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  • Bug#1095739: mdanalysis FTBFS on i386

    From Adrian Bunk@21:1/5 to All on Tue Feb 11 12:40:01 2025
    Source: mdanalysis
    Version: 2.8.0-1
    Severity: serious
    Tags: ftbfs patch
    X-Debbugs-Cc: Drew Parsons <dparsons@debian.org>

    https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=i386&ver=2.8.0-1&stamp=1739236579&raw=0

    ...
    =================================== FAILURES ===================================
    ___________________ TestAlign.test_AlignTraj_custom_weights ____________________

    self = <MDAnalysisTests.analysis.test_align.TestAlign object at 0xec988fa8> universe = <Universe with 3341 atoms>, reference = <Universe with 3341 atoms> tmpdir = local('/tmp/pytest-of-buildd/pytest-0/test_AlignTraj_custom_weights0')

    def test_AlignTraj_custom_weights(self, universe, reference, tmpdir):
    weights = np.zeros(universe.atoms.n_atoms)
    ca = universe.select_atoms('name CA')
    weights[ca.indices] = 1

    outfile = str(tmpdir.join('align_test.dcd'))

    x = align.AlignTraj(universe, reference,
    filename=outfile, select='name CA').run()
    x_weights = align.AlignTraj(universe, reference,
    filename=outfile, weights=weights).run()

    assert_allclose(x.results.rmsd, x_weights.results.rmsd, rtol=0, atol=1.5e-7)
    E AssertionError:
    E Not equal to tolerance rtol=0, atol=1.5e-07
    E
    E Mismatched elements: 1 / 98 (1.02%)
    E Max absolute difference among violations: 2.63986569e-07
    E Max relative difference among violations: 1.
    E ACTUAL: array([0. , 0.42343 , 0.593659, 0.736831, 0.82772 , 0.915449,
    E 1.003441, 1.115641, 1.203921, 1.316863, 1.41319 , 1.524446,
    E 1.614766, 1.700183, 1.793369, 1.872636, 1.955786, 2.016655,...
    E DESIRED: array([2.639866e-07, 4.234303e-01, 5.936586e-01, 7.368313e-01,
    E 8.277203e-01, 9.154491e-01, 1.003441e+00, 1.115641e+00,
    E 1.203921e+00, 1.316863e+00, 1.413190e+00, 1.524446e+00,...

    /build/reproducible-path/mdanalysis-2.8.0/testsuite/MDAnalysisTests/analysis/test_align.py:320: AssertionError
    =========================== short test summary info ============================
    FAILED testsuite/MDAnalysisTests/analysis/test_align.py::TestAlign::test_AlignTraj_custom_weights
    = 1 failed, 19082 passed, 558 skipped, 19 deselected, 7 xfailed, 2 xpassed, 170060 warnings in 671.48s (0:11:11) =
    ...


    Fix/Workaround:

    --- debian/rules.old 2025-02-11 02:55:50.128875372 +0000
    +++ debian/rules 2025-02-11 02:56:03.624875712 +0000
    @@ -11,7 +11,7 @@
    SKIP_TEST_LIST += test_all_import[.analysis.hole2] journal.pcbi.1004568

    ifneq (,$(findstring $(DEB_HOST_ARCH), i386))
    - export DEB_CFLAGS_MAINT_APPEND += -ffloat-store
    + export DEB_CFLAGS_MAINT_APPEND += -ffloat-store -fexcess-precision=fast
    export PYBUILD_TEST_ARGS += -v

    SKIP_TEST_LIST += test_multiprocess_COG[u4] test_ramachandran

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Debian Bug Tracking System@21:1/5 to All on Tue Feb 11 16:30:02 2025
    Processing control commands:

    tags -1 ftbfs
    Bug #1095739 [src:mdanalysis] mdanalysis FTBFS on i386
    Ignoring request to alter tags of bug #1095739 to the same tags previously set

    --
    1095739: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1095739
    Debian Bug Tracking System
    Contact owner@bugs.debian.org with problems

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Debian Bug Tracking System@21:1/5 to All on Fri Feb 14 14:40:01 2025
    This is a multi-part message in MIME format...

    Your message dated Fri, 14 Feb 2025 13:35:08 +0000
    with message-id <E1tivqW-001YOz-JL@fasolo.debian.org>
    and subject line Bug#1095739: fixed in mdanalysis 2.8.0-2
    has caused the Debian Bug report #1095739,
    regarding mdanalysis FTBFS on i386
    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 owner@bugs.debian.org
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    --
    1095739: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1095739
    Debian Bug Tracking System
    Contact owner@bugs.debian.org with problems

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