RStudio-Server crashes using Seurat/VlnPlot after upgrading to R 4.1.0

We recently upgraded software on one of our computational nodes:

  • Ubuntu 20.04
  • R 4.1.0
  • RStudio Server 1.4.1106

Ever since the upgrade, multiple users cannot run VlnPlot() or DimPlot() through the Seurat package. Their RStudio session crashes right away. We use a web browser to connect to RStudio Server, and once either of those commands are run, an error message pops up:

The previous R session was abnormally terminated due to an unexpected crash. You may have lost workspace data as a result of this crash.

/var/log/syslog only shows a one line error that's not super helpful, as far as I can tell:

ERROR session hadabend; LOGGED FROM: rstudio::core::Error {anonymous}::rInit(const rstudio::r::session::RInitInfo&) src/cpp/session/SessionMain.cpp:680

We've tried renaming .rstudio in each home directory to force a brand new environment with no old settings, but even installing the latest version of Seurat into a blank environment and running their tutorial with their sample data, the same problem comes up. I can't figure out what the problem might be, nor how to find a helpful log entry for it.

Any ideas for what to look at? I'm a Linux guy and I know my way around a terminal, but R and RStudio are not my areas of expertise. Thanks in advance!

R 4.1 breaks the current release of RStudio. There's a RStudio v1.4.1717-3 preview available.

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Wow, I had no idea about that. Is that documented anywhere? I saw that RStudio v1.3.1073-1 added "compatibility with R 4.1.0's graphics engine" back in 2020, and I didn't see that v1.4.1106 required R < 4.1 in any of the documentation or release notes.

Regardless, I'll try that upgrade and test it out tomorrow. Thanks!

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That did it! Upgrading to 1.4.1717 fixed plotting using R 4.1. I wish they would be more clear about version compatibility though. Thanks so much!

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