0s autopkgtest [16:47:45]: starting date and time: 2024-03-24 16:47:45+0000 0s autopkgtest [16:47:45]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:47:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uf3ect6w/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 catfishq --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-catfishq-20240324-164744-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/ 69s autopkgtest [16:48:54]: testbed dpkg architecture: arm64 69s autopkgtest [16:48:54]: testbed apt version: 2.7.12 69s autopkgtest [16:48:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 69s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 70s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 70s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 70s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 70s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 70s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 70s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 70s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 70s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 70s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 70s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 70s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 70s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 72s Fetched 9847 kB in 2s (5589 kB/s) 72s Reading package lists... 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Calculating upgrade... 76s The following packages will be REMOVED: 76s libssl3 76s The following NEW packages will be installed: 76s libssl3t64 76s The following packages have been kept back: 76s curl 76s The following packages will be upgraded: 76s openssl 76s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 76s Need to get 2777 kB of archives. 76s After this operation, 139 kB of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 76s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 77s Fetched 2777 kB in 1s (3732 kB/s) 77s (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.) 77s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 77s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 77s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 77s wget depends on libssl3 (>= 3.0.0). 77s u-boot-tools depends on libssl3 (>= 3.0.0). 77s tnftp depends on libssl3 (>= 3.0.0). 77s tcpdump depends on libssl3 (>= 3.0.0). 77s systemd-resolved depends on libssl3 (>= 3.0.0). 77s systemd depends on libssl3 (>= 3.0.0). 77s sudo depends on libssl3 (>= 3.0.0). 77s sbsigntool depends on libssl3 (>= 3.0.0). 77s rsync depends on libssl3 (>= 3.0.0). 77s python3-cryptography depends on libssl3 (>= 3.0.0). 77s openssh-server depends on libssl3 (>= 3.0.10). 77s openssh-client depends on libssl3 (>= 3.0.10). 77s mtd-utils depends on libssl3 (>= 3.0.0). 77s mokutil depends on libssl3 (>= 3.0.0). 77s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 77s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 77s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 77s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 77s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 77s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 77s libnvme1 depends on libssl3 (>= 3.0.0). 77s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 77s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 77s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 77s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 77s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 77s kmod depends on libssl3 (>= 3.0.0). 77s dhcpcd-base depends on libssl3 (>= 3.0.0). 77s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 77s 77s (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.) 77s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 77s Selecting previously unselected package libssl3t64:arm64. 77s (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.) 77s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 77s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 77s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 77s Setting up openssl (3.0.13-0ubuntu2) ... 77s Processing triggers for man-db (2.12.0-3) ... 78s Processing triggers for libc-bin (2.39-0ubuntu6) ... 78s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 80s sh: Attempting to set up Debian/Ubuntu apt sources automatically 80s sh: Distribution appears to be Ubuntu 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s eatmydata is already the newest version (131-1). 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s dbus is already the newest version (1.14.10-4ubuntu1). 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s rng-tools-debian is already the newest version (2.4). 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s The following packages will be REMOVED: 83s cloud-init* python3-configobj* python3-debconf* 83s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 83s After this operation, 3256 kB disk space will be freed. 83s (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.) 83s Removing cloud-init (24.1.2-0ubuntu1) ... 84s Removing python3-configobj (5.0.8-3) ... 84s Removing python3-debconf (1.5.86) ... 84s Processing triggers for man-db (2.12.0-3) ... 84s (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.) 84s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 85s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 85s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 85s invoke-rc.d: policy-rc.d denied execution of try-restart. 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s linux-generic is already the newest version (6.8.0-11.11+1). 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 86s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 88s Reading package lists... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s Calculating upgrade... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [16:49:15]: rebooting testbed after setup commands that affected boot 118s autopkgtest [16:49:43]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 122s autopkgtest [16:49:47]: @@@@@@@@@@@@@@@@@@@@ apt-source catfishq 124s Get:1 http://ftpmaster.internal/ubuntu noble/universe catfishq 1.4.0+ds-1 (dsc) [1943 B] 124s Get:2 http://ftpmaster.internal/ubuntu noble/universe catfishq 1.4.0+ds-1 (tar) [5596 B] 124s Get:3 http://ftpmaster.internal/ubuntu noble/universe catfishq 1.4.0+ds-1 (diff) [4144 B] 125s gpgv: Signature made Wed Mar 23 03:29:00 2022 UTC 125s gpgv: using RSA key E50AFD55ADD27AAB97163A8B21D20589974B3E96 125s gpgv: issuer "tmancill@debian.org" 125s gpgv: Can't check signature: No public key 125s dpkg-source: warning: cannot verify inline signature for ./catfishq_1.4.0+ds-1.dsc: no acceptable signature found 125s autopkgtest [16:49:50]: testing package catfishq version 1.4.0+ds-1 125s autopkgtest [16:49:50]: build not needed 125s autopkgtest [16:49:50]: test run-unit-test: preparing testbed 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s Starting pkgProblemResolver with broken count: 0 133s Starting 2 pkgProblemResolver with broken count: 0 133s Done 133s The following additional packages will be installed: 133s catfishq libdeflate0 libhts3 libhtscodecs2 python3-pysam 133s The following NEW packages will be installed: 133s autopkgtest-satdep catfishq libdeflate0 libhts3 libhtscodecs2 python3-pysam 133s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 4953 kB/4953 kB of archives. 133s After this operation, 42.0 MB of additional disk space will be used. 133s Get:1 /tmp/autopkgtest.m7HxS0/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 134s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 134s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 134s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 134s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 134s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 catfishq all 1.4.0+ds-1 [9432 B] 135s Fetched 4953 kB in 1s (6028 kB/s) 135s Selecting previously unselected package libdeflate0:arm64. 135s (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.) 135s Preparing to unpack .../0-libdeflate0_1.19-1_arm64.deb ... 135s Unpacking libdeflate0:arm64 (1.19-1) ... 135s Selecting previously unselected package libhtscodecs2:arm64. 135s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_arm64.deb ... 135s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 135s Selecting previously unselected package libhts3:arm64. 135s Preparing to unpack .../2-libhts3_1.18+ds-1_arm64.deb ... 135s Unpacking libhts3:arm64 (1.18+ds-1) ... 135s Selecting previously unselected package python3-pysam. 135s Preparing to unpack .../3-python3-pysam_0.22.0+ds-1_arm64.deb ... 135s Unpacking python3-pysam (0.22.0+ds-1) ... 136s Selecting previously unselected package catfishq. 136s Preparing to unpack .../4-catfishq_1.4.0+ds-1_all.deb ... 136s Unpacking catfishq (1.4.0+ds-1) ... 136s Selecting previously unselected package autopkgtest-satdep. 136s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 136s Unpacking autopkgtest-satdep (0) ... 136s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 136s Setting up libdeflate0:arm64 (1.19-1) ... 136s Setting up libhts3:arm64 (1.18+ds-1) ... 136s Setting up python3-pysam (0.22.0+ds-1) ... 136s Setting up catfishq (1.4.0+ds-1) ... 136s /usr/lib/python3/dist-packages/catfishq/cat_fastq.py:25: SyntaxWarning: invalid escape sequence '\s' 136s channel_regex_pattern = re.compile("(^|\s)ch=(?P\d+)") 136s /usr/lib/python3/dist-packages/catfishq/cat_fastq.py:29: SyntaxWarning: invalid escape sequence '\d' 136s channel_range_regex_pattern = re.compile("^(?P\d+)(-(?P\d+))?$") 136s Setting up autopkgtest-satdep (0) ... 136s Processing triggers for man-db (2.12.0-3) ... 137s Processing triggers for libc-bin (2.39-0ubuntu6) ... 140s (Reading database ... 74794 files and directories currently installed.) 140s Removing autopkgtest-satdep (0) ... 141s autopkgtest [16:50:06]: test run-unit-test: [----------------------- 141s Test recursive directory descent and dedup 142s Searching . for FASTQ files 142s Found 4 files 142s PASS 142s autopkgtest [16:50:07]: test run-unit-test: -----------------------] 143s run-unit-test PASS 143s autopkgtest [16:50:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 143s autopkgtest [16:50:08]: @@@@@@@@@@@@@@@@@@@@ summary 143s run-unit-test PASS 149s Creating nova instance adt-noble-arm64-catfishq-20240324-164744-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...