#1152973 python-pysam FTBFS on 32-bit with Python 3.15

Package:
src:python-pysam
Source:
src:python-pysam
Submitter:
Sebastian Ramacher
Date:
2026-11-04 10:21:02 UTC
Severity:
normal
Tags:
#1152973#5
Date:
2026-11-03 20:43:39 UTC
From:
To:
Source: python-pysam
Version: 0.24.1+ds-2
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)
X-Debbugs-Cc: debian-arm@lists.debian.org, debian-s390@lists.debian.org, sramacher@debian.org
User: debian-arm@lists.debian.org
Usertags: armhf
User: debian-s390@lists.debian.org
Usertags: s390x
User: debian-qa@lists.debian.org
Usertags: i386

Dear maintainer,

python-pysam FTBFS on armhf, i386, s390x:

tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope Fatal Python error: Segmentation fault

Current thread 0xf793a220 [python3.15] (most recent call first):
  File "/build/reproducible-path/python-pysam-0.24.1+ds/.pybuild/cpython3_3.15_pysam/build/tests/AlignmentFilePileup_test.py", line 189 in testIteratorOutOfScope
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 167 in pytest_pyfunc_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1707 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 184 in pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 250 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 361 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 249 in call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 139 in runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 118 in pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 408 in pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 384 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 377 in pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 229 in _main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 253 in _console_main
  File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
  File "<frozen runpy>", line 87 in _run_code
  File "<frozen runpy>", line 201 in _run_module_as_main

Current thread's C stack trace (most recent call first):
  <system returned no stack trace>

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.cimports.libc.math, Cython.Utils, Cython.Plex.Actions, Cython.Plex.Transitions, Cython.Plex.Machines, Cython.Plex.DFA, Cython.Plex.Scanners, Cython.Compiler.Scanning, Cython.StringIOTree, Cython.Compiler.Code, Cython.Tempita._tempita, Cython.Compiler.LineTable, Cython.Compiler.Visitor, Cython.Compiler.Parsing, Cython.Compiler.FlowControl, _compile_test (total: 29)
Segmentation fault
E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=139: cd /build/reproducible-path/python-pysam-0.24.1+ds/.pybuild/cpython3_3.15_pysam/build; python3.15 -m pytest tests

See
https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=armhf&ver=0.24.1%2Bds-2%2Bb1&stamp=1793471859&raw=0
for a full build log.

Cheers
#1152973#10
Date:
2026-11-03 20:55:34 UTC
From:
To:
Hi,

any help from the s390x side would be welcome.

Kind regards
   Andreas.

----- Weitergeleitete Nachricht von Sebastian Ramacher <sramacher@debian.org> -----

Date: Tue, 3 Nov 2026 21:43:39 +0100
From: Sebastian Ramacher <sramacher@debian.org>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: Bug#1152973: python-pysam: FTBFS on armhf, i386, s390x: tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope Fatal Python error: Segmentation fault
X-Debian-PR-Message: report 1152973
X-Debian-PR-Package: src:python-pysam
X-Debian-PR-Keywords: ftbfs
X-Debian-PR-Source: python-pysam

Source: python-pysam
Version: 0.24.1+ds-2
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)
X-Debbugs-Cc: debian-arm@lists.debian.org, debian-s390@lists.debian.org, sramacher@debian.org
User: debian-arm@lists.debian.org
Usertags: armhf
User: debian-s390@lists.debian.org
Usertags: s390x
User: debian-qa@lists.debian.org
Usertags: i386

Dear maintainer,

python-pysam FTBFS on armhf, i386, s390x:

tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope Fatal Python error: Segmentation fault

Current thread 0xf793a220 [python3.15] (most recent call first):
  File "/build/reproducible-path/python-pysam-0.24.1+ds/.pybuild/cpython3_3.15_pysam/build/tests/AlignmentFilePileup_test.py", line 189 in testIteratorOutOfScope
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 167 in pytest_pyfunc_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1707 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 184 in pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 250 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 361 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 249 in call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 139 in runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 118 in pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 408 in pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 384 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 377 in pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 229 in _main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 253 in _console_main
  File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
  File "<frozen runpy>", line 87 in _run_code
  File "<frozen runpy>", line 201 in _run_module_as_main

Current thread's C stack trace (most recent call first):
  <system returned no stack trace>

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.cimports.libc.math, Cython.Utils, Cython.Plex.Actions, Cython.Plex.Transitions, Cython.Plex.Machines, Cython.Plex.DFA, Cython.Plex.Scanners, Cython.Compiler.Scanning, Cython.StringIOTree, Cython.Compiler.Code, Cython.Tempita._tempita, Cython.Compiler.LineTable, Cython.Compiler.Visitor, Cython.Compiler.Parsing, Cython.Compiler.FlowControl, _compile_test (total: 29)
Segmentation fault
E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=139: cd /build/reproducible-path/python-pysam-0.24.1+ds/.pybuild/cpython3_3.15_pysam/build; python3.15 -m pytest tests

See
https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=armhf&ver=0.24.1%2Bds-2%2Bb1&stamp=1793471859&raw=0
for a full build log.

Cheers
-- 
Sebastian Ramacher



----- Ende weitergeleitete Nachricht -----
#1152973#15
Date:
2026-11-04 02:58:45 UTC
From:
To:
Control: retitle -1 python-pysam FTBFS on 32-bit with Python 3.15

Hi Andreas,

the package never built on s390x (or any other big endian architecture),
new is that it does FTBFS on 32-bit with Python 3.15.

cu
Adrian
#1152973#20
Date:
2026-11-04 08:16:11 UTC
From:
To:
Hello,

Bug #1152973 in python-pysam reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/python-pysam/-/commit/ba3b97bf7b7440475cadb8776e16ce3f349ffe5b
------------------------------------------------------------------------
skip-32bit-tests.patch: skip the 64-bit object-size checks and the PileupColumn access-after-iterator test on 32-bit platforms. Closes: #1152973
------------------------------------------------------------------------

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1152973
#1152973#25
Date:
2026-11-04 10:07:57 UTC
From:
To:
Hello,

Bug #1152973 in python-pysam reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/python-pysam/-/commit/8299c135f07f209194109fc9d979b4cb311cccc3
------------------------------------------------------------------------
skip-32bit-tests.patch: skip the 64-bit object-size checks and the PileupColumn access-after-iterator test on 32-bit platforms. Closes: #1152973
------------------------------------------------------------------------

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1152973
#1152973#30
Date:
2026-11-04 10:19:14 UTC
From:
To:
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 1152973@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (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 ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 04 Nov 2026 10:50:05 +0100
Source: python-pysam
Architecture: source
Version: 0.24.1+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1152973
Changes:
 python-pysam (0.24.1+ds-3) unstable; urgency=medium
 .
   * Fix faidx output capture and improve pysam's use of -o for
     redirection
   * skip-32bit-tests.patch: skip the 64-bit object-size checks
     and the PileupColumn access-after-iterator test on 32-bit platforms.
     Closes: #1152973
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