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Merge remote branch 'origin/develop' into develop

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Conflicts:
	var/spack/repos/builtin/packages/r-gmp/package.py
	var/spack/repos/builtin/packages/r-rmpfr/package.py
This commit is contained in:
Tom Merrick 2017-05-22 08:42:44 -05:00
commit 38ff43dfdc
22 changed files with 254 additions and 11 deletions
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1
var/spack/repos/builtin/packages/armadillo/package.py
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@ -33,6 +33,7 @@ class Armadillo(Package):
homepage = "http://arma.sourceforge.net/"
url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
version('7.900.1', '5ef71763bd429a3d481499878351f3be')
version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d')
version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')

57
var/spack/repos/builtin/packages/boost/call_once_variadic.patch Normal file
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@ -0,0 +1,57 @@
diff --git a/boost/thread/pthread/once.hpp b/boost/thread/pthread/once.hpp
index ccfb051..0bef038 100644
--- a/boost/thread/pthread/once.hpp
+++ b/boost/thread/pthread/once.hpp
@@ -42,7 +42,7 @@ namespace boost
}
#ifdef BOOST_THREAD_PROVIDES_ONCE_CXX11
-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
+#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
template<typename Function, class ...ArgTypes>
inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args);
#else
@@ -65,7 +65,7 @@ namespace boost
private:
volatile thread_detail::uintmax_atomic_t epoch;
-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
+#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
template<typename Function, class ...ArgTypes>
friend void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args);
#else
@@ -118,7 +118,7 @@ namespace boost
// http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2007/n2444.html
-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
+#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
template<typename Function, class ...ArgTypes>
diff --git a/boost/thread/pthread/once_atomic.hpp b/boost/thread/pthread/once_atomic.hpp
index 9e2f876..923f07b 100644
--- a/boost/thread/pthread/once_atomic.hpp
+++ b/boost/thread/pthread/once_atomic.hpp
@@ -115,7 +115,7 @@ namespace boost
#endif
-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
+#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
template<typename Function, class ...ArgTypes>
inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
diff --git a/boost/thread/win32/once.hpp b/boost/thread/win32/once.hpp
index cafcfd4..9b37b31 100644
--- a/boost/thread/win32/once.hpp
+++ b/boost/thread/win32/once.hpp
@@ -227,7 +227,7 @@ namespace boost
}
}
-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
+#if !defined BOOST_NO_CXX11_VARIADIC_TEMPLATES && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
//#if defined(BOOST_THREAD_RVALUE_REFERENCES_DONT_MATCH_FUNTION_PTR)
inline void call_once(once_flag& flag, void (*f)())
{

2
var/spack/repos/builtin/packages/boost/package.py
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@ -148,6 +148,8 @@ class Boost(Package):
patch('xl_1_62_0_le.patch', when='@1.62.0%xl_r')
patch('xl_1_62_0_le.patch', when='@1.62.0%xl')
patch('call_once_variadic.patch', when='@:1.56.0%gcc@5:')
def url_for_version(self, version):
url = "http://downloads.sourceforge.net/project/boost/boost/{0}/boost_{1}.tar.bz2"
return url.format(version.dotted, version.underscored)

1
var/spack/repos/builtin/packages/cmake/package.py
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@ -33,6 +33,7 @@ class Cmake(Package):
list_url = 'https://cmake.org/files/'
list_depth = 1
version('3.8.1', 'e8ef820ddf7a650845252bca846696e7')
version('3.8.0', 'f28cba717ba38ad82a488daed8f45b5b')
version('3.7.2', '79bd7e65cd81ea3aa2619484ad6ff25a')
version('3.7.1', 'd031d5a06e9f1c5367cdfc56fbd2a1c8')

17
var/spack/repos/builtin/packages/flex/package.py
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@ -23,6 +23,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
class Flex(AutotoolsPackage):
@ -39,6 +40,9 @@ class Flex(AutotoolsPackage):
version('2.6.0', '760be2ee9433e822b6eb65318311c19d')
version('2.5.39', '5865e76ac69c05699f476515592750d7')
variant('lex', default=True,
description="Provide symlinks for lex and libl")
depends_on('bison', type='build')
depends_on('gettext@0.19:', type='build')
depends_on('help2man', type='build')
@ -61,3 +65,16 @@ def url_for_version(self, version):
url += "/archive/flex-{0}.tar.gz".format(version.dashed)
return url
@run_after('install')
def symlink_lex(self):
if self.spec.satisfies('+lex'):
dso = dso_suffix
for dir, flex, lex in \
((self.prefix.bin, 'flex', 'lex'),
(self.prefix.lib, 'libfl.a', 'libl.a'),
(self.prefix.lib, 'libfl.' + dso, 'libl.' + dso)):
with working_dir(dir):
if (os.path.isfile(flex) and not
os.path.lexists(lex)):
symlink(flex, lex)

9
var/spack/repos/builtin/packages/gcc/package.py
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@ -170,6 +170,15 @@ def patch(self):
'typedef void* dispatch_block_t',
new_header)
# Use installed libz
if self.version >= Version('6'):
filter_file('@zlibdir@',
'-L{0}'.format(spec['zlib'].prefix.lib),
'gcc/Makefile.in')
filter_file('@zlibinc@',
'-I{0}'.format(spec['zlib'].prefix.include),
'gcc/Makefile.in')
def configure_args(self):
spec = self.spec

1
var/spack/repos/builtin/packages/gobject-introspection/package.py
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@ -44,6 +44,7 @@ class GobjectIntrospection(Package):
depends_on("cairo")
depends_on("bison", type="build")
depends_on("flex", type="build")
depends_on("pkg-config@0.9.0:", type="build")
# This package creates several scripts from
# toosl/g-ir-tool-template.in. In their original form these

1
var/spack/repos/builtin/packages/hpx5/package.py
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@ -39,6 +39,7 @@ class Hpx5(AutotoolsPackage):
homepage = "http://hpx.crest.iu.edu"
url = "http://hpx.crest.iu.edu/release/hpx-3.1.0.tar.gz"
version('4.1.0', '43cb78758506f77416b95276a472f84f')
version('4.0.0', 'b40dc03449ae1039cbb48ee149952b22')
version('3.1.0', '9e90b8ac46788c009079632828c77628')
version('2.0.0', '3d2ff3aab6c46481f9ec65c5b2bfe7a6')

1
var/spack/repos/builtin/packages/hwloc/package.py
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@ -44,6 +44,7 @@ class Hwloc(AutotoolsPackage):
list_url = "http://www.open-mpi.org/software/hwloc/"
list_depth = 2
version('1.11.7', '867a5266675e5bf1ef4ab66c459653f8')
version('1.11.6', 'b4e95eadd2fbdb6d40bbd96be6f03c84')
version('1.11.5', '8f5fe6a9be2eb478409ad5e640b2d3ba')
version('1.11.4', 'b6f23eb59074fd09fdd84905d50b103d')

3
var/spack/repos/builtin/packages/julia/package.py
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@ -37,7 +37,8 @@ class Julia(Package):
git='https://github.com/JuliaLang/julia.git', branch='master')
version('release-0.5',
git='https://github.com/JuliaLang/julia.git', branch='release-0.5')
version('0.5.1', 'bce119b98f274e0f07ce01498c463ad5', preferred=True)
version('0.5.2', '8c3fff150a6f96cf0536fb3b4eaa5cbb', preferred=True)
version('0.5.1', 'bce119b98f274e0f07ce01498c463ad5')
version('0.5.0', 'b61385671ba74767ab452363c43131fb')
version('release-0.4',
git='https://github.com/JuliaLang/julia.git', branch='release-0.4')

1
var/spack/repos/builtin/packages/libdrm/package.py
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@ -38,6 +38,7 @@ class Libdrm(Package):
version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
depends_on('pkg-config@0.9.0:', type='build')
depends_on('libpciaccess@0.10:', when=(sys.platform != 'darwin'))
depends_on('libpthread-stubs')

1
var/spack/repos/builtin/packages/libxml2/package.py
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@ -34,6 +34,7 @@ class Libxml2(AutotoolsPackage):
version('2.9.4', 'ae249165c173b1ff386ee8ad676815f5')
version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
version('2.7.8', '8127a65e8c3b08856093099b52599c86')
variant('python', default=False, description='Enable Python support')

16
var/spack/repos/builtin/packages/magics/package.py
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@ -23,6 +23,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import glob
class Magics(Package):
@ -42,7 +43,7 @@ class Magics(Package):
# The patch changes the hardcoded path to python in shebang to enable the
# usage of the first python installation that appears in $PATH
patch('no_hardcoded_python.patch')
patch('no_hardcoded_python.patch', when='@:2.29.6')
# The patch reorders includes and adds namespaces where necessary to
# resolve ambiguity of invocations of isnan and isinf functions. The
@ -63,7 +64,8 @@ class Magics(Package):
depends_on('python', type='build')
depends_on('perl', type='build')
depends_on('perl-xml-parser', type='build')
depends_on('grib-api')
depends_on('eccodes', when='@2.30.0:')
depends_on('grib-api', when='@:2.29.6')
depends_on('proj')
depends_on('boost')
depends_on('expat')
@ -73,8 +75,8 @@ class Magics(Package):
depends_on('qt', when='+metview+qt')
def patch(self):
filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl',
'tools/xml2cc_new.pl')
for plfile in glob.glob('*/*.pl'):
filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', plfile)
def install(self, spec, prefix):
options = []
@ -83,9 +85,13 @@ def install(self, spec, prefix):
options.append('-DENABLE_PYTHON=OFF')
options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
options.append('-DPROJ4_PATH=%s' % spec['proj'].prefix)
options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
options.append('-DENABLE_TESTS=OFF')
if self.version >= Version('2.30.0'):
options.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix)
else:
options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
if '+bufr' in spec:
options.append('-DENABLE_BUFR=ON')
options.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix)

11
var/spack/repos/builtin/packages/meme/package.py
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@ -35,9 +35,20 @@ class Meme(AutotoolsPackage):
version('4.11.4', '371f513f82fa0888205748e333003897')
variant('mpi', default=True, description='Enable MPI support')
depends_on('zlib', type=('link'))
depends_on('libxml2', type=('link'))
depends_on('libxslt', type=('link'))
depends_on('libgcrypt', type=('link'))
depends_on('perl', type=('build', 'run'))
depends_on('python@2.7:', type=('build', 'run'))
depends_on('mpi', when='+mpi')
# disable mpi support
def configure_args(self):
spec = self.spec
args = []
if '~mpi' in spec:
args += ['--enable-serial']
return args

81
var/spack/repos/builtin/packages/mpifileutils/package.py Normal file
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@ -0,0 +1,81 @@
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Mpifileutils(AutotoolsPackage):
"""mpiFileUtils is a suite of MPI-based tools to manage large datasets,
which may vary from large directory trees to large files.
High-performance computing users often generate large datasets with
parallel applications that run with many processes (millions in some
cases). However those users are then stuck with single-process tools
like cp and rm to manage their datasets. This suite provides
MPI-based tools to handle typical jobs like copy, remove, and compare
for such datasets, providing speedups of up to 20-30x."""
homepage = "https://github.com/hpc/mpifileutils"
url = "https://github.com/hpc/mpifileutils/releases/download/v0.6/mpifileutils-0.6.tar.gz"
version('0.6', '620bcc4966907481f1b1a965b28fc9bf')
depends_on('mpi')
depends_on('libcircle')
depends_on('lwgrp')
depends_on('dtcmp')
depends_on('libarchive')
variant('xattr', default=True,
description="Enable code for extended attributes")
variant('lustre', default=False,
description="Enable optimizations and features for Lustre")
# install experimental tools
# (coming with v0.7)
# variant('experimental', default=False,
# description="Install experimental tools")
def configure_args(self):
args = []
if '+lustre' in self.spec:
args.append('--enable-lustre')
else:
args.append('--disable-lustre')
# coming with v0.7
# if '+experimental' in self.spec:
# args.append('--enable-experimental')
# else:
# args.append('--disable-experimental')
return args
@property
def build_targets(self):
targets = []
if '+xattr' in self.spec:
targets.append('CFLAGS=-DDCOPY_USE_XATTRS')
return targets

10
var/spack/repos/builtin/packages/ncview/package.py
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@ -36,3 +36,13 @@ class Ncview(AutotoolsPackage):
depends_on('udunits2')
depends_on('libpng')
depends_on('libxaw')
def configure_args(self):
spec = self.spec
config_args = []
if spec.satisfies('^netcdf+mpi'):
config_args.append('CC={0}'.format(spec['mpi'].mpicc))
return config_args

3
var/spack/repos/builtin/packages/qt/package.py
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@ -73,6 +73,9 @@ class Qt(Package):
# https://github.com/xboxdrv/xboxdrv/issues/188
patch('btn_trigger_happy.patch', when='@5.7.0:')
# https://github.com/LLNL/spack/issues/1517
patch('qt5-pcre.patch', when='@5:')
patch('qt4-corewlan-new-osx.patch', when='@4')
patch('qt4-pcre-include-conflict.patch', when='@4')
patch('qt4-el-capitan.patch', when='@4')

33
var/spack/repos/builtin/packages/qt/qt5-pcre.patch Normal file
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@ -0,0 +1,33 @@
--- a/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/runtime/RegExp.cpp 2016-09-17 20:55:14.000000000 +0000
+++ b/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/runtime/RegExp.cpp 2017-05-17 01:55:10.000000000 +0000
@@ -44,7 +44,7 @@
#include "JIT.h"
#include "WRECGenerator.h"
#endif
-#include <pcre/pcre.h>
+#include "../pcre/pcre.h"
#endif
--- a/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.cpp 2016-09-17 20:55:14.000000000 +0000
+++ b/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.cpp 2017-05-17 01:55:51.000000000 +0000
@@ -32,7 +32,7 @@
#include "MacroAssembler.h"
#include "RegexCompiler.h"
-#include "pcre.h" // temporary, remove when fallback is removed.
+#include "../pcre/pcre.h" // temporary, remove when fallback is removed.
#if ENABLE(YARR_JIT)
--- a/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h 2016-09-17 20:55:14.000000000 +0000
+++ b/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h 2017-05-17 01:55:36.000000000 +0000
@@ -34,7 +34,7 @@
#include "RegexPattern.h"
#include <UString.h>
-#include <pcre.h>
+#include "../pcre/pcre.h"
struct JSRegExp; // temporary, remove when fallback is removed.
#if CPU(X86) && !COMPILER(MSVC)

2
var/spack/repos/builtin/packages/r-gmp/package.py
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@ -31,7 +31,7 @@ class RGmp(RPackage):
using the C library GMP (GNU Multiple Precision Arithmetic)."""
homepage = "http://mulcyber.toulouse.inra.fr/projects/gmp"
url = "https://cran.r-project.org/src/contrib/gmp_0.5-12.tar.gz"
url = "https://cran.r-project.org/src/contrib/gmp_0.5-13.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/gmp"
version('0.5-13.1', '4a45d45e53bf7140720bd44f10b075ed')

2
var/spack/repos/builtin/packages/r-rmpfr/package.py
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@ -33,7 +33,7 @@ class RRmpfr(RPackage):
is based on the GMP (GNU Multiple Precision) Library."""
homepage = "http://rmpfr.r-forge.r-project.org"
url = "https://cran.r-project.org/src/contrib/Rmpfr_0.6-0.tar.gz"
url = "https://cran.r-project.org/src/contrib/Rmpfr_0.6-1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/Rmpfr"
version('0.6-1', '55d4ec257bd2a9233bafee9e444d0265')

3
var/spack/repos/builtin/packages/r/package.py
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@ -36,10 +36,11 @@ class R(AutotoolsPackage):
Please consult the R project homepage for further information."""
homepage = "https://www.r-project.org"
url = "https://cloud.r-project.org/src/base/R-3/R-3.3.2.tar.gz"
url = "https://cloud.r-project.org/src/base/R-3/R-3.4.0.tar.gz"
extendable = True
version('3.4.0', '75083c23d507b9c16d5c6afbd7a827e7')
version('3.3.3', '0ac211ec15e813a24f8f4a5a634029a4')
version('3.3.2', '2437014ef40641cdc9673e89c040b7a8')
version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')

9
var/spack/repos/builtin/packages/spark/package.py
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@ -22,10 +22,11 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import re
import shutil
from spack import *
class Spark(Package):
"""Apache Spark is a fast and general engine
@ -72,4 +73,8 @@ def setup_environment(self, spack_env, run_env):
hadoop = self.spec['hadoop'].command
hadoop_classpath = hadoop('classpath', return_output=True)
# Remove whitespaces, as they can compromise syntax in
# module files
hadoop_classpath = re.sub('[\s+]', '', hadoop_classpath)
run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath)