R/4.2.3-cpeGNU-22.12-raw (R-4.2.3-cpeGNU-22.12-raw.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-raw.
EasyConfig:
name = 'R'
version = '4.2.3'
versionsuffix = '-raw'
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.
"""
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', # R-4.2.3.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', 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 $LDFLAGS" && '
configopts = "--with-pic --enable-threads --enable-R-shlib"
# some recommended packages may fail in a parallel build (e.g. Matrix), and
# we're installing them anyway below
configopts += " --with-recommended-packages=no"
# specify that at least EasyBuild v3.5.0 is required,
# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK
easybuild_version = '3.5.0'
exts_default_options = {
'source_urls': [
'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'https://cran.r-project.org/src/contrib/', # current version of packages
'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
],
'source_tmpl': '%(name)s_%(version)s.tar.gz',
}
# !! order of packages is important !!
# packages updated on 1st November 2021
exts_list = [
# include packages that are part of the base installation of R,
# both to make sure they are available (via sanity check),
# and to be able to pass the check for required dependencies when installing extensions in parallel
'base',
'compiler',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'parallel',
'splines',
'stats',
'stats4',
'tcltk',
'tools',
'utils',
#
# Do firsts because of potential problems
#
('Rmpi', '0.7-1', {
'easyblock': 'RPackage',
'patches': ['Rmpi-%(version)s_Cray.patch'],
'installopts': '--configure-args="--with-Rmpi-type=CRAY --with-Rmpi-include=$CRAY_MPICH_DIR/include --with-Rmpi-libpath=$CRAY_MPICH_DIR/lib" ',
'checksums': ['17dae27dea9317aacabc2255dfcf2538fb3195472cedd521256ced9a20dd2dc1'],
}),
]
moduleclass = 'lang'