RStudio Server#

The ‘RStudio Server’ app allows you to run an RStudio session on the cluster. In the ‘R version’ drop-down menu, you can choose the R module version that will be loaded for your session (such as R/4.4.1-gfbf-2023b).

The R-bundle-CRAN module is also loaded by default, providing hundreds of frequently-used R packages.

If needed, the R-bundle-Bioconductor module can be loaded as well to get access to many preinstalled bioinformatics packages.

A very large number of widely used R packages are already available by default. The following modules are always loaded with RStudio:

  • R-bundle-CRAN - packages for general usage available on the CRAN website

  • R-bundle-Bioconductor - bioinformatics packages available on the Bioconductor website

It is also possible to use locally installed R packages with RStudio, see: R package management.

RStudio furthermore allows to create RStudio Projects to manage your R environments. When creating RStudio Projects, we recommend using the command-line tool vsc-Rproject which provides a convenient way to manage your R environments when working with RStudio Projects on our HPC systems.

For more information on how to use RStudio, check out the official documentation.

Notes

  • Navigating between your different directories is possible using the file explorer. If you are navigating by clicking the folder, you will notice that you can see all user folders. You do not have access to these, and you will receive an error when you try to open them. You will also notice that you cannot use the same way of navigating after this. Another solution is to click the three dots on the right (…) and enter your path.

  • The ‘Tools-Install packages’ interface does not allow you to select any other path than the default in your $VSC_HOME. It is recommended to use the install.packages() function instead.

  • By default, RStudio Server stores its cache in $VSC_HOME/.local/share/rstudio. This cache can get very large, and cause you to exceed the quota of your home directory. To avoid this, you can redirect this cache to your $VSC_DATA directory by setting the $XDG_DATA_HOME environment variable in your ~/.bashrc:

    echo "export XDG_DATA_HOME=$VSC_DATA/.local/share" >> ~/.bashrc

    VUB The RStudio app automatically sets this environment variable for you in your app session.

  • Additionally, we recommend changing the default behaviour of RStudio to NOT restore the .RData file (which stores your saved R objects from a previous session) into the workspace on startup, and to NEVER ‘Save the workspace to .RData’ on exit. You can do this via the RStudio interface: Tools > Global Options > General > Workspace. These user preferences are persistent across RStudio sessions, and are saved in your rstudio-prefs.json file. This file (if present) is located in $XDG_CONFIG_HOME/rstudio or $VSC_HOME/.config/rstudio.

    VUB Alternatively, you can tick the ‘Clean workspace at startup’ checkbox in the resources form. However, note that this setting is overridden by your user preferences: namely, the value of the "load_workspace" parameter in your rstudio-prefs.json file takes priority.