name = 'R'
version = '3.1.1'

homepage = 'http://www.r-project.org/'
description = """R is a free software environment for statistical local_computing and graphics."""

toolchain = {'name': 'ictce', 'version': '5.5.0'}

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=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', '6.2'),
    ('ncurses', '5.9'),
    ('libpng', '1.6.9'),  # for plotting in R
    # Java bindings are built if Java is found, might as well provide it
    ('Java', '1.7.0_79', '', True),
]

local_name_tmpl = '%(name)s_%(version)s.tar.gz'
local_ext_options = {
    'source_urls': [
        # package archive
        'http://cran.r-project.org/src/contrib/Archive/%(name)s',
        'http://cran.freestatistics.org/src/contrib',  # alternative for packages
    ],
    'source_tmpl': local_name_tmpl,
}
# Bioconductor packages have a different download url
local_bioconductor_options = {
    'source_urls': [
        'http://www.bioconductor.org/packages/release/bioc/src/contrib/',
        'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'],
    'source_tmpl': local_name_tmpl,
}
# !! order of packages is important !!
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!
    ('irace', '1.04', local_ext_options),
    ('rJava', '0.9-6', local_ext_options),
    ('lattice', '0.20-29', local_ext_options),
    ('RColorBrewer', '1.0-5', local_ext_options),
    ('latticeExtra', '0.6-26', local_ext_options),
    ('Matrix', '1.1-3', local_ext_options),
    ('png', '0.1-7', local_ext_options),
    ('Rcpp', '0.11.1', local_ext_options),
    ('quadprog', '1.5-5', local_ext_options),
    ('BB', '2014.1-1', local_ext_options),
    ('rlecuyer', '0.3-3', local_ext_options),
    ('snow', '0.3-13', local_ext_options),
    ('MASS', '7.3-33', local_ext_options),
    ('class', '7.3-10', local_ext_options),
    ('e1071', '1.6-3', local_ext_options),
    ('nnet', '7.3-8', local_ext_options),
    ('car', '2.0-20', local_ext_options),
    ('colorspace', '1.2-4', local_ext_options),
    ('DEoptimR', '1.0-1', local_ext_options),
    ('robustbase', '0.91-1', local_ext_options),
    ('sp', '1.0-15', local_ext_options),
    ('vcd', '1.3-1', local_ext_options),
    ('snowfall', '1.84-6', local_ext_options),
    ('rpart', '4.1-8', local_ext_options),
    ('randomForest', '4.6-7', local_ext_options),
    ('mice', '2.21', local_ext_options),
    ('nlme', '3.1-117', local_ext_options),
    ('mgcv', '1.7-29', local_ext_options),
    ('logistf', '1.21', local_ext_options),
    ('akima', '0.5-11', local_ext_options),
    ('bitops', '1.0-6', local_ext_options),
    ('boot', '1.3-11', local_ext_options),
    ('cluster', '1.15.2', local_ext_options),
    ('coda', '0.16-1', local_ext_options),
    ('codetools', '0.2-8', local_ext_options),
    ('DBI', '0.2-7', local_ext_options),
    ('foreign', '0.8-61', local_ext_options),
    ('survival', '2.37-7', local_ext_options),
    ('gam', '1.09.1', local_ext_options),
    ('gamlss.data', '4.2-7', local_ext_options),
    ('gamlss.dist', '4.2-7', local_ext_options),
    ('hwriter', '1.3', local_ext_options),
    ('KernSmooth', '2.23-12', local_ext_options),
    ('zoo', '1.7-11', local_ext_options),
    ('lmtest', '0.9-33', local_ext_options),
    ('mnormt', '1.4-7', local_ext_options),
    ('mvtnorm', '0.9-99992', local_ext_options),
    ('numDeriv', '2012.9-1', local_ext_options),
    ('pscl', '1.04.4', local_ext_options),
    ('RSQLite', '0.11.4', local_ext_options),
    ('sandwich', '2.3-0', local_ext_options),
    ('sfsmisc', '1.0-25', local_ext_options),
    ('spatial', '7.3-8', local_ext_options),
    ('VGAM', '0.9-4', local_ext_options),
    ('waveslim', '1.7.3', local_ext_options),
    ('xtable', '1.7-3', local_ext_options),
    ('profileModel', '0.5-9', local_ext_options),
    ('brglm', '0.5-9', local_ext_options),
    ('deSolve', '1.10-8', local_ext_options),
    ('tseriesChaos', '0.1-13', local_ext_options),
    ('tseries', '0.10-32', local_ext_options),
    ('neuRosim', '0.2-10', local_ext_options),
    ('fastICA', '1.2-0', local_ext_options),
    ('R.methodsS3', '1.6.1', local_ext_options),
    ('R.oo', '1.18.0', local_ext_options),
    ('R.utils', '1.32.4', local_ext_options),
    ('R.matlab', '3.0.1', local_ext_options),
    ('Rniftilib', '0.0-32', local_ext_options),
    ('iterators', '1.0.7', local_ext_options),
    ('foreach', '1.4.2', local_ext_options),
    ('BBmisc', '1.6', local_ext_options),
    ('digest', '0.6.4', local_ext_options),
    ('base64enc', '0.1-1', local_ext_options),
    ('sendmailR', '1.1-2', local_ext_options),
    ('brew', '1.0-6', local_ext_options),
    ('plyr', '1.8.1', local_ext_options),
    ('stringr', '0.6.2', local_ext_options),
    ('fail', '1.2', local_ext_options),
    ('BatchJobs', '1.2', local_ext_options),
    ('BiocGenerics', '0.10.0', local_bioconductor_options),
    ('Biobase', '2.24.0', local_bioconductor_options),
    ('IRanges', '1.22.8', local_bioconductor_options),
    ('GenomeInfoDb', '1.0.2', local_bioconductor_options),
    ('AnnotationDbi', '1.26.0', local_bioconductor_options),
    ('XVector', '0.4.0', local_bioconductor_options),
    ('zlibbioc', '1.10.0', local_bioconductor_options),
    ('Biostrings', '2.32.0', local_bioconductor_options),
    ('GenomicRanges', '1.16.3', local_bioconductor_options),
    ('Rsamtools', '1.16.0', local_bioconductor_options),
    ('BSgenome', '1.32.0', local_bioconductor_options),
    ('BiocParallel', '0.6.1', local_bioconductor_options),
    ('GenomicAlignments', '1.0.2', local_bioconductor_options),
    ('ShortRead', '1.22.0', local_bioconductor_options),
    ('graph', '1.42.0', local_bioconductor_options),
    ('gbm', '2.1', local_ext_options),
    ('dichromat', '2.0-0', local_ext_options),
    ('Formula', '1.1-1', local_ext_options),
    ('Hmisc', '3.14-4', local_ext_options),
    ('munsell', '0.4.2', local_ext_options),
    ('labeling', '0.2', local_ext_options),
    ('scales', '0.2.4', local_ext_options),
    ('fastcluster', '1.1.13', local_ext_options),
    ('reshape2', '1.4', local_ext_options),
    ('gtable', '0.1.2', local_ext_options),
    ('proto', '0.3-10', local_ext_options),
    ('ggplot2', '1.0.0', local_ext_options),
    ('reshape', '0.8.5', local_ext_options),
    ('gsalib', '2.0', local_ext_options),
    ('ape', '3.1-2', local_ext_options),
    ('igraph', '0.7.1', local_ext_options),
    ('fastmatch', '1.0-4', local_ext_options),
    ('phangorn', '1.99-7', local_ext_options),
    ('gdsfmt', '1.0.4', local_ext_options),
    ('SNPRelate', '0.9.19', local_ext_options),
    ('getopt', '1.20.0', local_ext_options),
    ('miscTools', '0.6-16', local_ext_options),
    ('maxLik', '1.2-0', local_ext_options),
    ('statmod', '1.4.20', local_ext_options),
    ('mlogit', '0.2-4', local_ext_options),
    ('optparse', '1.2.0', local_ext_options),
    ('permute', '0.8-3', local_ext_options),
    ('vegan', '2.0-10', local_ext_options),
    ('gtools', '3.4.1', local_ext_options),
    ('combinat', '0.0-8', local_ext_options),
    ('klaR', '0.6-11', local_ext_options),
]

moduleclass = 'lang'