19s autopkgtest [15:25:29]: starting date and time: 2024-07-12 15:25:29+0000 19s autopkgtest [15:25:29]: git checkout: fd3bed09 nova: allow more retries for quota issues 19s autopkgtest [15:25:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.06dlcit_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-15.secgroup --name adt-oracular-arm64-epcr-20240712-152505-juju-7f2275-prod-proposed-migration-environment-3-d7a5f6e3-7c9c-4904-9900-323ec15c9e79 --image adt/ubuntu-oracular-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,keyserver.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/ 196s autopkgtest [15:28:20]: testbed dpkg architecture: arm64 196s autopkgtest [15:28:24]: testbed apt version: 2.9.6 196s autopkgtest [15:28:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 197s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 198s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 198s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [344 kB] 198s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [43.3 kB] 198s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 198s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [89.9 kB] 198s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2104 B] 198s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 198s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 198s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [359 kB] 198s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [7988 B] 198s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [7596 B] 198s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 202s Fetched 1036 kB in 2s (621 kB/s) 202s Reading package lists... 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 241s Calculating upgrade... 242s The following packages will be upgraded: 242s libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales openssh-client 242s openssh-server openssh-sftp-server 242s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 242s Need to get 10.6 MB of archives. 242s After this operation, 28.7 kB disk space will be freed. 242s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-devtools arm64 2.39-3.1ubuntu3 [27.7 kB] 242s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6-dev arm64 2.39-3.1ubuntu3 [1591 kB] 243s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-dev-bin arm64 2.39-3.1ubuntu3 [19.7 kB] 243s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6 arm64 2.39-3.1ubuntu3 [2770 kB] 243s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-bin arm64 2.39-3.1ubuntu3 [579 kB] 243s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-sftp-server arm64 1:9.6p1-3ubuntu17 [36.7 kB] 243s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-server arm64 1:9.6p1-3ubuntu17 [502 kB] 243s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-client arm64 1:9.6p1-3ubuntu17 [888 kB] 243s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 locales all 2.39-3.1ubuntu3 [4220 kB] 243s Preconfiguring packages ... 243s Fetched 10.6 MB in 1s (11.1 MB/s) 244s (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 ... 78392 files and directories currently installed.) 244s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_arm64.deb ... 244s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 244s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_arm64.deb ... 244s Unpacking libc6-dev:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 244s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_arm64.deb ... 244s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 244s Preparing to unpack .../libc6_2.39-3.1ubuntu3_arm64.deb ... 246s Unpacking libc6:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 246s Setting up libc6:arm64 (2.39-3.1ubuntu3) ... 246s Error: Could not restart systemd, systemd binary not working 246s (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 ... 78392 files and directories currently installed.) 246s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_arm64.deb ... 246s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 246s Setting up libc-bin (2.39-3.1ubuntu3) ... 246s (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 ... 78392 files and directories currently installed.) 246s Preparing to unpack .../openssh-sftp-server_1%3a9.6p1-3ubuntu17_arm64.deb ... 246s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 246s Preparing to unpack .../openssh-server_1%3a9.6p1-3ubuntu17_arm64.deb ... 246s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 246s Preparing to unpack .../openssh-client_1%3a9.6p1-3ubuntu17_arm64.deb ... 246s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 246s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 246s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 246s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 246s Setting up locales (2.39-3.1ubuntu3) ... 246s Generating locales (this might take a while)... 249s en_US.UTF-8... done 249s Generation complete. 249s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 249s Setting up libc-devtools (2.39-3.1ubuntu3) ... 249s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 249s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 249s Installing new version of config file /etc/pam.d/sshd ... 252s Setting up libc6-dev:arm64 (2.39-3.1ubuntu3) ... 252s Processing triggers for systemd (256-1ubuntu1) ... 252s Processing triggers for man-db (2.12.1-2) ... 252s Processing triggers for ufw (0.36.2-6) ... 252s Reading package lists... 253s Building dependency tree... 253s Reading state information... 254s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 257s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 257s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 257s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 257s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 259s Reading package lists... 259s Reading package lists... 259s Building dependency tree... 259s Reading state information... 260s Calculating upgrade... 260s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 260s Reading package lists... 261s Building dependency tree... 261s Reading state information... 261s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 268s autopkgtest [15:29:38]: rebooting testbed after setup commands that affected boot 304s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 314s autopkgtest [15:30:24]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 343s autopkgtest [15:30:53]: @@@@@@@@@@@@@@@@@@@@ apt-source epcr 349s Get:1 http://ftpmaster.internal/ubuntu oracular/universe epcr 2.3.12-1-9 (dsc) [2026 B] 349s Get:2 http://ftpmaster.internal/ubuntu oracular/universe epcr 2.3.12-1-9 (tar) [76.8 kB] 349s Get:3 http://ftpmaster.internal/ubuntu oracular/universe epcr 2.3.12-1-9 (diff) [55.9 kB] 349s gpgv: Signature made Mon Dec 7 20:11:34 2020 UTC 349s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 349s gpgv: issuer "tille@debian.org" 349s gpgv: Can't check signature: No public key 349s dpkg-source: warning: cannot verify inline signature for ./epcr_2.3.12-1-9.dsc: no acceptable signature found 349s autopkgtest [15:30:59]: testing package epcr version 2.3.12-1-9 350s autopkgtest [15:31:00]: build not needed 350s autopkgtest [15:31:00]: test run-unit-test: preparing testbed 355s Reading package lists... 356s Building dependency tree... 356s Reading state information... 356s Starting pkgProblemResolver with broken count: 0 357s Starting 2 pkgProblemResolver with broken count: 0 357s Done 357s The following additional packages will be installed: 357s ncbi-epcr 357s Suggested packages: 357s bioperl 357s The following NEW packages will be installed: 357s autopkgtest-satdep ncbi-epcr 357s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 357s Need to get 154 kB/155 kB of archives. 357s After this operation, 469 kB of additional disk space will be used. 357s Get:1 /tmp/autopkgtest.Tbpc0G/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 358s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 ncbi-epcr arm64 2.3.12-1-9 [154 kB] 358s Fetched 154 kB in 0s (363 kB/s) 359s Selecting previously unselected package ncbi-epcr. 359s (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 ... 78392 files and directories currently installed.) 359s Preparing to unpack .../ncbi-epcr_2.3.12-1-9_arm64.deb ... 359s Unpacking ncbi-epcr (2.3.12-1-9) ... 359s Selecting previously unselected package autopkgtest-satdep. 359s Preparing to unpack .../1-autopkgtest-satdep.deb ... 359s Unpacking autopkgtest-satdep (0) ... 359s Setting up ncbi-epcr (2.3.12-1-9) ... 359s Setting up autopkgtest-satdep (0) ... 359s Processing triggers for man-db (2.12.1-2) ... 381s (Reading database ... 78411 files and directories currently installed.) 381s Removing autopkgtest-satdep (0) ... 386s autopkgtest [15:31:36]: test run-unit-test: [----------------------- 386s * Adding gingko.fasta 386s * Adding File gingko.mmap 386s  - Adding Sequence MG922664.1 386s = Resetting... OKTotal number of sequences: 1 386s Number of hash entries: 20 386s Average number of sequences per hash entry: 1 386s Maximal number of sequences per hash entry: 1 386s Null hash entries: 0 386s Total number of hits: 313964 386s Average number of hits per hash entry: 15698.2 386s Maximal number of hits per hash entry: 48023 386s  - Adding Sequence MG922664.1 386s = Dumping 386s = Dumping OK 386s = File rbcL-primer.txt, STSes 1-2 386s autopkgtest [15:31:36]: test run-unit-test: -----------------------] 387s run-unit-test PASS 387s autopkgtest [15:31:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 387s autopkgtest [15:31:37]: @@@@@@@@@@@@@@@@@@@@ summary 387s run-unit-test PASS 449s nova [W] Skipping flock in bos03-arm64 449s Creating nova instance adt-oracular-arm64-epcr-20240712-152505-juju-7f2275-prod-proposed-migration-environment-3-d7a5f6e3-7c9c-4904-9900-323ec15c9e79 from image adt/ubuntu-oracular-arm64-server-20240712.img (UUID a9c53646-2a41-49d7-a14b-d40262a2cb6c)...