RStudio
A graphical RStudio is available through our cluster Web Portals. Information on accessing the web portal is available on Access the Web Portal) documentation page.
RStudio Server
The RStudio Server app is available on our cluster Web Portals. To get started, connect to one of cluster Web Portals and choose Rstudio from the Interactive Apps menu or the dashboard and then follow the instructions for launching an interactive app. In the submission form, you can alos select between a number of R versions.
Change User R Package Path
To change the default path where packages installed by the user are stored, you need to add the following line of code in your $HOME/.bashrc:
export R_LIBS_USER=path_to_your_local_r_packages
Configure the Graphic Device
When you plot in a RStudio session, you may encounter the following error:
Error in RStudioGD() :
Shadow graphics device error: r error 4 (R code execution error)
In addition: Warning message:
In grDevices:::png("/tmp/RtmpcRxRaB/4v3450e3627g4432fa27f516348657267.png", :
unable to open connection to X11 display ''
To fix the problem, you need to configure your RStudio session to use Cairo for plotting.
You can do it in your code as follows:
options(bitmapType='cairo')
Alternatively, you can put the above code in .Rprofile in your home directory and the option will be picked up automatically.
Clean RStudio
If RStudio becomes slow to respond or completely stops responding, terminate the RStudio session and then run the following script at a shell command line:
ycrc_clean_rstudio.sh
This will remove any temporary files created by RStudio and allow it to start anew.
Run RStudio in Remote Desktop
While we don't generally encourage our users to run a production R code in RStudio, there are cases that it could be beneficial. For example, when a user needs to monitor the R code's progress continuously.
RStudio Server is not user friendly for long-running R code. When your CAS session timeout, you won't be able to reconnect while the code is running. You will need to wait until the code finishes beforeyou can connect to the same session again.
If you need to monitor your R code's progress continuously within the same R session without concerns about disconnection, you can run RStudio Desktop within a Remote Desktop environment.
Using R module with RStudio Desktop
First, start a Remote Desktop instance in the web portal. From the terminal in the Remote Desktop, run the following commands:
module load R
module load RStudio
rstudio
Using R Conda with RStudio Desktop
If you want to use R in a Conda environment, start a Remote Desktop instance in the web portal first.
From the terminal in the Remote Desktop, do not load the modules for R and RStudio.
Instead, install 'rstudio-desktop' into your R Conda environment if you have not done so,
and then call rstudio.
module load miniconda
conda activate my_r_env
conda install rstudio-desktop
rstudio
Troubleshoot
RStudio with Conda R
If you see NOT_FOUND in "Conda R Environment", it means your Conda R environment has not been properly installed. You may need to reinstall your Conda R environment and make sure r-base r-essentials are both included.
RStudio Server does not respond
If you encounter a grey screen after clicking the "Connect to RStudio Server" button, terminate the RStudio session and run clean-rstudio.sh in a [terminal](/clusters-at-yale/access/ood#terminal.