0s autopkgtest [15:15:56]: starting date and time: 2025-03-15 15:15:56+0000 0s autopkgtest [15:15:56]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:15:56]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f44v7d6m/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 phyml --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.76 lxd-armhf-10.145.243.76:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [15:16:17]: testbed dpkg architecture: armhf 23s autopkgtest [15:16:19]: testbed apt version: 2.9.33 27s autopkgtest [15:16:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [15:16:25]: testbed release detected to be: None 37s autopkgtest [15:16:33]: updating testbed package index (apt update) 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 40s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 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 [326 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 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 [332 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 40s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 41s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 55s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 56s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 56s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 56s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 66s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 68s Fetched 41.0 MB in 29s (1436 kB/s) 69s Reading package lists... 76s autopkgtest [15:17:12]: upgrading testbed (apt dist-upgrade and autopurge) 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 79s Starting 2 pkgProblemResolver with broken count: 0 79s Done 80s Entering ResolveByKeep 80s 80s Calculating upgrade... 81s The following packages will be upgraded: 81s libc-bin libc6 locales python3-jinja2 sos strace 81s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Need to get 8642 kB of archives. 81s After this operation, 23.6 kB of additional disk space will be used. 81s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 83s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 87s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 87s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 87s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 88s Preconfiguring packages ... 88s Fetched 8642 kB in 7s (1329 kB/s) 88s (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.) 88s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 89s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 89s Setting up libc6:armhf (2.41-1ubuntu2) ... 89s (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.) 89s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 89s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 89s Setting up libc-bin (2.41-1ubuntu2) ... 90s (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.) 90s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 90s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 90s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 90s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 90s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 90s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 90s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 91s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 91s Setting up sos (4.9.0-5) ... 92s Setting up locales (2.41-1ubuntu2) ... 93s Generating locales (this might take a while)... 95s en_US.UTF-8... done 95s Generation complete. 95s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 95s Setting up strace (6.13+ds-1ubuntu1) ... 95s Processing triggers for man-db (2.13.0-1) ... 97s Processing triggers for systemd (257.3-1ubuntu3) ... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Starting pkgProblemResolver with broken count: 0 101s Starting 2 pkgProblemResolver with broken count: 0 101s Done 101s Solving dependencies... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s autopkgtest [15:17:40]: rebooting testbed after setup commands that affected boot 148s autopkgtest [15:18:24]: 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 174s autopkgtest [15:18:50]: @@@@@@@@@@@@@@@@@@@@ apt-source phyml 186s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (dsc) [2131 B] 186s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (tar) [1804 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (diff) [27.1 kB] 186s gpgv: Signature made Sat Nov 30 06:14:54 2024 UTC 186s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 186s gpgv: Can't check signature: No public key 186s dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-4build1.dsc: no acceptable signature found 186s autopkgtest [15:19:02]: testing package phyml version 3:3.3.20220408-4build1 188s autopkgtest [15:19:04]: build not needed 191s autopkgtest [15:19:07]: test run-unit-test: preparing testbed 192s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s Starting pkgProblemResolver with broken count: 0 193s Starting 2 pkgProblemResolver with broken count: 0 193s Done 194s The following NEW packages will be installed: 194s hwloc-nox libgfortran5 libhwloc15 libmpich12 libslurm42t64 mpi-default-bin 194s mpich phyml 194s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 194s Need to get 4290 kB of archives. 194s After this operation, 12.3 MB of additional disk space will be used. 194s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 195s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libhwloc15 armhf 2.12.0-1 [147 kB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libslurm42t64 armhf 24.11.1-1 [769 kB] 195s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpich12 armhf 4.2.1-5 [1574 kB] 195s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf hwloc-nox armhf 2.12.0-1 [213 kB] 195s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf mpich armhf 4.2.1-5 [214 kB] 195s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf mpi-default-bin armhf 1.18 [2504 B] 195s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf phyml armhf 3:3.3.20220408-4build1 [1039 kB] 196s Fetched 4290 kB in 1s (5227 kB/s) 196s Selecting previously unselected package libgfortran5:armhf. 196s (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.) 196s Preparing to unpack .../0-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 196s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 196s Selecting previously unselected package libhwloc15:armhf. 196s Preparing to unpack .../1-libhwloc15_2.12.0-1_armhf.deb ... 196s Unpacking libhwloc15:armhf (2.12.0-1) ... 196s Selecting previously unselected package libslurm42t64. 196s Preparing to unpack .../2-libslurm42t64_24.11.1-1_armhf.deb ... 196s Unpacking libslurm42t64 (24.11.1-1) ... 196s Selecting previously unselected package libmpich12:armhf. 196s Preparing to unpack .../3-libmpich12_4.2.1-5_armhf.deb ... 196s Unpacking libmpich12:armhf (4.2.1-5) ... 196s Selecting previously unselected package hwloc-nox. 196s Preparing to unpack .../4-hwloc-nox_2.12.0-1_armhf.deb ... 196s Unpacking hwloc-nox (2.12.0-1) ... 196s Selecting previously unselected package mpich. 196s Preparing to unpack .../5-mpich_4.2.1-5_armhf.deb ... 196s Unpacking mpich (4.2.1-5) ... 196s Selecting previously unselected package mpi-default-bin. 196s Preparing to unpack .../6-mpi-default-bin_1.18_armhf.deb ... 196s Unpacking mpi-default-bin (1.18) ... 196s Selecting previously unselected package phyml. 196s Preparing to unpack .../7-phyml_3%3a3.3.20220408-4build1_armhf.deb ... 196s Unpacking phyml (3:3.3.20220408-4build1) ... 196s Setting up libslurm42t64 (24.11.1-1) ... 196s Setting up libhwloc15:armhf (2.12.0-1) ... 196s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 196s Setting up libmpich12:armhf (4.2.1-5) ... 196s Setting up hwloc-nox (2.12.0-1) ... 196s Setting up mpich (4.2.1-5) ... 196s update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode 196s update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode 196s Setting up mpi-default-bin (1.18) ... 196s Setting up phyml (3:3.3.20220408-4build1) ... 196s Processing triggers for man-db (2.13.0-1) ... 197s Processing triggers for libc-bin (2.41-1ubuntu2) ... 206s autopkgtest [15:19:22]: test run-unit-test: [----------------------- 209s + export PHYMLCPUS=1 209s + PHYMLCPUS=1 209s + echo 'DNA interleaved sequence file, default parameters single processor:' 209s + /usr/bin/phyml -i nucleic 209s DNA interleaved sequence file, default parameters single processor: 209s 209s 209s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 209s 209s 209s 209s 209s 209s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 209s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 209s 209s . Sequence filename: nucleic 209s . Data type: dna 209s . Alphabet size: 4 209s . Sequence format: interleaved 209s . Number of data sets: 1 209s . Nb of bootstrapped data sets: 0 209s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 209s . Model name: HKY85 209s . Ts/tv ratio: estimated 209s . Proportion of invariable sites: 0.000000 209s . RAS model: discrete Gamma 209s . Number of subst. rate catgs: 4 209s . Gamma distribution parameter: estimated 209s . 'Middle' of each rate class: mean 209s . Nucleotide equilibrium frequencies: empirical 209s . Optimise tree topology: yes 209s . Starting tree: BioNJ 209s . Add random input tree: no 209s . Optimise branch lengths: yes 209s . Minimum length of an edge: 1e-08 209s . Optimise substitution model parameters: yes 209s . Run ID: none 209s . Random seed: 1742051965 209s . Subtree patterns aliasing: no 209s . Version: 3.3.3:3.3.20220408-4build1 209s . Byte alignment: 1 209s . AVX enabled: no 209s . SSE enabled: no 209s 209s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 209s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 209s 209s 209s 209s . 382 patterns found (out of a total of 886 sites). 209s 209s . 582 sites without polymorphism (65.69%). 209s 209s 209s . Computing pairwise distances... 209s 209s . Building BioNJ tree... 209s 209s . This analysis requires at least 11 MB of memory space. 209s 209s 210s . Score of initial tree: -5680.04 210s 210s . Starting first round of SPRs... 212s 215s 3s | 1 | lnL= -5429.7 | depth= 3/ 40 | improvements= 16 | delta_lnL= 42.1/ 1000.0 + 215s 6s | 2 | lnL= -5435.5 | depth= 2/ 24 | improvements= 14 | delta_lnL= 7.3/ 1000.0 215s 215s . Second round of optimization... 217s 219s 8s | 3 | lnL= -5440.1 | depth= 7/ 21 | improvements= 20 | delta_lnL= 25.7/ 1000.0 221s 10s | 4 | lnL= -5435.4 | depth= 2/ 16 | improvements= 18 | delta_lnL= 3.0/ 1000.0 222s 12s | 5 | lnL= -5447.2 | depth= 1/ 12 | improvements= 21 | delta_lnL= 0.0/ 1000.0 222s 13s | 6 | lnL= -5447.2 | depth= 4/ 9 | improvements= 23 | delta_lnL= 20.7/ 51.4 223s 13s | 7 | lnL= -5438.6 | depth= 2/ 8 | improvements= 23 | delta_lnL= 7.1/ 51.4 224s 14s | 8 | lnL= -5436.6 | depth= 5/ 6 | improvements= 13 | delta_lnL= 12.1/ 51.4 224s 15s | 9 | lnL= -5442.9 | depth= 1/ 9 | improvements= 10 | delta_lnL= 0.0/ 51.4 225s 15s | 10 | lnL= -5428.5 | depth= 2/ 7 | improvements= 18 | delta_lnL= 4.4/ 41.5 + 226s 16s | 11 | lnL= -5424.2 | depth= 1/ 6 | improvements= 14 | delta_lnL= 0.0/ 41.5 + 227s 17s | 12 | lnL= -5446.0 | depth= 1/ 5 | improvements= 15 | delta_lnL= 0.0/ 41.5 227s 18s | 13 | lnL= -5460.1 | depth= 1/ 5 | improvements= 22 | delta_lnL= 0.0/ 41.5 228s 18s | 14 | lnL= -5431.2 | depth= 2/ 5 | improvements= 12 | delta_lnL= 14.6/ 20.0 228s 19s | 15 | lnL= -5423.8 | depth= 2/ 6 | improvements= 14 | delta_lnL= 0.7/ 20.0 + 229s 19s | 16 | lnL= -5428.4 | depth= 2/ 6 | improvements= 12 | delta_lnL= 4.2/ 20.0 229s 19s | 17 | lnL= -5449.4 | depth= 2/ 6 | improvements= 15 | delta_lnL= 11.6/ 20.0 230s 20s | 18 | lnL= -5428.1 | depth= 1/ 6 | improvements= 14 | delta_lnL= 0.0/ 29.2 230s 21s | 19 | lnL= -5422.5 | depth= 1/ 5 | improvements= 7 | delta_lnL= 0.0/ 29.2 + 231s 21s | 20 | lnL= -5425.1 | depth= 1/ 5 | improvements= 19 | delta_lnL= 0.0/ 29.2 232s 22s | 21 | lnL= -5420.8 | depth= 1/ 5 | improvements= 10 | delta_lnL= 0.0/ 29.2 + 232s 23s | 22 | lnL= -5430.5 | depth= 2/ 5 | improvements= 15 | delta_lnL= 1.2/ 20.0 232s 23s | 23 | lnL= -5442.4 | depth= 1/ 6 | improvements= 12 | delta_lnL= 0.0/ 20.0 233s 23s | 24 | lnL= -5443.3 | depth= 2/ 5 | improvements= 14 | delta_lnL= 1.0/ 20.0 233s 24s | 25 | lnL= -5426.2 | depth= 2/ 6 | improvements= 17 | delta_lnL= 5.7/ 20.0 234s 24s | 26 | lnL= -5432.4 | depth= 3/ 6 | improvements= 15 | delta_lnL= 3.8/ 20.0 234s 25s | 27 | lnL= -5425.4 | depth= 3/ 7 | improvements= 5 | delta_lnL= 10.8/ 20.0 234s 234s . Third round of optimization... 237s 239s 28s | 28 | lnL= -5420.8 | depth= 1/ 10 | improvements= 3 | delta_lnL= 0.0/ 100.0 | triple moves= 5 242s 30s | 29 | lnL= -5420.3 | depth= 3/ 8 | improvements= 1 | delta_lnL= 5.3/ 100.0 | triple moves= 5 + 245s 33s | 30 | lnL= -5420.3 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 245s 36s | 31 | lnL= -5420.3 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 245s 245s . Final optimisation steps... 247s 247s 247s . Log likelihood of the current tree: -5420.25583662907320104. 247s 248s . Calculating fast branch supports (using 'aBayes'). 248s 248s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'.+ echo 'AA interleaved sequence file, default parameters single processor:' 248s + /usr/bin/phyml -i proteic -d aa 248s 248s 248s . Time used 0h0m39s 248s 248s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 248s AA interleaved sequence file, default parameters single processor: 248s 248s 248s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 248s 248s 248s 248s 248s 248s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 248s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 248s 248s . Sequence filename: proteic 248s . Data type: aa 248s . Alphabet size: 20 248s . Sequence format: interleaved 248s . Number of data sets: 1 248s . Nb of bootstrapped data sets: 0 248s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 248s . Model name: LG 248s . Proportion of invariable sites: 0.000000 248s . RAS model: discrete Gamma 248s . Number of subst. rate catgs: 4 248s . Gamma distribution parameter: estimated 248s . 'Middle' of each rate class: mean 248s . Amino-acid equilibrium frequencies: empirical 248s . Optimise tree topology: yes 248s . Starting tree: BioNJ 248s . Add random input tree: no 248s . Optimise branch lengths: yes 248s . Minimum length of an edge: 1e-08 248s . Optimise substitution model parameters: yes 248s . Run ID: none 248s . Random seed: 1742052004 248s . Subtree patterns aliasing: no 248s . Version: 3.3.3:3.3.20220408-4build1 248s . Byte alignment: 1 248s . AVX enabled: no 248s . SSE enabled: no 248s 248s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 248s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 248s 248s 248s 248s . 429 patterns found (out of a total of 547 sites). 248s 248s . 136 sites without polymorphism (24.86%). 248s 248s 248s . Computing pairwise distances... 248s 248s . Building BioNJ tree... 248s 248s . This analysis requires at least 39 MB of memory space. 248s 248s 251s . Score of initial tree: -12569.85 251s 251s . Starting first round of SPRs... 263s 276s 15s | 1 | lnL= -12467.2 | depth= 1/ 40 | improvements= 16 | delta_lnL= 0.0/ 1000.0 276s 28s | 2 | lnL= -12476.4 | depth= 2/ 24 | improvements= 14 | delta_lnL= 6.9/ 1000.0 276s 276s . Second round of optimization... 287s 299s 39s | 3 | lnL= -12473.8 | depth= 2/ 21 | improvements= 14 | delta_lnL= 4.0/ 1000.0 311s 51s | 4 | lnL= -12487.0 | depth= 2/ 16 | improvements= 20 | delta_lnL= 14.0/ 1000.0 314s 63s | 5 | lnL= -12477.1 | depth= 3/ 12 | improvements= 17 | delta_lnL= 26.7/ 1000.0 317s 66s | 6 | lnL= -12467.2 | depth= 2/ 9 | improvements= 21 | delta_lnL= 6.2/ 27.9 319s 69s | 7 | lnL= -12492.8 | depth= 1/ 7 | improvements= 23 | delta_lnL= 0.0/ 27.9 322s 71s | 8 | lnL= -12477.8 | depth= 2/ 5 | improvements= 16 | delta_lnL= 6.5/ 27.9 325s 74s | 9 | lnL= -12490.8 | depth= 3/ 6 | improvements= 17 | delta_lnL= 41.8/ 27.9 330s 77s | 10 | lnL= -12494.3 | depth= 2/ 7 | improvements= 25 | delta_lnL= 8.2/ 20.0 333s 82s | 11 | lnL= -12460.3 | depth= 2/ 6 | improvements= 18 | delta_lnL= 6.4/ 20.0 333s 85s | 12 | lnL= -12466.4 | depth= 2/ 6 | improvements= 20 | delta_lnL= 8.1/ 20.0 333s 333s . Third round of optimization... 346s 366s 98s | 13 | lnL= -12443.3 | depth= 1/ 10 | improvements= 4 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 366s 118s | 14 | lnL= -12443.1 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 366s 366s . Final optimisation steps... 374s 374s 374s . Log likelihood of the current tree: -12443.04877140561256965. 374s 380s . Calculating fast branch supports (using 'aBayes'). 380s 380s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 380s 380s . Time used 0h2m12s 380s 380s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 380s AA sequential sequence file, with customization single processor: 380s + echo 'AA sequential sequence file, with customization single processor:' 380s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 380s 380s 380s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 380s 380s 380s 380s 380s 380s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 380s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 380s 380s . Sequence filename: example.nex 380s . Data type: dna 380s . Alphabet size: 4 380s . Sequence format: interleaved 380s . Number of data sets: 1 380s . Nb of bootstrapped data sets: 0 380s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 380s . Model name: HKY85 380s . Ts/tv ratio: estimated 380s . Proportion of invariable sites: 0.000000 380s . RAS model: discrete Gamma 380s . Number of subst. rate catgs: 4 380s . Gamma distribution parameter: estimated 380s . 'Middle' of each rate class: mean 380s . Nucleotide equilibrium frequencies: empirical 380s . Optimise tree topology: yes 380s . Starting tree: BioNJ 380s . Add random input tree: no 380s . Optimise branch lengths: yes 380s . Minimum length of an edge: 1e-08 380s . Optimise substitution model parameters: yes 380s . Run ID: none 380s . Random seed: 1742052136 380s . Subtree patterns aliasing: no 380s . Version: 3.3.3:3.3.20220408-4build1 380s . Byte alignment: 1 380s . AVX enabled: no 380s . SSE enabled: no 380s 380s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 380s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 380s 380s 380s 380s . 1037 patterns found (out of a total of 2888 sites). 380s 380s . 1378 sites without polymorphism (47.71%). 380s 380s 380s . Computing pairwise distances... 380s 380s . Building BioNJ tree... 380s 380s . This analysis requires at least 3 MB of memory space. 380s 380s 381s . Score of initial tree: -12664.54 381s 381s . Starting first round of SPRs... 381s 381s 1s | 1 | lnL= -12572.8 | depth= 1/ 40 | improvements= 2 | delta_lnL= 0.0/ 1000.0 381s 381s . Second round of optimization... 381s 381s 1s | 2 | lnL= -12572.8 | depth= 1/ 36 | improvements= 3 | delta_lnL= 0.0/ 1000.0 381s 381s . Third round of optimization... 381s 382s 1s | 3 | lnL= -12563.6 | depth= 1/ 20 | improvements= 1 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 382s 2s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 382s 382s . Final optimisation steps... 382s 382s 382s . Log likelihood of the current tree: -12563.11885905565213761. 382s 383s . Calculating fast branch supports (using 'aBayes').+ export PHYMLCPUS=2 383s + PHYMLCPUS=2 383s + echo 'DNA interleaved sequence file, default parameters using 2 processors:' 383s + /usr/bin/phyml -i nucleic 383s 383s 383s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 383s 383s . Time used 0h0m3s 383s 383s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 383s DNA interleaved sequence file, default parameters using 2 processors: 383s 383s 383s . Running the analysis on 2 CPUs.. 383s 383s . Command line: /usr/lib/phyml/bin/phyml-mpi -i nucleic 383s 383s 383s 383s 383s 383s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 383s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 383s 383s . Sequence filename: nucleic 383s . Data type: dna 383s . Alphabet size: 4 383s . Sequence format: interleaved 383s . Number of data sets: 1 383s . Nb of bootstrapped data sets: 0 383s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 383s . Model name: HKY85 383s . Ts/tv ratio: estimated 383s . Proportion of invariable sites: 0.000000 383s . RAS model: discrete Gamma 383s . Number of subst. rate catgs: 4 383s . Gamma distribution parameter: estimated 383s . 'Middle' of each rate class: mean 383s . Nucleotide equilibrium frequencies: empirical 383s . Optimise tree topology: yes 383s . Starting tree: BioNJ 383s . Add random input tree: no 383s . Optimise branch lengths: yes 383s . Minimum length of an edge: 1e-08 383s . Optimise substitution model parameters: yes 383s . Run ID: none 383s . Random seed: 1742052139 383s . Subtree patterns aliasing: no 383s . Version: 3.3.3:3.3.20220408-4build1 383s . Byte alignment: 1 383s . AVX enabled: no 383s . SSE enabled: no 383s 383s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 383s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 383s 383s 383s 383s . 382 patterns found (out of a total of 886 sites). 383s 383s . 582 sites without polymorphism (65.69%). 383s 383s 383s . Computing pairwise distances... 383s 383s . Building BioNJ tree... 383s 383s . This analysis requires at least 11 MB of memory space. 383s 383s 384s . Score of initial tree: -5680.04 384s 384s . Starting first round of SPRs... 387s 389s 4s | 1 | lnL= -5435.3 | depth= 1/ 40 | improvements= 22 | delta_lnL= 0.0/ 1000.0 392s 6s | 2 | lnL= -5452.9 | depth= 5/ 24 | improvements= 16 | delta_lnL= 5.8/ 1000.0 394s 9s | 3 | lnL= -5427.9 | depth= 2/ 14 | improvements= 23 | delta_lnL= 7.6/ 1000.0 + 394s 11s | 4 | lnL= -5428.1 | depth= 3/ 8 | improvements= 11 | delta_lnL= 2.6/ 1000.0 394s 394s . Second round of optimization... 396s 396s 13s | 5 | lnL= -5424.5 | depth= 13/ 13 | improvements= 17 | delta_lnL= 26.2/ 1000.0 + 397s 13s | 6 | lnL= -5430.5 | depth= 5/ 17 | improvements= 14 | delta_lnL= 9.8/ 20.0 397s 14s | 7 | lnL= -5436.6 | depth= 2/ 13 | improvements= 20 | delta_lnL= 0.7/ 20.0 398s 14s | 8 | lnL= -5425.8 | depth= 2/ 10 | improvements= 12 | delta_lnL= 8.9/ 20.0 398s 14s | 9 | lnL= -5435.2 | depth= 2/ 8 | improvements= 15 | delta_lnL= 6.0/ 20.0 399s 15s | 10 | lnL= -5451.7 | depth= 2/ 6 | improvements= 21 | delta_lnL= 2.0/ 20.0 400s 16s | 11 | lnL= -5438.3 | depth= 2/ 6 | improvements= 13 | delta_lnL= 10.4/ 20.0 400s 17s | 12 | lnL= -5422.1 | depth= 2/ 6 | improvements= 10 | delta_lnL= 17.3/ 20.0 + 401s 17s | 13 | lnL= -5441.2 | depth= 3/ 6 | improvements= 18 | delta_lnL= 4.7/ 20.0 401s 18s | 14 | lnL= -5434.5 | depth= 3/ 7 | improvements= 13 | delta_lnL= 7.1/ 34.6 402s 18s | 15 | lnL= -5432.9 | depth= 2/ 7 | improvements= 7 | delta_lnL= 4.0/ 34.6 402s 18s | 16 | lnL= -5427.2 | depth= 1/ 6 | improvements= 7 | delta_lnL= 0.0/ 34.6 402s 19s | 17 | lnL= -5423.3 | depth= 1/ 5 | improvements= 9 | delta_lnL= 0.0/ 34.6 403s 19s | 18 | lnL= -5428.6 | depth= 1/ 5 | improvements= 17 | delta_lnL= 0.0/ 20.0 403s 20s | 19 | lnL= -5422.3 | depth= 2/ 5 | improvements= 10 | delta_lnL= 1.9/ 20.0 404s 20s | 20 | lnL= -5426.8 | depth= 1/ 6 | improvements= 17 | delta_lnL= 0.0/ 20.0 405s 21s | 21 | lnL= -5421.7 | depth= 2/ 5 | improvements= 9 | delta_lnL= 1.7/ 20.0 + 405s 22s | 22 | lnL= -5444.7 | depth= 2/ 6 | improvements= 23 | delta_lnL= 11.0/ 20.0 406s 22s | 23 | lnL= -5444.3 | depth= 3/ 6 | improvements= 19 | delta_lnL= 18.3/ 20.0 406s 23s | 24 | lnL= -5431.1 | depth= 2/ 7 | improvements= 14 | delta_lnL= 7.7/ 20.0 407s 23s | 25 | lnL= -5433.5 | depth= 2/ 6 | improvements= 16 | delta_lnL= 8.8/ 20.0 407s 24s | 26 | lnL= -5437.9 | depth= 2/ 6 | improvements= 10 | delta_lnL= 13.7/ 36.7 408s 24s | 27 | lnL= -5421.5 | depth= 1/ 6 | improvements= 8 | delta_lnL= 0.0/ 36.7 + 409s 25s | 28 | lnL= -5441.3 | depth= 1/ 5 | improvements= 16 | delta_lnL= 0.0/ 36.7 409s 26s | 29 | lnL= -5427.8 | depth= 1/ 5 | improvements= 11 | delta_lnL= 0.0/ 36.7 410s 26s | 30 | lnL= -5425.8 | depth= 2/ 5 | improvements= 9 | delta_lnL= 20.7/ 27.3 411s 27s | 31 | lnL= -5428.8 | depth= 2/ 6 | improvements= 19 | delta_lnL= 5.3/ 27.3 411s 28s | 32 | lnL= -5421.1 | depth= 1/ 6 | improvements= 9 | delta_lnL= 0.0/ 27.3 + 412s 28s | 33 | lnL= -5419.9 | depth= 1/ 5 | improvements= 12 | delta_lnL= 0.0/ 27.3 + 412s 29s | 34 | lnL= -5419.7 | depth= 1/ 5 | improvements= 4 | delta_lnL= 0.0/ 41.4 + 412s 412s . Third round of optimization... 414s 417s 31s | 35 | lnL= -5416.0 | depth= 1/ 10 | improvements= 5 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 420s 34s | 36 | lnL= -5415.8 | depth= 0/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 420s 37s | 37 | lnL= -5415.8 | depth= 0/ 6 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 420s 420s . Final optimisation steps... 422s 422s 422s . Log likelihood of the current tree: -5415.79613287899428542. 422s 423s . Calculating fast branch supports (using 'aBayes'). 423s 423s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 423s 423s . Time used 0h0m40s 423s 423s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 423s AA interleaved sequence file, default parameters using 2 processors: 423s + echo 'AA interleaved sequence file, default parameters using 2 processors:' 423s + /usr/bin/phyml -i proteic -d aa 424s 424s 424s . Running the analysis on 2 CPUs.. 424s 424s . Command line: /usr/lib/phyml/bin/phyml-mpi -i proteic -d aa 424s 424s 424s 424s 424s 424s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 424s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 424s 424s . Sequence filename: proteic 424s . Data type: aa 424s . Alphabet size: 20 424s . Sequence format: interleaved 424s . Number of data sets: 1 424s . Nb of bootstrapped data sets: 0 424s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 424s . Model name: LG 424s . Proportion of invariable sites: 0.000000 424s . RAS model: discrete Gamma 424s . Number of subst. rate catgs: 4 424s . Gamma distribution parameter: estimated 424s . 'Middle' of each rate class: mean 424s . Amino-acid equilibrium frequencies: empirical 424s . Optimise tree topology: yes 424s . Starting tree: BioNJ 424s . Add random input tree: no 424s . Optimise branch lengths: yes 424s . Minimum length of an edge: 1e-08 424s . Optimise substitution model parameters: yes 424s . Run ID: none 424s . Random seed: 1742052179 424s . Subtree patterns aliasing: no 424s . Version: 3.3.3:3.3.20220408-4build1 424s . Byte alignment: 1 424s . AVX enabled: no 424s . SSE enabled: no 424s 424s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 424s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 424s 424s 424s 424s . 429 patterns found (out of a total of 547 sites). 424s 424s . 136 sites without polymorphism (24.86%). 424s 424s 424s . Computing pairwise distances... 424s 424s . Building BioNJ tree... 424s 424s . This analysis requires at least 39 MB of memory space. 424s 424s 427s . Score of initial tree: -12569.85 427s 427s . Starting first round of SPRs... 439s 439s 15s | 1 | lnL= -12459.3 | depth= 1/ 40 | improvements= 13 | delta_lnL= 0.0/ 1000.0 439s 439s . Second round of optimization... 450s 461s 26s | 2 | lnL= -12466.7 | depth= 1/ 36 | improvements= 22 | delta_lnL= 0.0/ 1000.0 472s 37s | 3 | lnL= -12486.2 | depth= 1/ 20 | improvements= 15 | delta_lnL= 0.0/ 1000.0 483s 48s | 4 | lnL= -12478.1 | depth= 2/ 16 | improvements= 26 | delta_lnL= 5.7/ 1000.0 486s 59s | 5 | lnL= -12483.3 | depth= 2/ 12 | improvements= 18 | delta_lnL= 16.7/ 1000.0 488s 62s | 6 | lnL= -12457.7 | depth= 2/ 9 | improvements= 17 | delta_lnL= 8.3/ 20.0 491s 64s | 7 | lnL= -12474.5 | depth= 1/ 7 | improvements= 12 | delta_lnL= 0.0/ 20.0 494s 67s | 8 | lnL= -12559.9 | depth= 2/ 5 | improvements= 16 | delta_lnL= 5.7/ 20.0 496s 70s | 9 | lnL= -12494.0 | depth= 3/ 6 | improvements= 17 | delta_lnL= 13.8/ 20.0 502s 72s | 10 | lnL= -12454.9 | depth= 2/ 7 | improvements= 12 | delta_lnL= 13.1/ 20.0 502s 78s | 11 | lnL= -12457.9 | depth= 2/ 6 | improvements= 12 | delta_lnL= 9.5/ 20.0 502s 502s . Third round of optimization... 515s 529s 91s | 12 | lnL= -12445.5 | depth= 3/ 10 | improvements= 6 | delta_lnL= 4.2/ 100.0 | triple moves= 5 + 543s 105s | 13 | lnL= -12444.6 | depth= 3/ 8 | improvements= 1 | delta_lnL= 5.0/ 100.0 | triple moves= 5 + 564s 119s | 14 | lnL= -12443.1 | depth= 2/ 6 | improvements= 1 | delta_lnL= 1.8/ 100.0 | triple moves= 6 + 564s 140s | 15 | lnL= -12443.0 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 6 + 564s 564s . Final optimisation steps... 571s 571s 572s . Log likelihood of the current tree: -12443.04864641573658446. 572s 578s . Calculating fast branch supports (using 'aBayes'). 578s 578s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 578s 578s . Time used 0h2m34s 578s 578s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 579s AA sequential sequence file, with customization using 2 processors: 579s + echo 'AA sequential sequence file, with customization using 2 processors:' 579s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 579s 579s 579s . Running the analysis on 2 CPUs.. 579s 579s . Command line: /usr/lib/phyml/bin/phyml-mpi -i example.nex -d nt -c 4 -a e 579s 579s 579s 579s 579s 579s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 579s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 579s 579s . Sequence filename: example.nex 579s . Data type: dna 579s . Alphabet size: 4 579s . Sequence format: interleaved 579s . Number of data sets: 1 579s . Nb of bootstrapped data sets: 0 579s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 579s . Model name: HKY85 579s . Ts/tv ratio: estimated 579s . Proportion of invariable sites: 0.000000 579s . RAS model: discrete Gamma 579s . Number of subst. rate catgs: 4 579s . Gamma distribution parameter: estimated 579s . 'Middle' of each rate class: mean 579s . Nucleotide equilibrium frequencies: empirical 579s . Optimise tree topology: yes 579s . Starting tree: BioNJ 579s . Add random input tree: no 579s . Optimise branch lengths: yes 579s . Minimum length of an edge: 1e-08 579s . Optimise substitution model parameters: yes 579s . Run ID: none 579s . Random seed: 1742052335 579s . Subtree patterns aliasing: no 579s . Version: 3.3.3:3.3.20220408-4build1 579s . Byte alignment: 1 579s . AVX enabled: no 579s . SSE enabled: no 579s 579s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 579s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 579s 579s 579s 579s . 1037 patterns found (out of a total of 2888 sites). 579s 579s . 1378 sites without polymorphism (47.71%). 579s 579s 579s . Computing pairwise distances... 579s 579s . Building BioNJ tree... 579s 579s . This analysis requires at least 3 MB of memory space. 579s 579s 579s . Score of initial tree: -12664.54 579s 579s . Starting first round of SPRs... 580s 580s 0s | 1 | lnL= -12681.3 | depth= 1/ 40 | improvements= 6 | delta_lnL= 0.0/ 1000.0 580s 580s . Second round of optimization... 580s 580s 1s | 2 | lnL= -12604.5 | depth= 1/ 36 | improvements= 5 | delta_lnL= 0.0/ 1000.0 580s 580s . Third round of optimization... 580s 581s 1s | 3 | lnL= -12563.9 | depth= 1/ 20 | improvements= 4 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 581s 2s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 581s 581s . Final optimisation steps... 581s 581s 581s . Log likelihood of the current tree: -12563.11885905565213761. 581s 581s . Calculating fast branch supports (using 'aBayes'). 581s 581s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 581s 581s . Time used 0h0m2s 581s 581s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 582s PASS 582s + echo PASS 582s autopkgtest [15:25:38]: test run-unit-test: -----------------------] 586s autopkgtest [15:25:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 586s run-unit-test PASS 590s autopkgtest [15:25:46]: @@@@@@@@@@@@@@@@@@@@ summary 590s run-unit-test PASS