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easyconfigs-it4i/r/R/R-3.4.0-intel-2017a-X11-20170314.eb
easybuild 40b461ca6f fix
2019-11-06 13:38:09 +01:00

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name = 'R'
version = '3.4.0'
x11ver = '20170314'
versionsuffix = '-X11-%s' % x11ver
homepage = 'http://www.r-project.org/'
description = """R is a free software environment for statistical local_computing and graphics."""
toolchain = {'name': 'intel', 'version': '2017a'}
sources = [SOURCE_TAR_GZ]
source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s']
preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"'
configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib"
# Actually use Tcl/Tk
configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh '
# Enable graphics capabilities for plotting.
configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff"
# some recommended packages may fail in a parallel build (e.g. Matrix),
# and we're installing them anyway below
configopts += " --with-recommended-packages=no"
dependencies = [
('X11', x11ver, '', True),
('Mesa', '17.0.2'),
('libGLU', '9.0.0', '', True),
('cairo', '1.14.8', '', True),
('libreadline', '7.0', '', True),
('ncurses', '6.0', '', True),
('bzip2', '1.0.6', '', True),
('XZ', '5.2.3', '', True),
('zlib', '1.2.11', '', True),
('SQLite', '3.17.0', '', True),
('PCRE', '8.40', '', True),
('libpng', '1.6.29', '', True), # for plotting in R
('libjpeg-turbo', '1.5.1', '', True), # for plottting in R
('LibTIFF', '4.0.7', '', True),
# Java bindings are built if Java is found, might as well provide it
('Java', '1.8.0_121', '', True),
('Tcl', '8.6.6', '', True), # for tcltk
('Tk', '8.6.6', '', True), # for tcltk
('cURL', '7.53.1', '', True), # for RCurl
('libxml2', '2.9.4', '', True), # for XML
('GDAL', '2.1.3', '-Python-2.7.13', True), # for rgdal
('PROJ', '4.9.3'), # for rgdal
('GMP', '6.1.2', '', True), # for igraph
('NLopt', '2.4.2'), # for nloptr
('FFTW', '3.3.6'), # for fftw
('libsndfile', '1.0.28'), # for seewave
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
# ('OpenSSL', '1.0.2h'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
name_tmpl = '%(name)s_%(version)s.tar.gz'
ext_options = {
'source_urls': [
# package archive
'http://cran.r-project.org/src/contrib/Archive/%(name)s',
'http://cran.r-project.org/src/contrib/', # current version of packages
# mirror alternative for current packages
'http://cran.freestatistics.org/src/contrib',
],
'source_tmpl': name_tmpl,
}
# !! order of packages is important !!
# packages updated on May 11th 2017
exts_list = [
# default libraries, only here to sanity check their presence
'base',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'splines',
'stats',
'stats4',
'tools',
'utils',
# non-standard libraries, should be specified with fixed versions!
('Rmpi', '0.6-6', ext_options),
('abind', '1.4-5', ext_options),
('magic', '1.5-6', ext_options),
('geometry', '0.3-6', dict(ext_options.items() +
[('patches', ['geometry-0.3-4-icc.patch'])])),
('bit', '1.1-12', ext_options),
('filehash', '2.4-1', ext_options),
('ff', '2.2-13', ext_options),
('bnlearn', '4.1.1', ext_options),
('bootstrap', '2017.2', ext_options),
('combinat', '0.0-8', ext_options),
('deal', '1.2-37', ext_options),
('fdrtool', '1.2.15', ext_options),
('formatR', '1.5', ext_options),
('gtools', '3.5.0', ext_options),
('gdata', '2.17.0', ext_options),
('GSA', '1.03', ext_options),
('highr', '0.6', ext_options),
('infotheo', '1.2.0', ext_options),
('lars', '1.2', ext_options),
('lazy', '1.2-15', ext_options),
('kernlab', '0.9-25', ext_options),
('mime', '0.5', ext_options),
('markdown', '0.8', ext_options),
('mlbench', '2.1-1', ext_options),
('NLP', '0.1-10', ext_options),
('mclust', '5.3', ext_options),
('RANN', '2.5', ext_options),
('rmeta', '2.16', ext_options),
('segmented', '0.5-1.4', ext_options),
('som', '0.3-5.1', ext_options),
('SuppDists', '1.1-9.4', ext_options),
('stabledist', '0.7-1', ext_options),
('survivalROC', '1.0.3', ext_options),
('pspline', '1.0-17', ext_options),
('timeDate', '3012.100', ext_options),
('longmemo', '1.0-0', ext_options),
('ADGofTest', '0.3', ext_options),
('ade4', '1.7-6', ext_options),
('AlgDesign', '1.1-7.3', ext_options),
('base64enc', '0.1-3', ext_options),
('BH', '1.62.0-1', ext_options),
('brew', '1.0-6', ext_options),
('Brobdingnag', '1.2-4', ext_options),
('corpcor', '1.6.9', ext_options),
('longitudinal', '1.1.12', ext_options),
('backports', '1.0.5', ext_options),
('checkmate', '1.8.2', ext_options),
('Rcpp', '0.12.10', ext_options),
('cubature', '1.3-8', ext_options),
('DEoptimR', '1.0-8', ext_options),
('digest', '0.6.12', ext_options),
('fastmatch', '1.1-0', ext_options),
('ffbase', '0.12.3', ext_options),
('iterators', '1.0.8', ext_options),
('maps', '3.1.1', ext_options),
('nnls', '1.4', ext_options),
('sendmailR', '1.2-1', ext_options),
('spam', '1.4-0', ext_options),
('subplex', '1.2-2', ext_options),
('stringi', '1.1.5', ext_options),
('magrittr', '1.5', ext_options),
('stringr', '1.2.0', ext_options),
('evaluate', '0.10', ext_options),
('logspline', '2.1.9', ext_options),
('ncbit', '2013.03.29', ext_options),
('permute', '0.9-4', ext_options),
('plotrix', '3.6-5', ext_options),
('randomForest', '4.6-12', ext_options),
('scatterplot3d', '0.3-40', ext_options),
('SparseM', '1.77', ext_options),
('tripack', '1.3-8', ext_options),
('irace', '2.3', ext_options),
('rJava', '0.9-8', ext_options),
('lattice', '0.20-35', ext_options),
('RColorBrewer', '1.1-2', ext_options),
('latticeExtra', '0.6-28', ext_options),
('Matrix', '1.2-10', ext_options),
('png', '0.1-7', ext_options),
('RcppArmadillo', '0.7.800.2.0', ext_options),
('plyr', '1.8.4', ext_options),
('pROC', '1.9.1', ext_options),
('quadprog', '1.5-5', ext_options),
('BB', '2014.10-1', ext_options),
('BBmisc', '1.11', ext_options),
('fail', '1.3', ext_options),
('rlecuyer', '0.3-4', ext_options),
('snow', '0.4-2', ext_options),
('MASS', '7.3-47', ext_options),
('tree', '1.0-37', ext_options),
('pls', '2.6-0', ext_options),
('class', '7.3-14', ext_options),
('e1071', '1.6-8', ext_options),
('nnet', '7.3-12', ext_options),
('nlme', '3.1-131', ext_options),
('minqa', '1.2.4', ext_options),
('RcppEigen', '0.3.3.3.0', ext_options),
('MatrixModels', '0.4-1', ext_options),
('quantreg', '5.33', ext_options),
('mgcv', '1.8-17', ext_options),
('colorspace', '1.3-2', ext_options),
('robustbase', '0.92-7', ext_options),
('sp', '1.2-4', ext_options),
('zoo', '1.8-0', ext_options),
('lmtest', '0.9-35', ext_options),
('vcd', '1.4-3', ext_options),
('snowfall', '1.84-6.1', ext_options),
('rpart', '4.1-11', ext_options),
('survival', '2.41-3', ext_options),
('mice', '2.30', ext_options),
('urca', '1.3-0', ext_options),
('fracdiff', '1.4-2', ext_options),
('logistf', '1.22', ext_options),
('akima', '0.6-2', ext_options),
('bitops', '1.0-6', ext_options),
('boot', '1.3-19', ext_options),
('mixtools', '1.1.0', ext_options),
('cluster', '2.0.6', ext_options),
('gclus', '1.3.1', ext_options),
('coda', '0.19-1', ext_options),
('codetools', '0.2-15', ext_options),
('foreach', '1.4.3', ext_options),
('doMC', '1.3.4', ext_options),
('DBI', '0.6-1', ext_options),
('foreign', '0.8-68', ext_options),
('gam', '1.14-4', ext_options),
('gamlss.data', '5.0-0', ext_options),
('gamlss.dist', '5.0-0', ext_options),
('hwriter', '1.3.2', ext_options),
('KernSmooth', '2.23-15', ext_options),
('xts', '0.9-7', ext_options),
('TTR', '0.23-1', ext_options),
('quantmod', '0.4-8', ext_options),
('mnormt', '1.5-5', ext_options),
('mvtnorm', '1.0-6', ext_options),
('pcaPP', '1.9-61', ext_options),
('numDeriv', '2016.8-1', ext_options),
('lava', '1.5', ext_options),
('prodlim', '1.6.1', ext_options),
('pscl', '1.4.9', ext_options),
('memoise', '1.1.0', ext_options),
('plogr', '0.1-1', ext_options),
('RSQLite', '1.1-2', ext_options),
('BatchJobs', '1.6', ext_options),
('sandwich', '2.3-4', ext_options),
('sfsmisc', '1.1-0', ext_options),
('spatial', '7.3-11', ext_options),
('VGAM', '1.0-3', ext_options),
('waveslim', '1.7.5', ext_options),
('xtable', '1.8-2', ext_options),
('profileModel', '0.5-9', ext_options),
('brglm', '0.5-9', ext_options),
('deSolve', '1.14', ext_options),
('tseriesChaos', '0.1-13', ext_options),
('tseries', '0.10-40', ext_options),
('fastICA', '1.2-0', ext_options),
('R.methodsS3', '1.7.1', ext_options),
('R.oo', '1.21.0', ext_options),
('cgdsr', '1.2.6', ext_options),
('R.utils', '2.5.0', ext_options),
('R.matlab', '3.6.1', ext_options),
('gbm', '2.1.3', ext_options),
('dichromat', '2.0-0', ext_options),
('Formula', '1.2-1', ext_options),
('acepack', '1.4.1', ext_options),
('reshape2', '1.4.2', ext_options),
('gtable', '0.2.0', ext_options),
('munsell', '0.4.3', ext_options),
('labeling', '0.3', ext_options),
('scales', '0.4.1', ext_options),
('proto', '1.0.0', ext_options),
('lazyeval', '0.2.0', ext_options),
('assertthat', '0.2.0', ext_options),
('tibble', '1.3.0', ext_options),
('ggplot2', '2.2.1', ext_options),
('gridExtra', '2.2.1', ext_options),
('chron', '2.3-50', ext_options),
('data.table', '1.10.4', ext_options),
('viridisLite', '0.2.0', ext_options),
('viridis', '0.4.0', ext_options),
('yaml', '2.1.14', ext_options),
('jsonlite', '1.4', ext_options),
('htmltools', '0.3.6', ext_options),
('htmlwidgets', '0.8', ext_options),
('knitr', '1.16', ext_options),
('htmlTable', '1.9', ext_options),
('Hmisc', '4.0-3', ext_options),
('fastcluster', '1.1.22', ext_options),
('registry', '0.3', ext_options),
('pkgmaker', '0.22', ext_options),
('rngtools', '1.2.4', ext_options),
('doParallel', '1.0.10', ext_options),
('gridBase', '0.4-7', ext_options),
('NMF', '0.20.6', ext_options),
('irlba', '2.1.2', ext_options),
('igraph', '1.0.1', ext_options),
('GeneNet', '1.2.13', ext_options),
('ape', '4.1', ext_options),
('RJSONIO', '1.3-0', ext_options),
('caTools', '1.17.1', ext_options),
('gplots', '3.0.1', ext_options),
('ROCR', '1.0-7', ext_options),
('httpuv', '1.3.3', ext_options),
('R6', '2.2.1', ext_options),
('rjson', '0.2.15', ext_options),
('sourcetools', '0.1.6', ext_options),
('shiny', '1.0.3', ext_options),
('seqinr', '3.3-6', ext_options),
('LearnBayes', '2.15', ext_options),
('deldir', '0.1-14', ext_options),
('gmodels', '2.16.2', ext_options),
('expm', '0.999-2', ext_options),
('spdep', '0.6-13', ext_options),
('dplyr', '0.5.0', ext_options),
('vegan', '2.4-3', ext_options),
('adegenet', '2.0.1', ext_options),
('prettyunits', '1.0.2', ext_options),
('progress', '1.1.2', ext_options),
('rncl', '0.8.2', ext_options),
('XML', '3.98-1.7', ext_options),
('crayon', '1.3.2', ext_options),
('praise', '1.0.0', ext_options),
('testthat', '1.0.2', ext_options),
('rprojroot', '1.2', ext_options),
('rmarkdown', '1.5', ext_options),
('curl', '2.6', ext_options),
('openssl', '0.9.6', ext_options),
('httr', '1.2.1', ext_options),
('reshape', '0.8.6', ext_options),
('xml2', '1.1.1', ext_options),
('bold', '0.4.0', ext_options),
('triebeard', '0.3.0', ext_options),
('urltools', '1.6.0', ext_options),
('httpcode', '0.2.0', ext_options),
('crul', '0.3.6', ext_options),
('rredlist', '0.3.0', ext_options),
('rentrez', '1.0.4', ext_options),
('rotl', '3.0.3', ext_options),
('solrium', '0.4.0', ext_options),
('ritis', '0.5.4', ext_options),
('worrms', '0.1.0', ext_options),
('natserv', '0.1.4', ext_options),
('taxize', '0.8.4', ext_options),
('tidyr', '0.6.2', ext_options),
('uuid', '0.1-2', ext_options),
('RNeXML', '2.0.7', ext_options),
('phylobase', '0.8.4', ext_options),
('adephylo', '1.1-10', ext_options),
('animation', '2.5', ext_options),
('bigmemory.sri', '0.1.3', ext_options),
('bigmemory', '4.5.19', dict(ext_options.items() + \
[('patches', ['bigmemory-4.5.19_icpc-wd308.patch'])])),
('calibrate', '1.7.2', ext_options),
('clusterGeneration', '1.3.4', ext_options),
('raster', '2.5-8', ext_options),
('dismo', '1.1-4', ext_options),
('extrafontdb', '1.0', ext_options),
('Rttf2pt1', '1.3.4', ext_options),
('extrafont', '0.17', ext_options),
('fields', '8.10', ext_options),
('shapefiles', '0.7', ext_options),
('fossil', '0.3.7', ext_options),
('geiger', '2.0.6', ext_options),
('glmnet', '2.0-10', ext_options),
('rgl', '0.98.1', ext_options),
('labdsv', '1.8-0', ext_options),
('stabs', '0.6-2', ext_options),
('modeltools', '0.2-21', ext_options),
('strucchange', '1.5-1', ext_options),
('TH.data', '1.0-8', ext_options),
('multlocal_comp', '1.4-6', ext_options),
('coin', '1.1-3', ext_options),
('party', '1.2-3', ext_options),
('mboost', '2.8-0', ext_options),
('msm', '1.6.4', ext_options),
('nor1mix', '1.2-2', ext_options),
('np', '0.60-3', ext_options),
('polynom', '1.3-9', ext_options),
('polspline', '1.1.12', ext_options),
('rms', '5.1-1', ext_options),
('RWekajars', '3.9.1-3', ext_options),
('RWeka', '0.4-34', ext_options),
('slam', '0.1-40', ext_options),
('tm', '0.7-1', ext_options),
('TraMineR', '2.0-5', ext_options),
('chemometrics', '1.4.2', ext_options),
('FNN', '1.1', ext_options),
('ipred', '0.9-6', ext_options),
('statmod', '1.4.29', ext_options),
('miscTools', '0.6-22', ext_options),
('maxLik', '1.3-4', ext_options),
('mlogit', '0.2-4', ext_options),
('getopt', '1.20.0', ext_options),
('gsalib', '2.1', ext_options),
('optparse', '1.3.2', ext_options),
('klaR', '0.6-12', ext_options),
('neuRosim', '0.2-12', ext_options),
('locfit', '1.5-9.1', ext_options),
('GGally', '1.3.0', ext_options),
('beanplot', '1.2', ext_options),
('clValid', '0.6-6', ext_options),
('matrixStats', '0.52.2', ext_options),
('DiscriMiner', '0.1-29', ext_options),
('ellipse', '0.3-8', ext_options),
('leaps', '3.0', ext_options),
('nloptr', '1.0.4', ext_options),
('lme4', '1.1-13', ext_options),
('pbkrtest', '0.4-7', ext_options),
('car', '2.1-4', ext_options),
('flashClust', '1.01-2', ext_options),
('FactoMineR', '1.35', ext_options),
('flexclust', '1.3-4', ext_options),
('flexmix', '2.3-14', ext_options),
('prabclus', '2.2-6', ext_options),
('diptest', '0.75-7', ext_options),
('trimcluster', '0.1-2', ext_options),
('fpc', '2.1-10', ext_options),
('BiasedUrn', '1.07', ext_options),
('TeachingDemos', '2.10', ext_options),
('kohonen', '3.0.2', dict(ext_options.items() + \
[('patches', ['kohonen-3.0.2_icpc-wd308.patch'])])),
('base64', '2.0', ext_options),
('doRNG', '1.6.6', ext_options),
('nleqslv', '3.2', ext_options),
('Deriv', '3.8.0', ext_options),
('RGCCA', '2.1.2', ext_options),
('pheatmap', '1.0.8', ext_options),
('openxlsx', '4.0.17', ext_options),
('pvclust', '2.0-0', ext_options),
('RCircos', '1.2.0', ext_options),
('lambda.r', '1.1.9', ext_options),
('futile.options', '1.0.0', ext_options),
('futile.logger', '1.4.3', ext_options),
('VennDiagram', '1.6.17', ext_options),
('xlsxjars', '0.6.1', ext_options),
('xlsx', '0.5.7', ext_options),
('forecast', '8.0', dict(ext_options.items() + \
[('patches', ['forecast-6.1_icpc-wd308.patch'])])),
('fma', '2.3', ext_options),
('expsmooth', '2.3', ext_options),
('fpp', '0.5', ext_options),
('maptools', '0.9-2', ext_options),
('tensor', '1.5', ext_options),
('polyclip', '1.6-1', ext_options),
('goftest', '1.1-1', ext_options),
('spatstat.utils', '1.6-0', ext_options),
('spatstat', '1.51-0', ext_options),
('rgdal', '1.2-7', ext_options),
('gdalUtils', '2.0.1.7', ext_options),
('pracma', '2.0.4', ext_options),
('RCurl', '1.95-4.8', ext_options),
('bio3d', '2.3-1', ext_options),
('AUC', '0.3.0', ext_options),
('interpretR', '0.2.4', ext_options),
('cvAUC', '1.1.0', ext_options),
('SuperLearner', '2.0-21', ext_options),
('lpSolve', '5.6.13', ext_options),
('mediation', '4.4.5', ext_options),
('ModelMetrics', '1.1.0', ext_options),
('caret', '6.0-76', ext_options),
('adabag', '4.1', ext_options),
('parallelMap', '1.3', ext_options),
('ParamHelpers', '1.10', ext_options),
('ggvis', '0.4.3', ext_options),
('mlr', '2.11', ext_options),
('unbalanced', '2.0', ext_options),
('RSNNS', '0.4-9', ext_options),
('abc.data', '1.0', ext_options),
('abc', '2.1', ext_options),
('lhs', '0.14', ext_options),
('tensorA', '0.36', ext_options),
('EasyABC', '1.5', ext_options),
('shape', '1.4.2', ext_options),
('whisker', '0.3-2', ext_options),
('rstudioapi', '0.6', ext_options),
('commonmark', '1.2', ext_options),
('desc', '1.1.0', ext_options),
('roxygen2', '6.0.1', ext_options),
('git2r', '0.18.0', ext_options),
('rversions', '1.0.3', ext_options),
('withr', '1.0.2', ext_options),
('devtools', '1.13.0', ext_options),
('Rook', '1.1-1', ext_options),
('Cairo', '1.5-9', dict(ext_options.items() +
[('patches', ['Cairo-1.5-9.patch'])])),
('RMTstat', '0.3', ext_options),
('Lmoments', '1.2-3', ext_options),
('distillery', '1.0-2', ext_options),
('extRemes', '2.0-8', ext_options),
('pixmap', '0.4-11', ext_options),
('tkrplot', '0.0-23', ext_options),
('misc3d', '0.8-4', ext_options),
('multicool', '0.1-10', dict(ext_options.items() + \
[('patches', ['multicool-0.1-10_icpc-wd308.patch'])])),
('ks', '1.10.6', ext_options),
('logcondens', '2.1.5', ext_options),
('Iso', '0.0-17', ext_options),
('penalized', '0.9-50', ext_options),
('clusterRepro', '0.5-1.1', ext_options),
('randomForestSRC', '2.4.2', ext_options),
('sm', '2.2-5.4', ext_options),
('psych', '1.7.5', ext_options),
('pbivnorm', '0.6.0', ext_options),
('lavaan', '0.5-23.1097', ext_options),
('matrixcalc', '1.0-3', ext_options),
('arm', '1.9-3', ext_options),
('mi', '1.0', ext_options),
('visNetwork', '1.0.3', ext_options),
('rgexf', '0.15.3', ext_options),
('influenceR', '0.1.0', ext_options),
('DiagrammeR', '0.9.0', ext_options),
('sem', '3.1-9', ext_options),
('jpeg', '0.1-8', ext_options),
('network', '1.13.0', ext_options),
('statnet.common', '3.3.0', ext_options),
('sna', '2.4', ext_options),
('glasso', '1.8', dict(ext_options.items() + \
[('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])),
('huge', '1.2.7', ext_options),
('d3Network', '0.5.2.1', ext_options),
('ggm', '2.3', ext_options),
('qgraph', '1.4.3', ext_options),
('diveRsity', '1.9.90', ext_options),
('doSNOW', '1.0.14', ext_options),
('phangorn', '2.2.0', ext_options),
('geepack', '1.2-1', ext_options),
('lubridate', '1.6.0', ext_options),
('biom', '0.3.12', ext_options),
('pim', '2.0.1', ext_options),
('minpack.lm', '1.2-1', ext_options),
('rootSolve', '1.7', ext_options),
('diagram', '1.6.3', ext_options),
('FME', '1.3.5', ext_options),
('bmp', '0.2', ext_options),
('readbitmap', '0.1-4', ext_options),
('purrr', '0.2.2', ext_options),
('downloader', '0.4', ext_options),
('imager', '0.40.2', dict(ext_options.items() + \
[('patches', ['imager-0.40.2_icpc-wd308.patch'])])),
('pracma', '2.0.4', ext_options),
('signal', '0.7-6', ext_options),
('tuneR', '1.3.2', ext_options),
('pastecs', '1.3-18', ext_options),
('audio', '0.1-5', ext_options),
('fftw', '1.0-4', ext_options),
('seewave', '2.0.5', ext_options),
('gsw', '1.0-3', ext_options),
('oce', '0.9-21', ext_options),
('ineq', '0.2-13', ext_options),
('soundecology', '1.3.2', ext_options),
]
moduleclass = 'lang'
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