Shell script to run the 3 main R package check types.

rpackagecheck.sh

#!/usr/bin/env sh

# Author: Sean Maden
#
# Script to install, build, and check R packages during development. Can perform
# one of 3 check types (R CHECK with and without '--as-cran', or BiocCheck).
# 
# Flags:
# -v : Build vignettes (otherwise use `... --no-build-vignettes`)
# -r : Run `R CMD CHECK ...`
# -b : Run `R BiocCheck ...`
# -c : Run CRAN check (e.g. `R CMD CHECK --as-cran ...`)
# 
# Returns:
# Builds the package, generates tarball containing the built binaries and check
# logs.

#------------
# parse flags
#------------
# initialize flag variables
packagepath=
buildvignettes=0
rcheck=0
bioccheck=0
crancheck=0

# parse provided flags
while getopts vrbchp: name; do
    case "$name" in
        'v')    buildvignettes=1;;
        'r')    rcheck=1;;
        'b')    bioccheck=1;;
        'c')    crancheck=1;;
        'p')    packagepath=$OPTARG;;
        \?)     echo "Invalid option provided: -$OPTARG" >&2;;
    esac
done

#-------------------------
# package setup for checks
#-------------------------
# check package path existence
if [ ! -d "$packagepath" ]; then
    echo 'ERROR: invalid package path provided'
    exit 1
fi

# prep the package
R CMD INSTALL $packagepath

# parse buildvignettes flag
if [ $buildvignettes == 0 ]; then
    echo 'Skipping vignette builds...'
    R CMD BUILD $packagepath --no-build-vignettes
else
    echo 'Building vignettes...'
    R CMD BUILD $packagepath
fi

# prep the tar path
packagename=$(basename $packagepath)
# get the version from description text
vers=$(sed '2q;d' $packagepath'/DESCRIPTION') 
vf=${vers:9}
tarpath=$packagename'_'$vf'.tar.gz' # detect the tar file

#---------------------
# run specified checks
#---------------------
if [ ! $rcheck == 0 ]; then
    echo 'Running `R CMD CHECK`...'
    R CMD CHECK $tarpath
fi
if [ ! $bioccheck == 0 ]; then
    echo 'Running `R CMD BiocCheck`...'
    R CMD BiocCheck $tarpath
fi
if [ ! $crancheck == 0 ]; then
    echo 'Running `R CMD CHECK --as-cran`...'
    R CMD CHECK --as-cran $tarpath
fi