Abstract

I give a walkthrough of a bash script that installs all of the R packages required by an R program (e.g., Shiny app, R file, R markdown file). This is useful for speeding up the workflow of adding a new Shiny app to a server.

Why do we need a script?

As explained in Dean Attali’s excellent post on how to setup an RStudio and Shiny server, you can install an R package (for example ‘mypackage’) for everyone on a server at the command line with:¹

sudo su - -c "R -q -e "install.packages('mypackage', repos='http://cran.rstudio.com/')""

Repeating this long command once or twice is fine, but if you have an app that requires several R packages such as:

# Dean Attali
# November 21 2014

# This is the server portion of a shiny app shows cancer data in the United
# States

source("helpers.R")  # have the helper functions avaiable

library(shiny)
library(magrittr)
library(plyr)
library(dplyr)
library(tidyr)
library(ggplot2)
library(shinyjs)

# Get the raw data
cDatRaw <- getData()
...

then you want to automate the task of installing missing R packages.

The bash script

For the impatient among you, here is the entire script:

The one argument passed to the script is the location of the R file that contains library(mypackage) or require(mypackage) commands (each on a separate line). The script will determine whether or not each required package is installed, and if it is not, the package will be installed from CRAN.

The first few lines simply check to make sure that a single argument is provided. If not, a usage reminder is echoed and the script exits. Otherwise, the argument is saved so that it is available in the variable $file.

if [ $# -ne 1 ]; then
  echo $0: usage: installAllRPackages.bash file
  exit 1
fi

file=$1

The next set of lines creates three temporary files in the ‘~/tmp’ directory (it must exist!) and sets a trap to delete them on exit.

tempfile() {
  tempprefix=$(basename "$0")
  mktemp ~/tmp/${tempprefix}.XXXXXX
}

TMP1=$(tempfile)
TMP2=$(tempfile)
TMP3=$(tempfile)

trap 'rm -f $TMP1 $TMP2 $TMP3' EXIT

The next two lines employ grep to search the R file for library and require commands, placing any lines containing the commands in the temporary file $TMP1.

grep library $file >> $TMP1
grep require $file >> $TMP1

Then, awk is used to extract the name of each package by looking inside the parenthesis on each line of the $TMP1 file. The end result is a $TMP2 file that contains the name of an R package on each line.

awk -F "[()]" '{ for (i=2; i<NF; i+=2) print $i }' $TMP1 >> $TMP2

The real meat of the script is in the final while loop. In each iteration of the loop, a package name is extracted from $TMP2 and stored in the variable $p. We will reuse the $TMP3 file, so we empty it with the truncate command at the start of each loop. Also inside the loop, the command

sudo su - -c "R -q -e "is.element('$p', installed.packages()[,1])"" >> $TMP3 

calls R to check to see if the package name is an element of the array returned from the installed.packages() command. The result is stored in the file $TMP3. If the R command returns [1] TRUE, then on to the next package. Otherwise, the package is installed. The entire while loop:

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