R

There are 3 version of R installed on KewHPC are 3.6.3, 4.0.2 and 4.1.2

Running R on KewHPC

In order to us R on KewHPC You'll need both a batch script such as this:

#!/bin/bash 
#SBATCH -c 1
#SBATCH -p all
#SBATCH -J R_job
#SBATCH -o /data/users_area/usr00kg/Rscript.out
#SBATCH -e /data/users_area/usr00kg/Rscript.err

module load R/4.0.2

Rscript job_script.R argument1 argument2

and an R script contaning your analysis:

#!/usr/bin/env Rscript
args <- commandArgs(TRUE)

argument1 = args[1]
....
....
etc.

Modules

Many commonly used R moules have been centrally installed. If you need any others ask Matt Clarke to install them centrally. You can also install packages locally in your /data/users_area or /home. This is especially useful if you need a specific version or are developing an R module.

Installing to Local Lib

Load up the version of R you need and enter the interactive R terminal.

module load R/3.6.3
R

Specify the location of your local library with "lib=".

install.packages("ggplot2",lib="/data/users_area/usr00kg/R_local_lib")

Loading from Local Lib

There are two ways of doing this:

Permanently Loading the Lib

This is done by adding your library to the "R_LIBS" variable by adding the following lines to the end of your ~/.bashrc file.

if [ -n $R_LIBS ]; then
    export R_LIBS=/data/users_area/usr00kg/R_local_lib:$R_LIBS
else
    export R_LIBS=/data/users_area/usr00kg/R_local_lib
fi

Within Your R script

By specifying the library when loading the library

library("ggplot2", lib.loc="/data/users_area/usr00kg/R_local_lib")