Your message dated Thu, 31 Oct 2024 08:11:39 +0000
with message-id <[email protected]>
and subject line Bug#1086156: fixed in python-biopython 1.84+dfsg-4
has caused the Debian Bug report #1086156,
regarding ftbfs: test failure: DSSP failed to produce an output
to be marked as done.
This means that you claim that the problem has been dealt with.
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1086156: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086156
Debian Bug Tracking System
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--- Begin Message ---
Source: python-biopython
Version: 1.84+dfsg-3
Severity: serious
Tags: ftbfs
Justification: ftbfs
I recently pushed a naive change to python-biopython, and Salsa
CI tripped on the test suite[1]:
ERROR: test_dssp (test_PDB_DSSP.DSSP_tool_test.test_dssp)
Test DSSP generation from PDB.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/builds/med-team/python-biopython/debian/output/source_dir/.pybuild/cpython3_3.12/build/Tests/test_PDB_DSSP.py",
line 105, in test_dssp
dssp = DSSP(model, pdbfile)
^^^^^^^^^^^^^^^^^^^^
File
"/builds/med-team/python-biopython/debian/output/source_dir/.pybuild/cpython3_3.12/build/Bio/PDB/DSSP.py",
line 387, in __init__
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/builds/med-team/python-biopython/debian/output/source_dir/.pybuild/cpython3_3.12/build/Bio/PDB/DSSP.py",
line 201, in dssp_dict_from_pdb_file
raise Exception("DSSP failed to produce an output")
Exception: DSSP failed to produce an output
[1]: https://salsa.debian.org/med-team/python-biopython/-/jobs/6495336/raw
dssp hasn't changed recently, but the libcifpp on which it
depends has been bumped on October 14th 2024. I haven't checked
for sure but maybe it is related?
Cheers, :)
--
.''`. Étienne Mollier <[email protected]>
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`. `' sent from /dev/pts/2, please excuse my verbosity
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--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.84+dfsg-4
Done: Étienne Mollier <[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.
Étienne Mollier <[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, 30 Oct 2024 21:45:42 +0100
Source: python-biopython
Architecture: source
Version: 1.84+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1086156
Changes:
python-biopython (1.84+dfsg-4) unstable; urgency=medium
.
* skip-scipy-in-codonalign.patch: comment about #1086108.
Bug #1086108 may be related and the patch removed once resolved.
* d/t/mini-ccd.cif: new: provide subset of data needed by the libcifpp.
* d/copyright: document origin of mini-ccd.cif.
* d/rules: configure libcifpp to use the mini-ccd.cif.
By instructing the libcifpp to use a local data directory with the
mini-ccd.cif providing the missing components.cif PDB/DSSP related
tests depending on a working libcifpp are back in "fair enough"
working conditions. The original components.cif is more than 400M and
changes constantly, making it problematic to maintain through Debian
packages while at the same time keeping it useful for end users,
Thanks to Maarten L. Hekkelman <[email protected]> (Closes: #1086156)
* d/t/run-unit-test: also fix PDB/dssp for autopkgtest.
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