0s autopkgtest [02:31:51]: starting date and time: 2026-02-05 02:31:51+0000 0s autopkgtest [02:31:51]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [02:31:51]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n99ix_81/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:glibc --apt-upgrade delly --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- lxd -r lxd-armhf-10.145.243.107 lxd-armhf-10.145.243.107:autopkgtest/ubuntu/resolute/armhf 27s autopkgtest [02:32:18]: testbed dpkg architecture: armhf 29s autopkgtest [02:32:20]: testbed apt version: 3.1.14 32s autopkgtest [02:32:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 34s autopkgtest [02:32:25]: testbed release detected to be: None 43s autopkgtest [02:32:34]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 46s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 46s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 46s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 46s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 46s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 47s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 47s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [250 kB] 47s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1364 kB] 48s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9664 B] 48s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 52s Get:13 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [310 kB] 52s Get:14 http://ftpmaster.internal/ubuntu resolute/main Sources [1413 kB] 52s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 52s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 54s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [176 kB] 56s Fetched 44.0 MB in 11s (3975 kB/s) 58s Reading package lists... 64s autopkgtest [02:32:55]: upgrading testbed (apt dist-upgrade and autopurge) 65s Reading package lists... 66s Building dependency tree... 66s Reading state information... 67s Calculating upgrade... 68s The following packages will be upgraded: 68s libc-bin libc-gconv-modules-extra libc6 libmd0 locales pollinate 68s python3-linkify-it python3-referencing sed 68s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 8120 kB of archives. 68s After this operation, 0 B of additional disk space will be used. 68s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf sed armhf 4.9-2build3 [191 kB] 68s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-gconv-modules-extra armhf 2.42-2ubuntu5 [1417 kB] 68s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6 armhf 2.42-2ubuntu5 [1632 kB] 69s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-bin armhf 2.42-2ubuntu5 [545 kB] 69s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libmd0 armhf 1.1.0-2build4 [23.4 kB] 69s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf locales all 2.42-2ubuntu5 [4255 kB] 69s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 69s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf pollinate all 4.33-4ubuntu5 [14.0 kB] 69s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 70s Preconfiguring packages ... 70s Fetched 8120 kB in 2s (4871 kB/s) 70s (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 ... 68395 files and directories currently installed.) 70s Preparing to unpack .../sed_4.9-2build3_armhf.deb ... 70s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 70s Setting up sed (4.9-2build3) ... 70s (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 ... 68395 files and directories currently installed.) 70s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_armhf.deb ... 70s Unpacking libc-gconv-modules-extra:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 71s Setting up libc-gconv-modules-extra:armhf (2.42-2ubuntu5) ... 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 ... 68395 files and directories currently installed.) 71s Preparing to unpack .../libc6_2.42-2ubuntu5_armhf.deb ... 71s readlink: /usr/lib/libeatmydata: No such file or directory 71s Unpacking libc6:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 71s Setting up libc6:armhf (2.42-2ubuntu5) ... 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 ... 68395 files and directories currently installed.) 71s Preparing to unpack .../libc-bin_2.42-2ubuntu5_armhf.deb ... 71s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 71s Setting up libc-bin (2.42-2ubuntu5) ... 72s (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 ... 68395 files and directories currently installed.) 72s Preparing to unpack .../libmd0_1.1.0-2build4_armhf.deb ... 72s Unpacking libmd0:armhf (1.1.0-2build4) over (1.1.0-2build3) ... 72s Setting up libmd0:armhf (1.1.0-2build4) ... 72s (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 ... 68395 files and directories currently installed.) 72s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 72s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 72s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 72s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 72s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 72s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 72s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 72s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 72s Setting up locales (2.42-2ubuntu5) ... 74s Generating locales (this might take a while)... 78s en_US.UTF-8... done 78s Generation complete. 78s Setting up pollinate (4.33-4ubuntu5) ... 78s apparmor_parser: Unable to replace "pollinate". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 78s 78s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 78s Setting up python3-referencing (0.36.2-1ubuntu2) ... 79s Processing triggers for systemd (259-1ubuntu3) ... 79s Processing triggers for man-db (2.13.1-1) ... 81s Processing triggers for install-info (7.2-5) ... 81s Processing triggers for libc-bin (2.42-2ubuntu5) ... 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s autopkgtest [02:33:18]: rebooting testbed after setup commands that affected boot 128s autopkgtest [02:33:59]: 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 154s autopkgtest [02:34:25]: @@@@@@@@@@@@@@@@@@@@ apt-source delly 165s Get:1 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (dsc) [2274 B] 165s Get:2 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (tar) [3739 kB] 165s Get:3 http://ftpmaster.internal/ubuntu resolute/universe delly 1.7.2-1 (diff) [5324 B] 165s gpgv: Signature made Sat Nov 15 10:23:20 2025 UTC 165s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 165s gpgv: issuer "emollier@debian.org" 165s gpgv: Can't check signature: No public key 165s dpkg-source: warning: cannot verify inline signature for ./delly_1.7.2-1.dsc: no acceptable signature found 165s autopkgtest [02:34:36]: testing package delly version 1.7.2-1 167s autopkgtest [02:34:38]: build not needed 170s autopkgtest [02:34:41]: test run-unit-test: preparing testbed 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 172s Solving dependencies... 173s The following NEW packages will be installed: 173s delly libboost-filesystem1.88.0 libboost-iostreams1.88.0 173s libboost-program-options1.88.0 libdeflate0 libhts3t64 libhtscodecs2 173s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 173s Need to get 1780 kB of archives. 173s After this operation, 9009 kB of additional disk space will be used. 173s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libboost-filesystem1.88.0 armhf 1.88.0-1.4ubuntu3 [286 kB] 174s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libboost-iostreams1.88.0 armhf 1.88.0-1.4ubuntu3 [260 kB] 174s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libboost-program-options1.88.0 armhf 1.88.0-1.4ubuntu3 [345 kB] 174s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 174s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2build1 [67.0 kB] 174s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 174s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf delly armhf 1.7.2-1 [376 kB] 175s Fetched 1780 kB in 1s (2485 kB/s) 175s Selecting previously unselected package libboost-filesystem1.88.0:armhf. 175s (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 ... 68395 files and directories currently installed.) 175s Preparing to unpack .../0-libboost-filesystem1.88.0_1.88.0-1.4ubuntu3_armhf.deb ... 175s Unpacking libboost-filesystem1.88.0:armhf (1.88.0-1.4ubuntu3) ... 175s Selecting previously unselected package libboost-iostreams1.88.0:armhf. 175s Preparing to unpack .../1-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_armhf.deb ... 175s Unpacking libboost-iostreams1.88.0:armhf (1.88.0-1.4ubuntu3) ... 175s Selecting previously unselected package libboost-program-options1.88.0:armhf. 175s Preparing to unpack .../2-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_armhf.deb ... 175s Unpacking libboost-program-options1.88.0:armhf (1.88.0-1.4ubuntu3) ... 175s Selecting previously unselected package libdeflate0:armhf. 175s Preparing to unpack .../3-libdeflate0_1.23-2_armhf.deb ... 175s Unpacking libdeflate0:armhf (1.23-2) ... 175s Selecting previously unselected package libhtscodecs2:armhf. 175s Preparing to unpack .../4-libhtscodecs2_1.6.1-2build1_armhf.deb ... 175s Unpacking libhtscodecs2:armhf (1.6.1-2build1) ... 175s Selecting previously unselected package libhts3t64:armhf. 175s Preparing to unpack .../5-libhts3t64_1.22.1+ds2-1_armhf.deb ... 175s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 175s Selecting previously unselected package delly. 175s Preparing to unpack .../6-delly_1.7.2-1_armhf.deb ... 175s Unpacking delly (1.7.2-1) ... 175s Setting up libhtscodecs2:armhf (1.6.1-2build1) ... 175s Setting up libboost-program-options1.88.0:armhf (1.88.0-1.4ubuntu3) ... 175s Setting up libdeflate0:armhf (1.23-2) ... 175s Setting up libboost-filesystem1.88.0:armhf (1.88.0-1.4ubuntu3) ... 175s Setting up libboost-iostreams1.88.0:armhf (1.88.0-1.4ubuntu3) ... 175s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 175s Setting up delly (1.7.2-1) ... 175s Processing triggers for man-db (2.13.1-1) ... 176s Processing triggers for libc-bin (2.42-2ubuntu5) ... 184s autopkgtest [02:34:55]: test run-unit-test: [----------------------- 186s Running Tests 186s Test 1 186s [2026-Feb-05 02:34:57] delly call -o sr.bcf -g ref.fa sr.bam 186s [2026-Feb-05 02:34:57] Paired-end and split-read scanning 186s [2026-Feb-05 02:34:57] Split-read clustering 186s [2026-Feb-05 02:34:57] Paired-end clustering 186s [2026-Feb-05 02:34:57] Split-read assembly 186s [2026-Feb-05 02:34:57] Generate REF and ALT probes 186s [2026-Feb-05 02:34:57] SV annotation 186s [2026-Feb-05 02:34:57] Genotyping 186s Test 2 186s [2026-Feb-05 02:34:57] Sample statistics 186s Sample:sr,ReadSize=150,Median=501,MAD=33,UniqueDiscordantPairs=9 186s [2026-Feb-05 02:34:57] Done. 186s [2026-Feb-05 02:34:57] delly lr -g ref.fa lr.bam -o lr.vcf 186s [2026-Feb-05 02:34:57] Split-read scanning 186s [2026-Feb-05 02:34:57] Split-read assembly 187s [2026-Feb-05 02:34:58] SV annotation 187s [2026-Feb-05 02:34:58] Genotyping 187s Test 3 187s [2026-Feb-05 02:34:58] Done. 187s [2026-Feb-05 02:34:58] delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf 187s [2026-Feb-05 02:34:58] Scanning Windows 187s [2026-Feb-05 02:34:58] Estimate GC bias 187s [2026-Feb-05 02:34:58] Count fragments 187s [2026-Feb-05 02:34:58] Genotyping 187s PASS 187s [2026-Feb-05 02:34:58] Done. 187s autopkgtest [02:34:58]: test run-unit-test: -----------------------] 191s run-unit-test PASS 191s autopkgtest [02:35:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 195s autopkgtest [02:35:06]: @@@@@@@@@@@@@@@@@@@@ summary 195s run-unit-test PASS