RStudio

This is the landing page for RStudio which contains examples, tutorials and other contributed resources for using RStudio on the UFS HPC.

RStudio is an IDE (Integrated Development Environment) for the statistical software R. If you only want to run R, go here.

Note that RStudio uses its own version of R, and mixing it with the stand-alone R package available on the UFS HPC will break RStudio.

UFS HPC Usage Example

RStudio is made available on the UFS HPC within its own Singularity container for use with qvnc. Unfortunately, this means, that software that is distributed within other Singularity containers will not be available.

Follow these steps to run RStudio via qvnc:

  1. Open a Terminal session and load the latest RStudio module:

    $ module load rstudio

    Note: If you need a specific version of RStudio, tab-complete (press tab several times) after typing rstudio to list the versions available and then complete the command with the desired version as follows:

    $ module load rstudio/2022022501_2021.09.2-382_R_4.1.2


    Where the version string is composed of the following components (Refer to above example):

    • The date/version of the container (2022022501)
    • The RStudio version (2021.09.2-382)
    • The R version (4.1.2)

  2. Now create a qvnc session:

    $ qvnc

  3. Once in your desktop environment, click on Activities in the upper left corner of the desktop, and then on the Application launcher: rstudio_1

  4. From the list of applications, find the RStudio icon and click on it to launch RStudio: rstudio_2

Installing Packages in RStudio

Packages from CRAN and a compressed archive can be installed via the GUI. To install a package from CRAN via the GUI, follow these steps:

  1. In the main application menu go to and click on Tools > Install Packages ...: rstudio_3

    The following dialog box should appear:

    rstudio_4

  2. Make sure the CRAN repository is selected:

    rstudio_5

  3. Enter the package name you wish to install in the Packages text box (for multiple packages, separate names with commas). The package name should start to autocomplete if it is in the CRAN repository:

    rstudio_6

    Note: It is recommended not to change the default install library (unless you know what you are doing)

  4. Make sure the Install Dependencies box is checked and click on the Install button. You should notice the installation process proceeding in the R Console (Notice that the GUI simply issues the install.packages()):

    rstudio_7

    The console output should indicate whether the installation was successful.

  5. To install packages from other repositories such as Bioconductor or GitHub, the console should be used with the commands outlined here

Performance Notes

  • 1 Node
  • The recommended resources required by RStudio will depend on the 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

  • No community guides are available.

Official site and documentation

Licensing Information

Primary Citation

  • RStudio Team (2022). RStudio: Integrated Development for R. RStudio, PBC, Boston, MA URL http://www.rstudio.com/.
  • Please remember to check (and cite) the citations for any packages used with RStudio

External Guides and Resources