0s autopkgtest [01:33:16]: starting date and time: 2026-02-05 01:33:16+0000 0s autopkgtest [01:33:16]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:33:16]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zih03lid/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:chiark-tcl --apt-upgrade delly --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 chiark-tcl/1.3.7build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-24.secgroup --name adt-resolute-arm64-delly-20260205-013316-juju-7f2275-prod-proposed-migration-environment-2-bbce6263-c22c-4ac8-88ee-79cce5362ec6 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-delly-20260205-013316-juju-7f2275-prod-proposed-migration-environment-2-bbce6263-c22c-4ac8-88ee-79cce5362ec6 from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 65s autopkgtest [01:34:21]: testbed dpkg architecture: arm64 65s autopkgtest [01:34:21]: testbed apt version: 3.1.14 65s autopkgtest [01:34:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s autopkgtest [01:34:21]: testbed release detected to be: None 66s autopkgtest [01:34:22]: updating testbed package index (apt update) 67s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 68s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1768 kB] 68s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 68s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 68s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [228 kB] 68s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [262 kB] 68s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7248 B] 68s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 68s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 68s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1540 kB] 68s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [40.2 kB] 68s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 68s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 72s Fetched 4091 kB in 2s (2196 kB/s) 73s Reading package lists... 73s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 73s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 74s Reading package lists... 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Calculating upgrade... 75s The following packages will be upgraded: 75s libc-bin libc-gconv-modules-extra libc6 locales python3-linkify-it 76s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 7881 kB of archives. 76s After this operation, 0 B of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 76s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 76s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 76s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 77s dpkg-preconfigure: unable to re-open stdin: No such file or directory 77s Fetched 7881 kB in 1s (9764 kB/s) 77s (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 ... 89360 files and directories currently installed.) 77s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 77s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 77s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 77s (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 ... 89360 files and directories currently installed.) 77s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 78s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 78s Setting up libc6:arm64 (2.42-2ubuntu5) ... 78s (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 ... 89360 files and directories currently installed.) 78s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 78s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 78s Setting up libc-bin (2.42-2ubuntu5) ... 78s (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 ... 89360 files and directories currently installed.) 78s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 78s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 79s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 79s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 79s Setting up locales (2.42-2ubuntu5) ... 79s Generating locales (this might take a while)... 81s en_US.UTF-8... done 81s Generation complete. 81s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 82s Processing triggers for man-db (2.13.1-1) ... 83s Processing triggers for systemd (259-1ubuntu3) ... 84s autopkgtest [01:34:40]: upgrading testbed (apt dist-upgrade and autopurge) 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 85s Calculating upgrade... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Solving dependencies... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s autopkgtest [01:34:45]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 89s autopkgtest [01:34:45]: @@@@@@@@@@@@@@@@@@@@ apt-source delly 91s Get:1 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (dsc) [2274 B] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (tar) [3739 kB] 91s Get:3 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (diff) [5324 B] 91s gpgv: Signature made Sat Nov 15 10:23:20 2025 UTC 91s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 91s gpgv: issuer "emollier@debian.org" 91s gpgv: Can't check signature: No public key 91s dpkg-source: warning: cannot verify inline signature for ./delly_1.7.2-1.dsc: no acceptable signature found 91s autopkgtest [01:34:47]: testing package delly version 1.7.2-1 91s autopkgtest [01:34:47]: build not needed 92s autopkgtest [01:34:48]: test run-unit-test: preparing testbed 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Solving dependencies... 93s The following NEW packages will be installed: 93s delly libboost-filesystem1.88.0 libboost-iostreams1.88.0 93s libboost-program-options1.88.0 libdeflate0 libhts3t64 libhtscodecs2 95s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 1853 kB of archives. 95s After this operation, 10.0 MB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-filesystem1.88.0 arm64 1.88.0-1.4ubuntu3 [290 kB] 95s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.88.0 arm64 1.88.0-1.4ubuntu3 [261 kB] 95s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-program-options1.88.0 arm64 1.88.0-1.4ubuntu3 [326 kB] 95s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 95s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2build1 [83.8 kB] 95s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 95s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 delly arm64 1.7.2-1 [404 kB] 95s Fetched 1853 kB in 2s (779 kB/s) 95s Selecting previously unselected package libboost-filesystem1.88.0:arm64. 95s (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 ... 89360 files and directories currently installed.) 95s Preparing to unpack .../0-libboost-filesystem1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 96s Unpacking libboost-filesystem1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 96s Selecting previously unselected package libboost-iostreams1.88.0:arm64. 96s Preparing to unpack .../1-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 96s Unpacking libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 96s Selecting previously unselected package libboost-program-options1.88.0:arm64. 96s Preparing to unpack .../2-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 96s Unpacking libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 96s Selecting previously unselected package libdeflate0:arm64. 96s Preparing to unpack .../3-libdeflate0_1.23-2_arm64.deb ... 96s Unpacking libdeflate0:arm64 (1.23-2) ... 96s Selecting previously unselected package libhtscodecs2:arm64. 96s Preparing to unpack .../4-libhtscodecs2_1.6.1-2build1_arm64.deb ... 96s Unpacking libhtscodecs2:arm64 (1.6.1-2build1) ... 96s Selecting previously unselected package libhts3t64:arm64. 96s Preparing to unpack .../5-libhts3t64_1.22.1+ds2-1_arm64.deb ... 96s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 96s Selecting previously unselected package delly. 96s Preparing to unpack .../6-delly_1.7.2-1_arm64.deb ... 96s Unpacking delly (1.7.2-1) ... 96s Setting up libhtscodecs2:arm64 (1.6.1-2build1) ... 96s Setting up libboost-program-options1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 96s Setting up libdeflate0:arm64 (1.23-2) ... 96s Setting up libboost-filesystem1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 96s Setting up libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 96s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 96s Setting up delly (1.7.2-1) ... 96s Processing triggers for man-db (2.13.1-1) ... 96s Processing triggers for libc-bin (2.42-2ubuntu5) ... 97s autopkgtest [01:34:53]: test run-unit-test: [----------------------- 98s Running Tests 98s Test 1 98s [2026-Feb-05 01:34:53] delly call -o sr.bcf -g ref.fa sr.bam 98s [2026-Feb-05 01:34:54] Paired-end and split-read scanning 98s [2026-Feb-05 01:34:54] Split-read clustering 98s [2026-Feb-05 01:34:54] Paired-end clustering 98s [2026-Feb-05 01:34:54] Split-read assembly 98s [2026-Feb-05 01:34:54] Generate REF and ALT probes 98s [2026-Feb-05 01:34:54] SV annotation 98s [2026-Feb-05 01:34:54] Genotyping 98s [2026-Feb-05 01:34:54] Sample statistics 98s Sample:sr,ReadSize=150,Median=501,MAD=33,UniqueDiscordantPairs=9 98s [2026-Feb-05 01:34:54] Done. 98s Test 2 98s [2026-Feb-05 01:34:54] delly lr -g ref.fa lr.bam -o lr.vcf 98s [2026-Feb-05 01:34:54] Split-read scanning 98s [2026-Feb-05 01:34:54] Split-read assembly 98s [2026-Feb-05 01:34:54] SV annotation 98s [2026-Feb-05 01:34:54] Genotyping 98s Test 3 98s [2026-Feb-05 01:34:54] Done. 98s [2026-Feb-05 01:34:54] delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf 98s [2026-Feb-05 01:34:54] Scanning Windows 98s [2026-Feb-05 01:34:54] Estimate GC bias 98s [2026-Feb-05 01:34:54] Count fragments 98s [2026-Feb-05 01:34:54] Genotyping 98s PASS 98s [2026-Feb-05 01:34:54] Done. 99s autopkgtest [01:34:55]: test run-unit-test: -----------------------] 99s autopkgtest [01:34:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 99s run-unit-test PASS 100s autopkgtest [01:34:56]: @@@@@@@@@@@@@@@@@@@@ summary 100s run-unit-test PASS