Your message dated Fri, 23 Sep 2022 06:19:03 +0000
with message-id <e1obc1f-00gbs4...@fasolo.debian.org>
and subject line Bug#1019515: fixed in gemmi 0.5.7+ds-1
has caused the Debian Bug report #1019515,
regarding gemmi: autopkgtest regression on arm64 i386 s390x and ppc64el:
numerical deltas
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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--
1019515: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1019515
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: gemmi
Version: 0.5.6+ds-2
Severity: serious
User: debian...@lists.debian.org
Usertags: regression
Dear maintainer(s),
With a recent upload of gemmi the autopkgtest of gemmi fails in testing
when that autopkgtest is run with the binary packages of gemmi from
unstable. It passes when run with only packages from testing. In tabular
form:
pass fail
gemmi from testing 0.5.6+ds-2
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration to testing [1]. Can
you please investigate the situation and fix it?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=gemmi
https://ci.debian.net/data/autopkgtest/testing/arm64/g/gemmi/25899714/log.gz
=================================== FAILURES
===================================
__________________________ TestProg.test_sfcalc_1pfe
___________________________
self = <test_prog.TestProg testMethod=test_sfcalc_1pfe>
@unittest.skipIf(sys.platform == 'win32', 'with MSVC it differs
slightly')
def test_sfcalc_1pfe(self):
self.do('''\
$ gemmi sfcalc --dmin=9 --rate=4 --blur=60 --rcut=1e-7 --test -v
tests/1pfe.cif.gz
[...]
RMSE=0.0010414 0.0001639% max|dF|=0.003530 R=0.000%
<dPhi>=8.067e-06
''') # noqa: E501
tests/test_prog.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_prog.py:36: in do
self.assertEqual(expected_lines, output_lines)
E AssertionError: Lists differ: ['RMSE=0.0010414 0.0001639%
max|dF|=0.003530 R=0.000% <dPhi>=8.067e-06'] != ['RMSE=0.0010127
0.0001594% max|dF|=0.003041 R=0.000% <dPhi>=7.880e-06']
E E First differing element 0:
E 'RMSE=0.0010414 0.0001639% max|dF|=0.003530 R=0.000%
<dPhi>=8.067e-06'
E 'RMSE=0.0010127 0.0001594% max|dF|=0.003041 R=0.000%
<dPhi>=7.880e-06'
E E - ['RMSE=0.0010414 0.0001639% max|dF|=0.003530 R=0.000%
<dPhi>=8.067e-06']
E ? - ^ ^^ -- ^ --
E E + ['RMSE=0.0010127 0.0001594% max|dF|=0.003041 R=0.000%
<dPhi>=7.880e-06']
E ? ^^ ^ + ++ ++ ^
__________________________ TestProg.test_sfcalc_5wkd
___________________________
self = <test_prog.TestProg testMethod=test_sfcalc_5wkd>
@unittest.skipIf(sys.platform == 'win32', 'with MSVC it differs
slightly')
def test_sfcalc_5wkd(self):
self.do('''\
$ gemmi sfcalc --blur=12 --dmin=2.5 --rate=2.5 --rcut=1e-7 --test
-v tests/5wkd.pdb
[...]
RMSE=3.3342e-05 4.703e-05% max|dF|=0.0001706 R=0.000%
<dPhi>=4.718e-06
''') # noqa: E501
tests/test_prog.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_prog.py:36: in do
self.assertEqual(expected_lines, output_lines)
E AssertionError: Lists differ: ['RMSE=3.3342e-05 4.703e-05%
max|dF|=0.0001706 R=0.000% <dPhi>=4.718e-06'] != ['RMSE=3.2830e-05
4.630e-05% max|dF|=0.0001628 R=0.000% <dPhi>=4.665e-06']
E E First differing element 0:
E 'RMSE=3.3342e-05 4.703e-05% max|dF|=0.0001706 R=0.000%
<dPhi>=4.718e-06'
E 'RMSE=3.2830e-05 4.630e-05% max|dF|=0.0001628 R=0.000%
<dPhi>=4.665e-06'
E E - ['RMSE=3.3342e-05 4.703e-05% max|dF|=0.0001706 R=0.000%
<dPhi>=4.718e-06']
E ? ^^^ ^ - --
^^^
E E + ['RMSE=3.2830e-05 4.630e-05% max|dF|=0.0001628 R=0.000%
<dPhi>=4.665e-06']
E ? ++ ^ ^^ ++
^^^
=========================== short test summary info
============================
FAILED tests/test_prog.py::TestProg::test_sfcalc_1pfe - AssertionError:
Lists...
FAILED tests/test_prog.py::TestProg::test_sfcalc_5wkd - AssertionError:
Lists...
======================== 2 failed, 169 passed in 1.42s
=========================
autopkgtest [17:13:32]: test command1
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: gemmi
Source-Version: 0.5.7+ds-1
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
gemmi, 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 1019...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated gemmi 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: Thu, 22 Sep 2022 10:02:00 -0400
Source: gemmi
Architecture: source
Version: 0.5.7+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1019515
Changes:
gemmi (0.5.7+ds-1) unstable; urgency=medium
.
* New upstream version 0.5.7+ds
* Drop upstream-integrated patches.
* Skip overly sensitive test (Closes: #1019515).
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