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#!/bin/bash
#
# Setup an R environment in a given directory.
#
# This works as follows. We create an ".Rprofile" file in the current
# directory that sets the .libPaths to the desired Rlib directory. We do the
# same with an .Renviron file because it's R so one place isn't enough. This
# essentially makes that the only source of packages read by anything that
# respects this .Rprofile. Next we install packages as normal using the
# install_if_not_exists.R script, which only installs packages if necessary
# and supports GitHub and local packages as well.
#
# This file is part of RSimpleVenv: https://github.com/GjjvdBurg/RSimpleVenv
#
# Author: G.J.J. van den Burg
# Date: 2019-06-19
# License: MIT
res='\033[1m\033[0m'
log() { echo -e "\e[32m$*${res}"; }
err() { echo -e "\e[31m$*${res}"; exit 1; }
install() {
log "Installing $1";
Rscript ./utils/install_if_not_exist.R "$1"
# exit on failure
if [ ! $? == 0 ]
then
err "Non-zero exit status after installing $1"
fi
}
if [ $# -ne 2 ]
then
echo "Usage: $0 packageFile rlib_dir"
exit 1
fi
PACKAGE_FILE="$1"
LIBDIR=$(realpath "$2")
mkdir -p ${LIBDIR}
# Ensure that this is the only libPath from now on.
echo ".libPaths(c('${LIBDIR}'))" > .Rprofile
echo "R_LIBS=${LIBDIR}" > .Renviron
echo "R_LIBS_USER=${LIBDIR}" >> .Renviron
# Here's a fun one: for some reason R tests lazy loading in vanilla mode by
# default, which overwrites all the environment and library stuff we just
# carefully set. This can break things when you have a different package
# version installed in your user R package library. Luckily, if you dig
# through the R source code (not in the documentation!), you can find out that
# there's an obscure environment variable that can be set to disable this
# behaviour. What fun! What an intuitively designed programming language! /s
export _R_CHECK_INSTALL_DEPENDS_="TRUE"
# Install devtools for GitHub-based packages
install devtools
# Install all packages from the provided package file
while read -r pkg
do
if [ -z ${pkg} ]
then
continue
fi
install "${pkg}"
done < ${PACKAGE_FILE}
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