0s autopkgtest [15:28:29]: starting date and time: 2024-03-23 15:28:29+0000 0s autopkgtest [15:28:29]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:28:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d8_1e8ce/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:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade sniffles --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 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-ppc64el-14.secgroup --name adt-noble-ppc64el-sniffles-20240323-152828-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 117s autopkgtest [15:30:26]: testbed dpkg architecture: ppc64el 117s autopkgtest [15:30:26]: testbed apt version: 2.7.12 117s autopkgtest [15:30:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 118s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 119s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 119s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 119s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 119s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 119s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 119s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 119s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 119s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 119s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 119s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 119s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 122s Fetched 9623 kB in 3s (3670 kB/s) 122s Reading package lists... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Calculating upgrade... 126s The following packages will be REMOVED: 126s libssl3 126s The following NEW packages will be installed: 126s libssl3t64 126s The following packages have been kept back: 126s curl 126s The following packages will be upgraded: 126s openssl 126s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 126s Need to get 3151 kB of archives. 126s After this operation, 73.7 kB of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 126s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 127s Fetched 3151 kB in 1s (4464 kB/s) 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 ... 70156 files and directories currently installed.) 127s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 127s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 127s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 127s wget depends on libssl3 (>= 3.0.0). 127s tnftp depends on libssl3 (>= 3.0.0). 127s tcpdump depends on libssl3 (>= 3.0.0). 127s systemd-resolved depends on libssl3 (>= 3.0.0). 127s systemd depends on libssl3 (>= 3.0.0). 127s sudo depends on libssl3 (>= 3.0.0). 127s rsync depends on libssl3 (>= 3.0.0). 127s python3-cryptography depends on libssl3 (>= 3.0.0). 127s openssh-server depends on libssl3 (>= 3.0.10). 127s openssh-client depends on libssl3 (>= 3.0.10). 127s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 127s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 127s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 127s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 127s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 127s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 127s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 127s libnvme1 depends on libssl3 (>= 3.0.0). 127s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 127s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 127s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 127s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 127s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 127s kmod depends on libssl3 (>= 3.0.0). 127s dhcpcd-base depends on libssl3 (>= 3.0.0). 127s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 127s 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 ... 70156 files and directories currently installed.) 127s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 127s Selecting previously unselected package libssl3t64: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 ... 70145 files and directories currently installed.) 127s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 127s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 127s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 127s Setting up openssl (3.0.13-0ubuntu2) ... 127s Processing triggers for man-db (2.12.0-3) ... 128s Processing triggers for libc-bin (2.39-0ubuntu6) ... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 129s sh: Attempting to set up Debian/Ubuntu apt sources automatically 129s sh: Distribution appears to be Ubuntu 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s eatmydata is already the newest version (131-1). 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... 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* 131s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 131s After this operation, 3256 kB disk space will be freed. 131s (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.) 131s 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) ... 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 ... 69769 files and directories currently installed.) 132s 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. 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s linux-generic is already the newest version (6.8.0-11.11+1). 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 134s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 134s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 137s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Calculating upgrade... 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... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s autopkgtest [15:30:47]: rebooting testbed after setup commands that affected boot 176s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 183s autopkgtest [15:31:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 185s autopkgtest [15:31:34]: @@@@@@@@@@@@@@@@@@@@ apt-source sniffles 187s Get:1 http://ftpmaster.internal/ubuntu noble/universe sniffles 2.2-1 (dsc) [2032 B] 187s Get:2 http://ftpmaster.internal/ubuntu noble/universe sniffles 2.2-1 (tar) [2815 kB] 187s Get:3 http://ftpmaster.internal/ubuntu noble/universe sniffles 2.2-1 (diff) [8368 B] 187s gpgv: Signature made Thu Aug 10 10:48:39 2023 UTC 187s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 187s gpgv: issuer "tille@debian.org" 187s gpgv: Can't check signature: No public key 187s dpkg-source: warning: cannot verify inline signature for ./sniffles_2.2-1.dsc: no acceptable signature found 188s autopkgtest [15:31:37]: testing package sniffles version 2.2-1 188s autopkgtest [15:31:37]: build not needed 191s autopkgtest [15:31:40]: test run-unit-test: preparing testbed 192s Reading package lists... 192s Building dependency tree... 192s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 192s The following additional packages will be installed: 192s libdeflate0 libhts3 libhtscodecs2 python3-pysam sniffles 192s Suggested packages: 192s bwa 192s The following NEW packages will be installed: 192s autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 python3-pysam sniffles 192s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 5806 kB/5807 kB of archives. 192s After this operation, 47.7 MB of additional disk space will be used. 192s Get:1 /tmp/autopkgtest.p0lQCC/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 192s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 193s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 193s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 193s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 193s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el sniffles all 2.2-1 [45.7 kB] 193s Fetched 5806 kB in 1s (7732 kB/s) 193s Selecting previously unselected package libdeflate0:ppc64el. 193s (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.) 193s Preparing to unpack .../0-libdeflate0_1.19-1_ppc64el.deb ... 193s Unpacking libdeflate0:ppc64el (1.19-1) ... 193s Selecting previously unselected package libhtscodecs2:ppc64el. 193s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_ppc64el.deb ... 193s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 193s Selecting previously unselected package libhts3:ppc64el. 193s Preparing to unpack .../2-libhts3_1.18+ds-1_ppc64el.deb ... 193s Unpacking libhts3:ppc64el (1.18+ds-1) ... 193s Selecting previously unselected package python3-pysam. 193s Preparing to unpack .../3-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 193s Unpacking python3-pysam (0.22.0+ds-1) ... 194s Selecting previously unselected package sniffles. 194s Preparing to unpack .../4-sniffles_2.2-1_all.deb ... 194s Unpacking sniffles (2.2-1) ... 194s Selecting previously unselected package autopkgtest-satdep. 194s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 194s Unpacking autopkgtest-satdep (0) ... 194s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 194s Setting up libdeflate0:ppc64el (1.19-1) ... 194s Setting up libhts3:ppc64el (1.18+ds-1) ... 194s Setting up python3-pysam (0.22.0+ds-1) ... 194s Setting up sniffles (2.2-1) ... 194s Setting up autopkgtest-satdep (0) ... 194s Processing triggers for man-db (2.12.0-3) ... 195s Processing triggers for libc-bin (2.39-0ubuntu6) ... 197s (Reading database ... 70145 files and directories currently installed.) 197s Removing autopkgtest-satdep (0) ... 197s autopkgtest [15:31:46]: test run-unit-test: [----------------------- 197s Running Sniffles2, build 2.2 197s Run Mode: call_sample 197s Start on: 2024/03/23 15:31:46 197s Working dir: /tmp/autopkgtest.p0lQCC/autopkgtest_tmp 197s Used command: /usr/bin/sniffles --input test.bam --snf test.snf 197s ============================== 197s Opening for reading: test.bam 197s Opening for writing: test.snf 197s 197s Analyzing 1 alignments total... 197s 197s (Estimating progress); 1/1 tasks done; parallel 0/4; 0 candidates. 197s Took 0.00s. 197s 197s Done. 197s Wrote 0 SV candidates to test.snf (for multi-sample calling). 197s FIXME: Please enhance these simple test. 198s autopkgtest [15:31:47]: test run-unit-test: -----------------------] 198s autopkgtest [15:31:47]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 198s run-unit-test PASS 198s autopkgtest [15:31:47]: @@@@@@@@@@@@@@@@@@@@ summary 198s run-unit-test PASS 209s Creating nova instance adt-noble-ppc64el-sniffles-20240323-152828-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...