Merge branch 'easybuilders:develop' into 20250115170157_new_pr_QGIS3402

pavelToman · Jan 24, 2025 · ec9f8ae · ec9f8ae
2 parents eaf9388 + bc1619f
commit ec9f8ae
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diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-10.3.0.eb
@@ -16,8 +16,12 @@ description = """Autoconf is an extensible package of M4 macros that produce she
 toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
 
 source_urls = [GNU_SOURCE]
-sources = [SOURCELOWER_TAR_XZ]
-checksums = ['f14c83cfebcc9427f2c3cea7258bd90df972d92eb26752da4ddad81c87a0faa4']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.36.1'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.37'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.38'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.39'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.40'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.40'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.40'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-Port-better-to-NVHPC.patch b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-Port-better-to-NVHPC.patch
@@ -0,0 +1,29 @@
+From 632282145ba1d617f480cde74eef938826fef4d5 Mon Sep 17 00:00:00 2001
+From: Paul Eggert <eggert@cs.ucla.edu>
+Date: Thu, 16 Jan 2025 11:24:12 -0800
+Subject: Port better to NVHPC
+
+See <https://savannah.gnu.org/support/?111172>.
+* lib/autoconf/fortran.m4 (_AC_FC_LIBRARY_LDFLAGS):
+Ignore -l options with embedded '='.
+---
+ lib/autoconf/fortran.m4 | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/lib/autoconf/fortran.m4 b/lib/autoconf/fortran.m4
+index 0fc7545d..4c39607c 100644
+--- a/lib/autoconf/fortran.m4
++++ b/lib/autoconf/fortran.m4
+@@ -664,7 +664,7 @@ while test $[@%:@] != 1; do
+ 	  ;;
+ 	  # Ignore these flags.
+ 	-lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -little \
+-	  |-LANG:=* | -LIST:* | -LNO:* | -link)
++	  | -[[lLR]]*=* | -LIST:* | -LNO:* | -link)
+ 	  ;;
+ 	-lkernel32)
+ 	  # Ignore this library only on Windows-like systems.
+-- 
+cgit v1.2.3-70-g09d2
+
+
diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71.eb
@@ -16,8 +16,12 @@ description = """Autoconf is an extensible package of M4 macros that produce she
 toolchain = SYSTEM
 
 source_urls = [GNU_SOURCE]
-sources = [SOURCELOWER_TAR_XZ]
-checksums = ['f14c83cfebcc9427f2c3cea7258bd90df972d92eb26752da4ddad81c87a0faa4']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    '431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c',  # autoconf-2.71.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 dependencies = [('M4', '1.4.18')]
 

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    'afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e',  # autoconf-2.72.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.42'),

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb
@@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e']
+patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
+checksums = [
+    'afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e',  # autoconf-2.72.tar.gz
+    '157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb',  # Autoconf-2.71-Port-better-to-NVHPC.patch
+]
 
 builddependencies = [
     ('binutils', '2.42'),

diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb
@@ -0,0 +1,39 @@
+easyblock = 'RPackage'
+
+name = 'arrow-R'
+version = '17.0.0.1'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://cran.r-project.org/web/packages/arrow'
+description = "R interface to the Apache Arrow C++ library"
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/Archive/arrow',  # package archive
+    'https://cran.r-project.org/src/contrib/',  # current version of packages
+    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+]
+sources = ['arrow_%(version)s.tar.gz']
+checksums = ['0214dbf5d958968172a6f67abbae916d33933625cf41dc22e89ab77a29cde75e']
+
+builddependencies = [
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('R', '4.4.2'),
+    ('R-bundle-CRAN', '2024.11'),
+    ('Arrow', '17.0.0'),  # arrow-R x.y.z[.N] only works with Arrow x.y.z
+]
+
+preinstallopts = "export LIBARROW_BUILD=false && "
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['arrow'],
+}
+
+options = {'modulename': 'arrow'}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb
@@ -0,0 +1,40 @@
+easyblock = 'Tarball'
+
+name = 'Beast'
+version = '2.7.7'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://beast2.org'
+description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using
+ strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies
+ but is also a framework for testing evolutionary hypotheses without conditioning on a single
+ tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted
+ proportional to its posterior probability. """
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'}
+
+source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/']
+sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]]
+checksums = [{
+    'BEAST.v2.7.7.Linux.x86.tgz': 'a866f3e5da4ef890a042f01849e32322aa0a8e16e3e1cb2c59f823de2611781a',
+    'BEAST.v2.7.7.Linux.aarch64.tgz': 'aa14e4a950fe2d9f3db24102a4e7365d8d42f79da1d9b1cdcf3016e927d18b9e',
+}]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Java', '11', '', SYSTEM),
+    ('beagle-lib', '4.0.1', versionsuffix),  # optional but recommended by developers
+    ('GTK3', '3.24.37'),  # optional for GUI tools
+]
+
+sanity_check_paths = {
+    'files': ['bin/beast'],
+    'dirs': []
+}
+
+sanity_check_commands = ["beast -help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'Tarball'
+
+name = 'Beast'
+version = '2.7.7'
+
+homepage = 'https://beast2.org'
+description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using
+ strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies
+ but is also a framework for testing evolutionary hypotheses without conditioning on a single
+ tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted
+ proportional to its posterior probability. """
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'}
+
+source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/']
+sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]]
+checksums = [{
+    'BEAST.v2.7.7.Linux.x86.tgz': 'a866f3e5da4ef890a042f01849e32322aa0a8e16e3e1cb2c59f823de2611781a',
+    'BEAST.v2.7.7.Linux.aarch64.tgz': 'aa14e4a950fe2d9f3db24102a4e7365d8d42f79da1d9b1cdcf3016e927d18b9e',
+}]
+
+dependencies = [
+    ('Java', '11', '', SYSTEM),
+    ('beagle-lib', '4.0.1'),  # optional but recommended by developers
+    ('GTK3', '3.24.37'),  # optional for GUI tools
+]
+
+sanity_check_paths = {
+    'files': ['bin/beast'],
+    'dirs': []
+}
+
+sanity_check_commands = ["beast -help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonBundle'
+
+name = 'Biotite'
+version = '0.41.0'
+
+homepage = 'https://www.biotite-python.org/'
+description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to
+identify homologous sequence regions in a protein family or you would like to
+find disulfide bonds in a protein structure: Biotite has the right tool for
+you. This package bundles popular tasks in computational molecular biology into
+a uniform Python library."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('biotite', version, {
+        'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb
@@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
 toolchain = {'name': 'GCC', 'version': '12.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+source_urls = ['https://archives.boost.io/release/%(version)s/source/']
 sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
 checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6']
 

diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb
@@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
 toolchain = {'name': 'GCC', 'version': '12.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+source_urls = ['https://archives.boost.io/release/%(version)s/source/']
 sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
 checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c']
 

diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb
@@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
 toolchain = {'name': 'GCC', 'version': '13.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+source_urls = ['https://archives.boost.io/release/%(version)s/source/']
 sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
 checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628']
 

diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb
@@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
 toolchain = {'name': 'GCC', 'version': '13.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+source_urls = ['https://archives.boost.io/release/%(version)s/source/']
 sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
 patches = ['Boost-1.85.0_fix-ppc-charconv.patch']
 checksums = [