R

R is a programming environment for performing statistical operations.

To find out more, visit the R website at: https://www.r-project.org

Running R

Module

Version

R

4.1.2-foss-2021b
4.2.1-foss-2022a
4.2.2-foss-2022b
4.3.2-gfbf-2023a
4.4.1-gfbf-2023b
4.4.2-gfbf-2024a

To see available versions when logged into the cluster, issue command

module spider R

Then, to use the desired R-version, issue command

module load R/<version>

How to install packages

There might be some packages missing in the R modules that are installed, or maybe you need a different version than what currently exists. In that case you could install the packages yourself. For example, following is the procedure to install the package called XYZ by the user user1 on SAGA (the steps are also similar on fram and betzy):

  • Login to saga

  • Load the module

  • Create a directory in which the packages should be installed.

    • NB: It is very important that you do not install the packages in your /home folder, as you might risk running out of storage quota.

  • Run R

        [user1@login-1.SAGA ~]$ module restore
        [user1@login-1.SAGA ~]$ module load R/4.0.0-foss-2020a
        [user1@login-1.SAGA ~]$ mkdir /cluster/projects/nnXXXXk/R
        [user1@login-1.SAGA ~]$ R

  • Use the R prompt to install the package

  • Here the packages are installed in the project area. This is a preffered choice because:

    1. You will not risk exceeding your quota

    2. All project members can link to this path in their R instances, instead of having to install one package multiple times.

      #Set the location for the packages to be installed
      > .libPaths("/cluster/projects/nnXXXXk/R")
      #Install the package
      >  install.packages("XYX", repo="cran.uib.no")
      #Check if the package can be  loaded
      > library(XYZ)

  • How to use an installed package: After installing, everytime the packages needed to be accessed the .libPaths("/cluster/projects/nnXXXXk/R") setting should be done. When submitting R Script as a job, the .libPath("/cluster/projects/nnXXXXk/R") should be specified before calling the package.

License Information

R is available under several open-source licenses. For more information, visit https://www.r-project.org/Licenses/

It is the user’s responsibility to make sure they adhere to the license agreements.