R-4.0.2_packages_install

#!/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 4.0.2
#
# 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
# Updated April 2019 for R 3.5.3 and PROJ.4 6.0.0
# Updated June 2019 for R 3.6.0, Texinfo 6.6 and TeX Live 2019
# Further updates to get a working set of Geographic packages (PROJ, GDAL etc) July 2019
# Updated April 2020 for R 3.6.3 and GNU 9.2.0 - some packages not currently installed
# - see below
# Updated June 2020 for R 4.0.2
# Updated September 2020 to set currect value for R_LIBS_SITE - WILL NEED TO CHANGE FOR EACH
# NEW R VERSION!
# Updated December 2020 to add Protobuf (new GNU 9.2.0 version) and JQ.
#
# Using Ian's require function to load modules
#
# Will need modules: see list of modules below.

set -e

VERSION=${VERSION:-4.0.2}   
INSTALL_PREFIX=${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 beta-modules
require gcc-libs/9.2.0
require compilers/gnu/9.2.0
require openblas/0.3.7-serial/gnu-9.2.0
require java/1.8.0_92
require fftw/3.3.8/gnu-9.2.0
require ghostscript/9.19/gnu-4.9.2
require texinfo/6.6/gnu-4.9.2
require texlive/2019
require gsl/2.6/gnu-9.2.0
require hdf/5-1.10.5/gnu-9.2.0
require udunits/2.2.26/gnu-9.2.0
require netcdf/4.7.4/gnu-9.2.0
require mpi/openmpi/3.1.5/gnu-9.2.0
require pcre2/10.35/gnu-9.2.0

# Not currently installed - 15/4/2020
# require jags/4.2.0/gnu.4.9.2-openblas
# require root/5.34.36/gnu-4.9.2-fftw-3.3.6-gsl-2.4
# require glpk/4.60/gnu-4.9.2

require perl/5.22.0
require libtool/2.4.6
require freetype/2.8.1/gnu-4.9.2
require graphicsmagick/1.3.21
require python/2.7.12
require sqlite/3.31.1/gnu-9.2.0
require proj.4/7.0.0/gnu-9.2.0
require sqlite/3.31.1/gnu-9.2.0
require proj.4/7.0.0/gnu-9.2.0
require gdal/3.0.4/gnu-9.2.0
require geos/3.8.1/gnu-9.2.0
require gmt/6.0.0/gnu-9.2.0
require v8/3.15
require protobuf/3.14.0/gnu-9.2.0
require jq/1.5/gnu-4.9.2

require r/4.0.2-openblas/gnu-9.2.0

export R_LIBS_SITE=/shared/ucl/apps/R/R-4.0.2-OpenBLAS/lib64/R/library:/home/ccspapp/Scratch//R/R-4.0.2-OpenBLAS/library


# 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_3.6.3.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
# Removed from packages to be built June 2019 as it fails to build with R 3.6.0

#   ${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 - Breaks install with R 3.5.3

# R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/ridge_2.1-3.tar.gz

R_input=${LOCALDIR}/R_packages_UCL_5_3.6.3.R
R --no-save < $R_input

# Now to install Bioconductor.

R_input=${LOCALDIR}/Bioconductor_UCL_1_3.6.3.R
R --no-save < $R_input