r-rich

Summary

Software Description

MSI now offers r-rich modules that provide compatible versions of R, RStudio, and common dependencies for R packages. These modules behave similarly to the previous R modules in most ways - you can use R interactively or in batch mode via the command line, or interactively using the RStudio interface.

The major difference between the r-rich modules and the earlier R modules is that you should not need to load additional modules in order to support installation of most R packages. For instance, in order to install the sf package for one of the older R modules, you would have needed to load modules for udunits, proj, gdal, and geos. With the r-rich modules, once you’ve loaded an r-rich module with the version of R you’d like to use, you can simply install the sf package without loading anything else.

This is accomplished by containerizing R, RStudio, and the dependencies using apptainer. This has the consequence that if you do need additional dependencies in order to install a particular package, other modules that you load are not likely to be compatible with the contents of the r-rich modules. So if you run into a package that you need to install that is not supported by a current r-rich module, please reach out to help@msi.umn.edu and we can help by either creating an updated r-rich module that meets your needs, or by providing support for you making your own modifications to a custom version of the module for your group’s use.

General Linux

Using the module via the command line works the same way that it always has - load the module and run R or Rscript as needed, e.g.

module load r-rich/4.6.0_msi1.2
R

To use the module via the RStudio OnDemand interface, you will need an additional step compared to the previous method.

  • Select RStudio Server from the list of Interactive Apps on the OnDemand website

  • Choose the Resources and Time Limit that you need for your work as usual

  • Under R Version select None (Custom Environment Provided)

  • Tick the box for Customize Environment

  • Fill in the custom environment with the following:

module purge
module load r-rich/4.6.0_msi1.2

  • Launch your job

Versioning of the new modules

The r-rich modules have a two-part versioning label, indicating both the version of R that is installed and the version of the environment that MSI is providing around that R module in terms of dependencies. For instance the module:

r-rich/4.6.0_msi1.2

provides R version 4.6.0, and the set of dependencies version 1.2. The set of dependencies that are included in any particular version of this module are too numerous to list in a useful way - there are over a thousand such dependencies in the 1.2 version.

The recommendation is to use the latest environment version available for the version of R you’d like to use, and try to install the packages you need. If that doesn’t work, reach out to help@msi.umn.edu for guidance on which module might be more appropriate, or assistance with getting an appropriate module installed if one doesn’t already exist.