Description

R is a free software environment for statistical computing and graphics.

Usage

module load 2023
module load R/4.3.2-gfbf-2023a

Installed packages

R module is installed with more than 700 packages. We are not listing them all here. However, you can always see them by calling the following command:

module load 2023
module show R/4.3.2-gfbf-2023a

If you believe a common R package is missing, please contact the helpdesk and we will install it for you.

Installing R packages

If you want to install your own specific packages, follow the guidelines described below. This is a recipe to install R packages from CRAN (http://cran.r-project.org/). As an example we demonstrate how to install the package far.

Many packages are already installed (see above), so try that first:

module load 2023
module load R/4.3.2-gfbf-2023a
R
> require(far)
Loading required package: far
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘far’

So, package far is not installed. To install it:

module load 2023
module load R/4.3.2-gfbf-2023a

locate the package on the CRAN website and download it to Snellius

wget http://cran.r-project.org/src/contrib/far_0.6-5.tar.gz

Tell the R program when to look for user installed packages

mkdir $HOME/rpackages
export R_LIBS=$HOME/rpackages:$R_LIBS

And install it

R CMD INSTALL -l $HOME/rpackages far_0.6-5.tar.gz

That is nearly all. The package is installed now in the directory 'rpackages' in your home directory. We advise to install all your R packages in this directory. Note that you'll also need to set the R_LIBS environment variable in your batch jobs.

NOTE: sometimes a package depends on another package. During installation, you will get a message like:

ERROR: dependencies 'yyyyyy' are not available for package 'xxxxxx'

In this case, install package 'yyyyyy' first.

Command line parameters in R

It is possible to call an R program on the command line with arguments for the R program.

Example:

file: test.r
argv = commandArgs(trailingOnly=TRUE)
cat("Number of arguments: ",length(argv),"\n")
cat("Argument number 2: ",argv[2],"\n")


call this script with the example command line arguments:

Rscript --no-save --slave test.r one two 123
# or
R --no-save --slave --args one two 123 < test.r
# or
R CMD BATCH --no-save --slave '--args one two 123' test.r outputfile
  • --no-save : do not save the workspace
  • --slave : run as quiet as possible (no welcome screen etc.)

The output:

Number of arguments:  3 
Argument number 2:  two

Notes:

  • 1st example: output goes to standard output
  • 2nd example: the arguments for the R script are directly after the --args flag. The output goes to standard output.
  • 3rd example: the output goes to the file 'outputfile'. If the name of the output file is ommitted, the output goes to 'test.r.Rout'.

NOTE: the arguments are available as strings. You can convert to number as follows:

#convert third argument to number:
x = as.numeric(argv[3])

Homepage

https://www.r-project.org/

More information

Cran website

  • No labels