R/4.6.1-cpeGNU-26.03-OpenMP (R-4.6.1-cpeGNU-26.03-OpenMP.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/4.6.1-cpeGNU-26.03-OpenMP.
EasyConfig:
#DOC This EasyConfig provides R compiled with the multithreaded LibSci libraries (hence the -OpenMP suffix)
#DOC and with packages for parallel computing and other packages offered by Cray-R already installed.
#DOC It also contains some packages for benchmarking.
name = 'R'
version = '4.6.1'
version_suffix = '-OpenMP'
local_bzip2_version = '1.0.8' # http://www.bzip.org/downloads.html
local_cairo_version = '1.18.4' # https://www.cairographics.org/
local_cURL_version = '8.21.0' # https://curl.haxx.se/download/ - Newer than 2026.1?
local_gzip_version = '1.14' # https://ftp.gnu.org/gnu/gzip/
local_libjpegturbo_version = '3.2.0' # https://github.com/libjpeg-turbo/libjpeg-turbo/releases
local_libpng_version = '1.6.58' # http://www.libpng.org/pub/png/libpng.html (Not yet in EB 2025a when checking)
local_libreadline_version = '8.3.3' # https://ftp.gnu.org/pub/gnu/readline/, also look at the patches
local_libtiff_version = '4.7.2' # https://download.osgeo.org/libtiff/
local_ncurses_version = '6.6' # https://ftp.gnu.org/pub/gnu/ncurses/
local_Pango_version = '1.57.1' # http://ftp.gnome.org/pub/GNOME/sources/pango/
local_PCRE2_version = '10.47' # https://github.com/PCRE2Project/pcre2/releases # Not yet in EB 2025a when checked for installation
local_Tk_version = '9.0.4' # https://tcl.tk/
local_XZ_version = '5.8.3' # https://tukaani.org/xz/
local_zlib_version = '2.3.3' # https://github.com/zlib-ng/zlib-ng/releases
local_cURL_version = '8.21.0' # https://curl.haxx.se/download/ - Newer than 2026.1?
local_libuv_version = '1.52.1' # https://github.com/libuv/libuv/releases
local_Zip_version = '3.0' # https://infozip.sourceforge.net/Zip.html
local_UnZip_version = '6.0' # https://infozip.sourceforge.net/UnZip.html
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 deps 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 setting OMP_NUM_THREADS.
"""
toolchain = {'name': 'cpeGNU', 'version': '26.03'}
toolchain_opts = {'openmp': True}
source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
sources = [SOURCE_TAR_GZ]
checksums = [
'4da6e61d2c0aac5f14a2e7e432cb5fcc269efe83da4293050ba7f03dff4e2cf4', # R-4.6.1.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.
build_deps = [
('buildtools', '%(toolchain_version)s', '', SYSTEM),
]
deps = [
# 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.
('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),
# For extra packages
('cURL', local_cURL_version),
('libuv', local_libuv_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.
pre_configure_opts = '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.
pre_configure_opts += 'export LDFLAGS="-fopenmp $LDFLAGS" && '
configure_opts = "--with-pic --enable-threads --enable-R-shlib"
# some recommended packages may fail in a parallel build (e.g. Matrix), and
# we're installing them anyway below
configure_opts += " --with-recommended-packages=no"
exts_default_opts = {
'source_urls': [
'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'https://cran.r-project.org/src/contrib/', # current version of packages
'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
],
'source_tmpl': '%(name)s_%(version)s.tar.gz',
}
# !! order of packages is important !!
# packages updated on 6th August 2026
exts_list = [
# include packages that are part of the base installation of R,
# both to make sure they are available (via sanity check),
# and to be able to pass the check for required deps when installing extensions in parallel
'base',
'compiler',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'parallel',
'splines',
'stats',
'stats4',
#'tcltk', # Not compatible yet with Tcl 9? Tcl 9 does not have a init.tcl.
'tools',
'utils',
#
# Do Rmpi first because of potential problems
#
#
# Parallel compputing packages
#
('Rmpi', '0.7-3.4', {
'easyblock': 'RPackage',
'patches': ['Rmpi-%(version)s_Cray.patch'],
'install_opts': '--configure-args="--with-Rmpi-type=CRAY --with-Rmpi-include=$CRAY_MPICH_DIR/include --with-Rmpi-libpath=$CRAY_MPICH_DIR/lib" ',
'checksums': [
'12096db54761e8b3337955b4f3ddb785d1ded2a1cce0b58e50e63e0bc659d464', # Rmpi_0.7-3.4.tar.gz
'910480ee4c154f4618207d54a723378d7fbe270ef4d4fd4c0fe02c75a667a671' # Rmpi-0.7-3.4_Cray.patch
],
}),
('Rcpp', '1.1.2', {
'checksums': ['2746cf2fb188e5f0a84dbf5c8f68915b54564ed33e5754572f174e7b32e7f4f3'],
}),
('codetools', '0.2-20', {
'checksums': ['3be6f375ec178723ddfd559d1e8e85bfeee04a5fbaf9f53f2f844e1669fea863'],
}),
('RUnit', '0.4.33.1', {
'checksums': ['8528fa3ba8d04a6e71783f01ba3e1163b5900c6b3c2bc81bad2349e220197f05'],
}),
('tinytest', '1.4.3', {
'checksums': ['ecc3a398690e72ca70127c1177e1f78b602dc5062f1597b897255bcc33c38375'],
}),
('backports', '1.5.1', {
'checksums': ['b8eeeabe3c27e1486f43e0b18dae57f0e870dd7c6979d3668df76bf0d4735bad'],
}),
('rlang', '1.3.0', {
'checksums': ['80aa537d49e72265f443a15e8936128af583caa5e572086518b503cbf064279c'],
}),
('parallelly', '1.48.0', {
'checksums': ['58fe71ccee8e4dc95591958c5428c5000350937024373b99b258a76da0927636'],
}),
('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', '2.3.4', {
'checksums': ['95e1068dee07d95c5e616dfd66e622cf245821acd358a77e790118c34ebd85ca'],
}),
('data.table', '1.18.4', {
'checksums': ['d65256f0050a6443770d5982b5098a2a8c894f9675ed17053416c7815cbddeb9'],
}),
('fs', '2.1.0', {
'checksums': ['7088af1117d65c4ceb144b532e323f197fc8243b1d704bf6edf40774789829cd'],
}),
('cli', '3.6.6', {
'checksums': ['b2b58d6dd82f5798b335e39c00591686a01fd3e94399ef898e146173e36f18f9'],
}),
('glue', '1.8.1', {
'checksums': ['1c55905d3efc3d5c199ceb0bd12218e97f0d4c64df6038ff41ecef415478a122'],
}),
('lifecycle', '1.0.5', {
'checksums': ['61841e3e6edba056a88355a3f1d6698ab8d5d9cb3c05f2af0ec5a44ab516f8ee'],
}),
('pkgconfig', '2.0.3', {
'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'],
}),
('vctrs', '0.7.3', {
'checksums': ['b45078413e06ac624dddb7221a3a43908b405c8abec09822cb86638d30b0435b'],
}),
('hms', '1.1.4', {
'checksums': ['efc525f797b62b3740d06c6fa8202593ab5aa4fc1edeefb76b6eb9be89e87b94'],
}),
('prettyunits', '1.2.0', {
'checksums': ['f059f27e2a5c82e351fe05b87ad712f7afc273c651450453f59d99af5deeacea'],
}),
('R6', '2.6.1', {
'checksums': ['59c6eba8b1b912eb7e104f65053235604be853425ee67c152ac4e86a1f2073b4'],
}),
('crayon', '1.5.3', {
'checksums': ['3e74a0685541efb5ea763b92cfd5c859df71c46b0605967a0b5dbb7326e9da69'],
}),
('progress', '1.2.3', {
'checksums': ['ea2b079b894de85c3ab12088c9c52aec06432245047a961d5b4b8aa6889f9276'],
}),
('rappdirs', '0.3.4', {
'checksums': ['2320ebc9ef3b1a32a1e63f94a6ce2c1c34d66782221a6531e786804f681abc66'],
}),
('stringi', '1.8.9', {
'checksums': ['427fcebd281d7ea850becce75e0807576dd394a723a814b2d487419b93275a33'],
}),
('withr', '3.0.3', {
'checksums': ['d86c6454164fc85678bfc85e2a6cce42f7461d45fa9a87de71f376e7956c991e'],
}),
('digest', '0.6.39', {
'checksums': ['8bf048b49b2d17077138fae758bda56bbd53278d9437f2fdeaedf979c90a13c9'],
}),
('batchtools', '0.9.18', {
'checksums': ['47ffd7be8f4e06d89207f58aa7fdf49343e2af5578b539447ca2338fc0e7f0cf'],
}),
('globals', '0.19.1', {
'checksums': ['b58d7ea423eb8772aa1be615d97722a6babf836360e01e533d176e108c216979'],
}),
('listenv', '1.0.0', {
'checksums': ['b12c71b839638b324857e134e31e7de4fc7595e00af5e7c634a78374bd1cd2aa'],
}),
('future', '1.75.0', {
'checksums': ['9cc444d36e0d0a7935ac76a027f807a44d505eed7eacccde0dd79a82c7f36ca1'],
}),
('future.apply', '1.20.2', {
'checksums': ['30d6b64c93a1c40fc1b07e21503fce811707fc30589145832ce0b8947ce74bdf'],
}),
('future.batchtools', '0.22.0', {
'checksums': ['dbd7022308a290dd359b5c1049a3ebfe5e83849cbb70017ac5e737b29d59be42'],
}),
#
# Some other popular packages available in Cray-R
#
('lattice', '0.22-9', { # Dependency for Matrix and others
'checksums': ['b72ad4ed2e5269fa7cf668e46f83a9b5d9d5f8fdcbc5b9886531ca19dffca4ba'],
}),
('Matrix', '1.7-6', { # Also dependency for survival
'checksums': ['694239dbe47e659d6d39a49af95157f46bd94977c283df00c4e8a016601cf143'],
}),
('MASS', '7.3-66', { # Dependency for class
'checksums': ['59c619c70bfca653f1c74aef880e69405daefd0134e716a1862ecc5334b4e155'],
}),
('class', '7.3-24', {
'checksums': ['e8c66e57e3f4214ced6fff135a0d9b55f7bd7d6c947b219063de57b275c507e1'],
}),
('foreign', '0.8-91', {
'checksums': ['fdf6c2c6077659a7dc069e58528d3c7cd93b6571c708d98994565386afce5298'],
}),
('KernSmooth', '2.23-26', {
'checksums': ['b465bdac197f7faa787e625412ae03d1b7c2c134b1c924cfeb775faf9c4da73e'],
}),
('nlme', '3.1-170', { # Dependency for mgcv
'checksums': ['d8e1a92cc295b046c9fd12bc1b875fe7921cc1db58f4407f0b97d625e8197b44'],
}),
('mgcv', '1.9-4', { # Needs nlme
'checksums': ['a98159698afb269e06a46cac1f945bf2b3427a2dd587c6f2efd67ede90089372'],
}),
('nnet', '7.3-21', {
'checksums': ['c3914e2b8fd2cc2df7afb60cfa106070fc43cd5b60f877f3790303fc6513895b'],
}),
('rpart', '4.1.27', {
'checksums': ['3183552d74f02749a70e2b989591c561ca0f7c146034f415748acc8480ca4050'],
}),
('spatial', '7.3-19', {
'checksums': ['6d9d26a64709d7da453ba3b31df8c9e9dbee64fd1b3097e45d1509ad26a9b9dc'],
}),
('survival', '3.8-9', { # Needs Matrix
'checksums': ['9aa8fadd4fb185ac48f260c9d0f69fd6dfff4a4e2724920618057aa1f5d5bfbe'],
}),
#
# Some benchmarking packages and their deps not yet included above.
#
('fansi', '1.0.7', { # Dependency for bench
'checksums': ['32a43f073aeb5c1d31c804014b95c2cb644bb4132119fcea313838b7ea4eb792'],
}),
('utf8', '1.2.6', { # Dependency for bench
'checksums': ['4589f8b72291329e70b7f3a8c20f2feb4e7764eebad2e6976bc9a3eee7686ce9'],
}),
('pillar', '1.11.1', { # Dependency for bench
'checksums': ['056ce154238c9b5b8d5dcbcb52e1bc51d33870ce08c8a9ca9496478bd59f4653'],
}),
('profmem', '0.7.0', { # Dependency for bench
'checksums': ['16efc5f13f4b78919c9d51c07acf62c051e0e3830ae3cc32c596f8daf569c3cb'],
}),
('magrittr', '2.0.5', { # Dependency for bench
'checksums': ['3f5b5b1d4e6d12807a95c50b6c88cb1d8af2c5eb5213f08bfe58f278eca2ed23'],
}),
('tibble', '3.3.1', { # Dependency for bench, benchmarkme
'checksums': ['fb309f8a1939021b237c7e85ff7ad6e8ff5acd57a6230d220a452094b492b28f'],
}),
('bench', '1.1.4', {
'checksums': ['b822f5b7648deecc6b516dcca4e932ce92e65eb166b997b04355218aceb1d083'],
}),
('microbenchmark', '1.5.0', {
'checksums': ['3d1e92a9206811ad128b28795d20a0d31da5f0c29ea7f1caaf1194ed3e49765f'],
}),
('SuppDists', '1.1-9.9', { # Random number generators used by the commonly used R-benchmark-25.R script
'checksums': ['7fbc0881948841bed1915cd5b998164167b1a265da6d955a8e85a1fcb3dea926'],
}),
('generics', '0.1.2', { # Dependency for bemchmarkme via dplyr
'checksums': ['63eab37a9148f820ce2d67bda3dab6dedb9db6890baa5284949c39ab1b4c5898'],
}),
('tidyselect', '1.2.1', { # Dependency for bemchmarkme via dplyr
'checksums': ['169e97ba0bbfbcdf4a80534322751f87a04370310c40e27f04aac6525d45903c'],
}),
('dplyr', '1.2.1', { # Dependency for bemchmarkme
'checksums': ['18d66fe2f24cda8b619c177326d39dd015229ab99695fa67d3fa31e4569390e0'],
}),
('curl', '7.1.0', { # Dependency for bemchmarkme via httr
'checksums': ['74f079b6306acc18fbe60c18dbaac805703fb6579e6ab398f3437377695fd8a9'],
}),
('jsonlite', '2.0.0', { # Dependency for bemchmarkme via httr
'checksums': ['75eb910c82b350ec33f094779da0f87bff154c232e4ae39c9896a9b89f3ac82d'],
}),
('mime', '0.13', { # Dependency for bemchmarkme via httr
'checksums': ['7132834cf3c3388eff12bad376d69fbcf8275acc37d36c290e59174fe3c7f3eb'],
}),
('sys', '3.4.3', { # Dependency for bemchmarkme via askpass via openssl via httr
'checksums': ['051e7332e3074db826efef9059067721864f9d70adc55bbcae3a72e5ae83913a'],
}),
('askpass', '1.2.1', { # Dependency for bemchmarkme via openssl via httr
'checksums': ['6c2106a74c44a748f2cea795d9686e27a0058a90debcfd8558b62b06aec0c7dd'],
}),
('openssl', '2.4.2', { # Dependency for bemchmarkme via httr
'checksums': ['1fc030ad0a008472eac7f086666a7623bdbe6d27c5fdb07b5510f56545d2f4e7'],
}),
('httr', '1.4.8', { # Dependency for bemchmarkme
'checksums': ['62acf6759814f0a2923d18904971e16e01d6147419ceb816dac02113fc3e09f8'],
}),
('stringr', '1.6.0', { # Dependency for bemchmarkme
'checksums': ['24f2fc5df980a7eb888659e22b9744d2316c558624015c7a7cd8c3ce3e370064'],
}),
('benchmarkmeData', '2.0.0', { # Dependency for bemchmarkme
'checksums': ['a8dacf85a1c548d011299dca78ec376a7fbea68d0b6482e763dca7685bad1417'],
}),
('benchmarkme', '1.0.8', {
'checksums': ['1d7100e001a355afc83815b1b698466135f4512c53528c324d13013b3c475f61'],
}),
]
# Set OMP_STACKSIZE to avoid crashes in LibSci
#env_mod_extra_vars = {
# 'OMP_STACKSIZE': '256M',
#}
env_mod_category = 'lang'