Your message dated Wed, 22 May 2024 14:55:14 +0000
with message-id <[email protected]>
and subject line Bug#1064147: fixed in python-biopython 1.83+dfsg1-3
has caused the Debian Bug report #1064147,
regarding ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1064147: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064147
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-biopython
Version: 1.81+dfsg-3
Severity: serious
Tags: ftbfs
Justification: ftbfs
While trying to pinpoint the root cause of test failures in the
packaging attempt of Biopython 1.83, I eventually realized that
the version 1.81 of Biopython is also affected by the same
issues. The relevant part of the test log looks like:
======================================================================
ERROR: test_embl7 (test_SeqIO.TestSeqIO.test_embl7)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 3388,
in test_embl7
self.perform_test(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626,
in perform_test
self.check_simple_write_read(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363,
in check_simple_write_read
records2 = list(SeqIO.parse(handle=handle, format=fmt))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line
72, in __next__
return next(self.records)
^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
447, in iterate
parser.close()
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
File "../Modules/pyexpat.c", line 416, in StartElement
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in
start_element_ns
self._cont_handler.startElementNS(pair, None,
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
163, in startEntryFieldElement
return self.startPropertyElement(attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
339, in startPropertyElement
record = self.records[-1]
~~~~~~~~~~~~^^^^
IndexError: list index out of range
======================================================================
ERROR: test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 2785,
in test_genbank8
self.perform_test(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626,
in perform_test
self.check_simple_write_read(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363,
in check_simple_write_read
records2 = list(SeqIO.parse(handle=handle, format=fmt))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line
72, in __next__
return next(self.records)
^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
447, in iterate
parser.close()
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
File "../Modules/pyexpat.c", line 416, in StartElement
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in
start_element_ns
self._cont_handler.startElementNS(pair, None,
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
163, in startEntryFieldElement
return self.startPropertyElement(attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
339, in startPropertyElement
record = self.records[-1]
~~~~~~~~~~~~^^^^
IndexError: list index out of range
I haven't checked but I heavily suspect that this is causing
also autopkgtest failures.
For information,
--
.''`. Étienne Mollier <[email protected]>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/0, please excuse my verbosity
`-
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.83+dfsg1-3
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, 22 May 2024 15:14:56 +0200
Source: python-biopython
Architecture: source
Version: 1.83+dfsg1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1064147
Changes:
python-biopython (1.83+dfsg1-3) unstable; urgency=medium
.
* Replace skip-xmlio-tests.patch by seqxml-parser.patch.
Instead of skipping the test, upstream introduced a change that fixed
the XML parser for use with the newer version of expat. (Closes: #1064147)
* d/control: declare compliance to standards version 4.7.0.
* d/python3-biopython.lintian-overrides: update file name.
Checksums-Sha1:
9f225796127c31f404287931989561ebe40e1836 3437 python-biopython_1.83+dfsg1-3.dsc
8e5a862cbf60fe56dc027e324cb0839374de788c 21664
python-biopython_1.83+dfsg1-3.debian.tar.xz
Checksums-Sha256:
75a30a08ed5acf9a129946d923095f33a21fb7bd46b0a12b6c0781a6d6fe05f6 3437
python-biopython_1.83+dfsg1-3.dsc
2abe3dc0c737d519adfdc249769f7ab21549e8bcd2ba17c87a32baa9b396b0b9 21664
python-biopython_1.83+dfsg1-3.debian.tar.xz
Files:
ce987a8a8d1d5b6552fa484cb9c00f6b 3437 python optional
python-biopython_1.83+dfsg1-3.dsc
ca0154424569a03529ae3e195868b14b 21664 python optional
python-biopython_1.83+dfsg1-3.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=05N3
-----END PGP SIGNATURE-----
pgpsyLqfNw0PF.pgp
Description: PGP signature
--- End Message ---
