RStudio crash affecting SCE subset `[` operation

[tavareshugo]

(last updated July 2025 - this bug might "resolve itself" with new Bioc releases)

In both the bulk and single-cell courses we've been experiencing a sporadic crash that we cannot replicate, but consistently happens to ~5 participants in the room:

• When performing a subset operation, e.g. sce[detected_genes, ] R/RStudio hangs for a really long time.
• Closing RStudio doesn't solve the issue, as several rsession processes remain running in the background.

As we haven't found a solution for this problem, if this occurs during the course, the solution is:

• In-person course
  • Open a terminal and run killall rstudio rsession.
  • Restart RStudio.
• Online course
  • Easy and quick: Ask Paul to restart the instance (@ tag him on Slack)
  • Fallback: Open a terminal on Guacamole and run: killall rsession, then refresh the RServer window.

Try running the code again - usually it works, as the crash doesn't tend to repeat itself.

If the crash does happen, please mention it to me or Paul J, so we are aware that the crash still affects current courses.

[tavareshugo]

This issue is still affecting courses Nov 2025, including online courses. We still could not find any solution:

• We are running the latest version of Bioc 3.22 (released Oct 2025).
• I have re-serialised the objects for the Bulk course using latest version, but still the bug occurs.