Installing R libraries

R is a programming environment for performing statistical operations. On this page we show how to install R libraries for your projects.

Selecting the module to load

We recommend to use the command module spider R to see all available versions:

$ module spider R

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

     Versions:
        R/3.5.1-foss-2018b
        R/3.5.1-intel-2018b
        R/3.6.0-foss-2019a
        R/3.6.0-fosscuda-2019a
        R/3.6.0-intel-2019a
        R/3.6.1-foss-2019a
        R/3.6.2-foss-2019b
        R/3.6.2-fosscuda-2019b
        R/3.6.2-intel-2019b
        R/4.0.0-foss-2020a
        R/4.0.0-fosscuda-2020a
        R/4.0.3-foss-2020b
        R/4.0.3-fosscuda-2020b
        R/4.1.0-foss-2021a
        R/4.1.2-foss-2021b
        R/4.2.1-foss-2022a

Then load one of these, for instance:

$ module load R/4.2.1-foss-2022a

We have also made bioconductor as a module with the base bioconductor packages. Not all packages found in bioconductor repository are pre-installed. This is because of compatibility issues, i.e. not all packages can be installed with the same set of dependencies and to make it easier for the user to select the exact version combinations for some packages.

$ module spider bioconductor

-----------------------------------------------------------------------------------------------------------------------------------------------------------
  R-bundle-Bioconductor:
-----------------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      R is a free software environment for statistical computing and graphics.

     Versions:
        R-bundle-Bioconductor/3.8-foss-2018b-R-3.5.1
        R-bundle-Bioconductor/3.8-intel-2018b-R-3.5.1
        R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0
        R-bundle-Bioconductor/3.11-foss-2020a-R-4.0.0
        R-bundle-Bioconductor/3.12-foss-2020b-R-4.0.3
        R-bundle-Bioconductor/3.13-foss-2021a-R-4.1.0
        R-bundle-Bioconductor/3.14-foss-2021b-R-4.1.2

How to install packages as a user

There might be some packages missing in the R module we have installed or maybe you need a different version than what we have. In that case you could install the packages yourself.

Warning

• Installing packages may take a long time, especially compared with installing on a Windows or Mac computer. The reason for this is that some packages will be compiled from source code to work on the operating system we have on the HPC systems.

• There is only restricted internet access from compute nodes, so you cannot easily install packages as part of your job. You need to install them using the login node and make sure to provide the path in the job script (examples below).

First log into the cluster and load one of the R modules or R bundles, for instance:

$ module restore
$ module load R/4.2.1-foss-2022a

Then create a directory which will hold the installed libraries:

$ mkdir ${HOME}/R

Then start the R prompt where we do the rest:

$ R

Use the R prompt to set the library path and install the package (adjust “user” to your username in the highlighted line):

# set the location for the packages to be installed
> .libPaths(c("/cluster/home/user/R", .libPaths()))

# install the package
> install.packages("somelibrary", repo="cran.uib.no")

# check whether the package can be loaded
> library(somelibrary)

To access the package in your scripts, you will need to add the .libPaths line to your scripts.

Keeping track of your R environment

A good way to keep track of your R environment is to use renv. This tool makes it possible to record and share your dependencies for better reproducibility.

Rscript example in a job

We have a separate page with examples for your First R calculation.

License Information

R is available under several open-source licenses. It is the user’s responsibility to make sure they adhere to the license agreements.