R/4.2.3-cpeGNU-22.12 (R-4.2.3-cpeGNU-22.12.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/4.2.3-cpeGNU-22.12.
EasyConfig:
name = 'R'
version = '4.2.3'
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 = '7.86.0' # https://curl.haxx.se/download/
local_gzip_version = '1.12' # https://ftp.gnu.org/gnu/gzip/
local_libjpegturbo_version = '2.1.4' # https://github.com/libjpeg-turbo/libjpeg-turbo/releases
local_libpng_version = '1.6.38' # http://www.libpng.org/pub/png/libpng.html
local_libreadline_version = '8.2' # https://ftp.gnu.org/pub/gnu/readline/
local_libtiff_version = '4.4.0' # https://download.osgeo.org/libtiff/
local_ncurses_version = '6.4' # https://ftp.gnu.org/pub/gnu/ncurses/
local_Pango_version = '1.50.12' # http://ftp.gnome.org/pub/GNOME/sources/pango/
local_PCRE2_version = '10.40' # https://ftp.pcre.org/pub/pcre/
local_Tk_version = '8.6.12' # https://tcl.tk/
local_XZ_version = '5.4.2' # https://tukaani.org/xz/
local_zlib_version = '1.2.12' # https://zlib.net/
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.
"""
usage = """
Note that there are some know restrictions to using parallel computing
in R on LUMI:
- The `detectCores` routine in the standard R package `parallel` fails to
detect the number of cores available to the application. Instead it
returns the full number of (virtual) cores on the system.
- `mpi.spawn.Rslaves` is not suppoted in `Rmpi` as Cray MPICH does not
support spawning processes (in fact, does not support `MPI_Comm_spawn`
used by this package).
"""
toolchain = {'name': 'cpeGNU', 'version': '22.12'}
toolchainopts = {'openmp': True}
source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
sources = [SOURCE_TAR_GZ]
checksums = ['55e4a9a6d43be314e2c03d0266a6fa5444afdce50b303bfc3b82b3979516e074']
# 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', '', True),
# ('pkg-config', '0.29.2'),
# ('Xvfb', '1.20.13'),
]
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', '3.0-6.0'), # 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),
# Extensions
# ('Mesa', '21.1.7'),
# ('libGLU', '9.0.2'),
# ('SQLite', '3.36'),
# ('Java', '11', '', True),
# ('libxml2', '2.9.10'), # for XML
# ('GMP', '6.2.1'), # for igraph
# ('NLopt', '2.7.0'), # for nloptr
# ('FFTW', '3.3.10'), # for fftw
# ('libsndfile', '1.0.31'), # for seewave
# ('ICU', '69.1'), # for rJava & gdsfmt
# ('HDF5', '1.12.1'), # for hdf5r
# ('UDUNITS', '2.2.28'), # for units
# ('GSL', '2.7'), # for RcppGSL
# ('ImageMagick', '7.1.0-4'), # for animation
# ('GLPK', '5.0'), # for Rglpk
# ('nodejs', '14.17.6'), # for V8 (required by rstan)
# ('GDAL', '3.3.2'), # for sf
# ('MPFR', '4.1.0'), # for Rmpfr
# ('libgit2', '1.1.1'),
# ('OpenSSL', '1.1', '', True),
]
# 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 $LDFLAGS" && '
configopts = "--with-pic --enable-threads --enable-R-shlib"
# some recommended packages may fail in a parallel build (e.g. Matrix), and
# we're installing them anyway below
configopts += " --with-recommended-packages=no"
# specify that at least EasyBuild v3.5.0 is required,
# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK
easybuild_version = '3.5.0'
exts_default_options = {
'source_urls': [
'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'https://cran.r-project.org/src/contrib/', # current version of packages
'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
],
'source_tmpl': '%(name)s_%(version)s.tar.gz',
}
# !! order of packages is important !!
# packages updated on 1st November 2021
exts_list = [
'base',
'compiler',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'parallel',
'splines',
'stats',
'stats4',
'tcltk',
'tools',
'utils',
('Rmpi', '0.7-1', {
'easyblock': 'RPackage',
'installopts': '--configure-args="--with-Rmpi-type=CRAY --with-Rmpi-include=$CRAY_MPICH_DIR/include --with-Rmpi-libpath=$CRAY_MPICH_DIR/lib" ',
'patches': ['Rmpi-%(version)s_Cray.patch'],
'checksums': [
{'Rmpi_0.7-1.tar.gz': '17dae27dea9317aacabc2255dfcf2538fb3195472cedd521256ced9a20dd2dc1'},
{'Rmpi-0.7-1_Cray.patch': '910480ee4c154f4618207d54a723378d7fbe270ef4d4fd4c0fe02c75a667a671'},
],
}),
('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', '1.1.1', {
'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'],
}),
('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', '1.84-6.2', {
'checksums': ['9b467ab2b992455c6e1aeabe375c5694761fa1cf8aaf4f003ca47102b656353b'],
}),
('doSNOW', '1.0.20', {
'checksums': ['917cabed166aa2d1ec291691c17e1e3d344e858543e1682e3a442cc0c504bbb8'],
}),
('base64url', '1.4', {
'checksums': ['1d058f138660e9155ebb331d7a2561e2541ee3321b8da90f6c41fd8dcc122c58'],
}),
('brew', '1.0-8', {
'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'],
}),
('checkmate', '2.2.0', {
'checksums': ['96ec14b057e875465f8ef194f35b8e124cd5b5919697692fb392706201359118'],
}),
('data.table', '1.14.8', {
'checksums': ['14b2ce5367df9c9bb58f373555066f5dcb629c156149b5565de36d69557139fd'],
}),
('fs', '1.6.2', {
'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'],
}),
('cli', '3.6.1', {
'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'],
}),
('glue', '1.6.2', {
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}),
('lifecycle', '1.0.3', {
'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'],
}),
('pkgconfig', '2.0.3', {
'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'],
}),
('vctrs', '0.6.3', {
'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'],
}),
('hms', '1.1.3', {
'checksums': ['e626f4c60af46efd53ea631b316a103e089470d8fd63c0e0c0efb99364990282'],
}),
('prettyunits', '1.1.1', {
'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'],
}),
('R6', '2.5.1', {
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}),
('crayon', '1.5.2', {
'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'],
}),
('progress', '1.2.2', {
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}),
('rappdirs', '0.3.3', {
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}),
('stringi', '1.7.12', {
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}),
('withr', '2.5.0', {
'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'],
}),
('digest', '0.6.33', {
'checksums': ['be702c886b1639be7eda4ea25a4261b30ce418c580f79bd78ec8d6cb4d327819'],
}),
('batchtools', '0.9.17', {
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}),
('globals', '0.16.2', {
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}),
('listenv', '0.9.0', {
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}),
('future', '1.33.0', {
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('future.apply', '1.11.0', {
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}),
('future.batchtools', '0.12.0', {
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}),
]
moduleclass = 'lang'