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Merge branch 'develop' into features/shared

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This commit is contained in:
Carson Woods
2019-10-31 21:29:33 -04:00
parent 3593a7be6a 43b18dada4
commit 0a71b1d5ac
2929 changed files with 27972 additions and 18723 deletions
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4
var/spack/repos/builtin.mock/packages/cmake-client/package.py
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@@ -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.")

4
var/spack/repos/builtin.mock/packages/dependent-install/package.py
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@@ -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'))

27
var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py Normal file
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@@ -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)

1
var/spack/repos/builtin.mock/packages/override-module-templates/package.py
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@@ -12,7 +12,6 @@ class OverrideModuleTemplates(Package):
version('1.0', 'foobarbaz')
dotkit_template = 'override.txt'
tcl_template = 'override.txt'
lmod_template = 'override.txt'

15
var/spack/repos/builtin/packages/abinit/package.py
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@@ -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+')
@@ -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

4
var/spack/repos/builtin/packages/abyss/package.py
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@@ -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.

2
var/spack/repos/builtin/packages/accfft/package.py
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@@ -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')

44
var/spack/repos/builtin/packages/ace/package.py Normal file
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@@ -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)

8
var/spack/repos/builtin/packages/ack/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/activeharmony/package.py
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@@ -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")

15
var/spack/repos/builtin/packages/acts-core/package.py
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@@ -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")
]

4
var/spack/repos/builtin/packages/adept-utils/package.py
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@@ -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')

38
var/spack/repos/builtin/packages/adiak/package.py Normal file
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@@ -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

22
var/spack/repos/builtin/packages/adios/package.py
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@@ -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')
@@ -79,12 +79,12 @@ 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
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')
@@ -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

22
var/spack/repos/builtin/packages/adios/zfp051.patch Normal file
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@@ -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
{

130
var/spack/repos/builtin/packages/adios2/package.py
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@@ -7,56 +7,61 @@
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 conversion if a different '
'endianness is detected between write and read.')
# 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('dataspaces', default=False,
description='Enable support for DATASPACES')
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
# optional language bindings, C++11 and C always provided
variant('python', default=False,
description='Enable the Python >= 2.7 bindings')
description='Enable the Python bindings')
variant('fortran', default=True,
description='Enable the Fortran bindings')
@@ -71,33 +76,32 @@ 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('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('libzmq', when='+dataman')
depends_on('libzmq', when='@2.4: +ssc')
depends_on('dataspaces@1.8.0:', when='+dataspaces')
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('zfp', when='+zfp')
# depends_on('sz@:1.4.12', when='+sz')
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@: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')
@@ -112,10 +116,9 @@ 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'),
@@ -123,31 +126,50 @@ 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 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'))
if spec.satisfies('+python'):
args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s'
% self.spec['python'].command.path)
return args

15
var/spack/repos/builtin/packages/adlbx/package.py
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@@ -11,13 +11,12 @@ 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')
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')
depends_on('exmcutils@master', when='@master')
depends_on('exmcutils@:0.5.3', when='@:0.8.0')
@@ -28,11 +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):

8
var/spack/repos/builtin/packages/adol-c/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/aegean/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/albert/package.py
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@@ -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')

5
var/spack/repos/builtin/packages/alglib/package.py
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@@ -16,10 +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')
def url_for_version(self, version):
return 'http://www.alglib.net/translator/re/alglib-{0}.cpp.gpl.tgz'.format(version.dotted)
version('3.11.0', sha256='34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0')
build_directory = 'src'

33
var/spack/repos/builtin/packages/allinea-reports/package.py
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@@ -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)

4
var/spack/repos/builtin/packages/allpaths-lg/package.py
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@@ -11,9 +11,9 @@ 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', 'bde9008e236d87708a48eb83af6d6d5b')
version('52488', sha256='035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542')
# compiles with gcc 4.7.0 to 4.9.4)
conflicts('%gcc@:4.6.4,5.1.0:')

2
var/spack/repos/builtin/packages/alsa-lib/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/amg2013/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/aml/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/amp/package.py
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@@ -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' %

2
var/spack/repos/builtin/packages/ampliconnoise/package.py
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@@ -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')

1
var/spack/repos/builtin/packages/amrex/package.py
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@@ -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

2
var/spack/repos/builtin/packages/andi/package.py
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@@ -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')

4
var/spack/repos/builtin/packages/angsd/package.py
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@@ -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')

10
var/spack/repos/builtin/packages/ant/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/antlr/package.py
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@@ -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')

9
var/spack/repos/builtin/packages/ants/package.py
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@@ -18,10 +18,15 @@ 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')
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)

2
var/spack/repos/builtin/packages/ape/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/apex/package.py
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@@ -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:")

2
var/spack/repos/builtin/packages/applewmproto/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/appres/package.py
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@@ -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')

7
var/spack/repos/builtin/packages/apr-util/package.py
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@@ -10,10 +10,11 @@ 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('1.6.0', '3b03dbff60728a4f4c33f5d929e8b35a')
version('1.5.4', '866825c04da827c6e5f53daff5569f42')
version('1.6.1', sha256='b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459')
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')

7
var/spack/repos/builtin/packages/apr/package.py
View File

@@ -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('1.6.2', '8672e78514e3fcef2643127c524bf0f9')
version('1.5.2', '98492e965963f852ab29f9e61b2ad700')
version('1.7.0', sha256='48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2')
version('1.6.2', sha256='4fc24506c968c5faf57614f5d0aebe0e9d0b90afa47a883e1a1ca94f15f4a42e')
version('1.5.2', sha256='1af06e1720a58851d90694a984af18355b65bb0d047be03ec7d659c746d6dbdb')

4
var/spack/repos/builtin/packages/aragorn/package.py
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@@ -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']

17
var/spack/repos/builtin/packages/arborx/package.py
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@@ -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:

2
var/spack/repos/builtin/packages/archer/package.py
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@@ -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')

6
var/spack/repos/builtin/packages/argobots/package.py
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@@ -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")

2
var/spack/repos/builtin/packages/argp-standalone/package.py
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@@ -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

2
var/spack/repos/builtin/packages/argtable/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/aria2/package.py
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@@ -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')

20
var/spack/repos/builtin/packages/arlecore/package.py
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@@ -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)

42
var/spack/repos/builtin/packages/arm-forge/package.py
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@@ -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",
)

11
var/spack/repos/builtin/packages/armadillo/package.py
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@@ -12,15 +12,10 @@ 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', 'd9762d6f097e0451d0cfadfbda295e7c')
version('7.950.1', 'c06eb38b12cae49cab0ce05f96147147')
# 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('8.100.1', sha256='54773f7d828bd3885c598f90122b530ded65d9b195c9034e082baea737cd138d')
version('7.950.1', sha256='a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b')
variant('hdf5', default=False, description='Include HDF5 support')

22
var/spack/repos/builtin/packages/arpack-ng/incompatible_isnan_fix.patch Normal file
View File

@@ -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

12
var/spack/repos/builtin/packages/arpack-ng/package.py
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@@ -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')
@@ -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')

8
var/spack/repos/builtin/packages/arrow/package.py
View File

@@ -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')

4
var/spack/repos/builtin/packages/asagi/package.py
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@@ -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')

51
var/spack/repos/builtin/packages/ascent/package.py
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@@ -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")
@@ -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")
@@ -120,8 +122,8 @@ 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):
"""
@@ -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()
@@ -353,12 +355,21 @@ 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
@@ -396,10 +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")

2
var/spack/repos/builtin/packages/asciidoc/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/asciidoctor/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/aspcud/package.py
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@@ -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'))

2
var/spack/repos/builtin/packages/aspell/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/aspell6-de/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/aspell6-en/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/aspell6-es/package.py
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@@ -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')

5
var/spack/repos/builtin/packages/aspera-cli/package.py
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@@ -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)
@@ -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)

2
var/spack/repos/builtin/packages/assimp/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/astra/package.py
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@@ -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):

2
var/spack/repos/builtin/packages/astral/package.py
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@@ -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')

10
var/spack/repos/builtin/packages/astyle/package.py
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@@ -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

4
var/spack/repos/builtin/packages/at-spi2-atk/package.py
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@@ -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:')

2
var/spack/repos/builtin/packages/at-spi2-core/package.py
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@@ -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:')

6
var/spack/repos/builtin/packages/atk/package.py
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@@ -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:')

10
var/spack/repos/builtin/packages/atlas/package.py
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@@ -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:')

2
var/spack/repos/builtin/packages/atom-dft/package.py
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@@ -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')

4
var/spack/repos/builtin/packages/atompaw/package.py
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@@ -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")

2
var/spack/repos/builtin/packages/atop/package.py
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@@ -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')

12
var/spack/repos/builtin/packages/augustus/package.py
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@@ -16,11 +16,11 @@ 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', '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'))
@@ -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'))

8
var/spack/repos/builtin/packages/autoconf/package.py
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@@ -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.

2
var/spack/repos/builtin/packages/autodock-vina/package.py
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@@ -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')

10
var/spack/repos/builtin/packages/autofact/package.py
View File

@@ -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)

2
var/spack/repos/builtin/packages/autogen/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/automaded/package.py
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@@ -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')

12
var/spack/repos/builtin/packages/automake/package.py
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@@ -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'))

2
var/spack/repos/builtin/packages/axel/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/axl/package.py
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@@ -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']

12
var/spack/repos/builtin/packages/bamtools/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/bamutil/package.py
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@@ -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'))

6
var/spack/repos/builtin/packages/barrnap/package.py
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@@ -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')

4
var/spack/repos/builtin/packages/bash-completion/package.py
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@@ -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')

31
var/spack/repos/builtin/packages/bash/package.py
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@@ -12,13 +12,33 @@ 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:')
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):

2
var/spack/repos/builtin/packages/bats/package.py
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@@ -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")

31
var/spack/repos/builtin/packages/bazel/package.py
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@@ -17,24 +17,19 @@ 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')
depends_on('java@8:', type=('build', 'link', 'run'))
depends_on('zip')

2
var/spack/repos/builtin/packages/bbmap/package.py
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@@ -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')

2
var/spack/repos/builtin/packages/bc/package.py
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@@ -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')

12
var/spack/repos/builtin/packages/bcftools/package.py
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@@ -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:')

9
var/spack/repos/builtin/packages/bcl2fastq2/package.py
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@@ -19,13 +19,8 @@ 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')
# 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('2.20.0.422', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3')
version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806')
conflicts('platform=darwin',
msg='malloc.h/etc requirements break build on macs')

2
var/spack/repos/builtin/packages/bdftopcf/package.py
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@@ -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')

4
var/spack/repos/builtin/packages/bdw-gc/package.py
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@@ -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')

4
var/spack/repos/builtin/packages/bear/package.py
View File

@@ -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')

8
var/spack/repos/builtin/packages/beast1/package.py
View File

@@ -13,8 +13,7 @@ class Beast1(Package):
homepage = "http://beast.community/"
version('1.10.4', sha256='be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8')
version('1.10.0', 'bcf2f2c074319360ec8a2ebad57d2e57')
version('1.8.4', 'cb8752340c1f77a22d39ca4fe09687b0')
version('1.8.4', sha256='c14e93976008463108aefa34ecc23287ab70703caccf4962e36e295207120d78')
variant('beagle', default=True, description='Build with libbeagle support')
@@ -25,8 +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)

2
var/spack/repos/builtin/packages/beast2/package.py
View File

@@ -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')

6
var/spack/repos/builtin/packages/bedops/package.py
View File

@@ -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):

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