Your message dated Wed, 18 Jan 2023 16:34:36 +0000 with message-id <e1pibow-0099kk...@fasolo.debian.org> and subject line Bug#1028995: fixed in mdtraj 1.9.7-5 has caused the Debian Bug report #1028995, regarding mdtraj: (autopkgtest) needs update for Python 3.11 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1028995: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028995 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: mdtraj Version: 1.9.7-4 Severity: serious User: debian...@lists.debian.org Usertags: needs-update User: debian-pyt...@lists.debian.org Usertags: python3.11 Control: affects -1 src:python3-defaults Hi Maintainer The autopkgtests of mdtraj fail with Python 3.11 as the default version (and Python 3.10 still supported) [1]. I've copied what I hope is the relevant part of the log below. Regards Graham [1] https://ci.debian.net/packages/m/mdtraj/testing/amd64/ Fatal Python error: Segmentation fault Current thread 0x00007f9669eda040 (most recent call first): File "/usr/lib/python3/dist-packages/mdtraj/core/trajectory.py", line 2062 in image_molecules File "/tmp/autopkgtest-lxc.czx2fspl/downtmp/build.1n0/src/tests/test_trajectory.py", line 732 in test_image_molecules File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195 in pytest_pyfunc_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/python.py", line 1789 in runtest File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 167 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 260 in <lambda> File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 339 in from_call File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 259 in call_runtest_hook File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 220 in call_and_report File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 131 in runtestprotocol File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 112 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 349 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 324 in _main File "/usr/lib/python3/dist-packages/_pytest/main.py", line 270 in wrap_session File "/usr/lib/python3/dist-packages/_pytest/main.py", line 317 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 167 in main File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 190 in console_main File "/usr/bin/pytest-3", line 33 in <module>
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--- Begin Message ---Source: mdtraj Source-Version: 1.9.7-5 Done: Drew Parsons <dpars...@debian.org> We believe that the bug you reported is fixed in the latest version of mdtraj, 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 1028...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Drew Parsons <dpars...@debian.org> (supplier of updated mdtraj 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 Jan 2023 16:38:41 +0100 Source: mdtraj Architecture: source Version: 1.9.7-5 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Changed-By: Drew Parsons <dpars...@debian.org> Closes: 1028995 Changes: mdtraj (1.9.7-5) unstable; urgency=medium . * debian patch python3.11_PR1758.patch adapts upstream PR1758 to fix build with python3.11. Also, skip test_image_molecules in debian/tests (segfaults). Closes: #1028995. * Standards-Version: 4.6.2 Checksums-Sha1: 6604e61de4b319ead77e71515f68f3c793bec499 2597 mdtraj_1.9.7-5.dsc 22018a7df807e0d6c96c67f3ac8dd546b2a032d7 299608 mdtraj_1.9.7-5.debian.tar.xz Checksums-Sha256: 05703412d690c7d2cb1552e2a2fa692fc2f92c5573a80ebfc2dd0d221186eca4 2597 mdtraj_1.9.7-5.dsc b62cee98dd4e0a30b626a02f25a6e49c564009a7b3b15cf4c5bb3bdc10a713cb 299608 mdtraj_1.9.7-5.debian.tar.xz Files: e21c0c12ab2a8546c13babffb8c8733c 2597 python optional mdtraj_1.9.7-5.dsc 2a664d45ee5ead483214f639233c49d8 299608 python optional mdtraj_1.9.7-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmPIGMsACgkQVz7x5L1a AfpMARAAlsY31O3U3uP5TTmG6clwrZ7rfyOctVG7GfEhO4EBO1f5f1Pkl/vVrkVH o0Ztn310qEqLgQdJTsSO8WjqZ7JN5jZDrzKxcsQp6zuhA9YDxXeP6gHGhPCrObux NgD8XF8Hl2drr/YUdwqvW5ITEQGtnjM/dmOHLZVtbq04qeWLsYuZl1n556ZsflqC V0uPiknsjuu5/J/03QEo0HkTzHUwqEFBenPvLxVlos6QnPoO2S6mlizivk1p8DjY PuTbP1T/3n3t9kGLL+RxoIPzKyIiyl8gojH+zu3CMBQE3adxlavMSWbYwJ1ZjIxz x8WqQ9GLqBvtFL24saPo3wvqFfGGvGDVnQNuqXnrv85yLG6lWSsuAwy0mqO41VRh F3SG8wWiUNEFbRYBOgYzlJAfknmuVdMFRqYsbssaaoj6gdOTQWTSeltQ4Sxlw7Y2 9zZAVC2XsBIncJ57EP6DMLrJQQJhCYePOKMvIpb5CZN8DPUN1aNBI0q1oany9jEv Al5mgzvf+z7WP1JO1vbALfPO88EG9veG4tWNpkX0LwxrJUOVNyO9GeYKEIKW+6iI tDyWeCxSM7VP8VwBi+0yRc4+CrsZwoH5MSTGeZvPzAhxhpPjsKe7fpuQ/yGxWapI HcIn6VrfBLWAog//oo1fISuPNWswvBWJT3IWcbVeUHZsOFDb5sY= =Mq2w -----END PGP SIGNATURE-----
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