RStudio Server#

The ‘RStudio Server’ app allows you to run an RStudio session on the cluster. In the ‘Toolchain year and R version’ drop-down menu, you can choose the version of R module that would be loaded for your session. Additionally, the R-bundle-CRAN and R-bundle-Bioconductor modules can be loaded on top of the base R module to provide easy access to hundreds of preinstalled packages.

It is also possible to use locally installed R packages with RStudio, see e.g. VSCdocR package management. RStudio furthermore allows to create RStudio projects to manage your R environments. When doing so, we recommend selecting the renv option to ensure a completely independent R environment. Without using renv, loading an RStudio project may lead to incomplete R library paths.

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

Note

  • 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, the RStudio app redirects the cache to your data directory by setting the $XDG_DATA_HOME variable (you can also set this in your ~/.bashrc):

    export XDG_DATA_HOME=$VSC_DATA/.local/share

  • 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.

    Alternatively, you can tick the ‘Clean workspace at startup’ checkbox in the resources form. Note, however, that your user preferences (stored in $XDG_DATA_HOME/rstudio-prefs.json, defined by the “load_workspace” parameter) take priority over this checkbox option.