Hi Paul, On 3/2/22 11:51 PM, Paul Gevers wrote:
I tried re-triggering it to check once again but looks like runners are not up unfortunately.You mean the salsa ones, right?
Yes
And so if you could trigger a test suite for this package at your end once, and help debug it, that'd be really nice.What do you propose I look for? I'm not very good at debugging random software.
Me neither, but I could propose to check for two things: a) As per Sascha's idea[1], if you can simply run the test once, and check there is nothing(no daemon/service) removing files in /tmp/.. dir b) If you could bypass the unlink (patch pasted below to do so) and check once, that would be great [1]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1005479#10 --- a/src/toil/jobStores/fileJobStore.py +++ b/src/toil/jobStores/fileJobStore.py @@ -489,13 +489,16 @@ return except OSError as e: if e.errno == errno.EEXIST: - # Overwrite existing file, emulating shutil.copyfile(). - os.unlink(localFilePath) - # It would be very unlikely to fail again for same reason but possible - # nonetheless in which case we should just give up. - os.link(jobStoreFilePath, localFilePath) - # Now we succeeded and don't need to copy - return + try: + # Overwrite existing file, emulating shutil.copyfile(). + os.unlink(localFilePath) + # It would be very unlikely to fail again for same reason but possible + # nonetheless in which case we should just give up. + os.link(jobStoreFilePath, localFilePath) + # Now we succeeded and don't need to copy + return + except: + pass elif e.errno == errno.EXDEV: # It's a cross-device link even though it didn't appear to be. # Just keep going and hit the file copy case.
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