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
