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R packages#

Note

Please keep in mind that this is not general documentation about installing R packages, but specific information about self-installed R packages at the HPC-UGent infrastructure.

The HPC-UGent infrastructure contains different generations of CPUs, with different microarchitectures, that are not necessarily compatible with each other. Additionally, we have multiple versions of R installed with different versions of toolchains, and by default, self-installed packages are installed in separate directories based only on R major and minor versions (only using x.y for R version x.y.z).

In this way, you might use self-installed R packages on incompatible CPU microarchitectures and/or compiled with incompatible toolchains, or for a different major version of the operating system, which might lead to hangs or other types of errors.

Since end of February 2025, we make sure that R packages that you install yourself will be installed in a directory that is specific to the operating system version, CPU microarchitecture, toolchain, and R version that is being used. The location of this directory by default is (by setting $R_LIBS_USER environment variable to) $VSC_DATA/local_R_LIBS/$VSC_OS_LOCAL/$VSC_ARCH_LOCAL/<R version>-<toolchain>.

Controlling the location for self-installed R packages#

If you would like to have another location (for example you are using a central location in your Virtual Organisation), you should set the environment variable $R_LIBS_BASEDIR to the desired location before you load any centrally installed R module. In this case, the location of the directory for self-installed R packages will be $R_LIBS_BASEDIR/local_R_LIBS/$VSC_OS_LOCAL/$VSC_ARCH_LOCAL/<R version>-<toolchain>. If this directory is not writable, you will still be able to use already installed R packages from that location, but you will not be able to install R packages yourself.

You can always check the default location(s) of R packages by issuing .libPaths() command in R. This command will show the package locations, ordered by their priorities.

Missing R packages intalled before#

Please be aware that if you have installed R packages yourself before end of February 2025, then you have to reinstall all of them. You might have to reinstall self installed R packages if you want to use them:

  • on a different cluster
  • with a different version of R
  • with an R compiled with a different version of toolchain
  • if the operating system was changed/updated.