0s autopkgtest [17:16:40]: starting date and time: 2024-03-24 17:16:40+0000 0s autopkgtest [17:16:40]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:16:40]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ixmwlnhl/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 bamkit --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@bos01-arm64-12.secgroup --name adt-noble-arm64-bamkit-20240324-171640-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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://us.ports.ubuntu.com/ubuntu-ports/ 111s autopkgtest [17:18:31]: testbed dpkg architecture: arm64 112s autopkgtest [17:18:32]: testbed apt version: 2.7.12 112s autopkgtest [17:18:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 112s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 113s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 113s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 113s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 113s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 113s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 113s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 114s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 114s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 114s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 116s Fetched 9850 kB in 2s (5232 kB/s) 116s Reading package lists... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s Calculating upgrade... 120s The following packages will be REMOVED: 120s libssl3 120s The following NEW packages will be installed: 120s libssl3t64 120s The following packages have been kept back: 120s curl 120s The following packages will be upgraded: 120s openssl 121s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 121s Need to get 2777 kB of archives. 121s After this operation, 139 kB of additional disk space will be used. 121s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 121s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 121s Fetched 2777 kB in 1s (4046 kB/s) 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 ... 75911 files and directories currently installed.) 122s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 122s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 122s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 122s wget depends on libssl3 (>= 3.0.0). 122s u-boot-tools depends on libssl3 (>= 3.0.0). 122s tnftp depends on libssl3 (>= 3.0.0). 122s tcpdump depends on libssl3 (>= 3.0.0). 122s systemd-resolved depends on libssl3 (>= 3.0.0). 122s systemd depends on libssl3 (>= 3.0.0). 122s sudo depends on libssl3 (>= 3.0.0). 122s sbsigntool depends on libssl3 (>= 3.0.0). 122s rsync depends on libssl3 (>= 3.0.0). 122s python3-cryptography depends on libssl3 (>= 3.0.0). 122s openssh-server depends on libssl3 (>= 3.0.10). 122s openssh-client depends on libssl3 (>= 3.0.10). 122s mtd-utils depends on libssl3 (>= 3.0.0). 122s mokutil depends on libssl3 (>= 3.0.0). 122s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 122s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 122s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 122s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 122s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 122s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 122s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 122s libnvme1 depends on libssl3 (>= 3.0.0). 122s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 122s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 122s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 122s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 122s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 122s kmod depends on libssl3 (>= 3.0.0). 122s dhcpcd-base depends on libssl3 (>= 3.0.0). 122s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 122s 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 ... 75911 files and directories currently installed.) 122s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 122s Selecting previously unselected package libssl3t64:arm64. 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 ... 75900 files and directories currently installed.) 122s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 122s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 122s Setting up libssl3t64:arm64 (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 (2.39-0ubuntu6) ... 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 124s sh: Attempting to set up Debian/Ubuntu apt sources automatically 124s sh: Distribution appears to be Ubuntu 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s eatmydata is already the newest version (131-1). 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s dbus is already the newest version (1.14.10-4ubuntu1). 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s rng-tools-debian is already the newest version (2.4). 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s The following packages will be REMOVED: 128s cloud-init* python3-configobj* python3-debconf* 128s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 128s After this operation, 3256 kB disk space will be freed. 128s (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 ... 75913 files and directories currently installed.) 128s Removing cloud-init (24.1.2-0ubuntu1) ... 129s Removing python3-configobj (5.0.8-3) ... 129s Removing python3-debconf (1.5.86) ... 129s Processing triggers for man-db (2.12.0-3) ... 129s (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 ... 75524 files and directories currently installed.) 129s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 130s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 130s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 130s invoke-rc.d: policy-rc.d denied execution of try-restart. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 131s linux-generic is already the newest version (6.8.0-11.11+1). 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 131s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 131s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 133s Reading package lists... 133s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [17:18:56]: rebooting testbed after setup commands that affected boot 281s autopkgtest [17:21:21]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 284s autopkgtest [17:21:24]: @@@@@@@@@@@@@@@@@@@@ apt-source bamkit 285s Get:1 http://ftpmaster.internal/ubuntu noble/universe bamkit 0.0.1+git20170413.ccd079d-3 (dsc) [2124 B] 285s Get:2 http://ftpmaster.internal/ubuntu noble/universe bamkit 0.0.1+git20170413.ccd079d-3 (tar) [7772 B] 285s Get:3 http://ftpmaster.internal/ubuntu noble/universe bamkit 0.0.1+git20170413.ccd079d-3 (diff) [6420 B] 285s gpgv: Signature made Mon Aug 16 11:31:23 2021 UTC 285s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 285s gpgv: issuer "npatra974@gmail.com" 285s gpgv: Can't check signature: No public key 285s dpkg-source: warning: cannot verify inline signature for ./bamkit_0.0.1+git20170413.ccd079d-3.dsc: no acceptable signature found 285s autopkgtest [17:21:25]: testing package bamkit version 0.0.1+git20170413.ccd079d-3 286s autopkgtest [17:21:26]: build not needed 286s autopkgtest [17:21:26]: test run-unit-test: preparing testbed 289s Reading package lists... 289s Building dependency tree... 289s Reading state information... 290s Starting pkgProblemResolver with broken count: 0 290s Starting 2 pkgProblemResolver with broken count: 0 290s Done 290s The following additional packages will be installed: 290s bamkit libdeflate0 libhts3 libhtscodecs2 python3-pysam samtools 290s Suggested packages: 290s cwltool 290s The following NEW packages will be installed: 290s autopkgtest-satdep bamkit libdeflate0 libhts3 libhtscodecs2 python3-pysam 290s samtools 290s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 290s Need to get 5542 kB/5543 kB of archives. 290s After this operation, 43.7 MB of additional disk space will be used. 290s Get:1 /tmp/autopkgtest.hlYVRX/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 291s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 291s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 291s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 291s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 291s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 bamkit all 0.0.1+git20170413.ccd079d-3 [14.9 kB] 291s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 292s Fetched 5542 kB in 1s (5888 kB/s) 292s Selecting previously unselected package libdeflate0:arm64. 292s (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 ... 75469 files and directories currently installed.) 292s Preparing to unpack .../0-libdeflate0_1.19-1_arm64.deb ... 292s Unpacking libdeflate0:arm64 (1.19-1) ... 292s Selecting previously unselected package libhtscodecs2:arm64. 292s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_arm64.deb ... 292s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 292s Selecting previously unselected package libhts3:arm64. 292s Preparing to unpack .../2-libhts3_1.18+ds-1_arm64.deb ... 292s Unpacking libhts3:arm64 (1.18+ds-1) ... 292s Selecting previously unselected package python3-pysam. 292s Preparing to unpack .../3-python3-pysam_0.22.0+ds-1_arm64.deb ... 292s Unpacking python3-pysam (0.22.0+ds-1) ... 292s Selecting previously unselected package bamkit. 292s Preparing to unpack .../4-bamkit_0.0.1+git20170413.ccd079d-3_all.deb ... 292s Unpacking bamkit (0.0.1+git20170413.ccd079d-3) ... 292s Selecting previously unselected package samtools. 292s Preparing to unpack .../5-samtools_1.19.2-1_arm64.deb ... 292s Unpacking samtools (1.19.2-1) ... 292s Selecting previously unselected package autopkgtest-satdep. 292s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 292s Unpacking autopkgtest-satdep (0) ... 292s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 292s Setting up libdeflate0:arm64 (1.19-1) ... 292s Setting up libhts3:arm64 (1.18+ds-1) ... 292s Setting up python3-pysam (0.22.0+ds-1) ... 292s Setting up bamkit (0.0.1+git20170413.ccd079d-3) ... 293s Setting up samtools (1.19.2-1) ... 293s Setting up autopkgtest-satdep (0) ... 293s Processing triggers for man-db (2.12.0-3) ... 293s Processing triggers for libc-bin (2.39-0ubuntu6) ... 296s (Reading database ... 75987 files and directories currently installed.) 296s Removing autopkgtest-satdep (0) ... 298s autopkgtest [17:21:38]: test run-unit-test: [----------------------- 298s PASS Tests 299s autopkgtest [17:21:39]: test run-unit-test: -----------------------] 299s autopkgtest [17:21:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 299s run-unit-test PASS 299s autopkgtest [17:21:39]: @@@@@@@@@@@@@@@@@@@@ summary 299s run-unit-test PASS 314s Creating nova instance adt-noble-arm64-bamkit-20240324-171640-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...