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easyconfigs-it4i/r/R/R-3.1.2-intel-2015b.eb
Josef Hrabal 27902b54aa _not_installed merged back 
Modules which was not installed merged back to root directory.
2017-04-05 12:53:18 +02:00

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name = 'R'
version = '3.1.2'
homepage = 'http://www.r-project.org/'
description = """R is a free software environment for statistical computing and graphics."""
toolchain = {'name': 'intel', 'version': '2015b'}
sources = [SOURCE_TAR_GZ]
source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s']
preconfigopts = 'BLAS_LIBS="$LIBBLAS_MT" LAPACK_LIBS="$LIBLAPACK_MT"'
configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --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"
dependencies = [
('libreadline', '6.3'),
('ncurses', '5.9'),
('libpng', '1.6.12'), # for plotting in R
('libjpeg-turbo', '1.4.0'), # for plottting in R
('Java', '1.8.0_51', '', True), # Java bindings are built if Java is found, might as well provide it
]
name_tmpl = '%(name)s_%(version)s.tar.gz'
ext_options = {
'source_urls': [
'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'http://cran.r-project.org/src/contrib/', # current version of packages
'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
],
'source_tmpl': name_tmpl,
}
# Bioconductor packages have a different download url
bioconductor_options = {
'source_urls': [
'http://www.bioconductor.org/packages/release/bioc/src/contrib/',
'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/',
'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/',
'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/',
'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/',
'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/',
],
'source_tmpl': name_tmpl,
}
# !! order of packages is important !!
# packages updated on January 8th 2015
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', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])),
('abind', '1.4-0', ext_options),
('magic', '1.5-6', ext_options),
('geometry', '0.3-4', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])),
('bit', '1.1-12', ext_options),
('filehash', '2.2-2', ext_options),
('ff', '2.2-13', ext_options),
('bnlearn', '3.6', ext_options),
('bootstrap', '2014.4', ext_options),
('combinat', '0.0-8', ext_options),
('deal', '1.2-37', ext_options),
('fdrtool', '1.2.13', ext_options),
('formatR', '1.0', ext_options),
('gtools', '3.4.1', ext_options),
('gdata', '2.13.3', ext_options),
('GSA', '1.03', ext_options),
('highr', '0.4', ext_options),
('infotheo', '1.2.0', ext_options),
('lars', '1.2', ext_options),
('lazy', '1.2-15', ext_options),
('kernlab', '0.9-19', ext_options),
('mime', '0.2', ext_options),
('markdown', '0.7.4', ext_options),
('mlbench', '2.1-1', ext_options),
('NLP', '0.1-5', ext_options),
('mclust', '4.4', ext_options),
('RANN', '2.4.1', ext_options),
('rmeta', '2.16', ext_options),
('segmented', '0.5-1.0', ext_options),
('som', '0.3-5', ext_options),
('SuppDists', '1.1-9.1', ext_options),
('stabledist', '0.6-6', ext_options),
('survivalROC', '1.0.3', ext_options),
('pspline', '1.0-16', ext_options),
('timeDate', '3011.99', ext_options),
('longmemo', '1.0-0', ext_options),
('ADGofTest', '0.3', ext_options),
('ade4', '1.6-2', ext_options),
('AlgDesign', '1.1-7.3', ext_options),
('base64enc', '0.1-2', ext_options),
('BH', '1.55.0-3', ext_options),
('brew', '1.0-6', ext_options),
('Brobdingnag', '1.2-4', ext_options),
('corpcor', '1.6.7', ext_options),
('longitudinal', '1.1.10', ext_options),
('checkmate', '1.5.1', ext_options),
('cubature', '1.1-2', ext_options),
('DEoptimR', '1.0-2', ext_options),
('digest', '0.6.8', ext_options),
('fastmatch', '1.0-4', ext_options),
('ffbase', '0.11.3', ext_options),
('iterators', '1.0.7', ext_options),
('maps', '2.3-9', ext_options),
('nnls', '1.4', ext_options),
('sendmailR', '1.2-1', ext_options),
('spam', '1.0-1', ext_options),
('subplex', '1.1-4', ext_options),
('stringr', '0.6.2', ext_options),
('evaluate', '0.5.5', ext_options),
('logspline', '2.1.5', ext_options),
('ncbit', '2013.03.29', ext_options),
('permute', '0.8-3', ext_options),
('plotrix', '3.5-10', ext_options),
('randomForest', '4.6-10', ext_options),
('scatterplot3d', '0.3-35', ext_options),
('SparseM', '1.6', ext_options),
('tripack', '1.3-6', ext_options),
('irace', '1.06', ext_options),
('rJava', '0.9-6', ext_options),
('lattice', '0.20-29', ext_options),
('RColorBrewer', '1.1-2', ext_options),
('latticeExtra', '0.6-26', ext_options),
('Matrix', '1.1-4', ext_options),
('png', '0.1-7', ext_options),
('Rcpp', '0.11.3', ext_options),
('RcppArmadillo', '0.4.600.0', ext_options),
('plyr', '1.8.1', ext_options),
('pROC', '1.7.3', ext_options),
('quadprog', '1.5-5', ext_options),
('BB', '2014.10-1', ext_options),
('BBmisc', '1.8', ext_options),
('fail', '1.2', ext_options),
('rlecuyer', '0.3-3', ext_options),
('snow', '0.3-13', ext_options),
('MASS', '7.3-35', ext_options),
('tree', '1.0-35', ext_options),
('pls', '2.4-3', ext_options),
('class', '7.3-11', ext_options),
('e1071', '1.6-4', ext_options),
('nnet', '7.3-8', ext_options),
('car', '2.0-22', ext_options),
('colorspace', '1.2-4', ext_options),
('robustbase', '0.92-2', ext_options),
('sp', '1.0-17', ext_options),
('vcd', '1.3-2', ext_options),
('snowfall', '1.84-6', ext_options),
('rpart', '4.1-8', ext_options),
('mice', '2.22', ext_options),
('nlme', '3.1-118', ext_options),
('urca', '1.2-8', ext_options),
('fracdiff', '1.4-2', ext_options),
('mgcv', '1.8-4', ext_options),
('logistf', '1.21', ext_options),
('akima', '0.5-11', ext_options),
('bitops', '1.0-6', ext_options),
('boot', '1.3-13', ext_options),
('mixtools', '1.0.2', ext_options),
('cluster', '1.15.3', ext_options),
('gclus', '1.3.1', ext_options),
('coda', '0.16-1', ext_options),
('codetools', '0.2-9', ext_options),
('foreach', '1.4.2', ext_options),
('doMC', '1.3.3', ext_options),
('DBI', '0.3.1', ext_options),
('foreign', '0.8-62', ext_options),
('survival', '2.37-7', ext_options),
('gam', '1.09.1', ext_options),
('gamlss.data', '4.2-7', ext_options),
('gamlss.dist', '4.3-1', ext_options),
('hwriter', '1.3.2', ext_options),
('KernSmooth', '2.23-13', ext_options),
('zoo', '1.7-11', ext_options),
('xts', '0.9-7', ext_options),
('TTR', '0.22-0', ext_options),
('quantmod', '0.4-3', ext_options),
('lmtest', '0.9-33', ext_options),
('mnormt', '1.5-1', ext_options),
('mvtnorm', '1.0-2', ext_options),
('pcaPP', '1.9-60', ext_options),
('numDeriv', '2012.9-1', ext_options),
('lava', '1.3', ext_options),
('prodlim', '1.5.1', ext_options),
('pscl', '1.4.6', ext_options),
('RSQLite', '1.0.0', ext_options),
('BatchJobs', '1.5', ext_options),
('sandwich', '2.3-2', ext_options),
('sfsmisc', '1.0-27', ext_options),
('spatial', '7.3-8', ext_options),
('VGAM', '0.9-6', ext_options),
('waveslim', '1.7.3', ext_options),
('xtable', '1.7-4', ext_options),
('profileModel', '0.5-9', ext_options),
('brglm', '0.5-9', ext_options),
('deSolve', '1.11', ext_options),
('tseriesChaos', '0.1-13', ext_options),
('tseries', '0.10-32', ext_options),
('fastICA', '1.2-0', ext_options),
('R.methodsS3', '1.6.1', ext_options),
('R.oo', '1.18.0', ext_options),
('cgdsr', '1.1.33', ext_options),
('R.utils', '1.34.0', ext_options),
('R.matlab', '3.1.1', ext_options),
('BiocGenerics', '0.12.1', bioconductor_options),
('Biobase', '2.26.0', bioconductor_options),
('S4Vectors', '0.4.0', bioconductor_options),
('IRanges', '2.0.1', bioconductor_options),
('GenomeInfoDb', '1.2.4', bioconductor_options),
('AnnotationDbi', '1.28.1', bioconductor_options),
('XVector', '0.6.0', bioconductor_options),
('zlibbioc', '1.12.0', bioconductor_options),
('Biostrings', '2.34.1', bioconductor_options),
('GenomicRanges', '1.18.4', bioconductor_options),
('Rsamtools', '1.18.2', bioconductor_options),
('BiocParallel', '1.0.2', bioconductor_options),
('GenomicAlignments', '1.2.1', bioconductor_options),
('ShortRead', '1.24.0', bioconductor_options),
('graph', '1.44.1', bioconductor_options),
('gbm', '2.1', ext_options),
('dichromat', '2.0-0', ext_options),
('Formula', '1.1-2', ext_options),
('acepack', '1.3-3.3', ext_options),
('Hmisc', '3.14-6', ext_options),
('munsell', '0.4.2', ext_options),
('labeling', '0.3', ext_options),
('scales', '0.2.4', ext_options),
('fastcluster', '1.1.15', ext_options),
('reshape2', '1.4.1', ext_options),
('chron', '2.3-45', ext_options),
('data.table', '1.9.4', ext_options),
('gtable', '0.1.2', ext_options),
('proto', '0.3-10', ext_options),
('ggplot2', '1.0.0', ext_options),
('igraph', '0.7.1', ext_options),
('GeneNet', '1.2.11', ext_options),
('ape', '3.2', ext_options),
('htmltools', '0.2.6', ext_options),
('RJSONIO', '1.3-0', ext_options),
('caTools', '1.17.1', ext_options),
('gplots', '2.16.0', ext_options),
('ROCR', '1.0-5', ext_options),
('httpuv', '1.3.2', ext_options),
('R6', '2.0.1', ext_options),
('shiny', '0.10.2.2', ext_options),
('adegenet', '1.4-2', ext_options),
('phylobase', '0.6.8', ext_options),
('adephylo', '1.1-6', ext_options),
('animation', '2.3', ext_options),
('bigmemory.sri', '0.1.3', ext_options),
('bigmemory', '4.4.6', ext_options),
('calibrate', '1.7.2', ext_options),
('clusterGeneration', '1.3.1', ext_options),
('raster', '2.3-12', ext_options),
('dismo', '1.0-5', ext_options),
('expm', '0.99-1.1', ext_options),
('extrafontdb', '1.0', ext_options),
('Rttf2pt1', '1.3.2', ext_options),
('extrafont', '0.17', ext_options),
('fields', '7.1', ext_options),
('shapefiles', '0.7', ext_options),
('fossil', '0.3.7', ext_options),
('geiger', '2.0.3', ext_options),
('glmnet', '1.9-8', ext_options),
('labdsv', '1.6-1', ext_options),
('MatrixModels', '0.3-1.1', ext_options),
('stabs', '0.5-0', ext_options),
('mboost', '2.4-1', ext_options),
('msm', '1.5', ext_options),
('nor1mix', '1.2-0', ext_options),
('np', '0.60-2', ext_options),
('polynom', '1.3-8', ext_options),
('quantreg', '5.05', ext_options),
('RcppEigen', '0.3.2.3.0', ext_options),
('polspline', '1.1.9', ext_options),
('TH.data', '1.0-6', ext_options),
('multcomp', '1.3-8', ext_options),
('rms', '4.2-1', ext_options),
('RWekajars', '3.7.11-1', ext_options),
('RWeka', '0.4-23', ext_options),
('slam', '0.1-32', ext_options),
('tm', '0.6', ext_options),
('TraMineR', '1.8-8', ext_options),
('chemometrics', '1.3.8', ext_options),
('FNN', '1.1', ext_options),
('ipred', '0.9-3', ext_options),
('knitr', '1.8', ext_options),
('statmod', '1.4.20', ext_options),
('miscTools', '0.6-16', ext_options),
('maxLik', '1.2-4', ext_options),
('mlogit', '0.2-4', ext_options),
('getopt', '1.20.0', ext_options),
('gsalib', '2.1', ext_options),
('reshape', '0.8.5', ext_options),
('optparse', '1.3.0', ext_options),
('klaR', '0.6-12', ext_options),
('neuRosim', '0.2-12', ext_options),
('affyio', '1.34.0', bioconductor_options),
('BiocInstaller', '1.16.1', bioconductor_options),
('preprocessCore', '1.28.0', bioconductor_options),
('affy', '1.44.0', bioconductor_options),
('GO.db', '3.0.0', bioconductor_options),
('limma', '3.22.4', bioconductor_options),
('RBGL', '1.42.0', bioconductor_options),
('org.Hs.eg.db', '3.0.0', bioconductor_options),
('AnnotationForge', '1.8.2', bioconductor_options),
('KEGG.db', '3.0.0', bioconductor_options),
('annaffy', '1.38.0', bioconductor_options),
('gcrma', '2.38.0', bioconductor_options),
('oligoClasses', '1.28.0', bioconductor_options),
('edgeR', '3.8.5', bioconductor_options),
('PFAM.db', '3.0.0', bioconductor_options),
('locfit', '1.5-9.1', ext_options),
('gridExtra', '0.9.1', ext_options),
('GGally', '0.5.0', ext_options),
('baySeq', '2.0.50', bioconductor_options),
('beanplot', '1.2', ext_options),
('clValid', '0.6-6', ext_options),
('qvalue', '1.40.0', bioconductor_options),
('impute', '1.40.0', bioconductor_options),
('matrixStats', '0.12.2', ext_options),
('samr', '2.0', ext_options),
('DEGseq', '1.20.0', bioconductor_options),
('DiscriMiner', '0.1-29', ext_options),
('ellipse', '0.3-8', ext_options),
('leaps', '2.9', ext_options),
('FactoMineR', '1.28', ext_options),
('modeltools', '0.2-21', ext_options),
('flexclust', '1.3-4', ext_options),
('flexmix', '2.3-12', ext_options),
('prabclus', '2.2-6', ext_options),
('diptest', '0.75-6', ext_options),
('trimcluster', '0.1-2', ext_options),
('fpc', '2.1-9', ext_options),
('BiasedUrn', '1.06.1', ext_options),
('hgu133plus2.db', '3.0.0', bioconductor_options),
('TeachingDemos', '2.9', ext_options),
('jsonlite', '0.9.14', ext_options),
('kohonen', '2.0.15', ext_options),
('base64', '1.1', ext_options),
('illuminaio', '0.8.0', bioconductor_options),
('registry', '0.2', ext_options),
('pkgmaker', '0.22', ext_options),
('rngtools', '1.2.4', ext_options),
('doRNG', '1.6', ext_options),
('bumphunter', '1.6.0', bioconductor_options),
('multtest', '2.22.0', bioconductor_options),
('siggenes', '1.40.0', bioconductor_options),
('nleqslv', '2.5', ext_options),
('DynDoc', '1.44.0', bioconductor_options),
('genoset', '1.20.0', bioconductor_options),
('RGCCA', '2.0', ext_options),
('pheatmap', '0.7.7', ext_options),
('multtest', '2.22.0', bioconductor_options),
('NOISeq', '2.8.0', bioconductor_options),
('openxlsx', '2.2.1', ext_options),
('Rgraphviz', '2.10.0', bioconductor_options),
('pvclust', '1.3-2', ext_options),
('RCircos', '1.1.2', ext_options),
('reshape', '0.8.5', ext_options),
('RNASeqPower', '1.6.0', bioconductor_options),
('VennDiagram', '1.6.9', ext_options),
('xlsxjars', '0.6.1', ext_options),
('xlsx', '0.5.7', ext_options),
]
moduleclass = 'lang'
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