0s autopkgtest [17:37:07]: starting date and time: 2024-03-24 17:37:07+0000 0s autopkgtest [17:37:07]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:37:07]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0yln8erv/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 bioawk --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-bioawk-20240324-172157-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/ 102s autopkgtest [17:38:49]: testbed dpkg architecture: arm64 102s autopkgtest [17:38:49]: testbed apt version: 2.7.12 102s autopkgtest [17:38:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 104s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 105s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 105s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 105s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 105s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 105s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 105s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 105s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 105s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 105s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 105s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 111s Fetched 9850 kB in 3s (3491 kB/s) 111s Reading package lists... 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Calculating upgrade... 118s The following packages will be REMOVED: 118s libssl3 118s The following NEW packages will be installed: 118s libssl3t64 118s The following packages have been kept back: 118s curl 118s The following packages will be upgraded: 118s openssl 118s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 118s Need to get 2777 kB of archives. 118s After this operation, 139 kB of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 118s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 119s Fetched 2777 kB in 1s (3908 kB/s) 119s (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.) 119s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 119s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 120s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 120s wget depends on libssl3 (>= 3.0.0). 120s u-boot-tools depends on libssl3 (>= 3.0.0). 120s tnftp depends on libssl3 (>= 3.0.0). 120s tcpdump depends on libssl3 (>= 3.0.0). 120s systemd-resolved depends on libssl3 (>= 3.0.0). 120s systemd depends on libssl3 (>= 3.0.0). 120s sudo depends on libssl3 (>= 3.0.0). 120s sbsigntool depends on libssl3 (>= 3.0.0). 120s rsync depends on libssl3 (>= 3.0.0). 120s python3-cryptography depends on libssl3 (>= 3.0.0). 120s openssh-server depends on libssl3 (>= 3.0.10). 120s openssh-client depends on libssl3 (>= 3.0.10). 120s mtd-utils depends on libssl3 (>= 3.0.0). 120s mokutil depends on libssl3 (>= 3.0.0). 120s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 120s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 120s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 120s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 120s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 120s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 120s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 120s libnvme1 depends on libssl3 (>= 3.0.0). 120s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 120s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 120s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 120s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 120s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 120s kmod depends on libssl3 (>= 3.0.0). 120s dhcpcd-base depends on libssl3 (>= 3.0.0). 120s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 120s 120s (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.) 120s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 120s Selecting previously unselected package libssl3t64:arm64. 120s (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.) 120s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 120s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 120s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 120s Setting up openssl (3.0.13-0ubuntu2) ... 120s Processing triggers for man-db (2.12.0-3) ... 121s Processing triggers for libc-bin (2.39-0ubuntu6) ... 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 125s sh: Attempting to set up Debian/Ubuntu apt sources automatically 125s sh: Distribution appears to be Ubuntu 126s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s eatmydata is already the newest version (131-1). 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 130s dbus is already the newest version (1.14.10-4ubuntu1). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 132s rng-tools-debian is already the newest version (2.4). 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s The following packages will be REMOVED: 133s cloud-init* python3-configobj* python3-debconf* 134s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 134s After this operation, 3256 kB disk space will be freed. 134s (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.) 134s Removing cloud-init (24.1.2-0ubuntu1) ... 135s Removing python3-configobj (5.0.8-3) ... 135s Removing python3-debconf (1.5.86) ... 136s Processing triggers for man-db (2.12.0-3) ... 136s (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.) 136s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 138s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 138s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 138s invoke-rc.d: policy-rc.d denied execution of try-restart. 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 140s linux-generic is already the newest version (6.8.0-11.11+1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 140s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 146s Reading package lists... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 147s Calculating upgrade... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [17:39:37]: rebooting testbed after setup commands that affected boot 304s autopkgtest [17:42:11]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 307s autopkgtest [17:42:14]: @@@@@@@@@@@@@@@@@@@@ apt-source bioawk 309s Get:1 http://ftpmaster.internal/ubuntu noble/universe bioawk 1.0-4 (dsc) [2025 B] 309s Get:2 http://ftpmaster.internal/ubuntu noble/universe bioawk 1.0-4 (tar) [72.1 kB] 309s Get:3 http://ftpmaster.internal/ubuntu noble/universe bioawk 1.0-4 (diff) [5268 B] 309s gpgv: Signature made Wed Mar 17 18:01:06 2021 UTC 309s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 309s gpgv: issuer "npatra974@gmail.com" 309s gpgv: Can't check signature: No public key 309s dpkg-source: warning: cannot verify inline signature for ./bioawk_1.0-4.dsc: no acceptable signature found 309s autopkgtest [17:42:16]: testing package bioawk version 1.0-4 310s autopkgtest [17:42:17]: build not needed 310s autopkgtest [17:42:17]: test run-unit-test: preparing testbed 316s Reading package lists... 316s Building dependency tree... 316s Reading state information... 317s Starting pkgProblemResolver with broken count: 0 317s Starting 2 pkgProblemResolver with broken count: 0 317s Done 318s The following additional packages will be installed: 318s bioawk samtools-test seqkit-examples 318s Recommended packages: 318s libio-pty-perl 318s The following NEW packages will be installed: 318s autopkgtest-satdep bioawk samtools-test seqkit-examples 318s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 318s Need to get 42.2 MB/42.2 MB of archives. 318s After this operation, 57.6 MB of additional disk space will be used. 318s Get:1 /tmp/autopkgtest.r9etC9/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 318s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 bioawk arm64 1.0-4 [58.5 kB] 319s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools-test all 1.19.2-1 [2401 kB] 319s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 seqkit-examples all 2.3.1+ds-2 [39.7 MB] 321s Fetched 42.2 MB in 2s (22.1 MB/s) 321s Selecting previously unselected package bioawk. 321s (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.) 321s Preparing to unpack .../bioawk_1.0-4_arm64.deb ... 321s Unpacking bioawk (1.0-4) ... 321s Selecting previously unselected package samtools-test. 321s Preparing to unpack .../samtools-test_1.19.2-1_all.deb ... 321s Unpacking samtools-test (1.19.2-1) ... 321s Selecting previously unselected package seqkit-examples. 321s Preparing to unpack .../seqkit-examples_2.3.1+ds-2_all.deb ... 321s Unpacking seqkit-examples (2.3.1+ds-2) ... 322s Selecting previously unselected package autopkgtest-satdep. 322s Preparing to unpack .../1-autopkgtest-satdep.deb ... 322s Unpacking autopkgtest-satdep (0) ... 322s Setting up bioawk (1.0-4) ... 322s Setting up seqkit-examples (2.3.1+ds-2) ... 322s Setting up samtools-test (1.19.2-1) ... 322s Setting up autopkgtest-satdep (0) ... 322s Processing triggers for man-db (2.12.0-3) ... 327s (Reading database ... 76259 files and directories currently installed.) 327s Removing autopkgtest-satdep (0) ... 328s autopkgtest [17:42:35]: test run-unit-test: [----------------------- 328s Test 1 - Get length for sequences 328s ================================= 328s PASS 328s Test 2 - Get reverse compliment 328s ================================== 328s PASS 328s Test 3 - Convert FASTA to tabular form 328s ================================== 328s PASS 328s Test 4 - Print feature length 328s ================================== 328s PASS 328s Test 5 - Extract mapped reads 328s ================================== 328s PASS 329s autopkgtest [17:42:36]: test run-unit-test: -----------------------] 329s autopkgtest [17:42:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 329s run-unit-test PASS 330s autopkgtest [17:42:37]: @@@@@@@@@@@@@@@@@@@@ summary 330s run-unit-test PASS 344s Creating nova instance adt-noble-arm64-bioawk-20240324-172157-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...