{bio,tools}[foss/2022a] R-bundle-Bioconductor v3.15, arrow-R v8.0.0

easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb

@@ -0,0 +1,69 @@
+easyblock = 'CMakeMake'
+
+name = 'Arrow'
+version = '8.0.0'
+
+homepage = 'https://arrow.apache.org'
+description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform
+ for in-memory data."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s']
+sources = ['apache-arrow-%(version)s.tar.gz']
+checksums = ['ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('Autotools', '20220317'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('pkgconf', '1.8.0'),
+]
+
+# Arrow strongly prefers included jemalloc, so not including it as a dependency
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),  # for numpy
+    ('Boost', '1.79.0'),
+    ('lz4', '1.9.3'),
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('zstd', '1.5.2'),
+    ('snappy', '1.1.9'),
+    ('RapidJSON', '1.1.0'),
+    ('RE2', '2022-06-01'),
+    ('utf8proc', '2.7.0'),
+]
+
+start_dir = 'cpp'
+
+# see https://arrow.apache.org/docs/developers/python.html
+configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON "
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON "
+configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON "
+configopts += "-DZSTD_ROOT=$EBROOTZSTD "
+
+# also install Python bindings
+local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
+local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && "
+local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
+local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON "
+local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ."
+postinstallcmds = [local_install_pyarrow_cmds]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT,
+              'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT],
+    'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "python -c 'import pyarrow'",
+    "python -c 'import pyarrow.parquet'",
+]
+
+moduleclass = 'data'

easybuild/easyconfigs/a/arrow-R/arrow-R-8.0.0-foss-2022a-R-4.2.1.eb

@@ -0,0 +1,34 @@
+easyblock = 'RPackage'
+
+name = 'arrow-R'
+version = '8.0.0'
+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': '2022a'}
+
+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 = ['6c9aa08c68b7b39cb7d6b9394c0b94a566c0fe9a85cea61f5ed19e460bdb05ad']
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('Arrow', '8.0.0'),
+]
+
+preinstallopts = "export LIBARROW_BINARY=true && "
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['arrow'],
+}
+
+options = {'modulename': 'arrow'}
+
+moduleclass = 'tools'

easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb

@@ -0,0 +1,36 @@
+# pkgconf should be used in preference to pkg-config
+# This is included for use only in software that fails to build when using pkgconf
+easyblock = 'ConfigureMake'
+
+name = 'pkg-config'
+version = '0.29.2'
+
+homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/'
+
+description = """
+ pkg-config is a helper tool used when compiling applications and libraries.
+ It helps you insert the correct compiler options on the command line so an
+ application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0`
+ for instance, rather than hard-coding values on where to find glib (or other
+ libraries).
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://pkg-config.freedesktop.org/releases/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591']
+
+builddependencies = [('binutils', '2.38')]
+
+# don't use PAX, it might break.
+tar_config_opts = True
+
+configopts = " --with-internal-glib"
+
+sanity_check_paths = {
+    'files': ['bin/pkg-config'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'