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R-3.5.1_packages_install
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#!/usr/bin/env bash
###############################################
# Installing UCL needed additional R and Bioconductor
# packages.
#
# This replaces the old ~ccaabaa/Software/R/extra-pkgs-order.txt file from
# previous version of R on Legion etc. It will need to be updated each time
# an extra package is added to the current R installation.
#
# For R 3.5.1
#
# by Brian Alston, June 2016
# Updated Sep 2016 to updated JAGS version
# Updated Nov 2016 for R 3.3.2 and extra modules for rgdal and rgeos packages.
# Updated Dec 2016 to use https://cloud.r-project.org/ as defult repro.
# Updated May 2017 for R 3.4.0 and to add udunits/2.2.20/gnu-4.9.2 module.
# Updated October 2017 for R 3.4.2
# Updated May 2018 for R 3.5.0
# Updated June 2018 to fix MPI support - now using mpi/openmpi/3.0.0/gnu-4.9.2
# Updated September 2018 for R 3.5.1 and ROOT 5.34.36
# Also updated for udunits 2.2.26
# Updated October 2018 to create ~/.R/Makevars to allow installaion of rstan
#
# Using Ian's require function to load modules
#
# Will need modules: see list of modules below.
set -e
VERSION=${VERSION:-3.5.1}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/R/R-${VERSION}-OpenBLAS}
export RLIB_MAIN=${RLIB_MAIN:-${INSTALL_PREFIX}/lib64/R/library}
export RLIB_DB=${RLIB_DB:-/home/ccspapp/Scratch/R/R-${VERSION}-OpenBLAS/library}
export REPROS=${REPROS:-https://cloud.r-project.org/}
LOCALDIR=${LOCALDIR:-/shared/ucl/apps/build_scripts/files/R_UCL}
export PATH=$INSTALL_PREFIX/bin:$PATH
dirname=$(dirname $0 2>/dev/null || pwd)
INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
source ${INCLUDES_DIR}/module_maker_inc.sh
source ${INCLUDES_DIR}/require_inc.sh
require gcc-libs/4.9.2
require compilers/gnu/4.9.2
require openblas/0.2.14/gnu-4.9.2
require java/1.8.0_92
require fftw/3.3.6-pl2/gnu-4.9.2
require ghostscript/9.19/gnu-4.9.2
require texinfo/5.2/gnu-4.9.2
require texlive/2015
require gsl/1.16/gnu-4.9.2
require hdf/5-1.8.15/gnu-4.9.2
require udunits/2.2.26/gnu-4.9.2
require netcdf/4.3.3.1/gnu-4.9.2
require jags/4.2.0/gnu.4.9.2-openblas
require root/5.34.36/gnu-4.9.2-fftw-3.3.6
require glpk/4.60/gnu-4.9.2
require mpi/openmpi/3.0.0/gnu-4.9.2
require perl/5.22.0
require libtool/2.4.6
require graphicsmagick/1.3.21
require python2/recommended
require gdal/2.0.0
require gmt/5.3.1
require proj.4/4.9.1
require geos/3.5.0/gnu-4.9.2
require r/3.5.1-openblas/gnu-4.9.2
require v8/3.15
require protobuf/12-2017/gnu-4.9.2
require jq/1.5/gnu-4.9.2
# Set up ~/.R/Makevars for rstan which needs C++ 2014 stuff
mkdir -p ~/.R
cd ~/.R
cat > Makevars <<EOF
CXX14 = g++ -std=c++1y
CXX14FLAGS = -Wno-unused-variable -Wno-unused-function -fPIC
EOF
# temp_dir=`mktemp -d -p /dev/shm`
temp_dir='/home/ccspapp/Software/R/Packages'
echo "Building in $temp_dir ..."
cd $temp_dir
module list
read -p "Press [Enter] key to start ..."
cd $temp_dir
mkdir -p $RLIB_DB
# Note: some old packages need to be installed from local files that have had minor updates applied eg:
#
# adapt fails to install on R > 3.0.1 with: ERROR: a 'NAMESPACE' file is required
#
# tar xvzf adapt_1.0-4.tar.gz
# cd adapt
# Create NAMESPACE with contents:
#
# exportPattern("^[^\\.]")
#
# cd ..
# tar cvzf adapt_1.0-4-ucl.tar.gz adapt
#
# Do this for all packages that fail with abover error.
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/adapt_1.0-4-ucl.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_1.R
R --no-save < $R_input
# No longer on CRAN current - July 2013
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/Design_2.3-0-ucl.tar.gz
# So build of RCurl picks up currect version of libcurl
export PATH=/shared/ucl/apps/curl/7.21.3/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:/shared/ucl/apps/curl/7.21.3/lib
export PKG_LIBS="-L/shared/ucl/apps/curl/7.21.3/lib"
R_input=${LOCALDIR}/R_packages_UCL_2.R
R --no-save < $R_input
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/OPE_0.7-ucl.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_3.R
R --no-save < $R_input
# No longer on CRAN - Aug 2014
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/NetworkAnalysis_0.3-1.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_4.R
R --no-save < $R_input
# For Julie Bertrand (j.bertrand@ucl.ac.uk) - added Jan 2014
# No longer on CRAN current - June 2016
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/ridge_2.1-3.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_5.R
R --no-save < $R_input
# Now to install Bioconductor.
R_input=${LOCALDIR}/Bioconductor_UCL_1.R
R --no-save < $R_input