[Debian-med-packaging] Bug#1005479: toil: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13

[Nilesh Patra]

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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