0s autopkgtest [16:28:41]: starting date and time: 2024-07-12 16:28:41+0000 0s autopkgtest [16:28:41]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [16:28:41]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dom61_og/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade epcr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- lxd -r lxd-armhf-10.145.243.27 lxd-armhf-10.145.243.27:autopkgtest/ubuntu/oracular/armhf 55s autopkgtest [16:29:36]: testbed dpkg architecture: armhf 57s autopkgtest [16:29:38]: testbed apt version: 2.9.6 57s autopkgtest [16:29:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 65s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [343 kB] 65s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 65s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.6 kB] 65s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 65s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [58.3 kB] 65s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf c-n-f Metadata [1444 B] 65s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf Packages [1368 B] 65s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf c-n-f Metadata [120 B] 65s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [303 kB] 65s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf c-n-f Metadata [6176 B] 65s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1448 B] 65s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf c-n-f Metadata [120 B] 67s Fetched 899 kB in 1s (1100 kB/s) 67s Reading package lists... 90s tee: /proc/self/fd/2: Permission denied 112s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 112s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 112s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 112s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 114s Reading package lists... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s Calculating upgrade... 116s The following packages will be upgraded: 116s inetutils-telnet libc-bin libc6 libssl3t64 locales openssh-client 116s openssh-server openssh-sftp-server openssl telnet 116s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 11.9 MB of archives. 116s After this operation, 285 kB of additional disk space will be used. 116s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc6 armhf 2.39-3.1ubuntu3 [2825 kB] 117s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc-bin armhf 2.39-3.1ubuntu3 [527 kB] 117s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libssl3t64 armhf 3.2.2-1ubuntu1 [1729 kB] 117s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu17 [35.6 kB] 117s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-server armhf 1:9.6p1-3ubuntu17 [502 kB] 117s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-client armhf 1:9.6p1-3ubuntu17 [888 kB] 117s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf locales all 2.39-3.1ubuntu3 [4220 kB] 117s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf openssl armhf 3.2.2-1ubuntu1 [1095 kB] 117s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf inetutils-telnet armhf 2:2.5-5ubuntu1 [94.4 kB] 117s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf telnet all 0.17+2.5-5ubuntu1 [3688 B] 118s Preconfiguring packages ... 118s Fetched 11.9 MB in 1s (10.8 MB/s) 118s (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 ... 58437 files and directories currently installed.) 118s Preparing to unpack .../libc6_2.39-3.1ubuntu3_armhf.deb ... 118s Unpacking libc6:armhf (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 119s Setting up libc6:armhf (2.39-3.1ubuntu3) ... 119s Error: Could not restart systemd, systemd binary not working 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 ... 58437 files and directories currently installed.) 119s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_armhf.deb ... 119s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 119s Setting up libc-bin (2.39-3.1ubuntu3) ... 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 ... 58437 files and directories currently installed.) 119s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_armhf.deb ... 119s Unpacking libssl3t64:armhf (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 119s Setting up libssl3t64:armhf (3.2.2-1ubuntu1) ... 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 ... 58437 files and directories currently installed.) 119s Preparing to unpack .../0-openssh-sftp-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 119s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 119s Preparing to unpack .../1-openssh-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 120s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 120s Preparing to unpack .../2-openssh-client_1%3a9.6p1-3ubuntu17_armhf.deb ... 120s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 120s Preparing to unpack .../3-locales_2.39-3.1ubuntu3_all.deb ... 120s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 120s Preparing to unpack .../4-openssl_3.2.2-1ubuntu1_armhf.deb ... 120s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 120s Preparing to unpack .../5-inetutils-telnet_2%3a2.5-5ubuntu1_armhf.deb ... 120s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 120s Preparing to unpack .../6-telnet_0.17+2.5-5ubuntu1_all.deb ... 120s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 121s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 121s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 121s Setting up locales (2.39-3.1ubuntu3) ... 122s Generating locales (this might take a while)... 125s en_US.UTF-8... done 125s Generation complete. 125s Setting up openssl (3.2.2-1ubuntu1) ... 125s Installing new version of config file /etc/ssl/openssl.cnf ... 125s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 125s Setting up telnet (0.17+2.5-5ubuntu1) ... 125s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 125s Installing new version of config file /etc/pam.d/sshd ... 126s Processing triggers for ufw (0.36.2-6) ... 126s Processing triggers for systemd (256-1ubuntu1) ... 127s Processing triggers for man-db (2.12.1-2) ... 128s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s autopkgtest [16:30:53]: rebooting testbed after setup commands that affected boot 202s autopkgtest [16:32:03]: testbed running kernel: Linux 6.5.0-41-generic #41~22.04.2-Ubuntu SMP PREEMPT_DYNAMIC Mon Jun 3 16:28:24 UTC 2 230s autopkgtest [16:32:31]: @@@@@@@@@@@@@@@@@@@@ apt-source epcr 241s Get:1 http://ftpmaster.internal/ubuntu oracular/universe epcr 2.3.12-1-9 (dsc) [2026 B] 241s Get:2 http://ftpmaster.internal/ubuntu oracular/universe epcr 2.3.12-1-9 (tar) [76.8 kB] 241s Get:3 http://ftpmaster.internal/ubuntu oracular/universe epcr 2.3.12-1-9 (diff) [55.9 kB] 241s gpgv: Signature made Mon Dec 7 20:11:34 2020 UTC 241s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 241s gpgv: issuer "tille@debian.org" 241s gpgv: Can't check signature: No public key 241s dpkg-source: warning: cannot verify inline signature for ./epcr_2.3.12-1-9.dsc: no acceptable signature found 241s autopkgtest [16:32:42]: testing package epcr version 2.3.12-1-9 243s autopkgtest [16:32:44]: build not needed 245s autopkgtest [16:32:46]: test run-unit-test: preparing testbed 255s Reading package lists... 256s Building dependency tree... 256s Reading state information... 256s Starting pkgProblemResolver with broken count: 0 257s Starting 2 pkgProblemResolver with broken count: 0 257s Done 258s The following additional packages will be installed: 258s ncbi-epcr 258s Suggested packages: 258s bioperl 258s The following NEW packages will be installed: 258s autopkgtest-satdep ncbi-epcr 258s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 258s Need to get 145 kB/146 kB of archives. 258s After this operation, 338 kB of additional disk space will be used. 258s Get:1 /tmp/autopkgtest.Cryr9u/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 258s Get:2 http://ftpmaster.internal/ubuntu oracular/universe armhf ncbi-epcr armhf 2.3.12-1-9 [145 kB] 259s Fetched 145 kB in 0s (382 kB/s) 259s Selecting previously unselected package ncbi-epcr. 259s (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 ... 58436 files and directories currently installed.) 259s Preparing to unpack .../ncbi-epcr_2.3.12-1-9_armhf.deb ... 259s Unpacking ncbi-epcr (2.3.12-1-9) ... 259s Selecting previously unselected package autopkgtest-satdep. 259s Preparing to unpack .../1-autopkgtest-satdep.deb ... 259s Unpacking autopkgtest-satdep (0) ... 259s Setting up ncbi-epcr (2.3.12-1-9) ... 259s Setting up autopkgtest-satdep (0) ... 259s Processing triggers for man-db (2.12.1-2) ... 272s (Reading database ... 58455 files and directories currently installed.) 272s Removing autopkgtest-satdep (0) ... 278s autopkgtest [16:33:19]: test run-unit-test: [----------------------- 280s * Adding gingko.fasta 280s * Adding File gingko.mmap 280s  - Adding Sequence MG922664.1 280s = Resetting... OKTotal number of sequences: 1 280s Number of hash entries: 20 280s Average number of sequences per hash entry: 1 280s Maximal number of sequences per hash entry: 1 280s Null hash entries: 0 280s Total number of hits: 313964 280s Average number of hits per hash entry: 15698.2 280s Maximal number of hits per hash entry: 48023 280s  - Adding Sequence MG922664.1 280s = Dumping 280s = Dumping OK 280s = File rbcL-primer.txt, STSes 1-2 281s autopkgtest [16:33:22]: test run-unit-test: -----------------------] 285s run-unit-test PASS 285s autopkgtest [16:33:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 288s autopkgtest [16:33:29]: @@@@@@@@@@@@@@@@@@@@ summary 288s run-unit-test PASS