0s autopkgtest [15:44:22]: starting date and time: 2025-03-15 15:44:22+0000 0s autopkgtest [15:44:22]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:44:22]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gn_1cipu/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,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade veryfasttree --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.21 lxd-armhf-10.145.243.21:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [15:44:43]: testbed dpkg architecture: armhf 23s autopkgtest [15:44:45]: testbed apt version: 2.9.33 26s autopkgtest [15:44:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [15:44:50]: testbed release detected to be: None 36s autopkgtest [15:44:58]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 42s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 65s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 65s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 67s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 67s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 67s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 83s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 85s Fetched 41.0 MB in 47s (874 kB/s) 86s Reading package lists... 92s autopkgtest [15:45:54]: upgrading testbed (apt dist-upgrade and autopurge) 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 96s Starting 2 pkgProblemResolver with broken count: 0 96s Done 97s Entering ResolveByKeep 97s 98s Calculating upgrade... 98s The following packages will be upgraded: 98s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 99s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 8683 kB of archives. 99s After this operation, 23.6 kB of additional disk space will be used. 99s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 110s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 110s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 111s Preconfiguring packages ... 111s Fetched 8683 kB in 12s (735 kB/s) 111s (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 ... 64655 files and directories currently installed.) 111s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 111s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Setting up libc6:armhf (2.41-1ubuntu2) ... 112s (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 ... 64655 files and directories currently installed.) 112s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 112s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Setting up libc-bin (2.41-1ubuntu2) ... 112s (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 ... 64655 files and directories currently installed.) 112s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 112s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 113s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 113s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 113s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 113s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 113s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 113s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 113s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 114s Setting up sos (4.9.0-5) ... 115s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 115s Setting up locales (2.41-1ubuntu2) ... 116s Generating locales (this might take a while)... 120s en_US.UTF-8... done 120s Generation complete. 120s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 121s Setting up strace (6.13+ds-1ubuntu1) ... 121s Processing triggers for man-db (2.13.0-1) ... 122s Processing triggers for systemd (257.3-1ubuntu3) ... 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 126s Solving dependencies... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [15:46:31]: rebooting testbed after setup commands that affected boot 177s autopkgtest [15:47:19]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 207s autopkgtest [15:47:49]: @@@@@@@@@@@@@@@@@@@@ apt-source veryfasttree 217s Get:1 http://ftpmaster.internal/ubuntu plucky/universe veryfasttree 4.0.4+dfsg-1 (dsc) [2137 B] 217s Get:2 http://ftpmaster.internal/ubuntu plucky/universe veryfasttree 4.0.4+dfsg-1 (tar) [164 kB] 217s Get:3 http://ftpmaster.internal/ubuntu plucky/universe veryfasttree 4.0.4+dfsg-1 (diff) [29.8 kB] 217s gpgv: Signature made Sat Nov 2 19:18:09 2024 UTC 217s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 217s gpgv: issuer "emollier@debian.org" 217s gpgv: Can't check signature: No public key 217s dpkg-source: warning: cannot verify inline signature for ./veryfasttree_4.0.4+dfsg-1.dsc: no acceptable signature found 217s autopkgtest [15:47:59]: testing package veryfasttree version 4.0.4+dfsg-1 219s autopkgtest [15:48:01]: build not needed 222s autopkgtest [15:48:04]: test run-unit-test: preparing testbed 224s Reading package lists... 224s Building dependency tree... 224s Reading state information... 225s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 227s The following NEW packages will be installed: 227s libgomp1 veryfasttree 227s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 227s Need to get 702 kB of archives. 227s After this operation, 1503 kB of additional disk space will be used. 227s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 227s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf veryfasttree armhf 4.0.4+dfsg-1 [574 kB] 228s Fetched 702 kB in 1s (613 kB/s) 228s Selecting previously unselected package libgomp1:armhf. 228s (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 ... 64655 files and directories currently installed.) 228s Preparing to unpack .../libgomp1_15-20250222-0ubuntu1_armhf.deb ... 228s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 228s Selecting previously unselected package veryfasttree. 228s Preparing to unpack .../veryfasttree_4.0.4+dfsg-1_armhf.deb ... 228s Unpacking veryfasttree (4.0.4+dfsg-1) ... 228s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 228s Setting up veryfasttree (4.0.4+dfsg-1) ... 228s Processing triggers for libc-bin (2.41-1ubuntu2) ... 228s Processing triggers for man-db (2.13.0-1) ... 237s autopkgtest [15:48:19]: test run-unit-test: [----------------------- 239s Command: VeryFastTree test.fasta 239s VeryFastTree Version 4.0.4 (OpenMP) 239s Alignment: test.fasta 239s Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000 239s Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 239s TopHits: 1.00*sqrtN close=default refresh=0.80 239s ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories 239s 0.10 seconds: Joined 200 of 201 239s Initial topology in 0.10 seconds 239s Refining topology: 31 rounds ME-NNIs, 2 rounds ME-SPRs, 15 rounds ML-NNIs 239s 0.24 seconds: SPR round 1 of 2, 101 of 406 nodes 239s 0.35 seconds: SPR round 1 of 2, 201 of 406 nodes 239s 0.46 seconds: SPR round 1 of 2, 301 of 406 nodes 239s 0.57 seconds: SPR round 1 of 2, 407 of 406 nodes 239s 0.70 seconds: SPR round 2 of 2, 101 of 406 nodes 239s 0.81 seconds: SPR round 2 of 2, 201 of 406 nodes 240s 0.92 seconds: SPR round 2 of 2, 301 of 406 nodes 240s 1.02 seconds: SPR round 2 of 2, 401 of 406 nodes 240s Total branch-length 85.602 after 1.06 sec 240s 1.17 seconds: ML Lengths 101 of 202 splits 240s 1.29 seconds: ML Lengths 201 of 202 splits 240s 1.50 seconds: ML NNI round 1 of 15, 101 of 202 splits, 18 changes (max delta 9.013) 240s 1.73 seconds: ML NNI round 1 of 15, 201 of 202 splits, 34 changes (max delta 10.111) 240s ML-NNI round 1: LogLk = -60072.254 NNIs 35 max delta 10.11 Time 1.74 241s 1.85 seconds: Site likelihoods with rate category 5 of 20 241s 1.96 seconds: Site likelihoods with rate category 10 of 20 241s 2.08 seconds: Site likelihoods with rate category 15 of 20 241s 2.19 seconds: Site likelihoods with rate category 20 of 20 241s Switched to using 20 rate categories (CAT approximation) 241s Rate categories were divided by 1.107 so that average rate = 1.0 241s CAT-based log-likelihoods may not be comparable across runs 241s Use -gamma for approximate but comparable Gamma(20) log-likelihoods 241s 2.47 seconds: ML NNI round 2 of 15, 101 of 202 splits, 8 changes (max delta 11.432) 241s 2.73 seconds: ML NNI round 2 of 15, 201 of 202 splits, 14 changes (max delta 11.432) 241s ML-NNI round 2: LogLk = -57877.783 NNIs 15 max delta 11.43 Time 2.74 242s 3.02 seconds: ML NNI round 3 of 15, 101 of 202 splits, 2 changes (max delta 0.026) 242s ML-NNI round 3: LogLk = -57873.310 NNIs 3 max delta 1.04 Time 3.11 242s 3.30 seconds: ML NNI round 4 of 15, 69 of 202 splits, 0 changes 242s ML-NNI round 4: LogLk = -57873.252 NNIs 0 max delta 0.00 Time 3.31 242s Turning off heuristics for final round of ML NNIs (converged) 242s 3.54 seconds: ML NNI round 5 of 15, 101 of 202 splits, 0 changes 242s 3.77 seconds: ML NNI round 5 of 15, 201 of 202 splits, 0 changes 242s ML-NNI round 5: LogLk = -57871.310 NNIs 0 max delta 0.00 Time 3.78 (final) 243s 3.91 seconds: ML Lengths 101 of 202 splits 243s 4.05 seconds: ML Lengths 201 of 202 splits 243s Optimize all lengths: LogLk = -57839.692 Time 4.06 243s 4.49 seconds: ML split tests for 100 of 201 internal splits 244s 4.91 seconds: ML split tests for 200 of 201 internal splits 244s Total time: 4.92 seconds Unique: 204/204 Bad splits: 0/201 244s TreeCompleted 244s Command: VeryFastTree 244s VeryFastTree Version 4.0.4 (OpenMP) 244s Alignment: standard input 244s Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000 244s Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 244s TopHits: 1.00*sqrtN close=default refresh=0.80 244s ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories 244s 0.10 seconds: Joined 200 of 201 244s Initial topology in 0.10 seconds 244s Refining topology: 31 rounds ME-NNIs, 2 rounds ME-SPRs, 15 rounds ML-NNIs 244s 0.24 seconds: SPR round 1 of 2, 101 of 406 nodes 244s 0.35 seconds: SPR round 1 of 2, 201 of 406 nodes 244s 0.46 seconds: SPR round 1 of 2, 301 of 406 nodes 244s 0.57 seconds: SPR round 1 of 2, 407 of 406 nodes 244s 0.70 seconds: SPR round 2 of 2, 101 of 406 nodes 244s 0.81 seconds: SPR round 2 of 2, 201 of 406 nodes 245s 0.92 seconds: SPR round 2 of 2, 301 of 406 nodes 245s 1.02 seconds: SPR round 2 of 2, 401 of 406 nodes 245s Total branch-length 85.602 after 1.06 sec 245s 1.18 seconds: ML Lengths 101 of 202 splits 245s 1.29 seconds: ML Lengths 201 of 202 splits 245s 1.51 seconds: ML NNI round 1 of 15, 101 of 202 splits, 18 changes (max delta 9.013) 245s 1.74 seconds: ML NNI round 1 of 15, 201 of 202 splits, 34 changes (max delta 10.111) 245s ML-NNI round 1: LogLk = -60072.254 NNIs 35 max delta 10.11 Time 1.75 245s 1.86 seconds: Site likelihoods with rate category 5 of 20 246s 1.97 seconds: Site likelihoods with rate category 10 of 20 246s 2.09 seconds: Site likelihoods with rate category 15 of 20 246s 2.20 seconds: Site likelihoods with rate category 20 of 20 246s Switched to using 20 rate categories (CAT approximation) 246s Rate categories were divided by 1.107 so that average rate = 1.0 246s CAT-based log-likelihoods may not be comparable across runs 246s Use -gamma for approximate but comparable Gamma(20) log-likelihoods 246s 2.48 seconds: ML NNI round 2 of 15, 101 of 202 splits, 8 changes (max delta 11.432) 246s 2.75 seconds: ML NNI round 2 of 15, 201 of 202 splits, 14 changes (max delta 11.432) 246s ML-NNI round 2: LogLk = -57877.783 NNIs 15 max delta 11.43 Time 2.76 247s 3.04 seconds: ML NNI round 3 of 15, 101 of 202 splits, 2 changes (max delta 0.026) 247s ML-NNI round 3: LogLk = -57873.310 NNIs 3 max delta 1.04 Time 3.14 247s 3.32 seconds: ML NNI round 4 of 15, 69 of 202 splits, 0 changes 247s ML-NNI round 4: LogLk = -57873.252 NNIs 0 max delta 0.00 Time 3.33 247s Turning off heuristics for final round of ML NNIs (converged) 247s 3.57 seconds: ML NNI round 5 of 15, 101 of 202 splits, 0 changes 247s 3.80 seconds: ML NNI round 5 of 15, 201 of 202 splits, 0 changes 247s ML-NNI round 5: LogLk = -57871.310 NNIs 0 max delta 0.00 Time 3.81 (final) 248s 3.95 seconds: ML Lengths 101 of 202 splits 248s 4.09 seconds: ML Lengths 201 of 202 splits 248s Optimize all lengths: LogLk = -57839.692 Time 4.10 248s 4.53 seconds: ML split tests for 100 of 201 internal splits 249s 4.96 seconds: ML split tests for 200 of 201 internal splits 249s Total time: 4.97 seconds Unique: 204/204 Bad splits: 0/201 249s TreeCompleted 249s autopkgtest [15:48:31]: test run-unit-test: -----------------------] 253s run-unit-test PASS 253s autopkgtest [15:48:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 257s autopkgtest [15:48:39]: @@@@@@@@@@@@@@@@@@@@ summary 257s run-unit-test PASS