[Debian-med-packaging] Bug#1131798: sniffles: autopkgtest failure with Python 3.14

[Graham Inggs]

Source: sniffles
Version: 2.6.0-1
Severity: important
Tags: forky sid
User: debian-python at lists.debian.org
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