Running Rscript in command line and loading packages

2
votes

I have a foo.R file which contains 

library("ggplot2")
cat("Its working")

I am trying to run foo.r via the command line using the Rscript commandRscript --default-packages=ggplot2 foo.R and it is giving me the following error: 

1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
2: package ‘ggplot2’ in options("defaultPackages") was not found 
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted

Any help on how to load packages while running "Rscript" is much appreciated.

2
rcommand-linepackagesrscript
Run Rscript -e 'cat(c(.libPaths(), installed.packages()[,1]), sep = "\n")' and compare it to what you get when running that in an interactive session. Sometimes Rscript is using a different R backend and / or set of libraries than you expect. - nrussell
Does Rscript foo.R work? - cory
Got it to work, I had to go in to R in the server (user@servername:~$ R), and then do '>install.packages("ggplot2")' This installed the package and now I can run the earlier Rscript command. I tested my code on RStudio and that's why I couldn't run through the terminal. Thanks guys, will keep posted if I run into other issues. - kasun61

2 Answers

1
votes

For future references, you could use function require instead of library to avoid this error: require just returns FALSE and raises a warning if the package is not installed instead of throwing an error. You can therefore do a construct as follows:

if(!require(ggplot2)){install.packages("ggplot2")}

What it does is trying to load the package and, if it is not installed, installs it.

0
votes

Or you could use this,

# --------- Helper Functions ------------ #
# Ref: https://gist.github.com/smithdanielle/9913897
# check.packages function: install and load multiple R packages.
# Check to see if packages are installed. Install them if they are not, then load them into the R session.
check.packages <- function (pkg) {
  print("Installing required packages, please wait...")
  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
  if (length(new.pkg)) {
    install.packages(new.pkg, dependencies = TRUE)
  }
  sapply(pkg, library, character.only = TRUE)
}

# Usage example
# packages<-c("ggplot2", "afex", "ez", "Hmisc", "pander", "plyr")
# check.packages(packages)

check.packages("tidyverse")