Your message dated Mon, 12 Feb 2024 07:49:12 +0000
with message-id <e1rzr3w-00aiou...@fasolo.debian.org>
and subject line Bug#1053865: fixed in prody 2.4.1+dfsg-1
has caused the Debian Bug report #1053865,
regarding prody: incompatible with python3-biopython > 1.79
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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--
1053865: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1053865
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: prody
Version: 2.3.1+dfsg-3
Severity: serious
Justification: FTBFS
Tags: sid ftbfs
Forwarded: https://github.com/prody/ProDy/issues/1723
Hello,
prody FTBFS with python3-biopython > 1.79:
======================================================================
FAIL: testBuildMSAlocal
(prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence/test_analysis.py",
line 1210, in testBuildMSAlocal
assert_array_equal(expect, result)
File
"/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
985, in assert_array_equal
assert_array_compare(operator.__eq__, x, y, err_msg=err_msg,
File "/usr/lib/python3.11/contextlib.py", line 81, in inner
return func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File
"/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line
862, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal
Mismatched elements: 2 / 2 (100%)
x: array([<Sequence: 1 (msa_3hsyA_3o21A[0]; length 380; 354 residues
and 26 gaps)>,
<Sequence: 2 (msa_3hsyA_3o21A[1]; length 380; 374 residues and 6
gaps)>],
dtype=object)
y: array([<Sequence: 1 (Unknown[0]; length 80; 59 residues and 21 gaps)>,
<Sequence: 2 (Unknown[1]; length 80; 64 residues and 16 gaps)>],
dtype=object)
The upstream knows about the issue.
Best,
Andrius
--- End Message ---
--- Begin Message ---
Source: prody
Source-Version: 2.4.1+dfsg-1
Done: Andrius Merkys <mer...@debian.org>
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 1053...@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 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 12 Feb 2024 02:30:45 -0500
Source: prody
Architecture: source
Version: 2.4.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1053865
Changes:
prody (2.4.1+dfsg-1) unstable; urgency=medium
.
* New upstream version 2.4.1+dfsg
* Exclude *.bat files.
* Bump copyright years.
* Update standards version to 4.6.2, no changes needed.
* Adjust debian/watch to recognize release candidates.
* Resolve biopython incompatibility by partially applying upstream patch from
PR#1816 (Closes: #1053865)
* Add license paragraph for prody/dynamics/editing.py.
* Switch to 'Testsuite: autopkgtest-pkg-pybuild'.
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ca79e8ea7a3cef7b62ea8938a1ef2e74cb676fb9 9436 prody_2.4.1+dfsg-1.debian.tar.xz
f9ebd7103ef74f64fc73a9ac619a3d93e95255e5 7994
prody_2.4.1+dfsg-1_source.buildinfo
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Files:
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295e44486fd6cb8cbe38f64aad51439e 16085288 science optional
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prody_2.4.1+dfsg-1.debian.tar.xz
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