R:How to install additional packages

Created by Potthoff, Sebastian on 24. Mar 2020

You may want to install R libraries that are not provided by the default installation. They can be installed to your home directory using the following procedure. Note that some packages might need external libraries. Requirements can usually be found in the package documentation. These libraries have to be loaded by using the module load command before using R.

  1. Load the base R module from the intel or foss toolchain
    module load intel
    module load R
  1. Create a folder in your home directory, where you wish to install your additional packages, e.g.

    mkdir -p ~/R/library/
  1. Start up R and use the .libPaths function to create an additional search/installation path for R
    > .libPaths('~/R/library/')

    # Check if the new path was added
    > .libPaths()
    [1] "/home/s/spottho1/R/library"
    [2] "/Applic.HPC/Easybuild/skylake/2019a/software/MPI/intel/2019.1.144-GCC-8.2.0-2.31.1/impi/2018.4.274/R/3.6.0/lib64/R/library"
  1. Install your required package (e.g. the 'DEoptim' package)
    > install.packages('DEoptim')

Notes:

  • Make sure to always include your personal library path with .libPaths also when running batch jobs
  • When switching to newer R versions in the future you might want to re-install your packages
  • Some packages can be tricky to install. If you need help don't hesitate to contact support