R packages
R users are encouraged to install their favorite R packages within the R_LIBS_USER directory which is by default in the user’s home directory. For exampl, you could using the following command to install a R package:
> install.packages("package name")
Since it can save users’ effort (and storage space) in managing the dependencies, commonly used R packages are installed and maintained centrally by the TG in the directory of /opt/R-packages. Centrally installed R packages are built for different R versions.
Note
Centally installed R packages only available for R version >= 4.0.1.
Using the centrally installed R packages
The centrally installed R packages are made available via the R-packages environment module with the version number matching the version of R.
For instance, to access the packages built for R version 4.1.0, one does:
$ module load R-packages/4.1.0
before starting the R session.
Note
Under the hood, the R-packages module simply sets the variable R_LIBS_SITE to the path where the packages are installed.
You can then load the package you want by
> library(package)
Note
If you are using rstudio, you don’t even need to load the R-packages module in advance. You could simply run the rstudio wrapper script in your VNC session. The dialog contains a tickbox for making the centally installed packages available.
Installing your own packages
When installing your own packages, you could define the installation location by setting the variable R_LIBS_USER before you start R. The default value defined by R is $HOME/R/x86_64-pc-linux-gnu-library/{version} where {version} is the R version.
Note
R packages are sometimes compiled against their dependent libraries and the R version you use to install them. You might need to re-install them for a different R version or after the dependent libraries are upgraded in the cluster.
Hereafter are instructions for installing specific packages: