Packages at Bianca (parallel session)

R libraries AKA R packages

  • UPPMAX have very many pre-installed packages

  • This is helpful especially for Bianca (with no internet)

  • You can install own packages on Bianca as well.

Questions

  • How to check for and use the UPPMAX pre-installed packages?

  • How to install packages on Bianca?

Objectives

  • Show how to check for R packages

  • Show how to install own packages on Bianca

Check current available packages

On UPPMAX the module R_packages is a package library containing almost all packages in the CRAN and BioConductor repositories. As of 2023-10-11 there are a total of:

  • A total of 23476 R packages are installed

  • A total of 23535 packages are available in CRAN and BioConductor

    • 19809 CRAN packages are installed, out of 19976 available

    • 3544 BioConductor-specific packages are installed, out of 3559 available

  • 121 other R packages are installed. These are not in CRAN/BioConductor, are only available in the CRAN/BioConductor archives, or are hosted on github, gitlab or elsewhere

There are many different ways to check if the package you are after is already installed - chances are it is! The simplest way is probably to simply try loading the package from within R .. code-block:: R

library(package-name)

Install own packages on Bianca

  • If an R package is not not available on Bianca already (like Conda repositories) you may have to use the wharf to install the library/package