[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]

control: severity -1 serious
control: tags -1 moreinfo

On Sat, 19 Feb 2022 19:11:52 +0100 Sascha Steinbiss <satta at debian.org> wrote:
> Unfortunately I cannot reproduce this.

+1

> toil 5.6.0-2 builds in unstable
> with no problems locally (amd64) and on the Reproducible Builds build
> cluster [1] on amd64, arm64, i386 and armhf. See attached diff of build
> logs.

CC'ed elbrus.
@Paul, could you please help reproduce this in the debci environment and
help us with any clues as to what might be wrong?

> My hunch after looking at the error message would be a timing issue with
> /tmp cleanups running while the tests are running? The tests take a long
> time so maybe something may have deleted test data at the wrong time?

Could be; also on looking at recent debci logs[2]

| File "/usr/lib/python3/dist-packages/toil/jobStores/fileJobStore.py", line 498, in read_file
|    os.link(jobStoreFilePath, local_path)
| OSError: [Errno 18] Invalid cross-device link: '/tmp/autopkgtest-lxc.rgt3f050/downtmp/build.YHo/src/jobstore-test-de9381ff-d8be-4b36-a691-be2c5fa759d2/files/no-job/file-d7145278c6b84845bd03cf5cff29e690/stream' -> '/home/debci/tmp/tmp1lgiu28c'

It looks (to me) that home and tmp are mounted on different partitions and os.link does not work
with such a setting.
Maybe you could simply do an atomic copy and try once.

> I will lower the severity since I cannot confirm this to be a constant
> FTBFS.

Unfortunately, that does not help us much. It is failing in debci even on a fresh run today as you can also see
in excuses[3] and so we need to fix it.
I have re-bumped to serious and added a moreinfo tag, so atleast this is
in the next tasks to check.

> [1]
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/toil.html
[2]: https://ci.debian.net/data/autopkgtest/testing/amd64/t/toil/19660240/log.gz
[3]: https://qa.debian.org/excuses.php?package=toil

Regards,
Nilesh
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