Unable to create R notebook in RStudio

[hexhowells]

When trying to open a R Notebook in RStudio (Running in a Galaxy workbook) I get the following error:

Error writing code to file /var/lib/condor/execute/dir_90804/bccd-ac5d-7e72-44da: system error 2 (No such file or directory)
Error in file(filename, "r") : cannot open the connection
Calls: sourceWithProgress -> parse -> file
In addition: Warning message:
In file(filename, "r") :
  cannot open file '/var/lib/condor/execute/dir_90804/bccd-ac5d-7e72-44da': Permission denied
Execution halted

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Steps to reproduce

1. Run RStudio in a Galaxy workflow
2. In RStudio: "File" > "New File" > "R Notebook"
3. Click Yes to the following prompt

[bgruening]

@hexhowells thanks for the report. I, unfortunately, do not understand enough about RStudio and why it needs to write in this folder. It looks like it should not look there. HOME is not pointing to this dir, so no clue why its looking there.

The file is also not there, I have checked and this is how it looks like:

root@42fa4f61d0b8:/data/jwd01/pulsar_staging/61740283/working# ls -l /var/lib/condor/execute/dir_525019
total 0
drwx------. 2 rstudio-server rstudio-server  6 Aug  5 08:52 tmp
drwx------. 3 rstudio-server rstudio-server 17 Aug  5 08:52 var

Do you need those packages to be updated? Maybe we can rebuild the container instead?

[hexhowells]

I'm still getting familiar with RStudio myself, but updating the packages might address the current issue of the outdated packages.

Rebuilding the container might be a more robust long-term solution, especially since the automated package updating seems to be encountering problems with that directory.