[Debian-med-packaging] Bug#1068960: python-pybedtools: FTBFS: testsuite error: 14 failed, 491 passed, 2 deselected, 3 xfailed

[Aurelien Jarno]

Source: python-pybedtools
Version: 0.9.1-1
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)

Dear maintainer,

python-pybedtools fails to build from source due to errors in the
testsuite. From my build log on amd64:

| =========================== short test summary info ============================
| FAILED pybedtools/test/test_gzip_support.py::test_gzipped_file_types_are_bed
| FAILED pybedtools/test/test_gzip_support.py::test_gzipped_files_can_be_intersected
| FAILED pybedtools/test/test_gzip_support.py::test_gzipped_files_are_iterable_as_normal
| FAILED pybedtools/test/test_gzip_support.py::test_str_representation_of_gzipped_files_is_the_same_as_normal
| FAILED pybedtools/test/test_gzip_support.py::test_head_of_gzipped_files_is_the_same_as_normal
| FAILED pybedtools/test/test_gzip_support.py::test_gzipped_output - FileNotFou...
| FAILED pybedtools/test/test_gzip_support.py::test_gzipping_is_default_when_extension_is_dot_gz
| FAILED pybedtools/test/test_gzip_support.py::test_gzipping_can_be_turned_off_even_for_dot_gz
| FAILED pybedtools/test/test_issues.py::test_issue_169 - UnicodeDecodeError: '...
| FAILED pybedtools/test/test_issues.py::test_issue_196 - OSError: Could not op...
| FAILED pybedtools/test/test_issues.py::test_issue_180 - OSError: Could not op...
| FAILED pybedtools/test/test_issues.py::test_issue_181 - OSError: Could not op...
| FAILED pybedtools/test/test_issues.py::test_issue_258 - gzip.BadGzipFile: Not...
| FAILED pybedtools/test/test_issues.py::test_issue_343 - UnicodeDecodeError: '...
| =========== 14 failed, 491 passed, 2 deselected, 3 xfailed in 9.27s ============
| E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build; python3.11 -m pytest -k "not test_chromsizes"
| dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
| make: *** [debian/rules:30: binary] Error 25
| dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

A full build log on riscv64 is available here:
https://buildd.debian.org/status/fetch.php?pkg=python-pybedtools&arch=riscv64&ver=0.9.1-1%2Bb2&stamp=1713040255&raw=0

Full build logs on amd64 and arm64 are also available on reproducible
builds:
https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/python-pybedtools_0.9.1-1.rbuild.log.gz
https://tests.reproducible-builds.org/debian/rbuild/unstable/arm64/python-pybedtools_0.9.1-1.rbuild.log.gz

Regards
Aurelien