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markrobinsonuzh / cytofWorkflow

MIT License
14 stars 3 forks source link

R session aborted #38

Closed yueli8 closed 4 months ago

yueli8 commented 4 months ago

Hello,

Thank you so much for developing so nice software.

When I ran following commands, it always shows R session aborted.

What can I do at present stage?

Thank you in advance for your great help!

Best,

Yue

da_res1 <- diffcyt(sce, 
    formula = da_formula1, contrast = contrast,
    analysis_type = "DA", method_DA = "diffcyt-DA-GLMM",
    clustering_to_use = "merging1", verbose = FALSE)

Screenshot from 2024-06-21 02-27-46

HelenaLC commented 4 months ago

What version of R are you using? What’s the output of your session info? Hard to advise without any information…

yueli8 commented 4 months ago

Hello HelenaLC,

Thank you so much for your quick response!

R version is R 4.4.0.

Please see following Screenshot.

Thank you in advance for your great help!

Best,

Yue

Screenshot from 2024-06-21 02-27-46

markrobinsonuzh commented 4 months ago

I'm not fully sure. But are you running this in VSCode ?

https://www.reddit.com/r/Ubuntu/comments/1d9ajpb/vscode_has_been_crashing_on_ubuntu_22044_lts_x86/

(at least several of the error message related to this are potentially VSCode-related)

yueli8 commented 4 months ago

Hello markrobinsonuzh,

Thank you so much for your great help!

I running all these commands in R studio version 4.4.0. The environment is Ubuntu 18.04.5 LTS.

Thank you again and really appreciated!

Best,

Yue

markrobinsonuzh commented 4 months ago

Hi Yue,

Do you have the latest version of RStudio?

From what I've found, for example:

https://stackoverflow.com/questions/67638836/r-crashing-while-displaying-ggplot-after-update-process-memory-read-out-of-rang

https://issues.apache.org/jira/browse/ARROW-13037

I believe this is fully unrelated to diffcyt / cytofWorkflow.

Best, Mark

yueli8 commented 4 months ago

Hello markrobinsonuzh,

Thank you so much for your quick response!

My RStudio is 4.4.0. My Ubuntu environment is 18.04.5 LTS.

Is that because my Ubuntu environment is too old ?I should upgrade my Ubuntu environment?

Thank you in advance for your great help!

Best,

Yue

markrobinsonuzh commented 4 months ago

Your version of R is 4.4.0, but what version of RStudio do you have? See here: https://posit.co/download/rstudio-desktop/

In any case, Ubuntu 18.04 is "end of life" for >1 year now, so it could be useful to upgrade: https://ubuntu.com/blog/18-04-end-of-standard-support

I will close the issue because it does not appear to be a cytofWorkflow issue (I also checked building it locally on my hardward and it was fine), but rather a local installation issue.