Hi, any help from the s390x side would be welcome.
Kind regards Andreas. ----- Weitergeleitete Nachricht von Sebastian Ramacher <[email protected]> ----- Date: Tue, 3 Nov 2026 21:43:39 +0100 From: Sebastian Ramacher <[email protected]> To: Debian Bug Tracking System <[email protected]> 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: [email protected], [email protected], [email protected] User: [email protected] Usertags: armhf User: [email protected] Usertags: s390x User: [email protected] 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 _______________________________________________ Debian-med-packaging mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging ----- Ende weitergeleitete Nachricht ----- -- https://fam-tille.de
