0s autopkgtest [19:53:43]: starting date and time: 2026-01-22 19:53:43+0000 0s autopkgtest [19:53:43]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [19:53:43]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k88hgovq/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults --apt-upgrade sniffles --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- lxd -r lxd-armhf-10.145.243.28 lxd-armhf-10.145.243.28:autopkgtest/ubuntu/resolute/armhf 23s autopkgtest [19:54:06]: testbed dpkg architecture: armhf 25s autopkgtest [19:54:08]: testbed apt version: 3.1.12 29s autopkgtest [19:54:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s autopkgtest [19:54:14]: testbed release detected to be: None 39s autopkgtest [19:54:22]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 41s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 42s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 42s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 42s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1011 kB] 42s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.6 kB] 42s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.2 kB] 42s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 42s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [95.3 kB] 42s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [658 kB] 42s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [4896 B] 42s Get:12 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [310 kB] 42s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 43s Get:14 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 43s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1371 kB] 43s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.2 MB] 43s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [175 kB] 47s Fetched 42.2 MB in 5s (7800 kB/s) 48s Reading package lists... 54s autopkgtest [19:54:37]: upgrading testbed (apt dist-upgrade and autopurge) 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 58s The following packages were automatically installed and are no longer required: 58s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 58s Use 'apt autoremove' to remove them. 58s The following NEW packages will be installed: 58s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 58s The following packages will be upgraded: 58s libplymouth5 libpython3-stdlib plymouth plymouth-theme-ubuntu-text python3 58s python3-gdbm python3-minimal 58s 7 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 6525 kB of archives. 58s After this operation, 22.5 MB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.2-1 [905 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.2-1 [2155 kB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-gdbm armhf 3.14.2-1 [11.1 kB] 59s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.14.2-1 [28.2 kB] 59s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.14.2-1 [22.9 kB] 59s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.2-1 [2270 kB] 59s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.2-1 [816 kB] 59s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.14.2-1 [10.9 kB] 59s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libplymouth5 armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [147 kB] 59s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf plymouth-theme-ubuntu-text armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [10.0 kB] 59s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf plymouth armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [150 kB] 60s Fetched 6525 kB in 1s (7273 kB/s) 60s Selecting previously unselected package libpython3.14-minimal:armhf. 60s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 66485 files and directories currently installed.) 60s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_armhf.deb ... 60s Unpacking libpython3.14-minimal:armhf (3.14.2-1) ... 60s Selecting previously unselected package python3.14-minimal. 60s Preparing to unpack .../python3.14-minimal_3.14.2-1_armhf.deb ... 60s Unpacking python3.14-minimal (3.14.2-1) ... 60s Preparing to unpack .../python3-gdbm_3.14.2-1_armhf.deb ... 60s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 60s Setting up libpython3.14-minimal:armhf (3.14.2-1) ... 60s Setting up python3.14-minimal (3.14.2-1) ... 62s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 66827 files and directories currently installed.) 62s Preparing to unpack .../python3-minimal_3.14.2-1_armhf.deb ... 62s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 62s Setting up python3-minimal (3.14.2-1) ... 62s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 66827 files and directories currently installed.) 62s Preparing to unpack .../0-python3_3.14.2-1_armhf.deb ... 62s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 62s Selecting previously unselected package libpython3.14-stdlib:armhf. 62s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_armhf.deb ... 62s Unpacking libpython3.14-stdlib:armhf (3.14.2-1) ... 63s Selecting previously unselected package python3.14. 63s Preparing to unpack .../2-python3.14_3.14.2-1_armhf.deb ... 63s Unpacking python3.14 (3.14.2-1) ... 63s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_armhf.deb ... 63s Unpacking libpython3-stdlib:armhf (3.14.2-1) over (3.13.7-1) ... 63s Preparing to unpack .../4-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 63s Unpacking libplymouth5:armhf (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 63s Preparing to unpack .../5-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 63s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 63s Preparing to unpack .../6-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 63s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 63s Setting up libpython3.14-stdlib:armhf (3.14.2-1) ... 63s Setting up libplymouth5:armhf (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 63s Setting up python3.14 (3.14.2-1) ... 64s Setting up libpython3-stdlib:armhf (3.14.2-1) ... 64s Setting up python3-gdbm (3.14.2-1) ... 64s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 64s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 65s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 65s Setting up python3 (3.14.2-1) ... 65s Processing triggers for libc-bin (2.42-2ubuntu4) ... 66s Processing triggers for systemd (259-1ubuntu2) ... 66s Processing triggers for man-db (2.13.1-1) ... 67s Processing triggers for initramfs-tools (0.150ubuntu7) ... 67s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 67s Processing triggers for initramfs-tools (0.150ubuntu7) ... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Solving dependencies... 70s The following packages will be REMOVED: 70s libpython3.13-minimal* libpython3.13-stdlib* python3.13* python3.13-minimal* 71s 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. 71s After this operation, 21.3 MB disk space will be freed. 71s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 67257 files and directories currently installed.) 71s Removing python3.13 (3.13.11-1) ... 71s Removing libpython3.13-stdlib:armhf (3.13.11-1) ... 71s Removing python3.13-minimal (3.13.11-1) ... 72s Removing libpython3.13-minimal:armhf (3.13.11-1) ... 72s Processing triggers for man-db (2.13.1-1) ... 72s Processing triggers for systemd (259-1ubuntu2) ... 73s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 66518 files and directories currently installed.) 73s Purging configuration files for libpython3.13-minimal:armhf (3.13.11-1) ... 73s Purging configuration files for python3.13-minimal (3.13.11-1) ... 75s autopkgtest [19:54:58]: rebooting testbed after setup commands that affected boot 118s autopkgtest [19:55:41]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 145s autopkgtest [19:56:08]: @@@@@@@@@@@@@@@@@@@@ apt-source sniffles 156s Get:1 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (dsc) [2056 B] 156s Get:2 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (tar) [2917 kB] 156s Get:3 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (diff) [8416 B] 157s gpgv: Signature made Sat Feb 15 22:05:44 2025 UTC 157s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 157s gpgv: issuer "tille@debian.org" 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./sniffles_2.6.0-1.dsc: no acceptable signature found 157s autopkgtest [19:56:20]: testing package sniffles version 2.6.0-1 159s autopkgtest [19:56:22]: build not needed 162s autopkgtest [19:56:25]: test run-unit-test: preparing testbed 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Solving dependencies... 164s The following NEW packages will be installed: 164s libdeflate0 libhts3t64 libhtscodecs2 python3-edlib python3-psutil 164s python3-pysam sniffles 165s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 5211 kB of archives. 165s After this operation, 42.8 MB of additional disk space will be used. 165s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 165s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2build1 [67.0 kB] 165s Get:3 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 165s Get:4 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-edlib armhf 1.2.7-7 [91.1 kB] 165s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-psutil armhf 7.1.0-1ubuntu1 [189 kB] 165s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pysam armhf 0.23.3+ds-2 [4358 kB] 165s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf sniffles all 2.6.0-1 [58.5 kB] 166s Fetched 5211 kB in 1s (6718 kB/s) 166s Selecting previously unselected package libdeflate0:armhf. 166s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 66518 files and directories currently installed.) 166s Preparing to unpack .../0-libdeflate0_1.23-2_armhf.deb ... 166s Unpacking libdeflate0:armhf (1.23-2) ... 166s Selecting previously unselected package libhtscodecs2:armhf. 166s Preparing to unpack .../1-libhtscodecs2_1.6.1-2build1_armhf.deb ... 166s Unpacking libhtscodecs2:armhf (1.6.1-2build1) ... 166s Selecting previously unselected package libhts3t64:armhf. 166s Preparing to unpack .../2-libhts3t64_1.22.1+ds2-1_armhf.deb ... 166s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 166s Selecting previously unselected package python3-edlib:armhf. 166s Preparing to unpack .../3-python3-edlib_1.2.7-7_armhf.deb ... 166s Unpacking python3-edlib:armhf (1.2.7-7) ... 166s Selecting previously unselected package python3-psutil. 166s Preparing to unpack .../4-python3-psutil_7.1.0-1ubuntu1_armhf.deb ... 166s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 166s Selecting previously unselected package python3-pysam. 166s Preparing to unpack .../5-python3-pysam_0.23.3+ds-2_armhf.deb ... 166s Unpacking python3-pysam (0.23.3+ds-2) ... 166s Selecting previously unselected package sniffles. 167s Preparing to unpack .../6-sniffles_2.6.0-1_all.deb ... 167s Unpacking sniffles (2.6.0-1) ... 167s Setting up libhtscodecs2:armhf (1.6.1-2build1) ... 167s Setting up libdeflate0:armhf (1.23-2) ... 167s Setting up python3-psutil (7.1.0-1ubuntu1) ... 167s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 167s Setting up python3-edlib:armhf (1.2.7-7) ... 167s Setting up python3-pysam (0.23.3+ds-2) ... 167s Setting up sniffles (2.6.0-1) ... 168s Processing triggers for man-db (2.13.1-1) ... 169s Processing triggers for libc-bin (2.42-2ubuntu4) ... 176s autopkgtest [19:56:39]: test run-unit-test: [----------------------- 179s 2026-01-22 19:56:42,011 INFO sniffles.main (1027): Running Sniffles2, build 2.6.0 179s 2026-01-22 19:56:42,011 INFO sniffles.main (1027): Run Mode: call_sample 179s 2026-01-22 19:56:42,011 INFO sniffles.main (1027): Start on: 2026/01/22 19:56:42 179s 2026-01-22 19:56:42,011 INFO sniffles.main (1027): Working dir: /tmp/autopkgtest.ylPxpi/autopkgtest_tmp 179s 2026-01-22 19:56:42,011 INFO sniffles.main (1027): Used command: /usr/bin/sniffles --input test.bam --snf test.snf 179s 2026-01-22 19:56:42,011 INFO sniffles.main (1027): ============================== 179s 2026-01-22 19:56:42,050 INFO sniffles.main (1027): Opening for reading: test.bam 179s 2026-01-22 19:56:42,053 INFO sniffles.main (1027): Opening for writing: test.snf 179s 2026-01-22 19:56:42,062 INFO sniffles.main (1027): 179s 2026-01-22 19:56:42,063 INFO sniffles.main (1027): Analyzing 1 alignments total... 179s 2026-01-22 19:56:42,063 INFO sniffles.main (1027): 179s 2026-01-22 19:56:42,063 INFO sniffles.worker (1027): Starting worker 0 179s 2026-01-22 19:56:42,070 ERROR sniffles.main (1027): Unhandled error while running sniffles. 179s Traceback (most recent call last): 179s File "/usr/bin/sniffles", line 580, in 179s Sniffles2_Main(processes) 179s ~~~~~~~~~~~~~~^^^^^^^^^^^ 179s File "/usr/bin/sniffles", line 492, in Sniffles2_Main 179s p.start() 179s ~~~~~~~^^ 179s File "/usr/lib/python3/dist-packages/sniffles/parallel.py", line 522, in start 179s self.process.start() 179s ~~~~~~~~~~~~~~~~~~^^ 179s File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start 179s self._popen = self._Popen(self) 179s ~~~~~~~~~~~^^^^^^ 179s File "/usr/lib/python3.14/multiprocessing/context.py", line 224, in _Popen 179s return _default_context.get_context().Process._Popen(process_obj) 179s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 179s File "/usr/lib/python3.14/multiprocessing/context.py", line 300, in _Popen 179s return Popen(process_obj) 179s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ 179s super().__init__(process_obj) 179s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 179s File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ 179s self._launch(process_obj) 179s ~~~~~~~~~~~~^^^^^^^^^^^^^ 179s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 47, in _launch 179s reduction.dump(process_obj, buf) 179s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 179s File "/usr/lib/python3.14/multiprocessing/reduction.py", line 60, in dump 179s ForkingPickler(file, protocol).dump(obj) 179s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^ 179s TypeError: cannot pickle '_thread.RLock' object 179s when serializing dict item '_lock' 179s when serializing psutil.Process state 179s when serializing psutil.Process object 179s when serializing dict item '_process' 179s when serializing sniffles.utils.resmon.ResourceMonitor state 179s when serializing sniffles.utils.resmon.ResourceMonitor object 179s when serializing dict item 'recycle' 179s when serializing sniffles.parallel.SnifflesWorker state 179s when serializing sniffles.parallel.SnifflesWorker object 179s when serializing tuple item 0 179s when serializing method reconstructor arguments 179s when serializing method object 179s when serializing dict item '_target' 179s when serializing multiprocessing.context.Process state 179s when serializing multiprocessing.context.Process object 179s autopkgtest [19:56:42]: test run-unit-test: -----------------------] 183s run-unit-test FAIL non-zero exit status 1 183s autopkgtest [19:56:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 187s autopkgtest [19:56:50]: @@@@@@@@@@@@@@@@@@@@ summary 187s run-unit-test FAIL non-zero exit status 1