We have been running this configuration on an HPC cluster without issues:
R 4.2.2+Bioconductor (and other versions)
Rstudio server 2023.12.0-369
OnDemand version: 4.0.3
Rstudio is launched from OnDemand. It starts a per-user dedicated instance of rstudio-server on a compute node and then automatically connects the user via rsession. With this configuration, everything starts normally in about 45 seconds and there are no warnings displayed.
A user recently requested installation of R 4.6.0. We added that as well as R 4.6.0+Bioconductor as new HPC modules, however the new version of R is not compatible with Rstudio server 2023.12.0-369, necessitating an upgrade of RStudio.
For upgrade testing, we tried:
R 4.6.0+Bioconductor
Rstudio server 2026.05.0-218 or
Rstudio server 2026.06.0-242
OnDemand version: 4.0.3 (no change)
R 4.6.0 starts up without issue, but starting with any version of R+Bioconductor results in the "R is taking longer to start than usual" message after 30 seconds:
The various buttons don't seem to help. If you just ignore the dialog, it will start without issue after about 1.5-2 minutes of total time. We could just communicate this to the user base, but it would be a better experience if it would start up faster or at least not display the above dialog. I can only guess that the huge number of packages included with our Bioconductor modules contributes to the slow startup time, although this is not seen when loading an R module from the command line.
Are there any configuration changes I can make to either speed up the rsession startup process or suppress the above startup warning dialog? I've tried the "clean up R/Rstudio state files" as recommended in many other posts regarding the "R is taking longer…" dialog, to no avail. Any assistance appreciated.