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 Libraries: rlibs.md
       - Transcribe: transcribe.md
       - VS Code Tunnel: vscodetunnel.md
   - FAQ:

mkdocs/docs/HPC/rlibs.md

@@ -0,0 +1,40 @@
+# R libraries
+
+Please keep in mind, that this is not a general manual
+abut installing `R` libraries, but only system specific information about self 
+installed R libraries at {{ hpcinfra }}.
+
+Our infrastructure contains different CPU architectures, 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 libraries are installed in separate directories based only
+on `R` major and minor versions.
+
+In this way, you might use self installed `R` libraries on incompatible architectures and/or
+compiled with incompatible toolchains, which might lead to hangs or other types of errors.
+
+When you load a centrally installed `R` module we make sure that self installed libraries 
+will be installed to an operational system, architecture, toolchain, and `R` version
+dependent directory. The location of this directory by default is
+(by setting `R_LIBS_USER` environmental variable to)
+`$VSC_DATA/local_R_LIBS/$VSC_OS_LOCAL/$VSC_ARCH_LOCAL/<R version>-<toolchain>`.
+
+If you would like to have another location (for example you are using a central location
+in your VO), you should set the environmental variable `R_LIBS_BASEDIR` to the desired location
+*before* you load any centrally installed `R` module. In this case, the location of the
+directory for self installed `R` libraries will be
+`$R_LIBS_BASEDIR/local_R_LIBS/$VSC_OS_LOCAL/$VSC_ARCH_LOCAL/<R version>-<toolchain>`.
+If this directory is not writable, you can still be able to use already installed 
+`R` libraries from that location, but you will not be able to install `R` libraries 
+yourself.
+
+You can always check the default location(s) of `R` libraries by issuing `.libPaths()` command
+in `R`. This command will show the library locations ordered by their priorities. 
+
+Please be aware that if you have installed an `R` libraries yourself in the past, 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. 
+