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#! /bin/bash
# COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh
# TESTING=1
# Use this when R is build & installed and the package list 'work in progress'
# PKGDEBUG=1
PKG=R
VERSION=4.0.5
BUILD=0
# https://www.r-project.org/
# https://cran.r-project.org/mirrors.html
# A caching proxy under /project/retarded/rproxy
CRANMIRROR=http://platsch:8010/cran/$PKG-$VERSION-$BUILD/cran
BIOCMIRROR=http://platsch:8010/bioconductor/$PKG-$VERSION-$BUILD/bioc
PREFIX=/pkg/$PKG-$VERSION-$BUILD
if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
# export GITHUB_PAT='5***b' 38 secret chars
. ./github_pat.source
if [ -z "$GITHUB_PAT" ] ; then
echo "# Error: GITHUB_PAT is not set, build of 'dynverse/dyno' is supposed to fail."
echo "# Check the dvteam mails for 'personal access token'"
exit 1
fi
# neither home nor /usr/local/package - but texlive kpsewhich for nghiavtr/BPSC
# mind: we need this path later on, since presumably Seurat or one of its
# dependencies screws up the PATH
PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin:/package/texlive/2020/bin
echo "# Ready player one."
date
set -xe
umask 022
BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
test -d $BUILD_TMPDIR && rm -fr $BUILD_TMPDIR/build/velocyto_fixup
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=$PREFIX/bin:\$PATH
PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH}
if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi
export PKG_CONFIG_PATH LD_LIBRARY_PATH
EOF
. $PREFIX/profile
NPROC=$(nproc)
export MAKEFLAGS="-j $NPROC"
BUILDDIR=$BUILD_TMPDIR/build
mkdir -p $BUILDDIR
cd $BUILDDIR
if [ -z "$PKGDEBUG" ]; then
# Start with some extra stuff. To keep the 'sf' package happy.
( # for 'dynverse/dyno', see UDUNITS2_INCLUDE, UDUNITS2_LIBS below
UNITSVER=2.2.26
# test -e udunits-$UNITSVER.tar.gz || wget --no-verbose ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-$UNITSVER.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/5803837c6019236d24a9c9795cc8b462/udunits-2.2.26.tar.gz
test -e udunits-$UNITSVER.tar.gz || wget -nv $BEEHIVE
test -d udunits-$UNITSVER || tar -xf udunits-$UNITSVER.tar.gz
cd udunits-$UNITSVER
CFLAGS='-O2 -fPIC' \
./configure --prefix=$PREFIX --libdir=$PREFIX/lib --enable-shared=no
make
make install
)
# The rest is for 'sf', with 'spdep' as the real culprit.
# sf is a pain in the ass, as it carries tons of system dependencies (GDAL, PROJ, ...)
# https://github.com/r-spatial/sf - Simple Features for R
# ('Simple' in the sense of brainless I guess)
# OTOH its needed by monocle3, which is related to AG Mundlos & M. Spielmann, a Nature publication ...
(
PROJVER=6.1.0
# test -e proj-$PROJVER.tar.gz || wget --no-verbose http://download.osgeo.org/proj/proj-$PROJVER.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/4ec5d9240b0e290670886519f250946c/proj-6.1.0.tar.gz
test -e proj-$PROJVER.tar.gz || wget -nv $BEEHIVE
test -d proj-$PROJVER || tar -xf proj-$PROJVER.tar.gz
cd proj-$PROJVER
./configure \
--prefix=$PREFIX \
--libdir=$PREFIX/lib \
--with-external-gtest=no
make
make install
)
(
GEOSVER=3.7.2
# test -e geos-$GEOSVER.tar.bz2 || wget --no-verbose http://download.osgeo.org/geos/geos-$GEOSVER.tar.bz2
BEEHIVE=https://beehive.molgen.mpg.de/8caa4d19d311c1a78feb2f57505dc0e3/geos-3.7.2.tar.bz2
test -e geos-$GEOSVER.tar.bz2 || wget -nv $BEEHIVE
test -d geos-$GEOSVER || tar -xf geos-$GEOSVER.tar.bz2
cd geos-$GEOSVER
./configure \
--prefix=$PREFIX \
--libdir=$PREFIX/lib
make
make install
)
(
GDALVER=2.4.1
# test -e gdal-$GDALVER.tar.xz || wget --no-verbose http://download.osgeo.org/gdal/$GDALVER/gdal-$GDALVER.tar.xz
BEEHIVE=https://beehive.molgen.mpg.de/ff98500aab063da563acade884518dfa/gdal-2.4.1.tar.xz
test -e gdal-$GDALVER.tar.xz || wget -nv $BEEHIVE
test -d gdal-$GDALVER || tar -xf gdal-$GDALVER.tar.xz
cd gdal-$GDALVER
export CFLAGS="-O2 -fPIC"
export CXXFLAGS="-O2 -fPIC"
./configure \
--prefix=$PREFIX \
--libdir=$PREFIX/lib
make
make install
)
# ###########
# Now Build R
# test -e R-$VERSION.tar.gz || wget --no-verbose https://cran.r-project.org/src/base/R-4/R-4.0.5.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/eb8fb47cc91ff287005c1633ef8599e6/R-4.0.5.tar.gz
test -e R-$VERSION.tar.gz || wget -nv $BEEHIVE
test -d R-$VERSION || tar -xf 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=$PREFIX \
--libdir=$PREFIX/lib \
--with-pic \
--with-recommended-packages \
--enable-shared \
--with-x \
--enable-R-shlib \
LDFLAGS=-Wl,-rpath,$PREFIX/lib/R/lib
export TZ=CEST # some tests need timezone
make
make check
make install
cd $BUILDDIR
cat <<- RCODEXXX | Rscript -
options(repos=structure(c(CRAN='$CRANMIRROR')))
options(BioC_mirror = '$BIOCMIRROR')
install.packages('BiocManager')
install.packages('remotes') # or installs from github will fail.
BiocManager::install(update = TRUE, ask = FALSE) # update the 'base' packages
RCODEXXX
# java stuff seems to be a troublemaker, install first
cat <<- RCODEXXX | Rscript -
options(repos=structure(c(CRAN='$CRANMIRROR')))
options(BioC_mirror = '$BIOCMIRROR')
BiocManager::install(c('rJava', 'RWeka', 'RWekajars'), update = FALSE)
RCODEXXX
echo "# State of lib/R/library after initial setup:"
ls -la $PREFIX/lib/R/library
fi ### -z "$PKGDEBUG"
unset DISPLAY # avoid warnings about 'RGL: unable to open X11 display'
export UDUNITS2_INCLUDE=$PREFIX/include
export UDUNITS2_LIBS=$PREFIX/lib
# List of packages
# Package names containing a '/' are treated as GitHub repositories
# SingleCellExperiment must come before aertslab/SCENIC, so just do all github stuff at the end
# Format hint:
# cat package_list | sed -e 's/\s\s*/\n/g' | sort -f | uniq | tr '\n' ' ' | fmt -w 120
cat <<- RCODEXXX > package_list
abind acepack ACME ade4 AdequacyModel affy affyio affyPLM akima ALL annotate AnnotationDbi AnnotationForge aod
ape apeglm arrayQualityMetrics ash assertthat AUCell bamsignals base64 base64enc batchelor BatchJobs BayesDA BBmisc
bdsmatrix beadarray BeadDataPackR beanplot beeswarm bgmm BH bigmemory bigmemory.sri Biobase BiocGenerics BiocParallel
biomaRt BioNet Biostrings biovizBase bit bitops boot bootstrap Boruta bpca BradleyTerry2 brew brglm BSgenome
BSgenome.Ecoli.NCBI.20080805 bumphunter c060 C50 Cairo car caret Category caTools CellNOptR checkmate ChIPpeakAnno
ChIPseeker chipseq chron circlize CircStats Ckmeans.1d.dp class clue cluster clusterProfiler CNEr coda codetools coin
colorspace combinat corpcor corrgram corrplot cowplot crayon cummeRbund curl cvTools data.table DBI DelayedArray
DelayedMatrixStats deldir DEoptimR DESeq2 devtools DEXSeq dichromat digest DirichletMultinomial dismo DNAcopy doMC
doParallel doRNG doSNOW dostats dplyr dtw dynamicTreeCut e1071 earth edgeR elasticnet energy entropy evaluate evd
exactRankTests exomeCopy ExomeDepth fail fANCOVA fastcluster fastICA fastmatch FDb.InfiniumMethylation.hg19 fdrtool
FField fields filehash flashClust foreach foreign formatR Formula futile.logger futile.options gbm gclus gcrma gdata
genefilter GeneNet geneplotter genetics GenomeInfoDb genomeIntervals GenomicAlignments GenomicFeatures GenomicRanges
GEOquery getopt GGally ggbio ggm ggplot2 ggpubr git2r glasso Glimma glmnet GlobalAncova GlobalOptions globaltest
gmp gnm GO.db GOstats GOTHiC gplots graph gRbase gridBase gridExtra gridSVG GSEABase GSEAlm gsl gsubfn gtable
gtools Gviz h2o haplo.stats HardyWeinberg hash hdf5r hdi hdrcde hexbin hflights hgu95av2 hgu95av2.db hgu95av2cdf
HiCcompare highr HiveR Hmisc HMM Homo.sapiens hsmm htmltools HTqPCR httpuv httr hwriter igraph illuminaio impute
infotheo inline intervals ipred IRanges iterators itertools jsonlite kernlab KernSmooth knitr ks kSamples labeling
Lahman lambda.r lars lattice latticeExtra lava lazyeval LEAP leaps LearnBayes lhs limma linprog lintr lme4 lmtest
locfit longitudinal lpSolve lpSolveAPI LSD lumi magrittr manipulate mapproj maps maptools maptree markdown MASS MAST
Matrix MatrixEQTL matrixStats mclust mda MEDIPS memoise meta MethylSeekR methylumi mgcv mice microbenchmark mime
minfi minqa misc3d mitools mixtools mlegp modeltools monocle multcomp multicool multiHiCcompare multtest munsell
muscle mvtnorm nleqslv nlme nloptr NMF nnet nor1mix numDeriv OmicCircos optparse org.Hs.eg.db OrganismDbi pamr
party partykit pbapply pbkrtest pcalg pcaMethods penalizedSVM peperr PerfMeas pheatmap pkgmaker plotmo plotrix
pls plus plyr ppcor pracma preprocessCore pROC prodlim profileModel proto proxy pwr qsea qtl quadprog quantreg
QuasR qvalue qvcalc R.cache R.matlab R.methodsS3 R.oo R.utils R2HTML R6 randomForest randomGLM raster rbenchmark
RBGL rbokeh RCircos RcisTarget RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl registry relaimpo relimp remotes
reshape reshape2 reticulate rex rFerns rgl Rgraphviz RGtk2 rhandsontable rhdf5 RhpcBLASctl Rhtslib rJava rjson
RJSONIO rlecuyer RMariaDB rmarkdown rmeta RMySQL RNAseq123 rnaseqGene rngtools robustbase ROC ROCR roxygen2 rpart
RPostgres RPostgreSQL RRF Rsamtools RSQLite rstudioapi rtracklayer RUnit rversions S4Vectors sandwich scales
scalreg scatterplot3d scDD SCnorm scone SCORPIUS sda segmented sendmailR seqinr seqLogo seriation setRNG Seurat sf
sfsmisc shape shiny shinythemes ShortRead siggenes simpleaffy SingleCellExperiment sm snow snowfall snpStats som
sp spam SparseM spatial splancs spls statmod stepPlr stringdist stringi stringr strucchange SummarizedExperiment
SuppDists survey svMisc svTools tables TeachingDemos testthat TFBSTools TFMPvalue tgp TH.data tidyr tidyverse
topGO TSP TxDb.Hsapiens.UCSC.hg19.knownGene VariantAnnotation vcd VennDiagram venneuler verification VGAM vsn
waveslim WGCNA whisker xlsx xlsxjars XML xml2 xtable XVector yaml yeastCC zinbwave zipfR zlibbioc zoo
aertslab/SCENIC aertslab/SCopeLoomR cole-trapnell-lab/leidenbase cole-trapnell-lab/monocle3 cole-trapnell-lab/RANNinf
dynverse/dyno jokergoo/ComplexHeatmap jokergoo/EnrichedHeatmap nghiavtr/BPSC
RCODEXXX
cat <<- RCODEXXX | Rscript -
XSAVE_PATH <- Sys.getenv('PATH')
options(repos=structure(c(CRAN='$CRANMIRROR')))
options(BioC_mirror = '$BIOCMIRROR')
pkgs <- scan('package_list', what = character())
for (pk in pkgs) {
pa <- unlist(strsplit(pk, '/')); p <- pa[1]; if (! is.na(pa[2])) p <- pa[2]
# there is no simple way to get rid of the error message, so avoid mimimi...
cat('* if there is no package, install it - errors here are part of the test!\n')
chk <- NULL; try(chk <- find.package(p))
if (is.null(chk)) {
cat( sprintf('* About to install: %s\n', pk), file='work_monitor_list', append = TRUE)
BiocManager::install(pk, Ncpus = $NPROC, update = FALSE)
ret <- library(p, character.only = TRUE, logical.return = TRUE)
if (! ret) q(save = "no", status = 2)
# the logic fails for 'cole-trapnell-lab/cicero-release', fixed below
detach( paste("package", p, sep = ":"), unload = TRUE, character.only=TRUE)
if (Sys.getenv('PATH') != XSAVE_PATH) {
cat( sprintf('*** PATH SCREWUP OCCURED (package %s)\n', pk))
cat( sprintf('*** expected: %s\n', XSAVE_PATH))
cat( sprintf('*** now: %s\n', Sys.getenv('PATH')))
}
Sys.setenv(PATH = XSAVE_PATH)
cat( sprintf('* REALY_DONE with: %s\n', pk))
} else {
cat( sprintf('* ALREADY_DONE with: %s\n', pk))
}
}
RCODEXXX
# simple test: can everything be found?
cat <<- RCODEXXX | Rscript -
pkgs <- scan('package_list', what = character())
for (pk in pkgs) {
pa <- unlist(strsplit(pk, '/')); p <- pa[1]; if (! is.na(pa[2])) p <- pa[2]
chk <- NULL; try(chk <- find.package(p))
if (is.null(chk)) {
cat( sprintf('* ERROR: Missing package: %s\n', pk))
q(save = "no", status = 3)
}
}
RCODEXXX
# stress test: load all packages (uses 4G, claims 16G)
cat <<- RCODEXXX | Rscript -
pkgs <- scan('package_list', what = character())
for (pk in pkgs) {
pa <- unlist(strsplit(pk, '/')); p <- pa[1]; if (! is.na(pa[2])) p <- pa[2]
ret <- library(p, character.only = TRUE, logical.return = TRUE)
if (! ret) {
cat( sprintf('* ERROR: Failed to load package/library: %s\n', pk))
q(save = "no", status = 4)
}
}
RCODEXXX
# do 'cole-trapnell-lab/cicero-release' seperately
echo "BiocManager::install('cole-trapnell-lab/cicero-release', update = FALSE)" | Rscript -
# rstudios rsession does a lot of magic to detect the true R binary, thus bypassing
# our friendly 'hints' from the wrapper.
# tell lib/R/library/sf/libs/sf.so about lib -- yes it's the beloved sf package again!
# the original rpath is only set to /pkg/R-x.y.z-0/lib/R/lib, add /pkg/R-x.y.z-0/lib.
patchelf --set-rpath $PREFIX/lib/R/lib:$PREFIX/lib \
$PREFIX/lib/R/library/sf/libs/sf.so
# same with 'GreenleafLab/ArchR', https://www.archrproject.com/index.html
cat <<- RCODEXXX | Rscript -
options(repos=structure(c(CRAN='$CRANMIRROR')))
options(BioC_mirror = '$BIOCMIRROR')
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
library(ArchR)
ArchR::installExtraPackages()
RCODEXXX
# finally a source build, this is/was intended to provide a clean velocyto.R package for G. Pacini.
# velocyto.R uses an inappropriate makefile and has a silly multitreading issue
cd $BUILDDIR
mkdir -p velocyto_fixup
cd velocyto_fixup
git clone https://github.com/velocyto-team/velocyto.R
cd velocyto.R
git checkout 0.6 --force
git clean -dffx
mv src/Makevars src/Makevars.weird
# yields just -fopenmp, which won't work on macs with clang
echo 'PKG_CXXFLAGS=-Wall $(SHLIB_OPENMP_CXXFLAGS)' > src/Makevars
# intercept the inane 'grab all cores' policy
# defaultNCores <- function() { parallel::detectCores(logical=F) }
cp -p R/momentum_routines.R R/momentum_routines.R.orig
sed -e '/^defaultNCores/ d' -i R/momentum_routines.R
cat <<__NCores_HACK >> R/momentum_routines.R
defaultNCores <- function() {
env <- Sys.getenv('VELOCYTO_CORES')
if (env != "") { return(as.integer(env)) }
parallel::detectCores(logical=F)
}
__NCores_HACK
R CMD INSTALL .
echo "# Game over ..."
date
exit