Your message dated Wed, 13 May 2026 14:39:05 +0000
with message-id <[email protected]>
and subject line Bug#1131072: fixed in python-biopython 1.87+dfsg-1
has caused the Debian Bug report #1131072,
regarding python-biopython: autopkgtest regression with NumPy 2.4
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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--
1131072: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1131072
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-biopython
Version: 1.86+dfsg-1
Severity: important
User: [email protected]
Usertags: numpy2.4
Dear maintainer,
According to https://ci.debian.net data, your package python-biopython has an
autopkgtest regression with numpy.
The following architectures failed: amd64, arm64.
Hopefully relevant excerpt from
https://ci.debian.net/packages/p/python-biopython/unstable/amd64/69506848/
follows:
129s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
152s test_PDB_binary_cif ... skipping. Error: Install msgpack to use
Bio.PDB.binaryCIF (e.g. pip install msgpack)
152s test_PDB_internal_coords ... skipping. Error: Install mmtf to use
Bio.PDB.mmtf (e.g. pip install mmtf-python)
152s FAIL
220s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
220s TypeError: only 0-dimensional arrays can be converted to Python scalars
220s ValueError: setting an array element with a sequence.
220s FAILED (failures = 1)
258s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
282s test_PDB_binary_cif ... skipping. Error: Install msgpack to use
Bio.PDB.binaryCIF (e.g. pip install msgpack)
282s test_PDB_internal_coords ... skipping. Error: Install mmtf to use
Bio.PDB.mmtf (e.g. pip install mmtf-python)
282s FAIL
337s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
337s TypeError: only 0-dimensional arrays can be converted to Python scalars
337s ValueError: setting an array element with a sequence.
337s FAILED (failures = 1)
338s dependencies FAIL non-zero exit status 1
561s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
584s FAIL
688s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
688s TypeError: only 0-dimensional arrays can be converted to Python scalars
688s ValueError: setting an array element with a sequence.
688s FAILED (failures = 1)
724s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
753s FAIL
853s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
853s TypeError: only 0-dimensional arrays can be converted to Python scalars
853s ValueError: setting an array element with a sequence.
853s FAILED (failures = 1)
855s full_suite FAIL non-zero exit status 1
855s dependencies FAIL non-zero exit status 1
855s full_suite FAIL non-zero exit status 1
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.87+dfsg-1
Done: Karsten Schöke <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-biopython, 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.
Karsten Schöke <[email protected]> (supplier of updated
python-biopython 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])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 13 May 2026 15:39:59 +0200
Source: python-biopython
Built-For-Profiles: nocheck
Architecture: source
Version: 1.87+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Karsten Schöke <[email protected]>
Closes: 1123673 1131072 1135451
Changes:
python-biopython (1.87+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Fix CVE-2025-68463 (Closes: #1123673, #1131072)
* Standards-Version: 4.7.4 (routine-update)
* d/rules: Sphinx no longer aborts the build on warnings. (Closes: #1135451)
* d/t/control: Remove obsolete skip-not-installable option
* d/rules: Updated the link to the Debian mathjax jslib after upstream
change.
* d/control: wrap-and-sort and change B-D
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