new file: c/Cube/Cube-4.4.3-gompi-2019.03.eb

new file:   c/Cube/Cube-4.4.3-intel-2017a.eb
	new file:   c/Cube/Cube-4.4.3-intel-2018a.eb
	new file:   c/Cube/Cube-4.4.3-intel-2019.02.eb
	new file:   c/CubeGUI/CubeGUI-4.4.3-gompi.2019.03.eb
	new file:   c/CubeGUI/CubeGUI-4.4.3-intel-2017a.eb
	new file:   c/CubeGUI/CubeGUI-4.4.3-intel-2018a.eb
	new file:   c/CubeGUI/CubeGUI-4.4.3-intel-2019.02.eb
	new file:   c/CubeLib/CubeLib-4.4.3-gompi-2019.03.eb
	new file:   c/CubeLib/CubeLib-4.4.3-intel-2017a.eb
	new file:   c/CubeLib/CubeLib-4.4.3-intel-2018a.eb
	new file:   c/CubeLib/CubeLib-4.4.3-intel-2019.02.eb
	new file:   c/CubeW/CubeW-4.4.2-gompi-2019.03.eb
	new file:   c/CubeW/CubeW-4.4.2-intel-2017a.eb
	new file:   c/CubeW/CubeW-4.4.2-intel-2018a.eb
	new file:   c/CubeW/CubeW-4.4.2-intel-2019.02.eb
	new file:   g/gompi/gompi-2019.03.eb
	new file:   q/Qualimap/Qualimap-2.2.1-intel-2017a.eb
	modified:   r/R/R-3.5.3-intel-2017a.eb
	modified:   t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb
	new file:   t/Trilinos/Trilinos-12.14.1-thyra_test.patch
	deleted:    q/Qualimap/Qualimap-2.2.1.eb
	deleted:    r/R/Makevars
	deleted:    r/R/R-3.5.3-intel-2017a.old
This commit is contained in:
Lukáš Krupčík 2019-04-29 11:26:43 +02:00
parent f367c9b4be
commit 8d889cdc7f
23 changed files with 513 additions and 557 deletions

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@ -0,0 +1,23 @@
# IT4Innovations 2019
easyblock = "Toolchain"
name = 'Cube'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'gompi', 'version': '2019.03'}
dependencies = [
('CubeW', '4.4.2'),
('CubeLib', '4.4.3'),
('CubeGUI', '4.4.3'),
]
moduleclass = 'perf'

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@ -0,0 +1,23 @@
# IT4Innovations 2019
easyblock = "Toolchain"
name = 'Cube'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2017a'}
dependencies = [
('CubeW', '4.4.2'),
('CubeLib', '4.4.3'),
('CubeGUI', '4.4.3'),
]
moduleclass = 'perf'

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@ -0,0 +1,23 @@
# IT4Innovations 2019
easyblock = "Toolchain"
name = 'Cube'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2018a'}
dependencies = [
('CubeW', '4.4.2'),
('CubeLib', '4.4.3'),
('CubeGUI', '4.4.3'),
]
moduleclass = 'perf'

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@ -0,0 +1,23 @@
# IT4Innovations 2019
easyblock = "Toolchain"
name = 'Cube'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2019.02'}
dependencies = [
('CubeW', '4.4.2'),
('CubeLib', '4.4.3'),
('CubeGUI', '4.4.3'),
]
moduleclass = 'perf'

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@ -0,0 +1,32 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeGUI'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'gompi', 'version': '2019.03'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubegui-%(version)s.tar.gz']
dependencies = [
('Qt', '4.8.7', '', True),
('CubeLib', '4.4.3')
]
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,34 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeGUI'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubegui-%(version)s.tar.gz']
dependencies = [
('Qt', '4.8.7', '', True),
('CubeLib', '4.4.3')
]
configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel'
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,34 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeGUI'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2018a'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubegui-%(version)s.tar.gz']
dependencies = [
('Qt', '4.8.7', '', True),
('CubeLib', '4.4.3')
]
configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel'
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,34 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeGUI'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2019.02'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubegui-%(version)s.tar.gz']
dependencies = [
('Qt', '4.8.7', '', True),
('CubeLib', '4.4.3')
]
configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel'
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,27 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeLib'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'gompi', 'version': '2019.03'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubelib-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,29 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeLib'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubelib-%(version)s.tar.gz']
configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel'
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,27 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeLib'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2018a'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubelib-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,27 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeLib'
version = '4.4.3'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2019.02'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubelib-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,27 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeW'
version = '4.4.2'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'gompi', 'version': '2019.03'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubew-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,27 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeW'
version = '4.4.2'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubew-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,27 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeW'
version = '4.4.2'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2018a'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubew-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

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@ -0,0 +1,27 @@
# IT4Innovations 2019
easyblock = 'EB_Score_minus_P'
name = 'CubeW'
version = '4.4.2'
homepage = 'http://www.scalasca.org/software/cube-4.x/download.html'
description = """Cube, which is used as performance report explorer for Scalasca and
Score-P, is a generic tool for displaying a multi-dimensional performance space
consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system
resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree
can be collapsed or expanded to achieve the desired level of granularity."""
toolchain = {'name': 'intel', 'version': '2019.02'}
toolchainopts = {'optarch': False}
source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/']
sources = ['cubew-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin', 'include', 'lib'],
}
moduleclass = 'perf'

22
g/gompi/gompi-2019.03.eb Normal file
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@ -0,0 +1,22 @@
# IT4Innovations 2019
easyblock = "Toolchain"
name = 'gompi'
version = '2019.03'
homepage = '(none)'
description = """GNU Compiler Collection (GCC) based compiler toolchain,
including OpenMPI for MPI support."""
toolchain = {'name': 'dummy', 'version': ''}
gccver = '6.3.0-2.27'
# compiler toolchain dependencies
dependencies = [
('GCC', gccver), # includes both GCC and binutils
('OpenMPI', '4.0.0', '', ('GCC', gccver)),
]
moduleclass = 'toolchain'

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@ -1,6 +1,6 @@
# IT4Innovations 2019
easyblock = "CmdCp"
easyblock = "Tarball"
name = 'Qualimap'
version = '2.2.1'
@ -13,21 +13,18 @@ description = """Qualimap 2 is a platform-independent application written in
toolchain = {'name': 'intel', 'version': '2017a'}
sources = ['qualimap_v2.2.1.zip']
sources = ['qualimap_v%(version)s.zip']
source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads']
dependencies = [
('Java', '1.8.0_121', '', True),
('R', '3.5.3'),
]
cmds_map = [('.*', "./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')]
modextrapaths = {"PATH": '.'}
sanity_check_paths = {
'files': ['bin/bazel'],
'dirs': [],
'files': ['qualimap'],
'dirs': ['lib', 'scripts', 'species'],
}
moduleclass = 'bio'

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@ -1,2 +0,0 @@
# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex<double>::_M_value" is inaccessible'
PKG_CXXFLAGS = -wd308

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@ -707,9 +707,7 @@ exts_list = [
('cgdsr', '1.2.10', {
'checksums': ['43bc02fb33c371464f9407d5e5e6419527e9360e3e394343862cca0aebe1d0f7'],
}),
('R.utils', '2.6.0', {
'checksums': ['5d64993d1209b512a4e97f2edecdbc185f4a369ee5fa2e334ed2cf017486470e'],
}),
('R.utils', '2.8.0'),
('R.matlab', '3.6.1', {
'checksums': ['1032579fd152d419eaf1f69bf6035fba7a71ef26e76136c48a6fc619e3887804'],
}),
@ -2091,7 +2089,30 @@ exts_list = [
('rtracklayer', '1.42.2'),
('BSgenome', '1.50.0'),
('gsmoothr', '0.1.7'),
('limma', '3.14.4'),
('limma', '3.38.3'),
('edgeR', '3.24.3'),
('DNAcopy', '1.56.0'),
('AnnotationDbi', '1.44.0'),
('annotate', '1.60.1'),
('genefilter', '1.64.0'),
('affyio', '1.52.0'),
('BiocManager', '1.30.4'),
('preprocessCore', '1.44.0'),
('affy', '1.60.0'),
('vsn', '3.50.0'),
('Ringo', '1.46.0'),
('R.filesets', '2.13.0'),
('R.devices', '2.16.0'),
('aroma.light', '3.12.0'),
('PSCBS', '0.64.0'),
('aroma.core', '3.1.3'),
('R.huge', '0.9.0'),
('aroma.apd', '0.6.0'),
('aroma.affymetrix', '3.1.1'),
('truncnorm', '1.0-8'),
('Rsolnp', '1.16'),
('Repitools', '1.28.0'),
('rtracklayer', '1.42.2'),
]
moduleclass = 'lang'

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@ -1,540 +0,0 @@
# IT4Innovations 2019
name = 'R'
version = '3.5.3'
homepage = 'http://www.r-project.org/'
description = """R is a free software environment for statistical computing and graphics."""
toolchain = {'name': 'intel', 'version': '2017a'}
sources = [SOURCE_TAR_GZ]
source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s']
preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"'
configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib"
# Actually use Tcl/Tk
configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh '
# Enable graphics capabilities for plotting.
configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff"
# some recommended packages may fail in a parallel build (e.g. Matrix),
# and we're installing them anyway below
configopts += " --with-recommended-packages=no"
dependencies = [
('cairo', '1.14.8', '', True),
('libreadline', '7.0', '', True),
('ncurses', '6.0', '', True),
('bzip2', '1.0.6', '', True),
('XZ', '5.2.3', '', True),
('zlib', '1.2.11', '', True),
('SQLite', '3.17.0', '', True),
('PCRE', '8.40', '', True),
('libpng', '1.6.29', '', True), # for plotting in R
('libjpeg-turbo', '1.5.1', '', True), # for plottting in R
('LibTIFF', '4.0.7', '', True),
# Java bindings are built if Java is found, might as well provide it
('Java', '1.8.0_144', '', True),
('Tcl', '8.6.6', '', True), # for tcltk
('Tk', '8.6.6', '', True), # for tcltk
('cURL', '7.53.1', '', True), # for RCurl
('libxml2', '2.9.4', '', True), # for XML
('GDAL', '2.1.3', '-Python-2.7.13', True), # for rgdal
('PROJ', '4.9.3'), # for rgdal
('GMP', '6.1.2', '', True), # for igraph
('NLopt', '2.4.2'), # for nloptr
('FFTW', '3.3.6'), # for fftw
('libsndfile', '1.0.28'), # for seewave
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
# ('OpenSSL', '1.0.2h'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
name_tmpl = '%(name)s_%(version)s.tar.gz'
ext_options = {
'source_urls': [
# package archive
'http://cran.r-project.org/src/contrib/Archive/%(name)s',
'http://cran.r-project.org/src/contrib/', # current version of packages
# mirror alternative for current packages
'http://cran.freestatistics.org/src/contrib',
'http://www.bioconductor.org/packages/release/bioc/src/contrib/'
],
'source_tmpl': name_tmpl,
}
# !! order of packages is important !!
# packages updated on May 11th 2017
exts_list = [
# default libraries, only here to sanity check their presence
'base',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'splines',
'stats',
'stats4',
'tools',
'utils',
# non-standard libraries, should be specified with fixed versions!
('Rmpi', '0.6-6', ext_options),
('abind', '1.4-5', ext_options),
('magic', '1.5-6', ext_options),
('geometry', '0.3-6', dict(ext_options.items() +
[('patches', ['geometry-0.3-4-icc.patch'])])),
('bit', '1.1-12', ext_options),
('filehash', '2.4-1', ext_options),
('ff', '2.2-13', ext_options),
('bnlearn', '4.1.1', ext_options),
('bootstrap', '2017.2', ext_options),
('combinat', '0.0-8', ext_options),
('deal', '1.2-37', ext_options),
('fdrtool', '1.2.15', ext_options),
('formatR', '1.5', ext_options),
('gtools', '3.5.0', ext_options),
('gdata', '2.17.0', ext_options),
('GSA', '1.03', ext_options),
('highr', '0.6', ext_options),
('infotheo', '1.2.0', ext_options),
('lars', '1.2', ext_options),
('lazy', '1.2-15', ext_options),
('kernlab', '0.9-25', ext_options),
('mime', '0.5', ext_options),
('markdown', '0.8', ext_options),
('mlbench', '2.1-1', ext_options),
('NLP', '0.1-10', ext_options),
('mclust', '5.3', ext_options),
('RANN', '2.5', ext_options),
('rmeta', '2.16', ext_options),
('segmented', '0.5-1.4', ext_options),
('som', '0.3-5.1', ext_options),
('SuppDists', '1.1-9.4', ext_options),
('stabledist', '0.7-1', ext_options),
('survivalROC', '1.0.3', ext_options),
('pspline', '1.0-17', ext_options),
('timeDate', '3012.100', ext_options),
('longmemo', '1.0-0', ext_options),
('ADGofTest', '0.3', ext_options),
('ade4', '1.7-6', ext_options),
('AlgDesign', '1.1-7.3', ext_options),
('base64enc', '0.1-3', ext_options),
('BH', '1.62.0-1', ext_options),
('brew', '1.0-6', ext_options),
('Brobdingnag', '1.2-4', ext_options),
('corpcor', '1.6.9', ext_options),
('longitudinal', '1.1.12', ext_options),
('backports', '1.0.5', ext_options),
('checkmate', '1.8.2', ext_options),
('Rcpp', '0.12.10', ext_options),
('cubature', '1.3-8', ext_options),
('DEoptimR', '1.0-8', ext_options),
('digest', '0.6.12', ext_options),
('fastmatch', '1.1-0', ext_options),
('ffbase', '0.12.3', ext_options),
('iterators', '1.0.8', ext_options),
('maps', '3.1.1', ext_options),
('nnls', '1.4', ext_options),
('sendmailR', '1.2-1', ext_options),
('spam', '1.4-0', ext_options),
('subplex', '1.2-2', ext_options),
('stringi', '1.1.5', ext_options),
('magrittr', '1.5', ext_options),
('stringr', '1.2.0', ext_options),
('evaluate', '0.10', ext_options),
('logspline', '2.1.9', ext_options),
('ncbit', '2013.03.29', ext_options),
('permute', '0.9-4', ext_options),
('plotrix', '3.6-5', ext_options),
('randomForest', '4.6-12', ext_options),
('scatterplot3d', '0.3-40', ext_options),
('SparseM', '1.77', ext_options),
('tripack', '1.3-8', ext_options),
('irace', '2.3', ext_options),
('rJava', '0.9-8', ext_options),
('lattice', '0.20-35', ext_options),
('RColorBrewer', '1.1-2', ext_options),
('latticeExtra', '0.6-28', ext_options),
('Matrix', '1.2-10', ext_options),
('png', '0.1-7', ext_options),
('RcppArmadillo', '0.7.800.2.0', ext_options),
('plyr', '1.8.4', ext_options),
('pROC', '1.9.1', ext_options),
('quadprog', '1.5-5', ext_options),
('BB', '2014.10-1', ext_options),
('BBmisc', '1.11', ext_options),
('fail', '1.3', ext_options),
('rlecuyer', '0.3-4', ext_options),
('snow', '0.4-2', ext_options),
('MASS', '7.3-47', ext_options),
('tree', '1.0-37', ext_options),
('pls', '2.6-0', ext_options),
('class', '7.3-14', ext_options),
('e1071', '1.6-8', ext_options),
('nnet', '7.3-12', ext_options),
('nlme', '3.1-131', ext_options),
('minqa', '1.2.4', ext_options),
('RcppEigen', '0.3.3.3.0', ext_options),
('MatrixModels', '0.4-1', ext_options),
('quantreg', '5.33', ext_options),
('mgcv', '1.8-17', ext_options),
('colorspace', '1.3-2', ext_options),
('robustbase', '0.92-7', ext_options),
('sp', '1.2-4', ext_options),
('zoo', '1.8-0', ext_options),
('lmtest', '0.9-35', ext_options),
('vcd', '1.4-3', ext_options),
('snowfall', '1.84-6.1', ext_options),
('rpart', '4.1-11', ext_options),
('survival', '2.41-3', ext_options),
('mice', '2.30', ext_options),
('urca', '1.3-0', ext_options),
('fracdiff', '1.4-2', ext_options),
('logistf', '1.22', ext_options),
('akima', '0.6-2', ext_options),
('bitops', '1.0-6', ext_options),
('boot', '1.3-19', ext_options),
('mixtools', '1.1.0', ext_options),
('cluster', '2.0.6', ext_options),
('gclus', '1.3.1', ext_options),
('coda', '0.19-1', ext_options),
('codetools', '0.2-15', ext_options),
('foreach', '1.4.3', ext_options),
('doMC', '1.3.4', ext_options),
('DBI', '0.6-1', ext_options),
('foreign', '0.8-68', ext_options),
('gam', '1.14-4', ext_options),
('gamlss.data', '5.0-0', ext_options),
('gamlss.dist', '5.0-0', ext_options),
('hwriter', '1.3.2', ext_options),
('KernSmooth', '2.23-15', ext_options),
('xts', '0.9-7', ext_options),
('TTR', '0.23-1', ext_options),
('quantmod', '0.4-8', ext_options),
('mnormt', '1.5-5', ext_options),
('mvtnorm', '1.0-6', ext_options),
('pcaPP', '1.9-61', ext_options),
('numDeriv', '2016.8-1', ext_options),
('lava', '1.5', ext_options),
('prodlim', '1.6.1', ext_options),
('pscl', '1.4.9', ext_options),
('memoise', '1.1.0', ext_options),
('plogr', '0.1-1', ext_options),
('RSQLite', '1.1-2', ext_options),
('BatchJobs', '1.6', ext_options),
('sandwich', '2.3-4', ext_options),
('sfsmisc', '1.1-0', ext_options),
('spatial', '7.3-11', ext_options),
('VGAM', '1.0-3', ext_options),
('waveslim', '1.7.5', ext_options),
('xtable', '1.8-2', ext_options),
('profileModel', '0.5-9', ext_options),
('brglm', '0.5-9', ext_options),
('deSolve', '1.14', ext_options),
('tseriesChaos', '0.1-13', ext_options),
('tseries', '0.10-40', ext_options),
('fastICA', '1.2-0', ext_options),
('R.methodsS3', '1.7.1', ext_options),
('R.oo', '1.21.0', ext_options),
('cgdsr', '1.2.6', ext_options),
('R.utils', '2.5.0', ext_options),
('R.matlab', '3.6.1', ext_options),
('gbm', '2.1.3', ext_options),
('dichromat', '2.0-0', ext_options),
('Formula', '1.2-1', ext_options),
('acepack', '1.4.1', ext_options),
('reshape2', '1.4.2', ext_options),
('gtable', '0.2.0', ext_options),
('munsell', '0.4.3', ext_options),
('labeling', '0.3', ext_options),
('scales', '0.4.1', ext_options),
('proto', '1.0.0', ext_options),
('lazyeval', '0.2.0', ext_options),
('assertthat', '0.2.0', ext_options),
('tibble', '1.3.0', ext_options),
('ggplot2', '2.2.1', ext_options),
('gridExtra', '2.2.1', ext_options),
('chron', '2.3-50', ext_options),
('data.table', '1.10.4', ext_options),
('viridisLite', '0.2.0', ext_options),
('viridis', '0.4.0', ext_options),
('yaml', '2.1.14', ext_options),
('jsonlite', '1.4', ext_options),
('htmltools', '0.3.6', ext_options),
('htmlwidgets', '0.8', ext_options),
('knitr', '1.16', ext_options),
('htmlTable', '1.9', ext_options),
('Hmisc', '4.0-3', ext_options),
('fastcluster', '1.1.22', ext_options),
('registry', '0.3', ext_options),
('pkgmaker', '0.22', ext_options),
('rngtools', '1.2.4', ext_options),
('doParallel', '1.0.10', ext_options),
('gridBase', '0.4-7', ext_options),
('NMF', '0.20.6', ext_options),
('irlba', '2.1.2', ext_options),
('igraph', '1.0.1', ext_options),
('GeneNet', '1.2.13', ext_options),
('ape', '4.1', ext_options),
('RJSONIO', '1.3-0', ext_options),
('caTools', '1.17.1', ext_options),
('gplots', '3.0.1', ext_options),
('ROCR', '1.0-7', ext_options),
('httpuv', '1.3.3', ext_options),
('R6', '2.2.1', ext_options),
('rjson', '0.2.15', ext_options),
('sourcetools', '0.1.6', ext_options),
('shiny', '1.0.3', ext_options),
('seqinr', '3.3-6', ext_options),
('LearnBayes', '2.15', ext_options),
('deldir', '0.1-14', ext_options),
('gmodels', '2.16.2', ext_options),
('expm', '0.999-2', ext_options),
('spdep', '0.6-13', ext_options),
('dplyr', '0.5.0', ext_options),
('vegan', '2.4-3', ext_options),
('adegenet', '2.0.1', ext_options),
('prettyunits', '1.0.2', ext_options),
('progress', '1.1.2', ext_options),
('rncl', '0.8.2', ext_options),
('XML', '3.98-1.7', ext_options),
('crayon', '1.3.2', ext_options),
('praise', '1.0.0', ext_options),
('testthat', '1.0.2', ext_options),
('rprojroot', '1.2', ext_options),
('rmarkdown', '1.5', ext_options),
('curl', '2.6', ext_options),
('openssl', '0.9.6', ext_options),
('httr', '1.2.1', ext_options),
('reshape', '0.8.6', ext_options),
('xml2', '1.1.1', ext_options),
('bold', '0.4.0', ext_options),
('triebeard', '0.3.0', ext_options),
('urltools', '1.6.0', ext_options),
('httpcode', '0.2.0', ext_options),
('crul', '0.3.6', ext_options),
('rredlist', '0.3.0', ext_options),
('rentrez', '1.0.4', ext_options),
('rotl', '3.0.3', ext_options),
('solrium', '0.4.0', ext_options),
('ritis', '0.5.4', ext_options),
('worrms', '0.1.0', ext_options),
('natserv', '0.1.4', ext_options),
('taxize', '0.8.4', ext_options),
('tidyr', '0.6.2', ext_options),
('uuid', '0.1-2', ext_options),
('RNeXML', '2.0.7', ext_options),
('phylobase', '0.8.4', ext_options),
('adephylo', '1.1-10', ext_options),
('animation', '2.5', ext_options),
('bigmemory.sri', '0.1.3', ext_options),
('bigmemory', '4.5.19', dict(ext_options.items() + \
[('patches', ['bigmemory-4.5.19_icpc-wd308.patch'])])),
('calibrate', '1.7.2', ext_options),
('clusterGeneration', '1.3.4', ext_options),
('raster', '2.5-8', ext_options),
('dismo', '1.1-4', ext_options),
('extrafontdb', '1.0', ext_options),
('Rttf2pt1', '1.3.4', ext_options),
('extrafont', '0.17', ext_options),
('fields', '8.10', ext_options),
('shapefiles', '0.7', ext_options),
('fossil', '0.3.7', ext_options),
('geiger', '2.0.6', ext_options),
('glmnet', '2.0-10', ext_options),
('rgl', '0.98.1', ext_options),
('labdsv', '1.8-0', ext_options),
('stabs', '0.6-2', ext_options),
('modeltools', '0.2-21', ext_options),
('strucchange', '1.5-1', ext_options),
('TH.data', '1.0-8', ext_options),
('multcomp', '1.4-6', ext_options),
('coin', '1.1-3', ext_options),
('party', '1.2-3', ext_options),
('mboost', '2.8-0', ext_options),
('msm', '1.6.4', ext_options),
('nor1mix', '1.2-2', ext_options),
('np', '0.60-3', ext_options),
('polynom', '1.3-9', ext_options),
('polspline', '1.1.12', ext_options),
('rms', '5.1-1', ext_options),
('RWekajars', '3.9.1-3', ext_options),
('RWeka', '0.4-34', ext_options),
('slam', '0.1-40', ext_options),
('tm', '0.7-1', ext_options),
('TraMineR', '2.0-5', ext_options),
('chemometrics', '1.4.2', ext_options),
('FNN', '1.1', ext_options),
('ipred', '0.9-6', ext_options),
('statmod', '1.4.29', ext_options),
('miscTools', '0.6-22', ext_options),
('maxLik', '1.3-4', ext_options),
('mlogit', '0.2-4', ext_options),
('getopt', '1.20.0', ext_options),
('gsalib', '2.1', ext_options),
('optparse', '1.3.2', ext_options),
('klaR', '0.6-12', ext_options),
('neuRosim', '0.2-12', ext_options),
('locfit', '1.5-9.1', ext_options),
('GGally', '1.3.0', ext_options),
('beanplot', '1.2', ext_options),
('clValid', '0.6-6', ext_options),
('matrixStats', '0.52.2', ext_options),
('DiscriMiner', '0.1-29', ext_options),
('ellipse', '0.3-8', ext_options),
('leaps', '3.0', ext_options),
('nloptr', '1.0.4', ext_options),
('lme4', '1.1-13', ext_options),
('pbkrtest', '0.4-7', ext_options),
('car', '2.1-4', ext_options),
('flashClust', '1.01-2', ext_options),
('FactoMineR', '1.35', ext_options),
('flexclust', '1.3-4', ext_options),
('flexmix', '2.3-14', ext_options),
('prabclus', '2.2-6', ext_options),
('diptest', '0.75-7', ext_options),
('trimcluster', '0.1-2', ext_options),
('fpc', '2.1-10', ext_options),
('BiasedUrn', '1.07', ext_options),
('TeachingDemos', '2.10', ext_options),
('kohonen', '3.0.2', dict(ext_options.items() + \
[('patches', ['kohonen-3.0.2_icpc-wd308.patch'])])),
('base64', '2.0', ext_options),
('doRNG', '1.6.6', ext_options),
('nleqslv', '3.2', ext_options),
('Deriv', '3.8.0', ext_options),
('RGCCA', '2.1.2', ext_options),
('pheatmap', '1.0.8', ext_options),
('openxlsx', '4.0.17', ext_options),
('pvclust', '2.0-0', ext_options),
('RCircos', '1.2.0', ext_options),
('lambda.r', '1.1.9', ext_options),
('futile.options', '1.0.0', ext_options),
('futile.logger', '1.4.3', ext_options),
('VennDiagram', '1.6.17', ext_options),
('xlsxjars', '0.6.1', ext_options),
('xlsx', '0.5.7', ext_options),
('forecast', '8.0', dict(ext_options.items() + \
[('patches', ['forecast-6.1_icpc-wd308.patch'])])),
('fma', '2.3', ext_options),
('expsmooth', '2.3', ext_options),
('fpp', '0.5', ext_options),
('maptools', '0.9-2', ext_options),
('tensor', '1.5', ext_options),
('polyclip', '1.6-1', ext_options),
('goftest', '1.1-1', ext_options),
('spatstat.utils', '1.6-0', ext_options),
('spatstat', '1.51-0', ext_options),
('rgdal', '1.2-7', ext_options),
('gdalUtils', '2.0.1.7', ext_options),
('pracma', '2.0.4', ext_options),
('RCurl', '1.95-4.8', ext_options),
('bio3d', '2.3-1', ext_options),
('AUC', '0.3.0', ext_options),
('interpretR', '0.2.4', ext_options),
('cvAUC', '1.1.0', ext_options),
('SuperLearner', '2.0-21', ext_options),
('lpSolve', '5.6.13', ext_options),
('mediation', '4.4.5', ext_options),
('ModelMetrics', '1.1.0', ext_options),
('caret', '6.0-76', ext_options),
('adabag', '4.1', ext_options),
('parallelMap', '1.3', ext_options),
('ParamHelpers', '1.10', ext_options),
('ggvis', '0.4.3', ext_options),
('mlr', '2.11', ext_options),
('unbalanced', '2.0', ext_options),
('RSNNS', '0.4-9', ext_options),
('abc.data', '1.0', ext_options),
('abc', '2.1', ext_options),
('lhs', '0.14', ext_options),
('tensorA', '0.36', ext_options),
('EasyABC', '1.5', ext_options),
('shape', '1.4.2', ext_options),
('whisker', '0.3-2', ext_options),
('rstudioapi', '0.6', ext_options),
('commonmark', '1.2', ext_options),
('desc', '1.1.0', ext_options),
('roxygen2', '6.0.1', ext_options),
('git2r', '0.18.0', ext_options),
('rversions', '1.0.3', ext_options),
('withr', '1.0.2', ext_options),
('devtools', '1.13.0', ext_options),
('Rook', '1.1-1', ext_options),
('Cairo', '1.5-9', dict(ext_options.items() +
[('patches', ['Cairo-1.5-9.patch'])])),
('RMTstat', '0.3', ext_options),
('Lmoments', '1.2-3', ext_options),
('distillery', '1.0-2', ext_options),
('extRemes', '2.0-8', ext_options),
('pixmap', '0.4-11', ext_options),
('tkrplot', '0.0-23', ext_options),
('misc3d', '0.8-4', ext_options),
('multicool', '0.1-10', dict(ext_options.items() + \
[('patches', ['multicool-0.1-10_icpc-wd308.patch'])])),
('ks', '1.10.6', ext_options),
('logcondens', '2.1.5', ext_options),
('Iso', '0.0-17', ext_options),
('penalized', '0.9-50', ext_options),
('clusterRepro', '0.5-1.1', ext_options),
('randomForestSRC', '2.4.2', ext_options),
('sm', '2.2-5.4', ext_options),
('psych', '1.7.5', ext_options),
('pbivnorm', '0.6.0', ext_options),
('lavaan', '0.5-23.1097', ext_options),
('matrixcalc', '1.0-3', ext_options),
('arm', '1.9-3', ext_options),
('mi', '1.0', ext_options),
('visNetwork', '1.0.3', ext_options),
('rgexf', '0.15.3', ext_options),
('influenceR', '0.1.0', ext_options),
('DiagrammeR', '0.9.0', ext_options),
('sem', '3.1-9', ext_options),
('jpeg', '0.1-8', ext_options),
('network', '1.13.0', ext_options),
('statnet.common', '3.3.0', ext_options),
('sna', '2.4', ext_options),
('glasso', '1.8', dict(ext_options.items() + \
[('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])),
('huge', '1.2.7', ext_options),
('d3Network', '0.5.2.1', ext_options),
('ggm', '2.3', ext_options),
('qgraph', '1.4.3', ext_options),
('diveRsity', '1.9.90', ext_options),
('doSNOW', '1.0.14', ext_options),
('phangorn', '2.2.0', ext_options),
('geepack', '1.2-1', ext_options),
('lubridate', '1.6.0', ext_options),
('biom', '0.3.12', ext_options),
('pim', '2.0.1', ext_options),
('minpack.lm', '1.2-1', ext_options),
('rootSolve', '1.7', ext_options),
('diagram', '1.6.3', ext_options),
('FME', '1.3.5', ext_options),
('bmp', '0.2', ext_options),
('readbitmap', '0.1-4', ext_options),
('purrr', '0.2.2', ext_options),
('downloader', '0.4', ext_options),
('imager', '0.40.2', dict(ext_options.items() + \
[('patches', ['imager-0.40.2_icpc-wd308.patch'])])),
('pracma', '2.0.4', ext_options),
('signal', '0.7-6', ext_options),
('tuneR', '1.3.2', ext_options),
('pastecs', '1.3-18', ext_options),
('audio', '0.1-5', ext_options),
('fftw', '1.0-4', ext_options),
('seewave', '2.0.5', ext_options),
('gsw', '1.0-3', ext_options),
('oce', '0.9-21', ext_options),
('ineq', '0.2-13', ext_options),
('soundecology', '1.3.2', ext_options),
# ('KFAS', '1.2.9', ext_options),
# qualimap dependencies
('Biobase', '2.42.0', ext_options),
('NOISeq', '2.26.1', ext_options),
]
moduleclass = 'lang'

View File

@ -16,12 +16,13 @@ source_urls = ['https://github.com/trilinos/Trilinos/archive/']
sources = ['%(namelower)s-release-12-14-1.tar.gz']
patches = [
('Trilinos-12.14.1-epetra_hdf5.patch'),
('Trilinos-12.14.1-thyra_test.patch'),
# ('Trilinos-12.12.1_fix-CEpetra-LAPACK.patch', 'packages/CTrilinos'),
# 'Trilinos-12.12.1_muelu-fix-function-signature.patch',
# 'Trilinos-12.12.1_fix-Sundance.patch',
]
configopts = '-DThyraEpetraAdapters_TestThyraDebugHang_MPI_4_DISABLE=ON '
configopts = '-DThyraEpetraAdapters_THYRADEBUGHANG_ENABLE=OFF '
configopts += '-DEpetraExt_ENABLE_HDF5=OFF '
builddependencies = [
@ -33,8 +34,8 @@ dependencies = [
('Py', '2.7', '', True),
('Boost', '1.68.0', versionsuffix),
('SCOTCH', '6.0.6'),
('SuiteSparse', '5.4.0', '-ParMETIS-4.0.3'),
('ParMETIS', '4.0.3'),
('SuiteSparse', '5.4.0', '-METIS-5.1.0'),
('METIS', '5.1.0', '', True),
('netCDF', '4.6.1'),
('MATIO', '1.5.12', '', ('GCCcore', '6.3.0')),
('GLM', '0.9.9.0', '', ('GCCcore', '6.3.0')),
@ -44,6 +45,9 @@ dependencies = [
# disable TrilinosCouplings package, doesn't build correctly (examples fail to compile)
skip_exts = ['TrilinosCouplings']
prebuildopts = "find packages/amesos2/test/solvers -type f -exec sed -i.bak 's/-lifcoremt_pic/-lifcoremt_pic -lcamd -lccolamd/g' {} + && "
# workaround for Teuchos.pyc not being found during "make install"
# see https://github.com/trilinos/Trilinos/issues/1749
preinstallopts = "cd %(builddir)s/trilinos-%(version)s-Source/packages/PyTrilinos/src/PyTrilinos && "

View File

@ -0,0 +1,10 @@
--- packages/thyra/adapters/epetra/test/CMakeLists.txt.orig 2019-04-26 08:08:36.271709024 +0200
+++ packages/thyra/adapters/epetra/test/CMakeLists.txt 2019-04-26 08:08:17.591718590 +0200
@@ -12,6 +12,7 @@
TRIBITS_ADD_EXECUTABLE_AND_TEST(
TestThyraDebugHang
+ EXCLUDE_IF_NOT_TRUE ${PACKAGE_NAME}_THYRADEBUGHANG_ENABLE
SOURCES
TestThyraDebugHang.cpp
${TEUCHOS_STD_PARALLEL_UNIT_TEST_MAIN}