0s autopkgtest [17:31:43]: starting date and time: 2024-03-24 17:31:43+0000 0s autopkgtest [17:31:43]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:31:43]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uv0el_s1/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 bamclipper --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@bos01-arm64-13.secgroup --name adt-noble-arm64-bamclipper-20240324-171632-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://us.ports.ubuntu.com/ubuntu-ports/ 122s autopkgtest [17:33:45]: testbed dpkg architecture: arm64 122s autopkgtest [17:33:45]: testbed apt version: 2.7.12 122s autopkgtest [17:33:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 123s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 124s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 124s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 124s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 124s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 126s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 126s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 126s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 126s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 126s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 126s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 126s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 126s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 132s Fetched 9850 kB in 4s (2705 kB/s) 132s Reading package lists... 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Calculating upgrade... 139s The following packages will be REMOVED: 139s libssl3 139s The following NEW packages will be installed: 139s libssl3t64 139s The following packages have been kept back: 139s curl 139s The following packages will be upgraded: 139s openssl 139s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 139s Need to get 2777 kB of archives. 139s After this operation, 139 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 142s Fetched 2777 kB in 2s (1274 kB/s) 142s (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.) 142s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 142s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 142s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 142s wget depends on libssl3 (>= 3.0.0). 142s u-boot-tools depends on libssl3 (>= 3.0.0). 142s tnftp depends on libssl3 (>= 3.0.0). 142s tcpdump depends on libssl3 (>= 3.0.0). 142s systemd-resolved depends on libssl3 (>= 3.0.0). 142s systemd depends on libssl3 (>= 3.0.0). 142s sudo depends on libssl3 (>= 3.0.0). 142s sbsigntool depends on libssl3 (>= 3.0.0). 142s rsync depends on libssl3 (>= 3.0.0). 142s python3-cryptography depends on libssl3 (>= 3.0.0). 142s openssh-server depends on libssl3 (>= 3.0.10). 142s openssh-client depends on libssl3 (>= 3.0.10). 142s mtd-utils depends on libssl3 (>= 3.0.0). 142s mokutil depends on libssl3 (>= 3.0.0). 142s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 142s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 142s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 142s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 142s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 142s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 142s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 142s libnvme1 depends on libssl3 (>= 3.0.0). 142s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 142s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 142s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 142s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 142s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 142s kmod depends on libssl3 (>= 3.0.0). 142s dhcpcd-base depends on libssl3 (>= 3.0.0). 142s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 142s 142s (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.) 142s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 143s Selecting previously unselected package libssl3t64:arm64. 143s (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.) 143s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 143s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 143s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 143s Setting up openssl (3.0.13-0ubuntu2) ... 143s Processing triggers for man-db (2.12.0-3) ... 144s Processing triggers for libc-bin (2.39-0ubuntu6) ... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 146s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 147s sh: Attempting to set up Debian/Ubuntu apt sources automatically 147s sh: Distribution appears to be Ubuntu 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s eatmydata is already the newest version (131-1). 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s dbus is already the newest version (1.14.10-4ubuntu1). 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s rng-tools-debian is already the newest version (2.4). 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s The following packages will be REMOVED: 156s cloud-init* python3-configobj* python3-debconf* 157s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 157s After this operation, 3256 kB disk space will be freed. 157s (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.) 157s Removing cloud-init (24.1.2-0ubuntu1) ... 159s Removing python3-configobj (5.0.8-3) ... 159s Removing python3-debconf (1.5.86) ... 159s Processing triggers for man-db (2.12.0-3) ... 159s (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.) 159s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 160s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 160s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 160s invoke-rc.d: policy-rc.d denied execution of try-restart. 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 162s linux-generic is already the newest version (6.8.0-11.11+1). 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 163s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 163s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 168s Reading package lists... 169s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s Calculating upgrade... 171s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s autopkgtest [17:34:36]: rebooting testbed after setup commands that affected boot 335s autopkgtest [17:37:18]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 338s autopkgtest [17:37:21]: @@@@@@@@@@@@@@@@@@@@ apt-source bamclipper 340s Get:1 http://ftpmaster.internal/ubuntu noble/universe bamclipper 1.0.0-3 (dsc) [2010 B] 340s Get:2 http://ftpmaster.internal/ubuntu noble/universe bamclipper 1.0.0-3 (tar) [5832 B] 340s Get:3 http://ftpmaster.internal/ubuntu noble/universe bamclipper 1.0.0-3 (diff) [36.0 kB] 340s gpgv: Signature made Fri Sep 30 06:43:50 2022 UTC 340s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 340s gpgv: issuer "tille@debian.org" 340s gpgv: Can't check signature: No public key 340s dpkg-source: warning: cannot verify inline signature for ./bamclipper_1.0.0-3.dsc: no acceptable signature found 340s autopkgtest [17:37:23]: testing package bamclipper version 1.0.0-3 341s autopkgtest [17:37:24]: build not needed 341s autopkgtest [17:37:24]: test run-unit-test: preparing testbed 346s Reading package lists... 346s Building dependency tree... 346s Reading state information... 347s Starting pkgProblemResolver with broken count: 0 347s Starting 2 pkgProblemResolver with broken count: 0 347s Done 348s The following additional packages will be installed: 348s bamclipper libdeflate0 libhts3 libhtscodecs2 parallel samtools 348s Suggested packages: 348s csh fish ksh tcsh zsh cwltool 348s The following NEW packages will be installed: 348s autopkgtest-satdep bamclipper libdeflate0 libhts3 libhtscodecs2 parallel 348s samtools 348s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 348s Need to get 3079 kB/3080 kB of archives. 348s After this operation, 6201 kB of additional disk space will be used. 348s Get:1 /tmp/autopkgtest.gKWV1b/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 349s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 349s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 349s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 349s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 349s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 parallel all 20231122+ds-1 [1944 kB] 350s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 bamclipper all 1.0.0-3 [6476 B] 351s Fetched 3079 kB in 2s (2041 kB/s) 351s Selecting previously unselected package libdeflate0:arm64. 351s (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.) 351s Preparing to unpack .../0-libdeflate0_1.19-1_arm64.deb ... 351s Unpacking libdeflate0:arm64 (1.19-1) ... 351s Selecting previously unselected package libhtscodecs2:arm64. 351s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_arm64.deb ... 351s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 351s Selecting previously unselected package libhts3:arm64. 351s Preparing to unpack .../2-libhts3_1.18+ds-1_arm64.deb ... 351s Unpacking libhts3:arm64 (1.18+ds-1) ... 351s Selecting previously unselected package samtools. 351s Preparing to unpack .../3-samtools_1.19.2-1_arm64.deb ... 351s Unpacking samtools (1.19.2-1) ... 351s Selecting previously unselected package parallel. 351s Preparing to unpack .../4-parallel_20231122+ds-1_all.deb ... 351s Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' 351s Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' 351s Unpacking parallel (20231122+ds-1) ... 351s Selecting previously unselected package bamclipper. 351s Preparing to unpack .../5-bamclipper_1.0.0-3_all.deb ... 351s Unpacking bamclipper (1.0.0-3) ... 351s Selecting previously unselected package autopkgtest-satdep. 351s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 351s Unpacking autopkgtest-satdep (0) ... 351s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 351s Setting up libdeflate0:arm64 (1.19-1) ... 351s Setting up parallel (20231122+ds-1) ... 351s Setting up libhts3:arm64 (1.18+ds-1) ... 351s Setting up samtools (1.19.2-1) ... 351s Setting up bamclipper (1.0.0-3) ... 351s Setting up autopkgtest-satdep (0) ... 351s Processing triggers for man-db (2.12.0-3) ... 352s Processing triggers for libc-bin (2.39-0ubuntu6) ... 357s (Reading database ... 75681 files and directories currently installed.) 357s Removing autopkgtest-satdep (0) ... 358s autopkgtest [17:37:41]: test run-unit-test: [----------------------- 359s SRR2075598.sam 359s sample.bam 359s sample.bam.bai 359s sample.primerclipped.bam 359s sample.primerclipped.bam.bai 359s trusight_myeloid.bedpe 359s PASS 359s autopkgtest [17:37:42]: test run-unit-test: -----------------------] 360s autopkgtest [17:37:43]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 360s run-unit-test PASS 360s autopkgtest [17:37:43]: @@@@@@@@@@@@@@@@@@@@ summary 360s run-unit-test PASS 376s Creating nova instance adt-noble-arm64-bamclipper-20240324-171632-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...