R/4.3.2-cpeGNU-23.09 (R-4.3.2-cpeGNU-23.09.eb)
Install with the EasyBuild-user module:
To access module help after installation and get reminded for which stacks and partitions the module is installed, usemodule spider R/4.3.2-cpeGNU-23.09.
EasyConfig:
name = 'R'
version = '4.3.2'
local_bzip2_version = '1.0.8' # http://www.bzip.org/downloads.html
local_cairo_version = '1.17.4' # https://www.cairographics.org/
local_cURL_version = '8.0.1' # https://curl.haxx.se/download/
local_gzip_version = '1.12' # https://ftp.gnu.org/gnu/gzip/
local_libjpegturbo_version = '2.1.5.1' # https://github.com/libjpeg-turbo/libjpeg-turbo/releases
local_libpng_version = '1.6.39' # http://www.libpng.org/pub/png/libpng.html
local_libreadline_version = '8.2' # https://ftp.gnu.org/pub/gnu/readline/
local_libtiff_version = '4.5.0' # https://download.osgeo.org/libtiff/
local_ncurses_version = '6.4' # https://ftp.gnu.org/pub/gnu/ncurses/
local_Pango_version = '1.50.14' # http://ftp.gnome.org/pub/GNOME/sources/pango/
local_PCRE2_version = '10.42' # https://ftp.pcre.org/pub/pcre/
local_Tk_version = '8.6.13' # https://tcl.tk/
local_XZ_version = '5.4.2' # https://tukaani.org/xz/
local_zlib_version = '1.2.13' # https://zlib.net/
local_Zip_version = '3.0'
local_UnZip_version = '6.0'
homepage = 'https://www.r-project.org/'
whatis = [
"Description: R is a free software environment for statistical computing and graphics."
]
description = """
This module provides a base R package, without many bells and whistles.
A fully-featured R has many dependencies that do not all make sense on
the compute nodes of LUMI, in particular when it comes to graphics.
Similarly, the build process as-is will not find a web browser nor
PDF viewer as these are not currently available on regular compute
nodes of LUMI.
This version of R links with the multithreaded version of
Cray LibSci, so its linear algebra routines support multithreading
by settingh OMP_NUM_THREADS.
"""
toolchain = {'name': 'cpeGNU', 'version': '23.09'}
toolchainopts = {'openmp': True}
source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
sources = [SOURCE_TAR_GZ]
checksums = [
'b3f5760ac2eee8026a3f0eefcb25b47723d978038eee8e844762094c860c452a', # R-4.3.2.tar.gz
]
# Note: R will not be able to tell which BLAS library was used as it is linked
# in automatically and does not appear in BLAS_LIBS so that the code in the
# configure script cannot figure out which BLAS is being used and set
# r_blas properly.
builddependencies = [
('buildtools', '%(toolchain_version)s', '', SYSTEM),
]
dependencies = [
# Base R
('ncurses', local_ncurses_version),
('libreadline', local_libreadline_version),
('zlib', local_zlib_version),
('bzip2', local_bzip2_version),
('gzip', local_gzip_version),
('XZ', local_XZ_version),
('Info-ZIP', f'{local_Zip_version}-{local_UnZip_version}'), # Not really needed as anything in this module is also in the system-installed versions.
# TODO: Add a zip/unzip command, though the system one might be OK as it only uses the commands.
('PCRE2', local_PCRE2_version),
('cURL', local_cURL_version), # for RCurl but also used by the base R package
('X11', '%(toolchain_version)s'),
('Tk', local_Tk_version), # for tcltk (base package)
('libpng', local_libpng_version), # for plotting in R
('libjpeg-turbo', local_libjpegturbo_version), # for plottting in R
('LibTIFF', local_libtiff_version),
('cairo', local_cairo_version),
('Pango', local_Pango_version),
]
# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols.
# Adding it to FLIBS makes sure it is present when needed.
preconfigopts = 'export FLIBS="$FLIBS -lm" && '
# We also need to ensure a single Cray LibSci library is used. It looks like R compiles
# some files with OpenMP if it figures out that the compiler supports OpenMP, but does
# not add the flag to the link options, resulting in problems with Cray LibSci. Hence
# we enforce OpenMP and manually add it to the linker flags as that is not done by
# the build process.
preconfigopts += 'export LDFLAGS="-fopenmp $LDFLAGS" && '
configopts = "--with-pic --enable-threads --enable-R-shlib"
# some recommended packages may fail in a parallel build (e.g. Matrix), and
# we're installing them anyway below
configopts += " --with-recommended-packages=no"
# specify that at least EasyBuild v3.5.0 is required,
# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK
easybuild_version = '3.5.0'
exts_default_options = {
'source_urls': [
'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'https://cran.r-project.org/src/contrib/', # current version of packages
'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
],
'source_tmpl': '%(name)s_%(version)s.tar.gz',
}
# !! order of packages is important !!
# packages updated on 1st November 2021
exts_list = [
# include packages that are part of the base installation of R,
# both to make sure they are available (via sanity check),
# and to be able to pass the check for required dependencies when installing extensions in parallel
'base',
'compiler',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'parallel',
'splines',
'stats',
'stats4',
'tcltk',
'tools',
'utils',
#
# Do firsts because of potential problems
#
('Rmpi', '0.7-2', {
'easyblock': 'RPackage',
'patches': ['Rmpi-%(version)s_Cray.patch'],
'installopts': '--configure-args="--with-Rmpi-type=CRAY --with-Rmpi-include=$CRAY_MPICH_DIR/include --with-Rmpi-libpath=$CRAY_MPICH_DIR/lib" ',
'checksums': ['8591fa9f50de52535a32b36e7ed142c6ca4e03fdfdbef79a1e27a63ed5322eef'],
}),
('Rcpp', '1.0.11', {
'checksums': ['df757c3068599c6c05367900bcad93547ba3422d59802dbaca20fd74d4d2fa5f'],
}),
('codetools', '0.2-19', {
'checksums': ['c4b7e567c87f33dad85de92f79641e5e5b5deede6d19a9dfa47133d191782dab'],
}),
('RUnit', '0.4.32', {
'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'],
}),
('tinytest', '1.4.1', {
'checksums': ['f6fc13887d096ba444fb722ef34cc88e079fc18be9668ffead1ba586a30b1c74'],
}),
('backports', '1.4.1', {
'checksums': ['845c3c59fbb05e5a892c4231b955a0afdd331d82b7cc815bcff0672023242474'],
}),
('rlang', '1.1.2', {
'checksums': ['2a0ee1dc6e5c59b283c32db5e74e869922a336197cb406fe92622b6ec66f8092'],
}),
('parallelly', '1.36.0', {
'checksums': ['b9c0a29155944aae8fdb4cab00c521c7ed16af250450dd2a3dd69d5661427c88'],
}),
('iterators', '1.0.14', {
'checksums': ['cef3075a0930e1408c764e4da56bbadd4f7d14315809df8f38dd51f80ccc677b'],
}),
('foreach', '1.5.2', {
'checksums': ['56338d8753f9f68f262cf532fd8a6d0fe25a71a2ff0107f3ce378feb926bafe4'],
}),
('doParallel', '1.0.17', {
'checksums': ['b96a25ad105a654d70c7b4ca27290dc9967bc47f4668b2763927a886b178abd7'],
}),
('doMPI', '0.2.2', {
'checksums': ['68a45715690f50ebb121ee868634ff269e8f9636599b8dd8f601bf714fa81c2a'],
}),
('snow', '0.4-4', {
'checksums': ['84587f46f222a96f3e2fde10ad6ec6ddbd878f4e917cd926d632f61a87db13c9'],
}),
('snowfall', '1.84-6.3', {
'checksums': ['2641932b01041e34b7afb1261f649755b4c8d6560080e0e2ee549ffdf3b8b143'],
}),
('doSNOW', '1.0.20', {
'checksums': ['917cabed166aa2d1ec291691c17e1e3d344e858543e1682e3a442cc0c504bbb8'],
}),
('base64url', '1.4', {
'checksums': ['1d058f138660e9155ebb331d7a2561e2541ee3321b8da90f6c41fd8dcc122c58'],
}),
('brew', '1.0-10', {
'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'],
}),
('checkmate', '2.3.1', {
'checksums': ['e7e6ba0cca400137f352a599ea29cf35a83f40a5ad26e7c4f06e6c35471884f6'],
}),
('data.table', '1.14.10', {
'checksums': ['014b41eb71a8ddad504baeaa3a2fbbf03406783f00f3adcce48567692978627e'],
}),
('fs', '1.6.3', {
'checksums': ['fa82061e50d7a4d94b7e404f9f2b699e75ae8fbfb575fabdfc2c39f536c0f971'],
}),
('cli', '3.6.2', {
'checksums': ['4c0749e3711b2b6ae90fd992784303bc8d98039599cac1deb397239a7018e151'],
}),
('glue', '1.6.2', {
'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'],
}),
('lifecycle', '1.0.4', {
'checksums': ['ada4d3c7e84b0c93105e888647c5754219a8334f6e1f82d5afaf83d4855b91cc'],
}),
('pkgconfig', '2.0.3', {
'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'],
}),
('vctrs', '0.6.5', {
'checksums': ['43167d2248fd699594044b5c8f1dbb7ed163f2d64761e08ba805b04e7ec8e402'],
}),
('hms', '1.1.3', {
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}),
('prettyunits', '1.2.0', {
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}),
('R6', '2.5.1', {
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}),
('crayon', '1.5.2', {
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}),
('progress', '1.2.3', {
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}),
('rappdirs', '0.3.3', {
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}),
('stringi', '1.8.3', {
'checksums': ['1602be8edd1dd8ac5a836f4077cbc9d6a312ca4b2c594a0486370e8c1e314925'],
}),
('withr', '2.5.2', {
'checksums': ['d5b6fa6d728fda5201310d6ad5921a43aae1c23029c25334bfc1e54cb13d4205'],
}),
('digest', '0.6.33', {
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}),
('batchtools', '0.9.17', {
'checksums': ['b6e1dd54e8b70c2bf38d2ad1884f6b60fc74c1100f910f46724aa723c0749be6'],
}),
('globals', '0.16.2', {
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}),
('listenv', '0.9.0', {
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}),
('future', '1.33.1', {
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}),
('future.apply', '1.11.1', {
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}),
('future.batchtools', '0.12.1', {
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}),
]
moduleclass = 'lang'