R/4.2.1-cpeGNU-22.06 (R-4.2.1-cpeGNU-22.06.eb)
This software is archived in the LUMI-EasyBuild-contrib GitHub repository as easybuild/easyconfigs/__archive__/r/R/R-4.2.1-cpeGNU-22.06.eb. The corresponding module would be R/4.2.1-cpeGNU-22.06.
name = 'R'
version = '4.2.1'
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': '22.06'}
toolchainopts = {'openmp': True}
source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
sources = [SOURCE_TAR_GZ]
checksums = [
'4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f', # R-4.1.2.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', '', True),
# ('pkg-config', '0.29.2'),
# ('Xvfb', '1.20.13'),
]
dependencies = [
# Base R
('ncurses', '6.2'),
('libreadline', '8.1.2'),
('zlib', '1.2.12'),
('bzip2', '1.0.8'),
('gzip', '1.12'),
('XZ', '5.2.5'),
('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', '10.40'),
('cURL', '7.83.1'), # for RCurl but also used by the base R package
('X11', '%(toolchain_version)s'),
('Tk', '8.6.12'), # for tcltk (base package)
('libpng', '1.6.37'), # for plotting in R
('libjpeg-turbo', '2.1.3'), # for plottting in R
('LibTIFF', '4.4.0'),
('cairo', '1.17.4'),
('Pango', '1.50.7'),
# 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 $LDFLAGS" && '
configopts = "--with-pic --enable-threads --enable-R-shlib"
# some recommended packages may fail in a parallel build (e.g. Matrix), and
# we're installing them anyway below
configopts += " --with-recommended-packages=no"
# specify that at least EasyBuild v3.5.0 is required,
# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK
easybuild_version = '3.5.0'
exts_default_options = {
'source_urls': [
'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'https://cran.r-project.org/src/contrib/', # current version of packages
'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
],
'source_tmpl': '%(name)s_%(version)s.tar.gz',
}
# !! order of packages is important !!
# packages updated on 1st November 2021
exts_list = [
# include packages that are part of the base installation of R,
# both to make sure they are available (via sanity check),
# and to be able to pass the check for required dependencies when installing extensions in parallel
'base',
'compiler',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'parallel',
'splines',
'stats',
'stats4',
'tcltk',
'tools',
'utils',
('Rmpi', '0.6-9.2', {
'easyblock': 'RPackage',
'patches': ['Rmpi-%(version)s_Cray.patch'],
'installopts': '--configure-args="--with-Rmpi-type=CRAY --with-Rmpi-include=$CRAY_MPICH_DIR/include --with-Rmpi-libpath=$CRAY_MPICH_DIR/lib" ',
'checksums': ['358ac1af97402e676f209261a231f36a35e60f0301edf8ca53dac11af3c3bd1a'],
}),
('abind', '1.4-5', {
'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'],
}),
('magic', '1.6-0', {
'checksums': ['4516d48c9618e3f395db873e886f5deb3b66b32ebe10d4c26c1420ac848acbbf'],
}),
('Rcpp', '1.0.8.3', {
'checksums': ['9da5b84cdaf56e972b41e669d496b1ece2e91bcd435505c68b9f2bd98375f8bf'],
}),
('RcppProgress', '0.4.2', {
'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'],
}),
('lpSolve', '5.6.15', {
'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'],
}),
('linprog', '0.9-4', {
'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'],
}),
('geometry', '0.4.6', {
'checksums': ['910465a8c8043faca73bcc7c81c9249b9938677ee6649468003b438a6503f5d8'],
}),
('bit', '4.0.4', {
'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'],
}),
('filehash', '2.4-3', {
'checksums': ['f394e2c93233e8ad1c104562ea9349855dc8e303131f559cd59834f9aa3e41bd'],
}),
('ff', '4.0.7', {
'checksums': ['0a47333d31c7afc3f95387166e21a3e4c763cbef47d9b5927753aef4ff8d83fa'],
}),
('bnlearn', '4.7.1', {
'checksums': ['243930daa7f71c63fe1aa6717e5d55a116a597b83e08745cbcbe9a418d7c1509'],
}),
('bootstrap', '2019.6', {
'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'],
}),
('combinat', '0.0-8', {
'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'],
}),
]
moduleclass = 'lang'