diff --git a/R-devel-2017-02-02-1.build.sh b/R-devel-2017-02-02-1.build.sh new file mode 100755 index 0000000..d2e6824 --- /dev/null +++ b/R-devel-2017-02-02-1.build.sh @@ -0,0 +1,132 @@ +#! /bin/bash + +PKG=R-devel +VERSION=2017-02-02 +BUILD=1 +PREFIX=/pkg/$PKG-$VERSION-$BUILD +#PREFIX=/dev/shm/$PKG-$VERSION-$BUILD + +set -xe +umask 022 + +BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp +test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR +mkdir -p $BUILD_TMPDIR/home +export TMPDIR=$BUILD_TMPDIR +export HOME=$BUILD_TMPDIR/home + +exec $PREFIX/profile <<-EOF + PATH=$PREFIX/bin:\$PATH +EOF +. $PREFIX/profile + +export MAKEFLAGS="-j $(nproc)" + +BUILDDIR=$PREFIX/build + +mkdir -p $BUILDDIR +cd $BUILDDIR + +test -s R-devel_$VERSION.tar.gz || cp /src/mariux/download/R-devel_$VERSION.tar.gz . +test -d R-devel || tar xvf R-devel_$VERSION.tar.gz +cd R-devel +./configure \ + --prefix=$PREFIX \ + --with-pic \ + --with-recommended-packages \ + --enable-shared \ + --with-x \ + --enable-R-shlib \ + LDFLAGS=-Wl,-rpath,$PREFIX/lib64/R/lib +make +TZ="CEST" make check +make install + +cd $BUILDDIR + +R --quiet --vanilla -e "update.packages(repos='https://cran.uni-muenster.de/',ask=FALSE)" + +# Some packages ( at least rhdf5 ) have problems with parallel builds +# bug report and suggested fix sent to maintainer +# +unset MAKEFLAGS + +# Bioconductor base packages +# +test -e biocLite.R || wget https://bioconductor.org/biocLite.R +R --quiet --vanilla -e "source('biocLite.R');biocLite()" + +# CRAN packages +# we install with BiocInstaller (biocLite), because some CRAN packages +# have dependencies into Bioconductor packages +# +PKG=( + AdequacyModel BBmisc BH BatchJobs BayesDA Boruta BradleyTerry2 C50 Cairo CircStats Ckmeans.1d.dp DBI + DEoptimR ExomeDepth FField Formula GGally GeneNet GlobalOptions HMM HardyWeinberg Hmisc KernSmooth + LSD Lahman LearnBayes MASS MatrixEQTL Matrix PerfMeas R.cache R.methodsS3 R.oo R.utils R2HTML R6 + RCircos RColorBrewer RCurl RGtk2 RJSONIO RMySQL ROCR RRF RSQLite RUnit RWeka RWekajars RcppArmadillo + RcppEigen Rcpp SparseM SuppDists TFMPvalue TH.data TSP TeachingDemos VGAM VennDiagram WGCNA XML + abind acepack ade4 akima aod ape ash assertthat base64 base64enc bdsmatrix beanplot beeswarm bgmm + bigmemory.sri bigmemory bigrf bit bitops boot bootstrap bpca brew brglm c060 caTools car caret + checkmate chron circlize class clue cluster coda codetools coin colorspace combinat corpcor + corrgram corrplot crayon curl data.table deldir devtools dichromat digest dismo doMC doParallel + doRNG doSNOW dostats dplyr dtw dynamicTreeCut e1071 earth elasticnet energy entropy evaluate evd + exactRankTests fANCOVA fail fastICA fastcluster fastmatch fdrtool fields filehash flashClust foreach + foreign formatR futile.logger futile.options gRbase gbm gclus gdata genetics getopt ggm ggplot2 git2r + glasso glmnet gmp gnm gplots gridBase gridExtra gridSVG grofit gsubfn gtable gtools h2o haplo.stats + harvestr hash hdi hdrcde hexbin hflights highr hsmm htmltools httpuv httr hwriter igraph inline intervals + ipred iterators itertools jsonlite kernlab knitr ks labeling lambda.r lars latticeExtra lattice lava + lazyeval leaps lhs linprog lint lintr lme4 lmtest locfit longitudinal lpSolve magrittr manipulate mapproj + maps maptools maptree markdown matrixStats mclust mda memoise meta mgcv mice microbenchmark mime minqa + misc3d mitools mixtools mlegp mnormt modeltools multcomp multicool munsell mvtnorm nleqslv nlme nloptr + nnet nor1mix numDeriv optparse pROC pamr party partykit pbapply pbkrtest pcalg penalizedSVM peperr pheatmap + pkgmaker plotmo plotrix pls plus plyr prodlim profileModel proto proxy pwr qtl quadprog quantreg qvcalc + rFerns rJava randomForest randomGLM raster rbenchmark registry relaimpo relimp reshape2 reshape rex + rggobi rgl rjson rlecuyer rmarkdown rmeta rngtools robustbase roxygen2 rpart rstudioapi rversions sandwich + scales scalreg scatterplot3d sda segmented sendmailR seqinr seriation setRNG setwidth sfsmisc shape + shiny sm snow snowfall som sp spam spatial spdep splancs spls statmod stepPlr stringdist stringi stringr + strucchange survey survival survrec svMisc svTools tables testthat tgp tidyr vcd venneuler verification + waveslim whisker xlsx xlsxjars xml2 xtable yaml zipfR zoo +) + +P=$(printf ',"%s"' "${PKG[@]}") # ,"ACME","ALL".... +P=${P#,} # "ACME","ALL",... + +R --quiet --vanilla -e "source('biocLite.R');biocLite(c($P))" + +# Bioconductor packages +# +PKG=( + ACME ALL AnnotationDbi AnnotationForge BSgenome.Ecoli.NCBI.20080805 BSgenome BeadDataPackR BioNet Biobase + BiocGenerics BiocInstaller BiocParallel Biostrings CNEr Category CellNOptR ChIPpeakAnno DESeq2 DESeq + DNAcopy DirichletMultinomial FDb.InfiniumMethylation.hg19 GEOquery GO.db GOTHiC GOstats GSEABase GSEAlm + GenomeGraphs GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GlobalAncova Gviz HTqPCR + Homo.sapiens IRanges MEDIPS OmicCircos OrganismDbi RBGL ROC Rgraphviz Rhtslib Rsamtools S4Vectors SVGAnnotation + ShortRead TFBSTools TxDb.Hsapiens.UCSC.hg19.knownGene VariantAnnotation XVector affyPLM affy affyio + annotate arrayQualityMetrics bamsignals beadarray biomaRt biovizBase bumphunter chipseq cummeRbund easyRNASeq + edgeR exomeCopy gcrma genefilter geneplotter genomeIntervals ggbio globaltest graph hgu95av2 hgu95av2cdf + illuminaio impute limma lumi methylumi minfi multtest muscle org.Hs.eg.db pcaMethods preprocessCore qvalue + rhdf5 rtracklayer seqLogo siggenes simpleaffy snpStats topGO vsn yeastCC zlibbioc + DEXSeq + qsea # 13.12.2016 lienhard + devtools # 29.03.2017 pacini + YosefLab/scone # 29.03.2017 pacini + rhondabacher/SCnorm # 29.03.2017 pacini + MAST # 29.03.2017 pacini + scDD # 03.03.2017 pacini +) + +P=$(printf ',"%s"' "${PKG[@]}") # ,"ACME","ALL".... +P=${P#,} # "ACME","ALL",... + +R --quiet --vanilla -e "source('biocLite.R');biocLite(c($P))" + + +R --quiet --vanilla -e 'library("devtools");install_github("nghiavtr/BPSC")' # 3.03.2017 pacini + + + +exit