Control R environment using modules

Setting up a semi-public repository

mkdir /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2

Note: need to do this only once per version; make sure that the folder does not already exist.

Create an R module

mkdir /cm/shared/apps/WUR/ABGC/modulefiles/R/

Note: need to do this only once per version; make sure that the folder does not already exist.

cp /cm/shared/modulefiles/R/3.0.2 /cm/shared/apps/WUR/ABGC/modulefiles/R/3.0.2_wur

Note: need to do this only once per version; make sure that the file does not already exist.

#%Module1.0#######################################################################
## R3 modulefile modified for WUR/ABGC use
##
proc ModulesHelp { } {

        puts stderr "\tAdds R v3.0.2 to your environment and sets WUR/ABGC libraries"
}

module-whatis   "Adds R v3.0.2 to your environment and set WUR/ABGC libraries"

set             r3_root        /cm/shared/apps/R3/
set             r3_wur_root    /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2/

prepend-path     PATH             $r3_root/bin
prepend-path     MANPATH          $r3_root/share/man
prepend-path     LD_LIBRARY_PATH  $r3_root/lib64
prepend-path     R_LIBS_SITE      $r3_wur_root

Load Module

module avail

 ----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
 bwa/0.5.9   bwa/0.7.5a  R/3.0.2_wur

module load R/3.0.2_wur

Install R package and check install path

install.packages('car')

 > installed.packages()
            Package      LibPath                                       
 car        "car"        "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"

See also

• Running parallel workloads in R on Slurm
• Installing domain specific software: installation by users
• Setting local variables
• Installing R packages locally
• Setting up and using a virtual environment for Python3