loop printing error when reading R session data

General
1

when running rstudio-server-2023.09.1+494-1.x86_64 with R 3.6, 4.0.0, 4.1.0, 4.2.2, or 4.3.2, on CentOS Linux release 7.9.2009 (Core).
rstudio loops pringing any error that happens while reading the previous session data. E.G., when I run R with my fingers from a bash shell, I get

Warning: namespace 'GenomicRanges' is not available and has been replaced
by .GlobalEnv when processing object 'airway'
Warning: namespace 'DESeq2' is not available and has been replaced
by .GlobalEnv when processing object 'dds'
[Previously saved workspace restored]

but running under rstudio 2023, I get a continuously scrolling

Loading required package: SummarizeExperiment
Loading required package: SummarizeExperiment
Loading required package: SummarizeExperiment
...

This endless spew does not occur with rstudio-server-rhel-2022.07.1-554-x86_64; that prints

Loading required package: SummarizedExperiment
Error in .requirePackage(package) :
  unable to find required package ‘SummarizedExperiment’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘SummarizedExperiment’
Loading required package: DESeq2
Error in .requirePackage(package) :
  unable to find required package ‘DESeq2’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DESeq2’

and then prompts for input.

Has anyone else run into this, and are there any workarounds to restore the RStudio 2022 behavior.? I need to run the 2023 version of RStudio to interoperate with R 4.3.2.

2

Unless things have changed recently RStudio works with R 3.3.0 and up.

3

Correct, but given a saved workspace error (which many of my users have based on testing), Rstudio 2023 loops printing a less than helpful message. RStudio 2022, while it doesn't work with R 4.3.2 (Incompatible Graphics Engine), does handle saved workspace errors gracefully.

4

Another suggestion: have you considered downversioning?

5

Some folks here really want R 4.3.2, and they also want the plot function to work in RStudio. Unfortunately, RStudio 2022 complains

R graphics engine version 16 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.

when used with R 4.3.2. So I can't update R without the current RStudio. They didn't like my idea of "just delete .RData", but that may be what's required..

6

Have you tried changing the graphics engine using Tools | Global Options | General | Advanced?

7

For serious workflows I would not countenance auto saving and auto loading workspaces.
In my humble but experienced opinion, one needs to fully control whats loaded and whats saved, not least because its possible to poison a workspace and find no way back than restarting clean ( i.e. erase the workspace).

My attitude was informed by blog posts from very experienced R folk like Project-oriented workflow and my subsequent personal experience.

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8

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