0s autopkgtest [15:17:05]: starting date and time: 2024-03-23 15:17:05+0000 0s autopkgtest [15:17:05]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:17:05]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dlg803s5/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@bos02-ppc64el-14.secgroup --name adt-noble-ppc64el-catfishq-20240323-151705-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 96s autopkgtest [15:18:41]: testbed dpkg architecture: ppc64el 96s autopkgtest [15:18:41]: testbed apt version: 2.7.12 96s autopkgtest [15:18:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 97s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 97s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 97s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 97s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 98s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 98s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 98s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 98s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 98s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 98s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 98s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 98s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 98s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 101s Fetched 9623 kB in 3s (3725 kB/s) 102s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s Calculating upgrade... 105s The following packages will be REMOVED: 105s libssl3 105s The following NEW packages will be installed: 105s libssl3t64 105s The following packages have been kept back: 105s curl 105s The following packages will be upgraded: 105s openssl 105s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 105s Need to get 3151 kB of archives. 105s After this operation, 73.7 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 106s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 106s Fetched 3151 kB in 1s (2433 kB/s) 106s (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 ... 70156 files and directories currently installed.) 106s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 106s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 107s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 107s wget depends on libssl3 (>= 3.0.0). 107s tnftp depends on libssl3 (>= 3.0.0). 107s tcpdump depends on libssl3 (>= 3.0.0). 107s systemd-resolved depends on libssl3 (>= 3.0.0). 107s systemd depends on libssl3 (>= 3.0.0). 107s sudo depends on libssl3 (>= 3.0.0). 107s rsync depends on libssl3 (>= 3.0.0). 107s python3-cryptography depends on libssl3 (>= 3.0.0). 107s openssh-server depends on libssl3 (>= 3.0.10). 107s openssh-client depends on libssl3 (>= 3.0.10). 107s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 107s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 107s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 107s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 107s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 107s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 107s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 107s libnvme1 depends on libssl3 (>= 3.0.0). 107s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 107s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 107s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 107s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 107s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 107s kmod depends on libssl3 (>= 3.0.0). 107s dhcpcd-base depends on libssl3 (>= 3.0.0). 107s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 107s 107s (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 ... 70156 files and directories currently installed.) 107s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 107s Selecting previously unselected package libssl3t64:ppc64el. 107s (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 ... 70145 files and directories currently installed.) 107s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 107s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 107s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 107s Setting up openssl (3.0.13-0ubuntu2) ... 107s Processing triggers for man-db (2.12.0-3) ... 107s Processing triggers for libc-bin (2.39-0ubuntu6) ... 107s Reading package lists... 111s Building dependency tree... 111s Reading state information...sh: Attempting to set up Debian/Ubuntu apt sources automatically 111s 111s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s eatmydata is already the newest version (131-1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s dbus is already the newest version (1.14.10-4ubuntu1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s rng-tools-debian is already the newest version (2.4). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s The following packages will be REMOVED: 111s cloud-init* python3-configobj* python3-debconf* 111s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 111s After this operation, 3256 kB disk space will be freed. 111s (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 ... 70158 files and directories currently installed.) 111s Removing cloud-init (24.1.2-0ubuntu1) ... 111s sh: Distribution appears to be Ubuntu 111s Removing python3-configobj (5.0.8-3) ... 111s Removing python3-debconf (1.5.86) ... 111s Processing triggers for man-db (2.12.0-3) ... 112s (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 ... 69769 files and directories currently installed.) 112s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 112s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 112s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 112s invoke-rc.d: policy-rc.d denied execution of try-restart. 115s Reading package lists...Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 115s 115s Building dependency tree... 115s Reading state information... 115s linux-generic is already the newest version (6.8.0-11.11+1). 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 116s Reading package lists... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s autopkgtest [15:19:02]: rebooting testbed after setup commands that affected boot 160s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 167s autopkgtest [15:19:52]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 169s autopkgtest [15:19:54]: @@@@@@@@@@@@@@@@@@@@ apt-source catfishq 171s Get:1 http://ftpmaster.internal/ubuntu noble/universe catfishq 1.4.0+ds-1 (dsc) [1943 B] 171s Get:2 http://ftpmaster.internal/ubuntu noble/universe catfishq 1.4.0+ds-1 (tar) [5596 B] 171s Get:3 http://ftpmaster.internal/ubuntu noble/universe catfishq 1.4.0+ds-1 (diff) [4144 B] 171s gpgv: Signature made Wed Mar 23 03:29:00 2022 UTC 171s gpgv: using RSA key E50AFD55ADD27AAB97163A8B21D20589974B3E96 171s gpgv: issuer "tmancill@debian.org" 171s gpgv: Can't check signature: No public key 171s dpkg-source: warning: cannot verify inline signature for ./catfishq_1.4.0+ds-1.dsc: no acceptable signature found 171s autopkgtest [15:19:56]: testing package catfishq version 1.4.0+ds-1 171s autopkgtest [15:19:56]: build not needed 171s autopkgtest [15:19:56]: test run-unit-test: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Starting pkgProblemResolver with broken count: 0 173s Starting 2 pkgProblemResolver with broken count: 0 173s Done 174s The following additional packages will be installed: 174s catfishq libdeflate0 libhts3 libhtscodecs2 python3-pysam 174s The following NEW packages will be installed: 174s autopkgtest-satdep catfishq libdeflate0 libhts3 libhtscodecs2 python3-pysam 174s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 5770 kB/5771 kB of archives. 174s After this operation, 47.5 MB of additional disk space will be used. 174s Get:1 /tmp/autopkgtest.9PG9Lq/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 174s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 174s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 174s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 174s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 175s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el catfishq all 1.4.0+ds-1 [9432 B] 176s Fetched 5770 kB in 2s (3359 kB/s) 176s Selecting previously unselected package libdeflate0:ppc64el. 176s (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 ... 69714 files and directories currently installed.) 176s Preparing to unpack .../0-libdeflate0_1.19-1_ppc64el.deb ... 176s Unpacking libdeflate0:ppc64el (1.19-1) ... 176s Selecting previously unselected package libhtscodecs2:ppc64el. 176s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_ppc64el.deb ... 176s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 176s Selecting previously unselected package libhts3:ppc64el. 176s Preparing to unpack .../2-libhts3_1.18+ds-1_ppc64el.deb ... 176s Unpacking libhts3:ppc64el (1.18+ds-1) ... 176s Selecting previously unselected package python3-pysam. 176s Preparing to unpack .../3-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 176s Unpacking python3-pysam (0.22.0+ds-1) ... 176s Selecting previously unselected package catfishq. 176s Preparing to unpack .../4-catfishq_1.4.0+ds-1_all.deb ... 176s Unpacking catfishq (1.4.0+ds-1) ... 176s Selecting previously unselected package autopkgtest-satdep. 176s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 176s Unpacking autopkgtest-satdep (0) ... 176s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 176s Setting up libdeflate0:ppc64el (1.19-1) ... 176s Setting up libhts3:ppc64el (1.18+ds-1) ... 176s Setting up python3-pysam (0.22.0+ds-1) ... 176s Setting up catfishq (1.4.0+ds-1) ... 176s /usr/lib/python3/dist-packages/catfishq/cat_fastq.py:25: SyntaxWarning: invalid escape sequence '\s' 176s channel_regex_pattern = re.compile("(^|\s)ch=(?P\d+)") 176s /usr/lib/python3/dist-packages/catfishq/cat_fastq.py:29: SyntaxWarning: invalid escape sequence '\d' 176s channel_range_regex_pattern = re.compile("^(?P\d+)(-(?P\d+))?$") 176s Setting up autopkgtest-satdep (0) ... 176s Processing triggers for man-db (2.12.0-3) ... 177s Processing triggers for libc-bin (2.39-0ubuntu6) ... 179s (Reading database ... 70131 files and directories currently installed.) 179s Removing autopkgtest-satdep (0) ... 180s autopkgtest [15:20:05]: test run-unit-test: [----------------------- 180s Test recursive directory descent and dedup 180s Searching . for FASTQ files 180s Found 4 files 180s PASS 180s autopkgtest [15:20:05]: test run-unit-test: -----------------------] 181s autopkgtest [15:20:06]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 181s run-unit-test PASS 181s autopkgtest [15:20:06]: @@@@@@@@@@@@@@@@@@@@ summary 181s run-unit-test PASS 192s Creating nova instance adt-noble-ppc64el-catfishq-20240323-151705-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...