#1013703 pyranges: FTBFS: pytest7 regression, py3.9 OK; py3.10 fails with Fatal Python error: Bus error

Package:
src:pyranges
Source:
pyranges
Submitter:
Louis-Philippe Véronneau
Date:
2022-07-07 20:39:03 UTC
Severity:
serious
Tags:
#1013703#5
Date:
2022-06-24 22:48:43 UTC
From:
To:
Hi,

During a selected rebuild of python packages in sid, your package failed
to build with pytest version 7.1.2-1.

The full build log is available from:
http://qa-logs.debian.net/2022/06/09/pytest/pyranges_0.0.111+ds-1_unstable_pytest-exp.log

I had a closer look at the error log and identified the regression as:
'py3.9 OK; py3.10 fails with Fatal Python error: Bus error'. Hopefully,
that's helpful!

All bugs filed during this rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=pytest7;users=debian-python@lists.debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=pytest7&fusertaguser=debian-python@lists.debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

If you reassign this bug to another package, please mark it as
'affects'-ing this package. See
https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it
with the one provided so that we can identify if something relevant
changed in the meantime.

#1013703#10
Date:
2022-07-01 18:53:45 UTC
From:
To:
Control: tag -1 moreinfo

Hi pollo,

I managed to build the package on my machine (I had to be very
very patient though, the build took a good fraction of the
afternoon, log says 5h15m21s).  There should be a build log in
attachment, for reference (please disregard the failure status,
it comes from me screwing up my autopkgtest infrastructure).

Interestingly, reproducible build of pyranges[1] fails due to
timeout at approximately the time your log chokes with the bus
error message.  I'm tempted to suspect this could have occurred
on your end too.

[1]: https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pyranges.html

If there is a problem, I would say that it is the test suite
which takes too long to execute.  Keeping track of the load
average makes me think tests are numerous and run sequentially.

Have a nice day,  :)

#1013703#17
Date:
2022-07-07 20:14:46 UTC
From:
To:
Version: 0.0.111+ds-2

Hello,

I adjusted the test suite of pyranges to run in parallel, to
speed up the process on multithreaded machines.  buildd reports
things went fine[1], and reproduciblebuilds.org[2] tests do not
end up in timeout anymore.  I believe this should settle the
migration to pytest 7 for that package hopefully.

[1]: https://buildd.debian.org/status/package.php?p=pyranges
[2]: https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pyranges.html

Have a nice day,  :)