Trying out an easy fix for setting the custom tmp folder. #1908
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lbergelson
approved these changes
Aug 9, 2023
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@kockan This seems sane to me. I might put a comment mentioning the timing issue in it.
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@kockan Have you tested that this fixes the issue? Can you reproduce it/ |
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@lbergelson Yes, it does. Here's a run with the main branch: vs. a run with the feature branch: |
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@lbergelson I am also worried about the "instantiating the intel libraries" part, though this comes before any of that really happens, so unless those require the default system tmp dir, it should be fine, but happy to look at alternatives if it actually might break those. |
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@kockan I had misread it when I posted (and deleted) that comment. I think it should be good. It happens before those still. |
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Picard command-line programs that check for R installation do so in the customCommandLineValidation() method under parseArgs(). If the user wants to set a custom tmp directory via the
--TMP_DIRflag, this will not go into effect since any usages of--TMP_DIRhappen after parseArgs(). Therefore RExecutor will try to copy the R script that checks whether R is installed to the default system tmp folder and attempt to run the script from that location.This is an attempt at fixing this timing issue by moving the work related to
--TMP_DIRinside parseArgs(), before customCommandLineValidation() is ever called. I'm not sure whether this is the best long-term solution, but it seems to fix the issue.Related issue: #1907