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Updated bin/generateEasyConfig.R for R 4.x
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@pneerincx
pneerincx committed Feb 1, 2021
1 parent d35b99e commit 2b3fecc
Showing 1 changed file with 90 additions and 37 deletions.
127 changes: 90 additions & 37 deletions bin/generateEasyConfig.R
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Original file line number Diff line number Diff line change
Expand Up @@ -23,38 +23,71 @@ repos$bioconductor$active = c('http://www.bioconductor.org/packages/release/bioc

#
# Default versions for dependecies.
# * This list is for R 3.6.x with foss 2018b.
# * When different versions of these dependencies are loaded in the environment with
#
# When different versions of these dependencies are loaded in the environment with
# module load dependency/version
# before this script is executed,
# then this script will pickup the new versions from the environment overruling the defaults.
# Extra dependencies will not get added automagically though:
# before this script is executed,
# then this script will pickup the new versions from the environment overruling the defaults.
# Extra dependencies will not get added automagically though:
# You will need to add those
# 1. here as well as
# 2. in the functions that write the EasyConfig files.
#
# This list is for R 3.6.x with foss 2018b:
#
#dependency_defaults <-list(
# 'pkg-config'='0.29.2',
# 'libreadline'='8.0',
# 'ncurses'='6.1',
# 'bzip2'='1.0.6',
# 'XZ'='5.2.4',
# 'zlib'='1.2.11',
# 'SQLite'='3.29.0',
# 'PCRE'='8.43',
# 'Java'='11.0.2',
# 'cURL'='7.63.0',
# 'libxml2'='2.9.8',
# 'libpng'='1.6.37',
# 'libjpeg-turbo'='2.0.2',
# 'LibTIFF'='4.0.10',
# 'cairo'='1.16.0',
# 'Pango'='1.43.0',
# 'GMP'='6.1.2',
# 'UDUNITS'='2.2.27.6',
# 'ImageMagick'='7.0.8-56',
# 'MariaDB-connector-c'='3.1.2',
# 'NLopt'='2.6.1'
#)
#
# This list is for R 4.0.x with foss 2018b:
#
dependency_defaults <-list(
'pkg-config'='0.29.2',
'libreadline'='8.0',
'ncurses'='6.1',
'bzip2'='1.0.6',
'XZ'='5.2.4',
'ncurses'='6.2',
'bzip2'='1.0.8',
'XZ'='5.2.5',
'zlib'='1.2.11',
'SQLite'='3.29.0',
'PCRE'='8.43',
'Java'='11.0.2',
'cURL'='7.63.0',
'libxml2'='2.9.8',
'SQLite'='3.34.0',
'PCRE2'='10.36',
'Java'='11-LTS',
'cURL'='7.74.0',
'libxml2'='2.9.10',
'libpng'='1.6.37',
'libjpeg-turbo'='2.0.2',
'LibTIFF'='4.0.10',
'cairo'='1.16.0',
'Pango'='1.43.0',
'GMP'='6.1.2',
'UDUNITS'='2.2.27.6',
'ImageMagick'='7.0.8-56',
'MariaDB-connector-c'='3.1.2',
'NLopt'='2.6.1'
'libjpeg-turbo'='2.0.6',
'LibTIFF'='4.2.0',
'cairo'='1.16.0-2',
'Pango'='1.48.0',
'OpenSSL'='1.1.1i',
'GMP'='6.2.1',
'UDUNITS'='2.2.28',
'ImageMagick'='7.0.10-59',
'MariaDB-connector-c'='3.1.11',
'NLopt'='2.7.0',
'HDF5'='1.10.7',
'nodejs'='14.15.4',
'unixODBC'='2.3.9',
'librsvg'='2.50.2'
)

#
Expand All @@ -77,6 +110,10 @@ Description:
Generates an EasyBuild EasyConfig file from an existing R environment.
Optionally you can first load a specific version of R using module load before generating the *.eb EasyConfig
WARNING: This script cannot parse version suffixes for dependencies.
If you need a dependency for R, that not only has a version (number),
but also a version suffix, you must patch that manually in the generated EasyConfigs.
Example usage:
module load EasyBuild
module load R
Expand All @@ -98,10 +135,10 @@ Explanation of options:
MM = month
release = incremental release number of an RPlus bundle in a given YY.MM.
Hence this is not a day! First release in given year and month is always 1.
--od path Output Directory where the generated *.eb EasyConfig file will be stored (optional).
--od path Output Directory where the generated *.eb EasyConfigs file will be stored (optional).
Will default to the current working directory as determined with getwd().
Name of the output file follows strict rules
and is automatically generated based on R version and toolchain.
Names of the output files follow strict rules
and are automatically generated based on R version and toolchain.
--ll LEVEL Log level (optional).
One of FINEST, FINER, FINE, DEBUG, INFO (default), WARNING, ERROR or CRITICAL.
")
Expand Down Expand Up @@ -288,8 +325,8 @@ writeECR <- function (fh, version, deps, packages, repos, toolchain.name, toolch
writeLines('description = """R is a free software environment for statistical computing and graphics."""', fh)
writeLines("moduleclass = 'lang'", fh)
writeLines(paste("toolchain = {'name': '", toolchain.name, "', 'version': '", toolchain.version, "'}", sep=''), fh)
writeLines("sources = [SOURCE_TAR_GZ]", fh)
writeLines("source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s']", fh)
writeLines("sources = [SOURCE_TAR_GZ]", fh)
writeLines("", fh)
writeLines("#", fh)
writeLines("# Specify that at least EasyBuild v3.5.0 is required,", fh)
Expand All @@ -308,7 +345,7 @@ writeECR <- function (fh, version, deps, packages, repos, toolchain.name, toolch
writeLines(paste(" ('XZ', '", deps[['XZ']], "'),", sep=''), fh)
writeLines(paste(" ('zlib', '", deps[['zlib']], "'),", sep=''), fh)
writeLines(paste(" ('SQLite', '", deps[['SQLite']], "'),", sep=''), fh)
writeLines(paste(" ('PCRE', '", deps[['PCRE']], "'),", sep=''), fh)
writeLines(paste(" ('PCRE2', '", deps[['PCRE2']], "'),", sep=''), fh)
writeLines(paste(" ('Java', '", deps[['Java']], "', '', True),", sep=''), fh)
writeLines(paste(" ('cURL', '", deps[['cURL']], "'),", sep=''), fh)
writeLines(paste(" ('libxml2', '", deps[['libxml2']], "'),", sep=''), fh)
Expand All @@ -321,15 +358,15 @@ writeECR <- function (fh, version, deps, packages, repos, toolchain.name, toolch
writeLines(" # Disabled TK, because the -no-X11 option does not work and still requires X11,", fh)
writeLines(" # which does not exist on headless compute nodes.", fh)
writeLines(" #", fh)
writeLines(" #('Tk', '8.6.9', '-no-X11'),", fh)
writeLines(" #('Tk', '8.6.11', '-no-X11'),", fh)
writeLines(" #", fh)
writeLines(" # OS dependency should be preferred if the os version is more recent then this version,", fh)
writeLines(" # it's nice to have an up to date openssl for security reasons.", fh)
writeLines(" #", fh)
writeLines(" #('OpenSSL', '1.0.2k'),", fh)
writeLines(paste(" ('OpenSSL', '", deps[['OpenSSL']], "'),", sep=''), fh)
writeLines("]", fh)
writeLines("", fh)
writeLines("osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]", fh)
writeLines("#osdependencies = [OS_PKG_OPENSSL_DEV]", fh)
writeLines("", fh)
writeLines("configopts = '--with-pic --enable-threads --enable-R-shlib'", fh)
writeLines("#", fh)
Expand All @@ -344,6 +381,11 @@ writeECR <- function (fh, version, deps, packages, repos, toolchain.name, toolch
writeLines("configopts += ' --with-x=no --with-tcltk=no'", fh)
writeLines("", fh)
writeLines("#", fh)
writeLines("# Dynamic patch to remove unnecessary dependency on X11 when using Cairo.", fh)
writeLines("# Makes the configure flag combination \"--with-x=no --with-cairo\" work.", fh)
writeLines("#", fh)
writeLines("configure_cmd_prefix = \"perl -pi -e 's/cairo-xlib.h/cairo.h/' configure m4/cairo.m4 && \"", fh)
writeLines("#", fh)
writeLines("# R package list.", fh)
writeLines("# Only default a.k.a. base packages are listed here just for sanity checking.", fh)
writeLines("# Additional packages go into RPlus module.", fh)
Expand Down Expand Up @@ -379,9 +421,9 @@ writeECRPlus <- function (fh, version, deps, packages, repos, toolchain.name, to
writeLines("# This Python should not be too new either: it's dependencies like for example on ncursus should be compatible with R's dependencies.", fh)
writeLines("# The alternative is to replace the https URLs with http URLs in the generated EasyConfig.", fh)
writeLines("#", fh)
writeLines("#builddependencies = [", fh)
writeLines("# ('Python', '3.7.4')", fh)
writeLines("#]", fh)
writeLines("builddependencies = [", fh)
writeLines(" ('Python', '3.9.1', '-bare')", fh)
writeLines("]", fh)
writeLines("", fh)
writeLines("dependencies = [", fh)
writeLines(" ('R', '%(version)s', '-bare'),", fh)
Expand All @@ -390,6 +432,10 @@ writeECRPlus <- function (fh, version, deps, packages, repos, toolchain.name, to
writeLines(paste(" ('ImageMagick', '", deps[['ImageMagick']], "'),", sep=''), fh)
writeLines(paste(" ('MariaDB-connector-c', '", deps[['MariaDB-connector-c']], "'),", sep=''), fh)
writeLines(paste(" ('NLopt', '", deps[['NLopt']], "'),", sep=''), fh)
writeLines(paste(" ('HDF5', '", deps[['HDF5']], "'),", sep=''), fh)
writeLines(paste(" ('nodejs', '", deps[['nodejs']], "'),", sep=''), fh)
writeLines(paste(" ('unixODBC', '", deps[['unixODBC']], "'),", sep=''), fh)
writeLines(paste(" ('librsvg', '", deps[['librsvg']], "'),", sep=''), fh)
writeLines("]", fh)
writeLines("", fh)
writeLines("#", fh)
Expand All @@ -401,12 +447,12 @@ writeECRPlus <- function (fh, version, deps, packages, repos, toolchain.name, to
writeLines(" 'dirs': [('library', '.')],", fh)
writeLines("}", fh)
writeLines("", fh)
writeLines("package_name_tmpl = '%(name)s_%(version)s.tar.gz'", fh)
writeLines("local_package_name_tmpl = '%(name)s_%(version)s.tar.gz'", fh)
writeLines("exts_defaultclass = 'RPackage'", fh)
writeLines("exts_filter = ('R -q --no-save', 'library(%(ext_name)s)')", fh)
writeLines("", fh)
for (this.repo in names(repos)) {
writeLines(paste(this.repo, '_options = {', sep=''), fh)
writeLines(paste('local_', this.repo, '_options = {', sep=''), fh)
writeLines(" 'source_urls': [", fh)
forget.this = lapply(unlist(repos[this.repo]),
function(url) {
Expand All @@ -420,7 +466,7 @@ writeECRPlus <- function (fh, version, deps, packages, repos, toolchain.name, to
}
)
writeLines(" ],", fh)
writeLines(" 'source_tmpl': package_name_tmpl,", fh)
writeLines(" 'source_tmpl': local_package_name_tmpl,", fh)
writeLines("}", fh)
}
writeLines("", fh)
Expand All @@ -433,7 +479,7 @@ writeECRPlus <- function (fh, version, deps, packages, repos, toolchain.name, to
forget.this = apply(subset(packages, Repo != 'base', select=c('Package', 'Version', 'Repo')), 1,
function(this.pkg) {
this.pkg <- as.list(this.pkg);
writeLines(sprintf(" ('%s', '%s', %s_options),", this.pkg$Package, this.pkg$Version, this.pkg$Repo), fh)
writeLines(sprintf(" ('%s', '%s', local_%s_options),", this.pkg$Package, this.pkg$Version, this.pkg$Repo), fh)
}
)
writeLines("]",fh)
Expand Down Expand Up @@ -642,6 +688,13 @@ logging::levellog(loglevels[['INFO']], paste('==================================
#
logging::levellog(loglevels[['INFO']], 'Run the EasyBuild "eb" command like this to insert checksums for the sources into the generated EasyConfigs:')
logging::levellog(loglevels[['INFO']], ': module load EasyBuild')
logging::levellog(loglevels[['INFO']], ': #')
logging::levellog(loglevels[['INFO']], ': # IMPORTANT: About Python dependency:')
logging::levellog(loglevels[['INFO']], ': # If the default version of Python in your environment is (too) old,')
logging::levellog(loglevels[['INFO']], ': # EasyBuild (and any other Python code) may fail to download data from HTTPS URLs.')
logging::levellog(loglevels[['INFO']], ': # In that case you must load a newer Python 3.x.')
logging::levellog(loglevels[['INFO']], ': #')
logging::levellog(loglevels[['INFO']], ': module load Python')
logging::levellog(loglevels[['INFO']], paste(': eb --inject-checksums=sha256 --stop=ready ', output.path.r, sep=''))
logging::levellog(loglevels[['INFO']], paste(': eb --inject-checksums=sha256 --stop=ready ', output.path.rplus, sep=''))
logging::levellog(loglevels[['INFO']], paste('=======================================================================', paste(rep('=', numberwidth), collapse=''), sep=''))

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