Apply suggestions from code review

Co-authored-by: Kenneth Hoste <[email protected]>

Author: hajgato

config/templates/hpc.template

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

mkdocs/docs/HPC/rlibs.md

@@ -1,37 +1,41 @@
-# R libraries
+# R packages
 
-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 }}.
+!!! 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 }}.
 
-Our infrastructure contains different CPU architectures, that are
+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 libraries are installed in separate directories based only
-on `R` major and minor versions.
+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` libraries on incompatible architectures and/or
-compiled with incompatible toolchains, which might lead to hangs or other types of errors.
+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.
 
-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)
+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 VO), you should set the environmental variable `R_LIBS_BASEDIR` to the desired location
+in your Virtual Organisation), you should set the environment variable `$R_LIBS_BASEDIR` to the desired location
 *before* you load any centrally installed `R` module. In this case, the location of the
-directory for self installed `R` libraries will be
+directory for self-installed `R` packages will be
 `$R_LIBS_BASEDIR/local_R_LIBS/$VSC_OS_LOCAL/$VSC_ARCH_LOCAL/<R version>-<toolchain>`.
 If this directory is not writable, you can still be able to use already installed 
-`R` libraries from that location, but you will not be able to install `R` libraries 
+`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` libraries by issuing `.libPaths()` command
+You can always check the default location(s) of `R` packages 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 
+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`