How to find and connect to an R session using ssh connection?

[mattwarkentin]

Hi,

I am using Positron (version info below) to connect via ssh to my institute's Linux-based HPC.

On this cluster, R is only available as a loadable module. So when first SSH'ing to the login node, there are no R sessions registered with Positron. Even after loading a version of R with module load R/4.2.0, I cannot find an R session to connect to for brief interactive analyses.

Is there a way to make Positron find the now-loaded R session? Any suggestions?

Cannot execute code because there is no registered runtime for the 'r' language.

Positron Version: 2025.06.0 (Universal) build 167
Code - OSS Version: 1.100.0
Commit: e7e5d55
Date: 2025-05-29T20:44:08.369Z
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Darwin arm64 24.5.0

[testlabauto]

Hello @mattwarkentin,

Thank you for using Positron.

Have you tried loading R in a terminal before launching Positron from that same terminal?

Also, is R available at any path such that it could be configured for custom discovery?:

settings:

Or could it be symlinked to a specific path for this same purpose?

[mattwarkentin]

Have you tried loading R in a terminal before launching Positron from that same terminal?

I am not sure I'm following. How would I load R in a terminal (on the HPC) and then use that same terminal to start a Positron remote SSH session which has to be done from my local machine?

Also, is R available at any path such that it could be configured for custom discovery?

Once R is loaded as a module, the path is to the binary is: /global/software/r/r-4.2.0/bin/R

[mattwarkentin]

Adding that path to the setting you described did help Positron discover the R binary after it is loaded as a module. But the R sessions still fails to start up with this error:

R 4.2.0 failed to start up (exit code -1)

The process exited abnormally (signal: 6 (SIGABRT) (core dumped))

[testlabauto]

Yes, I see what you mean regarding my first suggestion. I was thinking the same thing just after replying. Sorry about that.

Regarding supplying the path in the setting, could you share the contents of the Output channel named after the relevant R kernel in this thread.

and also the Kernel Supervisor logs:

I can share the SIGABRT details with a senior developer and see if they have any insight.

As an aside to unfortunately temper your expectations: there is a lot of support for environment modules on Workbench, but none of our desktop stuff has traditionally supported it.

[testlabauto]

And some additional notes from a dev who I have been chatting with:

• look up the R module definition and adding those environment variables to Positron (this can be done in the settings under Environment Variables), or
• adding something to .bash_profile that loads the R module when in Positron

[mattwarkentin]

Okay I started with the simplest solution first and it seemed to work. I added the module load R/4.2.0 to my .bash_profile on the HPC so that the R binary would be loaded and available for the connecting session when using Positron Remote SSH. This, along with adding the path for custom R binary discovery seems to work.

Thanks for your help, @testlabauto.

So, to summarize for whoever stumbles upon this thread who might be facing the same challenge (i.e., make sure Positron is able to find and load R on an HPC where R must be loaded as a module):

1. Load the R module on startup/connection to the HPC via ssh (such as through your .bash_profile)
2. Add the path the R binary to the Positron settings so it can find your custom location (I found this by loading R via module load R/4.2.0 and which R).

[jmcphers]

OK, glad that worked! I filed an issue here to consider having Positron support this natively. #8075