0s autopkgtest [21:26:29]: starting date and time: 2025-03-15 21:26:29+0000 0s autopkgtest [21:26:29]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:26:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c6am1bx3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade progressivemauve --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-2@bos03-7.secgroup --name adt-plucky-amd64-progressivemauve-20250315-212629-juju-7f2275-prod-proposed-migration-environment-2-174f9af4-1b81-4b65-bd20-a9688461e567 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 51s autopkgtest [21:27:20]: testbed dpkg architecture: amd64 51s autopkgtest [21:27:20]: testbed apt version: 2.9.31ubuntu1 52s autopkgtest [21:27:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [21:27:21]: testbed release detected to be: None 53s autopkgtest [21:27:22]: updating testbed package index (apt update) 53s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 54s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 54s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 54s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 54s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 54s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 54s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 54s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 54s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 54s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 54s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 54s Fetched 1265 kB in 1s (1509 kB/s) 55s Reading package lists... 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s Calculating upgrade... 56s The following package was automatically installed and is no longer required: 56s libnl-genl-3-200 56s Use 'sudo apt autoremove' to remove it. 56s The following NEW packages will be installed: 56s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 56s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 56s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 56s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 56s The following packages will be upgraded: 56s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 56s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 56s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 56s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 56s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 56s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 56s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 56s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 56s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 56s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 56s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 56s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 56s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 56s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 56s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 56s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 56s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 56s parted pci.ids pciutils pinentry-curses python-apt-common python3 56s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 56s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 56s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 56s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 56s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 56s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 56s xz-utils 56s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 829 MB of archives. 56s After this operation, 325 MB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 57s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 57s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 57s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 57s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 57s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 57s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 57s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 57s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 57s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 57s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 57s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 57s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 57s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 57s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 57s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 57s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 57s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 57s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 57s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 57s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 57s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 57s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 57s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 57s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 57s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 57s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 57s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 57s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 57s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 57s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 57s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 57s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 57s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 57s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 57s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 57s 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] 58s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 58s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 58s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 58s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 58s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 58s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 58s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 58s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 58s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 58s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 58s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 58s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 58s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 58s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 58s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 58s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 58s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 58s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 58s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 58s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 58s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 58s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 58s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 58s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 58s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 58s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 58s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 58s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 58s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 58s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 58s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 58s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 58s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 58s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 58s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 58s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 58s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 58s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 58s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 58s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 58s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 58s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 58s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 58s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 58s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 58s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 58s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 58s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 58s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 58s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 58s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 58s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 58s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 58s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 58s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 58s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 58s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 58s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 58s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 58s 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] 59s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 59s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 59s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 59s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 59s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 59s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 59s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 95s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 95s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 95s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 95s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 95s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 95s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 95s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 95s 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] 102s 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] 104s 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] 116s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 116s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 116s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 116s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 116s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 116s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 117s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 117s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 117s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 117s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 117s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 117s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 117s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 117s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 117s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 117s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 117s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 117s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 117s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 118s Preconfiguring packages ... 118s Fetched 829 MB in 1min 1s (13.5 MB/s) 118s (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 ... 109140 files and directories currently installed.) 118s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 118s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 118s Setting up ncurses-bin (6.5+20250216-2) ... 118s (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 ... 109140 files and directories currently installed.) 118s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 118s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 118s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 118s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 119s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 119s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 119s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 119s Checking for services that may need to be restarted... 119s Checking init scripts... 119s Checking for services that may need to be restarted... 119s Checking init scripts... 119s Stopping some services possibly affected by the upgrade (will be restarted later): 119s cron: stopping...done. 119s 119s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 119s Setting up libc6:amd64 (2.41-1ubuntu1) ... 120s Checking for services that may need to be restarted... 120s Checking init scripts... 120s Restarting services possibly affected by the upgrade: 120s cron: restarting...done. 120s 120s Services restarted successfully. 120s (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.) 121s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 121s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 121s Setting up ncurses-base (6.5+20250216-2) ... 121s (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.) 122s Preparing to unpack .../libsystemd0_257.3-1ubuntu3_amd64.deb ... 122s Unpacking libsystemd0:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Setting up libsystemd0:amd64 (257.3-1ubuntu3) ... 122s (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 ... 109146 files and directories currently installed.) 122s Preparing to unpack .../libnss-systemd_257.3-1ubuntu3_amd64.deb ... 122s Unpacking libnss-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Preparing to unpack .../systemd-sysv_257.3-1ubuntu3_amd64.deb ... 122s Unpacking systemd-sysv (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Preparing to unpack .../systemd-resolved_257.3-1ubuntu3_amd64.deb ... 122s Unpacking systemd-resolved (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Preparing to unpack .../libpam-systemd_257.3-1ubuntu3_amd64.deb ... 122s Unpacking libpam-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Preparing to unpack .../libsystemd-shared_257.3-1ubuntu3_amd64.deb ... 122s Unpacking libsystemd-shared:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Setting up libsystemd-shared:amd64 (257.3-1ubuntu3) ... 122s (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 ... 109146 files and directories currently installed.) 122s Preparing to unpack .../systemd_257.3-1ubuntu3_amd64.deb ... 122s Unpacking systemd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Preparing to unpack .../systemd-timesyncd_257.3-1ubuntu3_amd64.deb ... 122s Unpacking systemd-timesyncd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Preparing to unpack .../systemd-cryptsetup_257.3-1ubuntu3_amd64.deb ... 122s Unpacking systemd-cryptsetup (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 122s Preparing to unpack .../udev_257.3-1ubuntu3_amd64.deb ... 122s Unpacking udev (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 123s Preparing to unpack .../libudev1_257.3-1ubuntu3_amd64.deb ... 123s Unpacking libudev1:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 123s Setting up libudev1:amd64 (257.3-1ubuntu3) ... 123s (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.) 123s Preparing to unpack .../libcap-ng0_0.8.5-4build1_amd64.deb ... 123s Unpacking libcap-ng0:amd64 (0.8.5-4build1) over (0.8.5-4) ... 123s Setting up libcap-ng0:amd64 (0.8.5-4build1) ... 123s (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 ... 109146 files and directories currently installed.) 123s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 123s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 123s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 123s (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 ... 109146 files and directories currently installed.) 123s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu6_amd64.deb ... 123s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu6) over (2.5.5-1ubuntu5) ... 123s Setting up libseccomp2:amd64 (2.5.5-1ubuntu6) ... 123s (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 ... 109146 files and directories currently installed.) 123s Preparing to unpack .../libselinux1_3.7-3ubuntu3_amd64.deb ... 123s Unpacking libselinux1:amd64 (3.7-3ubuntu3) over (3.7-3ubuntu2) ... 123s Setting up libselinux1:amd64 (3.7-3ubuntu3) ... 123s (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 ... 109146 files and directories currently installed.) 123s Preparing to unpack .../libapparmor1_4.1.0~beta5-0ubuntu8_amd64.deb ... 123s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu5) ... 123s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 123s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 124s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 124s (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.) 124s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 124s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 124s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 124s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 125s Setting up python3-minimal (3.13.2-2) ... 125s (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 ... 109146 files and directories currently installed.) 125s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ... 125s Unpacking python3 (3.13.2-2) over (3.13.2-1) ... 125s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ... 125s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ... 125s Preparing to unpack .../2-media-types_13.0.0_all.deb ... 125s Unpacking media-types (13.0.0) over (12.0.0) ... 125s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ... 125s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 125s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ... 125s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 125s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ... 125s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 125s Setting up libtinfo6:amd64 (6.5+20250216-2) ... 125s (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 ... 109146 files and directories currently installed.) 125s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 125s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 125s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 125s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 125s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 125s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 125s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 125s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 125s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 126s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 126s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 126s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 126s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 126s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 126s Selecting previously unselected package libdebuginfod-common. 126s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 126s Unpacking libdebuginfod-common (0.192-4) ... 126s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 126s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 126s Setting up libsemanage-common (3.7-2.1build1) ... 126s (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 ... 109155 files and directories currently installed.) 126s Preparing to unpack .../libsemanage2_3.7-2.1build1_amd64.deb ... 126s Unpacking libsemanage2:amd64 (3.7-2.1build1) over (3.7-2.1) ... 126s Setting up libsemanage2:amd64 (3.7-2.1build1) ... 126s (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.) 126s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ... 126s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ... 126s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ... 126s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ... 126s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ... 126s Unpacking libglib2.0-0t64:amd64 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.../23-parted_3.6-5_amd64.deb ... 129s Unpacking parted (3.6-5) over (3.6-4build1) ... 129s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 129s 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' 129s 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' 129s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 129s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 129s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 129s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 129s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 129s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 129s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 129s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 129s Unpacking strace 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(2.44-3ubuntu1) over (2.44-2ubuntu1) ... 129s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ... 129s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 129s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ... 129s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 129s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ... 129s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 129s Preparing to unpack .../39-hwdata_0.393-3_all.deb ... 129s Unpacking hwdata (0.393-3) over (0.392-1) ... 129s Selecting previously unselected package pnp.ids. 129s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ... 129s Unpacking pnp.ids (0.393-3) ... 129s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ... 129s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 129s Selecting previously unselected package bpftool. 129s Preparing to unpack .../42-bpftool_7.6.0+6.14.0-10.10_amd64.deb ... 129s Unpacking bpftool (7.6.0+6.14.0-10.10) ... 130s Preparing to unpack .../43-python3-markupsafe_2.1.5-1build4_amd64.deb ... 130s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ... 130s Preparing to unpack .../44-python3-jinja2_3.1.5-2ubuntu1_all.deb ... 130s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 130s Preparing to unpack .../45-cloud-init-base_25.1-0ubuntu3_all.deb ... 130s Unpacking cloud-init-base (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 130s Preparing to unpack .../46-libbrotli1_1.1.0-2build4_amd64.deb ... 130s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 130s Preparing to unpack .../47-curl_8.12.1-3ubuntu1_amd64.deb ... 130s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 130s Preparing to unpack .../48-libcurl4t64_8.12.1-3ubuntu1_amd64.deb ... 130s Unpacking libcurl4t64:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 130s Preparing to unpack .../49-exfatprogs_1.2.8-1_amd64.deb ... 130s Unpacking exfatprogs (1.2.8-1) over (1.2.7-3) ... 130s Preparing to unpack .../50-libcurl3t64-gnutls_8.12.1-3ubuntu1_amd64.deb ... 130s Unpacking libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 130s Preparing to unpack .../51-fwupd_2.0.6-4_amd64.deb ... 130s Unpacking fwupd (2.0.6-4) over (2.0.6-3) ... 131s Preparing to unpack .../52-libfwupd3_2.0.6-4_amd64.deb ... 131s Unpacking libfwupd3:amd64 (2.0.6-4) over (2.0.6-3) ... 131s Preparing to unpack .../53-libmm-glib0_1.23.4-0ubuntu3_amd64.deb ... 131s Unpacking libmm-glib0:amd64 (1.23.4-0ubuntu3) over (1.23.4-0ubuntu2) ... 131s Preparing to unpack .../54-htop_3.4.0-2_amd64.deb ... 131s Unpacking htop (3.4.0-2) over (3.3.0-5) ... 131s Preparing to unpack .../55-linux-firmware_20250310.git9e1370d3-0ubuntu1_amd64.deb ... 131s Unpacking linux-firmware (20250310.git9e1370d3-0ubuntu1) over (20250204.git0fd450ee-0ubuntu1) ... 134s Preparing to unpack .../56-initramfs-tools_0.146ubuntu1_all.deb ... 134s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 134s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ... 134s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 134s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 134s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 134s Selecting previously unselected package libdebuginfod1t64:amd64. 134s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ... 134s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 134s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ... 134s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 134s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 134s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 134s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ... 134s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ... 134s Selecting previously unselected package linux-modules-6.14.0-10-generic. 134s Preparing to unpack .../63-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 134s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 135s Selecting previously unselected package linux-image-6.14.0-10-generic. 135s Preparing to unpack .../64-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 135s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ... 135s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic. 135s Preparing to unpack .../65-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 135s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 136s Preparing to unpack .../66-linux-generic_6.14.0-10.10_amd64.deb ... 136s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 136s Preparing to unpack .../67-linux-image-generic_6.14.0-10.10_amd64.deb ... 136s 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(1.0.6-6) over (1.0.6-5) ... 140s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 140s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 140s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 140s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 140s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 140s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 141s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 141s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 141s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 141s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 141s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 141s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 141s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 141s Setting up media-types (13.0.0) ... 141s Installing new version of config file /etc/mime.types ... 141s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 141s Setting up ubuntu-kernel-accessories (1.549) ... 141s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 141s Setting up pci.ids (0.0~2025.03.09-1) ... 141s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 141s Setting up apt-utils (2.9.33) ... 141s Setting up libdebuginfod-common (0.192-4) ... 141s Setting up exfatprogs (1.2.8-1) ... 141s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 141s Setting up bpftool (7.6.0+6.14.0-10.10) ... 141s Setting up libestr0:amd64 (0.1.11-2) ... 141s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 141s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 141s Setting up dosfstools (4.2-1.2) ... 141s Setting up rsyslog (8.2412.0-2ubuntu2) ... 141s info: The user `syslog' is already a member of `adm'. 142s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 142s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 142s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 142s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 142s Setting up systemd (257.3-1ubuntu3) ... 142s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 142s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 142s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 143s Setting up libparted2t64:amd64 (3.6-5) ... 143s 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' 143s 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' 143s Setting up linux-headers-generic (6.14.0-10.10) ... 143s Setting up libjemalloc2:amd64 (5.3.0-3) ... 143s Setting up locales (2.41-1ubuntu1) ... 143s Installing new version of config file /etc/locale.alias ... 143s Generating locales (this might take a while)... 145s en_US.UTF-8... done 145s Generation complete. 145s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 145s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 145s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 145s Installing new version of config file /etc/apparmor.d/fusermount3 ... 145s Installing new version of config file /etc/apparmor.d/lsusb ... 145s Installing new version of config file /etc/apparmor.d/openvpn ... 146s Reloading AppArmor profiles 147s Setting up libftdi1-2:amd64 (1.5-8build1) ... 147s Setting up libglib2.0-data (2.84.0-1) ... 147s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 147s Setting up libncurses6:amd64 (6.5+20250216-2) ... 147s Setting up strace (6.13+ds-1ubuntu1) ... 147s Setting up xz-utils (5.6.4-1) ... 147s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 148s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 148s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 148s Setting up udev (257.3-1ubuntu3) ... 149s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 151s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 151s Setting up libpci3:amd64 (1:3.13.0-2) ... 151s Setting up whiptail (0.52.24-4ubuntu2) ... 151s Setting up python-apt-common (2.9.9build1) ... 151s Setting up pnp.ids (0.393-3) ... 151s Setting up libnl-3-200:amd64 (3.7.0-1) ... 151s Setting up python3.13-minimal (3.13.2-2) ... 151s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 151s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 151s Setting up libc-dev-bin (2.41-1ubuntu1) ... 151s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 151s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 151s Setting up rsync (3.4.1+ds1-3) ... 152s rsync.service is a disabled or a static unit not running, not starting it. 152s Setting up python3.13-gdbm (3.13.2-2) ... 152s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 152s Setting up systemd-resolved (257.3-1ubuntu3) ... 153s Setting up initramfs-tools-bin (0.146ubuntu1) ... 153s Setting up ncurses-term (6.5+20250216-2) ... 153s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 153s Setting up libpython3.13:amd64 (3.13.2-2) ... 153s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 153s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 153s Setting up systemd-sysv (257.3-1ubuntu3) ... 153s Setting up linux-headers-virtual (6.14.0-10.10) ... 153s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 153s Setting up python3.13 (3.13.2-2) ... 153s Setting up htop (3.4.0-2) ... 153s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 155s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 155s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 155s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 155s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 155s Setting up parted (3.6-5) ... 155s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 155s Setting up python3 (3.13.2-2) ... 156s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 156s Setting up python3-markupsafe (2.1.5-1build4) ... 156s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 158s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 158s Setting up hwdata (0.393-3) ... 158s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 158s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 158s No schema files found: doing nothing. 158s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 158s Setting up linux-perf (6.14.0-10.10) ... 158s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 158s Setting up pciutils (1:3.13.0-2) ... 158s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 158s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 158s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 158s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 158s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 158s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 158s Setting up curl (8.12.1-3ubuntu1) ... 158s Setting up linux-image-virtual (6.14.0-10.10) ... 158s Setting up initramfs-tools-core (0.146ubuntu1) ... 158s Setting up linux-tools-common (6.14.0-10.10) ... 158s Setting up python3-systemd (235-1build6) ... 158s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 158s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 158s Setting up linux-image-generic (6.14.0-10.10) ... 158s Setting up python3-dbus (1.3.2-5build5) ... 158s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 158s Setting up initramfs-tools (0.146ubuntu1) ... 158s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 158s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 158s update-initramfs: deferring update (trigger activated) 158s Setting up linux-generic (6.14.0-10.10) ... 158s Setting up ubuntu-minimal (1.549) ... 158s Setting up python3-apt (2.9.9build1) ... 159s Setting up python3-bcrypt (4.2.0-2.1build1) ... 159s Setting up python3-yaml (6.0.2-1build2) ... 159s Setting up libfwupd3:amd64 (2.0.6-4) ... 159s Setting up python3-lazr.uri (1.0.6-6) ... 159s Setting up binutils (2.44-3ubuntu1) ... 159s Setting up ubuntu-standard (1.549) ... 159s Setting up cloud-init-base (25.1-0ubuntu3) ... 160s Setting up linux-virtual (6.14.0-10.10) ... 160s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 160s Setting up python3-gi (3.50.0-4build1) ... 161s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 161s Setting up fwupd (2.0.6-4) ... 161s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 161s fwupd.service is a disabled or a static unit not running, not starting it. 161s Setting up cloud-init (25.1-0ubuntu3) ... 161s Processing triggers for man-db (2.13.0-1) ... 163s Processing triggers for dbus (1.16.2-1ubuntu1) ... 163s Processing triggers for shared-mime-info (2.4-5) ... 163s Warning: program compiled against libxml 212 using older 209 163s Processing triggers for libc-bin (2.41-1ubuntu1) ... 163s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 163s /etc/kernel/postinst.d/initramfs-tools: 163s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 163s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 174s /etc/kernel/postinst.d/zz-update-grub: 174s Sourcing file `/etc/default/grub' 174s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 174s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 174s Generating grub configuration file ... 174s Found linux image: /boot/vmlinuz-6.14.0-10-generic 174s Found initrd image: /boot/initrd.img-6.14.0-10-generic 174s Found linux image: /boot/vmlinuz-6.12.0-16-generic 174s Found initrd image: /boot/initrd.img-6.12.0-16-generic 174s Found linux image: /boot/vmlinuz-6.11.0-8-generic 174s Found initrd image: /boot/initrd.img-6.11.0-8-generic 174s Warning: os-prober will not be executed to detect other bootable partitions. 174s Systems on them will not be added to the GRUB boot configuration. 174s Check GRUB_DISABLE_OS_PROBER documentation entry. 174s Adding boot menu entry for UEFI Firmware Settings ... 174s done 174s Processing triggers for initramfs-tools (0.146ubuntu1) ... 174s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 174s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 186s Solving dependencies... 186s The following packages will be REMOVED: 186s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 186s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 186s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 186s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 186s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 186s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 186s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 186s linux-tools-6.12.0-16-generic* 187s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 187s After this operation, 545 MB disk space will be freed. 187s (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.) 187s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 187s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 187s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 187s Removing libpython3.12t64:amd64 (3.12.9-1) ... 187s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 187s Removing libnsl2:amd64 (1.3.0-3build3) ... 187s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 187s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 188s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 190s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 190s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 192s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 192s /etc/kernel/postrm.d/initramfs-tools: 192s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 192s /etc/kernel/postrm.d/zz-update-grub: 192s Sourcing file `/etc/default/grub' 192s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 193s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 193s Generating grub configuration file ... 193s Found linux image: /boot/vmlinuz-6.14.0-10-generic 193s Found initrd image: /boot/initrd.img-6.14.0-10-generic 193s Found linux image: /boot/vmlinuz-6.12.0-16-generic 193s Found initrd image: /boot/initrd.img-6.12.0-16-generic 193s Warning: os-prober will not be executed to detect other bootable partitions. 193s Systems on them will not be added to the GRUB boot configuration. 193s Check GRUB_DISABLE_OS_PROBER documentation entry. 193s Adding boot menu entry for UEFI Firmware Settings ... 193s done 193s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 193s W: Removing the running kernel 193s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 193s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 193s /etc/kernel/postrm.d/initramfs-tools: 193s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 193s /etc/kernel/postrm.d/zz-update-grub: 193s Sourcing file `/etc/default/grub' 193s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 193s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 193s Generating grub configuration file ... 194s Found linux image: /boot/vmlinuz-6.14.0-10-generic 194s Found initrd image: /boot/initrd.img-6.14.0-10-generic 194s Warning: os-prober will not be executed to detect other bootable partitions. 194s Systems on them will not be added to the GRUB boot configuration. 194s Check GRUB_DISABLE_OS_PROBER documentation entry. 194s Adding boot menu entry for UEFI Firmware Settings ... 194s done 194s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 194s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 196s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 196s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 196s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 196s Processing triggers for libc-bin (2.41-1ubuntu1) ... 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 ... 76972 files and directories currently installed.) 196s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 196s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 196s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 196s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 196s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 196s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 196s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 196s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 197s autopkgtest [21:29:46]: upgrading testbed (apt dist-upgrade and autopurge) 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 197s Starting 2 pkgProblemResolver with broken count: 0 197s Done 198s Entering ResolveByKeep 198s 198s Calculating upgrade... 198s The following packages will be upgraded: 198s libc-bin libc-dev-bin libc6 libc6-dev locales 198s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Need to get 10.5 MB of archives. 198s After this operation, 1024 B of additional disk space will be used. 198s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 199s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 199s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 199s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 199s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 200s Preconfiguring packages ... 200s Fetched 10.5 MB in 1s (8640 kB/s) 200s (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.) 200s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 200s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 200s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 200s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc6:amd64 (2.41-1ubuntu2) ... 201s (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.) 201s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 201s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc-bin (2.41-1ubuntu2) ... 201s (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.) 201s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 201s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up locales (2.41-1ubuntu2) ... 202s Generating locales (this might take a while)... 203s en_US.UTF-8... done 203s Generation complete. 203s Setting up libc-dev-bin (2.41-1ubuntu2) ... 203s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 203s Processing triggers for man-db (2.13.0-1) ... 204s Processing triggers for systemd (257.3-1ubuntu3) ... 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 206s Done 206s Solving dependencies... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 206s autopkgtest [21:29:55]: rebooting testbed after setup commands that affected boot 229s autopkgtest [21:30:18]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 232s autopkgtest [21:30:21]: @@@@@@@@@@@@@@@@@@@@ apt-source progressivemauve 235s Get:1 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (dsc) [2413 B] 235s Get:2 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (tar) [96.1 kB] 235s Get:3 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (diff) [18.1 kB] 235s gpgv: Signature made Mon Apr 8 15:02:20 2024 UTC 235s gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 235s gpgv: issuer "juliank@ubuntu.com" 235s gpgv: Can't check signature: No public key 235s dpkg-source: warning: cannot verify inline signature for ./progressivemauve_1.2.0+4713+dfsg-5build3.dsc: no acceptable signature found 235s autopkgtest [21:30:24]: testing package progressivemauve version 1.2.0+4713+dfsg-5build3 236s autopkgtest [21:30:25]: build not needed 236s autopkgtest [21:30:25]: test run-unit-test: preparing testbed 236s Reading package lists... 237s Building dependency tree... 237s Reading state information... 237s Starting pkgProblemResolver with broken count: 0 237s Starting 2 pkgProblemResolver with broken count: 0 237s Done 237s The following NEW packages will be installed: 237s libboost-filesystem1.83.0 libboost-iostreams1.83.0 237s libboost-program-options1.83.0 libgenome0 libgomp1 libmems1t64 libmuscle1 237s progressivemauve 238s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 238s Need to get 3050 kB of archives. 238s After this operation, 15.0 MB of additional disk space will be used. 238s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.1ubuntu2 [287 kB] 238s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.1ubuntu2 [260 kB] 238s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.1ubuntu2 [323 kB] 238s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgenome0 amd64 1.3.11+svn20110227.4616-6 [132 kB] 238s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 238s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmuscle1 amd64 3.7+4565-8 [276 kB] 238s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmems1t64 amd64 1.6.0+4725-11 [643 kB] 238s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 progressivemauve amd64 1.2.0+4713+dfsg-5build3 [981 kB] 239s Fetched 3050 kB in 1s (3912 kB/s) 239s Selecting previously unselected package libboost-filesystem1.83.0:amd64. 239s (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.) 239s Preparing to unpack .../0-libboost-filesystem1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 239s Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 239s Selecting previously unselected package libboost-iostreams1.83.0:amd64. 239s Preparing to unpack .../1-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 239s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 239s Selecting previously unselected package libboost-program-options1.83.0:amd64. 239s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_amd64.deb ... 239s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 239s Selecting previously unselected package libgenome0:amd64. 239s Preparing to unpack .../3-libgenome0_1.3.11+svn20110227.4616-6_amd64.deb ... 239s Unpacking libgenome0:amd64 (1.3.11+svn20110227.4616-6) ... 239s Selecting previously unselected package libgomp1:amd64. 239s Preparing to unpack .../4-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 239s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 239s Selecting previously unselected package libmuscle1. 239s Preparing to unpack .../5-libmuscle1_3.7+4565-8_amd64.deb ... 239s Unpacking libmuscle1 (3.7+4565-8) ... 239s Selecting previously unselected package libmems1t64:amd64. 239s Preparing to unpack .../6-libmems1t64_1.6.0+4725-11_amd64.deb ... 239s Unpacking libmems1t64:amd64 (1.6.0+4725-11) ... 239s Selecting previously unselected package progressivemauve. 239s Preparing to unpack .../7-progressivemauve_1.2.0+4713+dfsg-5build3_amd64.deb ... 239s Unpacking progressivemauve (1.2.0+4713+dfsg-5build3) ... 239s Setting up libboost-program-options1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 239s Setting up libgenome0:amd64 (1.3.11+svn20110227.4616-6) ... 239s Setting up libboost-filesystem1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 239s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 239s Setting up libboost-iostreams1.83.0:amd64 (1.83.0-4.1ubuntu2) ... 239s Setting up libmuscle1 (3.7+4565-8) ... 239s Setting up libmems1t64:amd64 (1.6.0+4725-11) ... 239s Setting up progressivemauve (1.2.0+4713+dfsg-5build3) ... 239s Processing triggers for man-db (2.13.0-1) ... 240s Processing triggers for libc-bin (2.41-1ubuntu2) ... 241s autopkgtest [21:30:30]: test run-unit-test: [----------------------- 241s Storing raw sequence at /tmp/rawseq1391.000 241s Sequence loaded successfully. 241s genome_1.gbk 2175 base pairs. 241s Storing raw sequence at /tmp/rawseq1391.001 241s Sequence loaded successfully. 241s genome_2.gbk 2199 base pairs. 241s Storing raw sequence at /tmp/rawseq1391.002 241s Sequence loaded successfully. 241s genome_3.gbk 2224 base pairs. 241s Using weight 9 mers for initial seeds 241s Creating sorted mer list 241s Create time was: 0 seconds. 241s Creating sorted mer list 241s Create time was: 0 seconds. 241s Creating sorted mer list 241s Create time was: 0 seconds. 241s 33%.. 241s 66%.. 241s 99%.. 241s done. 241s using default bp penalty: 77720 241s using default bp estimate min score: 233160 241s Starting with 152 multi-matches 241s Computing genome content distance matrix... 241s 241s 241s Genome conservation distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s Writing guide tree to /tmp/guide_tree1391.000 241s reading tree... 241s initializing alignment tree... 241s Constructing seed occurrence lists for repeat detection 241s Calculating pairwise breakpoint distances 241s Pair 0, 1 has 30 initial LCBs 241s Using scaled bp penalty: 22995.7 241s Pair (0,1) has 1 well-supported breakpoints 241s Pair 0, 2 has 29 initial LCBs 241s Using scaled bp penalty: 10025.6 241s Pair (0,2) has 1 well-supported breakpoints 241s Pair 1, 2 has 31 initial LCBs 241s Using scaled bp penalty: 13766.1 241s Pair (1,2) has 1 well-supported breakpoints 241s genome content distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s bp distance matrix: 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 241s Aligning... 241s Aligning node 2 to 3 via 1! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 44 tracking matches 241s There are 88 / 220 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 27 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 3%..7%.. 241s 11%..14%..18%.. 241s 22%..25%..29%.. 241s 33%..37%.. 241s 40%..44%..48%.. 241s 51%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 57862 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 0 new matches outside LCBs 241s 0,0 has an additional 5 matches 241s Restoring backed up alignment tree... 241s 1,0 has 5 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 35 tracking matches 241s There are 70 / 175 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 7 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 241s 14%.. 241s 28%..done 241s Arrived at 3 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 8 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 3 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 57862, new anchor score: 50704 241s propagating ancestral breakpoints 241s performing a gapped alignment 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s Aligning node 1 to 4 via 0! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 60 tracking matches 241s There are 239 / 300 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 89 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 1%..2%..3%..4%..5%..6%..7%..8%.. 241s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 241s 20%..21%..22%..23%..24%..25%..26%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 5 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 99201 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 3 new matches outside LCBs 241s 1,0 have 1 new matches outside LCBs 241s 0,0 has an additional 3 matches 241s 1,0 has an additional 1 matches 241s Restoring backed up alignment tree... 241s 0,2 has 3 pairwise matches 241s 1,2 has 1 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 38 tracking matches 241s There are 152 / 190 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 2 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 99201, new anchor score: 102789 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 0 new matches outside LCBs 241s 1,0 have 0 new matches outside LCBs 241s Restoring backed up alignment tree... 241s 0,2 has 0 pairwise matches 241s 1,2 has 0 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 38 tracking matches 241s There are 152 / 190 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 2 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 102789, new anchor score: 102789 241s propagating ancestral breakpoints 241s performing a gapped alignment 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s Performing final pass iterative refinement 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s root alignment has 1 superintervals 241s root alignment length: 2328 241s Organisms have 52.8% GC 241s Storing raw sequence at /tmp/rawseq1392.000 241s Sequence loaded successfully. 241s genome_1.gbk 2175 base pairs. 241s Storing raw sequence at /tmp/rawseq1392.001 241s Sequence loaded successfully. 241s genome_2.gbk 2199 base pairs. 241s Storing raw sequence at /tmp/rawseq1392.002 241s Sequence loaded successfully. 241s genome_3.gbk 2224 base pairs. 241s Using weight 9 mers for initial seeds 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s 33%.. 241s 66%.. 241s 99%.. 241s done. 241s using default bp penalty: 77720 241s using default bp estimate min score: 233160 241s Starting with 152 multi-matches 241s Computing genome content distance matrix... 241s 241s 241s Genome conservation distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s Writing guide tree to threeway.tree 241s reading tree... 241s initializing alignment tree... 241s Constructing seed occurrence lists for repeat detection 241s Calculating pairwise breakpoint distances 241s Pair 0, 1 has 30 initial LCBs 241s Using scaled bp penalty: 22995.7 241s Pair (0,1) has 1 well-supported breakpoints 241s Pair 0, 2 has 29 initial LCBs 241s Using scaled bp penalty: 10025.6 241s Pair (0,2) has 1 well-supported breakpoints 241s Pair 1, 2 has 31 initial LCBs 241s Using scaled bp penalty: 13766.1 241s Pair (1,2) has 1 well-supported breakpoints 241s genome content distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s bp distance matrix: 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 241s Aligning... 241s Aligning node 2 to 3 via 1! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 44 tracking matches 241s There are 88 / 220 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 27 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 3%..7%.. 241s 11%..14%..18%.. 241s 22%..25%..29%.. 241s 33%..37%.. 241s 40%..44%..48%.. 241s 51%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 57862 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 0 new matches outside LCBs 241s 0,0 has an additional 5 matches 241s Restoring backed up alignment tree... 241s 1,0 has 5 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 35 tracking matches 241s There are 70 / 175 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 7 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 241s 14%.. 241s 28%..done 241s Arrived at 3 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 8 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 3 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 57862, new anchor score: 50704 241s propagating ancestral breakpoints 241s performing a gapped alignment 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s Aligning node 1 to 4 via 0! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 60 tracking matches 241s There are 239 / 300 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 89 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 1%..2%..3%..4%..5%..6%..7%..8%.. 241s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 241s 20%..21%..22%..23%..24%..25%..26%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 5 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 99201 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 3 new matches outside LCBs 241s 1,0 have 1 new matches outside LCBs 241s 0,0 has an additional 3 matches 241s 1,0 has an additional 1 matches 241s Restoring backed up alignment tree... 241s 0,2 has 3 pairwise matches 241s 1,2 has 1 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 38 tracking matches 241s There are 152 / 190 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 2 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 99201, new anchor score: 102789 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 0 new matches outside LCBs 241s 1,0 have 0 new matches outside LCBs 241s Restoring backed up alignment tree... 241s 0,2 has 0 pairwise matches 241s 1,2 has 0 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 38 tracking matches 241s There are 152 / 190 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 2 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 102789, new anchor score: 102789 241s propagating ancestral breakpoints 241s performing a gapped alignment 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s Performing final pass iterative refinement 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s root alignment has 1 superintervals 241s root alignment length: 2328 241s Organisms have 52.8% GC 241s Storing raw sequence at /tmp/rawseq1393.000 241s Sequence loaded successfully. 241s genome_1.gbk 2175 base pairs. 241s Storing raw sequence at /tmp/rawseq1393.001 241s Sequence loaded successfully. 241s genome_2.gbk 2199 base pairs. 241s Storing raw sequence at /tmp/rawseq1393.002 241s Sequence loaded successfully. 241s genome_3.gbk 2224 base pairs. 241s Using weight 9 mers for initial seeds 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s 33%.. 241s 66%.. 241s 99%.. 241s done. 241s using default bp penalty: 77720 241s using default bp estimate min score: 233160 241s Starting with 152 multi-matches 241s Computing genome content distance matrix... 241s 241s 241s Genome conservation distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s Writing guide tree to /tmp/guide_tree1393.000 241s reading tree... 241s initializing alignment tree... 241s Constructing seed occurrence lists for repeat detection 241s Calculating pairwise breakpoint distances 241s Pair 0, 1 has 30 initial LCBs 241s Using scaled bp penalty: 22995.7 241s Pair (0,1) has 1 well-supported breakpoints 241s Pair 0, 2 has 29 initial LCBs 241s Using scaled bp penalty: 10025.6 241s Pair (0,2) has 1 well-supported breakpoints 241s Pair 1, 2 has 31 initial LCBs 241s Using scaled bp penalty: 13766.1 241s Pair (1,2) has 1 well-supported breakpoints 241s genome content distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s bp distance matrix: 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 241s Aligning... 241s Aligning node 2 to 3 via 1! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 44 tracking matches 241s There are 88 / 220 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 27 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 3%..7%.. 241s 11%..14%..18%.. 241s 22%..25%..29%.. 241s 33%..37%.. 241s 40%..44%..48%.. 241s 51%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 57862 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 0 new matches outside LCBs 241s 0,0 has an additional 5 matches 241s Restoring backed up alignment tree... 241s 1,0 has 5 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 35 tracking matches 241s There are 70 / 175 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 7 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 241s 14%.. 241s 28%..done 241s Arrived at 3 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 8 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 3 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 57862, new anchor score: 50704 241s propagating ancestral breakpoints 241s performing a gapped alignment 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s Aligning node 1 to 4 via 0! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 60 tracking matches 241s There are 239 / 300 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 89 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 1%..2%..3%..4%..5%..6%..7%..8%.. 241s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 241s 20%..21%..22%..23%..24%..25%..26%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 5 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 99201 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 3 new matches outside LCBs 241s 1,0 have 1 new matches outside LCBs 241s 0,0 has an additional 3 matches 241s 1,0 has an additional 1 matches 241s Restoring backed up alignment tree... 241s 0,2 has 3 pairwise matches 241s 1,2 has 1 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 38 tracking matches 241s There are 152 / 190 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 2 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 99201, new anchor score: 102789 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 0 new matches outside LCBs 241s 1,0 have 0 new matches outside LCBs 241s Restoring backed up alignment tree... 241s 0,2 has 0 pairwise matches 241s 1,2 has 0 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 38 tracking matches 241s There are 152 / 190 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 2 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 102789, new anchor score: 102789 241s propagating ancestral breakpoints 241s performing a gapped alignment 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s Performing final pass iterative refinement 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s root alignment has 1 superintervals 241s root alignment length: 2328 241s Sequence loaded successfully. 241s genome_1.gbk 2175 base pairs. 241s Sequence loaded successfully. 241s genome_2.gbk 2199 base pairs. 241s Sequence loaded successfully. 241s genome_3.gbk 2224 base pairs. 241s Organisms have 52.8% GC 241s Storing raw sequence at /tmp/rawseq1395.000 241s Sequence loaded successfully. 241s genome_1.gbk 2175 base pairs. 241s Storing raw sequence at /tmp/rawseq1395.001 241s Sequence loaded successfully. 241s genome_2.gbk 2199 base pairs. 241s Storing raw sequence at /tmp/rawseq1395.002 241s Sequence loaded successfully. 241s genome_3.gbk 2224 base pairs. 241s Using weight 9 mers for initial seeds 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s 33%.. 241s 66%.. 241s 99%.. 241s done. 241s Storing raw sequence at /tmp/rawseq1396.000 241s Sequence loaded successfully. 241s genome_1.gbk 2175 base pairs. 241s Storing raw sequence at /tmp/rawseq1396.001 241s Sequence loaded successfully. 241s genome_2.gbk 2199 base pairs. 241s Storing raw sequence at /tmp/rawseq1396.002 241s Sequence loaded successfully. 241s genome_3.gbk 2224 base pairs. 241s Using weight 9 mers for initial seeds 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s Sorted mer list loaded successfully 241s using default bp penalty: 77720 241s using default bp estimate min score: 233160 241s Starting with 152 multi-matches 241s Computing genome content distance matrix... 241s 241s 241s Genome conservation distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s Writing guide tree to /tmp/guide_tree1396.000 241s reading tree... 241s initializing alignment tree... 241s Constructing seed occurrence lists for repeat detection 241s Calculating pairwise breakpoint distances 241s Pair 0, 1 has 30 initial LCBs 241s Using scaled bp penalty: 22995.7 241s Pair (0,1) has 1 well-supported breakpoints 241s Pair 0, 2 has 29 initial LCBs 241s Using scaled bp penalty: 10025.6 241s Pair (0,2) has 1 well-supported breakpoints 241s Pair 1, 2 has 31 initial LCBs 241s Using scaled bp penalty: 13766.1 241s Pair (1,2) has 1 well-supported breakpoints 241s genome content distance matrix: 241s 0 0.4396 0.54463 241s 0.4396 0 0.507065 241s 0.54463 0.507065 0 241s 241s bp distance matrix: 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 0.9 0.9 0.9 241s 241s Aligning... 241s Aligning node 2 to 3 via 1! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 44 tracking matches 241s There are 88 / 220 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 27 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 3%..7%.. 241s 11%..14%..18%.. 241s 22%..25%..29%.. 241s 33%..37%.. 241s 40%..44%..48%.. 241s 51%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 3 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 57862 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 241s 0,0 have 0 new matches outside LCBs 241s 0,0 has an additional 5 matches 241s Restoring backed up alignment tree... 241s 1,0 has 5 pairwise matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 35 tracking matches 241s There are 70 / 175 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 7 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.4396 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 241s 14%.. 241s 28%..done 241s Arrived at 3 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 8 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(2) has 1 intervals 241s descendant 1(3) has 1 intervals 241s propagateDescendantBreakpoints yields 3 intervals 241s Creating ancestral ordering 241s Previous anchoring score: 57862, new anchor score: 50704 241s propagating ancestral breakpoints 241s performing a gapped alignment 241s 241s 0%.. 241s 100%..Fix left ends 241s 241s done. 241s Aligning node 1 to 4 via 0! 241s get ancestral matches 241s Performing Sum-of-pairs Greedy Breakpoint Elimination 241s construct LCB tracking matches 241s There are 60 tracking matches 241s There are 239 / 300 components used 241s init tracking match LCB tracking 241s pairwise score tracking matches 241s get pairwise LCBs 241s there are 89 pairwise LCBs 241s scaling bp penalty by conservation weight: 241s 0.54463 241s 0.507065 241s 241s 241s scaling bp penalty by bp weight: 241s 0.9 241s 0.9 241s 241s Greedy BPE 241s Scoring with scaled breakpoint penalty: 4000 241s 1%..2%..3%..4%..5%..6%..7%..8%.. 241s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 241s 20%..21%..22%..23%..24%..25%..26%..done 241s Arrived at 1 intervals 241s Adding unaligned intervals 241s addUnalignedIntervals yields 5 intervals 241s Merging unaligned intervals 241s Marbling gaps 241s Propagating descendant breakpoints 241s descendant 0(1) has 1 intervals 241s descendant 1(4) has 1 intervals 241s propagateDescendantBreakpoints yields 1 intervals 241s Creating ancestral ordering 241s Previous anchoring score: -1.79769e+308, new anchor score: 99201 241s Backing up alignment tree... 241s propagating ancestral breakpoints 241s recursive anchor search 242s 0,0 have 3 new matches outside LCBs 242s 1,0 have 1 new matches outside LCBs 242s 0,0 has an additional 3 matches 242s 1,0 has an additional 1 matches 242s Restoring backed up alignment tree... 242s 0,2 has 3 pairwise matches 242s 1,2 has 1 pairwise matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 38 tracking matches 242s There are 152 / 190 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 2 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.54463 242s 0.507065 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 4000 242s done 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(4) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Previous anchoring score: 99201, new anchor score: 102789 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 0 new matches outside LCBs 242s 1,0 have 0 new matches outside LCBs 242s Restoring backed up alignment tree... 242s 0,2 has 0 pairwise matches 242s 1,2 has 0 pairwise matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 38 tracking matches 242s There are 152 / 190 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 2 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.54463 242s 0.507065 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 4000 242s done 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(4) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Previous anchoring score: 102789, new anchor score: 102789 242s propagating ancestral breakpoints 242s performing a gapped alignment 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s Performing final pass iterative refinement 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s root alignment has 1 superintervals 242s root alignment length: 2328 242s Organisms have 52.8% GC 242s Storing raw sequence at /tmp/rawseq1397.000 242s Sequence loaded successfully. 242s genome_1.gbk 2175 base pairs. 242s Storing raw sequence at /tmp/rawseq1397.001 242s Sequence loaded successfully. 242s genome_2.gbk 2199 base pairs. 242s Using weight 9 mers for initial seeds 242s Sorted mer list loaded successfully 242s Sorted mer list loaded successfully 242s 49%.. 242s 99%.. 242s Exception FileNotOpened thrown from 242s Unknown() in gnFileSource.cpp 67 242s Called by Unknown() 242s done. 242s using default bp penalty: 50000 242s using default bp estimate min score: 232989 242s Starting with 55 multi-matches 242s Computing genome content distance matrix... 242s 242s 242s Genome conservation distance matrix: 242s 0 0.4396 242s 0.4396 0 242s 242s Writing guide tree to /tmp/guide_tree1397.000 242s reading tree... 242s initializing alignment tree... 242s Constructing seed occurrence lists for repeat detection 242s Calculating pairwise breakpoint distances 242s Pair 0, 1 has 30 initial LCBs 242s Using scaled bp penalty: 22978.9 242s Pair (0,1) has 1 well-supported breakpoints 242s genome content distance matrix: 242s 0 0.4396 242s 0.4396 0 242s 242s bp distance matrix: 242s 0.9 0.9 242s 0.9 0.9 242s 242s Aligning... 242s Aligning node 1 to 2 via 0! 242s get ancestral matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 44 tracking matches 242s There are 88 / 132 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 27 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.4396 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 4000 242s 3%..7%.. 242s 11%..14%..18%.. 242s 22%..25%..29%.. 242s 33%..37%.. 242s 40%..44%..48%.. 242s 51%..done 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(2) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Previous anchoring score: -1.79769e+308, new anchor score: 57862 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 0 new matches outside LCBs 242s 0,0 has an additional 5 matches 242s Restoring backed up alignment tree... 242s 1,0 has 5 pairwise matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 35 tracking matches 242s There are 70 / 105 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 7 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.4396 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 4000 242s 242s 14%.. 242s 28%..done 242s Arrived at 3 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 8 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(2) has 1 intervals 242s propagateDescendantBreakpoints yields 3 intervals 242s Creating ancestral ordering 242s Previous anchoring score: 57862, new anchor score: 50704 242s propagating ancestral breakpoints 242s performing a gapped alignment 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s Performing final pass iterative refinement 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s root alignment has 1 superintervals 242s root alignment length: 2249 242s Organisms have 53.2% GC 242s Storing raw sequence at /tmp/rawseq1398.000 242s Sequence loaded successfully. 242s genome_1.gbk 2175 base pairs. 242s Storing raw sequence at /tmp/rawseq1398.001 242s Sequence loaded successfully. 242s genome_2.gbk 2199 base pairs. 242s Storing raw sequence at /tmp/rawseq1398.002 242s Sequence loaded successfully. 242s genome_3.gbk 2224 base pairs. 242s Using weight 9 mers for initial seeds 242s Sorted mer list loaded successfully 242s Sorted mer list loaded successfully 242s Sorted mer list loaded successfully 242s 33%.. 242s 66%.. 242s 99%.. 242s done. 242s using default bp penalty: 77720 242s using default bp estimate min score: 233160 242s Starting with 152 multi-matches 242s Computing genome content distance matrix... 242s 242s 242s Genome conservation distance matrix: 242s 0 0.4396 0.54463 242s 0.4396 0 0.507065 242s 0.54463 0.507065 0 242s 242s Writing guide tree to /tmp/guide_tree1398.000 242s reading tree... 242s initializing alignment tree... 242s Constructing seed occurrence lists for repeat detection 242s Calculating pairwise breakpoint distances 242s Pair 0, 1 has 30 initial LCBs 242s Using scaled bp penalty: 22995.7 242s Pair (0,1) has 1 well-supported breakpoints 242s Pair 0, 2 has 29 initial LCBs 242s Using scaled bp penalty: 10025.6 242s Pair (0,2) has 1 well-supported breakpoints 242s Pair 1, 2 has 31 initial LCBs 242s Using scaled bp penalty: 13766.1 242s Pair (1,2) has 1 well-supported breakpoints 242s genome content distance matrix: 242s 0 0.4396 0.54463 242s 0.4396 0 0.507065 242s 0.54463 0.507065 0 242s 242s bp distance matrix: 242s 0.9 0.9 0.9 242s 0.9 0.9 0.9 242s 0.9 0.9 0.9 242s 242s Aligning... 242s Aligning node 2 to 3 via 1! 242s get ancestral matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 44 tracking matches 242s There are 88 / 220 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 27 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.4396 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 5000 242s 3%..7%.. 242s 11%..14%..18%.. 242s 22%..25%..29%.. 242s 33%..37%.. 242s 40%..44%..48%.. 242s 51%..done 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(2) has 1 intervals 242s descendant 1(3) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Previous anchoring score: -1.79769e+308, new anchor score: 57862 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 0 new matches outside LCBs 242s 0,0 has an additional 5 matches 242s Restoring backed up alignment tree... 242s 1,0 has 5 pairwise matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 35 tracking matches 242s There are 70 / 175 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 7 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.4396 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 5000 242s 242s 14%.. 242s 28%..done 242s Arrived at 3 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 8 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(2) has 1 intervals 242s descendant 1(3) has 1 intervals 242s propagateDescendantBreakpoints yields 3 intervals 242s Creating ancestral ordering 242s Previous anchoring score: 57862, new anchor score: 48704 242s propagating ancestral breakpoints 242s performing a gapped alignment 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s Aligning node 1 to 4 via 0! 242s get ancestral matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 60 tracking matches 242s There are 239 / 300 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 89 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.54463 242s 0.507065 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 5000 242s 1%..2%..3%..4%..5%..6%..7%..8%.. 242s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 242s 20%..21%..22%..23%..24%..25%..26%..done 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 5 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(4) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Previous anchoring score: -1.79769e+308, new anchor score: 99201 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 3 new matches outside LCBs 242s 1,0 have 1 new matches outside LCBs 242s 0,0 has an additional 3 matches 242s 1,0 has an additional 1 matches 242s Restoring backed up alignment tree... 242s 0,2 has 3 pairwise matches 242s 1,2 has 1 pairwise matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 38 tracking matches 242s There are 152 / 190 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 2 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.54463 242s 0.507065 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 5000 242s done 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(4) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Previous anchoring score: 99201, new anchor score: 102789 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 0 new matches outside LCBs 242s 1,0 have 0 new matches outside LCBs 242s Restoring backed up alignment tree... 242s 0,2 has 0 pairwise matches 242s 1,2 has 0 pairwise matches 242s Performing Sum-of-pairs Greedy Breakpoint Elimination 242s construct LCB tracking matches 242s There are 38 tracking matches 242s There are 152 / 190 components used 242s init tracking match LCB tracking 242s pairwise score tracking matches 242s get pairwise LCBs 242s there are 2 pairwise LCBs 242s scaling bp penalty by conservation weight: 242s 0.54463 242s 0.507065 242s 242s 242s scaling bp penalty by bp weight: 242s 0.9 242s 0.9 242s 242s Greedy BPE 242s Scoring with scaled breakpoint penalty: 5000 242s done 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(4) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Previous anchoring score: 102789, new anchor score: 102789 242s propagating ancestral breakpoints 242s performing a gapped alignment 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s Performing final pass iterative refinement 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s root alignment has 1 superintervals 242s root alignment length: 2328 242s Organisms have 52.8% GC 242s Sequence loaded successfully. 242s all_virii.fasta 2175 base pairs. 242s Sequence loaded successfully. 242s all_virii.fasta 2199 base pairs. 242s Sequence loaded successfully. 242s all_virii.fasta 2224 base pairs. 242s Using 9-mers for initial seeds 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s 242s Searching with seed pattern 11100100100100111 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s 32%.. 242s 65%.. 242s 99%.. 242s 242s Searching with seed pattern 111001010100111 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s 33%.. 242s 66%.. 242s 99%.. 242s 242s Searching with seed pattern 111010010010111 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s Creating sorted mer list 242s Create time was: 0 seconds. 242s 32%.. 242s 65%.. 242s 99%.. 242s done 242s using default bp penalty: 77720 242s using default bp estimate min score: 233160 242s 242s Assuming collinear genomes... 242s Starting with 291 multi-matches 242s Computing genome content distance matrix... 242s 242s 242s Genome conservation distance matrix: 242s 0 0.220697 0.310296 242s 0.220697 0 0.291861 242s 0.310296 0.291861 0 242s 242s Writing guide tree to /tmp/guide_tree1399.000 242s reading tree... 242s initializing alignment tree... 242s Aligning... 242s Aligning node 3 to 4 via 1! 242s get ancestral matches 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(3) has 1 intervals 242s descendant 1(4) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Prev alignment len: 18446744073709551615, new alignment length: 3832 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 0 new matches outside LCBs 242s Restoring backed up alignment tree... 242s 1,0 has 0 pairwise matches 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(3) has 1 intervals 242s descendant 1(4) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Prev alignment len: 3832, new alignment length: 3832 242s propagating ancestral breakpoints 242s performing a gapped alignment 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s Aligning node 1 to 2 via 0! 242s get ancestral matches 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 5 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(2) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Prev alignment len: 18446744073709551615, new alignment length: 4373 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 14 new matches outside LCBs 242s 1,0 have 17 new matches outside LCBs 242s 0,0 has an additional 38 matches 242s 1,0 has an additional 41 matches 242s Restoring backed up alignment tree... 242s 0,2 has 38 pairwise matches 242s 1,2 has 41 pairwise matches 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 3 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(2) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Prev alignment len: 4373, new alignment length: 3825 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 2 new matches outside LCBs 242s 1,0 have 1 new matches outside LCBs 242s 0,0 has an additional 2 matches 242s 1,0 has an additional 1 matches 242s Restoring backed up alignment tree... 242s 0,2 has 2 pairwise matches 242s 1,2 has 1 pairwise matches 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 1 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(2) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Prev alignment len: 3825, new alignment length: 3802 242s Backing up alignment tree... 242s propagating ancestral breakpoints 242s recursive anchor search 242s 0,0 have 0 new matches outside LCBs 242s 1,0 have 0 new matches outside LCBs 242s Restoring backed up alignment tree... 242s 0,2 has 0 pairwise matches 242s 1,2 has 0 pairwise matches 242s Arrived at 1 intervals 242s Adding unaligned intervals 242s addUnalignedIntervals yields 1 intervals 242s Merging unaligned intervals 242s Marbling gaps 242s Propagating descendant breakpoints 242s descendant 0(1) has 1 intervals 242s descendant 1(2) has 1 intervals 242s propagateDescendantBreakpoints yields 1 intervals 242s Creating ancestral ordering 242s Prev alignment len: 3802, new alignment length: 3802 242s propagating ancestral breakpoints 242s performing a gapped alignment 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s Performing final pass iterative refinement 242s 242s 0%.. 242s 100%..Fix left ends 242s 242s done. 242s root alignment has 1 superintervals 242s root alignment length: 2328 242s autopkgtest [21:30:31]: test run-unit-test: -----------------------] 243s autopkgtest [21:30:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 243s run-unit-test PASS 243s autopkgtest [21:30:32]: @@@@@@@@@@@@@@@@@@@@ summary 243s run-unit-test PASS 261s nova [W] Skipping flock for amd64 261s Creating nova instance adt-plucky-amd64-progressivemauve-20250315-212629-juju-7f2275-prod-proposed-migration-environment-2-174f9af4-1b81-4b65-bd20-a9688461e567 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 261s nova [W] Timed out waiting for c62137b2-3036-4918-9b70-7f4f8a7de152 to get deleted.