0s autopkgtest [20:09:08]: starting date and time: 2024-03-25 20:09:08+0000 0s autopkgtest [20:09:08]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [20:09:08]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.06n1jzqo/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-3@bos02-ppc64el-23.secgroup --name adt-noble-ppc64el-delly-20240325-200908-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 102s autopkgtest [20:10:50]: testbed dpkg architecture: ppc64el 103s autopkgtest [20:10:51]: testbed apt version: 2.7.12 103s autopkgtest [20:10:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 104s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3992 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 105s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 105s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 105s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 106s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 106s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 106s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 106s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4231 kB] 106s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 106s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 106s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 109s Fetched 9677 kB in 3s (2887 kB/s) 109s Reading package lists... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade... 113s The following packages will be REMOVED: 113s libssl3 113s The following NEW packages will be installed: 113s libssl3t64 113s The following packages have been kept back: 113s curl 113s The following packages will be upgraded: 113s openssl 113s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 113s Need to get 3151 kB of archives. 113s After this operation, 73.7 kB of additional disk space will be used. 113s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 114s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 114s Fetched 3151 kB in 1s (2475 kB/s) 115s (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 ... 70156 files and directories currently installed.) 115s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 115s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 115s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 115s wget depends on libssl3 (>= 3.0.0). 115s tnftp depends on libssl3 (>= 3.0.0). 115s tcpdump depends on libssl3 (>= 3.0.0). 115s systemd-resolved depends on libssl3 (>= 3.0.0). 115s systemd depends on libssl3 (>= 3.0.0). 115s sudo depends on libssl3 (>= 3.0.0). 115s rsync depends on libssl3 (>= 3.0.0). 115s python3-cryptography depends on libssl3 (>= 3.0.0). 115s openssh-server depends on libssl3 (>= 3.0.10). 115s openssh-client depends on libssl3 (>= 3.0.10). 115s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 115s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 115s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 115s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 115s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 115s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 115s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 115s libnvme1 depends on libssl3 (>= 3.0.0). 115s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 115s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 115s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 115s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 115s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 115s kmod depends on libssl3 (>= 3.0.0). 115s dhcpcd-base depends on libssl3 (>= 3.0.0). 115s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 115s 115s (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 ... 70156 files and directories currently installed.) 115s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 115s Selecting previously unselected package libssl3t64:ppc64el. 115s (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 ... 70145 files and directories currently installed.) 115s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 115s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 115s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 115s Setting up openssl (3.0.13-0ubuntu2) ... 115s Processing triggers for man-db (2.12.0-3) ... 115s Processing triggers for libc-bin (2.39-0ubuntu6) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 117s sh: Attempting to set up Debian/Ubuntu apt sources automatically 117s sh: Distribution appears to be Ubuntu 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s eatmydata is already the newest version (131-1). 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s dbus is already the newest version (1.14.10-4ubuntu1). 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s rng-tools-debian is already the newest version (2.4). 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s The following packages will be REMOVED: 119s cloud-init* python3-configobj* python3-debconf* 119s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 119s After this operation, 3256 kB disk space will be freed. 119s (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 ... 70158 files and directories currently installed.) 119s Removing cloud-init (24.1.2-0ubuntu1) ... 120s Removing python3-configobj (5.0.8-3) ... 120s Removing python3-debconf (1.5.86) ... 120s Processing triggers for man-db (2.12.0-3) ... 120s (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 ... 69769 files and directories currently installed.) 120s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 121s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 121s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 121s invoke-rc.d: policy-rc.d denied execution of try-restart. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s linux-generic is already the newest version (6.8.0-11.11+1). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 122s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 122s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 124s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s autopkgtest [20:11:13]: rebooting testbed after setup commands that affected boot 290s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 299s autopkgtest [20:14:07]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 302s autopkgtest [20:14:10]: @@@@@@@@@@@@@@@@@@@@ apt-source delly 305s Get:1 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (dsc) [2113 B] 305s Get:2 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (tar) [3744 kB] 305s Get:3 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (diff) [5312 B] 305s gpgv: Signature made Tue Dec 19 15:01:08 2023 UTC 305s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 305s gpgv: Can't check signature: No public key 305s dpkg-source: warning: cannot verify inline signature for ./delly_1.1.8-1build1.dsc: no acceptable signature found 305s autopkgtest [20:14:13]: testing package delly version 1.1.8-1build1 306s autopkgtest [20:14:14]: build not needed 308s autopkgtest [20:14:16]: test run-unit-test: preparing testbed 310s Reading package lists... 310s Building dependency tree... 310s Reading state information... 310s Starting pkgProblemResolver with broken count: 0 310s Starting 2 pkgProblemResolver with broken count: 0 310s Done 310s The following additional packages will be installed: 310s delly libboost-filesystem1.83.0 libboost-iostreams1.83.0 310s libboost-program-options1.83.0 libdeflate0 libgomp1 libhts3 libhtscodecs2 311s The following NEW packages will be installed: 311s autopkgtest-satdep delly libboost-filesystem1.83.0 libboost-iostreams1.83.0 311s libboost-program-options1.83.0 libdeflate0 libgomp1 libhts3 libhtscodecs2 311s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 311s Need to get 2465 kB/2466 kB of archives. 311s After this operation, 11.1 MB of additional disk space will be used. 311s Get:1 /tmp/autopkgtest.eKH7KB/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 311s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-filesystem1.83.0 ppc64el 1.83.0-2ubuntu1 [373 kB] 311s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 311s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 311s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 311s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 311s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 312s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 312s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el delly ppc64el 1.1.8-1build1 [446 kB] 312s Fetched 2465 kB in 1s (1923 kB/s) 312s Selecting previously unselected package libboost-filesystem1.83.0:ppc64el. 312s (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 ... 69714 files and directories currently installed.) 312s Preparing to unpack .../0-libboost-filesystem1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 312s Unpacking libboost-filesystem1.83.0:ppc64el (1.83.0-2ubuntu1) ... 312s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 312s Preparing to unpack .../1-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 312s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 312s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 312s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 312s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 312s Selecting previously unselected package libgomp1:ppc64el. 312s Preparing to unpack .../3-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 312s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 312s Selecting previously unselected package libdeflate0:ppc64el. 312s Preparing to unpack .../4-libdeflate0_1.19-1_ppc64el.deb ... 312s Unpacking libdeflate0:ppc64el (1.19-1) ... 312s Selecting previously unselected package libhtscodecs2:ppc64el. 312s Preparing to unpack .../5-libhtscodecs2_1.6.0-1_ppc64el.deb ... 312s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 312s Selecting previously unselected package libhts3:ppc64el. 312s Preparing to unpack .../6-libhts3_1.18+ds-1_ppc64el.deb ... 312s Unpacking libhts3:ppc64el (1.18+ds-1) ... 312s Selecting previously unselected package delly. 312s Preparing to unpack .../7-delly_1.1.8-1build1_ppc64el.deb ... 312s Unpacking delly (1.1.8-1build1) ... 312s Selecting previously unselected package autopkgtest-satdep. 312s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 312s Unpacking autopkgtest-satdep (0) ... 312s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 312s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 312s Setting up libdeflate0:ppc64el (1.19-1) ... 312s Setting up libboost-filesystem1.83.0:ppc64el (1.83.0-2ubuntu1) ... 312s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 312s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 312s Setting up libhts3:ppc64el (1.18+ds-1) ... 312s Setting up delly (1.1.8-1build1) ... 312s Setting up autopkgtest-satdep (0) ... 312s Processing triggers for man-db (2.12.0-3) ... 313s Processing triggers for libc-bin (2.39-0ubuntu6) ... 315s (Reading database ... 69761 files and directories currently installed.) 315s Removing autopkgtest-satdep (0) ... 316s autopkgtest [20:14:24]: test run-unit-test: [----------------------- 316s Running Tests 316s Test 1 316s [2024-Mar-25 20:14:24] delly call -o sr.bcf -g ref.fa sr.bam 316s [2024-Mar-25 20:14:24] Paired-end and split-read scanning 316s [2024-Mar-25 20:14:24] Split-read clustering 316s [2024-Mar-25 20:14:24] Paired-end clustering 316s [2024-Mar-25 20:14:24] Split-read assembly 316s [2024-Mar-25 20:14:24] Generate REF and ALT probes 316s [2024-Mar-25 20:14:24] SV annotation 316s [2024-Mar-25 20:14:24] Genotyping 316s [2024-Mar-25 20:14:24] Sample statistics 316s Sample:sr,ReadSize=150,Median=501,MAD=33,UniqueDiscordantPairs=9 316s [2024-Mar-25 20:14:24] Done. 316s Test 2 316s [2024-Mar-25 20:14:24] delly lr -g ref.fa lr.bam -o lr.vcf 316s [2024-Mar-25 20:14:24] Split-read scanning 316s [2024-Mar-25 20:14:24] Split-read assembly 317s [2024-Mar-25 20:14:25] SV annotation 317s [2024-Mar-25 20:14:25] Genotyping 317s [2024-Mar-25 20:14:25] Done. 317s Test 3 317s [2024-Mar-25 20:14:25] delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf 317s [2024-Mar-25 20:14:25] Scanning Windows 317s [2024-Mar-25 20:14:25] Estimate GC bias 317s [2024-Mar-25 20:14:25] Count fragments 317s [2024-Mar-25 20:14:25] Genotyping 317s [2024-Mar-25 20:14:25] PASS 317s Done. 317s autopkgtest [20:14:25]: test run-unit-test: -----------------------] 318s run-unit-test PASS 318s autopkgtest [20:14:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 318s autopkgtest [20:14:26]: @@@@@@@@@@@@@@@@@@@@ summary 318s run-unit-test PASS 330s Creating nova instance adt-noble-ppc64el-delly-20240325-200908-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...