Helix/bwVisu/RStudio

RStudio is an integrated development environment (IDE) for programming with R. It can handle Python code, too.

Change R Version

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 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 downloaded 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/your/home/directory
   module load devel/java_jdk
   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 when you choose custom in the dropdown menu when starting the job.

7. (Re)start RStudio

Add R packages

• Add a new package to RStudio
  1. Login to bwForCluster Helix or start the RStudio app on bwVisu and switch to the Terminal tab.
  2. Follow the instructions from the R page
• Note: For some packages, not all development dependencies are available through bwVisu. Some packages may have to be installed on the Login nodes after a ssh-login.
• To create dashboards, you can use RShiny with bwVisu RStudio as well.