R-3.5.3-0.build.sh

#! /bin/bash

# https://www.r-project.org/

# export GITHUB_PAT='5***b' 38 secret chars :)
. ./github_pat.source
if [ -z "$GITHUB_PAT" ] ; then
  echo "# Error: GITHUB_PAT is not set, build of 'dynverse/dyno' is supposed to fail."
  echo "#        Check the dvteam mails for 'personal access token'"
  exit 1
fi

PKG=R
VERSION=3.5.3
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 </dev/null

mkdir -p $PREFIX
cat >$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)"

# We need the environment (MAKEFLAGS, GITHUB_PAT), so '--vanilla' is no longer an option
#   --vanilla  : Combine --no-save, --no-restore, --no-site-file --no-init-file and --no-environ
STRACCIATELLA='--no-save --no-restore --no-site-file --no-init-file'

BUILDDIR=$BUILD_TMPDIR/build
mkdir -p $BUILDDIR
cd $BUILDDIR

( # for 'dynverse/dyno'
  test -e udunits-2.2.26.tar.gz || wget ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.26.tar.gz
  test -d udunits-2.2.26        || tar xvf udunits-2.2.26.tar.gz
  cd udunits-2.2.26
  CFLAGS='-O2 -fPIC' \
  ./configure --prefix=$PREFIX --libdir=$PREFIX/lib64 --enable-shared=no
  make
  make install
)
export UDUNITS2_INCLUDE=$PREFIX/include
export UDUNITS2_LIBS=$PREFIX/lib64

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 $STRACCIATELLA --quiet -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 $STRACCIATELLA --quiet -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 $STRACCIATELLA --quiet -e "source('biocLite.R');biocLite(c($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
	RhpcBLASctl          #  8.04.2019 Kreitler
)

P=$(printf ',"%s"' "${PKG[@]}")		# ,"ACME","ALL"....
P=${P#,}				# "ACME","ALL",...

R $STRACCIATELLA --quiet -e "source('biocLite.R');biocLite(c($P))"

# Finally the things that come from github

R $STRACCIATELLA --quiet -e 'library("devtools");install_github("jokergoo/ComplexHeatmap");install_github("jokergoo/EnrichedHeatmap")'  # 15.02.2019 kretzmer

# dynverse/dyno likes to have Slingshot, SCORPIUS and Monocle3 from a singularity context, well
# at least rcannood/SCORPIUS builds w/o fuzz.
R $STRACCIATELLA --quiet -e 'library("devtools");install_github("rcannood/SCORPIUS", build_vignettes = TRUE)'
R $STRACCIATELLA --quiet -e 'library("devtools");install_github("dynverse/dyno")'  # 8.04.2019 Virginie Stanislas

# BPSC needs kpsewhich from '/usr/local/package/bin/kpsewhich', so extend the path here and now
PATH=$PATH:/usr/local/package/bin
R $STRACCIATELLA --quiet -e 'library("devtools");install_github("nghiavtr/BPSC")'   # 3.03.2017 pacini

exit