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Groups > linux.debian.bugs.rc > #331287

Bug#1024425: python-pysam: FTBFS with Python 3.11 as a supported version

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Source: python-pysam
Version: 0.19.1+ds-1
Severity: serious
Tags: ftbfs
User: debian-python@lists.debian.org
Usertags: python3.11

Hi Maintainer

python-pysam FTBFS during the recent rebuild adding Python 3.11 as a
supported version [1].  I've copied what I hope is the relevant part
of the log below.

Regards
Graham


[1] https://buildd.debian.org/status/package.php?p=python-pysam


tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope
Fatal Python error: Segmentation fault

Current thread 0x00007f7e0ad1d040 (most recent call first):
  File "/usr/lib/python3.11/unittest/case.py", line 237 in handle
  File "/usr/lib/python3.11/unittest/case.py", line 766 in assertRaises
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build/tests/AlignmentFilePileup_test.py",
line 220 in testIteratorOutOfScope
  File "/usr/lib/python3.11/unittest/case.py", line 579 in _callTestMethod
  File "/usr/lib/python3.11/unittest/case.py", line 623 in run
  File "/usr/lib/python3.11/unittest/case.py", line 678 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 327 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 166 in
pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 259 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 338 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 258 in
call_runtest_hook
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 219 in
call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 130 in
runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 111 in
pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in
pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 322 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 268 in
wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 315 in
pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in
_multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 164 in main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 187 in console_main
  File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 5 in <module>
  File "<frozen runpy>", line 88 in _run_code
  File "<frozen runpy>", line 198 in _run_module_as_main

Extension modules: pysam.libcutils, pysam.libchtslib,
pysam.libcsamtools, pysam.libcbcftools, pysam.libcfaidx,
pysam.libctabixproxies, pysam.libctabix, pysam.libcalignmentfile,
pysam.libcalignedsegment, pysam.libcsamfile, pysam.libcvcf,
pysam.libcbcf, pysam.libcbgzf, Cython.Plex.Actions,
Cython.Plex.Scanners, Cython.Compiler.Scanning,
Cython.Tempita._tempita, Cython.Compiler.Visitor,
Cython.Compiler.FlowControl, _compile_test (total: 20)
Segmentation fault
E: pybuild pybuild:379: test: plugin distutils failed with: exit
code=139: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build;
python3.11 -m pytest tests

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Bug#1024425: python-pysam: FTBFS with Python 3.11 as a supported version Graham Inggs <ginggs@debian.org> - 2022-11-19 11:30 +0100
  Bug#1024425: [Debian-med-packaging] Bug#1024425: python-pysam: FTBFS with Python 3.11 as a supported version Étienne Mollier <emollier@emlwks999.eu> - 2022-11-19 16:50 +0100
  Processed: Re: [Debian-med-packaging] Bug#1024425: python-pysam:  FTBFS with Python 3.11 as a supported version "Debian Bug Tracking System" <owner@bugs.debian.org> - 2022-11-19 16:50 +0100
  Processed: python-pysam ftbfs with python3.11 reduced severity "Debian Bug Tracking System" <owner@bugs.debian.org> - 2022-11-29 22:50 +0100
  Bug#1024425: python-pysam ftbfs with python3.11 reduced severity Étienne Mollier <emollier@emlwks999.eu> - 2022-11-29 22:50 +0100

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