R: Add version 3.6.0

Fix the error below by adding the package path to `PATH`:

    * DONE (exNSS4)
    Loading required package: exNSS4
    building package exSexpr ...
    Converting Rd files to LaTeX
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
      Running 'texi2dvi' on 'Rd2.tex' failed.
    Messages:
    You don't have a working TeX binary (tex) installed anywhere in
    your PATH, and texi2dvi cannot proceed without one.  If you want to use
    this script, you'll need to install TeX (if you don't have it) or change
    your PATH or TEX environment variable (if you do).  See the --help
    output for more details.

    For information about obtaining TeX, please see http://tug.org/texlive,
    or do a web search for TeX and your operating system or distro.
    Output:

    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
      Running 'texi2dvi' on 'Rd2.tex' failed.
    Messages:
    You don't have a working TeX binary (tex) installed anywhere in
    your PATH, and texi2dvi cannot proceed without one.  If you want to use
    this script, you'll need to install TeX (if you don't have it) or change
    your PATH or TEX environment variable (if you do).  See the --help
    output for more details.

    For information about obtaining TeX, please see http://tug.org/texlive,
    or do a web search for TeX and your operating system or distro.
    Output:

    Error in running tools::texi2pdf()
    * checking for file '/dev/shm/R-3.6.0-0.build.tmp/RtmpR8JydU/Pkgs/exSexpr/DESCRIPTION' ... OK
    * preparing 'exSexpr':
    * checking DESCRIPTION meta-information ... OK
    * installing the package to process help pages
    * saving partial Rd database
    * building the PDF package manual
    Hmm ... looks like a package
    Creating pdf output from LaTeX ...
    Error: R CMD build failed (no tarball) for package exSexpr

The errors below are in the build log.

    $ grep ^Error R-3.6.0-0.build.log
    Error: package ‘S4Vectors’ 0.18.3 was found, but >= 0.19.11 is required
    by ‘GenomicRanges’
    Error : package ‘S4Vectors’ 0.18.3 is loaded, but >= 0.19.11 is required
    by ‘GenomicRanges’
    Error: loading failed
    Error in reconcilePropertiesAndPrototype(name, slots, prototype,
    superClasses,  :
    Error: unable to load R code in package ‘ensembldb’

R-3.6.0-0.build.sh

@@ -0,0 +1,179 @@
+#! /bin/bash
+
+# https://www.r-project.org/
+
+# export GITHUB_PAT='5***b' 38 secret chars :)
+. ./github_pat.source
+if [ -z "$GITHUB_PAT" ] ; then
+  echo "# Error: GITHUB_PAT is not set, build of 'dynverse/dyno' is supposed to fail."
+  echo "#        Check the dvteam mails for 'personal access token'"
+  exit 1
+fi
+
+PKG=R
+VERSION=3.6.0
+BUILD=0
+
+PREFIX=/pkg/$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:/usr/local/package/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