[Debian-med-packaging] Bug#1110800: biomaj3-core: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
Lucas Nussbaum
lucas at debian.org
Mon Aug 11 08:36:52 BST 2025
Source: biomaj3-core
Version: 3.0.28-4
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-core_3.0.28-4_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):
> debian/rules binary
> dh binary --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:311: python3.13 setup.py config
> /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
> warnings.warn(msg)
> /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
> !!
>
> ********************************************************************************
> Please consider removing the following classifiers in favor of a SPDX license expression:
>
> License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> self._finalize_license_expression()
> running config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:311: /usr/bin/python3 setup.py build
> /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
> warnings.warn(msg)
> /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
> !!
>
> ********************************************************************************
> Please consider removing the following classifiers in favor of a SPDX license expression:
>
> License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> self._finalize_license_expression()
> running build
> running build_py
> creating /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/biomaj_core
> copying biomaj_core/utils.py -> /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/biomaj_core
> copying biomaj_core/bmajindex.py -> /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/biomaj_core
> copying biomaj_core/config.py -> /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/biomaj_core
> copying biomaj_core/__init__.py -> /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/biomaj_core
> running egg_info
> creating biomaj_core.egg-info
> writing biomaj_core.egg-info/PKG-INFO
> writing dependency_links to biomaj_core.egg-info/dependency_links.txt
> writing requirements to biomaj_core.egg-info/requires.txt
> writing top-level names to biomaj_core.egg-info/top_level.txt
> writing manifest file 'biomaj_core.egg-info/SOURCES.txt'
> reading manifest file 'biomaj_core.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> adding license file 'LICENSE'
> writing manifest file 'biomaj_core.egg-info/SOURCES.txt'
> copying biomaj_core/mimes-bio.txt -> /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/biomaj_core
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:311: cd /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build; python3.13 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0
> rootdir: /build/reproducible-path/biomaj3-core-3.0.28
> plugins: typeguard-4.4.2
> collected 0 items / 1 error
>
> ==================================== ERRORS ====================================
> _ ERROR collecting .pybuild/cpython3_3.13_biomaj-core/build/tests/test_biomaj.py _
> ImportError while importing test module '/build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/tests/test_biomaj.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/test_biomaj.py:8: in <module>
> from biomaj_core.config import BiomajConfig
> biomaj_core/config.py:10: in <module>
> from biomaj_core.bmajindex import BmajIndex
> 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 ===============================
> biomaj_core/utils.py:11
> /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build/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/test_biomaj.py
> !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
> ========================= 1 warning, 1 error in 0.29s ==========================
> E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /build/reproducible-path/biomaj3-core-3.0.28/.pybuild/cpython3_3.13_biomaj-core/build; python3.13 -m pytest tests
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
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