Your message dated Tue, 27 Dec 2022 12:32:44 +0000
with message-id <[email protected]>
and subject line Bug#1024425: fixed in python-pysam 0.20.0+ds-2
has caused the Debian Bug report #1024425,
regarding python-pysam: FTBFS with Python 3.11 as a supported version
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1024425: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024425
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-pysam
Version: 0.19.1+ds-1
Severity: serious
Tags: ftbfs
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: python-pysam
Source-Version: 0.20.0+ds-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-pysam, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated python-pysam package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 27 Dec 2022 11:41:25 +0100
Source: python-pysam
Architecture: source
Version: 0.20.0+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1024425
Changes:
python-pysam (0.20.0+ds-2) unstable; urgency=medium
.
* disable-tests-python3.11.patch: add; work around test failure.
Thanks to John Marshall and Graham Inggs (Closes: #1024425)
* d/control: restore dependency on python3-all-dev.
* d/control: restore autodep8-python autopkgtest.
* Standards-Version: 4.6.2 (routine-update)
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