[Debian-med-packaging] Bug#1110798: biomaj3-download: FTBFS: make[1]: *** [debian/rules:29: override_dh_auto_test] Error 2

[Lucas Nussbaum]

Source: biomaj3-download
Version: 3.2.12-2
Severity: serious
Justification: FTBFS
Tags: forky sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20250809 ftbfs-forky

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

The full build log is available from:
http://qa-logs.debian.net/2025/08/09/biomaj3-download_3.2.12-2_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20250809;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250809&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

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 mine
so that we can identify if something relevant changed in the meantime.

-- 
Relevant part of the build log (hopefully):
> make[1]: Entering directory '/build/reproducible-path/biomaj3-download-3.2.12'
> LOCAL_IRODS=0 NETWORK=0 python3 -m pytest -v tests/biomaj_tests.py
> ============================= test session starts ==============================
> platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3
> cachedir: .pytest_cache
> rootdir: /build/reproducible-path/biomaj3-download-3.2.12
> plugins: typeguard-4.4.2
> collecting ... collected 0 items / 1 error
> 
> ==================================== ERRORS ====================================
> ____________________ ERROR collecting tests/biomaj_tests.py ____________________
> ImportError while importing test module '/build/reproducible-path/biomaj3-download-3.2.12/tests/biomaj_tests.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3.13/importlib/__init__.py:88: in import_module
>     return _bootstrap._gcd_import(name[level:], package, level)
> tests/biomaj_tests.py:21: in <module>
>     from biomaj_core.config import BiomajConfig
> /usr/lib/python3/dist-packages/biomaj_core/config.py:10: in <module>
>     from biomaj_core.bmajindex import BmajIndex
> /usr/lib/python3/dist-packages/biomaj_core/bmajindex.py:5: in <module>
>     from elasticsearch import Elasticsearch
> /usr/lib/python3/dist-packages/elasticsearch/__init__.py:32: in <module>
>     raise ImportError(
> E   ImportError: An incompatible version of elastic-transport is installed. Must be between v8.0.0 and v9.0.0. Install the correct version with the following command: $ python -m pip install 'elastic-transport>=8, <9'
> =============================== warnings summary ===============================
> tests/biomaj_tests.py:453
>   /build/reproducible-path/biomaj3-download-3.2.12/tests/biomaj_tests.py:453: SyntaxWarning: invalid escape sequence '\s'
>     "<a[\s]+href=\"([\w\-\.]+\">[\w\-\.]+.tar.gz)<\/a>[\s]+([0-9]{2}-[A-Za-z]{3}-[0-9]{4}[\s][0-9]{2}:[0-9]{2})[\s]+([0-9]+[A-Za-z])",
> 
> tests/biomaj_tests.py:454
>   /build/reproducible-path/biomaj3-download-3.2.12/tests/biomaj_tests.py:454: SyntaxWarning: invalid escape sequence '\s'
>     "<a[\s]+href=\"[\w\-\.]+\">([\w\-\.]+.tar.gz)<\/a>[\s]+([0-9]{2}-[A-Za-z]{3}-[0-9]{4}[\s][0-9]{2}:[0-9]{2})[\s]+([0-9]+[A-Za-z])",
> 
> ../../../usr/lib/python3/dist-packages/biomaj_core/utils.py:11
>   /usr/lib/python3/dist-packages/biomaj_core/utils.py:11: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
>     import pkg_resources
> 
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> ERROR tests/biomaj_tests.py
> !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
> ========================= 3 warnings, 1 error in 0.37s =========================
> make[1]: *** [debian/rules:29: override_dh_auto_test] Error 2