0s autopkgtest [02:22:08]: starting date and time: 2024-03-23 02:22:08+0000 0s autopkgtest [02:22:08]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [02:22:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1ed1unr8/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 htsjdk --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-2@bos02-s390x-17.secgroup --name adt-noble-s390x-htsjdk-20240323-022208-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/ 109s autopkgtest [02:23:57]: testbed dpkg architecture: s390x 110s autopkgtest [02:23:58]: testbed apt version: 2.7.12 110s autopkgtest [02:23:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 111s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 111s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4035 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 113s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 113s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [661 kB] 113s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 113s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 113s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 113s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4189 kB] 114s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 114s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.5 kB] 114s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 116s Fetched 9622 kB in 5s (2129 kB/s) 116s Reading package lists... 118s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade... 119s The following packages will be REMOVED: 119s libssl3 119s The following NEW packages will be installed: 119s libssl3t64 119s The following packages have been kept back: 119s curl 119s The following packages will be upgraded: 119s openssl 119s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 119s Need to get 2685 kB of archives. 119s After this operation, 239 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 120s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 121s Fetched 2685 kB in 2s (1304 kB/s) 121s (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.) 121s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 121s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 121s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 121s wget depends on libssl3 (>= 3.0.0). 121s tnftp depends on libssl3 (>= 3.0.0). 121s tcpdump depends on libssl3 (>= 3.0.0). 121s systemd-resolved depends on libssl3 (>= 3.0.0). 121s systemd depends on libssl3 (>= 3.0.0). 121s sudo depends on libssl3 (>= 3.0.0). 121s s390-tools depends on libssl3 (>= 3.0.0). 121s rsync depends on libssl3 (>= 3.0.0). 121s python3-cryptography depends on libssl3 (>= 3.0.0). 121s openssh-server depends on libssl3 (>= 3.0.10). 121s openssh-client depends on libssl3 (>= 3.0.10). 121s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 121s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 121s libssh-4:s390x depends on libssl3 (>= 3.0.0). 121s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 121s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 121s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 121s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 121s libnvme1 depends on libssl3 (>= 3.0.0). 121s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 121s libkmod2:s390x depends on libssl3 (>= 3.0.0). 121s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 121s libcurl4:s390x depends on libssl3 (>= 3.0.0). 121s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 121s kmod depends on libssl3 (>= 3.0.0). 121s dhcpcd-base depends on libssl3 (>= 3.0.0). 121s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 121s 122s (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.) 122s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 122s Selecting previously unselected package libssl3t64:s390x. 122s (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.) 122s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 122s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 122s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 122s Setting up openssl (3.0.13-0ubuntu2) ... 122s Processing triggers for man-db (2.12.0-3) ... 122s Processing triggers for libc-bin (2.39-0ubuntu2) ... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 123s Unknown architecture, assuming PC-style ttyS0 123s sh: Attempting to set up Debian/Ubuntu apt sources automatically 123s sh: Distribution appears to be Ubuntu 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s eatmydata is already the newest version (131-1). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s dbus is already the newest version (1.14.10-4ubuntu1). 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 rng-tools-debian is already the newest version (2.4). 125s 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 The following packages will be REMOVED: 125s cloud-init* python3-configobj* python3-debconf* 125s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 125s After this operation, 3256 kB disk space will be freed. 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 ... 52172 files and directories currently installed.) 125s Removing cloud-init (24.1.2-0ubuntu1) ... 126s Removing python3-configobj (5.0.8-3) ... 126s Removing python3-debconf (1.5.86) ... 126s Processing triggers for man-db (2.12.0-3) ... 126s (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.) 126s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 127s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 127s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 127s invoke-rc.d: policy-rc.d denied execution of try-restart. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s linux-generic is already the newest version (6.8.0-11.11+1). 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 128s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 128s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 130s Reading package lists... 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s Calculating upgrade... 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 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [02:24:18]: rebooting testbed after setup commands that affected boot 145s autopkgtest [02:24:33]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 147s autopkgtest [02:24:35]: @@@@@@@@@@@@@@@@@@@@ apt-source htsjdk 153s Get:1 http://ftpmaster.internal/ubuntu noble/universe htsjdk 4.1.0+dfsg-1 (dsc) [2649 B] 153s Get:2 http://ftpmaster.internal/ubuntu noble/universe htsjdk 4.1.0+dfsg-1 (tar) [46.9 MB] 153s Get:3 http://ftpmaster.internal/ubuntu noble/universe htsjdk 4.1.0+dfsg-1 (diff) [39.4 kB] 154s gpgv: Signature made Sun Feb 11 21:45:33 2024 UTC 154s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 154s gpgv: Can't check signature: No public key 154s dpkg-source: warning: cannot verify inline signature for ./htsjdk_4.1.0+dfsg-1.dsc: no acceptable signature found 156s autopkgtest [02:24:44]: testing package htsjdk version 4.1.0+dfsg-1 156s beagle-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 156s chromhmm-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 156s drop-seq-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 156s fastqc-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 156s jalview-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 156s command1 SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 157s picard-tools-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 157s pilon-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 157s autopkgtest [02:24:45]: build not needed 160s beagle-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s chromhmm-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s drop-seq-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s fastqc-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s jalview-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s command1 SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s picard-tools-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s autopkgtest [02:24:49]: @@@@@@@@@@@@@@@@@@@@ summary 161s beagle-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s chromhmm-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s drop-seq-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s fastqc-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s jalview-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s command1 SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s picard-tools-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s pilon-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s beagle-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s chromhmm-run-sample-analysis SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s drop-seq-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s fastqc-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s jalview-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s command1 SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s picard-tools-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s pilon-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 161s pilon-run-unit-test SKIP Test lists explicitly supported architectures, but the current architecture s390x isn't listed. 172s Creating nova instance adt-noble-s390x-htsjdk-20240323-022208-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...