add R module set R package location docs

config/templates/hpc.template

@@ -59,6 +59,7 @@ nav:
       - OpenFOAM: openFOAM.md
       - Python: python.md
       - Python virtual environments: setting_up_python_virtual_environments.md
+      - R packages: r-packages.md
       - Transcribe: transcribe.md
       - VS Code Tunnel: vscodetunnel.md
   - FAQ:

mkdocs/docs/HPC/r-packages.md

@@ -0,0 +1,47 @@
+# 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 {{ hpcinfra }}.
+
+The {{ hpcinfra }} 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 an `R` packages yourself in the past (before end of February 2025),
+you might have to reinstall those 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 operational system is changed/updated. 
+