0s autopkgtest [16:46:19]: starting date and time: 2025-11-17 16:46:19+0000 0s autopkgtest [16:46:19]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:46:19]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z5q9v06f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:dnarrange --apt-upgrade dnarrange --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=dnarrange/1.6.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-3.secgroup --name adt-resolute-amd64-dnarrange-20251117-164619-juju-7f2275-prod-proposed-migration-environment-20-db418cc9-f879-4f24-a943-1263e874b480 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-dnarrange-20251117-164619-juju-7f2275-prod-proposed-migration-environment-20-db418cc9-f879-4f24-a943-1263e874b480 from image adt/ubuntu-resolute-amd64-server-20251117.img (UUID 9762b0cc-7c5b-4854-acd5-cc74ad0de8c6)... 48s autopkgtest [16:47:07]: testbed dpkg architecture: amd64 48s autopkgtest [16:47:07]: testbed apt version: 3.1.11 49s autopkgtest [16:47:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 49s autopkgtest [16:47:08]: testbed release detected to be: None 51s autopkgtest [16:47:09]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [73.2 kB] 51s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9852 B] 51s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 51s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [779 kB] 51s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [113 kB] 51s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [153 kB] 51s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3236 B] 51s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B] 51s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB] 51s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 51s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [254 kB] 51s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [543 kB] 51s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [20.1 kB] 51s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [13.4 kB] 51s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [6516 B] 51s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [680 B] 53s Fetched 2149 kB in 1s (2001 kB/s) 54s Reading package lists... 55s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 57s The following packages will be upgraded: 57s apt libapt-pkg7.0 libcrypt-dev libcrypt1 libunwind8 usbutils 57s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 2978 kB of archives. 57s After this operation, 46.1 kB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt1 amd64 1:4.5.1-1 [90.7 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.12 [1148 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.12 [1474 kB] 57s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 usbutils amd64 1:019-1 [83.9 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libunwind8 amd64 1.8.3-0ubuntu1 [59.6 kB] 58s dpkg-preconfigure: unable to re-open stdin: No such file or directory 58s Fetched 2978 kB in 1s (4856 kB/s) 58s (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 ... 83372 files and directories currently installed.) 58s Preparing to unpack .../libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 58s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) over (1:4.4.38-1build1) ... 58s Preparing to unpack .../libcrypt1_1%3a4.5.1-1_amd64.deb ... 58s Unpacking libcrypt1:amd64 (1:4.5.1-1) over (1:4.4.38-1build1) ... 58s Setting up libcrypt1:amd64 (1:4.5.1-1) ... 58s (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 ... 83372 files and directories currently installed.) 58s Preparing to unpack .../libapt-pkg7.0_3.1.12_amd64.deb ... 58s Unpacking libapt-pkg7.0:amd64 (3.1.12) over (3.1.11) ... 58s Preparing to unpack .../archives/apt_3.1.12_amd64.deb ... 58s Unpacking apt (3.1.12) over (3.1.11) ... 58s Preparing to unpack .../usbutils_1%3a019-1_amd64.deb ... 58s Unpacking usbutils (1:019-1) over (1:018-2) ... 58s Preparing to unpack .../libunwind8_1.8.3-0ubuntu1_amd64.deb ... 58s Unpacking libunwind8:amd64 (1.8.3-0ubuntu1) over (1.8.1-0.1ubuntu1) ... 58s Setting up libunwind8:amd64 (1.8.3-0ubuntu1) ... 58s Setting up usbutils (1:019-1) ... 58s Setting up libcrypt-dev:amd64 (1:4.5.1-1) ... 59s Setting up libapt-pkg7.0:amd64 (3.1.12) ... 59s Setting up apt (3.1.12) ... 59s Processing triggers for man-db (2.13.1-1) ... 61s Processing triggers for libc-bin (2.42-2ubuntu2) ... 61s autopkgtest [16:47:20]: upgrading testbed (apt dist-upgrade and autopurge) 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Solving dependencies... 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s autopkgtest [16:47:23]: rebooting testbed after setup commands that affected boot 97s autopkgtest [16:47:56]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 100s autopkgtest [16:47:59]: @@@@@@@@@@@@@@@@@@@@ apt-source dnarrange 101s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/universe dnarrange 1.6.3-1 (dsc) [1699 B] 101s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/universe dnarrange 1.6.3-1 (tar) [1734 kB] 101s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/universe dnarrange 1.6.3-1 (tar) [30.8 kB] 101s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/universe dnarrange 1.6.3-1 (diff) [2740 B] 101s gpgv: Signature made Sat Nov 1 16:35:01 2025 UTC 101s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 101s gpgv: issuer "nilesh@debian.org" 101s gpgv: Can't check signature: No public key 101s dpkg-source: warning: cannot verify inline signature for ./dnarrange_1.6.3-1.dsc: no acceptable signature found 102s autopkgtest [16:48:01]: testing package dnarrange version 1.6.3-1 102s autopkgtest [16:48:01]: build not needed 103s autopkgtest [16:48:02]: test run-unit-test: preparing testbed 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s Solving dependencies... 104s The following NEW packages will be installed: 104s dnarrange python3-all 104s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 104s Need to get 20.8 kB of archives. 104s After this operation, 96.3 kB of additional disk space will be used. 104s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 dnarrange all 1.6.3-1 [19.9 kB] 104s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.7-1 [884 B] 104s Fetched 20.8 kB in 0s (791 kB/s) 104s Selecting previously unselected package dnarrange. 104s (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 ... 83372 files and directories currently installed.) 104s Preparing to unpack .../dnarrange_1.6.3-1_all.deb ... 104s Unpacking dnarrange (1.6.3-1) ... 104s Selecting previously unselected package python3-all. 104s Preparing to unpack .../python3-all_3.13.7-1_amd64.deb ... 104s Unpacking python3-all (3.13.7-1) ... 104s Setting up python3-all (3.13.7-1) ... 104s Setting up dnarrange (1.6.3-1) ... 105s autopkgtest [16:48:04]: test run-unit-test: [----------------------- 105s # dnarrange 105s 105s number of groups: 0 107s --- tests.out 2022-05-29 08:18:16.000000000 +0000 107s +++ - 2025-11-17 16:48:05.622035677 +0000 107s @@ -22,8 +22,10 @@ 107s -m PROB, --max-mismap=PROB 107s discard any alignment with mismap probability > PROB 107s (default=1.0) 107s + --insert=NAME find insertions of the sequence with this name 107s --shrink shrink the output 107s -v, --verbose show progress messages 107s + -w W, --width=W line-wrap width of group summary lines (default=79) 107s 107s TEST dnarrange alns.maf 107s # dnarrange alns.maf 107s autopkgtest [16:48:06]: test run-unit-test: -----------------------] 108s run-unit-test FAIL non-zero exit status 1 108s autopkgtest [16:48:07]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 108s autopkgtest [16:48:07]: @@@@@@@@@@@@@@@@@@@@ summary 108s run-unit-test FAIL non-zero exit status 1