rcps-buildscripts/R-4.0.2_single_package_install at master · themkots/rcps-buildscripts · GitHub

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#!/usr/bin/env bash

###############################################
# Installing a single R additional package
#
# by Brian Alston, October 2016 V1.1
# Updated Dec 2016 to use https://cloud.r-project.org/ as defult repro.
# Updated May 2017 to default to R 3.4.0
# Updated March 2018 to default to R 3.4.2
# Updated October 2018 to default to R 3.5.1
# Updated June 2019 to defULT TO R 3.6.0
# Updated July 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.

#
# usage: R-4.0.2_single_package_install <R package name> <extra args for install.packages>
#
# Will need modules: r/recommended or possibly r/new

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


if [ $# -lt 1 ]; then
	echo "usage: R-4.0.2_single_package_install <R package name> <extra args for install.packages>"
	exit 1
fi
PACKAGE=$1
if [ $# -eq 2 ]; then
    EXTRAS=$2
    echo "extra args - $EXTRAS"
fi

temp_dir=`mktemp -d -p /dev/shm`
# temp_dir='/home/ccspapp/Software/R'
echo "Building in $temp_dir ..."
cd $temp_dir
module list
read -p "Press [Enter] key to start ..."

cat > R_script <<EOF
mainLib <- Sys.getenv ("RLIB_MAIN");
dbLib <- Sys.getenv ("RLIB_DB");
repros <- Sys.getenv ("REPROS");
mainLib;
dbLib;
repros;

install.packages ("$PACKAGE", lib=mainLib, repos=repros, $EXTRAS);

EOF

echo "Installing $PACKAGE and dependencies ..."
R --no-save < R_script
echo "Done."