installr

#! /bin/ash
set -e

usage() {
    echo "Usage: $0 [ -c | -d ] [ -e ] [ -a pkgs ] [ -t pkgs ] [ -r ] [ -p ] REMOTES ..."
    echo
    echo "Options:"
    echo "  -c    install C and C++ compilers and keep them"
    echo "  -d    install C and C++ compilers, temporarily"
    echo "  -a    install Alpine packages and keep them"
    echo "  -t    install Alpine packages, temporarily"
    echo "  -p    do not remove pak after the installation (ignored if -r is given)".
    echo "  -e    use renv to restore the renv.lock file if present."
    echo
    echo "REMOTES may be:"
    echo "  * package names from CRAN/Bioconductor, e.g.    ggplot2"
    echo "  * slugs of GitHub repos, e.g.                   tidyverse/ggplot2"
    echo "  * GitHub branch, tag or commit, e.g             tidyverse/ggplot2@v1.0.0"
    echo "  * URLs to package .tar.gz files, e.g.           url::https://x.com/pkg.tar.gz"
    echo "  * path to a local directory, e.g.               local::."
    exit 2
}

error() {
    echo $1 >&2
    exit 2
}

unset KEEP_PAK


while getopts 'pecda:t:?h' o
do
    case $o in
        a) APKG_FIN=$OPTARG ; shift ;;
        t) APKG_TMP=$OPTARG ; shift ;;
        c) APKG_COMPILERS=true ;;
        d) APKG_COMPILERS_TMP=true ;;
        p) KEEP_PAK=true ;;
        e) USE_RENV=true ;;
        h|?) usage ;;
    esac
    shift
done

APKG_GCC="gcc musl-dev g++"

if [[ -n "$APKG_COMPILERS"  ]]; then
    APKG_FIN="$APKG_FIN $APKG_GCC"
fi

if [[ -n "$APKG_COMPILERS_TMP" ]]; then
    APKG_TMP="$APKG_TMP $APKG_GCC"
fi

echo
echo --------------------------------------
[[ -n "$APKG_FIN" ]] && echo Adding "$APKG_FIN"
[[ -n "$APKG_TMP" ]] && echo Temporarily adding "$APKG_TMP"
apk add --no-cache $APKG_FIN $APKG_TMP

echo
echo --------------------------------------
echo "Installing pak (if needed)"
Rscript -e 'if (! requireNamespace("pak", quietly=TRUE)) install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'

if [[ $# -eq 0 ]]; then
    echo
    echo --------------------------------------
    echo No R packages to install
else
    echo
    echo --------------------------------------
    echo Installing "$@"
    Rscript -e 'pak::pkg_install(commandArgs(TRUE))' "$@"
fi

echo
echo --------------------------------------
echo Cleaning up pak cache
Rscript -e 'pak::cache_clean(); pak::meta_clean(TRUE)'
rm -rf /tmp/Rtmp*
if [[ -z "$KEEP_PAK" ]]; then
    echo
    echo --------------------------------------
    echo Removing pak
    Rscript -e 'remove.packages("pak")'
fi


echo --------------------------------------
echo "Activating and Restoring renv.lock file if needed."
if [[ "$USE_RENV" == true ]]; then
    if [[ -f "./renv.lock" ]]; then
    Rscript -e 'renv::consent(provided = TRUE)'
    Rscript -e 'renv::restore()'
    else
    echo "renv.lock file is not present in the current directory."
  fi
fi
rm -rf /tmp/Rtmp*

echo
echo --------------------------------------
[[ -n "$APKG_TMP" ]] && echo Removing "$APKG_TMP"
apk del $APKG_TMP

echo
echo --------------------------------------
echo Cleaning up cache

rm -rf /var/cache/apk/*