RStudio User Guide

Table of contents

1. How to change the R version in RStudio
   1. Change the R version to one of the available versions on Helix
   2. Change the R version to a version unavailable on Helix
2. How to add R packages to Rstudio

How to change the R version in RStudio

By default, the default R version on Helix is used. You can view the current default version by executing module -t -d avail 2>&1 | grep math/R on Helix.

Change the R version to one of the available versions on Helix

1. Open or create the file .bashrc in your home directory, either by opening a shell on Helix or by starting the RStudio app on bwVisu and opening the file there.
2. Add the following line to your .bashrc file:

   export R_MODULE_VERSION=<available R version on Helix>
   

   for example export R_MODULE_VERSION=4.2.1.
3. (Re)start RStudio

Change the R version to a version unavailable on Helix

1. Open a shell on Helix by sshing into Helix or by starting the RStudio app on bwVisu and switching to the Terminal tab:
2. Download your desired R version, unpack it and change into the unpacked directory:

   tar -xf R-x.y.z.tar.gz
   cd R-x.y.z.tar.gz
   

   where x.y.z denotes the version of your download R installation files.
3. Patch the configuration file to make it compatible with your shell environment on Helix:

   sed '/date-time conversions do not work in 2020/s/^/: #/' -i configure
   

4. Install R into a chosen location in your home directory:

   ./configure prefix=$HOME/path/in/you/home/directory
   make
   make install
   

5. Make your installed R version the default by exporting the location of its binary to your PATH: Open or create the file .bashrc in your home directory and add the following line:

   export "$PATH=/path/to/your/R/installation/directory/bin:$PATH"
   

   Please make sure that the suffix /bin is added to the path to the installation location of your custom R version. This is the default location where the binaries of R will be usually installed.
6. Test the installation: Reload your bash environment and obtain the version of the R binary in your path:

   source $HOME/.bashrc && R --version
   

   If the displayed version number is equal to the one of your custom R installation, then the installation was successfull and your custom R version will be automatically loaded in RStudio.
7. (Re)start RStudio

How to add R packages to RStudio

1. Open a shell on Helix by sshing into Helix or by starting the RStudio app on bwVisu and switching to the Terminal tab.

2. Execute

   module load math/R/4.2.1
   

3. Load the R environment by executing

   R
   

4. Run the following installation command:

   install.packages("name-of-the-package")
   

   If the package will not install because another package could no be installed, try to run the installation command for that package first. After that, retry to install package. If the installation worked, you'll be able to load the package in RStudio.