Your message dated Tue, 07 Jul 2026 20:21:46 +0000
with message-id <[email protected]>
and subject line Bug#1130357: fixed in sniffles 2.8.0-1
has caused the Debian Bug report #1130357,
regarding sniffles: autopkgtest failure with Python 3.14
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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--
1130357: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1130357
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: sniffles
Version: 2.6.0-1
Severity: important
Tags: forky sid
User: [email protected]
Usertags: python3.14
Hi Maintainer
The autopkgtests of this package failed in Ubuntu with Python 3.14 as
the default version. I've copied what I hope is the relevant part of
the log below.
Regards
Graham
67s autopkgtest [16:07:27]: test run-unit-test: [-----------------------
67s 2026-03-24 16:07:26,897 INFO sniffles.main (2037): Running
Sniffles2, build 2.6.0
67s 2026-03-24 16:07:26,897 INFO sniffles.main (2037): Run Mode: call_sample
67s 2026-03-24 16:07:26,898 INFO sniffles.main (2037): Start on:
2026/03/24 16:07:26
67s 2026-03-24 16:07:26,898 INFO sniffles.main (2037): Working dir:
/tmp/autopkgtest.QhQ4KR/autopkgtest_tmp
67s 2026-03-24 16:07:26,898 INFO sniffles.main (2037): Used
command: /usr/bin/sniffles --input test.bam --snf test.snf
67s 2026-03-24 16:07:26,898 INFO sniffles.main (2037):
==============================
67s 2026-03-24 16:07:26,907 INFO sniffles.main (2037): Opening for
reading: test.bam
67s 2026-03-24 16:07:26,907 INFO sniffles.main (2037): Opening for
writing: test.snf
67s 2026-03-24 16:07:26,910 INFO sniffles.main (2037):
67s 2026-03-24 16:07:26,910 INFO sniffles.main (2037): Analyzing 1
alignments total...
67s 2026-03-24 16:07:26,910 INFO sniffles.main (2037):
67s 2026-03-24 16:07:26,910 INFO sniffles.worker (2037): Starting worker 0
67s 2026-03-24 16:07:26,913 ERROR sniffles.main (2037): Unhandled
error while running sniffles.
67s Traceback (most recent call last):
67s File "/usr/bin/sniffles", line 580, in <module>
67s Sniffles2_Main(processes)
67s ~~~~~~~~~~~~~~^^^^^^^^^^^
67s File "/usr/bin/sniffles", line 492, in Sniffles2_Main
67s p.start()
67s ~~~~~~~^^
67s File "/usr/lib/python3/dist-packages/sniffles/parallel.py",
line 522, in start
67s self.process.start()
67s ~~~~~~~~~~~~~~~~~~^^
67s File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start
67s self._popen = self._Popen(self)
67s ~~~~~~~~~~~^^^^^^
67s File "/usr/lib/python3.14/multiprocessing/context.py", line
224, in _Popen
67s return _default_context.get_context().Process._Popen(process_obj)
67s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
67s File "/usr/lib/python3.14/multiprocessing/context.py", line
300, in _Popen
67s return Popen(process_obj)
67s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py",
line 35, in __init__
67s super().__init__(process_obj)
67s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
67s File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line
20, in __init__
67s self._launch(process_obj)
67s ~~~~~~~~~~~~^^^^^^^^^^^^^
67s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py",
line 47, in _launch
67s reduction.dump(process_obj, buf)
67s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
67s File "/usr/lib/python3.14/multiprocessing/reduction.py", line 60, in dump
67s ForkingPickler(file, protocol).dump(obj)
67s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
67s TypeError: cannot pickle '_thread.RLock' object
67s when serializing dict item '_lock'
67s when serializing psutil.Process state
67s when serializing psutil.Process object
67s when serializing dict item '_process'
67s when serializing sniffles.utils.resmon.ResourceMonitor state
67s when serializing sniffles.utils.resmon.ResourceMonitor object
67s when serializing dict item 'recycle'
67s when serializing sniffles.parallel.SnifflesWorker state
67s when serializing sniffles.parallel.SnifflesWorker object
67s when serializing tuple item 0
67s when serializing method reconstructor arguments
67s when serializing method object
67s when serializing dict item '_target'
67s when serializing multiprocessing.context.Process state
67s when serializing multiprocessing.context.Process object
67s autopkgtest [16:07:27]: test run-unit-test: -----------------------]
68s autopkgtest [16:07:28]: test run-unit-test: - - - - - - - - - -
results - - - - - - - - - -
68s run-unit-test FAIL non-zero exit status 1
--- End Message ---
--- Begin Message ---
Source: sniffles
Source-Version: 2.8.0-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sniffles, 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.
Andreas Tille <[email protected]> (supplier of updated sniffles 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: Tue, 07 Jul 2026 21:39:23 +0200
Source: sniffles
Architecture: source
Version: 2.8.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1130357
Changes:
sniffles (2.8.0-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Closes: #1130357
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* d/watch: version=5
* d/copyright: No Files-Excluded needed any more
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Files:
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sniffles_2.8.0.orig.tar.xz
65b4588c5e18c6722a615baa52c804e3 8428 science optional
sniffles_2.8.0-1.debian.tar.xz
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sniffles_2.8.0-1_amd64.buildinfo
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