Your message dated Fri, 14 Feb 2025 13:35:08 +0000
with message-id <e1tivqw-001yoz...@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.
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immediately.)
--
1095739: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1095739
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: mdanalysis
Version: 2.8.0-1
Severity: serious
Tags: ftbfs patch
X-Debbugs-Cc: Drew Parsons <dpars...@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
--- End Message ---
--- Begin Message ---
Source: mdanalysis
Source-Version: 2.8.0-2
Done: Drew Parsons <dpars...@debian.org>
We believe that the bug you reported is fixed in the latest version of
mdanalysis, 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 1095...@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 mdanalysis 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: SHA512
Format: 1.8
Date: Fri, 14 Feb 2025 12:40:15 +0100
Source: mdanalysis
Architecture: source
Version: 2.8.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Closes: 1095739
Changes:
mdanalysis (2.8.0-2) unstable; urgency=medium
.
* Depends: python3-biopython only on arches where it is available
(biopython is optional for mdanalysis, needed for analysis.align)
* run armel tests verbose to identify stalling distance tests
* build i386 with -fexcess-precision=fast (better than relaxing test
tolerance). Closes: #1095739
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mdanalysis_2.8.0-2_source.buildinfo
Checksums-Sha256:
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mdanalysis_2.8.0-2.dsc
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Files:
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66fcfc9939b491d54bd16153a708e542 11112 python optional
mdanalysis_2.8.0-2.debian.tar.xz
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mdanalysis_2.8.0-2_source.buildinfo
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