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  • Bug#1104387: mdanalysis: FTBFS randomly: E: Build killed with signal TE

    From Lucas Nussbaum@21:1/5 to All on Tue Apr 29 16:00:03 2025
    Source: mdanalysis
    Version: 2.9.0-7
    Severity: important
    Justification: FTBFS
    Tags: trixie sid ftbfs
    User: lucas@debian.org
    Usertags: ftbfs-20250428 ftbfs-trixie ftbfs-randomly

    Hi,

    Your package fails to build randomly on amd64: In the exact same
    environment, sometimes it builds fine, and sometimes it fails.

    Relevant part (hopefully):
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy[all-np_slice0-None-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy[all-np_slice0-box1-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy[index 0 to 8 -np_slice1-None-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy[index 0 to 8 -np_slice1-box1-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy[index 9-np_slice2-None-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy[index 9-np_slice2-box1-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy_tric[index 0 to 8 -np_slice0-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestSelfDistanceArrayDCD_TRIC::test_atomgroup_matches_numpy_tric[index 9-np_slice1-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestTriclinicDistances::test_transforms[S_mol-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestTriclinicDistances::test_transforms[S_mol_single-serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestTriclinicDistances::test_selfdist[serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestTriclinicDistances::test_distarray[serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestTriclinicDistances::test_pbc_dist[serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::TestTriclinicDistances::test_pbc_wrong_wassenaar_distance[serial] PASSED [ 44%]
    testsuite/MDAnalysisTests/lib/test_distances.py::test_issue_3725[None]
    E: Build killed with signal TERM after 150 minutes of inactivity


    The full build log is available from: http://qa-logs.debian.net/2025/04/28/mdanalysis_2.9.0-7_unstable.log

    You can find other build logs (including successful ones) in: http://qa-logs.debian.net/2025/04/28/

    All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20250428;users=lucas@debian.org
    or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250428&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

    A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

    If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects

    If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Drew Parsons@21:1/5 to All on Sun May 11 23:40:02 2025
    Source: mdanalysis
    Followup-For: Bug #1104387
    Control: tags -1 ftbfs
    Control: forwarded -1 https://github.com/MDAnalysis/mdanalysis/issues/4906

    There is a degree of flakiness in the mdanalysis tests, known upstream, https://github.com/MDAnalysis/mdanalysis/issues/4209 https://github.com/MDAnalysis/mdanalysis/issues/4906

    test_distance often comes up, but the failures are random all over the
    place. They will pass on a repeat.

    So it's hard to know where to start with the problem. Running no
    tests at all doesn't seem the best way. Skip every failing test one by
    one as they come up, until the probability of failure is sufficiently
    reduced to not trigger your testing system?

    But given the discussion on Issue #4906, perhaps for now we can
    address it by skipping test_distances entirely, until #4906 is fixed.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)