diff --git a/R-3.5.2-0.build.sh b/R-3.5.2-0.build.sh new file mode 100755 index 0000000..838d254 --- /dev/null +++ b/R-3.5.2-0.build.sh @@ -0,0 +1,161 @@ +#! /bin/bash + +# https://github.com/MathurinD/STASNet ??? +# http://bioconductor.org/packages/stats/ +# +# ^Rcpp (>= 0.10.4) +# ^BH +# RhpcBLASctl +# ^ Rgraphviz +# ^ pheatmap +# ^ lattice +# ^ lhs +# parallel +# + +# https://www.r-project.org/ + +PKG=R +VERSION=3.5.2 +BUILD=0 + +PREFIX=/pkg/$PKG-$VERSION-$BUILD +if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi + +# neither home nor /usr/local/package +PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin +export PATH + +set -xe +umask 022 + +BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp +test -d $BUILD_TMPDIR && rm -r $BUILD_TMPDIR +mkdir -p $BUILD_TMPDIR/home +export TMPDIR=$BUILD_TMPDIR +export HOME=$BUILD_TMPDIR/home + +exec $PREFIX/profile <<-EOF + PATH=$PREFIX/bin:\$PATH + if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi +EOF +. $PREFIX/profile + +export MAKEFLAGS="-j $(nproc)" + +BUILDDIR=$BUILD_TMPDIR/build +mkdir -p $BUILDDIR +cd $BUILDDIR + +test -e R-$VERSION.tar.gz || wget https://cran.r-project.org/src/base/R-3/R-$VERSION.tar.gz +test -d R-$VERSION || tar xvf R-$VERSION.tar.gz +cd R-$VERSION + +sed -i 's/en_GB/en_US/g' tests/reg-tests-3.R tests/reg-tests-3.Rout.save + +./configure \ + --prefix=$PREFIX \ + --with-pic \ + --with-recommended-packages \ + --enable-shared \ + --with-x \ + --enable-R-shlib \ + LDFLAGS=-Wl,-rpath,$PREFIX/lib64/R/lib + +export TZ=CEST # some tests need timezone +make +make check +make install + +cd $BUILDDIR + +R --quiet --vanilla -e "update.packages(repos='https://cran.uni-muenster.de/',ask=FALSE)" + +# 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 remotes 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($P))" + +# Bioconductor packages, and user request even if they are from cran, reason: see above + +PKG=( + ACME ALL AnnotationDbi AnnotationForge BSgenome.Ecoli.NCBI.20080805 BSgenome BeadDataPackR BioNet Biobase + BiocGenerics BiocInstaller BiocParallel Biostrings CNEr Category CellNOptR ChIPpeakAnno DESeq2 DESeq + DNAcopy DirichletMultinomial FDb.InfiniumMethylation.hg19 GEOquery GO.db GOTHiC GOstats GSEABase GSEAlm + GenomeGraphs GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GlobalAncova Gviz HTqPCR + Homo.sapiens IRanges MEDIPS OmicCircos OrganismDbi RBGL ROC Rgraphviz Rhtslib Rsamtools S4Vectors + ShortRead TFBSTools TxDb.Hsapiens.UCSC.hg19.knownGene VariantAnnotation XVector affyPLM affy affyio + annotate arrayQualityMetrics bamsignals beadarray biomaRt biovizBase bumphunter chipseq cummeRbund easyRNASeq + edgeR exomeCopy gcrma genefilter geneplotter genomeIntervals ggbio globaltest graph hgu95av2 hgu95av2cdf + illuminaio impute limma lumi methylumi minfi multtest muscle org.Hs.eg.db pcaMethods preprocessCore qvalue + rhdf5 rtracklayer seqLogo siggenes simpleaffy snpStats topGO vsn yeastCC zlibbioc + DEXSeq + qsea # 13.12.2016 lienhard + devtools # 29.03.2017 pacini + YosefLab/scone # 29.03.2017 pacini + rhondabacher/SCnorm # 29.03.2017 pacini + MAST # 29.03.2017 pacini + scDD # 03.03.2017 pacini + zinbwave # 15.03.2018 stanisla + monocle # 21.06.2018 pacinihdf5r + hdf5r Seurat # 20.08.2018 kretzmer + # digest # 29.08.2018 stanisla (update request, already present see above) + QuasR MethylSeekR # 30.08.2018 alena + rnaseqGene apeglm # 4.09.2018 alena + RNAseq123 Glimma # 4.09.2018 alena +) + +P=$(printf ',"%s"' "${PKG[@]}") # ,"ACME","ALL".... +P=${P#,} # "ACME","ALL",... + +R --quiet --vanilla -e "source('biocLite.R');biocLite(c($P))" + +# BPSC needs kpsewhich from '/usr/local/package/bin/kpsewhich', so extend the path here and now +PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/package/bin +export PATH +. $PREFIX/profile +R --quiet --vanilla -e 'library("devtools");install_github("nghiavtr/BPSC")' # 3.03.2017 pacini +R --quiet --vanilla -e 'library("devtools");install_github("jokergoo/ComplexHeatmap");install_github("jokergoo/EnrichedHeatmap")' # 15.02.2019 kretzmer + +exit