0s autopkgtest [13:56:55]: starting date and time: 2024-07-12 13:56:55+0000 0s autopkgtest [13:56:55]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [13:56:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.38ysy961/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@lcy02-94.secgroup --name adt-oracular-amd64-fastdnaml-20240712-135655-juju-7f2275-prod-proposed-migration-environment-2-9f77fe15-c38a-40c4-827a-6d2766374e3f --image adt/ubuntu-oracular-amd64-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/ 94s autopkgtest [13:58:29]: testbed dpkg architecture: amd64 94s autopkgtest [13:58:29]: testbed apt version: 2.9.6 94s autopkgtest [13:58:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 94s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 94s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [45.3 kB] 94s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 94s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [345 kB] 94s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [73.0 kB] 94s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [99.7 kB] 94s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B] 94s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 94s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 94s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 94s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [374 kB] 94s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [240 kB] 94s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B] 94s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 94s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B] 94s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 96s Fetched 1378 kB in 0s (5276 kB/s) 96s Reading package lists... 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Calculating upgrade... 99s The following packages will be upgraded: 99s binutils binutils-common binutils-x86-64-linux-gnu gir1.2-glib-2.0 99s libbinutils libc-bin libc-dev-bin libc-devtools libc6 libc6-dev 99s libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data libgprofng0 99s libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssl 99s 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 21.2 MB of archives. 99s After this operation, 423 kB of additional disk space will be used. 99s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB] 99s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB] 99s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB] 99s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB] 99s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB] 99s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.2.2-1ubuntu1 [2138 kB] 99s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 gir1.2-glib-2.0 amd64 2.80.4-1ubuntu1 [182 kB] 99s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-0t64 amd64 2.80.4-1ubuntu1 [1545 kB] 99s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB] 99s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB] 99s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.2.2-1ubuntu1 [1122 kB] 99s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.62.1-2 [75.1 kB] 99s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42.50.20240710-1ubuntu1 [860 kB] 99s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42.50.20240710-1ubuntu1 [95.6 kB] 99s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42.50.20240710-1ubuntu1 [97.6 kB] 99s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240710-1ubuntu1 [2477 kB] 99s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42.50.20240710-1ubuntu1 [574 kB] 99s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42.50.20240710-1ubuntu1 [18.1 kB] 99s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42.50.20240710-1ubuntu1 [243 kB] 99s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42.50.20240710-1ubuntu1 [14.4 kB] 99s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libnss3 amd64 2:3.102-1 [1399 kB] 100s Preconfiguring packages ... 100s Fetched 21.2 MB in 0s (58.5 MB/s) 100s (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 ... 74487 files and directories currently installed.) 100s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ... 100s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 100s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ... 100s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 100s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ... 100s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 100s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ... 100s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 101s Setting up libc6:amd64 (2.39-3.1ubuntu3) ... 101s Error: Could not restart systemd, systemd binary not working 101s (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 ... 74487 files and directories currently installed.) 101s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ... 101s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 101s Setting up libc-bin (2.39-3.1ubuntu3) ... 101s (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 ... 74487 files and directories currently installed.) 101s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_amd64.deb ... 101s Unpacking libssl3t64:amd64 (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 101s Setting up libssl3t64:amd64 (3.2.2-1ubuntu1) ... 101s (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 ... 74487 files and directories currently installed.) 101s Preparing to unpack .../00-gir1.2-glib-2.0_2.80.4-1ubuntu1_amd64.deb ... 101s Unpacking gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 101s Preparing to unpack .../01-libglib2.0-0t64_2.80.4-1ubuntu1_amd64.deb ... 101s Unpacking libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 101s Preparing to unpack .../02-libglib2.0-data_2.80.4-1ubuntu1_all.deb ... 101s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 101s Preparing to unpack .../03-locales_2.39-3.1ubuntu3_all.deb ... 101s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 102s Preparing to unpack .../04-openssl_3.2.2-1ubuntu1_amd64.deb ... 102s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 102s Preparing to unpack .../05-libnghttp2-14_1.62.1-2_amd64.deb ... 102s Unpacking libnghttp2-14:amd64 (1.62.1-2) over (1.62.1-1) ... 102s Preparing to unpack .../06-libgprofng0_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../07-libctf0_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking libctf0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../08-libctf-nobfd0_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../09-binutils-x86-64-linux-gnu_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../10-libbinutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking libbinutils:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../11-binutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../12-binutils-common_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking binutils-common:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../13-libsframe1_2.42.50.20240710-1ubuntu1_amd64.deb ... 102s Unpacking libsframe1:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 102s Preparing to unpack .../14-libnss3_2%3a3.102-1_amd64.deb ... 102s Unpacking libnss3:amd64 (2:3.102-1) over (2:3.101-1) ... 103s Setting up binutils-common:amd64 (2.42.50.20240710-1ubuntu1) ... 103s Setting up libnghttp2-14:amd64 (1.62.1-2) ... 103s Setting up libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) ... 103s Setting up libnss3:amd64 (2:3.102-1) ... 103s Setting up locales (2.39-3.1ubuntu3) ... 103s Generating locales (this might take a while)... 105s en_US.UTF-8... done 105s Generation complete. 105s Setting up libsframe1:amd64 (2.42.50.20240710-1ubuntu1) ... 105s Setting up libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) ... 105s No schema files found: doing nothing. 105s Setting up libglib2.0-data (2.80.4-1ubuntu1) ... 105s Setting up gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) ... 105s Setting up libbinutils:amd64 (2.42.50.20240710-1ubuntu1) ... 105s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 105s Setting up openssl (3.2.2-1ubuntu1) ... 105s Installing new version of config file /etc/ssl/openssl.cnf ... 105s Setting up libc-devtools (2.39-3.1ubuntu3) ... 105s Setting up libctf0:amd64 (2.42.50.20240710-1ubuntu1) ... 105s Setting up libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) ... 105s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ... 105s Setting up binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) ... 105s Setting up binutils (2.42.50.20240710-1ubuntu1) ... 105s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 105s Processing triggers for systemd (256-1ubuntu1) ... 106s Processing triggers for man-db (2.12.1-2) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 109s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 109s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 110s Reading package lists... 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [13:58:48]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 113s autopkgtest [13:58:48]: @@@@@@@@@@@@@@@@@@@@ apt-source fastdnaml 113s Get:1 http://ftpmaster.internal/ubuntu oracular/universe fastdnaml 1.2.2-16 (dsc) [1407 B] 113s Get:2 http://ftpmaster.internal/ubuntu oracular/universe fastdnaml 1.2.2-16 (tar) [70.0 kB] 113s Get:3 http://ftpmaster.internal/ubuntu oracular/universe fastdnaml 1.2.2-16 (diff) [8544 B] 114s gpgv: Signature made Sun Apr 7 09:24:25 2024 UTC 114s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 114s gpgv: Can't check signature: No public key 114s dpkg-source: warning: cannot verify inline signature for ./fastdnaml_1.2.2-16.dsc: no acceptable signature found 114s autopkgtest [13:58:49]: testing package fastdnaml version 1.2.2-16 114s autopkgtest [13:58:49]: build not needed 114s autopkgtest [13:58:49]: test Makefile: preparing testbed 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 116s The following additional packages will be installed: 116s fastdnaml 116s Suggested packages: 116s phylip 116s The following NEW packages will be installed: 116s autopkgtest-satdep fastdnaml 116s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 58.6 kB/59.3 kB of archives. 116s After this operation, 238 kB of additional disk space will be used. 116s Get:1 /tmp/autopkgtest.oAUuKm/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 116s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 fastdnaml amd64 1.2.2-16 [58.6 kB] 116s Fetched 58.6 kB in 0s (1978 kB/s) 116s Selecting previously unselected package fastdnaml. 116s (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 ... 74486 files and directories currently installed.) 116s Preparing to unpack .../fastdnaml_1.2.2-16_amd64.deb ... 116s Unpacking fastdnaml (1.2.2-16) ... 116s Selecting previously unselected package autopkgtest-satdep. 116s Preparing to unpack .../1-autopkgtest-satdep.deb ... 116s Unpacking autopkgtest-satdep (0) ... 116s Setting up fastdnaml (1.2.2-16) ... 116s Setting up autopkgtest-satdep (0) ... 116s Processing triggers for man-db (2.12.1-2) ... 119s (Reading database ... 74566 files and directories currently installed.) 119s Removing autopkgtest-satdep (0) ... 120s autopkgtest [13:58:55]: test Makefile: [----------------------- 120s cat /usr/share/doc/fastdnaml/examples/tests/fastdnaml.data | fastDNAml-util printdata | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints 120s 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 120s /tmp/autopkgtest.oAUuKm/wrapper.sh: Killing leaked background processes: 3175 120s PID TTY STAT TIME COMMAND 120s 3175 ? S 0:00 /bin/sh /usr/lib/fastdnaml/bin/fastDNAml_boot -boots 1 -max 2 -out -nice 10 fastdnaml.data.tmp 2 120s autopkgtest [13:58:55]: test Makefile: -----------------------] 120s Makefile PASS 120s autopkgtest [13:58:55]: test Makefile: - - - - - - - - - - results - - - - - - - - - - 121s autopkgtest [13:58:56]: @@@@@@@@@@@@@@@@@@@@ summary 121s Makefile PASS 134s nova [W] Skipping flock for amd64 134s Creating nova instance adt-oracular-amd64-fastdnaml-20240712-135655-juju-7f2275-prod-proposed-migration-environment-2-9f77fe15-c38a-40c4-827a-6d2766374e3f from image adt/ubuntu-oracular-amd64-server-20240711.img (UUID 4d65b1cc-a829-44fc-a8ac-cdd52093f9db)...