Add R-devel-2017-02-02-1

Rebuild and add scDD and nghiavtr/BPSC

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 </dev/null
+
+mkdir -p $PREFIX
+cat >$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