-
-
Save imm0rtalpony/6953ce12483cffd1dff958643062a6a8 to your computer and use it in GitHub Desktop.
Bash script to install all R packages required by an R program
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
#Install any packages required by an R file that aren't already installed | |
if [ $# -ne 1 ]; then | |
echo $0: usage: installAllRPackages.bash file | |
exit 1 | |
fi | |
file=$1 | |
tempfile() { | |
tempprefix=$(basename "$0") | |
mktemp ~/tmp/${tempprefix}.XXXXXX | |
} | |
TMP1=$(tempfile) | |
TMP2=$(tempfile) | |
TMP3=$(tempfile) | |
trap 'rm -f $TMP1 $TMP2 $TMP3' EXIT | |
grep library $file >> $TMP1 | |
grep require $file >> $TMP1 | |
awk -F "[()]" '{ for (i=2; i<NF; i+=2) print $i }' $TMP1 >> $TMP2 | |
while read p; do | |
truncate -s 0 $TMP3 | |
sudo su - -c "R -q -e \"is.element('$p', installed.packages()[,1])\"" >> $TMP3 | |
if grep -Fxq "[1] TRUE" $TMP3 | |
then | |
echo "$p package already installed" | |
else | |
echo "installing $p package" | |
sudo su - -c "R -q -e \"install.packages('$p', repos='http://cran.rstudio.com/')\"" | |
fi | |
done <$TMP2 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment