Bug#1058454: marked as done (prody: autopkgtest regression on i386)

Debian Bug Tracking System Fri, 28 Nov 2025 04:07:26 -0800

Your message dated Fri, 28 Nov 2025 12:05:07 +0000
with message-id <[email protected]>
and subject line Bug#1058454: fixed in prody 2.6.1+dfsg-1
has caused the Debian Bug report #1058454,
regarding prody: autopkgtest regression on i386
to be marked as done.


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-- 
1058454: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1058454
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---

Source: prody
Version: 2.3.1+dfsg-3
Severity: serious
Tags: sid trixie
User: [email protected]
Usertags: regression

Hi Maintainer

The autopkgtest of prody 2.3.1+dfsg-3 is failing when tested with
numpy 1:1.24.2-2 [1].  I've copied what I hope is the relevant part of
the log below.

Regards
Graham


[1] https://ci.debian.net/packages/p/prody/testing/i386/


345s =================================== FAILURES
===================================
345s ______________________ TestANMResults.testHessianSymmetry
______________________
345s
345s self = <prody.tests.dynamics.test_enms.TestANMResults
testMethod=testHessianSymmetry>
345s
345s def testHessianSymmetry(self):
345s hessian = anm._getHessian()
345s > assert_equal(hessian, hessian.T, 'hessian is not symmetric')
345s
345s tests/dynamics/test_enms.py:123:
345s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
345s
345s args = (<built-in function eq>, array([[ 6.9137506 , 0.02186812,
0.9401404 , ..., 0. ,
345s 0. , 0. ...33, 2.28102867],
345s [ 0. , 0. , 0. , ..., 0.89212883,
345s 2.28102867, 2.72983555]]))
345s kwds = {'err_msg': 'hessian is not symmetric', 'header': 'Arrays
are not equal', 'strict': False, 'verbose': True}
345s
345s @wraps(func)
345s def inner(*args, **kwds):
345s with self._recreate_cm():
345s > return func(*args, **kwds)
345s E AssertionError:
345s E Arrays are not equal
345s E hessian is not symmetric
345s E Mismatched elements: 6 / 51984 (0.0115%)
345s E Max absolute difference: 4.4408921e-16
345s E Max relative difference: 7.83963072e-16
345s E x: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s E y: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s
345s /usr/lib/python3.11/contextlib.py:81: AssertionError
345s _____________________ TestEXANMResults.testHessianSymmetry
_____________________
345s
345s self = <prody.tests.dynamics.test_enms.TestEXANMResults
testMethod=testHessianSymmetry>
345s
345s def testHessianSymmetry(self):
345s hessian = exanm._getHessian()
345s > assert_equal(hessian, hessian.T, 'hessian is not symmetric')
345s
345s tests/dynamics/test_enms.py:174:
345s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
345s
345s args = (<built-in function eq>, array([[ 8.02436812, 0.27315085,
4.13687748, ..., 0. ,
345s 0. , 0. ...01, -3.66113893],
345s [ 0. , 0. , 0. , ..., 1.48069236,
345s -3.66113893, 28.20730453]]))
345s kwds = {'err_msg': 'hessian is not symmetric', 'header': 'Arrays
are not equal', 'strict': False, 'verbose': True}
345s
345s @wraps(func)
345s def inner(*args, **kwds):
345s with self._recreate_cm():
345s > return func(*args, **kwds)
345s E AssertionError:
345s E Arrays are not equal
345s E hessian is not symmetric
345s E Mismatched elements: 148 / 13089924 (0.00113%)
345s E Max absolute difference: 8.8817842e-16
345s E Max relative difference: 2.78880522e-16
345s E x: array([[ 8.024368, 0.273151, 4.136877, ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.273151, 3.353604, -0.105517, ..., 0. , 0. ,...
345s E y: array([[ 8.024368, 0.273151, 4.136877, ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.273151, 3.353604, -0.105517, ..., 0. , 0. ,...
345s
345s /usr/lib/python3.11/contextlib.py:81: AssertionError
345s ______________________ TestANM.testBuildMatrixCoordsArray
______________________
345s
345s self = <prody.tests.dynamics.test_enms.TestANM
testMethod=testBuildMatrixCoordsArray>
345s
345s def testBuildMatrixCoordsArray(self):
345s """Test output when *coords* is an array."""
345s
345s self.buildMatrix(COORDS)
345s > assert_equal(self.getMatrix(), self.getExpected(),
345s 'failed to get correct matrix')
345s
345s tests/dynamics/test_enms.py:288:
345s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
345s
345s args = (<built-in function eq>, array([[ 6.9137506 , 0.02186812,
0.9401404 , ..., 0. ,
345s 0. , 0. ...33, 2.28102867],
345s [ 0. , 0. , 0. , ..., 0.89212883,
345s 2.28102867, 2.72983555]]))
345s kwds = {'err_msg': 'failed to get correct matrix', 'header':
'Arrays are not equal', 'strict': False, 'verbose': True}
345s
345s @wraps(func)
345s def inner(*args, **kwds):
345s with self._recreate_cm():
345s > return func(*args, **kwds)
345s E AssertionError:
345s E Arrays are not equal
345s E failed to get correct matrix
345s E Mismatched elements: 1 / 51984 (0.00192%)
345s E Max absolute difference: 1.77635684e-15
345s E Max relative difference: 1.43455679e-16
345s E x: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s E y: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. ,
345s E 0. ],
345s E [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,...
345s
345s /usr/lib/python3.11/contextlib.py:81: AssertionError

--- End Message ---

--- Begin Message ---

Source: prody
Source-Version: 2.6.1+dfsg-1
Done: Andrius Merkys <[email protected]>

We believe that the bug you reported is fixed in the latest version of
prody, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (supplier of updated prody 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 [email protected])


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Hash: SHA512

Format: 1.8
Date: Fri, 28 Nov 2025 06:44:43 -0500
Source: prody
Architecture: source
Version: 2.6.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1058454 1071807 1114707
Changes:
 prody (2.6.1+dfsg-1) unstable; urgency=medium
 .
   * New upstream version 2.6.1+dfsg (Closes: #1058454, #1071807, #1114707)
   * Adjust debian/watch to mangle numbered release candidates.
   * Exclude prody/proteins/hpbmodule/hpb_Python* with prebuilt shared
     libraries.
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--- End Message ---

Bug#1058454: marked as done (prody: autopkgtest regression on i386)

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