17:16:13 -0500 Subject: [PATCH 486/499] cpu: fix clang flags for generic x86_64 (#13491) * cpu: differentiate flags used for pristine LLVM vs. Apple's version --- lib/spack/llnl/util/cpu/microarchitectures.json | 17 ++++++++++++----- lib/spack/spack/test/architecture.py | 7 ++++--- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index 23cff4bf9af..bb3b4db21a1 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -61,11 +61,18 @@ "flags": "-march={name} -mtune={name}" } ], - "clang": { - "versions": ":", - "family": "x86-64", - "flags": "-march={family} -mcpu=generic" - }, + "clang": [ + { + "versions": "0.0.0-apple:", + "family": "x86-64", + "flags": "-march={family}" + }, + { + "versions": ":", + "family": "x86-64", + "flags": "-march={family} -mcpu=generic" + } + ], "intel": { "versions": ":", "name": "pentium4", diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index 30aba652143..0a37ef9558b 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -176,8 +176,9 @@ def test_arch_spec_container_semantic(item, architecture_str): ('gcc@4.7.2', 'ivybridge', '-march=core-avx-i -mtune=core-avx-i'), # Check mixed toolchains ('clang@8.0.0', 'broadwell', ''), + ('clang@3.5', 'x86_64', '-march=x86-64 -mcpu=generic'), # Check clang compilers with 'apple' suffix - ('clang@9.1.0-apple', 'x86_64', '-march=x86-64 -mcpu=generic') + ('clang@9.1.0-apple', 'x86_64', '-march=x86-64') ]) @pytest.mark.filterwarnings("ignore:microarchitecture specific") def test_optimization_flags( @@ -199,9 +200,9 @@ def test_optimization_flags( (spack.spec.CompilerSpec('gcc@4.4.0-special'), '9.2.0', 'icelake', '-march=icelake-client -mtune=icelake-client'), # Check that the special case for Apple's clang is treated correctly - # i.e. it won't try to dtect the version again + # i.e. it won't try to detect the version again (spack.spec.CompilerSpec('clang@9.1.0-apple'), None, 'x86_64', - '-march=x86-64 -mcpu=generic'), + '-march=x86-64'), ]) def test_optimization_flags_with_custom_versions( compiler, real_version, target_str, expected_flags, monkeypatch, config From a97faeb3c7115f9eb17a63d14464296e8168c767 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Wed, 30 Oct 2019 18:47:48 -0500 Subject: [PATCH 487/499] Documentation: Database.query methods share docstrings (#13515) Currently, query arguments in the Spack core are documented on the Database._query method, where the functionality is defined. For users of the spack python command, this makes the python builtin method help less than ideally useful, as help(spack.store.db.query) and help(spack.store.db.query_local) do not show relevant information. This PR updates the doc attributes for the Database.query and Database.query_local arguments to mirror everything after the first line of the Database._query docstring. --- lib/spack/spack/database.py | 94 +++++++++++++++++++++---------------- 1 file changed, 53 insertions(+), 41 deletions(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index a1748fc5852..e6e82f9803d 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -206,6 +206,50 @@ def __getattribute__(self, name): "Cannot access attribute '{0}' of lock".format(name)) +_query_docstring = """ + + Args: + query_spec: queries iterate through specs in the database and + return those that satisfy the supplied ``query_spec``. If + query_spec is `any`, This will match all specs in the + database. If it is a spec, we'll evaluate + ``spec.satisfies(query_spec)`` + + known (bool or any, optional): Specs that are "known" are those + for which Spack can locate a ``package.py`` file -- i.e., + Spack "knows" how to install them. Specs that are unknown may + represent packages that existed in a previous version of + Spack, but have since either changed their name or + been removed + + installed (bool or any, or InstallStatus or iterable of + InstallStatus, optional): if ``True``, includes only installed + specs in the search; if ``False`` only missing specs, and if + ``any``, all specs in database. If an InstallStatus or iterable + of InstallStatus, returns specs whose install status + (installed, deprecated, or missing) matches (one of) the + InstallStatus. (default: True) + + explicit (bool or any, optional): A spec that was installed + following a specific user request is marked as explicit. If + instead it was pulled-in as a dependency of a user requested + spec it's considered implicit. + + start_date (datetime, optional): filters the query discarding + specs that have been installed before ``start_date``. + + end_date (datetime, optional): filters the query discarding + specs that have been installed after ``end_date``. + + hashes (container): list or set of hashes that we can use to + restrict the search + + Returns: + list of specs that match the query + + """ + + class Database(object): """Per-process lock objects for each install prefix.""" @@ -1158,48 +1202,8 @@ def _query( end_date=None, hashes=None ): - """Run a query on the database + """Run a query on the database.""" - Args: - query_spec: queries iterate through specs in the database and - return those that satisfy the supplied ``query_spec``. If - query_spec is `any`, This will match all specs in the - database. If it is a spec, we'll evaluate - ``spec.satisfies(query_spec)`` - - known (bool or any, optional): Specs that are "known" are those - for which Spack can locate a ``package.py`` file -- i.e., - Spack "knows" how to install them. Specs that are unknown may - represent packages that existed in a previous version of - Spack, but have since either changed their name or - been removed - - installed (bool or any, or InstallStatus or iterable of - InstallStatus, optional): if ``True``, includes only installed - specs in the search; if ``False`` only missing specs, and if - ``any``, all specs in database. If an InstallStatus or iterable - of InstallStatus, returns specs whose install status - (installed, deprecated, or missing) matches (one of) the - InstallStatus. (default: True) - - explicit (bool or any, optional): A spec that was installed - following a specific user request is marked as explicit. If - instead it was pulled-in as a dependency of a user requested - spec it's considered implicit. - - start_date (datetime, optional): filters the query discarding - specs that have been installed before ``start_date``. - - end_date (datetime, optional): filters the query discarding - specs that have been installed after ``end_date``. - - hashes (container): list or set of hashes that we can use to - restrict the search - - Returns: - list of specs that match the query - - """ # TODO: Specs are a lot like queries. Should there be a # TODO: wildcard spec object, and should specs have attributes # TODO: like installed and known that can be queried? Or are @@ -1246,11 +1250,17 @@ def _query( return results + _query.__doc__ += _query_docstring + def query_local(self, *args, **kwargs): + """Query only the local Spack database.""" with self.read_transaction(): return sorted(self._query(*args, **kwargs)) + query_local.__doc__ += _query_docstring + def query(self, *args, **kwargs): + """Query the Spack database including all upstream databases.""" upstream_results = [] for upstream_db in self.upstream_dbs: # queries for upstream DBs need to *not* lock - we may not @@ -1265,6 +1275,8 @@ def query(self, *args, **kwargs): return sorted(results) + query.__doc__ += _query_docstring + def query_one(self, query_spec, known=any, installed=True): """Query for exactly one spec that matches the query spec. From 187706f1084c951ee44514c28da7a04b427a8db9 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 31 Oct 2019 09:42:18 -0600 Subject: [PATCH 488/499] portage: fix lapacke linkage (#13517) --- var/spack/repos/builtin/packages/portage/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/portage/package.py b/var/spack/repos/builtin/packages/portage/package.py index 91fc5fa4dc5..283fcef39a1 100644 --- a/var/spack/repos/builtin/packages/portage/package.py +++ b/var/spack/repos/builtin/packages/portage/package.py @@ -51,7 +51,7 @@ def cmake_args(self): else: options.append('-DENABLE_MPI=OFF') - options.append("-DLAPACKE_LIBRARIES=" + + options.append("-DLAPACKE_LIBRARY=" + self.spec["lapack"].libs.joined(";")) return options From 3d60c3ec10b2aa755f1eceda8c97da9b9fe495f8 Mon Sep 17 00:00:00 2001 From: Robert Maynard Date: Thu, 31 Oct 2019 12:04:19 -0400 Subject: [PATCH 489/499] VTK-m: Add support for the 1.5 release (#13514) --- var/spack/repos/builtin/packages/vtk-m/package.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/vtk-m/package.py b/var/spack/repos/builtin/packages/vtk-m/package.py index 317343bc82c..8c763ed4266 100644 --- a/var/spack/repos/builtin/packages/vtk-m/package.py +++ b/var/spack/repos/builtin/packages/vtk-m/package.py @@ -18,14 +18,15 @@ class VtkM(CMakePackage, CudaPackage): architectures.""" homepage = "https://m.vtk.org/" - url = "https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.3.0" + url = "https://gitlab.kitware.com/vtk/vtk-m/-/archive/v1.5.0/vtk-m-v1.5.0.tar.gz" git = "https://gitlab.kitware.com/vtk/vtk-m.git" version('master', branch='master') - version('1.4.0', sha256="60e1ce73a8c6beda8aed5f2d3ae670b6b0c78c068c6eff4ece769e6d719d5065") - version('1.3.0', sha256="72c2c8525a77a456fe0b6a1af0328dad6b9a688f402a3d3ebfa8942e0b5dba1a") - version('1.2.0', sha256="9103d954284661f6f03e5b18be6d7bc94254603e6abc8fce67f617f4ad325a0e") - version('1.1.0', sha256="a1746b1547d6fb901ea7d7ed50834e8832d6d41ddd497c84d02e1481100d43bc") + version('1.5.0', sha256="cd38957bb552e28b5197e4f738d5bb0b2c6f4025c3e17a66c8b19ee501273fbe") + version('1.4.0', sha256="8d83cca7cd5e204d10da151ce4f1846c1f7414c7c1e579173d15c5ea0631555a") + version('1.3.0', sha256="f88c1b0a1980f695240eeed9bcccfa420cc089e631dc2917c9728a2eb906df2e") + version('1.2.0', sha256="607272992e05f8398d196f0acdcb4af025a4a96cd4f66614c6341f31d4561763") + version('1.1.0', sha256="78618c81ca741b1fbba0853cb5d7af12c51973b514c268fc96dfb36b853cdb18") # use release, instead of release with debug symbols b/c vtkm libs # can overwhelm compilers with too many symbols From 738f2e14cefb1e35bbc973564343386188ead06d Mon Sep 17 00:00:00 2001 From: Julien Loiseau Date: Thu, 31 Oct 2019 10:32:54 -0700 Subject: [PATCH 490/499] MeshToolKit package (#12870) * Adding flecsph package * Correcting header * Boost version update * Correcting Flake8 errors * Correcting headers * Develop preferred in FleCSI * Removing FleCSPH branch of FleCSI * MeshToolKit package * formatting * Formatting * Correcting MSTK package * Format * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Update package.py * Format * Format * Correcting package behavior * Correcting format * Corrections * Update var/spack/repos/builtin/packages/mstk/package.py Co-Authored-By: Adam J. Stewart * Multiline --- .../repos/builtin/packages/mstk/package.py | 93 +++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mstk/package.py diff --git a/var/spack/repos/builtin/packages/mstk/package.py b/var/spack/repos/builtin/packages/mstk/package.py new file mode 100644 index 00000000000..53c3d3333b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/mstk/package.py @@ -0,0 +1,93 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Mstk(CMakePackage): + """MSTK is a mesh framework that allows users to represent, + manipulate and query unstructured 3D arbitrary topology meshes + in a general manner without the need to code their own data + structures. MSTK is a flexible framework in that it allows a + variety of underlying representations for the mesh while + maintaining a common interface. It allows users to choose from + different mesh representations either at initialization (implemented) + or during the program execution (not yet implemented) so that the + optimal data structures are used for the particular algorithm. + The interaction of users and applications with MSTK is through a + functional interface that acts as though the mesh always contains + vertices, edges, faces and regions and maintains connectivity between + all these entities.""" + + homepage = "https://github.com/MeshToolkit/MSTK" + git = "https://github.com/MeshToolkit/MSTK" + + maintainers = ['julienloiseau'] + + version('master', branch='master') + + variant('parallel', default='none', description='Enable Parallel Support', + values=('none', 'metis', 'zoltan', 'parmetis'), multi=True) + variant('exodusii', default=False, description='Enable ExodusII') + variant('use_markers', default=True, description="Enable MSTK to use markers") + + depends_on("cmake@3.8:", type='build') + + # Parallel variant + depends_on("mpi", when='parallel=metis') + depends_on("mpi", when='parallel=zoltan') + depends_on("mpi", when='parallel=parmetis') + depends_on("zoltan -fortran", when='parallel=zoltan') + depends_on("zoltan -fortran +parmetis", when='parallel=parmetis') + depends_on("zoltan -fortran +parmetis", when="parallel=zoltan +exodusii") + depends_on("metis", when="parallel=zoltan +exodusii") + + depends_on("metis", when='parallel=metis') + depends_on("metis", when='parallel=parmetis') + + # Exodusii variant + # The default exodusii build with mpi support + # It includes netcdf which includes hdf5 + depends_on("exodusii", when='+exodusii') + + def cmake_args(self): + options = [] + if '+use_markers' in self.spec: + options.append('-DMSTK_USE_MARKERS=ON') + else: + options.append('-DMSTK_USE_MARKERS=OFF') + + # Parallel variant + if not self.spec.satisfies('parallel=none'): + # Use mpi for compilation + options.append('-DCMAKE_CXX_COMPILER=' + self.spec['mpi'].mpicxx) + options.append('-DCMAKE_C_COMPILER=' + self.spec['mpi'].mpicc) + options.append('-DENABLE_PARALLEL=ON') + else: + options.append('-DENABLE_PARALLEL=OFF') + + if ("parmetis" in self.spec or "zoltan" in self.spec and + "+exodusii" in self.spec): + options.append("-DENABLE_METIS=ON") + options.append("-DENABLE_ZOLTAN=ON") + options.append('-DZOLTAN_NEEDS_ParMETIS=ON') + else: + if "zoltan" in self.spec: + options.append("-DENABLE_ZOLTAN=ON") + else: + options.append("-DENABLE_ZOLTAN=OFF") + if "metis" in self.spec: + options.append("-DENABLE_METIS=ON") + else: + options.append("-DENABLE_METIS=OFF") + options.append('-DZOLTAN_NEEDS_ParMETIS=OFF') + + # ExodusII variant + if '+exodusii' in self.spec: + options.append('-DENABLE_ExodusII=ON') + else: + options.append('-DENABLE_ExodusII=OFF') + + return options From e7f574aad5e89be222fbee0dff72f685f87f165c Mon Sep 17 00:00:00 2001 From: t-karatsu <49965247+t-karatsu@users.noreply.github.com> Date: Fri, 1 Nov 2019 02:38:23 +0900 Subject: [PATCH 491/499] ipopt: Add condition for 'aarch64' to Ipopt/config.guess (#13499) --- .../builtin/packages/ipopt/ipopt_aarch64_build.patch | 12 ++++++++++++ var/spack/repos/builtin/packages/ipopt/package.py | 1 + 2 files changed, 13 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ipopt/ipopt_aarch64_build.patch diff --git a/var/spack/repos/builtin/packages/ipopt/ipopt_aarch64_build.patch b/var/spack/repos/builtin/packages/ipopt/ipopt_aarch64_build.patch new file mode 100644 index 00000000000..18a653d2bd9 --- /dev/null +++ b/var/spack/repos/builtin/packages/ipopt/ipopt_aarch64_build.patch @@ -0,0 +1,12 @@ +--- spack-src/Ipopt/config.guess.org 2019-10-30 13:52:51.920159919 +0900 ++++ spack-src/Ipopt/config.guess 2019-10-30 13:55:27.956506585 +0900 +@@ -835,6 +835,9 @@ + arm*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; ++ aarch64:Linux:*:*) ++ echo ${UNAME_MACHINE}-unknown-linux-gnu ++ exit ;; + avr32*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py index fd9c87fba1e..44db2ba779c 100644 --- a/var/spack/repos/builtin/packages/ipopt/package.py +++ b/var/spack/repos/builtin/packages/ipopt/package.py @@ -39,6 +39,7 @@ class Ipopt(AutotoolsPackage): depends_on('metis@4.0:', when='+metis') patch('ipopt_ppc_build.patch', when='arch=ppc64le') + patch('ipopt_aarch64_build.patch', when='arch=aarch64') flag_handler = build_system_flags build_directory = 'spack-build' From a334007808e70c45c71a420ff1f71d8f8b0db3e2 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 31 Oct 2019 11:46:05 -0600 Subject: [PATCH 492/499] kokkos: turn host_values into a property (#13518) * kokkos: turn host_values into a property * Update package.py * Update package.py --- var/spack/repos/builtin/packages/kokkos/package.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py index dc971737554..cf7c486da90 100644 --- a/var/spack/repos/builtin/packages/kokkos/package.py +++ b/var/spack/repos/builtin/packages/kokkos/package.py @@ -67,6 +67,11 @@ class Kokkos(Package): variant('enable_lambda', default=False, description="set enable_lambda Kokkos CUDA option") + host_values = ('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX', + 'Power7', 'Power8', 'Power9', + 'WSM', 'SNB', 'HSW', 'BDW', 'SKX', + 'KNC', 'KNL') + gpu_values = ('Kepler30', 'Kepler32', 'Kepler35', 'Kepler37', 'Maxwell50', 'Maxwell52', 'Maxwell53', 'Pascal60', 'Pascal61', @@ -82,9 +87,7 @@ class Kokkos(Package): variant( 'host_arch', default='none', - values=('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX', - 'Power7', 'Power8', 'Power9', - 'WSM', 'SNB', 'HSW', 'BDW', 'SKX', 'KNC', 'KNL'), + values=host_values, description='Set the host architecture to use' ) From b4a51084abd891910a83554deda80d0e45f0cc61 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 31 Oct 2019 12:48:54 -0500 Subject: [PATCH 493/499] Add GRASS 7.8.0 (#13026) * Add GRASS 7.8.0 * Add new variants/dependencies * Remove unused dep * Filter entire libiconv line --- .../repos/builtin/packages/grass/package.py | 142 ++++++++++++------ 1 file changed, 96 insertions(+), 46 deletions(-) diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py index ca070112a0b..cc6057bf4dd 100644 --- a/var/spack/repos/builtin/packages/grass/package.py +++ b/var/spack/repos/builtin/packages/grass/package.py @@ -12,84 +12,102 @@ class Grass(AutotoolsPackage): used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.""" - homepage = "http://grass.osgeo.org" + homepage = "https://grass.osgeo.org" + url = "https://grass.osgeo.org/grass78/source/grass-7.8.0.tar.gz" + list_url = "https://grass.osgeo.org/download/software/sources/" - version('7.6.1', sha256='9e25c99cafd16ed8f5e2dca75b5a10dc2af0568dbedf3fc39f1c5a0a9c840b0b') - version('7.4.4', sha256='96a39e273103f7375a670eba94fa3e5dad2819c5c5664c9aee8f145882a94e8c') - version('7.4.3', sha256='004e65693ee97fd4d5dc7ad244e3286a115dccd88964d04be61c07db6574b399') - version('7.4.2', sha256='18eb19bc0aa4cd7be3f30f79ac83f9d0a29c63657f4c1b05bf4c5d5d57a8f46d') - version('7.4.1', sha256='560b8669caaafa9e8dbd4bbf2b4b4bbab7dca1cc46ee828eaf26c744fe0635fc') - version('7.4.0', sha256='cb6fa188e030a3a447fc5451fbe0ecbeb4069ee2fd1bf52ed8e40e9b89e293cc') + maintainers = ['adamjstewart'] - variant('cxx', default=True, description='Add c++ functionality') - variant('tiff', default=True, description='Add TIFF functionality') - variant('png', default=True, description='Add PNG functionality') - variant('postgres', default=False, description='Add PostgreSQL functionality') - variant('mysql', default=False, description='Add MySQL functionality') - variant('sqlite', default=True, description='Add SQLite functionality') - variant('opengl', default=True, description='Add OpenGL functionality') - variant('fftw', default=True, description='Add FFTW functionality') - variant('blas', default=False, description='Add BLAS functionality') - variant('lapack', default=False, description='Add LAPACK functionality') - variant('cairo', default=True, description='Add Cairo functionality') - variant('freetype', default=True, description='Add FreeType functionality') - variant('readline', default=False, description='Add Readline functionality') - variant('regex', default=True, description='Add regex functionality') - variant('pthread', default=False, description='Add POSIX threads functionality') - variant('openmp', default=False, description='Add OpenMP functionality') - variant('opencl', default=False, description='Add OpenCL functionality') - variant('bzlib', default=False, description='Add BZIP2 functionality') + version('7.8.0', sha256='4b1192294e959ffd962282344e4ff325c4472f73abe605e246a1da3beda7ccfa') + version('7.6.1', sha256='9e25c99cafd16ed8f5e2dca75b5a10dc2af0568dbedf3fc39f1c5a0a9c840b0b') + version('7.4.4', sha256='96a39e273103f7375a670eba94fa3e5dad2819c5c5664c9aee8f145882a94e8c') + version('7.4.3', sha256='004e65693ee97fd4d5dc7ad244e3286a115dccd88964d04be61c07db6574b399') + version('7.4.2', sha256='18eb19bc0aa4cd7be3f30f79ac83f9d0a29c63657f4c1b05bf4c5d5d57a8f46d') + version('7.4.1', sha256='560b8669caaafa9e8dbd4bbf2b4b4bbab7dca1cc46ee828eaf26c744fe0635fc') + version('7.4.0', sha256='cb6fa188e030a3a447fc5451fbe0ecbeb4069ee2fd1bf52ed8e40e9b89e293cc') + + variant('cxx', default=True, description='Support C++ functionality') + variant('tiff', default=False, description='Support TIFF functionality') + variant('png', default=False, description='Support PNG functionality') + variant('postgres', default=False, description='Support PostgreSQL functionality') + variant('mysql', default=False, description='Support MySQL functionality') + variant('sqlite', default=False, description='Support SQLite functionality') + variant('opengl', default=False, description='Support OpenGL functionality') + variant('odbc', default=False, description='Support ODBC functionality') + variant('fftw', default=False, description='Support FFTW functionality') + variant('blas', default=False, description='Support BLAS functionality') + variant('lapack', default=False, description='Support LAPACK functionality') + variant('cairo', default=False, description='Support Cairo functionality') + variant('freetype', default=False, description='Support FreeType functionality') + variant('readline', default=False, description='Support Readline functionality') + variant('regex', default=False, description='Support regex functionality') + variant('pthread', default=False, description='Support POSIX threads functionality') + variant('openmp', default=False, description='Support OpenMP functionality') + variant('opencl', default=False, description='Support OpenCL functionality') + variant('bzlib', default=False, description='Support BZIP2 functionality') + variant('zstd', default=False, description='Support Zstandard functionality') + variant('gdal', default=True, description='Enable GDAL/OGR support') + variant('liblas', default=False, description='Enable libLAS support') + variant('wxwidgets', default=False, description='Enable wxWidgets support') variant('netcdf', default=False, description='Enable NetCDF support') - variant('geos', default=False, description='Geometry Engine for v.buffer') + variant('geos', default=False, description='Enable GEOS support') + variant('x', default=False, description='Use the X Window System') - # required components - depends_on('gmake@3.8.1:', type='build') + # http://htmlpreview.github.io/?https://github.com/OSGeo/grass/blob/master/REQUIREMENTS.html + # General requirements + depends_on('gmake@3.81:', type='build') + depends_on('libiconv') depends_on('zlib') depends_on('flex', type='build') depends_on('bison', type='build') depends_on('proj') depends_on('proj@:4', when='@:7.5') - depends_on('proj@:5', when='@:7.7') - depends_on('gdal') - depends_on('python@2.7:2.9', type=('build', 'run')) - depends_on('libx11') + # GRASS 7.8.0 was supposed to support PROJ 6, but it still checks for + # share/proj/epsg, which was removed in PROJ 6 + depends_on('proj@:5', when='@:7.8') + depends_on('python@2.7:', type=('build', 'run')) + depends_on('python@2.7:2.8', when='@:7.6', type=('build', 'run')) + depends_on('py-six', when='@7.8:', type=('build', 'run')) - # optional pieces + # Optional packages depends_on('libtiff', when='+tiff') depends_on('libpng', when='+png') depends_on('postgresql', when='+postgres') depends_on('mariadb', when='+mysql') depends_on('sqlite', when='+sqlite') depends_on('gl', when='+opengl') + depends_on('unixodbc', when='+odbc') depends_on('fftw', when='+fftw') depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') - depends_on('cairo', when='+cairo') + depends_on('cairo@1.5.8:', when='+cairo') depends_on('freetype', when='+freetype') depends_on('readline', when='+readline') depends_on('opencl', when='+opencl') depends_on('bzip2', when='+bzlib') + depends_on('zstd', when='+zstd') + depends_on('gdal', when='+gdal') # required? + depends_on('liblas', when='+liblas') + depends_on('wxwidgets', when='+wxwidgets') + depends_on('py-wxpython@2.8.10.1:', when='+wxwidgets', type=('build', 'run')) depends_on('netcdf-c', when='+netcdf') depends_on('geos', when='+geos') + depends_on('libx11', when='+x') def url_for_version(self, version): - base = 'https://grass.osgeo.org' - return '{0}/grass{1}/source/grass-{2}.tar.gz'.format( - base, version.up_to(2).joined, version.dotted - ) + url = "https://grass.osgeo.org/grass{0}/source/grass-{1}.tar.gz" + return url.format(version.up_to(2).joined, version) + # https://grasswiki.osgeo.org/wiki/Compile_and_Install def configure_args(self): spec = self.spec args = [ - '--without-odbc', '--without-nls', + # TODO: add packages for these optional dependencies '--without-opendwg', - '--with-x', - '--with-gdal={0}/bin/gdal-config'.format( - spec['gdal'].prefix), - '--with-proj-share={0}/share/proj'.format( - spec['proj'].prefix), + '--without-pdal', + '--with-proj-share={0}'.format(spec['proj'].prefix.share.proj), ] if '+cxx' in spec: @@ -127,6 +145,11 @@ def configure_args(self): else: args.append('--without-opengl') + if '+odbc' in spec: + args.append('--with-odbc') + else: + args.append('--without-odbc') + if '+fftw' in spec: args.append('--with-fftw') else: @@ -182,6 +205,29 @@ def configure_args(self): else: args.append('--without-bzlib') + if '+zstd' in spec: + args.append('--with-zstd') + else: + args.append('--without-zstd') + + if '+gdal' in spec: + args.append('--with-gdal={0}/gdal-config'.format( + spec['gdal'].prefix.bin)) + else: + args.append('--without-gdal') + + if '+liblas' in spec: + args.append('--with-liblas={0}/liblas-config'.format( + spec['liblas'].prefix.bin)) + else: + args.append('--without-liblas') + + if '+wxwidgets' in spec: + args.append('--with-wxwidgets={0}/wx-config'.format( + spec['wxwidgets'].prefix.bin)) + else: + args.append('--without-wxwidgets') + if '+netcdf' in spec: args.append('--with-netcdf={0}/bin/nc-config'.format( spec['netcdf-c'].prefix)) @@ -194,6 +240,11 @@ def configure_args(self): else: args.append('--without-geos') + if '+x' in spec: + args.append('--with-x') + else: + args.append('--without-x') + return args # see issue: https://github.com/spack/spack/issues/11325 @@ -202,5 +253,4 @@ def configure_args(self): @run_after('configure') def fix_iconv_linking(self): makefile = FileFilter('include/Make/Platform.make') - makefile.filter(r'^ICONVLIB\s*=\s*', 'ICONVLIB = -liconv') - return None + makefile.filter(r'^ICONVLIB\s*=.*', 'ICONVLIB = -liconv') From 14fdaca4b4ce4d52fbdae4aa34d31775baa45f9c Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Thu, 31 Oct 2019 13:00:59 -0500 Subject: [PATCH 494/499] Bump up PGMath Library to latest version. More transparent name of the branch, version name equals branch name. (#13511) --- var/spack/repos/builtin/packages/pgmath/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/pgmath/package.py b/var/spack/repos/builtin/packages/pgmath/package.py index bd554890a0c..e096a596d84 100644 --- a/var/spack/repos/builtin/packages/pgmath/package.py +++ b/var/spack/repos/builtin/packages/pgmath/package.py @@ -11,10 +11,11 @@ class Pgmath(CMakePackage): """Flang's math library""" homepage = "https://github.com/flang-compiler/flang" - url = "https://github.com/flang-compiler/flang/archive/flang_20180612.tar.gz" + url = "https://github.com/flang-compiler/flang/archive/flang_20190329.tar.gz" git = "https://github.com/flang-compiler/flang.git" - version('develop', branch='master') + version('master', branch='master') + version('20190329', sha256='b8c621da53829f8c53bad73125556fb1839c9056d713433b05741f7e445199f2') version('20180921', sha256='f33bd1f054e474f1e8a204bb6f78d42f8f6ecf7a894fdddc3999f7c272350784') version('20180612', sha256='6af858bea013548e091371a97726ac784edbd4ff876222575eaae48a3c2920ed') From 536486f0e57b9bb6e6fe643472e8254a9d2aa5e8 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 31 Oct 2019 14:20:46 -0500 Subject: [PATCH 495/499] Travis CI: Test Python 3.8 (#13347) * Travis CI: Test Python 3.8 * Fix use of deprecated cgi.escape method * Fix version comparison * Fix flake8 F811 change in Python 3.8 * Make flake8 happy * Use Python 3.8 for all test categories --- .travis.yml | 26 +++++++++++++++----------- lib/spack/docs/getting_started.rst | 2 +- lib/spack/spack/cmd/flake8.py | 12 ++++++++++++ lib/spack/spack/cmd/list.py | 10 +++++++--- 4 files changed, 35 insertions(+), 15 deletions(-) diff --git a/.travis.yml b/.travis.yml index a79a5126b19..f8f0778caef 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,12 +18,12 @@ jobs: fast_finish: true include: - stage: 'style checks' - python: '3.7' + python: '3.8' os: linux language: python env: TEST_SUITE=flake8 # Shell integration with module files - - python: '3.7' + - python: '3.8' os: linux language: python env: [ TEST_SUITE=bootstrap ] @@ -46,10 +46,14 @@ jobs: language: python env: TEST_SUITE=unit - python: '3.7' + os: linux + language: python + env: TEST_SUITE=unit + - python: '3.8' os: linux language: python env: [ TEST_SUITE=unit, COVERAGE=true ] - - python: '3.7' + - python: '3.8' os: linux language: python env: TEST_SUITE=doc @@ -64,41 +68,41 @@ jobs: language: python env: [ TEST_SUITE=build, 'SPEC=mpich' ] # astyle (MakefilePackage) - - python: '3.7' + - python: '3.8' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=astyle' ] # tut (WafPackage) - - python: '3.7' + - python: '3.8' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=tut' ] # py-setuptools (PythonPackage) - - python: '3.7' + - python: '3.8' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=py-setuptools' ] # perl-dbi (PerlPackage) -# - python: '2.7' +# - python: '3.8' # os: linux # language: python # env: [ TEST_SUITE=build, 'SPEC=perl-dbi' ] # openjpeg (CMakePackage + external cmake) - - python: '3.7' + - python: '3.8' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=openjpeg' ] # r-rcpp (RPackage + external R) - - python: '3.7' + - python: '3.8' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=r-rcpp' ] # mpich (AutotoolsPackage) - - python: '3.7' + - python: '3.8' os: linux language: python env: [ TEST_SUITE=build, 'SPEC=mpich' ] - - python: '3.6' + - python: '3.8' stage: 'docker build' os: linux language: python diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst index 319d7f3c880..4d316b3bfa0 100644 --- a/lib/spack/docs/getting_started.rst +++ b/lib/spack/docs/getting_started.rst @@ -16,7 +16,7 @@ Prerequisites Spack has the following minimum requirements, which must be installed before Spack is run: -#. Python 2 (2.6 or 2.7) or 3 (3.4 - 3.7) to run Spack +#. Python 2 (2.6 or 2.7) or 3 (3.5 - 3.8) to run Spack #. A C/C++ compiler for building #. The ``make`` executable for building #. The ``git`` and ``curl`` commands for fetching diff --git a/lib/spack/spack/cmd/flake8.py b/lib/spack/spack/cmd/flake8.py index 61f7dd567f1..cc5b168c4b4 100644 --- a/lib/spack/spack/cmd/flake8.py +++ b/lib/spack/spack/cmd/flake8.py @@ -178,6 +178,12 @@ def add_pattern_exemptions(line, codes): def filter_file(source, dest, output=False): """Filter a single file through all the patterns in pattern_exemptions.""" + + # Prior to Python 3.8, `noqa: F811` needed to be placed on the `@when` line + # Starting with Python 3.8, it must be placed on the `def` line + # https://gitlab.com/pycqa/flake8/issues/583 + ignore_f811_on_previous_line = False + with open(source) as infile: parent = os.path.dirname(dest) mkdirp(parent) @@ -197,6 +203,12 @@ def filter_file(source, dest, output=False): line_errors.append(code) break + if 'F811' in line_errors: + ignore_f811_on_previous_line = True + elif ignore_f811_on_previous_line: + line_errors.append('F811') + ignore_f811_on_previous_line = False + if line_errors: line = add_pattern_exemptions(line, line_errors) diff --git a/lib/spack/spack/cmd/list.py b/lib/spack/spack/cmd/list.py index 570dcc7e27e..fe6983ce74e 100644 --- a/lib/spack/spack/cmd/list.py +++ b/lib/spack/spack/cmd/list.py @@ -7,7 +7,6 @@ from __future__ import division import argparse -import cgi import fnmatch import os import re @@ -23,6 +22,11 @@ import spack.cmd.common.arguments as arguments from spack.version import VersionList +if sys.version_info > (3, 1): + from html import escape +else: + from cgi import escape + description = "list and search available packages" section = "basic" level = "short" @@ -217,7 +221,7 @@ def head(n, span_id, title, anchor=None): out.write('

      \n') out.write(('
    • ' '%s' - '
      • \n') % (pkg.homepage, cgi.escape(pkg.homepage))) + '\n') % (pkg.homepage, escape(pkg.homepage, True))) out.write('
    \n') out.write('
    Spack package:
    \n') @@ -249,7 +253,7 @@ def head(n, span_id, title, anchor=None): out.write('
    Description:
    \n') out.write('
    \n') - out.write(cgi.escape(pkg.format_doc(indent=2))) + out.write(escape(pkg.format_doc(indent=2), True)) out.write('\n') out.write('
    \n') out.write('\n') From 4b56933643a2509fc694688bf1e4c20a6aa30b13 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 31 Oct 2019 14:21:05 -0500 Subject: [PATCH 496/499] Docs: unlock requirement versions (#13384) --- lib/spack/docs/requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/spack/docs/requirements.txt b/lib/spack/docs/requirements.txt index 190b018a0b4..f5c50b01991 100644 --- a/lib/spack/docs/requirements.txt +++ b/lib/spack/docs/requirements.txt @@ -1,7 +1,7 @@ # These dependencies should be installed using pip in order # to build the documentation. -sphinx==2.0.1 -sphinxcontrib-programoutput==0.14 -sphinx-rtd-theme==0.4.3 +sphinx +sphinxcontrib-programoutput +sphinx-rtd-theme python-levenshtein From 6ec39b6c81aa7a9b5853170026492567dd2cb55b Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Thu, 31 Oct 2019 12:56:38 -0700 Subject: [PATCH 497/499] Bugfix: BundlePackage staging/installation (#13524) 4af4487 added a mirror_id function to most FetchStrategy implementations that is used to calculate resource locations in mirrors. It left out BundleFetchStrategy which broke all packages making use of BundlePackage (e.g. xsdk). This adds a noop implementation of mirror_id to BundleFetchStrategy so that the download/installation of BundlePackages can proceed as normal. --- lib/spack/spack/fetch_strategy.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 393e3af9d12..370ccef593b 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -225,6 +225,9 @@ def source_id(self): """BundlePackages don't have a source id.""" return '' + def mirror_id(self): + """BundlePackages don't have a mirror id.""" + @pattern.composite(interface=FetchStrategy) class FetchStrategyComposite(object): From 93e87474fb67629aeeb43310482ccd67fb400cce Mon Sep 17 00:00:00 2001 From: Daniel Topa Date: Thu, 31 Oct 2019 15:57:50 -0600 Subject: [PATCH 498/499] dd Open MPI v. 4.0.2 (#13257) Verification builds on LANL Darwin x86_64, ARM, and, Power9: x86_64: OPTANE dantopa@cn733:pr-openmpi-4.0.2.spack $ spack arch linux-centos7-skylake_avx512 $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 2m 15.65s. Build: 6m 13.17s. Total: 8m 28.82s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.0.2-jrypg7vfnk6nl5if2rnzt65wdrjelxsq NEHALEM $ spack arch linux-centos7-nehalem $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 50.48s. Build: 9m 11.45s. Total: 10m 1.93s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-nehalem/gcc-4.8.5/openmpi-4.0.2-4jz3bcwjci44taizt4jqzxqh4y75uswc ARM $ spack arch linux-rhel7-aarch64 $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 1m 10.47s. Build: 11m 41.45s. Total: 12m 51.92s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/openmpi-4.0.2-ygr77roadqzdnsdgqz3uactjqnb5nayn POWER9 $ spack arch linux-rhel7-power9le $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ==> Warning: Using GCC 4.8 to optimize for Power 8 might not work if you are not on Red Hat Enterprise Linux 7, where a custom backport of the feature has been done. Upstream support from GCC starts in version 4.9 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 23.95s. Build: 9m 7.67s. Total: 9m 31.62s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-power8le/gcc-4.8.5/openmpi-4.0.2-cid4wfzr2iwgz6ybhkexludwu7koi266 $ spack find -ldf openmpi ==> 4 installed packages -- linux-centos7-haswell / gcc@4.8.5 ---------------------------- jrypg7v openmpi@4.0.2%gcc lliismp hwloc@1.11.11%gcc 7dqpxas libpciaccess@0.13.5%gcc viidrh5 libxml2@2.9.9%gcc yhvj3br numactl@2.0.12%gcc pkmj6e7 zlib@1.2.11%gcc -- linux-centos7-nehalem / gcc@4.8.5 ---------------------------- 4jz3bcw openmpi@4.0.2%gcc pcauu6w hwloc@1.11.11%gcc yiqf6bj libpciaccess@0.13.5%gcc wpfgqf2 libxml2@2.9.9%gcc fd2xpnm numactl@2.0.12%gcc xguzaxf zlib@1.2.11%gcc -- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------ ygr77ro openmpi@4.0.2%gcc omy3xi2 hwloc@1.11.11%gcc 6a4he35 libpciaccess@0.13.5%gcc txqo4cc libxml2@2.9.9%gcc m5neuus numactl@2.0.12%gcc 67s2oqn zlib@1.2.11%gcc -- linux-rhel7-power8le / gcc@4.8.5 ----------------------------- cid4wfz openmpi@4.0.2%gcc zcdnwb3 hwloc@1.11.11%gcc lencfon libpciaccess@0.13.5%gcc bve4jop libxml2@2.9.9%gcc kajzqwg numactl@2.0.12%gcc tjbynt2 zlib@1.2.11%gcc Thu Oct 17 19:02:50 MDT 2019 Signed-off-by: Daniel Topa --- var/spack/repos/builtin/packages/openmpi/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index fe625f97c74..d4107dff313 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -78,9 +78,10 @@ class Openmpi(AutotoolsPackage): version('develop', branch='master') # Current - version('4.0.1', sha256='cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709') # libmpi.so.40.20.1 + version('4.0.2', sha256='900bf751be72eccf06de9d186f7b1c4b5c2fa9fa66458e53b77778dffdfe4057') # libmpi.so.40.20.2 # Still supported + version('4.0.1', sha256='cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709') # libmpi.so.40.20.1 version('4.0.0', sha256='2f0b8a36cfeb7354b45dda3c5425ef8393c9b04115570b615213faaa3f97366b') # libmpi.so.40.20.0 version('3.1.4', preferred=True, sha256='17a69e0054db530c7dc119f75bd07d079efa147cf94bf27e590905864fe379d6') # libmpi.so.40.10.4 version('3.1.3', sha256='8be04307c00f51401d3fb9d837321781ea7c79f2a5a4a2e5d4eaedc874087ab6') # libmpi.so.40.10.3 From 43b18dada4442f688f2a3ef6629671cd9fd866a8 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Thu, 31 Oct 2019 18:35:13 -0500 Subject: [PATCH 499/499] hypre: add version 2.18.2 (#13527) --- var/spack/repos/builtin/packages/hypre/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 44ff3efc16a..c3397575524 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -20,6 +20,7 @@ class Hypre(Package): maintainers = ['ulrikeyang', 'osborn9', 'balay'] version('develop', branch='master') + version('2.18.2', sha256='28007b5b584eaf9397f933032d8367788707a2d356d78e47b99e551ab10cc76a') version('2.18.1', sha256='220f9c4ad024e815add8dad8950eaa2d8f4f231104788cf2a3c5d9da8f94ba6e') version('2.18.0', sha256='62591ac69f9cc9728bd6d952b65bcadd2dfe52b521081612609804a413f49b07') version('2.17.0', sha256='4674f938743aa29eb4d775211b13b089b9de84bfe5e9ea00c7d8782ed84a46d7')