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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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LinkPeaks, FindMarkers functions not working on RStudio AWS Server #1706

Closed chsnys closed 2 months ago

chsnys commented 4 months ago 
# insert reproducible example here

Hi, while i write the same code with same versions of packages in Desktop RStudio app, the LinkPeaks, FindMarkers functions are running smoothly and i am seeing output within 5 mins, but when i am running the same code using these functions in AWS RStudio server, the code is not running and i am seeing R session aborted within two hours. the server has double the capacity of RAM, the Desktop Application has, i am not seeing how much the function is processing even when i set Verbose to TRUE. can you please provide support to this issue?

timoast commented 3 months ago

Hi @chsnys, not sure what to suggest here, this sounds like it could be some issue with RStudio/AWS rather than Signac. Maybe you can try running as an Rscript on aws to narrow down whether the issue is specific to aws or RStudio? If you're able to provide a small reproducible example I can try on an AWS instance and see if I can reproduce the issue

timoast commented 2 months ago

Closing this now as I haven't heard back, please reopen if you are able to provide the reproducible example