boegel
commented
7 years ago @shahzebsiddiqui looks like PROJ is missing as a dependency, based on https://github.com/OSGeo/proj.4/blob/master/src/projects.h?
Closed shahzebsiddiqui closed 5 months ago
boegel
commented
7 years ago @shahzebsiddiqui looks like PROJ is missing as a dependency, based on https://github.com/OSGeo/proj.4/blob/master/src/projects.h?
shahzebsiddiqui
commented
7 years ago Is this something to do with PROJ build. I am using PROJ 4.8.0, is the project.h missing from the build.
Did a quick check for header files I only see the following:
[hpcswadm@amrndhl1157 R]$ ls -l /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/PROJ/4.8.0/include
total 51
-rw-r--r-- 1 hpcswadm hpcswadm 1001 Apr 3 08:49 org_proj4_Projections.h
-rw-r--r-- 1 hpcswadm hpcswadm 4820 Apr 3 08:49 proj_api.hAny suggestions what do to.
shahzebsiddiqui
commented
7 years ago @boegel Do we have an update on PROJ?
Does this PR https://github.com/hpcugent/easybuild-easyconfigs/pull/4295 resolve the issue?
shahzebsiddiqui
commented
7 years ago Okay, I finally figured out how to build R. There were few dependencies that had to be added to easyconfig file that were not present in current spec file.
The rgdal issue was resolved when building with PROJ 4.9.3. Also I ran into issue with cairo package, i made sure this was part of the dependency from EB and not system package. Cairo introduced several dependencies such as X11, GLib, gettext, etc...
[hpcswadm@amrndhl1157 R]$ cat R-3.3.1-intel-2017.01.eb
name = 'R'
version = '3.3.1'
homepage = 'http://www.r-project.org/'
description = """R is a free software environment for statistical computing and graphics."""
toolchain = {'name': 'intel', 'version': '2017.01'}
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', '6.3'),
('ncurses', '6.0'),
('bzip2', '1.0.6'),
('XZ', '5.2.2'),
('zlib', '1.2.8'),
('SQLite', '3.13.0'),
('PCRE', '8.38'),
('libpng', '1.6.23'), # for plotting in R
('libjpeg-turbo', '1.5.0'), # for plottting in R
('LibTIFF', '4.0.6'),
('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it
('Tcl', '8.6.5'), # for tcltk
('Tk', '8.6.5'), # for tcltk
('cURL', '7.49.1'), # for RCurl
('libxml2', '2.9.4'), # for XML
('GDAL', '2.1.0'), # for rgdal
('PROJ', '4.9.3'), # for rgdal
('GMP', '6.1.1'), # for igraph
('cairo','1.14.6'), # Cairo
# 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': [
'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,
}
# !! order of packages is important !!
# packages updated on July 8th 2016
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', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])),
('abind', '1.4-3', 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', '2.3', ext_options),
('ff', '2.2-13', ext_options),
('bnlearn', '4.0', ext_options),
('bootstrap', '2015.2', ext_options),
('combinat', '0.0-8', ext_options),
('deal', '1.2-37', ext_options),
('fdrtool', '1.2.15', ext_options),
('formatR', '1.4', 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', '0.9-24', ext_options),
('mime', '0.5', ext_options),
('markdown', '0.7.7', ext_options),
('mlbench', '2.1-1', ext_options),
('NLP', '0.1-9', ext_options),
('mclust', '5.2', 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', '1.1-9.2', ext_options),
('stabledist', '0.7-0', 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', '1.7-4', ext_options),
('AlgDesign', '1.1-7.3', ext_options),
('base64enc', '0.1-3', ext_options),
('BH', '1.60.0-2', ext_options),
('brew', '1.0-6', ext_options),
('Brobdingnag', '1.2-4', ext_options),
('corpcor', '1.6.8', ext_options),
('longitudinal', '1.1.12', ext_options),
('backports', '1.0.3', ext_options),
('checkmate', '1.8.1', ext_options),
('cubature', '1.1-2', ext_options),
('DEoptimR', '1.0-6', ext_options),
('digest', '0.6.9', ext_options),
('fastmatch', '1.0-4', ext_options),
('ffbase', '0.12.3', ext_options),
('iterators', '1.0.8', ext_options),
('maps', '3.1.0', ext_options),
('nnls', '1.4', ext_options),
('sendmailR', '1.2-1', ext_options),
('spam', '1.3-0', ext_options),
('subplex', '1.1-6', ext_options),
('stringi', '1.1.1', ext_options),
('magrittr', '1.5', ext_options),
('stringr', '1.0.0', ext_options),
('evaluate', '0.9', ext_options),
('logspline', '2.1.9', ext_options),
('ncbit', '2013.03.29', ext_options),
('permute', '0.9-0', ext_options),
('plotrix', '3.6-2', ext_options),
('randomForest', '4.6-12', ext_options),
('scatterplot3d', '0.3-37', ext_options),
('SparseM', '1.7', ext_options),
('tripack', '1.3-7', ext_options),
('irace', '1.07', ext_options),
('rJava', '0.9-8', ext_options),
('lattice', '0.20-33', ext_options),
('RColorBrewer', '1.1-2', ext_options),
('latticeExtra', '0.6-28', ext_options),
('Matrix', '1.2-6', ext_options),
('png', '0.1-7', ext_options),
('Rcpp', '0.12.5', ext_options),
('RcppArmadillo', '0.7.100.3.1', ext_options),
('plyr', '1.8.4', ext_options),
('pROC', '1.8', ext_options),
('quadprog', '1.5-5', ext_options),
('BB', '2014.10-1', ext_options),
('BBmisc', '1.9', ext_options),
('fail', '1.3', ext_options),
('rlecuyer', '0.3-4', ext_options),
('snow', '0.4-1', ext_options),
('MASS', '7.3-45', ext_options),
('tree', '1.0-37', ext_options),
('pls', '2.5-0', ext_options),
('class', '7.3-14', ext_options),
('e1071', '1.6-7', ext_options),
('nnet', '7.3-12', ext_options),
('nlme', '3.1-128', ext_options),
('minqa', '1.2.4', ext_options),
('RcppEigen', '0.3.2.8.1', ext_options),
('MatrixModels', '0.4-1', ext_options),
('quantreg', '5.26', ext_options),
('mgcv', '1.8-12', ext_options),
('colorspace', '1.2-6', ext_options),
('robustbase', '0.92-6', ext_options),
('sp', '1.2-3', ext_options),
('zoo', '1.7-13', ext_options),
('lmtest', '0.9-34', ext_options),
('vcd', '1.4-1', ext_options),
('snowfall', '1.84-6.1', ext_options),
('rpart', '4.1-10', ext_options),
('survival', '2.39-5', ext_options),
('mice', '2.25', ext_options),
('urca', '1.2-9', ext_options),
('fracdiff', '1.4-2', ext_options),
('logistf', '1.21', ext_options),
('akima', '0.5-12', ext_options),
('bitops', '1.0-6', ext_options),
('boot', '1.3-18', ext_options),
('mixtools', '1.0.4', ext_options),
('cluster', '2.0.4', ext_options),
('gclus', '1.3.1', ext_options),
('coda', '0.18-1', ext_options),
('codetools', '0.2-14', ext_options),
('foreach', '1.4.3', ext_options),
('doMC', '1.3.4', ext_options),
('DBI', '0.4-1', ext_options),
('foreign', '0.8-66', ext_options),
('gam', '1.12', ext_options),
('gamlss.data', '4.3-4', ext_options),
('gamlss.dist', '4.3-6', 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', '0.4-5', ext_options),
('mnormt', '1.5-4', ext_options),
('mvtnorm', '1.0-5', ext_options),
('pcaPP', '1.9-60', ext_options),
('numDeriv', '2014.2-1', ext_options),
('lava', '1.4.3', ext_options),
('prodlim', '1.5.7', ext_options),
('pscl', '1.4.9', ext_options),
('RSQLite', '1.0.0', 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', '1.0-2', 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', '1.13', ext_options),
('tseriesChaos', '0.1-13', ext_options),
('tseries', '0.10-35', ext_options),
('fastICA', '1.2-0', ext_options),
('R.methodsS3', '1.7.1', ext_options),
('R.oo', '1.20.0', ext_options),
('cgdsr', '1.2.5', ext_options),
('R.utils', '2.3.0', ext_options),
('R.matlab', '3.6.0', ext_options),
('gbm', '2.1.1', ext_options),
('dichromat', '2.0-0', ext_options),
('Formula', '1.2-1', ext_options),
('acepack', '1.3-3.3', ext_options),
('reshape2', '1.4.1', ext_options),
('gtable', '0.2.0', ext_options),
('munsell', '0.4.3', ext_options),
('labeling', '0.3', ext_options),
('scales', '0.4.0', ext_options),
('proto', '0.3-10', ext_options),
('ggplot2', '2.1.0', ext_options),
('gridExtra', '2.2.1', ext_options),
('chron', '2.3-47', ext_options),
('data.table', '1.9.6', ext_options),
('Hmisc', '3.17-4', ext_options),
('fastcluster', '1.1.20', 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', '2.0.0', ext_options),
('igraph', '1.0.1', ext_options),
('GeneNet', '1.2.13', ext_options),
('ape', '3.5', ext_options),
('htmltools', '0.3.5', 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),
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('jsonlite', '1.0', ext_options),
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('shiny', '0.13.2', ext_options),
('seqinr', '3.2-0', ext_options),
('LearnBayes', '2.15', ext_options),
('deldir', '0.1-12', ext_options),
('gmodels', '2.16.2', ext_options),
('spdep', '0.6-5', ext_options),
('assertthat', '0.1', ext_options),
('lazyeval', '0.2.0', ext_options),
('tibble', '1.1', ext_options),
('dplyr', '0.5.0', ext_options),
('vegan', '2.4-0', ext_options),
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('rncl', '0.6.0', ext_options),
('XML', '3.98-1.4', ext_options),
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('crayon', '1.3.2', ext_options),
('praise', '1.0.0', ext_options),
('testthat', '1.0.2', ext_options),
('yaml', '2.1.13', ext_options),
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('openssl', '0.9.4', ext_options),
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('reshape', '0.8.5', ext_options),
('xml2', '1.0.0', ext_options),
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('rredlist', '0.1.0', ext_options),
('rentrez', '1.0.2', ext_options),
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('tidyr', '0.5.1', ext_options),
('uuid', '0.1-2', ext_options),
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('phylobase', '0.8.2', ext_options),
('adephylo', '1.1-6', ext_options),
('animation', '2.4', 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', '1.1-1', ext_options),
('expm', '0.999-0', ext_options),
('extrafontdb', '1.0', ext_options),
('Rttf2pt1', '1.3.4', ext_options),
('extrafont', '0.17', ext_options),
('fields', '8.4-1', ext_options),
('shapefiles', '0.7', ext_options),
('fossil', '0.3.7', ext_options),
('geiger', '2.0.6', ext_options),
('glmnet', '2.0-5', ext_options),
('rgl', '0.95.1441', ext_options),
('labdsv', '1.8-0', ext_options),
('stabs', '0.5-1', ext_options),
('modeltools', '0.2-21', ext_options),
('strucchange', '1.5-1', ext_options),
('TH.data', '1.0-7', ext_options),
('multcomp', '1.4-5', ext_options),
('coin', '1.1-2', ext_options),
('party', '1.0-25', ext_options),
('mboost', '2.6-0', ext_options),
('msm', '1.6.1', ext_options),
('nor1mix', '1.2-1', ext_options),
('np', '0.60-2', ext_options),
('polynom', '1.3-8', ext_options),
('polspline', '1.1.12', ext_options),
('rms', '4.5-0', ext_options),
('RWekajars', '3.9.0-1', ext_options),
('RWeka', '0.4-29', ext_options),
('slam', '0.1-35', ext_options),
('tm', '0.6-2', ext_options),
('TraMineR', '1.8-12', ext_options),
('chemometrics', '1.3.9', ext_options),
('FNN', '1.1', ext_options),
('ipred', '0.9-5', ext_options),
('statmod', '1.4.24', ext_options),
('miscTools', '0.6-16', 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),
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('locfit', '1.5-9.1', ext_options),
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('ellipse', '0.3-8', ext_options),
('leaps', '2.9', ext_options),
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('lme4', '1.1-12', ext_options),
('pbkrtest', '0.4-6', ext_options),
('car', '2.1-2', ext_options),
('flashClust', '1.01-2', ext_options),
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('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', '2.0.19', ext_options),
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('nleqslv', '3.0.2', ext_options),
('RGCCA', '2.0', ext_options),
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('openxlsx', '3.0.0', ext_options),
('pvclust', '2.0-0', ext_options),
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('fma', '2.2', ext_options),
('expsmooth', '2.3', ext_options),
('fpp', '0.5', ext_options),
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('pracma', '1.9.3', ext_options),
('RCurl', '1.95-4.8', ext_options),
('bio3d', '2.2-4', ext_options),
('AUC', '0.3.0', ext_options),
('interpretR', '0.2.4', ext_options),
('cvAUC', '1.1.0', ext_options),
('SuperLearner', '2.0-19', ext_options),
('lpSolve', '5.6.13', ext_options),
('mediation', '4.4.5', ext_options),
('caret', '6.0-70', ext_options),
('adabag', '4.1', ext_options),
('parallelMap', '1.3', ext_options),
('ParamHelpers', '1.7', ext_options),
('ggvis', '0.4.2', ext_options),
('mlr', '2.8', ext_options),
('unbalanced', '2.0', ext_options),
('RSNNS', '0.4-7', ext_options),
('abc.data', '1.0', ext_options),
('abc', '2.1', ext_options),
('lhs', '0.13', 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),
('roxygen2', '5.0.1', ext_options),
('git2r', '0.15.0', ext_options),
('rversions', '1.0.2', ext_options),
('withr', '1.0.2', ext_options),
('devtools', '1.12.0', ext_options),
('Rook', '1.1-1', ext_options),
('rjson', '0.2.15', ext_options),
('Cairo', '1.5-9', ext_options),
('RMTstat', '0.3', ext_options),
('Lmoments', '1.2-3', ext_options),
('distillery', '1.0-2', ext_options),
('extRemes', '2.0-7', ext_options),
('pixmap', '0.4-11', ext_options),
('tkrplot', '0.0-23', ext_options),
('misc3d', '0.8-4', ext_options),
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('ks', '1.10.4', ext_options),
('logcondens', '2.1.4', ext_options),
('Iso', '0.0-17', ext_options),
('penalized', '0.9-47', ext_options),
('clusterRepro', '0.5-1.1', ext_options),
('randomForestSRC', '2.2.0', ext_options),
('sm', '2.2-5.4', ext_options),
('psych', '1.6.6', ext_options),
('pbivnorm', '0.6.0', ext_options),
('lavaan', '0.5-20', ext_options),
('matrixcalc', '1.0-3', ext_options),
('arm', '1.8-6', ext_options),
('mi', '1.0', ext_options),
('htmlwidgets', '0.6', ext_options),
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('DiagrammeR', '0.8.2', ext_options),
('sem', '3.1-7', ext_options),
('jpeg', '0.1-8', ext_options),
('sna', '2.3-2', 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', '1.3.4', ext_options),
('diveRsity', '1.9.89', ext_options),
('doSNOW', '1.0.14', ext_options),
('phangorn', '2.0.4', ext_options),
('geepack', '1.2-0.2', ext_options),
('lubridate', '1.5.6', ext_options),
('biom', '0.3.12', ext_options),
('pim', '2.0.0.2', 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),
]
moduleclass = 'lang'[hpcswadm@amrndhl1157 R]$ eb R-3.3.1-intel-2017.01.eb --robot --package -D
== temporary log file in case of crash /dev/shm/tmp/eb-T4azac/easybuild-_BVXhA.log
Dry run: printing build status of easyconfigs and dependencies
CFGS=/hpc/hpcswadm/easybuild
* [x] $CFGS/M4/M4-1.4.17.eb (module: Core | M4/.1.4.17)
* [x] $CFGS/Bison/Bison-3.0.4.eb (module: Core | Bison/.3.0.4)
* [x] $CFGS/flex/flex-2.6.0.eb (module: Core | flex/.2.6.0)
* [x] $CFGS/zlib/zlib-1.2.8.eb (module: Core | zlib/.1.2.8)
* [x] $CFGS/binutils/binutils-2.27.eb (module: Core | binutils/.2.27)
* [x] $CFGS/ncurses/ncurses-6.0.eb (module: Core | ncurses/.6.0)
* [x] $CFGS/GCCcore/GCCcore-5.4.0.eb (module: Core | GCCcore/.5.4.0)
* [x] $CFGS/zlib/zlib-1.2.8-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | zlib/.1.2.8)
* [x] $CFGS/M4/M4-1.4.17-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | M4/.1.4.17)
* [x] $CFGS/gettext/gettext-0.19.8.eb (module: Core | gettext/.0.19.8)
* [x] $CFGS/Bison/Bison-3.0.4-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | Bison/.3.0.4)
* [x] $CFGS/flex/flex-2.6.0-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | flex/.2.6.0)
* [x] $CFGS/binutils/binutils-2.27-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | binutils/.2.27)
* [x] $CFGS/icc/icc-2017.1.132-GCC-5.4.0-2.27.eb (module: Core | icc/.2017.1.132-GCC-5.4.0-2.27)
* [x] $CFGS/ifort/ifort-2017.1.132-GCC-5.4.0-2.27.eb (module: Core | ifort/.2017.1.132-GCC-5.4.0-2.27)
* [x] $CFGS/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.27.eb (module: Core | iccifort/.2017.1.132-GCC-5.4.0-2.27)
* [x] $CFGS/ncurses/ncurses-6.0-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | ncurses/.6.0)
* [x] $CFGS/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.27.eb (module: Compiler/intel/2017.1.132-GCC-5.4.0-2.27 | impi/2017.1.132)
* [x] $CFGS/iimpi/iimpi-2017.01-GCC-5.4.0-2.27.eb (module: Core | iimpi/.2017.01-GCC-5.4.0-2.27)
* [x] $CFGS/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.27.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | imkl/2017.1.132)
* [x] $CFGS/intel/intel-2017.01.eb (module: Core | intel/2017.01)
* [x] $CFGS/Autoconf/Autoconf-2.69-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Autoconf/.2.69)
* [x] $CFGS/PCRE/PCRE-8.38-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | PCRE/8.38)
* [x] $CFGS/Automake/Automake-1.15-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Automake/.1.15)
* [x] $CFGS/Tcl/Tcl-8.6.5-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Tcl/.8.6.5)
* [x] $CFGS/libpng/libpng-1.6.23-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | libpng/.1.6.23)
* [x] $CFGS/libtool/libtool-2.4.6-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | libtool/.2.4.6)
* [x] $CFGS/libreadline/libreadline-6.3-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | libreadline/.6.3)
* [x] $CFGS/bzip2/bzip2-1.0.6-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | bzip2/.1.0.6)
* [x] $CFGS/Autotools/Autotools-20150215-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Autotools/.20150215)
* [x] $CFGS/SQLite/SQLite-3.13.0-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | SQLite/.3.13.0)
* [x] $CFGS/XZ/XZ-5.2.2-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | XZ/.5.2.2)
* [x] $CFGS/LibTIFF/LibTIFF-4.0.6-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | LibTIFF/.4.0.6)
* [x] $CFGS/NASM/NASM-2.12.02-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | NASM/.2.12.02)
* [x] $CFGS/libjpeg-turbo/libjpeg-turbo-1.5.0-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | libjpeg-turbo/.1.5.0)
* [x] $CFGS/Java/Java-1.8.0_92.eb (module: Core | Java/1.8.0_92)
* [x] $CFGS/Tk/Tk-8.6.5-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Tk/.8.6.5)
* [x] $CFGS/cURL/cURL-7.49.1-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | cURL/.7.49.1)
* [x] $CFGS/libxml2/libxml2-2.9.4-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | libxml2/.2.9.4)
* [x] $CFGS/PROJ/PROJ-4.9.3-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | PROJ/.4.9.3)
* [x] $CFGS/GMP/GMP-6.1.1-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | GMP/6.1.1)
* [x] $CFGS/expat/expat-2.2.0-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | expat/.2.2.0)
* [x] $CFGS/Szip/Szip-2.1-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Szip/.2.1)
* [x] $CFGS/HDF5/HDF5-1.8.16-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | HDF5/1.8.16)
* [x] $CFGS/CMake/CMake-3.7.1-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | CMake/3.7.1)
* [x] $CFGS/freetype/freetype-2.7-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | freetype/.2.7)
* [x] $CFGS/Doxygen/Doxygen-1.8.11-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Doxygen/.1.8.11)
* [ ] $CFGS/pixman/pixman-0.34.0-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | pixman/.0.34.0)
* [x] $CFGS/netCDF/netCDF-4.4.1-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | netCDF/4.4.1)
* [x] $CFGS/GDAL/GDAL-2.1.0-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | GDAL/.2.1.0)
* [ ] $CFGS/libffi/libffi-3.2.1-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | libffi/.3.2.1)
* [ ] $CFGS/gettext/gettext-0.19.8-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | gettext/.0.19.8)
* [x] $CFGS/fontconfig/fontconfig-2.12.1-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | fontconfig/.2.12.1)
* [ ] $CFGS/Python/Python-2.7.12-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | Python/2.7.12)
* [x] $CFGS/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | pkg-config/.0.29.1)
* [ ] $CFGS/GLib/GLib-2.49.5-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | GLib/.2.49.5)
* [ ] $CFGS/X11/X11-20160819-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | X11/.20160819)
* [ ] $CFGS/cairo/cairo-1.14.6-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | cairo/.1.14.6)
* [ ] $CFGS/R/R-3.3.1-intel-2017.01.eb (module: MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132 | R/3.3.1)
== Temporary log file(s) /dev/shm/tmp/eb-T4azac/easybuild-_BVXhA.log* have been removed.
== Temporary directory /dev/shm/tmp/eb-T4azac has been removed.
[hpcswadm@amrndhl1157 R]$ eb R-3.3.1-intel-2017.01.eb --robot --package
== temporary log file in case of crash /dev/shm/tmp/eb-unNqWt/easybuild-nHlNol.log
== resolving dependencies ...
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/pixman/pixman-0.34.0-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/pixman/.0.34.0...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/pixman/0.34.0/easybuild/easybuild-pixman-0.34.0-20170426.135916.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/libffi/libffi-3.2.1-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/libffi/.3.2.1...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/libffi/3.2.1/easybuild/easybuild-libffi-3.2.1-20170426.140020.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/gettext/gettext-0.19.8-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/gettext/.0.19.8...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/gettext/0.19.8/easybuild/easybuild-gettext-0.19.8-20170426.141646.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/X11/X11-20160819-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/X11/.20160819...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== installing bundle component xorg-macros v1.19.0 (1/71)...
== installing bundle component libpthread-stubs v0.3 (2/71)...
== installing bundle component bigreqsproto v1.1.2 (3/71)...
== installing bundle component compositeproto v0.4.2 (4/71)...
== installing bundle component damageproto v1.2.1 (5/71)...
== installing bundle component dmxproto v2.3.1 (6/71)...
== installing bundle component dri2proto v2.8 (7/71)...
== installing bundle component dri3proto v1.0 (8/71)...
== installing bundle component fixesproto v5.0 (9/71)...
== installing bundle component fontsproto v2.1.3 (10/71)...
== installing bundle component glproto v1.4.17 (11/71)...
== installing bundle component inputproto v2.3.1 (12/71)...
== installing bundle component kbproto v1.0.7 (13/71)...
== installing bundle component presentproto v1.0 (14/71)...
== installing bundle component randrproto v1.5.0 (15/71)...
== installing bundle component recordproto v1.14.2 (16/71)...
== installing bundle component renderproto v0.11 (17/71)...
== installing bundle component resourceproto v1.2.0 (18/71)...
== installing bundle component scrnsaverproto v1.2.2 (19/71)...
== installing bundle component videoproto v2.3.3 (20/71)...
== installing bundle component xcmiscproto v1.2.2 (21/71)...
== installing bundle component xextproto v7.3.0 (22/71)...
== installing bundle component xf86bigfontproto v1.2.0 (23/71)...
== installing bundle component xf86dgaproto v2.1 (24/71)...
== installing bundle component xf86driproto v2.1.1 (25/71)...
== installing bundle component xf86vidmodeproto v2.3.1 (26/71)...
== installing bundle component xineramaproto v1.2.1 (27/71)...
== installing bundle component xproto v7.0.28 (28/71)...
== installing bundle component libXau v1.0.8 (29/71)...
== installing bundle component libXdmcp v1.1.2 (30/71)...
== installing bundle component xcb-proto v1.11 (31/71)...
== installing bundle component libxcb v1.11.1 (32/71)...
== installing bundle component xtrans v1.3.5 (33/71)...
== installing bundle component libxkbcommon v0.6.1 (34/71)...
== installing bundle component libX11 v1.6.3 (35/71)...
== installing bundle component libXext v1.3.3 (36/71)...
== installing bundle component libFS v1.0.7 (37/71)...
== installing bundle component libICE v1.0.9 (38/71)...
== installing bundle component libSM v1.2.2 (39/71)...
== installing bundle component libXScrnSaver v1.2.2 (40/71)...
== installing bundle component libXt v1.1.5 (41/71)...
== installing bundle component libXmu v1.1.2 (42/71)...
== installing bundle component libXpm v3.5.11 (43/71)...
== installing bundle component libXaw v1.0.13 (44/71)...
== installing bundle component libXfixes v5.0.2 (45/71)...
== installing bundle component libXcomposite v0.4.4 (46/71)...
== installing bundle component libXrender v0.9.9 (47/71)...
== installing bundle component libXcursor v1.1.14 (48/71)...
== installing bundle component libXdamage v1.1.4 (49/71)...
== installing bundle component libfontenc v1.1.3 (50/71)...
== installing bundle component libXfont v1.5.1 (51/71)...
== installing bundle component libXft v2.3.2 (52/71)...
== installing bundle component libXi v1.7.6 (53/71)...
== installing bundle component libXinerama v1.1.3 (54/71)...
== installing bundle component libXrandr v1.5.0 (55/71)...
== installing bundle component libXres v1.0.7 (56/71)...
== installing bundle component libXtst v1.2.2 (57/71)...
== installing bundle component libXv v1.0.10 (58/71)...
== installing bundle component libXvMC v1.0.9 (59/71)...
== installing bundle component libXxf86dga v1.1.4 (60/71)...
== installing bundle component libXxf86vm v1.1.4 (61/71)...
== installing bundle component libdmx v1.1.3 (62/71)...
== installing bundle component libpciaccess v0.13.4 (63/71)...
== installing bundle component libxkbfile v1.0.9 (64/71)...
== installing bundle component libxshmfence v1.2 (65/71)...
== installing bundle component xcb-util v0.4.0 (66/71)...
== installing bundle component xcb-util-image v0.4.0 (67/71)...
== installing bundle component xcb-util-keysyms v0.4.0 (68/71)...
== installing bundle component xcb-util-renderutil v0.3.9 (69/71)...
== installing bundle component xcb-util-wm v0.4.1 (70/71)...
== installing bundle component xcb-util-cursor v0.1.3 (71/71)...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/X11/20160819/easybuild/easybuild-X11-20160819-20170426.151450.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/Python/Python-2.7.12-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/Python/2.7.12...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== installing extension setuptools 23.1.0 (1/30)...
== installing extension pip 8.1.2 (2/30)...
== installing extension nose 1.3.7 (3/30)...
== installing extension numpy 1.11.1 (4/30)...
== installing extension scipy 0.17.1 (5/30)...
== installing extension blist 1.3.6 (6/30)...
== installing extension mpi4py 1.3.1 (7/30)...
== installing extension paycheck 1.0.2 (8/30)...
== installing extension pbr 1.10.0 (9/30)...
== installing extension lockfile 0.12.2 (10/30)...
== installing extension Cython 0.24 (11/30)...
== installing extension six 1.10.0 (12/30)...
== installing extension dateutil 2.5.3 (13/30)...
== installing extension deap 1.0.2 (14/30)...
== installing extension decorator 4.0.10 (15/30)...
== installing extension arff 2.1.0 (16/30)...
== installing extension pycrypto 2.6.1 (17/30)...
== installing extension ecdsa 0.13 (18/30)...
== installing extension cryptography 1.4 (19/30)...
== installing extension paramiko 2.0.1 (20/30)...
== installing extension pyparsing 2.1.5 (21/30)...
== installing extension netifaces 0.10.4 (22/30)...
== installing extension netaddr 0.7.18 (23/30)...
== installing extension funcsigs 1.0.2 (24/30)...
== installing extension mock 2.0.0 (25/30)...
== installing extension pytz 2016.4 (26/30)...
== installing extension pandas 0.18.1 (27/30)...
== installing extension enum34 1.1.6 (28/30)...
== installing extension bitstring 3.1.5 (29/30)...
== installing extension virtualenv 15.0.2 (30/30)...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/Python/2.7.12/easybuild/easybuild-Python-2.7.12-20170426.155133.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/GLib/GLib-2.49.5-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/GLib/.2.49.5...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/GLib/2.49.5/easybuild/easybuild-GLib-2.49.5-20170426.155809.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/cairo/cairo-1.14.6-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/cairo/.1.14.6...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/cairo/1.14.6/easybuild/easybuild-cairo-1.14.6-20170426.160431.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/R/R-3.3.1-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/R/3.3.1...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== installing extension base (1/414)...
== installing extension datasets (2/414)...
== installing extension graphics (3/414)...
== installing extension grDevices (4/414)...
== installing extension grid (5/414)...
== installing extension methods (6/414)...
== installing extension splines (7/414)...
== installing extension stats (8/414)...
== installing extension stats4 (9/414)...
== installing extension tools (10/414)...
== installing extension utils (11/414)...
== installing extension Rmpi 0.6-6 (12/414)...
== installing extension abind 1.4-3 (13/414)...
== installing extension magic 1.5-6 (14/414)...
== installing extension geometry 0.3-6 (15/414)...
== installing extension bit 1.1-12 (16/414)...
== installing extension filehash 2.3 (17/414)...
== installing extension ff 2.2-13 (18/414)...
== installing extension bnlearn 4.0 (19/414)...
== installing extension bootstrap 2015.2 (20/414)...
== installing extension combinat 0.0-8 (21/414)...
== installing extension deal 1.2-37 (22/414)...
== installing extension fdrtool 1.2.15 (23/414)...
== installing extension formatR 1.4 (24/414)...
== installing extension gtools 3.5.0 (25/414)...
== installing extension gdata 2.17.0 (26/414)...
== installing extension GSA 1.03 (27/414)...
== installing extension highr 0.6 (28/414)...
== installing extension infotheo 1.2.0 (29/414)...
== installing extension lars 1.2 (30/414)...
== installing extension lazy 1.2-15 (31/414)...
== installing extension kernlab 0.9-24 (32/414)...
== installing extension mime 0.5 (33/414)...
== installing extension markdown 0.7.7 (34/414)...
== installing extension mlbench 2.1-1 (35/414)...
== installing extension NLP 0.1-9 (36/414)...
== installing extension mclust 5.2 (37/414)...
== installing extension RANN 2.5 (38/414)...
== installing extension rmeta 2.16 (39/414)...
== installing extension segmented 0.5-1.4 (40/414)...
== installing extension som 0.3-5.1 (41/414)...
== installing extension SuppDists 1.1-9.2 (42/414)...
== installing extension stabledist 0.7-0 (43/414)...
== installing extension survivalROC 1.0.3 (44/414)...
== installing extension pspline 1.0-17 (45/414)...
== installing extension timeDate 3012.100 (46/414)...
== installing extension longmemo 1.0-0 (47/414)...
== installing extension ADGofTest 0.3 (48/414)...
== installing extension ade4 1.7-4 (49/414)...
== installing extension AlgDesign 1.1-7.3 (50/414)...
== installing extension base64enc 0.1-3 (51/414)...
== installing extension BH 1.60.0-2 (52/414)...
== installing extension brew 1.0-6 (53/414)...
== installing extension Brobdingnag 1.2-4 (54/414)...
== installing extension corpcor 1.6.8 (55/414)...
== installing extension longitudinal 1.1.12 (56/414)...
== installing extension backports 1.0.3 (57/414)...
== installing extension checkmate 1.8.1 (58/414)...
== installing extension cubature 1.1-2 (59/414)...
== installing extension DEoptimR 1.0-6 (60/414)...
== installing extension digest 0.6.9 (61/414)...
== installing extension fastmatch 1.0-4 (62/414)...
== installing extension ffbase 0.12.3 (63/414)...
== installing extension iterators 1.0.8 (64/414)...
== installing extension maps 3.1.0 (65/414)...
== installing extension nnls 1.4 (66/414)...
== installing extension sendmailR 1.2-1 (67/414)...
== installing extension spam 1.3-0 (68/414)...
== installing extension subplex 1.1-6 (69/414)...
== installing extension stringi 1.1.1 (70/414)...
== installing extension magrittr 1.5 (71/414)...
== installing extension stringr 1.0.0 (72/414)...
== installing extension evaluate 0.9 (73/414)...
== installing extension logspline 2.1.9 (74/414)...
== installing extension ncbit 2013.03.29 (75/414)...
== installing extension permute 0.9-0 (76/414)...
== installing extension plotrix 3.6-2 (77/414)...
== installing extension randomForest 4.6-12 (78/414)...
== installing extension scatterplot3d 0.3-37 (79/414)...
== installing extension SparseM 1.7 (80/414)...
== installing extension tripack 1.3-7 (81/414)...
== installing extension irace 1.07 (82/414)...
== installing extension rJava 0.9-8 (83/414)...
== installing extension lattice 0.20-33 (84/414)...
== installing extension RColorBrewer 1.1-2 (85/414)...
== installing extension latticeExtra 0.6-28 (86/414)...
== installing extension Matrix 1.2-6 (87/414)...
== installing extension png 0.1-7 (88/414)...
== installing extension Rcpp 0.12.5 (89/414)...
== installing extension RcppArmadillo 0.7.100.3.1 (90/414)...
== installing extension plyr 1.8.4 (91/414)...
== installing extension pROC 1.8 (92/414)...
== installing extension quadprog 1.5-5 (93/414)...
== installing extension BB 2014.10-1 (94/414)...
== installing extension BBmisc 1.9 (95/414)...
== installing extension fail 1.3 (96/414)...
== installing extension rlecuyer 0.3-4 (97/414)...
== installing extension snow 0.4-1 (98/414)...
== installing extension MASS 7.3-45 (99/414)...
== installing extension tree 1.0-37 (100/414)...
== installing extension pls 2.5-0 (101/414)...
== installing extension class 7.3-14 (102/414)...
== installing extension e1071 1.6-7 (103/414)...
== installing extension nnet 7.3-12 (104/414)...
== installing extension nlme 3.1-128 (105/414)...
== installing extension minqa 1.2.4 (106/414)...
== installing extension RcppEigen 0.3.2.8.1 (107/414)...
== installing extension MatrixModels 0.4-1 (108/414)...
== installing extension quantreg 5.26 (109/414)...
== installing extension mgcv 1.8-12 (110/414)...
== installing extension colorspace 1.2-6 (111/414)...
== installing extension robustbase 0.92-6 (112/414)...
== installing extension sp 1.2-3 (113/414)...
== installing extension zoo 1.7-13 (114/414)...
== installing extension lmtest 0.9-34 (115/414)...
== installing extension vcd 1.4-1 (116/414)...
== installing extension snowfall 1.84-6.1 (117/414)...
== installing extension rpart 4.1-10 (118/414)...
== installing extension survival 2.39-5 (119/414)...
== installing extension mice 2.25 (120/414)...
== installing extension urca 1.2-9 (121/414)...
== installing extension fracdiff 1.4-2 (122/414)...
== installing extension logistf 1.21 (123/414)...
== installing extension akima 0.5-12 (124/414)...
== installing extension bitops 1.0-6 (125/414)...
== installing extension boot 1.3-18 (126/414)...
== installing extension mixtools 1.0.4 (127/414)...
== installing extension cluster 2.0.4 (128/414)...
== installing extension gclus 1.3.1 (129/414)...
== installing extension coda 0.18-1 (130/414)...
== installing extension codetools 0.2-14 (131/414)...
== installing extension foreach 1.4.3 (132/414)...
== installing extension doMC 1.3.4 (133/414)...
== installing extension DBI 0.4-1 (134/414)...
== installing extension foreign 0.8-66 (135/414)...
== installing extension gam 1.12 (136/414)...
== installing extension gamlss.data 4.3-4 (137/414)...
== installing extension gamlss.dist 4.3-6 (138/414)...
== installing extension hwriter 1.3.2 (139/414)...
== installing extension KernSmooth 2.23-15 (140/414)...
== installing extension xts 0.9-7 (141/414)...
== installing extension TTR 0.23-1 (142/414)...
== installing extension quantmod 0.4-5 (143/414)...
== installing extension mnormt 1.5-4 (144/414)...
== installing extension mvtnorm 1.0-5 (145/414)...
== installing extension pcaPP 1.9-60 (146/414)...
== installing extension numDeriv 2014.2-1 (147/414)...
== installing extension lava 1.4.3 (148/414)...
== installing extension prodlim 1.5.7 (149/414)...
== installing extension pscl 1.4.9 (150/414)...
== installing extension RSQLite 1.0.0 (151/414)...
== installing extension BatchJobs 1.6 (152/414)...
== installing extension sandwich 2.3-4 (153/414)...
== installing extension sfsmisc 1.1-0 (154/414)...
== installing extension spatial 7.3-11 (155/414)...
== installing extension VGAM 1.0-2 (156/414)...
== installing extension waveslim 1.7.5 (157/414)...
== installing extension xtable 1.8-2 (158/414)...
== installing extension profileModel 0.5-9 (159/414)...
== installing extension brglm 0.5-9 (160/414)...
== installing extension deSolve 1.13 (161/414)...
== installing extension tseriesChaos 0.1-13 (162/414)...
== installing extension tseries 0.10-35 (163/414)...
== installing extension fastICA 1.2-0 (164/414)...
== installing extension R.methodsS3 1.7.1 (165/414)...
== installing extension R.oo 1.20.0 (166/414)...
== installing extension cgdsr 1.2.5 (167/414)...
== installing extension R.utils 2.3.0 (168/414)...
== installing extension R.matlab 3.6.0 (169/414)...
== installing extension gbm 2.1.1 (170/414)...
== installing extension dichromat 2.0-0 (171/414)...
== installing extension Formula 1.2-1 (172/414)...
== installing extension acepack 1.3-3.3 (173/414)...
== installing extension reshape2 1.4.1 (174/414)...
== installing extension gtable 0.2.0 (175/414)...
== installing extension munsell 0.4.3 (176/414)...
== installing extension labeling 0.3 (177/414)...
== installing extension scales 0.4.0 (178/414)...
== installing extension proto 0.3-10 (179/414)...
== installing extension ggplot2 2.1.0 (180/414)...
== installing extension gridExtra 2.2.1 (181/414)...
== installing extension chron 2.3-47 (182/414)...
== installing extension data.table 1.9.6 (183/414)...
== installing extension Hmisc 3.17-4 (184/414)...
== installing extension fastcluster 1.1.20 (185/414)...
== installing extension registry 0.3 (186/414)...
== installing extension pkgmaker 0.22 (187/414)...
== installing extension rngtools 1.2.4 (188/414)...
== installing extension doParallel 1.0.10 (189/414)...
== installing extension gridBase 0.4-7 (190/414)...
== installing extension NMF 0.20.6 (191/414)...
== installing extension irlba 2.0.0 (192/414)...
== installing extension igraph 1.0.1 (193/414)...
== installing extension GeneNet 1.2.13 (194/414)...
== installing extension ape 3.5 (195/414)...
== installing extension htmltools 0.3.5 (196/414)...
== installing extension RJSONIO 1.3-0 (197/414)...
== installing extension caTools 1.17.1 (198/414)...
== installing extension gplots 3.0.1 (199/414)...
== installing extension ROCR 1.0-7 (200/414)...
== installing extension httpuv 1.3.3 (201/414)...
== installing extension R6 2.1.2 (202/414)...
== installing extension jsonlite 1.0 (203/414)...
== installing extension rjson 0.2.15 (204/414)...
== installing extension shiny 0.13.2 (205/414)...
== installing extension seqinr 3.2-0 (206/414)...
== installing extension LearnBayes 2.15 (207/414)...
== installing extension deldir 0.1-12 (208/414)...
== installing extension gmodels 2.16.2 (209/414)...
== installing extension spdep 0.6-5 (210/414)...
== installing extension assertthat 0.1 (211/414)...
== installing extension lazyeval 0.2.0 (212/414)...
== installing extension tibble 1.1 (213/414)...
== installing extension dplyr 0.5.0 (214/414)...
== installing extension vegan 2.4-0 (215/414)...
== installing extension adegenet 2.0.1 (216/414)...
== installing extension rncl 0.6.0 (217/414)...
== installing extension XML 3.98-1.4 (218/414)...
== installing extension memoise 1.0.0 (219/414)...
== installing extension crayon 1.3.2 (220/414)...
== installing extension praise 1.0.0 (221/414)...
== installing extension testthat 1.0.2 (222/414)...
== installing extension yaml 2.1.13 (223/414)...
== installing extension knitr 1.13 (224/414)...
== installing extension rmarkdown 0.9.6 (225/414)...
== installing extension curl 0.9.7 (226/414)...
== installing extension openssl 0.9.4 (227/414)...
== installing extension httr 1.2.1 (228/414)...
== installing extension reshape 0.8.5 (229/414)...
== installing extension xml2 1.0.0 (230/414)...
== installing extension bold 0.3.5 (231/414)...
== installing extension rredlist 0.1.0 (232/414)...
== installing extension rentrez 1.0.2 (233/414)...
== installing extension rotl 3.0.0 (234/414)...
== installing extension taxize 0.7.8 (235/414)...
== installing extension tidyr 0.5.1 (236/414)...
== installing extension uuid 0.1-2 (237/414)...
== installing extension RNeXML 2.0.7 (238/414)...
== installing extension phylobase 0.8.2 (239/414)...
== installing extension adephylo 1.1-6 (240/414)...
== installing extension animation 2.4 (241/414)...
== installing extension bigmemory.sri 0.1.3 (242/414)...
== installing extension bigmemory 4.5.19 (243/414)...
== installing extension calibrate 1.7.2 (244/414)...
== installing extension clusterGeneration 1.3.4 (245/414)...
== installing extension raster 2.5-8 (246/414)...
== installing extension dismo 1.1-1 (247/414)...
== installing extension expm 0.999-0 (248/414)...
== installing extension extrafontdb 1.0 (249/414)...
== installing extension Rttf2pt1 1.3.4 (250/414)...
== installing extension extrafont 0.17 (251/414)...
== installing extension fields 8.4-1 (252/414)...
== installing extension shapefiles 0.7 (253/414)...
== installing extension fossil 0.3.7 (254/414)...
== installing extension geiger 2.0.6 (255/414)...
== installing extension glmnet 2.0-5 (256/414)...
== installing extension rgl 0.95.1441 (257/414)...
== installing extension labdsv 1.8-0 (258/414)...
== installing extension stabs 0.5-1 (259/414)...
== installing extension modeltools 0.2-21 (260/414)...
== installing extension strucchange 1.5-1 (261/414)...
== installing extension TH.data 1.0-7 (262/414)...
== installing extension multcomp 1.4-5 (263/414)...
== installing extension coin 1.1-2 (264/414)...
== installing extension party 1.0-25 (265/414)...
== installing extension mboost 2.6-0 (266/414)...
== installing extension msm 1.6.1 (267/414)...
== installing extension nor1mix 1.2-1 (268/414)...
== installing extension np 0.60-2 (269/414)...
== installing extension polynom 1.3-8 (270/414)...
== installing extension polspline 1.1.12 (271/414)...
== installing extension rms 4.5-0 (272/414)...
== installing extension RWekajars 3.9.0-1 (273/414)...
== installing extension RWeka 0.4-29 (274/414)...
== installing extension slam 0.1-35 (275/414)...
== installing extension tm 0.6-2 (276/414)...
== installing extension TraMineR 1.8-12 (277/414)...
== installing extension chemometrics 1.3.9 (278/414)...
== installing extension FNN 1.1 (279/414)...
== installing extension ipred 0.9-5 (280/414)...
== installing extension statmod 1.4.24 (281/414)...
== installing extension miscTools 0.6-16 (282/414)...
== installing extension maxLik 1.3-4 (283/414)...
== installing extension mlogit 0.2-4 (284/414)...
== installing extension getopt 1.20.0 (285/414)...
== installing extension gsalib 2.1 (286/414)...
== installing extension optparse 1.3.2 (287/414)...
== installing extension klaR 0.6-12 (288/414)...
== installing extension neuRosim 0.2-12 (289/414)...
== installing extension locfit 1.5-9.1 (290/414)...
== installing extension GGally 1.2.0 (291/414)...
== installing extension beanplot 1.2 (292/414)...
== installing extension clValid 0.6-6 (293/414)...
== installing extension matrixStats 0.50.2 (294/414)...
== installing extension DiscriMiner 0.1-29 (295/414)...
== installing extension ellipse 0.3-8 (296/414)...
== installing extension leaps 2.9 (297/414)...
== installing extension nloptr 1.0.4 (298/414)...
== installing extension lme4 1.1-12 (299/414)...
== installing extension pbkrtest 0.4-6 (300/414)...
== installing extension car 2.1-2 (301/414)...
== installing extension flashClust 1.01-2 (302/414)...
== installing extension FactoMineR 1.33 (303/414)...
== installing extension flexclust 1.3-4 (304/414)...
== installing extension flexmix 2.3-13 (305/414)...
== installing extension prabclus 2.2-6 (306/414)...
== installing extension diptest 0.75-7 (307/414)...
== installing extension trimcluster 0.1-2 (308/414)...
== installing extension fpc 2.1-10 (309/414)...
== installing extension BiasedUrn 1.07 (310/414)...
== installing extension TeachingDemos 2.10 (311/414)...
== installing extension kohonen 2.0.19 (312/414)...
== installing extension base64 2.0 (313/414)...
== installing extension doRNG 1.6 (314/414)...
== installing extension nleqslv 3.0.2 (315/414)...
== installing extension RGCCA 2.0 (316/414)...
== installing extension pheatmap 1.0.8 (317/414)...
== installing extension openxlsx 3.0.0 (318/414)...
== installing extension pvclust 2.0-0 (319/414)...
== installing extension RCircos 1.1.3 (320/414)...
== installing extension lambda.r 1.1.7 (321/414)...
== installing extension futile.options 1.0.0 (322/414)...
== installing extension futile.logger 1.4.1 (323/414)...
== installing extension VennDiagram 1.6.17 (324/414)...
== installing extension xlsxjars 0.6.1 (325/414)...
== installing extension xlsx 0.5.7 (326/414)...
== installing extension forecast 7.1 (327/414)...
== installing extension fma 2.2 (328/414)...
== installing extension expsmooth 2.3 (329/414)...
== installing extension fpp 0.5 (330/414)...
== installing extension maptools 0.8-39 (331/414)...
== installing extension deldir 0.1-12 (332/414)...
== installing extension tensor 1.5 (333/414)...
== installing extension polyclip 1.5-6 (334/414)...
== installing extension goftest 1.0-3 (335/414)...
== installing extension spatstat 1.46-1 (336/414)...
== installing extension rgdal 1.1-10 (337/414)...
== installing extension gdalUtils 2.0.1.7 (338/414)...
== installing extension pracma 1.9.3 (339/414)...
== installing extension RCurl 1.95-4.8 (340/414)...
== installing extension bio3d 2.2-4 (341/414)...
== installing extension AUC 0.3.0 (342/414)...
== installing extension interpretR 0.2.4 (343/414)...
== installing extension cvAUC 1.1.0 (344/414)...
== installing extension SuperLearner 2.0-19 (345/414)...
== installing extension lpSolve 5.6.13 (346/414)...
== installing extension mediation 4.4.5 (347/414)...
== installing extension caret 6.0-70 (348/414)...
== installing extension adabag 4.1 (349/414)...
== installing extension parallelMap 1.3 (350/414)...
== installing extension ParamHelpers 1.7 (351/414)...
== installing extension ggvis 0.4.2 (352/414)...
== installing extension mlr 2.8 (353/414)...
== installing extension unbalanced 2.0 (354/414)...
== installing extension RSNNS 0.4-7 (355/414)...
== installing extension abc.data 1.0 (356/414)...
== installing extension abc 2.1 (357/414)...
== installing extension lhs 0.13 (358/414)...
== installing extension tensorA 0.36 (359/414)...
== installing extension EasyABC 1.5 (360/414)...
== installing extension shape 1.4.2 (361/414)...
== installing extension whisker 0.3-2 (362/414)...
== installing extension rstudioapi 0.6 (363/414)...
== installing extension roxygen2 5.0.1 (364/414)...
== installing extension git2r 0.15.0 (365/414)...
== installing extension rversions 1.0.2 (366/414)...
== installing extension withr 1.0.2 (367/414)...
== installing extension devtools 1.12.0 (368/414)...
== installing extension Rook 1.1-1 (369/414)...
== installing extension rjson 0.2.15 (370/414)...
== installing extension Cairo 1.5-9 (371/414)...
== installing extension RMTstat 0.3 (372/414)...
== installing extension Lmoments 1.2-3 (373/414)...
== installing extension distillery 1.0-2 (374/414)...
== installing extension extRemes 2.0-7 (375/414)...
== installing extension pixmap 0.4-11 (376/414)...
== installing extension tkrplot 0.0-23 (377/414)...
== installing extension misc3d 0.8-4 (378/414)...
== installing extension multicool 0.1-9 (379/414)...
== installing extension ks 1.10.4 (380/414)...
== installing extension logcondens 2.1.4 (381/414)...
== installing extension Iso 0.0-17 (382/414)...
== installing extension penalized 0.9-47 (383/414)...
== installing extension clusterRepro 0.5-1.1 (384/414)...
== installing extension randomForestSRC 2.2.0 (385/414)...
== installing extension sm 2.2-5.4 (386/414)...
== installing extension psych 1.6.6 (387/414)...
== installing extension pbivnorm 0.6.0 (388/414)...
== installing extension lavaan 0.5-20 (389/414)...
== installing extension matrixcalc 1.0-3 (390/414)...
== installing extension arm 1.8-6 (391/414)...
== installing extension mi 1.0 (392/414)...
== installing extension htmlwidgets 0.6 (393/414)...
== installing extension visNetwork 1.0.1 (394/414)...
== installing extension DiagrammeR 0.8.2 (395/414)...
== installing extension sem 3.1-7 (396/414)...
== installing extension jpeg 0.1-8 (397/414)...
== installing extension sna 2.3-2 (398/414)...
== installing extension glasso 1.8 (399/414)...
== installing extension huge 1.2.7 (400/414)...
== installing extension d3Network 0.5.2.1 (401/414)...
== installing extension ggm 2.3 (402/414)...
== installing extension qgraph 1.3.4 (403/414)...
== installing extension diveRsity 1.9.89 (404/414)...
== installing extension doSNOW 1.0.14 (405/414)...
== installing extension phangorn 2.0.4 (406/414)...
== installing extension geepack 1.2-0.2 (407/414)...
== installing extension lubridate 1.5.6 (408/414)...
== installing extension biom 0.3.12 (409/414)...
== installing extension pim 2.0.0.2 (410/414)...
== installing extension minpack.lm 1.2-1 (411/414)...
== installing extension rootSolve 1.7 (412/414)...
== installing extension diagram 1.6.3 (413/414)...
== installing extension FME 1.3.5 (414/414)...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/R/3.3.1/easybuild/easybuild-R-3.3.1-20170426.191344.log, /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/R/3.3.1/easybuild/easybuild-R-3.3.1-20170426.191344.log.1, /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/R/3.3.1/easybuild/easybuild-R-3.3.1-20170426.191344.log.2
== Build succeeded for 8 out of 8
== Temporary log file(s) /dev/shm/tmp/eb-unNqWt/easybuild-nHlNol.log* have been removed.
== Temporary directory /dev/shm/tmp/eb-unNqWt has been removed.
Micket
commented
5 months ago This is long since outdated, and we have current builds of PROJ, R and rgdal so i'm sure whatever issue was here isn't relevant anymore.
I am running into the same issue when I tried build rgdal with foss-2016 toolchain. I am now trying with intel-2017.01. I don't know how to fix this, I am missing something.
Log Files in 3 parts : easybuild-R-3.3.1-intel-2017.01.part1.txt easybuild-R-3.3.1-intel-2017.01.part2.txt easybuild-R-3.3.1-intel-2017.01.part3.txt