0s autopkgtest [03:04:01]: starting date and time: 2026-02-05 03:04:01+0000 0s autopkgtest [03:04:01]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [03:04:01]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f4bdfax8/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade delly --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-ppc64el-20.secgroup --name adt-resolute-ppc64el-delly-20260205-030401-juju-7f2275-prod-proposed-migration-environment-15-f0a37cf9-b359-4778-9a79-04ddfc1237df --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-delly-20260205-030401-juju-7f2275-prod-proposed-migration-environment-15-f0a37cf9-b359-4778-9a79-04ddfc1237df from image adt/ubuntu-resolute-ppc64el-server-20260205.img (UUID f866c950-0b62-4023-bac6-0f13279e15ed)... 54s autopkgtest [03:04:55]: testbed dpkg architecture: ppc64el 54s autopkgtest [03:04:55]: testbed apt version: 3.1.14 54s autopkgtest [03:04:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 55s autopkgtest [03:04:56]: testbed release detected to be: None 55s autopkgtest [03:04:56]: updating testbed package index (apt update) 57s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 57s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 57s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 57s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 57s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 57s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [257 kB] 57s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1449 kB] 57s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [21.6 kB] 57s Fetched 3839 kB in 2s (2449 kB/s) 58s Reading package lists... 59s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 59s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 59s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 59s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Reading package lists... 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s The following packages will be upgraded: 60s libc-bin libc-gconv-modules-extra libc6 locales pollinate 60s python3-referencing sed 60s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 8612 kB of archives. 60s After this operation, 0 B of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el sed ppc64el 4.9-2build3 [211 kB] 60s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-gconv-modules-extra ppc64el 2.42-2ubuntu5 [1448 kB] 61s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc6 ppc64el 2.42-2ubuntu5 [1913 kB] 61s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-bin ppc64el 2.42-2ubuntu5 [748 kB] 61s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el locales all 2.42-2ubuntu5 [4255 kB] 61s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el pollinate all 4.33-4ubuntu5 [14.0 kB] 61s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 61s dpkg-preconfigure: unable to re-open stdin: No such file or directory 61s Fetched 8612 kB in 1s (16.4 MB/s) 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 ... 82008 files and directories currently installed.) 62s Preparing to unpack .../sed_4.9-2build3_ppc64el.deb ... 62s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 62s Setting up sed (4.9-2build3) ... 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 ... 82008 files and directories currently installed.) 62s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_ppc64el.deb ... 62s Unpacking libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 62s Setting up libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) ... 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 ... 82008 files and directories currently installed.) 62s Preparing to unpack .../libc6_2.42-2ubuntu5_ppc64el.deb ... 62s Unpacking libc6:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 63s Setting up libc6:ppc64el (2.42-2ubuntu5) ... 63s (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 ... 82008 files and directories currently installed.) 63s Preparing to unpack .../libc-bin_2.42-2ubuntu5_ppc64el.deb ... 63s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 63s Setting up libc-bin (2.42-2ubuntu5) ... 64s (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 ... 82008 files and directories currently installed.) 64s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 64s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 64s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 64s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 64s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 64s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 64s Setting up locales (2.42-2ubuntu5) ... 65s Generating locales (this might take a while)... 66s en_US.UTF-8... done 66s Generation complete. 66s Setting up pollinate (4.33-4ubuntu5) ... 77s Setting up python3-referencing (0.36.2-1ubuntu2) ... 77s Processing triggers for man-db (2.13.1-1) ... 79s Processing triggers for install-info (7.2-5) ... 79s Processing triggers for systemd (259-1ubuntu3) ... 80s autopkgtest [03:05:21]: upgrading testbed (apt dist-upgrade and autopurge) 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Solving dependencies... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s autopkgtest [03:05:22]: rebooting testbed after setup commands that affected boot 121s autopkgtest [03:06:02]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 123s autopkgtest [03:06:04]: @@@@@@@@@@@@@@@@@@@@ apt-source delly 125s Get:1 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (dsc) [2274 B] 125s Get:2 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (tar) [3739 kB] 125s Get:3 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (diff) [5324 B] 125s gpgv: Signature made Sat Nov 15 10:23:20 2025 UTC 125s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 125s gpgv: issuer "emollier@debian.org" 125s gpgv: Can't check signature: No public key 125s dpkg-source: warning: cannot verify inline signature for ./delly_1.7.2-1.dsc: no acceptable signature found 125s autopkgtest [03:06:06]: testing package delly version 1.7.2-1 126s autopkgtest [03:06:07]: build not needed 126s autopkgtest [03:06:07]: test run-unit-test: preparing testbed 126s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Solving dependencies... 127s The following NEW packages will be installed: 127s delly libboost-filesystem1.88.0 libboost-iostreams1.88.0 127s libboost-program-options1.88.0 libdeflate0 libhts3t64 libhtscodecs2 127s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 2142 kB of archives. 127s After this operation, 10.7 MB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-filesystem1.88.0 ppc64el 1.88.0-1.4ubuntu3 [296 kB] 127s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-iostreams1.88.0 ppc64el 1.88.0-1.4ubuntu3 [262 kB] 127s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-program-options1.88.0 ppc64el 1.88.0-1.4ubuntu3 [334 kB] 127s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 127s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2build1 [119 kB] 127s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.22.1+ds2-1 [617 kB] 127s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el delly ppc64el 1.7.2-1 [452 kB] 127s Fetched 2142 kB in 0s (12.4 MB/s) 127s Selecting previously unselected package libboost-filesystem1.88.0:ppc64el. 127s (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 ... 82008 files and directories currently installed.) 127s Preparing to unpack .../0-libboost-filesystem1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 127s Unpacking libboost-filesystem1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 127s Selecting previously unselected package libboost-iostreams1.88.0:ppc64el. 127s Preparing to unpack .../1-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 127s Unpacking libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 128s Selecting previously unselected package libboost-program-options1.88.0:ppc64el. 128s Preparing to unpack .../2-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 128s Unpacking libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 128s Selecting previously unselected package libdeflate0:ppc64el. 128s Preparing to unpack .../3-libdeflate0_1.23-2_ppc64el.deb ... 128s Unpacking libdeflate0:ppc64el (1.23-2) ... 128s Selecting previously unselected package libhtscodecs2:ppc64el. 128s Preparing to unpack .../4-libhtscodecs2_1.6.1-2build1_ppc64el.deb ... 128s Unpacking libhtscodecs2:ppc64el (1.6.1-2build1) ... 128s Selecting previously unselected package libhts3t64:ppc64el. 128s Preparing to unpack .../5-libhts3t64_1.22.1+ds2-1_ppc64el.deb ... 128s Unpacking libhts3t64:ppc64el (1.22.1+ds2-1) ... 128s Selecting previously unselected package delly. 128s Preparing to unpack .../6-delly_1.7.2-1_ppc64el.deb ... 128s Unpacking delly (1.7.2-1) ... 128s Setting up libhtscodecs2:ppc64el (1.6.1-2build1) ... 128s Setting up libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 128s Setting up libdeflate0:ppc64el (1.23-2) ... 128s Setting up libboost-filesystem1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 128s Setting up libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 128s Setting up libhts3t64:ppc64el (1.22.1+ds2-1) ... 128s Setting up delly (1.7.2-1) ... 128s Processing triggers for man-db (2.13.1-1) ... 128s Processing triggers for libc-bin (2.42-2ubuntu5) ... 129s autopkgtest [03:06:10]: test run-unit-test: [----------------------- 130s Running Tests 130s Test 1 130s [2026-Feb-05 03:06:11] delly call -o sr.bcf -g ref.fa sr.bam 130s [2026-Feb-05 03:06:11] Paired-end and split-read scanning 130s [2026-Feb-05 03:06:11] Split-read clustering 130s [2026-Feb-05 03:06:11] Paired-end clustering 130s [2026-Feb-05 03:06:11] Split-read assembly 130s [2026-Feb-05 03:06:11] Generate REF and ALT probes 130s [2026-Feb-05 03:06:11] SV annotation 130s [2026-Feb-05 03:06:11] Genotyping 130s [2026-Feb-05 03:06:11] Sample statistics 130s Sample:sr,ReadSize=150,Median=501,MAD=33,UniqueDiscordantPairs=9 130s [2026-Feb-05 03:06:11] Done. 130s Test 2 130s [2026-Feb-05 03:06:11] delly lr -g ref.fa lr.bam -o lr.vcf 130s [2026-Feb-05 03:06:11] Split-read scanning 130s [2026-Feb-05 03:06:11] Split-read assembly 130s [2026-Feb-05 03:06:12] SV annotation 130s [2026-Feb-05 03:06:12] Genotyping 130s [2026-Feb-05 03:06:12] Done. 130s Test 3 130s [2026-Feb-05 03:06:12] delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf 130s [2026-Feb-05 03:06:12] Scanning Windows 130s [2026-Feb-05 03:06:12] Estimate GC bias 130s [2026-Feb-05 03:06:12] Count fragments 130s [2026-Feb-05 03:06:12] Genotyping 130s [2026-Feb-05 03:06:12] Done. 130s PASS 131s autopkgtest [03:06:12]: test run-unit-test: -----------------------] 131s autopkgtest [03:06:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 131s run-unit-test PASS 131s autopkgtest [03:06:12]: @@@@@@@@@@@@@@@@@@@@ summary 131s run-unit-test PASS