R

This is the landing page for R which contains guides, tutorials and other contributed resources for using R on the UFS HPC

UFS HPC usage example

R can be loaded as an environmental module as follows:

  1. Open a Terminal

  2. Load the R module:

    $ module load R

  3. Note that the command above will load the latest available version of R. To load a specific version of R, type the command as above and then tab complete (press tab multiple times) to see the versions available. Then load the chosen version as follows:

    $ module load R/3.6.1

  4. You may now invoke the R interpreter:

    $ R

    or for an R script:

    $ Rscript <script>

Installing packages in R

Packages are installed into a user's home directory. However, it is important to only use these packages with the R version they were installed with.

To install packages from the R interpreter, issue these commands according to the source of the desired package:

  • To install packages from Bioconductor:

    $ BiocManager::install("package name")

  • To install packages from CRAN:

    $ install.packages("package name")

  • To install packages from GitHub:

    $ remotes::install_github('username/packagename')

Performance Notes

  • 1 Node
  • The recommended resources required by R will depend each use case, however, here are some helpful hints:
    • If your workload is calculation heavy - use more cores
    • If you work with large datasets - use more memory

Benchmarks

No benchmarks are available.

UFS HPC Community Guides and Tutorials

Official site and documentation

Licensing Information

Primary Citation

  • R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/
  • Please remember to check (and cite) the citations for any packages used with R
    • To check for the citation of a package, issue and run the following command within R: 
          $ citation(*package_name*)

External Guides and Resources