0s autopkgtest [16:44:53]: starting date and time: 2024-03-24 16:44:53+0000 0s autopkgtest [16:44:53]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:44:53]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.x5iabdkr/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 bamkit --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@bos03-arm64-19.secgroup --name adt-noble-arm64-bamkit-20240324-164453-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/ 85s autopkgtest [16:46:18]: testbed dpkg architecture: arm64 86s autopkgtest [16:46:19]: testbed apt version: 2.7.12 86s autopkgtest [16:46:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 86s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 86s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 86s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 87s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 87s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 87s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 87s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 87s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 87s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 87s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 87s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 87s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 87s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 89s Fetched 9847 kB in 2s (5781 kB/s) 89s Reading package lists... 91s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Calculating upgrade... 92s The following packages will be REMOVED: 92s libssl3 92s The following NEW packages will be installed: 92s libssl3t64 92s The following packages have been kept back: 92s curl 92s The following packages will be upgraded: 92s openssl 93s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 93s Need to get 2777 kB of archives. 93s After this operation, 139 kB of additional disk space will be used. 93s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 93s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 94s Fetched 2777 kB in 1s (3851 kB/s) 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 ... 74819 files and directories currently installed.) 94s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 94s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 94s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 94s wget depends on libssl3 (>= 3.0.0). 94s u-boot-tools 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 sbsigntool 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 mtd-utils depends on libssl3 (>= 3.0.0). 94s mokutil depends on libssl3 (>= 3.0.0). 94s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 94s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 94s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 94s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 94s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 94s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 94s libnvme1 depends on libssl3 (>= 3.0.0). 94s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 94s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 94s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 94s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 94s libcryptsetup12:arm64 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:arm64 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 ... 74819 files and directories currently installed.) 94s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 94s Selecting previously unselected package libssl3t64:arm64. 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 ... 74808 files and directories currently installed.) 94s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 94s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 94s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 94s Setting up openssl (3.0.13-0ubuntu2) ... 94s Processing triggers for man-db (2.12.0-3) ... 95s Processing triggers for libc-bin (2.39-0ubuntu6) ... 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 97s sh: Attempting to set up Debian/Ubuntu apt sources automatically 97s sh: Distribution appears to be Ubuntu 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s eatmydata is already the newest version (131-1). 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s dbus is already the newest version (1.14.10-4ubuntu1). 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 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... 101s The following packages will be REMOVED: 101s 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 ... 74821 files and directories currently installed.) 101s Removing cloud-init (24.1.2-0ubuntu1) ... 102s Removing python3-configobj (5.0.8-3) ... 102s Removing python3-debconf (1.5.86) ... 102s Processing triggers for man-db (2.12.0-3) ... 103s (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 ... 74432 files and directories currently installed.) 103s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 103s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 103s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 103s invoke-rc.d: policy-rc.d denied execution of try-restart. 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s linux-generic is already the newest version (6.8.0-11.11+1). 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 104s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 106s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [16:46:41]: rebooting testbed after setup commands that affected boot 137s autopkgtest [16:47:09]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 139s autopkgtest [16:47:12]: @@@@@@@@@@@@@@@@@@@@ apt-source bamkit 141s Get:1 http://ftpmaster.internal/ubuntu noble/universe bamkit 0.0.1+git20170413.ccd079d-3 (dsc) [2124 B] 141s Get:2 http://ftpmaster.internal/ubuntu noble/universe bamkit 0.0.1+git20170413.ccd079d-3 (tar) [7772 B] 141s Get:3 http://ftpmaster.internal/ubuntu noble/universe bamkit 0.0.1+git20170413.ccd079d-3 (diff) [6420 B] 142s gpgv: Signature made Mon Aug 16 11:31:23 2021 UTC 142s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 142s gpgv: issuer "npatra974@gmail.com" 142s gpgv: Can't check signature: No public key 142s dpkg-source: warning: cannot verify inline signature for ./bamkit_0.0.1+git20170413.ccd079d-3.dsc: no acceptable signature found 142s autopkgtest [16:47:15]: testing package bamkit version 0.0.1+git20170413.ccd079d-3 142s autopkgtest [16:47:15]: build not needed 142s autopkgtest [16:47:15]: test run-unit-test: preparing testbed 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 150s The following additional packages will be installed: 150s bamkit libdeflate0 libhts3 libhtscodecs2 python3-pysam samtools 150s Suggested packages: 150s cwltool 150s The following NEW packages will be installed: 150s autopkgtest-satdep bamkit libdeflate0 libhts3 libhtscodecs2 python3-pysam 150s samtools 150s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 5542 kB/5543 kB of archives. 150s After this operation, 43.7 MB of additional disk space will be used. 150s Get:1 /tmp/autopkgtest.Q5YKRU/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 150s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 150s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 150s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 150s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 151s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 bamkit all 0.0.1+git20170413.ccd079d-3 [14.9 kB] 151s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 151s Fetched 5542 kB in 1s (6619 kB/s) 151s Selecting previously unselected package libdeflate0:arm64. 151s (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 ... 74377 files and directories currently installed.) 151s Preparing to unpack .../0-libdeflate0_1.19-1_arm64.deb ... 151s Unpacking libdeflate0:arm64 (1.19-1) ... 151s Selecting previously unselected package libhtscodecs2:arm64. 151s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_arm64.deb ... 151s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 151s Selecting previously unselected package libhts3:arm64. 151s Preparing to unpack .../2-libhts3_1.18+ds-1_arm64.deb ... 151s Unpacking libhts3:arm64 (1.18+ds-1) ... 151s Selecting previously unselected package python3-pysam. 151s Preparing to unpack .../3-python3-pysam_0.22.0+ds-1_arm64.deb ... 151s Unpacking python3-pysam (0.22.0+ds-1) ... 152s Selecting previously unselected package bamkit. 152s Preparing to unpack .../4-bamkit_0.0.1+git20170413.ccd079d-3_all.deb ... 152s Unpacking bamkit (0.0.1+git20170413.ccd079d-3) ... 152s Selecting previously unselected package samtools. 152s Preparing to unpack .../5-samtools_1.19.2-1_arm64.deb ... 152s Unpacking samtools (1.19.2-1) ... 152s Selecting previously unselected package autopkgtest-satdep. 152s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 152s Unpacking autopkgtest-satdep (0) ... 152s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 152s Setting up libdeflate0:arm64 (1.19-1) ... 152s Setting up libhts3:arm64 (1.18+ds-1) ... 152s Setting up python3-pysam (0.22.0+ds-1) ... 152s Setting up bamkit (0.0.1+git20170413.ccd079d-3) ... 152s Setting up samtools (1.19.2-1) ... 152s Setting up autopkgtest-satdep (0) ... 152s Processing triggers for man-db (2.12.0-3) ... 153s Processing triggers for libc-bin (2.39-0ubuntu6) ... 155s (Reading database ... 74895 files and directories currently installed.) 155s Removing autopkgtest-satdep (0) ... 156s autopkgtest [16:47:29]: test run-unit-test: [----------------------- 157s PASS Tests 157s autopkgtest [16:47:30]: test run-unit-test: -----------------------] 158s run-unit-test PASS 158s autopkgtest [16:47:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 158s autopkgtest [16:47:31]: @@@@@@@@@@@@@@@@@@@@ summary 158s run-unit-test PASS 169s Creating nova instance adt-noble-arm64-bamkit-20240324-164453-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...