Getting VsCode to work interactively with R

Step 1: Creating an ssh key to use VSCode

Setup VSCode to run on a compute node using instructions outlined here.

Step 2: ssh to Biowulf and start an interactive session

ssh user@biowulf.nih.gov

sinteractive --gres=lscratch:5 #don't forget to allocate lscratch space  

Step 3: Set up the R Extension on VSCode

Once you have an sinteractive session and allocated compute node (e.g., CN1234), start VSCode and connect to the compute node. Install the "R Extension for Visual Studio Code".

Open the "R Extension" settings.

Add the following line below R › Rpath: Linux Path:

/home/$USER/bin/R  #replace $USER with your biowulf username  

Step 4: Set up Biowulf to work with VSCode R Extension

On Biowulf, create the file /home/$USER/bin/R with the following content:

mkdir ~/bin
nano ~/bin/R  

Paste the following into nano:

#! /bin/bash

module load R/4.2
exec R "$@"

Make /home/$USER/bin/R executable:

chmod +x R  

When R is called in vscode, /home/$USER/bin/R will be called and the content will be run.

If you see an error regarding vscDebugger not being found. You will need to install this package.

On Biowulf enter the following:

CN1234 $ module load R
CN1234 $ R
> remotes::install_github("ManuelHentschel/vscDebugger")
> q()

Step 5: Attach the VSCode R Extension

Assuming you are still connected to a computational node on VSCode, open a new .R file in VSCode. At the bottom of the page, you will see R: (not attached) (See below).

To attach the R extension, simply click R: (not attached). That's it! The IDE should now be ready to use. You will be able to view figures and R object interactively as you work.