0s autopkgtest [18:45:09]: starting date and time: 2024-03-25 18:45:09+0000 0s autopkgtest [18:45:09]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:45:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8y1vt05e/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:delly,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade delly --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=delly/1.1.8-1build2 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-20.secgroup --name adt-noble-s390x-delly-20240325-184509-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 113s autopkgtest [18:47:02]: testbed dpkg architecture: s390x 114s autopkgtest [18:47:03]: testbed apt version: 2.7.12 114s autopkgtest [18:47:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 115s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 115s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 115s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4045 kB] 116s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 116s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 116s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [693 kB] 116s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 116s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 116s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 116s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4173 kB] 117s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 117s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 117s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 119s Fetched 9648 kB in 4s (2627 kB/s) 120s Reading package lists... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s Calculating upgrade... 124s The following packages will be REMOVED: 124s libssl3 124s The following NEW packages will be installed: 124s libssl3t64 124s The following packages have been kept back: 124s curl 124s The following packages will be upgraded: 124s openssl 124s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 124s Need to get 2685 kB of archives. 124s After this operation, 239 kB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 125s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 125s Fetched 2685 kB in 1s (2873 kB/s) 125s (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 ... 52170 files and directories currently installed.) 125s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 125s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 125s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 125s wget depends on libssl3 (>= 3.0.0). 125s tnftp depends on libssl3 (>= 3.0.0). 125s tcpdump depends on libssl3 (>= 3.0.0). 125s systemd-resolved depends on libssl3 (>= 3.0.0). 125s systemd depends on libssl3 (>= 3.0.0). 125s sudo depends on libssl3 (>= 3.0.0). 125s s390-tools depends on libssl3 (>= 3.0.0). 125s rsync depends on libssl3 (>= 3.0.0). 125s python3-cryptography depends on libssl3 (>= 3.0.0). 125s openssh-server depends on libssl3 (>= 3.0.10). 125s openssh-client depends on libssl3 (>= 3.0.10). 125s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 125s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 125s libssh-4:s390x depends on libssl3 (>= 3.0.0). 125s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 125s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 125s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 125s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 125s libnvme1 depends on libssl3 (>= 3.0.0). 125s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 125s libkmod2:s390x depends on libssl3 (>= 3.0.0). 125s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 125s libcurl4:s390x depends on libssl3 (>= 3.0.0). 125s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 125s kmod depends on libssl3 (>= 3.0.0). 125s dhcpcd-base depends on libssl3 (>= 3.0.0). 125s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 125s 125s (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 ... 52170 files and directories currently installed.) 125s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 125s Selecting previously unselected package libssl3t64:s390x. 125s (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 ... 52159 files and directories currently installed.) 125s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 125s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 126s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 126s Setting up openssl (3.0.13-0ubuntu2) ... 126s Processing triggers for man-db (2.12.0-3) ... 126s Processing triggers for libc-bin (2.39-0ubuntu6) ... 126s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 127s Unknown architecture, assuming PC-style ttyS0 127s sh: Attempting to set up Debian/Ubuntu apt sources automatically 127s sh: Distribution appears to be Ubuntu 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s eatmydata is already the newest version (131-1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s dbus is already the newest version (1.14.10-4ubuntu1). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 131s rng-tools-debian is already the newest version (2.4). 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s The following packages will be REMOVED: 131s cloud-init* python3-configobj* python3-debconf* 132s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 132s After this operation, 3256 kB disk space will be freed. 132s (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 ... 52172 files and directories currently installed.) 132s Removing cloud-init (24.1.2-0ubuntu1) ... 132s Removing python3-configobj (5.0.8-3) ... 132s Removing python3-debconf (1.5.86) ... 132s Processing triggers for man-db (2.12.0-3) ... 133s (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 ... 51783 files and directories currently installed.) 133s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 133s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 133s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 133s invoke-rc.d: policy-rc.d denied execution of try-restart. 137s Reading package lists...Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 137s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 137s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 137s Reading package lists... 137s 137s Building dependency tree... 137s Reading state information... 137s linux-generic is already the newest version (6.8.0-11.11+1). 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Calculating upgrade... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s autopkgtest [18:47:28]: rebooting testbed after setup commands that affected boot 157s autopkgtest [18:47:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 160s autopkgtest [18:47:49]: @@@@@@@@@@@@@@@@@@@@ apt-source delly 163s Get:1 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (dsc) [2113 B] 163s Get:2 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (tar) [3744 kB] 163s Get:3 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (diff) [5312 B] 163s gpgv: Signature made Tue Dec 19 15:01:08 2023 UTC 163s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 163s gpgv: Can't check signature: No public key 163s dpkg-source: warning: cannot verify inline signature for ./delly_1.1.8-1build1.dsc: no acceptable signature found 163s autopkgtest [18:47:52]: testing package delly version 1.1.8-1build1 163s autopkgtest [18:47:52]: build not needed 168s autopkgtest [18:47:57]: test run-unit-test: preparing testbed 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 174s The following additional packages will be installed: 174s delly libboost-filesystem1.83.0 libboost-iostreams1.83.0 174s libboost-program-options1.83.0 libdeflate0 libgomp1 libhts3 libhtscodecs2 174s The following NEW packages will be installed: 174s autopkgtest-satdep delly libboost-filesystem1.83.0 libboost-iostreams1.83.0 174s libboost-program-options1.83.0 libdeflate0 libgomp1 libhts3 libhtscodecs2 174s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 2341 kB/2342 kB of archives. 174s After this operation, 10.1 MB of additional disk space will be used. 174s Get:1 /tmp/autopkgtest.4tveag/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [700 B] 174s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libboost-filesystem1.83.0 s390x 1.83.0-2ubuntu1 [372 kB] 174s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libboost-iostreams1.83.0 s390x 1.83.0-2ubuntu1 [340 kB] 174s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2ubuntu1 [418 kB] 174s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 174s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 174s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 175s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 175s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x delly s390x 1.1.8-1build1 [463 kB] 176s Fetched 2341 kB in 2s (990 kB/s) 176s Selecting previously unselected package libboost-filesystem1.83.0:s390x. 176s (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 ... 51728 files and directories currently installed.) 176s Preparing to unpack .../0-libboost-filesystem1.83.0_1.83.0-2ubuntu1_s390x.deb ... 176s Unpacking libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 176s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 176s Preparing to unpack .../1-libboost-iostreams1.83.0_1.83.0-2ubuntu1_s390x.deb ... 176s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 176s Selecting previously unselected package libboost-program-options1.83.0:s390x. 176s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-2ubuntu1_s390x.deb ... 176s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 176s Selecting previously unselected package libgomp1:s390x. 176s Preparing to unpack .../3-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 176s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 176s Selecting previously unselected package libdeflate0:s390x. 176s Preparing to unpack .../4-libdeflate0_1.19-1_s390x.deb ... 176s Unpacking libdeflate0:s390x (1.19-1) ... 176s Selecting previously unselected package libhtscodecs2:s390x. 176s Preparing to unpack .../5-libhtscodecs2_1.6.0-1_s390x.deb ... 176s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 176s Selecting previously unselected package libhts3:s390x. 176s Preparing to unpack .../6-libhts3_1.18+ds-1_s390x.deb ... 176s Unpacking libhts3:s390x (1.18+ds-1) ... 176s Selecting previously unselected package delly. 176s Preparing to unpack .../7-delly_1.1.8-1build1_s390x.deb ... 176s Unpacking delly (1.1.8-1build1) ... 176s Selecting previously unselected package autopkgtest-satdep. 176s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 176s Unpacking autopkgtest-satdep (0) ... 176s Setting up libhtscodecs2:s390x (1.6.0-1) ... 176s Setting up libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 176s Setting up libdeflate0:s390x (1.19-1) ... 176s Setting up libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 176s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 176s Setting up libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 176s Setting up libhts3:s390x (1.18+ds-1) ... 176s Setting up delly (1.1.8-1build1) ... 176s Setting up autopkgtest-satdep (0) ... 176s Processing triggers for man-db (2.12.0-3) ... 180s Processing triggers for libc-bin (2.39-0ubuntu6) ... 180s (Reading database ... 51775 files and directories currently installed.) 180s Removing autopkgtest-satdep (0) ... 181s autopkgtest [18:48:10]: test run-unit-test: [----------------------- 181s [2024-Mar-25 18:48:08] delly call -o sr.bcf -g ref.fa sr.bam 181s Running Tests 181s Test 1 181s [2024-Mar-25 18:48:08] Paired-end and split-read scanning 181s [2024-Mar-25 18:48:08] Split-read clustering 181s [2024-Mar-25 18:48:08] Paired-end clustering 181s [2024-Mar-25 18:48:08] Split-read assembly 181s [2024-Mar-25 18:48:08] Generate REF and ALT probes 181s [2024-Mar-25 18:48:08] SV annotation 181s [2024-Mar-25 18:48:09] Genotyping 181s [2024-Mar-25 18:48:09] Sample statistics 181s Sample:sr,ReadSize=150,Median=501,MAD=33,UniqueDiscordantPairs=9 181s [2024-Mar-25 18:48:09] Done. 181s Test 2 181s [2024-Mar-25 18:48:09] delly lr -g ref.fa lr.bam -o lr.vcf 181s [2024-Mar-25 18:48:09] Split-read scanning 181s [2024-Mar-25 18:48:09] Split-read assembly 182s [2024-Mar-25 18:48:11] SV annotation 182s [2024-Mar-25 18:48:11] Genotyping 182s Test 3 182s [2024-Mar-25 18:48:11] Done. 182s [2024-Mar-25 18:48:11] delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf 182s [2024-Mar-25 18:48:11] Scanning Windows 182s [2024-Mar-25 18:48:11] Estimate GC bias 182s [2024-Mar-25 18:48:11] Count fragments 183s [2024-Mar-25 18:48:12] Genotyping 183s [2024-Mar-25 18:48:12] Done. 183s PASS 183s autopkgtest [18:48:12]: test run-unit-test: -----------------------] 183s run-unit-test PASS 183s autopkgtest [18:48:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 184s autopkgtest [18:48:13]: @@@@@@@@@@@@@@@@@@@@ summary 184s run-unit-test PASS 199s Creating nova instance adt-noble-s390x-delly-20240325-184509-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...