[Debian-med-packaging] Bug#1104599: pyranges: FTBFS randomly: failing tests

[Santiago Vila]

Package: src:pyranges
Version: 0.0.111+ds-8
Severity: important
Tags: ftbfs trixie sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
.pybuild/cpython3_3.13_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[NaN, NaN, NaN, '+', '-']
  Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first.
    v.loc[:, "Strand"] = type_v.cat.add_categories(["."])

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - Exceptio...
========= 1 failed, 530 passed, 416111 warnings in 2734.06s (0:45:34) ==========
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyranges/build; python3.13 -m pytest -v -n 2
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:22: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

Note: The failing tests are not always the same, and the failure
rate I get is around 6%. I agree that this is not RC, but still
it might be worth to be investigated.

I've put several build logs here:

https://people.debian.org/~sanvila/build-logs/202505/


About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

[ Note: The above offer, for a FTBFS-randomly bug like this one,
  should be interpreted as "where the randomness is reproducible
  with the given failure rate" ]

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:pyranges, so that this is still
visible in the BTS web page for this package.

Thanks.