0s autopkgtest [21:52:38]: starting date and time: 2025-03-15 21:52:38+0000 0s autopkgtest [21:52:38]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:52:38]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6u4qij_1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-23.secgroup --name adt-plucky-amd64-phyml-20250315-211546-juju-7f2275-prod-proposed-migration-environment-20-f4196310-c375-497e-867a-b5f4b43f2761 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 49s autopkgtest [21:53:27]: testbed dpkg architecture: amd64 49s autopkgtest [21:53:27]: testbed apt version: 2.9.31ubuntu1 49s autopkgtest [21:53:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [21:53:28]: testbed release detected to be: None 50s autopkgtest [21:53:28]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 51s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 51s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 51s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 51s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 51s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 52s Fetched 1265 kB in 1s (1482 kB/s) 53s Reading package lists... 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 54s Calculating upgrade... 55s The following package was automatically installed and is no longer required: 55s libnl-genl-3-200 55s Use 'sudo apt autoremove' to remove it. 55s The following NEW packages will be installed: 55s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 55s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 55s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 55s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 55s The following packages will be upgraded: 55s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 55s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 55s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 55s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 55s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 55s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 55s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 55s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 55s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 55s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 55s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 55s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 55s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 55s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 55s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 55s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 55s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 55s parted pci.ids pciutils pinentry-curses python-apt-common python3 55s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 55s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 55s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 55s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 55s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 55s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 55s xz-utils 55s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 829 MB of archives. 55s After this operation, 325 MB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 55s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 55s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 55s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 56s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 56s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 56s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 56s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 56s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 56s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 56s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 56s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 56s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 56s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 56s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 56s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 56s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 56s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 56s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 56s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 56s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 56s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 56s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 56s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 56s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 56s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 56s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 56s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 56s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 56s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 56s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 56s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 56s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 56s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 56s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 56s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 56s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 56s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 57s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 57s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 57s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 57s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 57s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 57s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 57s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 57s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 57s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 57s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 57s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 57s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 57s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 57s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 57s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 57s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 57s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 57s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 57s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 57s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 57s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 57s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 57s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 57s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 57s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 57s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 57s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 57s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 57s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 57s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 57s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 57s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 57s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 57s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 57s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 57s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 57s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 57s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 57s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 57s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 57s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 57s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 57s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 57s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 57s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 57s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 57s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 57s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 57s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 57s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 57s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 57s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 57s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 57s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 57s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 57s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 57s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 57s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 57s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 57s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 57s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 57s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 57s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 58s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 58s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 58s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 58s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 58s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 58s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 58s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 58s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 81s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 81s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 81s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 81s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 81s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 81s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 81s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 81s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 83s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 84s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 91s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 91s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 91s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 91s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 91s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 91s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 91s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 92s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 92s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 92s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 92s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 92s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 92s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 92s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 92s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 92s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 92s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 92s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 92s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 93s Preconfiguring packages ... 93s Fetched 829 MB in 37s (22.3 MB/s) 93s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 101s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 101s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 101s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 101s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 101s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 101s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 101s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 101s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 101s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 101s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 102s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 102s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 102s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 102s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 102s Selecting previously unselected package libdebuginfod-common. 102s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 102s Unpacking libdebuginfod-common (0.192-4) ... 102s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 102s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 102s Setting up libsemanage-common (3.7-2.1build1) ... 102s (Reading database ... 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(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 ... 109155 files and directories currently installed.) 102s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ... 102s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ... 102s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ... 102s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ... 102s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ... 102s Unpacking libglib2.0-0t64:amd64 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.../23-parted_3.6-5_amd64.deb ... 105s Unpacking parted (3.6-5) over (3.6-4build1) ... 105s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 105s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 105s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 105s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 105s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 105s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 105s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 105s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 106s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 106s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 106s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 106s Unpacking strace 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(2.44-3ubuntu1) over (2.44-2ubuntu1) ... 106s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ... 106s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 106s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ... 106s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 106s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ... 106s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 106s Preparing to unpack .../39-hwdata_0.393-3_all.deb ... 106s Unpacking hwdata (0.393-3) over (0.392-1) ... 106s Selecting previously unselected package pnp.ids. 106s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ... 106s Unpacking pnp.ids (0.393-3) ... 106s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ... 106s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 106s Selecting previously unselected package bpftool. 106s Preparing to unpack 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.../49-exfatprogs_1.2.8-1_amd64.deb ... 107s Unpacking exfatprogs (1.2.8-1) over (1.2.7-3) ... 107s Preparing to unpack .../50-libcurl3t64-gnutls_8.12.1-3ubuntu1_amd64.deb ... 107s Unpacking libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 107s Preparing to unpack .../51-fwupd_2.0.6-4_amd64.deb ... 108s Unpacking fwupd (2.0.6-4) over (2.0.6-3) ... 108s Preparing to unpack .../52-libfwupd3_2.0.6-4_amd64.deb ... 108s Unpacking libfwupd3:amd64 (2.0.6-4) over (2.0.6-3) ... 108s Preparing to unpack .../53-libmm-glib0_1.23.4-0ubuntu3_amd64.deb ... 108s Unpacking libmm-glib0:amd64 (1.23.4-0ubuntu3) over (1.23.4-0ubuntu2) ... 108s Preparing to unpack .../54-htop_3.4.0-2_amd64.deb ... 108s Unpacking htop (3.4.0-2) over (3.3.0-5) ... 108s Preparing to unpack .../55-linux-firmware_20250310.git9e1370d3-0ubuntu1_amd64.deb ... 108s Unpacking linux-firmware (20250310.git9e1370d3-0ubuntu1) over (20250204.git0fd450ee-0ubuntu1) ... 112s Preparing to unpack .../56-initramfs-tools_0.146ubuntu1_all.deb ... 112s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 112s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ... 112s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 112s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 112s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 112s Selecting previously unselected package libdebuginfod1t64:amd64. 112s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ... 112s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 112s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ... 112s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 112s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 112s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 112s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ... 112s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ... 112s Selecting previously unselected package linux-modules-6.14.0-10-generic. 112s Preparing to unpack .../63-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 112s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 112s Selecting previously unselected package linux-image-6.14.0-10-generic. 112s Preparing to unpack .../64-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 112s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ... 112s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic. 112s Preparing to unpack .../65-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 112s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 114s Preparing to unpack .../66-linux-generic_6.14.0-10.10_amd64.deb ... 114s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 114s Preparing to unpack .../67-linux-image-generic_6.14.0-10.10_amd64.deb ... 114s 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(1.0.6-6) over (1.0.6-5) ... 119s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 119s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 119s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 119s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 119s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 119s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 119s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 119s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 120s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 120s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 120s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 120s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 120s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 120s Setting up media-types (13.0.0) ... 120s Installing new version of config file /etc/mime.types ... 120s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 120s Setting up ubuntu-kernel-accessories (1.549) ... 120s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 120s Setting up pci.ids (0.0~2025.03.09-1) ... 120s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 120s Setting up apt-utils (2.9.33) ... 120s Setting up libdebuginfod-common (0.192-4) ... 120s Setting up exfatprogs (1.2.8-1) ... 120s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 120s Setting up bpftool (7.6.0+6.14.0-10.10) ... 120s Setting up libestr0:amd64 (0.1.11-2) ... 120s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 120s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 120s Setting up dosfstools (4.2-1.2) ... 120s Setting up rsyslog (8.2412.0-2ubuntu2) ... 120s info: The user `syslog' is already a member of `adm'. 121s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 121s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 121s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 121s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 121s Setting up systemd (257.3-1ubuntu3) ... 121s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 121s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 122s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 122s Setting up libparted2t64:amd64 (3.6-5) ... 122s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 122s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 122s Setting up linux-headers-generic (6.14.0-10.10) ... 122s Setting up libjemalloc2:amd64 (5.3.0-3) ... 122s Setting up locales (2.41-1ubuntu1) ... 122s Installing new version of config file /etc/locale.alias ... 123s Generating locales (this might take a while)... 125s en_US.UTF-8... done 125s Generation complete. 125s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 125s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 125s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 125s Installing new version of config file /etc/apparmor.d/fusermount3 ... 125s Installing new version of config file /etc/apparmor.d/lsusb ... 125s Installing new version of config file /etc/apparmor.d/openvpn ... 126s Reloading AppArmor profiles 128s Setting up libftdi1-2:amd64 (1.5-8build1) ... 128s Setting up libglib2.0-data (2.84.0-1) ... 128s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 128s Setting up libncurses6:amd64 (6.5+20250216-2) ... 128s Setting up strace (6.13+ds-1ubuntu1) ... 128s Setting up xz-utils (5.6.4-1) ... 128s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 129s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 129s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 129s Setting up udev (257.3-1ubuntu3) ... 130s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 132s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 132s Setting up libpci3:amd64 (1:3.13.0-2) ... 132s Setting up whiptail (0.52.24-4ubuntu2) ... 132s Setting up python-apt-common (2.9.9build1) ... 132s Setting up pnp.ids (0.393-3) ... 132s Setting up libnl-3-200:amd64 (3.7.0-1) ... 132s Setting up python3.13-minimal (3.13.2-2) ... 133s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 133s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 133s Setting up libc-dev-bin (2.41-1ubuntu1) ... 133s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 133s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 133s Setting up rsync (3.4.1+ds1-3) ... 134s rsync.service is a disabled or a static unit not running, not starting it. 134s Setting up python3.13-gdbm (3.13.2-2) ... 134s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 134s Setting up systemd-resolved (257.3-1ubuntu3) ... 135s Setting up initramfs-tools-bin (0.146ubuntu1) ... 135s Setting up ncurses-term (6.5+20250216-2) ... 135s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 135s Setting up libpython3.13:amd64 (3.13.2-2) ... 135s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 135s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 135s Setting up systemd-sysv (257.3-1ubuntu3) ... 135s Setting up linux-headers-virtual (6.14.0-10.10) ... 135s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 135s Setting up python3.13 (3.13.2-2) ... 136s Setting up htop (3.4.0-2) ... 136s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 139s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 139s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 139s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 139s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 139s Setting up parted (3.6-5) ... 139s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 139s Setting up python3 (3.13.2-2) ... 139s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 139s Setting up python3-markupsafe (2.1.5-1build4) ... 139s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 142s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 142s Setting up hwdata (0.393-3) ... 142s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 142s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 142s No schema files found: doing nothing. 142s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 142s Setting up linux-perf (6.14.0-10.10) ... 142s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 142s Setting up pciutils (1:3.13.0-2) ... 142s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 142s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 142s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 142s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 142s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 142s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 142s Setting up curl (8.12.1-3ubuntu1) ... 142s Setting up linux-image-virtual (6.14.0-10.10) ... 142s Setting up initramfs-tools-core (0.146ubuntu1) ... 142s Setting up linux-tools-common (6.14.0-10.10) ... 142s Setting up python3-systemd (235-1build6) ... 142s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 142s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 142s Setting up linux-image-generic (6.14.0-10.10) ... 142s Setting up python3-dbus (1.3.2-5build5) ... 143s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 143s Setting up initramfs-tools (0.146ubuntu1) ... 143s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 143s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 143s update-initramfs: deferring update (trigger activated) 143s Setting up linux-generic (6.14.0-10.10) ... 143s Setting up ubuntu-minimal (1.549) ... 143s Setting up python3-apt (2.9.9build1) ... 143s Setting up python3-bcrypt (4.2.0-2.1build1) ... 143s Setting up python3-yaml (6.0.2-1build2) ... 143s Setting up libfwupd3:amd64 (2.0.6-4) ... 143s Setting up python3-lazr.uri (1.0.6-6) ... 143s Setting up binutils (2.44-3ubuntu1) ... 143s Setting up ubuntu-standard (1.549) ... 143s Setting up cloud-init-base (25.1-0ubuntu3) ... 145s Setting up linux-virtual (6.14.0-10.10) ... 145s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 145s Setting up python3-gi (3.50.0-4build1) ... 146s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 146s Setting up fwupd (2.0.6-4) ... 146s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 146s fwupd.service is a disabled or a static unit not running, not starting it. 146s Setting up cloud-init (25.1-0ubuntu3) ... 146s Processing triggers for man-db (2.13.0-1) ... 149s Processing triggers for dbus (1.16.2-1ubuntu1) ... 149s Processing triggers for shared-mime-info (2.4-5) ... 149s Warning: program compiled against libxml 212 using older 209 149s Processing triggers for libc-bin (2.41-1ubuntu1) ... 149s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 149s /etc/kernel/postinst.d/initramfs-tools: 149s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 149s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 161s /etc/kernel/postinst.d/zz-update-grub: 161s Sourcing file `/etc/default/grub' 161s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 161s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 161s Generating grub configuration file ... 162s Found linux image: /boot/vmlinuz-6.14.0-10-generic 162s Found initrd image: /boot/initrd.img-6.14.0-10-generic 162s Found linux image: /boot/vmlinuz-6.12.0-16-generic 162s Found initrd image: /boot/initrd.img-6.12.0-16-generic 162s Found linux image: /boot/vmlinuz-6.11.0-8-generic 162s Found initrd image: /boot/initrd.img-6.11.0-8-generic 162s Warning: os-prober will not be executed to detect other bootable partitions. 162s Systems on them will not be added to the GRUB boot configuration. 162s Check GRUB_DISABLE_OS_PROBER documentation entry. 162s Adding boot menu entry for UEFI Firmware Settings ... 162s done 162s Processing triggers for initramfs-tools (0.146ubuntu1) ... 162s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 162s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Solving dependencies... 177s The following packages will be REMOVED: 177s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 177s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 177s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 177s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 177s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 177s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 177s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 177s linux-tools-6.12.0-16-generic* 178s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 178s After this operation, 545 MB disk space will be freed. 178s (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 ... 148643 files and directories currently installed.) 178s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 178s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 178s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 178s Removing libpython3.12t64:amd64 (3.12.9-1) ... 178s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 178s Removing libnsl2:amd64 (1.3.0-3build3) ... 178s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 178s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 179s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 182s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 182s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 185s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 185s /etc/kernel/postrm.d/initramfs-tools: 185s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 186s /etc/kernel/postrm.d/zz-update-grub: 186s Sourcing file `/etc/default/grub' 186s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 186s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 186s Generating grub configuration file ... 186s Found linux image: /boot/vmlinuz-6.14.0-10-generic 186s Found initrd image: /boot/initrd.img-6.14.0-10-generic 186s Found linux image: /boot/vmlinuz-6.12.0-16-generic 186s Found initrd image: /boot/initrd.img-6.12.0-16-generic 186s Warning: os-prober will not be executed to detect other bootable partitions. 186s Systems on them will not be added to the GRUB boot configuration. 186s Check GRUB_DISABLE_OS_PROBER documentation entry. 186s Adding boot menu entry for UEFI Firmware Settings ... 186s done 186s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 187s W: Removing the running kernel 187s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 187s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 187s /etc/kernel/postrm.d/initramfs-tools: 187s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 187s /etc/kernel/postrm.d/zz-update-grub: 187s Sourcing file `/etc/default/grub' 187s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 187s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 187s Generating grub configuration file ... 187s Found linux image: /boot/vmlinuz-6.14.0-10-generic 187s Found initrd image: /boot/initrd.img-6.14.0-10-generic 187s Warning: os-prober will not be executed to detect other bootable partitions. 187s Systems on them will not be added to the GRUB boot configuration. 187s Check GRUB_DISABLE_OS_PROBER documentation entry. 187s Adding boot menu entry for UEFI Firmware Settings ... 187s done 187s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 188s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 190s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 190s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 190s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 190s Processing triggers for libc-bin (2.41-1ubuntu1) ... 190s (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 ... 76972 files and directories currently installed.) 190s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 190s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 190s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 190s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 190s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 190s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 190s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 190s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 190s autopkgtest [21:55:48]: upgrading testbed (apt dist-upgrade and autopurge) 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 191s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 192s Entering ResolveByKeep 193s 193s Calculating upgrade... 193s The following packages will be upgraded: 193s libc-bin libc-dev-bin libc6 libc6-dev locales 193s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Need to get 10.5 MB of archives. 193s After this operation, 1024 B of additional disk space will be used. 193s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 194s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 194s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 194s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 195s Preconfiguring packages ... 195s Fetched 10.5 MB in 1s (8299 kB/s) 195s (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 ... 76968 files and directories currently installed.) 195s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 195s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 195s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 195s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc6:amd64 (2.41-1ubuntu2) ... 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 ... 76968 files and directories currently installed.) 196s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 196s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc-bin (2.41-1ubuntu2) ... 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 ... 76968 files and directories currently installed.) 196s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 196s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up locales (2.41-1ubuntu2) ... 197s Generating locales (this might take a while)... 199s en_US.UTF-8... done 199s Generation complete. 199s Setting up libc-dev-bin (2.41-1ubuntu2) ... 199s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 199s Processing triggers for man-db (2.13.0-1) ... 200s Processing triggers for systemd (257.3-1ubuntu3) ... 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 202s Solving dependencies... 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s autopkgtest [21:56:01]: rebooting testbed after setup commands that affected boot 225s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 233s autopkgtest [21:56:31]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 236s autopkgtest [21:56:34]: @@@@@@@@@@@@@@@@@@@@ apt-source phyml 238s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (dsc) [2131 B] 238s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (tar) [1804 kB] 238s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phyml 3:3.3.20220408-4build1 (diff) [27.1 kB] 238s gpgv: Signature made Sat Nov 30 06:14:54 2024 UTC 238s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 238s gpgv: Can't check signature: No public key 238s dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-4build1.dsc: no acceptable signature found 238s autopkgtest [21:56:36]: testing package phyml version 3:3.3.20220408-4build1 239s autopkgtest [21:56:37]: build not needed 239s autopkgtest [21:56:37]: test run-unit-test: preparing testbed 240s Reading package lists... 240s Building dependency tree... 240s Reading state information... 240s Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 241s The following NEW packages will be installed: 241s libamd-comgr2 libamdhip64-5 libevent-pthreads-2.1-7t64 libfabric1 libgomp1 241s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 241s libibumad3 libllvm17t64 libmunge2 libopenmpi40 libpciaccess0 libpmix2t64 241s libpsm-infinipath1 libpsm2-2 librdmacm1t64 libucx0 libxnvctrl0 241s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common phyml 241s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 241s Need to get 58.2 MB of archives. 241s After this operation, 239 MB of additional disk space will be used. 241s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-21 [26.0 MB] 246s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 248s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 248s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 248s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 249s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 249s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 249s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 249s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 55.0-1ubuntu1 [71.5 kB] 249s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 249s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 249s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 249s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 249s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 249s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 249s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 249s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 249s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-5 [714 kB] 249s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 55.0-1ubuntu1 [29.7 kB] 249s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 55.0-1ubuntu1 [42.7 kB] 249s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.18.1+ds-2 [1293 kB] 249s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 249s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-common all 5.0.7-1 [97.9 kB] 249s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-bin amd64 5.0.7-1 [192 kB] 249s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 mpi-default-bin amd64 1.18 [2510 B] 249s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 phyml amd64 3:3.3.20220408-4build1 [1081 kB] 250s Fetched 58.2 MB in 8s (7271 kB/s) 250s Selecting previously unselected package libllvm17t64:amd64. 250s (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 ... 76968 files and directories currently installed.) 250s Preparing to unpack .../00-libllvm17t64_1%3a17.0.6-21_amd64.deb ... 250s Unpacking libllvm17t64:amd64 (1:17.0.6-21) ... 251s Selecting previously unselected package libamd-comgr2:amd64. 251s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 251s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 251s Selecting previously unselected package libhsakmt1:amd64. 251s Preparing to unpack .../02-libhsakmt1_5.7.0-1build1_amd64.deb ... 251s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 251s Selecting previously unselected package libhsa-runtime64-1. 251s Preparing to unpack .../03-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 251s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 251s Selecting previously unselected package libamdhip64-5. 251s Preparing to unpack .../04-libamdhip64-5_5.7.1-5_amd64.deb ... 251s Unpacking libamdhip64-5 (5.7.1-5) ... 251s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 251s Preparing to unpack .../05-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 251s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 251s Selecting previously unselected package libpsm-infinipath1. 251s Preparing to unpack .../06-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 251s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 251s Selecting previously unselected package libpsm2-2. 251s Preparing to unpack .../07-libpsm2-2_11.2.185-2.1_amd64.deb ... 251s Unpacking libpsm2-2 (11.2.185-2.1) ... 251s Selecting previously unselected package librdmacm1t64:amd64. 251s Preparing to unpack .../08-librdmacm1t64_55.0-1ubuntu1_amd64.deb ... 251s Unpacking librdmacm1t64:amd64 (55.0-1ubuntu1) ... 251s Selecting previously unselected package libfabric1:amd64. 251s Preparing to unpack .../09-libfabric1_1.17.0-3.1_amd64.deb ... 251s Unpacking libfabric1:amd64 (1.17.0-3.1) ... 251s Selecting previously unselected package libgomp1:amd64. 251s Preparing to unpack .../10-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 251s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 251s Selecting previously unselected package libhwloc15:amd64. 251s Preparing to unpack .../11-libhwloc15_2.12.0-1_amd64.deb ... 251s Unpacking libhwloc15:amd64 (2.12.0-1) ... 252s Selecting previously unselected package libmunge2:amd64. 252s Preparing to unpack .../12-libmunge2_0.5.16-1_amd64.deb ... 252s Unpacking libmunge2:amd64 (0.5.16-1) ... 252s Selecting previously unselected package libpciaccess0:amd64. 252s Preparing to unpack .../13-libpciaccess0_0.17-3build1_amd64.deb ... 252s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 252s Selecting previously unselected package libxnvctrl0:amd64. 252s Preparing to unpack .../14-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 252s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 252s Selecting previously unselected package ocl-icd-libopencl1:amd64. 252s Preparing to unpack .../15-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 252s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 252s Selecting previously unselected package libhwloc-plugins:amd64. 252s Preparing to unpack .../16-libhwloc-plugins_2.12.0-1_amd64.deb ... 252s Unpacking libhwloc-plugins:amd64 (2.12.0-1) ... 252s Selecting previously unselected package libpmix2t64:amd64. 252s Preparing to unpack .../17-libpmix2t64_5.0.6-5_amd64.deb ... 252s Unpacking libpmix2t64:amd64 (5.0.6-5) ... 252s Selecting previously unselected package libibumad3:amd64. 252s Preparing to unpack .../18-libibumad3_55.0-1ubuntu1_amd64.deb ... 252s Unpacking libibumad3:amd64 (55.0-1ubuntu1) ... 252s Selecting previously unselected package libibmad5:amd64. 252s Preparing to unpack .../19-libibmad5_55.0-1ubuntu1_amd64.deb ... 252s Unpacking libibmad5:amd64 (55.0-1ubuntu1) ... 252s Selecting previously unselected package libucx0:amd64. 252s Preparing to unpack .../20-libucx0_1.18.1+ds-2_amd64.deb ... 252s Unpacking libucx0:amd64 (1.18.1+ds-2) ... 252s Selecting previously unselected package libopenmpi40:amd64. 252s Preparing to unpack .../21-libopenmpi40_5.0.7-1_amd64.deb ... 252s Unpacking libopenmpi40:amd64 (5.0.7-1) ... 252s Selecting previously unselected package openmpi-common. 252s Preparing to unpack .../22-openmpi-common_5.0.7-1_all.deb ... 252s Unpacking openmpi-common (5.0.7-1) ... 252s Selecting previously unselected package openmpi-bin. 252s Preparing to unpack .../23-openmpi-bin_5.0.7-1_amd64.deb ... 252s Unpacking openmpi-bin (5.0.7-1) ... 252s Selecting previously unselected package mpi-default-bin. 252s Preparing to unpack .../24-mpi-default-bin_1.18_amd64.deb ... 252s Unpacking mpi-default-bin (1.18) ... 252s Selecting previously unselected package phyml. 252s Preparing to unpack .../25-phyml_3%3a3.3.20220408-4build1_amd64.deb ... 252s Unpacking phyml (3:3.3.20220408-4build1) ... 252s Setting up libpciaccess0:amd64 (0.17-3build1) ... 252s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 252s Setting up libibumad3:amd64 (55.0-1ubuntu1) ... 252s Setting up libibmad5:amd64 (55.0-1ubuntu1) ... 252s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 252s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 252s Setting up libmunge2:amd64 (0.5.16-1) ... 252s Setting up libllvm17t64:amd64 (1:17.0.6-21) ... 252s Setting up libhwloc15:amd64 (2.12.0-1) ... 252s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 252s Setting up libpsm2-2 (11.2.185-2.1) ... 252s Setting up openmpi-common (5.0.7-1) ... 252s Setting up librdmacm1t64:amd64 (55.0-1ubuntu1) ... 252s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 252s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 252s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 252s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 252s Setting up libfabric1:amd64 (1.17.0-3.1) ... 252s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 252s Setting up libpmix2t64:amd64 (5.0.6-5) ... 252s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 252s Setting up libamdhip64-5 (5.7.1-5) ... 252s Setting up libucx0:amd64 (1.18.1+ds-2) ... 252s Setting up libopenmpi40:amd64 (5.0.7-1) ... 252s Setting up openmpi-bin (5.0.7-1) ... 252s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 252s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 252s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 252s Setting up mpi-default-bin (1.18) ... 252s Setting up phyml (3:3.3.20220408-4build1) ... 252s Processing triggers for man-db (2.13.0-1) ... 253s Processing triggers for libc-bin (2.41-1ubuntu2) ... 254s autopkgtest [21:56:52]: test run-unit-test: [----------------------- 255s DNA interleaved sequence file, default parameters single processor: 255s + export PHYMLCPUS=1 255s + PHYMLCPUS=1 255s + echo 'DNA interleaved sequence file, default parameters single processor:' 255s + /usr/bin/phyml -i nucleic 255s 255s 255s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 255s 255s 255s 255s 255s 255s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 255s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 255s 255s . Sequence filename: nucleic 255s . Data type: dna 255s . Alphabet size: 4 255s . Sequence format: interleaved 255s . Number of data sets: 1 255s . Nb of bootstrapped data sets: 0 255s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 255s . Model name: HKY85 255s . Ts/tv ratio: estimated 255s . Proportion of invariable sites: 0.000000 255s . RAS model: discrete Gamma 255s . Number of subst. rate catgs: 4 255s . Gamma distribution parameter: estimated 255s . 'Middle' of each rate class: mean 255s . Nucleotide equilibrium frequencies: empirical 255s . Optimise tree topology: yes 255s . Starting tree: BioNJ 255s . Add random input tree: no 255s . Optimise branch lengths: yes 255s . Minimum length of an edge: 1e-08 255s . Optimise substitution model parameters: yes 255s . Run ID: none 255s . Random seed: 1742075813 255s . Subtree patterns aliasing: no 255s . Version: 3.3.3:3.3.20220408-4build1 255s . Byte alignment: 1 255s . AVX enabled: no 255s . SSE enabled: no 255s 255s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 255s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 255s 255s 255s 255s . 382 patterns found (out of a total of 886 sites). 255s 255s . 582 sites without polymorphism (65.69%). 255s 255s 255s . Computing pairwise distances... 255s 255s . Building BioNJ tree... 255s 255s . This analysis requires at least 11 MB of memory space. 255s 255s 255s . Score of initial tree: -5680.04 255s 255s . Starting first round of SPRs... 257s 257s 2s | 1 | lnL= -5446.4 | depth= 5/ 40 | improvements= 13 | delta_lnL= 9.5/ 1000.0 257s 257s . Second round of optimization... 259s 260s 4s | 2 | lnL= -5452.1 | depth= 7/ 36 | improvements= 23 | delta_lnL= 24.2/ 1000.0 261s 5s | 3 | lnL= -5456.0 | depth= 5/ 20 | improvements= 14 | delta_lnL= 83.9/ 1000.0 262s 6s | 4 | lnL= -5451.9 | depth= 2/ 16 | improvements= 24 | delta_lnL= 9.7/ 1000.0 263s 7s | 5 | lnL= -5428.4 | depth= 4/ 12 | improvements= 18 | delta_lnL= 7.6/ 1000.0 + 264s 8s | 6 | lnL= -5427.5 | depth= 6/ 9 | improvements= 12 | delta_lnL= 16.5/ 167.9 + 264s 9s | 7 | lnL= -5427.7 | depth= 5/ 10 | improvements= 17 | delta_lnL= 9.2/ 167.9 265s 9s | 8 | lnL= -5434.9 | depth= 1/ 9 | improvements= 15 | delta_lnL= 0.0/ 167.9 266s 10s | 9 | lnL= -5429.9 | depth= 3/ 7 | improvements= 19 | delta_lnL= 4.0/ 167.9 267s 11s | 10 | lnL= -5427.0 | depth= 1/ 7 | improvements= 18 | delta_lnL= 0.0/ 33.0 + 267s 11s | 11 | lnL= -5424.2 | depth= 5/ 5 | improvements= 17 | delta_lnL= 24.0/ 33.0 + 267s 12s | 12 | lnL= -5428.3 | depth= 3/ 9 | improvements= 16 | delta_lnL= 5.1/ 33.0 268s 12s | 13 | lnL= -5431.2 | depth= 3/ 7 | improvements= 13 | delta_lnL= 54.0/ 33.0 268s 13s | 14 | lnL= -5425.9 | depth= 2/ 7 | improvements= 16 | delta_lnL= 14.5/ 48.0 268s 13s | 15 | lnL= -5438.7 | depth= 1/ 6 | improvements= 16 | delta_lnL= 0.0/ 48.0 269s 13s | 16 | lnL= -5436.4 | depth= 1/ 5 | improvements= 15 | delta_lnL= 0.0/ 48.0 269s 13s | 17 | lnL= -5425.3 | depth= 3/ 5 | improvements= 12 | delta_lnL= 6.2/ 48.0 269s 14s | 18 | lnL= -5459.1 | depth= 4/ 7 | improvements= 22 | delta_lnL= 19.7/ 29.0 270s 14s | 19 | lnL= -5444.0 | depth= 4/ 8 | improvements= 17 | delta_lnL= 10.0/ 29.0 270s 15s | 20 | lnL= -5448.6 | depth= 1/ 8 | improvements= 20 | delta_lnL= 0.0/ 29.0 270s 270s . Third round of optimization... 271s 273s 16s | 21 | lnL= -5421.5 | depth= 2/ 10 | improvements= 13 | delta_lnL= 3.9/ 100.0 | triple moves= 5 + 275s 18s | 22 | lnL= -5420.8 | depth= 1/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 275s 20s | 23 | lnL= -5420.8 | depth= 0/ 6 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 275s 275s . Final optimisation steps... 276s 276s 276s . Log likelihood of the current tree: -5420.255803559439300443046. 276s 277s . Calculating fast branch supports (using 'aBayes'). 277s 277s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 277s 277s . Time used 0h0m22s 277s 277s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 277s AA interleaved sequence file, default parameters single processor: 277s + echo 'AA interleaved sequence file, default parameters single processor:' 277s + /usr/bin/phyml -i proteic -d aa 277s 277s 277s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 277s 277s 277s 277s 277s 277s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 277s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 277s 277s . Sequence filename: proteic 277s . Data type: aa 277s . Alphabet size: 20 277s . Sequence format: interleaved 277s . Number of data sets: 1 277s . Nb of bootstrapped data sets: 0 277s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 277s . Model name: LG 277s . Proportion of invariable sites: 0.000000 277s . RAS model: discrete Gamma 277s . Number of subst. rate catgs: 4 277s . Gamma distribution parameter: estimated 277s . 'Middle' of each rate class: mean 277s . Amino-acid equilibrium frequencies: empirical 277s . Optimise tree topology: yes 277s . Starting tree: BioNJ 277s . Add random input tree: no 277s . Optimise branch lengths: yes 277s . Minimum length of an edge: 1e-08 277s . Optimise substitution model parameters: yes 277s . Run ID: none 277s . Random seed: 1742075835 277s . Subtree patterns aliasing: no 277s . Version: 3.3.3:3.3.20220408-4build1 277s . Byte alignment: 1 277s . AVX enabled: no 277s . SSE enabled: no 277s 277s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 277s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 277s 277s 277s 277s . 429 patterns found (out of a total of 547 sites). 277s 277s . 136 sites without polymorphism (24.86%). 277s 277s 277s . Computing pairwise distances... 277s 277s . Building BioNJ tree... 277s 277s . This analysis requires at least 39 MB of memory space. 277s 277s 279s . Score of initial tree: -12569.85 279s 279s . Starting first round of SPRs... 288s 297s 11s | 1 | lnL= -12498.2 | depth= 2/ 40 | improvements= 25 | delta_lnL= 76.2/ 1000.0 306s 20s | 2 | lnL= -12493.5 | depth= 2/ 24 | improvements= 26 | delta_lnL= 39.6/ 1000.0 313s 29s | 3 | lnL= -12476.9 | depth= 2/ 14 | improvements= 23 | delta_lnL= 10.4/ 1000.0 321s 36s | 4 | lnL= -12494.7 | depth= 2/ 8 | improvements= 20 | delta_lnL= 33.9/ 1000.0 324s 44s | 5 | lnL= -12526.7 | depth= 3/ 8 | improvements= 21 | delta_lnL= 15.2/ 1000.0 324s 47s | 6 | lnL= -12452.3 | depth= 2/ 9 | improvements= 14 | delta_lnL= 28.1/ 152.3 324s 324s . Second round of optimization... 327s 330s 50s | 7 | lnL= -12472.2 | depth= 1/ 12 | improvements= 19 | delta_lnL= 0.0/ 152.3 333s 53s | 8 | lnL= -12481.5 | depth= 3/ 9 | improvements= 19 | delta_lnL= 18.1/ 152.3 335s 56s | 9 | lnL= -12479.6 | depth= 4/ 7 | improvements= 24 | delta_lnL= 92.6/ 152.3 338s 58s | 10 | lnL= -12473.4 | depth= 2/ 8 | improvements= 18 | delta_lnL= 4.1/ 36.1 340s 61s | 11 | lnL= -12489.2 | depth= 2/ 6 | improvements= 18 | delta_lnL= 12.7/ 36.1 342s 63s | 12 | lnL= -12479.5 | depth= 3/ 6 | improvements= 20 | delta_lnL= 3.4/ 36.1 344s 65s | 13 | lnL= -12469.9 | depth= 1/ 7 | improvements= 19 | delta_lnL= 0.0/ 36.1 346s 67s | 14 | lnL= -12476.1 | depth= 2/ 5 | improvements= 19 | delta_lnL= 31.5/ 25.4 348s 69s | 15 | lnL= -12474.4 | depth= 1/ 6 | improvements= 11 | delta_lnL= 0.0/ 25.4 348s 71s | 16 | lnL= -12460.6 | depth= 3/ 5 | improvements= 12 | delta_lnL= 11.2/ 25.4 348s 348s . Third round of optimization... 356s 369s 79s | 17 | lnL= -12443.1 | depth= 2/ 10 | improvements= 8 | delta_lnL= 6.7/ 100.0 | triple moves= 5 + 369s 92s | 18 | lnL= -12443.1 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 369s 369s . Final optimisation steps... 374s 374s 374s . Log likelihood of the current tree: -12443.048590728625640622340. 374s 379s . Calculating fast branch supports (using 'aBayes'). 379s 379s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 379s 379s . Time used 0h1m41s 379s 379s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 379s + echo 'AA sequential sequence file, with customization single processor:' 379s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 379s AA sequential sequence file, with customization single processor: 379s 379s 379s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 379s 379s 379s 379s 379s 379s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 379s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 379s 379s . Sequence filename: example.nex 379s . Data type: dna 379s . Alphabet size: 4 379s . Sequence format: interleaved 379s . Number of data sets: 1 379s . Nb of bootstrapped data sets: 0 379s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 379s . Model name: HKY85 379s . Ts/tv ratio: estimated 379s . Proportion of invariable sites: 0.000000 379s . RAS model: discrete Gamma 379s . Number of subst. rate catgs: 4 379s . Gamma distribution parameter: estimated 379s . 'Middle' of each rate class: mean 379s . Nucleotide equilibrium frequencies: empirical 379s . Optimise tree topology: yes 379s . Starting tree: BioNJ 379s . Add random input tree: no 379s . Optimise branch lengths: yes 379s . Minimum length of an edge: 1e-08 379s . Optimise substitution model parameters: yes 379s . Run ID: none 379s . Random seed: 1742075936 379s . Subtree patterns aliasing: no 379s . Version: 3.3.3:3.3.20220408-4build1 379s . Byte alignment: 1 379s . AVX enabled: no 379s . SSE enabled: no 379s 379s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 379s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 379s 379s 379s 379s . 1037 patterns found (out of a total of 2888 sites). 379s 379s . 1378 sites without polymorphism (47.71%). 379s 379s 379s . Computing pairwise distances... 379s 379s . Building BioNJ tree... 379s 379s . This analysis requires at least 3 MB of memory space. 379s 379s 379s . Score of initial tree: -12664.54 379s 379s . Starting first round of SPRs... 379s 379s 1s | 1 | lnL= -12579.8 | depth= 1/ 40 | improvements= 5 | delta_lnL= 0.0/ 1000.0 379s 379s . Second round of optimization... 379s 379s 1s | 2 | lnL= -12602.3 | depth= 1/ 36 | improvements= 5 | delta_lnL= 0.0/ 1000.0 379s 379s . Third round of optimization... 379s 379s 1s | 3 | lnL= -12566.7 | depth= 1/ 20 | improvements= 2 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 379s 1s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 379s 379s . Final optimisation steps... 380s 380s 380s . Log likelihood of the current tree: -12563.118859055624852771871. 380s 380s . Calculating fast branch supports (using 'aBayes'). 380s 380s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 380s 380s . Time used 0h0m2s 380s 380s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 380s + export PHYMLCPUS=2 380s + PHYMLCPUS=2 380s DNA interleaved sequence file, default parameters using 2 processors: 380s + echo 'DNA interleaved sequence file, default parameters using 2 processors:' 380s + /usr/bin/phyml -i nucleic 380s 380s 380s . Running the analysis on 2 CPUs.. 380s 380s . Command line: /usr/lib/phyml/bin/phyml-mpi -i nucleic 380s 380s 380s 380s 380s 380s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 380s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 380s 380s . Sequence filename: nucleic 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: 1742075938 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 . 382 patterns found (out of a total of 886 sites). 380s 380s . 582 sites without polymorphism (65.69%). 380s 380s 380s . Computing pairwise distances... 380s 380s . Building BioNJ tree... 380s 380s . This analysis requires at least 11 MB of memory space. 380s 380s 381s . Score of initial tree: -5680.04 381s 381s . Starting first round of SPRs... 383s 385s 3s | 1 | lnL= -5472.6 | depth= 5/ 40 | improvements= 24 | delta_lnL= 16.4/ 1000.0 387s 5s | 2 | lnL= -5450.9 | depth= 3/ 24 | improvements= 16 | delta_lnL= 14.8/ 1000.0 388s 7s | 3 | lnL= -5442.8 | depth= 7/ 14 | improvements= 20 | delta_lnL= 17.1/ 1000.0 389s 8s | 4 | lnL= -5431.9 | depth= 3/ 13 | improvements= 21 | delta_lnL= 7.3/ 1000.0 + 390s 9s | 5 | lnL= -5425.3 | depth= 4/ 9 | improvements= 16 | delta_lnL= 26.9/ 1000.0 + 390s 10s | 6 | lnL= -5425.9 | depth= 1/ 10 | improvements= 5 | delta_lnL= 0.0/ 50.0 390s 390s . Second round of optimization... 390s 391s 10s | 7 | lnL= -5426.2 | depth= 2/ 10 | improvements= 16 | delta_lnL= 1.2/ 50.0 391s 11s | 8 | lnL= -5424.5 | depth= 4/ 8 | improvements= 12 | delta_lnL= 53.3/ 50.0 + 392s 11s | 9 | lnL= -5432.0 | depth= 2/ 8 | improvements= 16 | delta_lnL= 8.1/ 50.0 393s 12s | 10 | lnL= -5427.1 | depth= 4/ 6 | improvements= 14 | delta_lnL= 4.8/ 106.7 393s 13s | 11 | lnL= -5423.4 | depth= 3/ 8 | improvements= 11 | delta_lnL= 8.1/ 106.7 + 394s 13s | 12 | lnL= -5425.7 | depth= 2/ 7 | improvements= 16 | delta_lnL= 2.9/ 106.7 394s 14s | 13 | lnL= -5428.5 | depth= 2/ 6 | improvements= 13 | delta_lnL= 5.3/ 106.7 395s 14s | 14 | lnL= -5439.5 | depth= 1/ 6 | improvements= 16 | delta_lnL= 0.0/ 20.0 395s 15s | 15 | lnL= -5434.6 | depth= 3/ 5 | improvements= 17 | delta_lnL= 6.4/ 20.0 395s 15s | 16 | lnL= -5432.3 | depth= 2/ 7 | improvements= 14 | delta_lnL= 16.2/ 20.0 396s 15s | 17 | lnL= -5431.4 | depth= 1/ 6 | improvements= 13 | delta_lnL= 0.0/ 20.0 396s 16s | 18 | lnL= -5432.5 | depth= 1/ 5 | improvements= 13 | delta_lnL= 0.0/ 32.3 396s 16s | 19 | lnL= -5429.6 | depth= 2/ 5 | improvements= 11 | delta_lnL= 3.1/ 32.3 396s 16s | 20 | lnL= -5432.6 | depth= 1/ 6 | improvements= 12 | delta_lnL= 0.0/ 32.3 396s 396s . Third round of optimization... 398s 401s 18s | 21 | lnL= -5420.3 | depth= 3/ 10 | improvements= 8 | delta_lnL= 5.4/ 100.0 | triple moves= 5 + 401s 20s | 22 | lnL= -5420.3 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 401s 401s . Final optimisation steps... 402s 402s 402s . Log likelihood of the current tree: -5420.255792516657493251842. 402s 402s . Calculating fast branch supports (using 'aBayes'). 402s 402s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 402s 402s . Time used 0h0m22s 402s 402s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 402s + echo 'AA interleaved sequence file, default parameters using 2 processors:' 402s + /usr/bin/phyml -i proteic -d aa 402s AA interleaved sequence file, default parameters using 2 processors: 403s 403s 403s . Running the analysis on 2 CPUs.. 403s 403s . Command line: /usr/lib/phyml/bin/phyml-mpi -i proteic -d aa 403s 403s 403s 403s 403s 403s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 403s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 403s 403s . Sequence filename: proteic 403s . Data type: aa 403s . Alphabet size: 20 403s . Sequence format: interleaved 403s . Number of data sets: 1 403s . Nb of bootstrapped data sets: 0 403s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 403s . Model name: LG 403s . Proportion of invariable sites: 0.000000 403s . RAS model: discrete Gamma 403s . Number of subst. rate catgs: 4 403s . Gamma distribution parameter: estimated 403s . 'Middle' of each rate class: mean 403s . Amino-acid equilibrium frequencies: empirical 403s . Optimise tree topology: yes 403s . Starting tree: BioNJ 403s . Add random input tree: no 403s . Optimise branch lengths: yes 403s . Minimum length of an edge: 1e-08 403s . Optimise substitution model parameters: yes 403s . Run ID: none 403s . Random seed: 1742075961 403s . Subtree patterns aliasing: no 403s . Version: 3.3.3:3.3.20220408-4build1 403s . Byte alignment: 1 403s . AVX enabled: no 403s . SSE enabled: no 403s 403s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 403s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 403s 403s 403s 403s . 429 patterns found (out of a total of 547 sites). 403s 403s . 136 sites without polymorphism (24.86%). 403s 403s 403s . Computing pairwise distances... 403s 403s . Building BioNJ tree... 403s 403s . This analysis requires at least 39 MB of memory space. 403s 403s 405s . Score of initial tree: -12569.85 405s 405s . Starting first round of SPRs... 413s 421s 10s | 1 | lnL= -12491.4 | depth= 4/ 40 | improvements= 24 | delta_lnL= 178.4/ 1000.0 429s 18s | 2 | lnL= -12530.4 | depth= 1/ 24 | improvements= 27 | delta_lnL= 0.0/ 1000.0 437s 26s | 3 | lnL= -12479.2 | depth= 2/ 14 | improvements= 20 | delta_lnL= 84.4/ 1000.0 437s 34s | 4 | lnL= -12488.2 | depth= 3/ 8 | improvements= 14 | delta_lnL= 10.0/ 1000.0 437s 437s . Second round of optimization... 445s 447s 42s | 5 | lnL= -12465.1 | depth= 1/ 13 | improvements= 18 | delta_lnL= 0.0/ 1000.0 449s 44s | 6 | lnL= -12460.2 | depth= 2/ 10 | improvements= 21 | delta_lnL= 16.3/ 20.0 451s 46s | 7 | lnL= -12469.9 | depth= 2/ 8 | improvements= 22 | delta_lnL= 21.2/ 20.0 453s 48s | 8 | lnL= -12465.7 | depth= 1/ 6 | improvements= 16 | delta_lnL= 0.0/ 20.0 455s 50s | 9 | lnL= -12479.0 | depth= 1/ 5 | improvements= 21 | delta_lnL= 0.0/ 20.0 460s 52s | 10 | lnL= -12472.7 | depth= 1/ 5 | improvements= 15 | delta_lnL= 0.0/ 42.3 462s 57s | 11 | lnL= -12459.8 | depth= 1/ 5 | improvements= 13 | delta_lnL= 0.0/ 42.3 464s 59s | 12 | lnL= -12477.3 | depth= 2/ 5 | improvements= 20 | delta_lnL= 23.7/ 42.3 466s 61s | 13 | lnL= -12468.5 | depth= 2/ 6 | improvements= 15 | delta_lnL= 6.4/ 42.3 466s 63s | 14 | lnL= -12482.1 | depth= 2/ 6 | improvements= 16 | delta_lnL= 17.6/ 47.4 466s 466s . Third round of optimization... 475s 488s 71s | 15 | lnL= -12444.4 | depth= 2/ 10 | improvements= 10 | delta_lnL= 10.0/ 100.0 | triple moves= 5 + 488s 85s | 16 | lnL= -12443.2 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 6 + 488s 488s . Final optimisation steps... 496s 496s 496s . Log likelihood of the current tree: -12443.048793431236845208332. 496s 500s . Calculating fast branch supports (using 'aBayes'). 500s 500s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 500s 500s . Time used 0h1m37s 500s 500s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 500s AA sequential sequence file, with customization using 2 processors: 500s + echo 'AA sequential sequence file, with customization using 2 processors:' 500s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 500s 500s 500s . Running the analysis on 2 CPUs.. 500s 500s . Command line: /usr/lib/phyml/bin/phyml-mpi -i example.nex -d nt -c 4 -a e 500s 500s 500s 500s 500s 500s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 500s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 500s 500s . Sequence filename: example.nex 500s . Data type: dna 500s . Alphabet size: 4 500s . Sequence format: interleaved 500s . Number of data sets: 1 500s . Nb of bootstrapped data sets: 0 500s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 500s . Model name: HKY85 500s . Ts/tv ratio: estimated 500s . Proportion of invariable sites: 0.000000 500s . RAS model: discrete Gamma 500s . Number of subst. rate catgs: 4 500s . Gamma distribution parameter: estimated 500s . 'Middle' of each rate class: mean 500s . Nucleotide equilibrium frequencies: empirical 500s . Optimise tree topology: yes 500s . Starting tree: BioNJ 500s . Add random input tree: no 500s . Optimise branch lengths: yes 500s . Minimum length of an edge: 1e-08 500s . Optimise substitution model parameters: yes 500s . Run ID: none 500s . Random seed: 1742076058 500s . Subtree patterns aliasing: no 500s . Version: 3.3.3:3.3.20220408-4build1 500s . Byte alignment: 1 500s . AVX enabled: no 500s . SSE enabled: no 500s 500s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 500s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 500s 500s 500s 500s . 1037 patterns found (out of a total of 2888 sites). 500s 500s . 1378 sites without polymorphism (47.71%). 500s 500s 500s . Computing pairwise distances... 500s 500s . Building BioNJ tree... 500s 500s . This analysis requires at least 3 MB of memory space. 500s 500s 500s . Score of initial tree: -12664.54 500s 500s . Starting first round of SPRs... 501s 501s 1s | 1 | lnL= -12564.0 | depth= 0/ 40 | improvements= 0 | delta_lnL= 0.0/ 1000.0 501s 501s . Second round of optimization... 501s 501s 1s | 2 | lnL= -12583.6 | depth= 1/ 36 | improvements= 4 | delta_lnL= 0.0/ 1000.0 501s 501s . Third round of optimization... 501s 501s 1s | 3 | lnL= -12563.9 | depth= 1/ 20 | improvements= 3 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 501s 1s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 501s 501s . Final optimisation steps... 502s 502s 502s . Log likelihood of the current tree: -12563.118859055624852771871. 502s 502s . Calculating fast branch supports (using 'aBayes'). 502s 502s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 502s 502s . Time used 0h0m2s 502s 502s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 502s PASS 502s + echo PASS 502s autopkgtest [22:01:00]: test run-unit-test: -----------------------] 503s run-unit-test PASS 503s autopkgtest [22:01:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 503s autopkgtest [22:01:01]: @@@@@@@@@@@@@@@@@@@@ summary 503s run-unit-test PASS 508s nova [W] Skipping flock for amd64 508s Creating nova instance adt-plucky-amd64-phyml-20250315-211546-juju-7f2275-prod-proposed-migration-environment-20-f4196310-c375-497e-867a-b5f4b43f2761 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 508s nova [W] Timed out waiting for 51883157-9f5e-431d-81be-c40eef1dd0ad to get deleted.