0s autopkgtest [23:36:18]: starting date and time: 2024-07-12 23:36:18+0000 0s autopkgtest [23:36:18]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [23:36:18]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j90uld9g/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 lucy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- lxd -r lxd-armhf-10.145.243.21 lxd-armhf-10.145.243.21:autopkgtest/ubuntu/oracular/armhf 55s autopkgtest [23:37:13]: testbed dpkg architecture: armhf 57s autopkgtest [23:37:15]: testbed apt version: 2.9.6 57s autopkgtest [23:37:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 65s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3288 B] 65s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 65s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.4 kB] 65s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [352 kB] 65s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [71.9 kB] 65s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf c-n-f Metadata [1428 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 [340 kB] 65s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf c-n-f Metadata [6916 B] 65s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1796 B] 65s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf c-n-f Metadata [120 B] 67s Fetched 960 kB in 1s (1185 kB/s) 67s Reading package lists... 85s tee: /proc/self/fd/2: Permission denied 107s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 109s Reading package lists... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade... 111s The following packages will be upgraded: 111s inetutils-telnet libc-bin libc6 libssl3t64 locales openssh-client 111s openssh-server openssh-sftp-server openssl telnet 112s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 11.9 MB of archives. 112s After this operation, 285 kB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc6 armhf 2.39-3.1ubuntu3 [2825 kB] 112s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc-bin armhf 2.39-3.1ubuntu3 [527 kB] 112s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libssl3t64 armhf 3.2.2-1ubuntu1 [1729 kB] 112s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu17 [35.6 kB] 112s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-server armhf 1:9.6p1-3ubuntu17 [502 kB] 112s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-client armhf 1:9.6p1-3ubuntu17 [888 kB] 112s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf locales all 2.39-3.1ubuntu3 [4220 kB] 112s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf openssl armhf 3.2.2-1ubuntu1 [1095 kB] 112s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf inetutils-telnet armhf 2:2.5-5ubuntu1 [94.4 kB] 112s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf telnet all 0.17+2.5-5ubuntu1 [3688 B] 113s Preconfiguring packages ... 113s Fetched 11.9 MB in 1s (13.0 MB/s) 113s (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.) 113s Preparing to unpack .../libc6_2.39-3.1ubuntu3_armhf.deb ... 113s Unpacking libc6:armhf (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 113s Setting up libc6:armhf (2.39-3.1ubuntu3) ... 114s Error: Could not restart systemd, systemd binary not working 114s (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.) 114s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_armhf.deb ... 114s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 114s Setting up libc-bin (2.39-3.1ubuntu3) ... 114s (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.) 114s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_armhf.deb ... 114s Unpacking libssl3t64:armhf (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 114s Setting up libssl3t64:armhf (3.2.2-1ubuntu1) ... 115s (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.) 115s Preparing to unpack .../0-openssh-sftp-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 115s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 115s Preparing to unpack .../1-openssh-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 115s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 115s Preparing to unpack .../2-openssh-client_1%3a9.6p1-3ubuntu17_armhf.deb ... 115s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 115s Preparing to unpack .../3-locales_2.39-3.1ubuntu3_all.deb ... 115s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 115s Preparing to unpack .../4-openssl_3.2.2-1ubuntu1_armhf.deb ... 115s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 115s Preparing to unpack .../5-inetutils-telnet_2%3a2.5-5ubuntu1_armhf.deb ... 115s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 115s Preparing to unpack .../6-telnet_0.17+2.5-5ubuntu1_all.deb ... 115s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 115s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 115s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 115s Setting up locales (2.39-3.1ubuntu3) ... 116s Generating locales (this might take a while)... 118s en_US.UTF-8... done 118s Generation complete. 118s Setting up openssl (3.2.2-1ubuntu1) ... 118s Installing new version of config file /etc/ssl/openssl.cnf ... 118s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 118s Setting up telnet (0.17+2.5-5ubuntu1) ... 118s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 118s Installing new version of config file /etc/pam.d/sshd ... 119s Processing triggers for ufw (0.36.2-6) ... 119s Processing triggers for systemd (256-1ubuntu1) ... 120s Processing triggers for man-db (2.12.1-2) ... 121s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [23:38:22]: rebooting testbed after setup commands that affected boot 198s autopkgtest [23:39:36]: 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 227s autopkgtest [23:40:05]: @@@@@@@@@@@@@@@@@@@@ apt-source lucy 238s Get:1 http://ftpmaster.internal/ubuntu oracular/universe lucy 1.20-4 (dsc) [1275 B] 238s Get:2 http://ftpmaster.internal/ubuntu oracular/universe lucy 1.20-4 (tar) [1458 kB] 238s Get:3 http://ftpmaster.internal/ubuntu oracular/universe lucy 1.20-4 (diff) [4632 B] 238s gpgv: Signature made Sun Mar 24 16:55:05 2024 UTC 238s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 238s gpgv: Can't check signature: No public key 238s dpkg-source: warning: cannot verify inline signature for ./lucy_1.20-4.dsc: no acceptable signature found 238s autopkgtest [23:40:16]: testing package lucy version 1.20-4 240s autopkgtest [23:40:18]: build not needed 243s autopkgtest [23:40:21]: test run-unit-test: preparing testbed 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 254s Starting pkgProblemResolver with broken count: 0 255s Starting 2 pkgProblemResolver with broken count: 0 255s Done 256s The following additional packages will be installed: 256s lucy 256s The following NEW packages will be installed: 256s autopkgtest-satdep lucy 257s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 257s Need to get 941 kB/942 kB of archives. 257s After this operation, 6223 kB of additional disk space will be used. 257s Get:1 /tmp/autopkgtest.24QIQM/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [700 B] 257s Get:2 http://ftpmaster.internal/ubuntu oracular/universe armhf lucy armhf 1.20-4 [941 kB] 258s Fetched 941 kB in 1s (1604 kB/s) 258s Selecting previously unselected package lucy. 258s (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.) 258s Preparing to unpack .../archives/lucy_1.20-4_armhf.deb ... 258s Unpacking lucy (1.20-4) ... 258s Selecting previously unselected package autopkgtest-satdep. 258s Preparing to unpack .../1-autopkgtest-satdep.deb ... 258s Unpacking autopkgtest-satdep (0) ... 258s Setting up lucy (1.20-4) ... 258s Setting up autopkgtest-satdep (0) ... 258s Processing triggers for man-db (2.12.1-2) ... 273s (Reading database ... 58457 files and directories currently installed.) 273s Removing autopkgtest-satdep (0) ... 279s autopkgtest [23:40:57]: test run-unit-test: [----------------------- 281s Test - 1 281s Less Useful Chunks Yank (lucy) 1.20p, by Hui-Hsien Chou and Michael Holmes, 281s with help from Granger, Anna, John and Terry Shea. 281s lucy: Warning! No vector file given; vector removal will not be done! 281s lucy: Warning! No splice file given; splice site will not be trimmed! 281s Phase 1: Checking the number of input sequences... 281s 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 1582 input sequences found. 281s Phase 2: Reading sequence name, length and position data... 281s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 116 empty sequences discarded. 281s Phase 3: Reading quality values and checking good sequence regions... 281s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 1582 quality sequences read; 147 low quality sequences dropped. 281s Phase 4: Comparing to 2nd sequence file... 281s 0 50 100 150 200 lucy: the 2nd sequences below (except salvaged) are not found in the first sequence file 281s lucy: >ATIEE17TF 281s 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 lucy: >ATIEO34TF 281s lucy: >ATIEO35TF 281s 1200 1250 1300 1350 1400 1450 1488 2nd sequences compared; 1307 sequences extended. 281s 73 low quality sequences salvaged. 281s Phase 7: Producing output sequence and quality files... 281s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 ---------------Passed!---------------------------- 281s Test - 2 281s ---------------Passed!---------------------------- 281s Test - 3 281s 1392 good sequences written in test1.seq and test1.qul. 281s Less Useful Chunks Yank (lucy) 1.20p, by Hui-Hsien Chou and Michael Holmes, 281s with help from Granger, Anna, John and Terry Shea. 281s lucy: Warning! No vector file given; vector removal will not be done! 281s lucy: Warning! No splice file given; splice site will not be trimmed! 281s Phase 1: Checking the number of input sequences... 281s 1 input sequences found. 281s Phase 2: Reading sequence name, length and position data... 281s 0 0 empty sequences discarded. 281s Phase 3: Reading quality values and checking good sequence regions... 281s 0 1 quality sequences read; 0 low quality sequences dropped. 281s Phase 4: 2nd sequences comparison skipped... 281s no 2nd sequence file provided. 281s Phase 7: Producing output sequence and quality files... 281s 0 1 good sequences written in test2.seq and test2.qul. 281s Less Useful Chunks Yank (lucy) 1.20p, by Hui-Hsien Chou and Michael Holmes, 281s with help from Granger, Anna, John and Terry Shea. 281s Phase 1: Checking the number of input sequences... 281s 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 1582 input sequences found. 281s Phase 2: Reading sequence name, length and position data... 281s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 116 empty sequences discarded. 281s Phase 3: Reading quality values and checking good sequence regions... 281s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 1582 quality sequences read; 147 low quality sequences dropped. 281s Phase 4: Comparing to 2nd sequence file... 281s 0 50 100 150 200 lucy: the 2nd sequences below (except salvaged) are not found in the first sequence file 281s lucy: >ATIEE17TF 282s 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 lucy: >ATIEO34TF 282s lucy: >ATIEO35TF 282s 1200 1250 1300 1350 1400 1450 1488 2nd sequences compared; 1307 sequences extended. 282s 73 low quality sequences salvaged. 282s Phase 5: Locating splice sites...Number of splice sequences: 4 287s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 1 short or no insert sequences discarded. 287s Phase 6: Kicking out vector sequences... 287s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 1 vector sequences discarded. 287s Phase 7: Producing output sequence and quality files... 287s 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350 1400 1450 1500 1550 1390 good sequences written in test3.seq and test3.qul. 287s 1582 sequence cleavage information written in lucy.info. 287s ---------------Passed!---------------------------- 288s autopkgtest [23:41:06]: test run-unit-test: -----------------------] 292s autopkgtest [23:41:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 292s run-unit-test PASS 296s autopkgtest [23:41:14]: @@@@@@@@@@@@@@@@@@@@ summary 296s run-unit-test PASS