0s autopkgtest [09:34:08]: starting date and time: 2024-03-23 09:34:08+0000 0s autopkgtest [09:34:08]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [09:34:08]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8du83hfc/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade wtdbg2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 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-3@bos02-s390x-21.secgroup --name adt-noble-s390x-wtdbg2-20240323-093407-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-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/ 83s autopkgtest [09:35:31]: testbed dpkg architecture: s390x 83s autopkgtest [09:35:31]: testbed apt version: 2.7.12 83s autopkgtest [09:35:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 84s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 84s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 84s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 84s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4029 kB] 85s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [651 kB] 85s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 85s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 85s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 85s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4144 kB] 85s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 85s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 85s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 87s Fetched 9558 kB in 2s (3867 kB/s) 87s Reading package lists... 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Calculating upgrade... 90s The following packages will be REMOVED: 90s libssl3 90s The following NEW packages will be installed: 90s libssl3t64 90s The following packages have been kept back: 90s curl 90s The following packages will be upgraded: 90s libbsd0 libc-bin libc6 locales openssl 91s 5 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 91s Need to get 10.5 MB of archives. 91s After this operation, 241 kB of additional disk space will be used. 91s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.39-0ubuntu6 [2847 kB] 92s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.39-0ubuntu6 [654 kB] 92s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 92s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 92s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libbsd0 s390x 0.12.1-1 [46.7 kB] 93s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x locales all 2.39-0ubuntu6 [4232 kB] 93s Preconfiguring packages ... 93s Fetched 10.5 MB in 3s (4066 kB/s) 93s (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.) 93s Preparing to unpack .../libc6_2.39-0ubuntu6_s390x.deb ... 94s Unpacking libc6:s390x (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 94s Setting up libc6:s390x (2.39-0ubuntu6) ... 94s (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.) 94s Preparing to unpack .../libc-bin_2.39-0ubuntu6_s390x.deb ... 94s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 94s Setting up libc-bin (2.39-0ubuntu6) ... 94s (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.) 94s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 94s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 94s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 94s wget depends on libssl3 (>= 3.0.0). 94s tnftp depends on libssl3 (>= 3.0.0). 94s tcpdump depends on libssl3 (>= 3.0.0). 94s systemd-resolved depends on libssl3 (>= 3.0.0). 94s systemd depends on libssl3 (>= 3.0.0). 94s sudo depends on libssl3 (>= 3.0.0). 94s s390-tools depends on libssl3 (>= 3.0.0). 94s rsync depends on libssl3 (>= 3.0.0). 94s python3-cryptography depends on libssl3 (>= 3.0.0). 94s openssh-server depends on libssl3 (>= 3.0.10). 94s openssh-client depends on libssl3 (>= 3.0.10). 94s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 94s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 94s libssh-4:s390x depends on libssl3 (>= 3.0.0). 94s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 94s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 94s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 94s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 94s libnvme1 depends on libssl3 (>= 3.0.0). 94s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 94s libkmod2:s390x depends on libssl3 (>= 3.0.0). 94s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 94s libcurl4:s390x depends on libssl3 (>= 3.0.0). 94s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 94s kmod depends on libssl3 (>= 3.0.0). 94s dhcpcd-base depends on libssl3 (>= 3.0.0). 94s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 94s 94s (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.) 94s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 94s Selecting previously unselected package libssl3t64:s390x. 94s (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.) 94s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 94s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 94s Preparing to unpack .../libbsd0_0.12.1-1_s390x.deb ... 94s Unpacking libbsd0:s390x (0.12.1-1) over (0.11.8-1) ... 95s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 95s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 95s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 95s Setting up locales (2.39-0ubuntu6) ... 95s Generating locales (this might take a while)... 97s en_US.UTF-8... done 97s Generation complete. 97s Setting up openssl (3.0.13-0ubuntu2) ... 97s Setting up libbsd0:s390x (0.12.1-1) ... 97s Processing triggers for man-db (2.12.0-3) ... 97s Processing triggers for libc-bin (2.39-0ubuntu6) ... 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 98s Unknown architecture, assuming PC-style ttyS0 98s sh: Attempting to set up Debian/Ubuntu apt sources automatically 98s sh: Distribution appears to be Ubuntu 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s eatmydata is already the newest version (131-1). 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s dbus is already the newest version (1.14.10-4ubuntu1). 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s rng-tools-debian is already the newest version (2.4). 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s The following packages will be REMOVED: 100s cloud-init* python3-configobj* python3-debconf* 101s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 101s After this operation, 3256 kB disk space will be freed. 101s (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.) 101s Removing cloud-init (24.1.2-0ubuntu1) ... 101s Removing python3-configobj (5.0.8-3) ... 101s Removing python3-debconf (1.5.86) ... 101s Processing triggers for man-db (2.12.0-3) ... 102s (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.) 102s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 102s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 102s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 102s invoke-rc.d: policy-rc.d denied execution of try-restart. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s linux-generic is already the newest version (6.8.0-11.11+1). 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s autopkgtest [09:35:54]: rebooting testbed after setup commands that affected boot 119s autopkgtest [09:36:07]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 122s autopkgtest [09:36:10]: @@@@@@@@@@@@@@@@@@@@ apt-source wtdbg2 129s Get:1 http://ftpmaster.internal/ubuntu noble/universe wtdbg2 2.5-9 (dsc) [2079 B] 129s Get:2 http://ftpmaster.internal/ubuntu noble/universe wtdbg2 2.5-9 (tar) [237 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble/universe wtdbg2 2.5-9 (diff) [121 MB] 129s gpgv: Signature made Thu Dec 1 16:43:57 2022 UTC 129s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 129s gpgv: issuer "tille@debian.org" 129s gpgv: Can't check signature: No public key 129s dpkg-source: warning: cannot verify inline signature for ./wtdbg2_2.5-9.dsc: no acceptable signature found 130s autopkgtest [09:36:18]: testing package wtdbg2 version 2.5-9 136s autopkgtest [09:36:24]: build not needed 141s autopkgtest [09:36:29]: test run-unit-test: preparing testbed 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Starting pkgProblemResolver with broken count: 0 144s Starting 2 pkgProblemResolver with broken count: 0 144s Done 144s The following additional packages will be installed: 144s bwa libdeflate0 libhts3 libhtscodecs2 minimap2 samtools wtdbg2-examples 144s Suggested packages: 144s cwltool 144s The following NEW packages will be installed: 144s autopkgtest-satdep bwa libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 144s wtdbg2-examples 144s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 123 MB/123 MB of archives. 144s After this operation, 125 MB of additional disk space will be used. 144s Get:1 /tmp/autopkgtest.7fVso7/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [728 B] 144s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x bwa s390x 0.7.17-7 [206 kB] 144s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 144s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 144s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 145s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x minimap2 s390x 2.24+dfsg-3build2 [396 kB] 145s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1 [613 kB] 145s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x wtdbg2-examples all 2.5-9 [121 MB] 148s Fetched 123 MB in 4s (29.7 MB/s) 148s Selecting previously unselected package bwa. 148s (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.) 148s Preparing to unpack .../0-bwa_0.7.17-7_s390x.deb ... 148s Unpacking bwa (0.7.17-7) ... 148s Selecting previously unselected package libdeflate0:s390x. 148s Preparing to unpack .../1-libdeflate0_1.19-1_s390x.deb ... 148s Unpacking libdeflate0:s390x (1.19-1) ... 149s Selecting previously unselected package libhtscodecs2:s390x. 149s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_s390x.deb ... 149s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 149s Selecting previously unselected package libhts3:s390x. 149s Preparing to unpack .../3-libhts3_1.18+ds-1_s390x.deb ... 149s Unpacking libhts3:s390x (1.18+ds-1) ... 149s Selecting previously unselected package minimap2. 149s Preparing to unpack .../4-minimap2_2.24+dfsg-3build2_s390x.deb ... 149s Unpacking minimap2 (2.24+dfsg-3build2) ... 149s Selecting previously unselected package samtools. 149s Preparing to unpack .../5-samtools_1.19.2-1_s390x.deb ... 149s Unpacking samtools (1.19.2-1) ... 149s Selecting previously unselected package wtdbg2-examples. 149s Preparing to unpack .../6-wtdbg2-examples_2.5-9_all.deb ... 149s Unpacking wtdbg2-examples (2.5-9) ... 149s Selecting previously unselected package autopkgtest-satdep. 149s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 149s Unpacking autopkgtest-satdep (0) ... 149s Setting up libhtscodecs2:s390x (1.6.0-1) ... 149s Setting up bwa (0.7.17-7) ... 149s Setting up minimap2 (2.24+dfsg-3build2) ... 149s Setting up libdeflate0:s390x (1.19-1) ... 149s Setting up wtdbg2-examples (2.5-9) ... 149s Setting up libhts3:s390x (1.18+ds-1) ... 149s Setting up samtools (1.19.2-1) ... 149s Setting up autopkgtest-satdep (0) ... 149s Processing triggers for man-db (2.12.0-3) ... 150s Processing triggers for libc-bin (2.39-0ubuntu6) ... 152s (Reading database ... 51875 files and directories currently installed.) 152s Removing autopkgtest-satdep (0) ... 152s autopkgtest [09:36:40]: test run-unit-test: [----------------------- 155s selfSampleData/reference.fasta 155s selfSampleData/pacbio_filtered.fastq 155s selfSampleData/README 155s selfSampleData/pacbio.spec 155s Begin Execution 155s /tmp/autopkgtest.7fVso7/build.SAk/src/debian/tests/run-unit-test: line 19: wtdbg2: command not found 156s autopkgtest [09:36:44]: test run-unit-test: -----------------------] 156s autopkgtest [09:36:44]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 156s run-unit-test FAIL non-zero exit status 127 157s autopkgtest [09:36:45]: @@@@@@@@@@@@@@@@@@@@ summary 157s run-unit-test FAIL non-zero exit status 127 168s Creating nova instance adt-noble-s390x-wtdbg2-20240323-093407-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...