3s autopkgtest [15:36:20]: starting date and time: 2024-07-12 15:36:20+0000 3s autopkgtest [15:36:20]: git checkout: fd3bed09 nova: allow more retries for quota issues 3s autopkgtest [15:36:20]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j4xevd63/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade fastdnaml --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-2@bos03-arm64-36.secgroup --name adt-oracular-arm64-fastdnaml-20240712-153617-juju-7f2275-prod-proposed-migration-environment-2-0364eeee-2460-43d9-a417-d87fb5cee8b7 --image adt/ubuntu-oracular-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,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/ 147s autopkgtest [15:38:44]: testbed dpkg architecture: arm64 147s autopkgtest [15:38:44]: testbed apt version: 2.9.6 147s autopkgtest [15:38:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 147s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 148s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 148s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [344 kB] 148s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [43.3 kB] 148s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 148s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [89.9 kB] 148s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2104 B] 148s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 148s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 148s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [359 kB] 148s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [7988 B] 148s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [7596 B] 148s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 150s Fetched 1036 kB in 1s (1169 kB/s) 150s Reading package lists... 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade... 158s The following packages will be upgraded: 158s libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales openssh-client 158s openssh-server openssh-sftp-server 158s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Need to get 10.6 MB of archives. 158s After this operation, 28.7 kB disk space will be freed. 158s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-devtools arm64 2.39-3.1ubuntu3 [27.7 kB] 158s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6-dev arm64 2.39-3.1ubuntu3 [1591 kB] 159s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-dev-bin arm64 2.39-3.1ubuntu3 [19.7 kB] 159s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6 arm64 2.39-3.1ubuntu3 [2770 kB] 160s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-bin arm64 2.39-3.1ubuntu3 [579 kB] 160s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-sftp-server arm64 1:9.6p1-3ubuntu17 [36.7 kB] 160s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-server arm64 1:9.6p1-3ubuntu17 [502 kB] 160s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-client arm64 1:9.6p1-3ubuntu17 [888 kB] 160s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 locales all 2.39-3.1ubuntu3 [4220 kB] 162s Preconfiguring packages ... 162s Fetched 10.6 MB in 3s (3753 kB/s) 162s (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.) 162s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_arm64.deb ... 162s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 162s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_arm64.deb ... 162s Unpacking libc6-dev:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 163s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_arm64.deb ... 163s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 163s Preparing to unpack .../libc6_2.39-3.1ubuntu3_arm64.deb ... 163s Unpacking libc6:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 163s Setting up libc6:arm64 (2.39-3.1ubuntu3) ... 164s Error: Could not restart systemd, systemd binary not working 164s (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.) 164s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_arm64.deb ... 164s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 164s Setting up libc-bin (2.39-3.1ubuntu3) ... 164s (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.) 164s Preparing to unpack .../openssh-sftp-server_1%3a9.6p1-3ubuntu17_arm64.deb ... 164s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 164s Preparing to unpack .../openssh-server_1%3a9.6p1-3ubuntu17_arm64.deb ... 164s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 164s Preparing to unpack .../openssh-client_1%3a9.6p1-3ubuntu17_arm64.deb ... 164s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 165s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 165s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 165s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 165s Setting up locales (2.39-3.1ubuntu3) ... 165s Generating locales (this might take a while)... 168s en_US.UTF-8... done 168s Generation complete. 169s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 169s Setting up libc-devtools (2.39-3.1ubuntu3) ... 169s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 169s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 169s Installing new version of config file /etc/pam.d/sshd ... 171s Setting up libc6-dev:arm64 (2.39-3.1ubuntu3) ... 171s Processing triggers for systemd (256-1ubuntu1) ... 174s Processing triggers for man-db (2.12.1-2) ... 175s Processing triggers for ufw (0.36.2-6) ... 175s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 178s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 178s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 178s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 179s Reading package lists... 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 181s Calculating upgrade... 181s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 182s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 185s autopkgtest [15:39:22]: rebooting testbed after setup commands that affected boot 234s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 272s autopkgtest [15:40:49]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 278s autopkgtest [15:40:55]: @@@@@@@@@@@@@@@@@@@@ apt-source fastdnaml 297s Get:1 http://ftpmaster.internal/ubuntu oracular/universe fastdnaml 1.2.2-16 (dsc) [1407 B] 297s Get:2 http://ftpmaster.internal/ubuntu oracular/universe fastdnaml 1.2.2-16 (tar) [70.0 kB] 297s Get:3 http://ftpmaster.internal/ubuntu oracular/universe fastdnaml 1.2.2-16 (diff) [8544 B] 298s gpgv: Signature made Sun Apr 7 09:24:25 2024 UTC 298s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 298s gpgv: Can't check signature: No public key 298s dpkg-source: warning: cannot verify inline signature for ./fastdnaml_1.2.2-16.dsc: no acceptable signature found 298s autopkgtest [15:41:15]: testing package fastdnaml version 1.2.2-16 301s autopkgtest [15:41:18]: build not needed 301s autopkgtest [15:41:18]: test Makefile: preparing testbed 305s Reading package lists... 305s Building dependency tree... 305s Reading state information... 305s Starting pkgProblemResolver with broken count: 0 305s Starting 2 pkgProblemResolver with broken count: 0 305s Done 306s The following additional packages will be installed: 306s fastdnaml 306s Suggested packages: 306s phylip 306s The following NEW packages will be installed: 306s autopkgtest-satdep fastdnaml 306s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 306s Need to get 57.2 kB/57.9 kB of archives. 306s After this operation, 245 kB of additional disk space will be used. 306s Get:1 /tmp/autopkgtest.2BFgxI/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 306s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 fastdnaml arm64 1.2.2-16 [57.2 kB] 307s Fetched 57.2 kB in 0s (187 kB/s) 307s Selecting previously unselected package fastdnaml. 307s (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.) 307s Preparing to unpack .../fastdnaml_1.2.2-16_arm64.deb ... 307s Unpacking fastdnaml (1.2.2-16) ... 307s Selecting previously unselected package autopkgtest-satdep. 307s Preparing to unpack .../1-autopkgtest-satdep.deb ... 307s Unpacking autopkgtest-satdep (0) ... 308s Setting up fastdnaml (1.2.2-16) ... 308s Setting up autopkgtest-satdep (0) ... 308s Processing triggers for man-db (2.12.1-2) ... 312s (Reading database ... 78472 files and directories currently installed.) 312s Removing autopkgtest-satdep (0) ... 322s autopkgtest [15:41:39]: test Makefile: [----------------------- 322s cat /usr/share/doc/fastdnaml/examples/tests/fastdnaml.data | fastDNAml-util printdata | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints 322s cat /usr/share/doc/fastdnaml/examples/tests/fastdnaml.data | fastDNAml-util printdata > fastdnaml.data.tmp; fastDNAml-util fastDNAml_boot -out -boots 2 -max 2 fastdnaml.data.tmp 2 322s /tmp/autopkgtest.2BFgxI/wrapper.sh: Killing leaked background processes: 1479 322s PID TTY STAT TIME COMMAND 322s 1479 ? S 0:00 /bin/sh /usr/lib/fastdnaml/bin/fastDNAml_boot -boots 1 -max 2 -out -nice 10 fastdnaml.data.tmp 2 323s autopkgtest [15:41:40]: test Makefile: -----------------------] 323s autopkgtest [15:41:40]: test Makefile: - - - - - - - - - - results - - - - - - - - - - 323s Makefile PASS 323s autopkgtest [15:41:40]: @@@@@@@@@@@@@@@@@@@@ summary 323s Makefile PASS 402s nova [W] Skipping flock in bos03-arm64 402s Creating nova instance adt-oracular-arm64-fastdnaml-20240712-153617-juju-7f2275-prod-proposed-migration-environment-2-0364eeee-2460-43d9-a417-d87fb5cee8b7 from image adt/ubuntu-oracular-arm64-server-20240712.img (UUID a9c53646-2a41-49d7-a14b-d40262a2cb6c)...