0s autopkgtest [13:28:54]: starting date and time: 2025-02-19 13:28:54+0000 0s autopkgtest [13:28:54]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:28:54]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gor4bjv1/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:sphinx --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- lxd -r lxd-armhf-10.145.243.53 lxd-armhf-10.145.243.53:autopkgtest/ubuntu/plucky/armhf 52s autopkgtest [13:29:46]: testbed dpkg architecture: armhf 54s autopkgtest [13:29:48]: testbed apt version: 2.9.14ubuntu1 58s autopkgtest [13:29:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [13:29:55]: testbed release detected to be: None 70s autopkgtest [13:30:04]: updating testbed package index (apt update) 72s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [249 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [110 kB] 73s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [110 kB] 73s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 73s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [744 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 73s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [101 kB] 73s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Components [4980 B] 73s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [760 B] 73s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Components [216 B] 73s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [649 kB] 73s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Components [292 kB] 73s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3116 B] 73s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Components [1072 B] 73s Get:17 http://ftpmaster.internal/ubuntu plucky/restricted Sources [16.3 kB] 73s Get:18 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 73s Get:19 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 75s Get:20 http://ftpmaster.internal/ubuntu plucky/main Sources [1386 kB] 75s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1369 kB] 75s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf Components [401 kB] 75s Get:23 http://ftpmaster.internal/ubuntu plucky/restricted armhf Packages [2900 B] 75s Get:24 http://ftpmaster.internal/ubuntu plucky/restricted armhf Components [196 B] 75s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.5 MB] 76s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf Components [3939 kB] 76s Get:27 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [173 kB] 76s Get:28 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Components [39.8 kB] 76s Get:29 http://ftpmaster.internal/ubuntu plucky-updates/main armhf Components [208 B] 76s Get:30 http://ftpmaster.internal/ubuntu plucky-updates/restricted armhf Components [212 B] 76s Get:31 http://ftpmaster.internal/ubuntu plucky-updates/universe armhf Components [212 B] 76s Get:32 http://ftpmaster.internal/ubuntu plucky-updates/multiverse armhf Components [212 B] 76s Get:33 http://ftpmaster.internal/ubuntu plucky-security/main armhf Components [204 B] 76s Get:34 http://ftpmaster.internal/ubuntu plucky-security/restricted armhf Components [212 B] 76s Get:35 http://ftpmaster.internal/ubuntu plucky-security/universe armhf Components [208 B] 76s Get:36 http://ftpmaster.internal/ubuntu plucky-security/multiverse armhf Components [212 B] 83s Fetched 46.6 MB in 8s (5675 kB/s) 84s Reading package lists... 91s autopkgtest [13:30:25]: upgrading testbed (apt dist-upgrade and autopurge) 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 94s Starting 2 pkgProblemResolver with broken count: 0 94s Done 95s Entering ResolveByKeep 95s 96s The following packages were automatically installed and are no longer required: 96s libassuan0 libicu74 libnsl2 libpython3.12-minimal libpython3.12-stdlib 96s libunwind8 linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic python3.12 96s python3.12-minimal 96s Use 'apt autoremove' to remove them. 96s The following NEW packages will be installed: 96s gcc-15-base libapt-pkg7.0 libicu76 libpython3.13-minimal 96s libpython3.13-stdlib linux-headers-6.12.0-15 linux-headers-6.12.0-15-generic 96s login.defs openssl-provider-legacy python3-bcrypt python3.13 96s python3.13-minimal 96s The following packages will be upgraded: 96s apparmor apport apport-core-dump-handler appstream apt apt-utils base-passwd 96s bash bash-completion bind9-dnsutils bind9-host bind9-libs binutils 96s binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils 96s btrfs-progs busybox-initramfs busybox-static ca-certificates cloud-init 96s cloud-init-base console-setup console-setup-linux coreutils cron 96s cron-daemon-common curl dash dbus dbus-bin dbus-daemon 96s dbus-session-bus-common dbus-system-bus-common dbus-user-session dhcpcd-base 96s diffutils dirmngr distro-info dmsetup dpkg dpkg-dev dracut-install e2fsprogs 96s e2fsprogs-l10n ed eject ethtool fdisk fwupd gcc-14-base gettext-base 96s gir1.2-girepository-2.0 gir1.2-glib-2.0 gir1.2-packagekitglib-1.0 gnupg 96s gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv 96s groff-base gzip htop ibverbs-providers init init-system-helpers 96s initramfs-tools initramfs-tools-bin initramfs-tools-core iproute2 iptables 96s iputils-ping iputils-tracepath keyboard-configuration keyboxd kpartx 96s krb5-locales libapparmor1 libappstream5 libapt-pkg6.0t64 libarchive13t64 96s libatomic1 libbinutils libblkid1 libblockdev-crypto3 libblockdev-fs3 96s libblockdev-loop3 libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 96s libblockdev-swap3 libblockdev-utils3 libblockdev3 libbpf1 libc-bin libc6 96s libcap-ng0 libcom-err2 libcrypt1 libctf-nobfd0 libctf0 libcurl3t64-gnutls 96s libcurl4t64 libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl 96s libedit2 libext2fs2t64 libfdisk1 libffi8 libfribidi0 libftdi1-2 libfwupd3 96s libgcc-s1 libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-bin 96s libglib2.0-data libgnutls30t64 libgpg-error-l10n libgpg-error0 libgpgme11t64 96s libgssapi-krb5-2 libgstreamer1.0-0 libgudev-1.0-0 libhogweed6t64 libibverbs1 96s libicu74 libip4tc2 libip6tc2 libjson-glib-1.0-0 libjson-glib-1.0-common 96s libk5crypto3 libkrb5-3 libkrb5support0 libldap-common libldap2 liblsof0 96s liblz4-1 libmaxminddb0 libmount1 libncurses6 libncursesw6 libnetplan1 96s libnettle8t64 libnewt0.52 libnftables1 libnftnl11 libnpth0t64 libnspr4 96s libnss-systemd libnss3 libnvme1t64 libp11-kit0 libpackagekit-glib2-18 96s libpam-systemd libpcap0.8t64 libpng16-16t64 libpolkit-agent-1-0 96s libpolkit-gobject-1-0 libprotobuf-c1 libpython3-stdlib libpython3.12-minimal 96s libpython3.12-stdlib libqmi-glib5 libqmi-proxy libreadline8t64 libsasl2-2 96s libsasl2-modules libsasl2-modules-db libselinux1 libsemanage-common 96s libsemanage2 libsframe1 libsmartcols1 libss2 libssl3t64 libstdc++6 96s libsystemd-shared libsystemd0 libtasn1-6 libtinfo6 libtraceevent1 96s libtraceevent1-plugin libudev1 libudisks2-0 libunistring5 liburcu8t64 96s libusb-1.0-0 libuuid1 libvolume-key1 libwrap0 libxdmcp6 libxkbcommon0 96s libxml2 libxtables12 libxxhash0 libyaml-0-2 libzstd1 linux-headers-generic 96s locales login logsave lshw lsof make mawk mount multipath-tools nano 96s ncurses-base ncurses-bin ncurses-term netcat-openbsd netplan-generator 96s netplan.io nftables openssl packagekit packagekit-tools passwd pci.ids 96s pinentry-curses polkitd pollinate powermgmt-base psmisc publicsuffix 96s python-apt-common python-babel-localedata python3 python3-apport python3-apt 96s python3-attr python3-babel python3-certifi python3-chardet 96s python3-cryptography python3-distro-info python3-gdbm python3-gi 96s python3-idna python3-jinja2 python3-json-pointer python3-jsonpatch 96s python3-jsonschema python3-jwt python3-launchpadlib python3-lazr.uri 96s python3-minimal python3-more-itertools python3-netplan python3-newt 96s python3-oauthlib python3-openssl python3-pkg-resources 96s python3-problem-report python3-pygments python3-referencing python3-rich 96s python3-setuptools python3-software-properties python3-urllib3 96s python3-wadllib python3.12 python3.12-gdbm python3.12-minimal 96s python3.13-gdbm readline-common rsync rsyslog software-properties-common 96s systemd systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 96s sysvinit-utils tar tzdata ubuntu-minimal ubuntu-standard ucf udev udisks2 96s ufw unattended-upgrades usb.ids util-linux uuid-runtime whiptail xauth 96s xfsprogs zstd 97s 300 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 135 MB of archives. 97s After this operation, 198 MB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf bash armhf 5.2.37-1ubuntu1 [677 kB] 97s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf bsdutils armhf 1:2.40.2-14ubuntu1 [110 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf coreutils armhf 9.5-1ubuntu1 [1275 kB] 97s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf dash armhf 0.5.12-12ubuntu1 [87.4 kB] 97s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf diffutils armhf 1:3.10-2 [172 kB] 97s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-15-base armhf 15-20250213-1ubuntu1 [53.2 kB] 97s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 15-20250213-1ubuntu1 [40.6 kB] 97s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libc6 armhf 2.40-4ubuntu1 [2866 kB] 98s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libxxhash0 armhf 0.8.3-2 [30.8 kB] 98s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf liblz4-1 armhf 1.10.0-3 [57.2 kB] 98s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf openssl-provider-legacy armhf 3.4.0-1ubuntu2 [29.4 kB] 98s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libssl3t64 armhf 3.4.0-1ubuntu2 [1756 kB] 98s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libzstd1 armhf 1.5.6+dfsg-2 [266 kB] 98s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 15-20250213-1ubuntu1 [725 kB] 98s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-timesyncd armhf 257.2-3ubuntu1 [42.1 kB] 98s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-session-bus-common all 1.16.0-1ubuntu1 [53.1 kB] 98s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-sysv armhf 257.2-3ubuntu1 [11.9 kB] 98s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libpam-systemd armhf 257.2-3ubuntu1 [238 kB] 98s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-user-session armhf 1.16.0-1ubuntu1 [9684 B] 98s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libapparmor1 armhf 4.1.0~beta1-0ubuntu5 [47.3 kB] 98s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-4 [13.8 kB] 98s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libselinux1 armhf 3.7-3ubuntu2 [73.2 kB] 98s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-system-bus-common all 1.16.0-1ubuntu1 [54.3 kB] 98s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-bin armhf 1.16.0-1ubuntu1 [37.9 kB] 98s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf dbus armhf 1.16.0-1ubuntu1 [28.1 kB] 98s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-daemon armhf 1.16.0-1ubuntu1 [111 kB] 98s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libdbus-1-3 armhf 1.16.0-1ubuntu1 [162 kB] 98s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-resolved armhf 257.2-3ubuntu1 [315 kB] 98s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-cryptsetup armhf 257.2-3ubuntu1 [126 kB] 98s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libncurses6 armhf 6.5+20250125-2 [88.8 kB] 98s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libncursesw6 armhf 6.5+20250125-2 [118 kB] 98s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libtinfo6 armhf 6.5+20250125-2 [91.9 kB] 98s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf bsdextrautils armhf 2.40.2-14ubuntu1 [94.2 kB] 98s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf eject armhf 2.40.2-14ubuntu1 [63.4 kB] 98s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf fdisk armhf 2.40.2-14ubuntu1 [157 kB] 98s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libblkid1 armhf 2.40.2-14ubuntu1 [169 kB] 98s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libmount1 armhf 2.40.2-14ubuntu1 [194 kB] 99s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libsmartcols1 armhf 2.40.2-14ubuntu1 [137 kB] 99s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libuuid1 armhf 2.40.2-14ubuntu1 [41.0 kB] 99s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf util-linux armhf 2.40.2-14ubuntu1 [1190 kB] 99s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf uuid-runtime armhf 2.40.2-14ubuntu1 [63.7 kB] 99s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libfdisk1 armhf 2.40.2-14ubuntu1 [217 kB] 99s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf mount armhf 2.40.2-14ubuntu1 [158 kB] 99s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf readline-common all 8.2-6 [56.5 kB] 99s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline8t64 armhf 8.2-6 [131 kB] 99s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt1 armhf 1:4.4.38-1 [91.7 kB] 99s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd-shared armhf 257.2-3ubuntu1 [2203 kB] 99s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf systemd armhf 257.2-3ubuntu1 [3028 kB] 99s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf udev armhf 257.2-3ubuntu1 [1402 kB] 99s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libnss-systemd armhf 257.2-3ubuntu1 [164 kB] 99s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libudev1 armhf 257.2-3ubuntu1 [193 kB] 99s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd0 armhf 257.2-3ubuntu1 [494 kB] 99s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libapt-pkg6.0t64 armhf 2.9.29 [1086 kB] 99s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf tar armhf 1.35+dfsg-3.1 [240 kB] 99s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg armhf 1.22.11ubuntu4 [1242 kB] 99s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf gzip armhf 1.13-1ubuntu2 [98.1 kB] 99s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf ncurses-bin armhf 6.5+20250125-2 [179 kB] 99s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libdebconfclient0 armhf 0.274ubuntu1 [11.2 kB] 99s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf base-passwd armhf 3.6.6 [53.4 kB] 99s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf init-system-helpers all 1.68 [39.0 kB] 99s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libc-bin armhf 2.40-4ubuntu1 [542 kB] 99s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf ncurses-base all 6.5+20250125-2 [25.8 kB] 99s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf ncurses-term all 6.5+20250125-2 [276 kB] 99s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf console-setup-linux all 1.226ubuntu3 [1880 kB] 100s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf console-setup all 1.226ubuntu3 [110 kB] 100s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf keyboard-configuration all 1.226ubuntu3 [212 kB] 100s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf sysvinit-utils armhf 3.14-1ubuntu1 [35.1 kB] 100s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf libapt-pkg7.0 armhf 2.9.30 [1065 kB] 100s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf apt armhf 2.9.30 [1390 kB] 100s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf apt-utils armhf 2.9.30 [214 kB] 100s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libgpg-error-l10n all 1.51-3 [8800 B] 100s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libgpg-error0 armhf 1.51-3 [64.8 kB] 100s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libnpth0t64 armhf 1.8-2 [7572 B] 100s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf gpg-wks-client armhf 2.4.4-2ubuntu22 [87.5 kB] 100s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf dirmngr armhf 2.4.4-2ubuntu22 [347 kB] 100s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf gpgsm armhf 2.4.4-2ubuntu22 [242 kB] 100s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg-utils armhf 2.4.4-2ubuntu22 [159 kB] 100s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf gpg-agent armhf 2.4.4-2ubuntu22 [237 kB] 100s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf gpg armhf 2.4.4-2ubuntu22 [525 kB] 100s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf gpgconf armhf 2.4.4-2ubuntu22 [116 kB] 100s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg all 2.4.4-2ubuntu22 [359 kB] 100s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf keyboxd armhf 2.4.4-2ubuntu22 [111 kB] 100s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu2 [40.6 kB] 100s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libnettle8t64 armhf 3.10.1-1 [188 kB] 100s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libhogweed6t64 armhf 3.10.1-1 [188 kB] 100s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libffi8 armhf 3.4.7-1 [21.1 kB] 100s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libp11-kit0 armhf 0.25.5-2ubuntu3 [261 kB] 100s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libtasn1-6 armhf 4.20.0-2 [38.2 kB] 100s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf libunistring5 armhf 1.3-1 [583 kB] 100s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.9-2ubuntu1 [961 kB] 100s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8build1 [19.0 kB] 100s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8build1 [49.9 kB] 100s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-common all 2.6.9+dfsg-1~exp2ubuntu1 [33.2 kB] 100s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf libldap2 armhf 2.6.9+dfsg-1~exp2ubuntu1 [177 kB] 100s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf gpgv armhf 2.4.4-2ubuntu22 [225 kB] 100s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf e2fsprogs-l10n all 1.47.2-1ubuntu1 [7030 B] 100s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf logsave armhf 1.47.2-1ubuntu1 [25.7 kB] 100s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf ubuntu-minimal armhf 1.547 [11.4 kB] 100s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf initramfs-tools all 0.145ubuntu2 [7948 B] 100s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf initramfs-tools-core all 0.145ubuntu2 [51.5 kB] 100s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libext2fs2t64 armhf 1.47.2-1ubuntu1 [207 kB] 100s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf e2fsprogs armhf 1.47.2-1ubuntu1 [588 kB] 101s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf dhcpcd-base armhf 1:10.1.0-7 [188 kB] 101s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf init armhf 1.68 [6296 B] 101s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libbpf1 armhf 1:1.5.0-2 [158 kB] 101s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf iptables armhf 1.8.11-2ubuntu1 [342 kB] 101s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libip4tc2 armhf 1.8.11-2ubuntu1 [21.7 kB] 101s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libip6tc2 armhf 1.8.11-2ubuntu1 [22.1 kB] 101s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libnftnl11 armhf 1.2.8-1 [53.3 kB] 101s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libxtables12 armhf 1.8.11-2ubuntu1 [33.0 kB] 101s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.13.0-1ubuntu1 [1096 kB] 101s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf iputils-ping armhf 3:20240905-1ubuntu1 [45.0 kB] 101s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf locales all 2.40-4ubuntu1 [4224 kB] 101s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf login.defs all 1:4.16.0-7ubuntu1 [38.5 kB] 101s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf login armhf 1:4.16.0-2+really2.40.2-14ubuntu1 [85.0 kB] 101s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf mawk armhf 1.3.4.20250131-1 [119 kB] 101s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf netcat-openbsd armhf 1.228-1 [42.4 kB] 101s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.2-1 [868 kB] 101s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.2-1 [2012 kB] 101s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cryptography armhf 43.0.0-1 [925 kB] 101s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf python3-minimal armhf 3.13.1-1~exp2 [27.6 kB] 101s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf python3 armhf 3.13.1-1~exp2 [23.9 kB] 101s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf python3-bcrypt armhf 4.2.0-2.1 [239 kB] 101s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf tzdata all 2025a-2ubuntu1 [198 kB] 101s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.2-1 [1969 kB] 101s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.2-1 [734 kB] 101s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-stdlib armhf 3.13.1-1~exp2 [10.2 kB] 101s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-girepository-2.0 armhf 1.82.0-4 [25.3 kB] 101s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-glib-2.0 armhf 2.83.3-2 [184 kB] 101s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf libgirepository-1.0-1 armhf 1.82.0-4 [109 kB] 101s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-data all 2.83.3-2 [52.7 kB] 101s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-bin armhf 2.83.3-2 [92.7 kB] 101s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 15-20250213-1ubuntu1 [7938 B] 101s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-0t64 armhf 2.83.3-2 [1452 kB] 102s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf netplan-generator armhf 1.1.2-2ubuntu1 [60.8 kB] 102s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf libyaml-0-2 armhf 0.2.5-2 [45.3 kB] 102s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf python3-netplan armhf 1.1.2-2ubuntu1 [24.2 kB] 102s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf netplan.io armhf 1.1.2-2ubuntu1 [67.7 kB] 102s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf libnetplan1 armhf 1.1.2-2ubuntu1 [123 kB] 102s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf ethtool armhf 1:6.11-1 [222 kB] 102s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf libsemanage-common all 3.7-2.1 [7198 B] 102s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf libsemanage2 armhf 3.7-2.1 [85.4 kB] 102s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf passwd armhf 1:4.16.0-7ubuntu1 [1041 kB] 102s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-4ubuntu1 [20.1 kB] 102s Get:145 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-4ubuntu1 [39.7 kB] 102s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-4ubuntu1 [17.3 kB] 102s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf dracut-install armhf 106-2ubuntu1 [38.7 kB] 102s Get:148 http://ftpmaster.internal/ubuntu plucky/main armhf initramfs-tools-bin armhf 0.145ubuntu2 [24.5 kB] 102s Get:149 http://ftpmaster.internal/ubuntu plucky/main armhf busybox-initramfs armhf 1:1.37.0-4ubuntu1 [188 kB] 102s Get:150 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12 armhf 3.12.9-1 [671 kB] 102s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-stdlib armhf 3.12.9-1 [1946 kB] 102s Get:152 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-minimal armhf 3.12.9-1 [2012 kB] 102s Get:153 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-minimal armhf 3.12.9-1 [825 kB] 102s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf cron armhf 3.0pl1-192ubuntu1 [84.2 kB] 102s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf rsync armhf 3.4.1-0syncable1 [422 kB] 102s Get:156 http://ftpmaster.internal/ubuntu plucky/main armhf python-apt-common all 2.9.8 [21.1 kB] 102s Get:157 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apt armhf 2.9.8 [174 kB] 102s Get:158 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-5 [13.6 kB] 102s Get:159 http://ftpmaster.internal/ubuntu plucky/main armhf python3-launchpadlib all 2.1.0-1 [126 kB] 102s Get:160 http://ftpmaster.internal/ubuntu plucky/main armhf python3-problem-report all 2.31.0-0ubuntu5 [25.5 kB] 102s Get:161 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apport all 2.31.0-0ubuntu5 [93.1 kB] 102s Get:162 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gi armhf 3.50.0-4 [260 kB] 102s Get:163 http://ftpmaster.internal/ubuntu plucky/main armhf apport-core-dump-handler all 2.31.0-0ubuntu5 [18.4 kB] 102s Get:164 http://ftpmaster.internal/ubuntu plucky/main armhf apport all 2.31.0-0ubuntu5 [83.0 kB] 102s Get:165 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-17ubuntu1 [53.5 kB] 102s Get:166 http://ftpmaster.internal/ubuntu plucky/main armhf libcom-err2 armhf 1.47.2-1ubuntu1 [25.6 kB] 102s Get:167 http://ftpmaster.internal/ubuntu plucky/main armhf libss2 armhf 1.47.2-1ubuntu1 [15.6 kB] 102s Get:168 http://ftpmaster.internal/ubuntu plucky/main armhf openssl armhf 3.4.0-1ubuntu2 [1159 kB] 102s Get:169 http://ftpmaster.internal/ubuntu plucky/main armhf ca-certificates all 20241223 [165 kB] 102s Get:170 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info armhf 1.13 [19.1 kB] 102s Get:171 http://ftpmaster.internal/ubuntu plucky/main armhf krb5-locales all 1.21.3-4ubuntu1 [14.7 kB] 102s Get:172 http://ftpmaster.internal/ubuntu plucky/main armhf libfribidi0 armhf 1.0.16-1 [24.3 kB] 102s Get:173 http://ftpmaster.internal/ubuntu plucky/main armhf libgssapi-krb5-2 armhf 1.21.3-4ubuntu1 [121 kB] 102s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf libkrb5-3 armhf 1.21.3-4ubuntu1 [314 kB] 102s Get:175 http://ftpmaster.internal/ubuntu plucky/main armhf libkrb5support0 armhf 1.21.3-4ubuntu1 [31.8 kB] 102s Get:176 http://ftpmaster.internal/ubuntu plucky/main armhf libk5crypto3 armhf 1.21.3-4ubuntu1 [78.6 kB] 102s Get:177 http://ftpmaster.internal/ubuntu plucky/main armhf libicu74 armhf 74.2-1ubuntu6 [10.5 MB] 102s Get:178 http://ftpmaster.internal/ubuntu plucky/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2ubuntu3 [599 kB] 103s Get:179 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pygments all 2.18.0+dfsg-2 [835 kB] 103s Get:180 http://ftpmaster.internal/ubuntu plucky/main armhf python3-rich all 13.9.4-1 [190 kB] 103s Get:181 http://ftpmaster.internal/ubuntu plucky/main armhf ucf all 3.0049 [43.3 kB] 103s Get:182 http://ftpmaster.internal/ubuntu plucky/main armhf rsyslog armhf 8.2412.0-2ubuntu1 [471 kB] 103s Get:183 http://ftpmaster.internal/ubuntu plucky/main armhf apparmor armhf 4.1.0~beta1-0ubuntu5 [589 kB] 103s Get:184 http://ftpmaster.internal/ubuntu plucky/main armhf bash-completion all 1:2.16.0-7 [214 kB] 103s Get:185 http://ftpmaster.internal/ubuntu plucky/main armhf libmaxminddb0 armhf 1.12.2-1 [16.9 kB] 103s Get:186 http://ftpmaster.internal/ubuntu plucky/main armhf liburcu8t64 armhf 0.15.0-1 [57.3 kB] 103s Get:187 http://ftpmaster.internal/ubuntu plucky/main armhf bind9-dnsutils armhf 1:9.20.0-2ubuntu4 [155 kB] 103s Get:188 http://ftpmaster.internal/ubuntu plucky/main armhf bind9-host armhf 1:9.20.0-2ubuntu4 [46.2 kB] 103s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf bind9-libs armhf 1:9.20.0-2ubuntu4 [1176 kB] 103s Get:190 http://ftpmaster.internal/ubuntu plucky/main armhf libedit2 armhf 3.1-20250104-1 [79.3 kB] 103s Get:191 http://ftpmaster.internal/ubuntu plucky/main armhf busybox-static armhf 1:1.37.0-4ubuntu1 [857 kB] 103s Get:192 http://ftpmaster.internal/ubuntu plucky/main armhf cron-daemon-common all 3.0pl1-192ubuntu1 [14.5 kB] 103s Get:193 http://ftpmaster.internal/ubuntu plucky/main armhf libdevmapper1.02.1 armhf 2:1.02.201-1ubuntu1 [137 kB] 103s Get:194 http://ftpmaster.internal/ubuntu plucky/main armhf dmsetup armhf 2:1.02.201-1ubuntu1 [80.4 kB] 103s Get:195 http://ftpmaster.internal/ubuntu plucky/main armhf ed armhf 1.21-1 [52.8 kB] 103s Get:196 http://ftpmaster.internal/ubuntu plucky/main armhf gettext-base armhf 0.23.1-1 [43.3 kB] 103s Get:197 http://ftpmaster.internal/ubuntu plucky/main armhf groff-base armhf 1.23.0-7 [949 kB] 103s Get:198 http://ftpmaster.internal/ubuntu plucky/main armhf libibverbs1 armhf 55.0-1ubuntu1 [58.5 kB] 103s Get:199 http://ftpmaster.internal/ubuntu plucky/main armhf ibverbs-providers armhf 55.0-1ubuntu1 [27.6 kB] 103s Get:200 http://ftpmaster.internal/ubuntu plucky/main armhf iputils-tracepath armhf 3:20240905-1ubuntu1 [13.3 kB] 103s Get:201 http://ftpmaster.internal/ubuntu plucky/main armhf nftables armhf 1.1.1-1build1 [70.8 kB] 103s Get:202 http://ftpmaster.internal/ubuntu plucky/main armhf libnftables1 armhf 1.1.1-1build1 [321 kB] 103s Get:203 http://ftpmaster.internal/ubuntu plucky/main armhf libpcap0.8t64 armhf 1.10.5-2ubuntu1 [140 kB] 103s Get:204 http://ftpmaster.internal/ubuntu plucky/main armhf libpng16-16t64 armhf 1.6.46-4 [171 kB] 103s Get:205 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.4-2 [19.0 kB] 103s Get:206 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.4-2 [53.8 kB] 103s Get:207 http://ftpmaster.internal/ubuntu plucky/main armhf libusb-1.0-0 armhf 2:1.0.27-2 [49.5 kB] 103s Get:208 http://ftpmaster.internal/ubuntu plucky/main armhf libxdmcp6 armhf 1:1.1.5-1 [9060 B] 103s Get:209 http://ftpmaster.internal/ubuntu plucky/main armhf libxkbcommon0 armhf 1.7.0-2 [113 kB] 103s Get:210 http://ftpmaster.internal/ubuntu plucky/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1 [311 kB] 103s Get:211 http://ftpmaster.internal/ubuntu plucky/main armhf lsof armhf 4.99.4+dfsg-1 [239 kB] 103s Get:212 http://ftpmaster.internal/ubuntu plucky/main armhf liblsof0 armhf 4.99.4+dfsg-1 [60.7 kB] 103s Get:213 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.3-1 [277 kB] 103s Get:214 http://ftpmaster.internal/ubuntu plucky/main armhf pci.ids all 0.0~2025.02.12-1 [284 kB] 103s Get:215 http://ftpmaster.internal/ubuntu plucky/main armhf powermgmt-base all 1.38 [7378 B] 103s Get:216 http://ftpmaster.internal/ubuntu plucky/main armhf psmisc armhf 23.7-2 [177 kB] 103s Get:217 http://ftpmaster.internal/ubuntu plucky/main armhf publicsuffix all 20250108.1153-0.1 [134 kB] 103s Get:218 http://ftpmaster.internal/ubuntu plucky/main armhf python3-distro-info all 1.13 [7798 B] 103s Get:219 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.2-1 [30.2 kB] 104s Get:220 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-gdbm armhf 3.12.9-1 [29.3 kB] 104s Get:221 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gdbm armhf 3.13.1-1 [8668 B] 104s Get:222 http://ftpmaster.internal/ubuntu plucky/main armhf ubuntu-standard armhf 1.547 [11.4 kB] 104s Get:223 http://ftpmaster.internal/ubuntu plucky/main armhf ufw all 0.36.2-9 [170 kB] 104s Get:224 http://ftpmaster.internal/ubuntu plucky/main armhf usb.ids all 2025.01.14-1 [223 kB] 104s Get:225 http://ftpmaster.internal/ubuntu plucky/main armhf xauth armhf 1:1.1.2-1.1 [23.0 kB] 104s Get:226 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl3t64-gnutls armhf 8.12.0+git20250209.89ed161+ds-1ubuntu1 [330 kB] 104s Get:227 http://ftpmaster.internal/ubuntu plucky/main armhf libappstream5 armhf 1.0.4-1 [211 kB] 104s Get:228 http://ftpmaster.internal/ubuntu plucky/main armhf appstream armhf 1.0.4-1 [67.3 kB] 104s Get:229 http://ftpmaster.internal/ubuntu plucky/main armhf libctf0 armhf 2.44-1ubuntu1 [74.4 kB] 104s Get:230 http://ftpmaster.internal/ubuntu plucky/main armhf libctf-nobfd0 armhf 2.44-1ubuntu1 [77.6 kB] 104s Get:231 http://ftpmaster.internal/ubuntu plucky/main armhf binutils-arm-linux-gnueabihf armhf 2.44-1ubuntu1 [995 kB] 104s Get:232 http://ftpmaster.internal/ubuntu plucky/main armhf libbinutils armhf 2.44-1ubuntu1 [405 kB] 104s Get:233 http://ftpmaster.internal/ubuntu plucky/main armhf binutils armhf 2.44-1ubuntu1 [3238 B] 104s Get:234 http://ftpmaster.internal/ubuntu plucky/main armhf binutils-common armhf 2.44-1ubuntu1 [216 kB] 104s Get:235 http://ftpmaster.internal/ubuntu plucky/main armhf libsframe1 armhf 2.44-1ubuntu1 [12.5 kB] 104s Get:236 http://ftpmaster.internal/ubuntu plucky/main armhf btrfs-progs armhf 6.12-1build1 [884 kB] 104s Get:237 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2 [109 kB] 104s Get:238 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-3 [8444 B] 104s Get:239 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonpatch all 1.32-5 [12.3 kB] 104s Get:240 http://ftpmaster.internal/ubuntu plucky/main armhf python3-attr all 25.1.0-1 [50.4 kB] 104s Get:241 http://ftpmaster.internal/ubuntu plucky/main armhf python3-referencing all 0.35.1-2ubuntu1 [21.9 kB] 104s Get:242 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonschema all 4.19.2-6ubuntu1 [65.5 kB] 104s Get:243 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jwt all 2.10.1-2 [21.0 kB] 104s Get:244 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-3 [89.9 kB] 104s Get:245 http://ftpmaster.internal/ubuntu plucky/main armhf cloud-init-base all 25.1~3geb1965a4-0ubuntu1 [615 kB] 104s Get:246 http://ftpmaster.internal/ubuntu plucky/main armhf curl armhf 8.12.0+git20250209.89ed161+ds-1ubuntu1 [247 kB] 104s Get:247 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl4t64 armhf 8.12.0+git20250209.89ed161+ds-1ubuntu1 [335 kB] 104s Get:248 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg-dev all 1.22.11ubuntu4 [1088 kB] 104s Get:249 http://ftpmaster.internal/ubuntu plucky/main armhf libdpkg-perl all 1.22.11ubuntu4 [279 kB] 104s Get:250 http://ftpmaster.internal/ubuntu plucky/main armhf make armhf 4.4.1-1 [180 kB] 104s Get:251 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive13t64 armhf 3.7.7-0ubuntu1 [335 kB] 104s Get:252 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.6+ds-1 [5636 B] 104s Get:253 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.6+ds-1 [59.5 kB] 104s Get:254 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.5-1 [5151 kB] 104s Get:255 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.5-1 [125 kB] 104s Get:256 http://ftpmaster.internal/ubuntu plucky/main armhf polkitd armhf 126-2 [92.5 kB] 104s Get:257 http://ftpmaster.internal/ubuntu plucky/main armhf libpolkit-agent-1-0 armhf 126-2 [15.1 kB] 104s Get:258 http://ftpmaster.internal/ubuntu plucky/main armhf libpolkit-gobject-1-0 armhf 126-2 [45.0 kB] 104s Get:259 http://ftpmaster.internal/ubuntu plucky/main armhf libprotobuf-c1 armhf 1.5.1-1ubuntu1 [18.1 kB] 104s Get:260 http://ftpmaster.internal/ubuntu plucky/main armhf libqmi-proxy armhf 1.35.6-1 [5878 B] 104s Get:261 http://ftpmaster.internal/ubuntu plucky/main armhf libqmi-glib5 armhf 1.35.6-1 [928 kB] 104s Get:262 http://ftpmaster.internal/ubuntu plucky/main armhf libpackagekit-glib2-18 armhf 1.3.0-3build1 [109 kB] 104s Get:263 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-packagekitglib-1.0 armhf 1.3.0-3build1 [25.5 kB] 104s Get:264 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg-l10n all 2.4.4-2ubuntu22 [66.4 kB] 104s Get:265 http://ftpmaster.internal/ubuntu plucky/main armhf htop armhf 3.3.0-5 [140 kB] 104s Get:266 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.3.0-1 [17.5 kB] 104s Get:267 http://ftpmaster.internal/ubuntu plucky/main armhf libnspr4 armhf 2:4.36-1ubuntu1 [94.5 kB] 104s Get:268 http://ftpmaster.internal/ubuntu plucky/main armhf libnss3 armhf 2:3.107-1ubuntu1 [1315 kB] 104s Get:269 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.24.2-1ubuntu1 [125 kB] 104s Get:270 http://ftpmaster.internal/ubuntu plucky/main armhf libvolume-key1 armhf 0.3.12-9 [39.1 kB] 104s Get:271 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.3.0-1 [22.4 kB] 104s Get:272 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.3.0-1 [34.5 kB] 104s Get:273 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.3.0-1 [6594 B] 104s Get:274 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.3.0-1 [13.4 kB] 104s Get:275 http://ftpmaster.internal/ubuntu plucky/main armhf libnvme1t64 armhf 1.11.1-2 [73.6 kB] 104s Get:276 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.3.0-1 [17.7 kB] 104s Get:277 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.3.0-1 [16.6 kB] 105s Get:278 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.3.0-1 [9010 B] 105s Get:279 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.3.0-1 [44.4 kB] 105s Get:280 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-8 [26.3 kB] 105s Get:281 http://ftpmaster.internal/ubuntu plucky/main armhf libgstreamer1.0-0 armhf 1.25.50-1 [1164 kB] 105s Get:282 http://ftpmaster.internal/ubuntu plucky/main armhf libgudev-1.0-0 armhf 1:238-6 [13.7 kB] 105s Get:283 http://ftpmaster.internal/ubuntu plucky/main armhf libicu76 armhf 76.1-1ubuntu2 [10.8 MB] 105s Get:284 http://ftpmaster.internal/ubuntu plucky/main armhf libsasl2-modules armhf 2.1.28+dfsg1-8build1 [62.7 kB] 105s Get:285 http://ftpmaster.internal/ubuntu plucky/main armhf udisks2 armhf 2.10.1-11ubuntu2 [278 kB] 105s Get:286 http://ftpmaster.internal/ubuntu plucky/main armhf libudisks2-0 armhf 2.10.1-11ubuntu2 [142 kB] 105s Get:287 http://ftpmaster.internal/ubuntu plucky/main armhf libwrap0 armhf 7.6.q-35 [45.6 kB] 105s Get:288 http://ftpmaster.internal/ubuntu plucky/main armhf linux-headers-6.12.0-15 all 6.12.0-15.15 [14.1 MB] 105s Get:289 http://ftpmaster.internal/ubuntu plucky/main armhf linux-headers-6.12.0-15-generic armhf 6.12.0-15.15 [1414 kB] 105s Get:290 http://ftpmaster.internal/ubuntu plucky/main armhf linux-headers-generic armhf 6.12.0-15.15+1 [10.8 kB] 105s Get:291 http://ftpmaster.internal/ubuntu plucky/main armhf packagekit-tools armhf 1.3.0-3build1 [28.0 kB] 105s Get:292 http://ftpmaster.internal/ubuntu plucky/main armhf packagekit armhf 1.3.0-3build1 [431 kB] 105s Get:293 http://ftpmaster.internal/ubuntu plucky/main armhf pollinate all 4.33-4ubuntu2 [12.4 kB] 105s Get:294 http://ftpmaster.internal/ubuntu plucky/main armhf python3-babel all 2.17.0-1 [101 kB] 105s Get:295 http://ftpmaster.internal/ubuntu plucky/main armhf python-babel-localedata all 2.17.0-1 [6678 kB] 106s Get:296 http://ftpmaster.internal/ubuntu plucky/main armhf python3-certifi all 2025.1.31+ds-1 [9816 B] 106s Get:297 http://ftpmaster.internal/ubuntu plucky/main armhf python3-chardet all 5.2.0+dfsg-2 [116 kB] 106s Get:298 http://ftpmaster.internal/ubuntu plucky/main armhf python3-idna all 3.10-1 [47.4 kB] 106s Get:299 http://ftpmaster.internal/ubuntu plucky/main armhf python3-more-itertools all 10.6.0-1 [57.7 kB] 106s Get:300 http://ftpmaster.internal/ubuntu plucky/main armhf python3-openssl all 25.0.0-1 [46.1 kB] 106s Get:301 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pkg-resources all 75.6.0-1 [144 kB] 106s Get:302 http://ftpmaster.internal/ubuntu plucky/main armhf python3-setuptools all 75.6.0-1 [645 kB] 106s Get:303 http://ftpmaster.internal/ubuntu plucky/main armhf software-properties-common all 0.108 [16.5 kB] 106s Get:304 http://ftpmaster.internal/ubuntu plucky/main armhf python3-software-properties all 0.108 [30.9 kB] 106s Get:305 http://ftpmaster.internal/ubuntu plucky/main armhf python3-urllib3 all 2.3.0-1 [94.0 kB] 106s Get:306 http://ftpmaster.internal/ubuntu plucky/main armhf python3-wadllib all 2.0.0-2 [36.2 kB] 106s Get:307 http://ftpmaster.internal/ubuntu plucky/main armhf unattended-upgrades all 2.12ubuntu2 [55.0 kB] 106s Get:308 http://ftpmaster.internal/ubuntu plucky/main armhf xfsprogs armhf 6.12.0-1ubuntu1 [958 kB] 106s Get:309 http://ftpmaster.internal/ubuntu plucky/main armhf zstd armhf 1.5.6+dfsg-2 [690 kB] 106s Get:310 http://ftpmaster.internal/ubuntu plucky/main armhf cloud-init all 25.1~3geb1965a4-0ubuntu1 [2102 B] 106s Get:311 http://ftpmaster.internal/ubuntu plucky/main armhf kpartx armhf 0.9.9-1ubuntu4 [35.0 kB] 106s Get:312 http://ftpmaster.internal/ubuntu plucky/main armhf multipath-tools armhf 0.9.9-1ubuntu4 [294 kB] 107s Preconfiguring packages ... 109s Fetched 135 MB in 10s (13.8 MB/s) 109s (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 ... 59970 files and directories currently installed.) 109s Preparing to unpack .../bash_5.2.37-1ubuntu1_armhf.deb ... 109s Unpacking bash (5.2.37-1ubuntu1) over (5.2.32-1ubuntu2) ... 109s Setting up bash (5.2.37-1ubuntu1) ... 109s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 109s (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 ... 59970 files and directories currently installed.) 109s Preparing to unpack .../bsdutils_1%3a2.40.2-14ubuntu1_armhf.deb ... 109s Unpacking bsdutils (1:2.40.2-14ubuntu1) over (1:2.40.2-1ubuntu1) ... 109s Setting up bsdutils (1:2.40.2-14ubuntu1) ... 109s (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 ... 59970 files and directories currently installed.) 109s Preparing to unpack .../coreutils_9.5-1ubuntu1_armhf.deb ... 109s Unpacking coreutils (9.5-1ubuntu1) over (9.4-3.1ubuntu1) ... 110s Setting up coreutils (9.5-1ubuntu1) ... 110s (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 ... 59970 files and directories currently installed.) 110s Preparing to unpack .../dash_0.5.12-12ubuntu1_armhf.deb ... 110s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 110s Setting up dash (0.5.12-12ubuntu1) ... 110s (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 ... 59970 files and directories currently installed.) 110s Preparing to unpack .../diffutils_1%3a3.10-2_armhf.deb ... 110s Unpacking diffutils (1:3.10-2) over (1:3.10-1build1) ... 110s Setting up diffutils (1:3.10-2) ... 110s Selecting previously unselected package gcc-15-base:armhf. 110s (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 ... 59970 files and directories currently installed.) 110s Preparing to unpack .../gcc-15-base_15-20250213-1ubuntu1_armhf.deb ... 110s Unpacking gcc-15-base:armhf (15-20250213-1ubuntu1) ... 110s Setting up gcc-15-base:armhf (15-20250213-1ubuntu1) ... 110s (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 ... 59975 files and directories currently installed.) 110s Preparing to unpack .../libgcc-s1_15-20250213-1ubuntu1_armhf.deb ... 110s Unpacking libgcc-s1:armhf (15-20250213-1ubuntu1) over (14.2.0-8ubuntu1) ... 110s Setting up libgcc-s1:armhf (15-20250213-1ubuntu1) ... 110s (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 ... 59975 files and directories currently installed.) 110s Preparing to unpack .../libc6_2.40-4ubuntu1_armhf.deb ... 110s Unpacking libc6:armhf (2.40-4ubuntu1) over (2.40-1ubuntu3) ... 111s Setting up libc6:armhf (2.40-4ubuntu1) ... 111s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59975 files and directories currently installed.) 111s Preparing to unpack .../libxxhash0_0.8.3-2_armhf.deb ... 111s Unpacking libxxhash0:armhf (0.8.3-2) over (0.8.2-2build1) ... 111s Setting up libxxhash0:armhf (0.8.3-2) ... 111s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59975 files and directories currently installed.) 111s Preparing to unpack .../liblz4-1_1.10.0-3_armhf.deb ... 111s Unpacking liblz4-1:armhf (1.10.0-3) over (1.9.4-3) ... 111s Setting up liblz4-1:armhf (1.10.0-3) ... 111s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59975 files and directories currently installed.) 111s Preparing to unpack .../libssl3t64_3.4.0-1ubuntu2_armhf.deb ... 111s Unpacking libssl3t64:armhf (3.4.0-1ubuntu2) over (3.3.1-2ubuntu2) ... 111s Selecting previously unselected package openssl-provider-legacy. 111s Preparing to unpack .../openssl-provider-legacy_3.4.0-1ubuntu2_armhf.deb ... 111s Unpacking openssl-provider-legacy (3.4.0-1ubuntu2) ... 111s Setting up libssl3t64:armhf (3.4.0-1ubuntu2) ... 111s Setting up openssl-provider-legacy (3.4.0-1ubuntu2) ... 111s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59978 files and directories currently installed.) 111s Preparing to unpack .../libzstd1_1.5.6+dfsg-2_armhf.deb ... 111s Unpacking libzstd1:armhf (1.5.6+dfsg-2) over (1.5.6+dfsg-1) ... 111s Setting up libzstd1:armhf (1.5.6+dfsg-2) ... 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59978 files and directories currently installed.) 112s Preparing to unpack .../libstdc++6_15-20250213-1ubuntu1_armhf.deb ... 112s Unpacking libstdc++6:armhf (15-20250213-1ubuntu1) over (14.2.0-8ubuntu1) ... 112s Setting up libstdc++6:armhf (15-20250213-1ubuntu1) ... 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59978 files and directories currently installed.) 112s Preparing to unpack .../0-systemd-timesyncd_257.2-3ubuntu1_armhf.deb ... 112s Unpacking systemd-timesyncd (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 112s Preparing to unpack .../1-dbus-session-bus-common_1.16.0-1ubuntu1_all.deb ... 112s Unpacking dbus-session-bus-common (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 112s Preparing to unpack .../2-systemd-sysv_257.2-3ubuntu1_armhf.deb ... 112s Unpacking systemd-sysv (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 112s Preparing to unpack .../3-libpam-systemd_257.2-3ubuntu1_armhf.deb ... 112s Unpacking libpam-systemd:armhf (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 112s Preparing to unpack .../4-dbus-user-session_1.16.0-1ubuntu1_armhf.deb ... 112s Unpacking dbus-user-session (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 112s Preparing to unpack .../5-libapparmor1_4.1.0~beta1-0ubuntu5_armhf.deb ... 112s Unpacking libapparmor1:armhf (4.1.0~beta1-0ubuntu5) over (4.1.0~beta1-0ubuntu4) ... 112s Preparing to unpack .../6-libcap-ng0_0.8.5-4_armhf.deb ... 112s Unpacking libcap-ng0:armhf (0.8.5-4) over (0.8.5-3build1) ... 112s Setting up libcap-ng0:armhf (0.8.5-4) ... 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59979 files and directories currently installed.) 112s Preparing to unpack .../libselinux1_3.7-3ubuntu2_armhf.deb ... 112s Unpacking libselinux1:armhf (3.7-3ubuntu2) over (3.7-3ubuntu1) ... 112s Setting up libselinux1:armhf (3.7-3ubuntu2) ... 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59979 files and directories currently installed.) 112s Preparing to unpack .../0-dbus-system-bus-common_1.16.0-1ubuntu1_all.deb ... 112s Unpacking dbus-system-bus-common (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 113s Preparing to unpack .../1-dbus-bin_1.16.0-1ubuntu1_armhf.deb ... 113s Unpacking dbus-bin (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 113s Preparing to unpack .../2-dbus_1.16.0-1ubuntu1_armhf.deb ... 113s Unpacking dbus (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 113s Preparing to unpack .../3-dbus-daemon_1.16.0-1ubuntu1_armhf.deb ... 113s Unpacking dbus-daemon (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 113s Preparing to unpack .../4-libdbus-1-3_1.16.0-1ubuntu1_armhf.deb ... 113s Unpacking libdbus-1-3:armhf (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 113s Preparing to unpack .../5-systemd-resolved_257.2-3ubuntu1_armhf.deb ... 113s Unpacking systemd-resolved (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 113s Preparing to unpack .../6-systemd-cryptsetup_257.2-3ubuntu1_armhf.deb ... 113s Unpacking systemd-cryptsetup (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 113s Preparing to unpack .../7-libncurses6_6.5+20250125-2_armhf.deb ... 113s Unpacking libncurses6:armhf (6.5+20250125-2) over (6.5-2) ... 113s Preparing to unpack .../8-libncursesw6_6.5+20250125-2_armhf.deb ... 113s Unpacking libncursesw6:armhf (6.5+20250125-2) over (6.5-2) ... 113s Preparing to unpack .../9-libtinfo6_6.5+20250125-2_armhf.deb ... 113s Unpacking libtinfo6:armhf (6.5+20250125-2) over (6.5-2) ... 113s Setting up libtinfo6:armhf (6.5+20250125-2) ... 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59979 files and directories currently installed.) 113s Preparing to unpack .../bsdextrautils_2.40.2-14ubuntu1_armhf.deb ... 113s Unpacking bsdextrautils (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 113s Preparing to unpack .../eject_2.40.2-14ubuntu1_armhf.deb ... 113s Unpacking eject (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 113s Preparing to unpack .../fdisk_2.40.2-14ubuntu1_armhf.deb ... 113s Unpacking fdisk (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 113s Preparing to unpack .../libblkid1_2.40.2-14ubuntu1_armhf.deb ... 113s Unpacking libblkid1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 113s Setting up libblkid1:armhf (2.40.2-14ubuntu1) ... 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59975 files and directories currently installed.) 113s Preparing to unpack .../libmount1_2.40.2-14ubuntu1_armhf.deb ... 113s Unpacking libmount1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 113s Setting up libmount1:armhf (2.40.2-14ubuntu1) ... 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59975 files and directories currently installed.) 114s Preparing to unpack .../libsmartcols1_2.40.2-14ubuntu1_armhf.deb ... 114s Unpacking libsmartcols1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 114s Setting up libsmartcols1:armhf (2.40.2-14ubuntu1) ... 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59975 files and directories currently installed.) 114s Preparing to unpack .../libuuid1_2.40.2-14ubuntu1_armhf.deb ... 114s Unpacking libuuid1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 114s Setting up libuuid1:armhf (2.40.2-14ubuntu1) ... 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59975 files and directories currently installed.) 114s Preparing to unpack .../util-linux_2.40.2-14ubuntu1_armhf.deb ... 114s Unpacking util-linux (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 114s Setting up util-linux (2.40.2-14ubuntu1) ... 115s fstrim.service is a disabled or a static unit not running, not starting it. 115s (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 ... 60021 files and directories currently installed.) 122s Preparing to unpack .../libunistring5_1.3-1_armhf.deb ... 122s Unpacking libunistring5:armhf (1.3-1) over (1.2-1) ... 122s Setting up libunistring5:armhf (1.3-1) ... 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 ... 60021 files and directories currently installed.) 123s Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-8build1_armhf.deb ... 123s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8build1) over (2.1.28+dfsg1-8) ... 123s Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-8build1_armhf.deb ... 123s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8build1) over (2.1.28+dfsg1-8) ... 123s Preparing to unpack .../libldap-common_2.6.9+dfsg-1~exp2ubuntu1_all.deb ... 123s Unpacking libldap-common (2.6.9+dfsg-1~exp2ubuntu1) over (2.6.8+dfsg-1~exp4ubuntu3) ... 123s Preparing to unpack .../libldap2_2.6.9+dfsg-1~exp2ubuntu1_armhf.deb ... 123s Unpacking libldap2:armhf (2.6.9+dfsg-1~exp2ubuntu1) over (2.6.8+dfsg-1~exp4ubuntu3) ... 123s Preparing to unpack .../gpgv_2.4.4-2ubuntu22_armhf.deb ... 123s Unpacking gpgv (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 123s Setting up gpgv (2.4.4-2ubuntu22) ... 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 ... 60020 files and directories currently installed.) 123s Preparing to unpack .../0-e2fsprogs-l10n_1.47.2-1ubuntu1_all.deb ... 123s Unpacking e2fsprogs-l10n (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 123s Preparing to unpack .../1-logsave_1.47.2-1ubuntu1_armhf.deb ... 123s Unpacking logsave (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 123s Preparing to unpack .../2-ubuntu-minimal_1.547_armhf.deb ... 123s Unpacking ubuntu-minimal (1.547) over (1.544) ... 123s Preparing to unpack .../3-initramfs-tools_0.145ubuntu2_all.deb ... 123s Unpacking initramfs-tools (0.145ubuntu2) over (0.142ubuntu35) ... 123s Preparing to unpack .../4-initramfs-tools-core_0.145ubuntu2_all.deb ... 123s Unpacking initramfs-tools-core (0.145ubuntu2) over (0.142ubuntu35) ... 123s Preparing to unpack .../5-libext2fs2t64_1.47.2-1ubuntu1_armhf.deb ... 123s Leaving 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' 123s Leaving 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 123s Leaving 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' 123s Leaving 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 123s Unpacking libext2fs2t64:armhf (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 123s Setting up libext2fs2t64:armhf (1.47.2-1ubuntu1) ... 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 ... 60020 files and directories currently installed.) 123s Preparing to unpack .../e2fsprogs_1.47.2-1ubuntu1_armhf.deb ... 123s Unpacking e2fsprogs (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 124s Preparing to unpack .../dhcpcd-base_1%3a10.1.0-7_armhf.deb ... 124s Unpacking dhcpcd-base (1:10.1.0-7) over (1:10.1.0-2) ... 124s Setting up libapparmor1:armhf (4.1.0~beta1-0ubuntu5) ... 124s Setting up mount (2.40.2-14ubuntu1) ... 124s Setting up systemd (257.2-3ubuntu1) ... 124s Installing new version of config file /etc/systemd/logind.conf ... 124s Installing new version of config file /etc/systemd/sleep.conf ... 124s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 124s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 124s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 125s Setting up systemd-sysv (257.2-3ubuntu1) ... 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 ... 60019 files and directories currently installed.) 125s Preparing to unpack .../00-init_1.68_armhf.deb ... 125s Unpacking init (1.68) over (1.67ubuntu1) ... 125s Preparing to unpack .../01-libbpf1_1%3a1.5.0-2_armhf.deb ... 125s Unpacking libbpf1:armhf (1:1.5.0-2) over (1:1.5.0-1) ... 125s Preparing to unpack .../02-iptables_1.8.11-2ubuntu1_armhf.deb ... 125s Unpacking iptables (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 125s Preparing to unpack .../03-libip4tc2_1.8.11-2ubuntu1_armhf.deb ... 125s Unpacking libip4tc2:armhf (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 125s Preparing to unpack .../04-libip6tc2_1.8.11-2ubuntu1_armhf.deb ... 125s Unpacking libip6tc2:armhf (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 125s Preparing to unpack .../05-libnftnl11_1.2.8-1_armhf.deb ... 125s Unpacking libnftnl11:armhf (1.2.8-1) over (1.2.7-1) ... 125s Preparing to unpack .../06-libxtables12_1.8.11-2ubuntu1_armhf.deb ... 125s Unpacking libxtables12:armhf (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 125s Preparing to unpack .../07-iproute2_6.13.0-1ubuntu1_armhf.deb ... 125s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 126s Preparing to unpack .../08-iputils-ping_3%3a20240905-1ubuntu1_armhf.deb ... 126s Unpacking iputils-ping (3:20240905-1ubuntu1) over (3:20240117-1build1) ... 126s Preparing to unpack .../09-locales_2.40-4ubuntu1_all.deb ... 126s Unpacking locales (2.40-4ubuntu1) over (2.40-1ubuntu3) ... 126s Selecting previously unselected package login.defs. 126s Preparing to unpack .../10-login.defs_1%3a4.16.0-7ubuntu1_all.deb ... 126s Unpacking login.defs (1:4.16.0-7ubuntu1) ... 126s Replacing files in old package login (1:4.15.3-3ubuntu2) ... 126s Setting up login.defs (1:4.16.0-7ubuntu1) ... 126s Installing new version of config file /etc/login.defs ... 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 ... 60026 files and directories currently installed.) 126s Preparing to unpack .../0-login_1%3a4.16.0-2+really2.40.2-14ubuntu1_armhf.deb ... 126s Unpacking login (1:4.16.0-2+really2.40.2-14ubuntu1) over (1:4.15.3-3ubuntu2) ... 126s Preparing to unpack .../1-mawk_1.3.4.20250131-1_armhf.deb ... 126s Unpacking mawk (1.3.4.20250131-1) over (1.3.4.20240905-1) ... 126s Preparing to unpack .../2-netcat-openbsd_1.228-1_armhf.deb ... 126s Unpacking netcat-openbsd (1.228-1) over (1.226-1.1) ... 126s Selecting previously unselected package libpython3.13-minimal:armhf. 126s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-1_armhf.deb ... 126s Unpacking libpython3.13-minimal:armhf (3.13.2-1) ... 126s Selecting previously unselected package python3.13-minimal. 126s Preparing to unpack .../4-python3.13-minimal_3.13.2-1_armhf.deb ... 126s Unpacking python3.13-minimal (3.13.2-1) ... 127s Preparing to unpack .../5-python3-cryptography_43.0.0-1_armhf.deb ... 127s Unpacking python3-cryptography (43.0.0-1) over (42.0.5-2build1) ... 127s Setting up libpython3.13-minimal:armhf (3.13.2-1) ... 127s Setting up python3.13-minimal (3.13.2-1) ... 128s (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 ... 60308 files and directories currently installed.) 128s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_armhf.deb ... 128s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.6-0ubuntu1) ... 128s Setting up python3-minimal (3.13.1-1~exp2) ... 129s (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 ... 60308 files and directories currently installed.) 129s Preparing to unpack .../00-python3_3.13.1-1~exp2_armhf.deb ... 129s Unpacking python3 (3.13.1-1~exp2) over (3.12.6-0ubuntu1) ... 129s Selecting previously unselected package python3-bcrypt. 129s Preparing to unpack .../01-python3-bcrypt_4.2.0-2.1_armhf.deb ... 129s Unpacking python3-bcrypt (4.2.0-2.1) ... 129s Preparing to unpack .../02-tzdata_2025a-2ubuntu1_all.deb ... 129s Unpacking tzdata (2025a-2ubuntu1) over (2024b-1ubuntu2) ... 129s Selecting previously unselected package libpython3.13-stdlib:armhf. 129s Preparing to unpack .../03-libpython3.13-stdlib_3.13.2-1_armhf.deb ... 129s Unpacking libpython3.13-stdlib:armhf (3.13.2-1) ... 129s Selecting previously unselected package python3.13. 129s Preparing to unpack .../04-python3.13_3.13.2-1_armhf.deb ... 129s Unpacking python3.13 (3.13.2-1) ... 129s Preparing to unpack .../05-libpython3-stdlib_3.13.1-1~exp2_armhf.deb ... 129s Unpacking libpython3-stdlib:armhf (3.13.1-1~exp2) over (3.12.6-0ubuntu1) ... 129s Preparing to unpack .../06-gir1.2-girepository-2.0_1.82.0-4_armhf.deb ... 129s Unpacking gir1.2-girepository-2.0:armhf (1.82.0-4) over (1.82.0-2) ... 129s Preparing to unpack .../07-gir1.2-glib-2.0_2.83.3-2_armhf.deb ... 129s Unpacking gir1.2-glib-2.0:armhf (2.83.3-2) over (2.82.2-3) ... 129s Preparing to unpack .../08-libgirepository-1.0-1_1.82.0-4_armhf.deb ... 129s Unpacking libgirepository-1.0-1:armhf (1.82.0-4) over (1.82.0-2) ... 129s Preparing to unpack .../09-libglib2.0-data_2.83.3-2_all.deb ... 129s Unpacking libglib2.0-data (2.83.3-2) over (2.82.2-3) ... 129s Preparing to unpack .../10-libglib2.0-bin_2.83.3-2_armhf.deb ... 129s Unpacking libglib2.0-bin (2.83.3-2) over (2.82.2-3) ... 129s Preparing to unpack .../11-libatomic1_15-20250213-1ubuntu1_armhf.deb ... 129s Unpacking libatomic1:armhf (15-20250213-1ubuntu1) over (14.2.0-8ubuntu1) ... 129s Preparing to unpack .../12-libglib2.0-0t64_2.83.3-2_armhf.deb ... 129s Unpacking libglib2.0-0t64:armhf (2.83.3-2) over (2.82.2-3) ... 129s Preparing to unpack .../13-netplan-generator_1.1.2-2ubuntu1_armhf.deb ... 129s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 129s Unpacking netplan-generator (1.1.2-2ubuntu1) over (1.1.1-1) ... 130s Preparing to unpack .../14-libyaml-0-2_0.2.5-2_armhf.deb ... 130s Unpacking libyaml-0-2:armhf (0.2.5-2) over (0.2.5-1build1) ... 130s Preparing to unpack .../15-python3-netplan_1.1.2-2ubuntu1_armhf.deb ... 130s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 130s for fn in glob1(directory, "%s.*" % fname): 130s Unpacking python3-netplan (1.1.2-2ubuntu1) over (1.1.1-1) ... 130s Preparing to unpack .../16-netplan.io_1.1.2-2ubuntu1_armhf.deb ... 130s Unpacking netplan.io (1.1.2-2ubuntu1) over (1.1.1-1) ... 130s Preparing to unpack .../17-libnetplan1_1.1.2-2ubuntu1_armhf.deb ... 130s Unpacking libnetplan1:armhf (1.1.2-2ubuntu1) over (1.1.1-1) ... 130s Preparing to unpack .../18-ethtool_1%3a6.11-1_armhf.deb ... 130s Unpacking ethtool (1:6.11-1) over (1:6.10-1) ... 130s Preparing to unpack .../19-libsemanage-common_3.7-2.1_all.deb ... 130s Unpacking libsemanage-common (3.7-2.1) over (3.7-2build1) ... 130s Setting up libsemanage-common (3.7-2.1) ... 130s (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 ... 60731 files and directories currently installed.) 130s Preparing to unpack .../libsemanage2_3.7-2.1_armhf.deb ... 130s Unpacking libsemanage2:armhf (3.7-2.1) over (3.7-2build1) ... 130s Setting up libsemanage2:armhf (3.7-2.1) ... 130s (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 ... 60731 files and directories currently installed.) 130s Preparing to unpack .../passwd_1%3a4.16.0-7ubuntu1_armhf.deb ... 130s Unpacking passwd (1:4.16.0-7ubuntu1) over (1:4.15.3-3ubuntu2) ... 130s Setting up passwd (1:4.16.0-7ubuntu1) ... 131s (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 ... 60766 files and directories currently installed.) 131s Preparing to unpack .../000-python3-newt_0.52.24-4ubuntu1_armhf.deb ... 131s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. 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Use glob.glob and pass a directory to its root_dir argument instead. 132s for fn in glob1(directory, "%s.*" % fname): 132s Unpacking python3-apt (2.9.8) over (2.9.0ubuntu2) ... 132s Preparing to unpack .../014-python3-lazr.uri_1.0.6-5_all.deb ... 132s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 132s for fn in glob1(directory, "%s.*" % fname): 132s Unpacking python3-lazr.uri (1.0.6-5) over (1.0.6-4) ... 132s Preparing to unpack .../015-python3-launchpadlib_2.1.0-1_all.deb ... 132s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 132s for fn in glob1(directory, "%s.*" % fname): 132s Unpacking python3-launchpadlib (2.1.0-1) over (2.0.0-1) ... 133s Preparing to unpack .../016-python3-problem-report_2.31.0-0ubuntu5_all.deb ... 133s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 133s for fn in glob1(directory, "%s.*" % fname): 133s Unpacking python3-problem-report (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 133s Preparing to unpack .../017-python3-apport_2.31.0-0ubuntu5_all.deb ... 133s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 133s for fn in glob1(directory, "%s.*" % fname): 133s Unpacking python3-apport (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 133s Preparing to unpack .../018-python3-gi_3.50.0-4_armhf.deb ... 133s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 133s for fn in glob1(directory, "%s.*" % fname): 133s Unpacking python3-gi (3.50.0-4) over (3.50.0-3build1) ... 133s Preparing to unpack .../019-apport-core-dump-handler_2.31.0-0ubuntu5_all.deb ... 133s Unpacking apport-core-dump-handler (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 133s Preparing to unpack .../020-apport_2.31.0-0ubuntu5_all.deb ... 133s Unpacking apport (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 133s Preparing to unpack .../021-gcc-14-base_14.2.0-17ubuntu1_armhf.deb ... 133s Unpacking gcc-14-base:armhf (14.2.0-17ubuntu1) over (14.2.0-8ubuntu1) ... 133s Preparing to unpack .../022-libcom-err2_1.47.2-1ubuntu1_armhf.deb ... 133s Unpacking libcom-err2:armhf (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 133s Preparing to unpack .../023-libss2_1.47.2-1ubuntu1_armhf.deb ... 133s Unpacking libss2:armhf (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 133s Preparing to unpack .../024-openssl_3.4.0-1ubuntu2_armhf.deb ... 133s Unpacking openssl (3.4.0-1ubuntu2) over (3.3.1-2ubuntu2) ... 134s Preparing to unpack .../025-ca-certificates_20241223_all.deb ... 134s Unpacking ca-certificates (20241223) over (20240203) ... 134s Preparing to unpack .../026-distro-info_1.13_armhf.deb ... 134s Unpacking distro-info (1.13) over (1.12) ... 134s Preparing to unpack .../027-krb5-locales_1.21.3-4ubuntu1_all.deb ... 134s Unpacking krb5-locales (1.21.3-4ubuntu1) over (1.21.3-3) ... 134s Preparing to unpack .../028-libfribidi0_1.0.16-1_armhf.deb ... 134s Unpacking libfribidi0:armhf (1.0.16-1) over (1.0.15-1) ... 134s Preparing to unpack .../029-libgssapi-krb5-2_1.21.3-4ubuntu1_armhf.deb ... 134s Unpacking libgssapi-krb5-2:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 134s Preparing to unpack .../030-libkrb5-3_1.21.3-4ubuntu1_armhf.deb ... 134s Unpacking libkrb5-3:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 134s Preparing to unpack .../031-libkrb5support0_1.21.3-4ubuntu1_armhf.deb ... 134s Unpacking libkrb5support0:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 134s Preparing to unpack .../032-libk5crypto3_1.21.3-4ubuntu1_armhf.deb ... 134s Unpacking libk5crypto3:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 134s Preparing to unpack .../033-libicu74_74.2-1ubuntu6_armhf.deb ... 134s Unpacking libicu74:armhf (74.2-1ubuntu6) over (74.2-1ubuntu4) ... 134s Preparing to unpack .../034-libxml2_2.12.7+dfsg+really2.9.14-0.2ubuntu3_armhf.deb ... 134s Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2ubuntu3) over (2.12.7+dfsg-3) ... 134s Preparing to unpack .../035-python3-pygments_2.18.0+dfsg-2_all.deb ... 135s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 135s for fn in glob1(directory, "%s.*" % fname): 135s Unpacking python3-pygments (2.18.0+dfsg-2) over (2.18.0+dfsg-1ubuntu1) ... 135s Preparing to unpack .../036-python3-rich_13.9.4-1_all.deb ... 135s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 135s for fn in glob1(directory, "%s.*" % fname): 135s Unpacking python3-rich (13.9.4-1) over (13.7.1-1) ... 135s Preparing to unpack .../037-ucf_3.0049_all.deb ... 135s Unpacking ucf (3.0049) over (3.0043+nmu1) ... 135s Preparing to unpack .../038-rsyslog_8.2412.0-2ubuntu1_armhf.deb ... 135s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2406.0-1ubuntu2) ... 136s Preparing to unpack .../039-apparmor_4.1.0~beta1-0ubuntu5_armhf.deb ... 137s Unpacking apparmor (4.1.0~beta1-0ubuntu5) over (4.1.0~beta1-0ubuntu4) ... 137s Preparing to unpack .../040-bash-completion_1%3a2.16.0-7_all.deb ... 137s Unpacking bash-completion (1:2.16.0-7) over (1:2.14.0-2) ... 137s Preparing to unpack .../041-libmaxminddb0_1.12.2-1_armhf.deb ... 137s Unpacking libmaxminddb0:armhf (1.12.2-1) over (1.11.0-1) ... 138s Preparing to unpack .../042-liburcu8t64_0.15.0-1_armhf.deb ... 138s Unpacking liburcu8t64:armhf (0.15.0-1) over (0.14.1-1) ... 138s Preparing to unpack .../043-bind9-dnsutils_1%3a9.20.0-2ubuntu4_armhf.deb ... 138s Unpacking bind9-dnsutils (1:9.20.0-2ubuntu4) over (1:9.20.0-2ubuntu3) ... 138s Preparing to unpack .../044-bind9-host_1%3a9.20.0-2ubuntu4_armhf.deb ... 138s Unpacking bind9-host (1:9.20.0-2ubuntu4) over (1:9.20.0-2ubuntu3) ... 138s Preparing to unpack .../045-bind9-libs_1%3a9.20.0-2ubuntu4_armhf.deb ... 138s Unpacking bind9-libs:armhf (1:9.20.0-2ubuntu4) over (1:9.20.0-2ubuntu3) ... 138s Preparing to unpack .../046-libedit2_3.1-20250104-1_armhf.deb ... 138s Unpacking libedit2:armhf (3.1-20250104-1) over (3.1-20240808-1) ... 138s Preparing to unpack .../047-busybox-static_1%3a1.37.0-4ubuntu1_armhf.deb ... 138s Unpacking busybox-static (1:1.37.0-4ubuntu1) over (1:1.36.1-9ubuntu1) ... 138s Preparing to unpack .../048-cron-daemon-common_3.0pl1-192ubuntu1_all.deb ... 138s Unpacking cron-daemon-common (3.0pl1-192ubuntu1) over (3.0pl1-189ubuntu1) ... 138s Preparing to unpack .../049-libdevmapper1.02.1_2%3a1.02.201-1ubuntu1_armhf.deb ... 138s Unpacking libdevmapper1.02.1:armhf (2:1.02.201-1ubuntu1) over (2:1.02.196-1ubuntu2) ... 138s Preparing to unpack .../050-dmsetup_2%3a1.02.201-1ubuntu1_armhf.deb ... 138s Unpacking dmsetup (2:1.02.201-1ubuntu1) over (2:1.02.196-1ubuntu2) ... 138s Preparing to unpack .../051-ed_1.21-1_armhf.deb ... 138s Unpacking ed (1.21-1) over (1.20.2-2) ... 138s Preparing to unpack .../052-gettext-base_0.23.1-1_armhf.deb ... 138s Unpacking gettext-base (0.23.1-1) over (0.22.5-2) ... 138s Preparing to unpack .../053-groff-base_1.23.0-7_armhf.deb ... 138s Unpacking groff-base (1.23.0-7) over (1.23.0-5) ... 138s Preparing to unpack .../054-libibverbs1_55.0-1ubuntu1_armhf.deb ... 138s Unpacking libibverbs1:armhf (55.0-1ubuntu1) over (52.0-2ubuntu1) ... 138s Preparing to unpack .../055-ibverbs-providers_55.0-1ubuntu1_armhf.deb ... 138s Unpacking ibverbs-providers:armhf (55.0-1ubuntu1) over (52.0-2ubuntu1) ... 139s Preparing to unpack .../056-iputils-tracepath_3%3a20240905-1ubuntu1_armhf.deb ... 139s Unpacking iputils-tracepath (3:20240905-1ubuntu1) over (3:20240117-1build1) ... 139s Preparing to unpack .../057-nftables_1.1.1-1build1_armhf.deb ... 139s Unpacking nftables (1.1.1-1build1) over (1.1.0-2) ... 139s Preparing to unpack .../058-libnftables1_1.1.1-1build1_armhf.deb ... 139s Unpacking libnftables1:armhf (1.1.1-1build1) over (1.1.0-2) ... 139s Preparing to unpack .../059-libpcap0.8t64_1.10.5-2ubuntu1_armhf.deb ... 139s Unpacking libpcap0.8t64:armhf (1.10.5-2ubuntu1) over (1.10.5-1ubuntu1) ... 139s Preparing to unpack .../060-libpng16-16t64_1.6.46-4_armhf.deb ... 139s Unpacking libpng16-16t64:armhf (1.6.46-4) over (1.6.44-2) ... 139s Preparing to unpack .../061-libtraceevent1-plugin_1%3a1.8.4-2_armhf.deb ... 139s Unpacking libtraceevent1-plugin:armhf (1:1.8.4-2) over (1:1.8.4-1) ... 139s Preparing to unpack .../062-libtraceevent1_1%3a1.8.4-2_armhf.deb ... 139s Unpacking libtraceevent1:armhf (1:1.8.4-2) over (1:1.8.4-1) ... 139s Preparing to unpack .../063-libusb-1.0-0_2%3a1.0.27-2_armhf.deb ... 139s Unpacking libusb-1.0-0:armhf (2:1.0.27-2) over (2:1.0.27-1) ... 139s Preparing to unpack .../064-libxdmcp6_1%3a1.1.5-1_armhf.deb ... 139s Unpacking libxdmcp6:armhf (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 139s Preparing to unpack .../065-libxkbcommon0_1.7.0-2_armhf.deb ... 139s Unpacking libxkbcommon0:armhf (1.7.0-2) over (1.7.0-1) ... 139s Preparing to unpack .../066-lshw_02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1_armhf.deb ... 139s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1) over (02.19.git.2021.06.19.996aaad9c7-2ubuntu2) ... 139s Preparing to unpack .../067-lsof_4.99.4+dfsg-1_armhf.deb ... 139s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 139s Preparing to unpack .../068-liblsof0_4.99.4+dfsg-1_armhf.deb ... 139s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 139s Preparing to unpack .../069-nano_8.3-1_armhf.deb ... 139s Unpacking nano (8.3-1) over (8.2-1) ... 139s Preparing to unpack .../070-pci.ids_0.0~2025.02.12-1_all.deb ... 139s Unpacking pci.ids (0.0~2025.02.12-1) over (0.0~2024.10.24-1) ... 139s Preparing to unpack .../071-powermgmt-base_1.38_all.deb ... 139s Unpacking powermgmt-base (1.38) over (1.37+nmu1ubuntu1) ... 139s Preparing to unpack .../072-psmisc_23.7-2_armhf.deb ... 139s Unpacking psmisc (23.7-2) over (23.7-1build1) ... 139s Preparing to unpack .../073-publicsuffix_20250108.1153-0.1_all.deb ... 139s Unpacking publicsuffix (20250108.1153-0.1) over (20231001.0357-0.1) ... 139s Preparing to unpack .../074-python3-distro-info_1.13_all.deb ... 140s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 140s for fn in glob1(directory, "%s.*" % fname): 140s Unpacking python3-distro-info (1.13) over (1.12) ... 140s Preparing to unpack .../075-python3.13-gdbm_3.13.2-1_armhf.deb ... 140s Unpacking python3.13-gdbm (3.13.2-1) over (3.13.0-2) ... 140s Preparing to unpack .../076-python3.12-gdbm_3.12.9-1_armhf.deb ... 140s Unpacking python3.12-gdbm (3.12.9-1) over (3.12.7-3) ... 140s Preparing to unpack .../077-python3-gdbm_3.13.1-1_armhf.deb ... 140s Unpacking python3-gdbm:armhf (3.13.1-1) over (3.12.7-1) ... 140s Preparing to unpack .../078-ubuntu-standard_1.547_armhf.deb ... 140s Unpacking ubuntu-standard (1.547) over (1.544) ... 140s Preparing to unpack .../079-ufw_0.36.2-9_all.deb ... 140s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 140s for fn in glob1(directory, "%s.*" % fname): 140s Unpacking ufw (0.36.2-9) over (0.36.2-8) ... 140s Preparing to unpack .../080-usb.ids_2025.01.14-1_all.deb ... 140s Unpacking usb.ids (2025.01.14-1) over (2024.07.04-1) ... 140s Preparing to unpack .../081-xauth_1%3a1.1.2-1.1_armhf.deb ... 140s Unpacking xauth (1:1.1.2-1.1) over (1:1.1.2-1build1) ... 140s Preparing to unpack .../082-libcurl3t64-gnutls_8.12.0+git20250209.89ed161+ds-1ubuntu1_armhf.deb ... 140s Unpacking libcurl3t64-gnutls:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) over (8.11.0-1ubuntu2) ... 140s Preparing to unpack .../083-libappstream5_1.0.4-1_armhf.deb ... 140s Unpacking libappstream5:armhf (1.0.4-1) over (1.0.3-1) ... 140s Preparing to unpack .../084-appstream_1.0.4-1_armhf.deb ... 140s Unpacking appstream (1.0.4-1) over (1.0.3-1) ... 141s Preparing to unpack .../085-libctf0_2.44-1ubuntu1_armhf.deb ... 141s Unpacking libctf0:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 141s Preparing to unpack .../086-libctf-nobfd0_2.44-1ubuntu1_armhf.deb ... 141s Unpacking libctf-nobfd0:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 141s Preparing to unpack .../087-binutils-arm-linux-gnueabihf_2.44-1ubuntu1_armhf.deb ... 141s Unpacking binutils-arm-linux-gnueabihf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 141s Preparing to unpack .../088-libbinutils_2.44-1ubuntu1_armhf.deb ... 141s Unpacking libbinutils:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 141s Preparing to unpack .../089-binutils_2.44-1ubuntu1_armhf.deb ... 141s Unpacking binutils (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 141s Preparing to unpack .../090-binutils-common_2.44-1ubuntu1_armhf.deb ... 141s Unpacking binutils-common:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 141s Preparing to unpack .../091-libsframe1_2.44-1ubuntu1_armhf.deb ... 141s Unpacking libsframe1:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 141s Preparing to unpack .../092-btrfs-progs_6.12-1build1_armhf.deb ... 141s Unpacking btrfs-progs (6.12-1build1) over (6.6.3-1.2) ... 141s Preparing to unpack .../093-python3-jinja2_3.1.5-2_all.deb ... 141s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 141s for fn in glob1(directory, "%s.*" % fname): 141s Unpacking python3-jinja2 (3.1.5-2) over (3.1.3-1ubuntu1) ... 141s Preparing to unpack .../094-python3-json-pointer_2.4-3_all.deb ... 141s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 141s for fn in glob1(directory, "%s.*" % fname): 141s Unpacking python3-json-pointer (2.4-3) over (2.4-2) ... 142s Preparing to unpack .../095-python3-jsonpatch_1.32-5_all.deb ... 142s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 142s for fn in glob1(directory, "%s.*" % fname): 142s Unpacking python3-jsonpatch (1.32-5) over (1.32-4) ... 142s Preparing to unpack .../096-python3-attr_25.1.0-1_all.deb ... 142s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 142s for fn in glob1(directory, "%s.*" % fname): 142s Unpacking python3-attr (25.1.0-1) over (23.2.0-2) ... 142s Preparing to unpack .../097-python3-referencing_0.35.1-2ubuntu1_all.deb ... 142s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 142s for fn in glob1(directory, "%s.*" % fname): 142s Unpacking python3-referencing (0.35.1-2ubuntu1) over (0.35.1-1ubuntu1) ... 142s Preparing to unpack .../098-python3-jsonschema_4.19.2-6ubuntu1_all.deb ... 142s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 142s for fn in glob1(directory, "%s.*" % fname): 142s Unpacking python3-jsonschema (4.19.2-6ubuntu1) over (4.19.2-3ubuntu1) ... 142s Preparing to unpack .../099-python3-jwt_2.10.1-2_all.deb ... 142s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 142s for fn in glob1(directory, "%s.*" % fname): 142s Unpacking python3-jwt (2.10.1-2) over (2.7.0-1) ... 142s Preparing to unpack .../100-python3-oauthlib_3.2.2-3_all.deb ... 142s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 142s for fn in glob1(directory, "%s.*" % fname): 142s Unpacking python3-oauthlib (3.2.2-3) over (3.2.2-2) ... 142s Preparing to unpack .../101-cloud-init-base_25.1~3geb1965a4-0ubuntu1_all.deb ... 143s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 143s for fn in glob1(directory, "%s.*" % fname): 143s Unpacking cloud-init-base (25.1~3geb1965a4-0ubuntu1) over (24.4-0ubuntu1) ... 143s dpkg: warning: unable to delete old directory '/lib/systemd/system/sshd-keygen@.service.d': Directory not empty 143s Preparing to unpack .../102-curl_8.12.0+git20250209.89ed161+ds-1ubuntu1_armhf.deb ... 143s Unpacking curl (8.12.0+git20250209.89ed161+ds-1ubuntu1) over (8.11.0-1ubuntu2) ... 143s Preparing to unpack .../103-libcurl4t64_8.12.0+git20250209.89ed161+ds-1ubuntu1_armhf.deb ... 143s Unpacking libcurl4t64:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) over (8.11.0-1ubuntu2) ... 143s Preparing to unpack .../104-dpkg-dev_1.22.11ubuntu4_all.deb ... 143s Unpacking dpkg-dev (1.22.11ubuntu4) over (1.22.11ubuntu3) ... 143s Preparing to unpack .../105-libdpkg-perl_1.22.11ubuntu4_all.deb ... 143s Unpacking libdpkg-perl (1.22.11ubuntu4) over (1.22.11ubuntu3) ... 143s Preparing to unpack .../106-make_4.4.1-1_armhf.deb ... 143s Unpacking make (4.4.1-1) over (4.3-4.1build2) ... 143s Preparing to unpack .../107-libarchive13t64_3.7.7-0ubuntu1_armhf.deb ... 143s Unpacking libarchive13t64:armhf (3.7.7-0ubuntu1) over (3.7.4-1.1) ... 143s Preparing to unpack .../108-libjson-glib-1.0-common_1.10.6+ds-1_all.deb ... 143s Unpacking libjson-glib-1.0-common (1.10.6+ds-1) over (1.10.0+ds-3) ... 143s Preparing to unpack .../109-libjson-glib-1.0-0_1.10.6+ds-1_armhf.deb ... 143s Unpacking libjson-glib-1.0-0:armhf (1.10.6+ds-1) over (1.10.0+ds-3) ... 143s Preparing to unpack .../110-fwupd_2.0.5-1_armhf.deb ... 144s Unpacking fwupd (2.0.5-1) over (2.0.2-1) ... 144s Preparing to unpack .../111-libfwupd3_2.0.5-1_armhf.deb ... 144s Unpacking libfwupd3:armhf (2.0.5-1) over (2.0.2-1) ... 144s Preparing to unpack .../112-polkitd_126-2_armhf.deb ... 144s Unpacking polkitd (126-2) over (125-2ubuntu1) ... 144s Preparing to unpack .../113-libpolkit-agent-1-0_126-2_armhf.deb ... 144s Unpacking libpolkit-agent-1-0:armhf (126-2) over (125-2ubuntu1) ... 144s Preparing to unpack .../114-libpolkit-gobject-1-0_126-2_armhf.deb ... 144s Unpacking libpolkit-gobject-1-0:armhf (126-2) over (125-2ubuntu1) ... 144s Preparing to unpack .../115-libprotobuf-c1_1.5.1-1ubuntu1_armhf.deb ... 144s Unpacking libprotobuf-c1:armhf (1.5.1-1ubuntu1) over (1.4.1-1ubuntu4) ... 145s Preparing to unpack .../116-libqmi-proxy_1.35.6-1_armhf.deb ... 145s Unpacking libqmi-proxy (1.35.6-1) over (1.35.2-0ubuntu2) ... 145s Preparing to unpack .../117-libqmi-glib5_1.35.6-1_armhf.deb ... 145s Unpacking libqmi-glib5:armhf (1.35.6-1) over (1.35.2-0ubuntu2) ... 145s Preparing to unpack .../118-libpackagekit-glib2-18_1.3.0-3build1_armhf.deb ... 145s Unpacking libpackagekit-glib2-18:armhf (1.3.0-3build1) over (1.3.0-2) ... 145s Preparing to unpack .../119-gir1.2-packagekitglib-1.0_1.3.0-3build1_armhf.deb ... 145s Unpacking gir1.2-packagekitglib-1.0 (1.3.0-3build1) over (1.3.0-2) ... 145s Preparing to unpack .../120-gnupg-l10n_2.4.4-2ubuntu22_all.deb ... 145s Unpacking gnupg-l10n (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 145s Preparing to unpack .../121-htop_3.3.0-5_armhf.deb ... 145s Unpacking htop (3.3.0-5) over (3.3.0-4build1) ... 145s Preparing to unpack .../122-libblockdev-utils3_3.3.0-1_armhf.deb ... 145s Unpacking libblockdev-utils3:armhf (3.3.0-1) over (3.2.1-1) ... 145s Preparing to unpack .../123-libnspr4_2%3a4.36-1ubuntu1_armhf.deb ... 145s Unpacking libnspr4:armhf (2:4.36-1ubuntu1) over (2:4.35-1.1ubuntu2) ... 145s Preparing to unpack .../124-libnss3_2%3a3.107-1ubuntu1_armhf.deb ... 145s Unpacking libnss3:armhf (2:3.107-1ubuntu1) over (2:3.103-1) ... 145s Preparing to unpack .../125-libgpgme11t64_1.24.2-1ubuntu1_armhf.deb ... 145s Unpacking libgpgme11t64:armhf (1.24.2-1ubuntu1) over (1.24.0-2ubuntu1) ... 145s Preparing to unpack .../126-libvolume-key1_0.3.12-9_armhf.deb ... 145s Unpacking libvolume-key1:armhf (0.3.12-9) over (0.3.12-8) ... 146s Preparing to unpack .../127-libblockdev-crypto3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev-crypto3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../128-libblockdev-fs3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev-fs3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../129-libblockdev-loop3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev-loop3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../130-libblockdev-mdraid3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev-mdraid3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../131-libnvme1t64_1.11.1-2_armhf.deb ... 146s Unpacking libnvme1t64 (1.11.1-2) over (1.11.1-1) ... 146s Preparing to unpack .../132-libblockdev-nvme3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev-nvme3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../133-libblockdev-part3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev-part3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../134-libblockdev-swap3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev-swap3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../135-libblockdev3_3.3.0-1_armhf.deb ... 146s Unpacking libblockdev3:armhf (3.3.0-1) over (3.2.1-1) ... 146s Preparing to unpack .../136-libftdi1-2_1.5-8_armhf.deb ... 146s Unpacking libftdi1-2:armhf (1.5-8) over (1.5-7build1) ... 146s Preparing to unpack .../137-libgstreamer1.0-0_1.25.50-1_armhf.deb ... 146s Unpacking libgstreamer1.0-0:armhf (1.25.50-1) over (1.24.9-1) ... 146s Preparing to unpack .../138-libgudev-1.0-0_1%3a238-6_armhf.deb ... 146s Unpacking libgudev-1.0-0:armhf (1:238-6) over (1:238-5ubuntu1) ... 146s Selecting previously unselected package libicu76:armhf. 146s Preparing to unpack .../139-libicu76_76.1-1ubuntu2_armhf.deb ... 146s Unpacking libicu76:armhf (76.1-1ubuntu2) ... 146s Preparing to unpack .../140-libsasl2-modules_2.1.28+dfsg1-8build1_armhf.deb ... 146s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-8build1) over (2.1.28+dfsg1-8) ... 147s Preparing to unpack .../141-udisks2_2.10.1-11ubuntu2_armhf.deb ... 147s Unpacking udisks2 (2.10.1-11ubuntu2) over (2.10.1-11ubuntu1) ... 147s Preparing to unpack .../142-libudisks2-0_2.10.1-11ubuntu2_armhf.deb ... 147s Unpacking libudisks2-0:armhf (2.10.1-11ubuntu2) over (2.10.1-11ubuntu1) ... 147s Preparing to unpack .../143-libwrap0_7.6.q-35_armhf.deb ... 147s Unpacking libwrap0:armhf (7.6.q-35) over (7.6.q-33) ... 147s Selecting previously unselected package linux-headers-6.12.0-15. 147s Preparing to unpack .../144-linux-headers-6.12.0-15_6.12.0-15.15_all.deb ... 147s Unpacking linux-headers-6.12.0-15 (6.12.0-15.15) ... 150s Selecting previously unselected package linux-headers-6.12.0-15-generic. 150s Preparing to unpack .../145-linux-headers-6.12.0-15-generic_6.12.0-15.15_armhf.deb ... 150s Unpacking linux-headers-6.12.0-15-generic (6.12.0-15.15) ... 152s Preparing to unpack .../146-linux-headers-generic_6.12.0-15.15+1_armhf.deb ... 152s Unpacking linux-headers-generic (6.12.0-15.15+1) over (6.11.0-8.8) ... 152s Preparing to unpack .../147-packagekit-tools_1.3.0-3build1_armhf.deb ... 152s Unpacking packagekit-tools (1.3.0-3build1) over (1.3.0-2) ... 152s Preparing to unpack .../148-packagekit_1.3.0-3build1_armhf.deb ... 152s Unpacking packagekit (1.3.0-3build1) over (1.3.0-2) ... 152s Preparing to unpack .../149-pollinate_4.33-4ubuntu2_all.deb ... 152s Unpacking pollinate (4.33-4ubuntu2) over (4.33-4ubuntu1) ... 152s Preparing to unpack .../150-python3-babel_2.17.0-1_all.deb ... 152s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 152s for fn in glob1(directory, "%s.*" % fname): 152s Unpacking python3-babel (2.17.0-1) over (2.16.0-1) ... 152s Preparing to unpack .../151-python-babel-localedata_2.17.0-1_all.deb ... 152s Unpacking python-babel-localedata (2.17.0-1) over (2.16.0-1) ... 153s Preparing to unpack .../152-python3-certifi_2025.1.31+ds-1_all.deb ... 153s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 153s for fn in glob1(directory, "%s.*" % fname): 153s Unpacking python3-certifi (2025.1.31+ds-1) over (2024.8.30+dfsg-1) ... 153s Preparing to unpack .../153-python3-chardet_5.2.0+dfsg-2_all.deb ... 153s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 153s for fn in glob1(directory, "%s.*" % fname): 153s Unpacking python3-chardet (5.2.0+dfsg-2) over (5.2.0+dfsg-1) ... 153s Preparing to unpack .../154-python3-idna_3.10-1_all.deb ... 154s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 154s for fn in glob1(directory, "%s.*" % fname): 154s Unpacking python3-idna (3.10-1) over (3.8-2) ... 154s Preparing to unpack .../155-python3-more-itertools_10.6.0-1_all.deb ... 154s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 154s for fn in glob1(directory, "%s.*" % fname): 154s Unpacking python3-more-itertools (10.6.0-1) over (10.5.0-1) ... 154s Preparing to unpack .../156-python3-openssl_25.0.0-1_all.deb ... 154s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 154s for fn in glob1(directory, "%s.*" % fname): 154s Unpacking python3-openssl (25.0.0-1) over (24.2.1-1) ... 154s Preparing to unpack .../157-python3-pkg-resources_75.6.0-1_all.deb ... 154s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 154s for fn in glob1(directory, "%s.*" % fname): 154s Unpacking python3-pkg-resources (75.6.0-1) over (75.2.0-1) ... 154s Preparing to unpack .../158-python3-setuptools_75.6.0-1_all.deb ... 154s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 154s for fn in glob1(directory, "%s.*" % fname): 154s Unpacking python3-setuptools (75.6.0-1) over (75.2.0-1) ... 155s Preparing to unpack .../159-software-properties-common_0.108_all.deb ... 155s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 155s for fn in glob1(directory, "%s.*" % fname): 155s Unpacking software-properties-common (0.108) over (0.105) ... 155s Preparing to unpack .../160-python3-software-properties_0.108_all.deb ... 155s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 155s for fn in glob1(directory, "%s.*" % fname): 155s Unpacking python3-software-properties (0.108) over (0.105) ... 155s Preparing to unpack .../161-python3-urllib3_2.3.0-1_all.deb ... 156s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 156s for fn in glob1(directory, "%s.*" % fname): 156s Unpacking python3-urllib3 (2.3.0-1) over (2.0.7-2ubuntu0.1) ... 156s Preparing to unpack .../162-python3-wadllib_2.0.0-2_all.deb ... 156s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 156s for fn in glob1(directory, "%s.*" % fname): 156s Unpacking python3-wadllib (2.0.0-2) over (2.0.0-1) ... 156s Preparing to unpack .../163-unattended-upgrades_2.12ubuntu2_all.deb ... 156s Unpacking unattended-upgrades (2.12ubuntu2) over (2.9.1+nmu4ubuntu1) ... 156s dpkg: warning: unable to delete old directory '/lib/systemd/system-sleep': Directory not empty 156s Preparing to unpack .../164-xfsprogs_6.12.0-1ubuntu1_armhf.deb ... 156s Unpacking xfsprogs (6.12.0-1ubuntu1) over (6.8.0-2.2ubuntu2) ... 156s Preparing to unpack .../165-zstd_1.5.6+dfsg-2_armhf.deb ... 156s Unpacking zstd (1.5.6+dfsg-2) over (1.5.6+dfsg-1) ... 156s Preparing to unpack .../166-cloud-init_25.1~3geb1965a4-0ubuntu1_all.deb ... 156s Unpacking cloud-init (25.1~3geb1965a4-0ubuntu1) over (24.4-0ubuntu1) ... 156s Preparing to unpack .../167-kpartx_0.9.9-1ubuntu4_armhf.deb ... 156s Unpacking kpartx (0.9.9-1ubuntu4) over (0.9.9-1ubuntu3) ... 156s Preparing to unpack .../168-multipath-tools_0.9.9-1ubuntu4_armhf.deb ... 156s Unpacking multipath-tools (0.9.9-1ubuntu4) over (0.9.9-1ubuntu3) ... 156s Setting up libip4tc2:armhf (1.8.11-2ubuntu1) ... 156s Setting up powermgmt-base (1.38) ... 156s Setting up distro-info (1.13) ... 156s Setting up liburcu8t64:armhf (0.15.0-1) ... 156s Setting up libibverbs1:armhf (55.0-1ubuntu1) ... 156s Setting up libxdmcp6:armhf (1:1.1.5-1) ... 156s Setting up pci.ids (0.0~2025.02.12-1) ... 156s Setting up libnewt0.52:armhf (0.52.24-4ubuntu1) ... 156s Setting up apt-utils (2.9.30) ... 156s Setting up bsdextrautils (2.40.2-14ubuntu1) ... 156s Setting up init (1.68) ... 156s Setting up ibverbs-providers:armhf (55.0-1ubuntu1) ... 156s Setting up gcc-14-base:armhf (14.2.0-17ubuntu1) ... 156s Setting up psmisc (23.7-2) ... 156s Setting up libyaml-0-2:armhf (0.2.5-2) ... 156s Setting up libip6tc2:armhf (1.8.11-2ubuntu1) ... 156s Setting up liblsof0 (4.99.4+dfsg-1) ... 156s Setting up libmaxminddb0:armhf (1.12.2-1) ... 156s Setting up python3.12-gdbm (3.12.9-1) ... 156s Setting up libedit2:armhf (3.1-20250104-1) ... 156s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-8build1) ... 156s Setting up netcat-openbsd (1.228-1) ... 156s Setting up libpython3.12-minimal:armhf (3.12.9-1) ... 156s Setting up binutils-common:armhf (2.44-1ubuntu1) ... 156s Setting up libctf-nobfd0:armhf (2.44-1ubuntu1) ... 156s Setting up gettext-base (0.23.1-1) ... 156s Setting up libnss-systemd:armhf (257.2-3ubuntu1) ... 156s Setting up libnftnl11:armhf (1.2.8-1) ... 156s Setting up krb5-locales (1.21.3-4ubuntu1) ... 157s Setting up libcom-err2:armhf (1.47.2-1ubuntu1) ... 157s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1) ... 157s Setting up locales (2.40-4ubuntu1) ... 158s Generating locales (this might take a while)... 160s en_US.UTF-8... done 160s Generation complete. 160s Setting up libldap-common (2.6.9+dfsg-1~exp2ubuntu1) ... 160s Installing new version of config file /etc/ldap/ldap.conf ... 160s Setting up libprotobuf-c1:armhf (1.5.1-1ubuntu1) ... 160s Setting up libsframe1:armhf (2.44-1ubuntu1) ... 160s Setting up python-babel-localedata (2.17.0-1) ... 160s Setting up libkrb5support0:armhf (1.21.3-4ubuntu1) ... 160s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8build1) ... 160s Setting up tzdata (2025a-2ubuntu1) ... 160s 160s Current default time zone: 'Etc/UTC' 160s Local time is now: Wed Feb 19 13:31:34 UTC 2025. 160s Universal Time is now: Wed Feb 19 13:31:34 UTC 2025. 160s Run 'dpkg-reconfigure tzdata' if you wish to change it. 160s 160s Setting up eject (2.40.2-14ubuntu1) ... 160s Setting up apparmor (4.1.0~beta1-0ubuntu5) ... 160s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 160s 160s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 160s 160s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 160s 161s Reloading AppArmor profiles 161s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "busybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "nautilus". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "toybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 162s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 162s 162s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 162s 162s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 162s 162s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 162s 162s Error: At least one profile failed to load 162s Setting up libglib2.0-data (2.83.3-2) ... 162s Setting up busybox-static (1:1.37.0-4ubuntu1) ... 162s Setting up systemd-cryptsetup (257.2-3ubuntu1) ... 162s Setting up libwrap0:armhf (7.6.q-35) ... 162s Setting up libnvme1t64 (1.11.1-2) ... 162s Setting up make (4.4.1-1) ... 162s Setting up libnspr4:armhf (2:4.36-1ubuntu1) ... 162s Setting up gnupg-l10n (2.4.4-2ubuntu22) ... 162s Setting up ed (1.21-1) ... 162s Setting up bash-completion (1:2.16.0-7) ... 162s Setting up libncurses6:armhf (6.5+20250125-2) ... 162s Setting up libdbus-1-3:armhf (1.16.0-1ubuntu1) ... 162s Setting up libfribidi0:armhf (1.0.16-1) ... 162s Setting up libpng16-16t64:armhf (1.6.46-4) ... 162s Setting up systemd-timesyncd (257.2-3ubuntu1) ... 162s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 162s Setting up libatomic1:armhf (15-20250213-1ubuntu1) ... 162s Setting up udev (257.2-3ubuntu1) ... 163s Setting up libss2:armhf (1.47.2-1ubuntu1) ... 163s Setting up usb.ids (2025.01.14-1) ... 163s Setting up dhcpcd-base (1:10.1.0-7) ... 163s Installing new version of config file /etc/dhcpcd.conf ... 163s Setting up ucf (3.0049) ... 163s Installing new version of config file /etc/ucf.conf ... 163s Setting up libncursesw6:armhf (6.5+20250125-2) ... 163s Setting up libk5crypto3:armhf (1.21.3-4ubuntu1) ... 163s Setting up busybox-initramfs (1:1.37.0-4ubuntu1) ... 164s Setting up libxtables12:armhf (1.8.11-2ubuntu1) ... 164s Setting up libdpkg-perl (1.22.11ubuntu4) ... 164s Setting up logsave (1.47.2-1ubuntu1) ... 164s Setting up libsasl2-2:armhf (2.1.28+dfsg1-8build1) ... 164s Setting up lsof (4.99.4+dfsg-1) ... 164s Setting up libfdisk1:armhf (2.40.2-14ubuntu1) ... 164s Setting up libicu74:armhf (74.2-1ubuntu6) ... 164s Setting up nano (8.3-1) ... 164s Installing new version of config file /etc/nanorc ... 164s Setting up libdevmapper1.02.1:armhf (2:1.02.201-1ubuntu1) ... 164s Setting up whiptail (0.52.24-4ubuntu1) ... 164s Setting up python-apt-common (2.9.8) ... 164s Setting up dracut-install (106-2ubuntu1) ... 164s Setting up dmsetup (2:1.02.201-1ubuntu1) ... 164s Setting up uuid-runtime (2.40.2-14ubuntu1) ... 164s uuidd.service is a disabled or a static unit not running, not starting it. 164s Setting up xauth (1:1.1.2-1.1) ... 164s Setting up groff-base (1.23.0-7) ... 164s Setting up libtraceevent1:armhf (1:1.8.4-2) ... 164s Setting up dbus-session-bus-common (1.16.0-1ubuntu1) ... 164s Setting up kpartx (0.9.9-1ubuntu4) ... 164s Setting up libpcap0.8t64:armhf (1.10.5-2ubuntu1) ... 164s Setting up libjson-glib-1.0-common (1.10.6+ds-1) ... 164s Setting up mawk (1.3.4.20250131-1) ... 164s Setting up libkrb5-3:armhf (1.21.3-4ubuntu1) ... 164s Setting up libusb-1.0-0:armhf (2:1.0.27-2) ... 164s Setting up libicu76:armhf (76.1-1ubuntu2) ... 164s Setting up linux-headers-6.12.0-15 (6.12.0-15.15) ... 164s Setting up keyboard-configuration (1.226ubuntu3) ... 166s Your console font configuration will be updated the next time your system 166s boots. If you want to update it now, run 'setupcon' from a virtual console. 166s update-initramfs: deferring update (trigger activated) 166s Setting up libbinutils:armhf (2.44-1ubuntu1) ... 166s Setting up dbus-system-bus-common (1.16.0-1ubuntu1) ... 166s Setting up openssl (3.4.0-1ubuntu2) ... 166s Installing new version of config file /etc/ssl/openssl.cnf ... 166s Setting up libgpg-error-l10n (1.51-3) ... 166s Setting up iputils-ping (3:20240905-1ubuntu1) ... 166s Setting up readline-common (8.2-6) ... 166s Setting up publicsuffix (20250108.1153-0.1) ... 166s Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2ubuntu3) ... 166s Setting up zstd (1.5.6+dfsg-2) ... 166s Setting up libldap2:armhf (2.6.9+dfsg-1~exp2ubuntu1) ... 166s Setting up dbus-bin (1.16.0-1ubuntu1) ... 166s Setting up libbpf1:armhf (1:1.5.0-2) ... 166s Setting up iputils-tracepath (3:20240905-1ubuntu1) ... 166s Setting up rsync (3.4.1-0syncable1) ... 167s rsync.service is a disabled or a static unit not running, not starting it. 167s Setting up python3.13-gdbm (3.13.2-1) ... 167s Setting up ethtool (1:6.11-1) ... 167s Setting up gnupg-utils (2.4.4-2ubuntu22) ... 167s Setting up initramfs-tools-bin (0.145ubuntu2) ... 167s Setting up ncurses-term (6.5+20250125-2) ... 167s Setting up login (1:4.16.0-2+really2.40.2-14ubuntu1) ... 167s Setting up cron-daemon-common (3.0pl1-192ubuntu1) ... 167s Setting up libxkbcommon0:armhf (1.7.0-2) ... 167s Setting up libctf0:armhf (2.44-1ubuntu1) ... 167s Setting up pinentry-curses (1.3.1-2ubuntu2) ... 167s Setting up python3.12-minimal (3.12.9-1) ... 168s Setting up libnftables1:armhf (1.1.1-1build1) ... 168s Setting up nftables (1.1.1-1build1) ... 168s Setting up iptables (1.8.11-2ubuntu1) ... 168s Setting up htop (3.3.0-5) ... 168s Setting up iproute2 (6.13.0-1ubuntu1) ... 169s Setting up btrfs-progs (6.12-1build1) ... 169s Setting up cron (3.0pl1-192ubuntu1) ... 169s Setting up rsyslog (8.2412.0-2ubuntu1) ... 169s Installing new version of config file /etc/apparmor.d/usr.sbin.rsyslogd ... 170s info: The user `syslog' is already a member of `adm'. 170s apparmor_parser: Unable to replace "rsyslogd". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 170s 171s Setting up e2fsprogs (1.47.2-1ubuntu1) ... 171s update-initramfs: deferring update (trigger activated) 172s Setting up libnss3:armhf (2:3.107-1ubuntu1) ... 172s Setting up dbus-daemon (1.16.0-1ubuntu1) ... 172s Setting up multipath-tools (0.9.9-1ubuntu4) ... 172s Setting up libftdi1-2:armhf (1.5-8) ... 172s Setting up ca-certificates (20241223) ... 176s Updating certificates in /etc/ssl/certs... 178s rehash: warning: skipping ca-certificates.crt, it does not contain exactly one certificate or CRL 178s 7 added, 1 removed; done. 178s Setting up libglib2.0-0t64:armhf (2.83.3-2) ... 178s No schema files found: doing nothing. 178s Setting up dbus (1.16.0-1ubuntu1) ... 178s A reboot is required to replace the running dbus-daemon. 178s Please reboot the system when convenient. 178s Setting up libblockdev-utils3:armhf (3.3.0-1) ... 178s Setting up linux-headers-6.12.0-15-generic (6.12.0-15.15) ... 178s Setting up libgssapi-krb5-2:armhf (1.21.3-4ubuntu1) ... 178s Setting up gir1.2-glib-2.0:armhf (2.83.3-2) ... 178s Setting up libreadline8t64:armhf (8.2-6) ... 178s Setting up libblockdev-nvme3:armhf (3.3.0-1) ... 178s Setting up libblockdev-fs3:armhf (3.3.0-1) ... 178s Setting up libtraceevent1-plugin:armhf (1:1.8.4-2) ... 178s Setting up gpgconf (2.4.4-2ubuntu22) ... 178s Setting up libpam-systemd:armhf (257.2-3ubuntu1) ... 179s Setting up libgirepository-1.0-1:armhf (1.82.0-4) ... 179s Setting up console-setup-linux (1.226ubuntu3) ... 180s Setting up initramfs-tools-core (0.145ubuntu2) ... 180s Setting up binutils-arm-linux-gnueabihf (2.44-1ubuntu1) ... 180s Setting up libarchive13t64:armhf (3.7.7-0ubuntu1) ... 180s Setting up libpython3.13-stdlib:armhf (3.13.2-1) ... 180s Setting up gpg (2.4.4-2ubuntu22) ... 180s Setting up libgudev-1.0-0:armhf (1:238-6) ... 180s Setting up libpolkit-gobject-1-0:armhf (126-2) ... 180s Setting up libgstreamer1.0-0:armhf (1.25.50-1) ... 180s Setcap worked! gst-ptp-helper is not suid! 180s Setting up libudisks2-0:armhf (2.10.1-11ubuntu2) ... 180s Setting up libpython3-stdlib:armhf (3.13.1-1~exp2) ... 180s Setting up systemd-resolved (257.2-3ubuntu1) ... 181s Setting up console-setup (1.226ubuntu3) ... 182s update-initramfs: deferring update (trigger activated) 182s Setting up gpg-agent (2.4.4-2ubuntu22) ... 182s Setting up libpython3.12-stdlib:armhf (3.12.9-1) ... 182s Setting up initramfs-tools (0.145ubuntu2) ... 182s update-initramfs: deferring update (trigger activated) 182s Setting up libblockdev-mdraid3:armhf (3.3.0-1) ... 182s Setting up libcurl4t64:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) ... 182s Setting up bind9-libs:armhf (1:9.20.0-2ubuntu4) ... 182s Setting up e2fsprogs-l10n (1.47.2-1ubuntu1) ... 182s Setting up python3.13 (3.13.2-1) ... 184s Setting up libblockdev-swap3:armhf (3.3.0-1) ... 184s Setting up python3.12 (3.12.9-1) ... 185s Setting up libblockdev-loop3:armhf (3.3.0-1) ... 185s Setting up gpgsm (2.4.4-2ubuntu22) ... 185s Setting up libcurl3t64-gnutls:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) ... 185s Setting up libglib2.0-bin (2.83.3-2) ... 185s Setting up libpackagekit-glib2-18:armhf (1.3.0-3build1) ... 185s Setting up libappstream5:armhf (1.0.4-1) ... 185s Setting up libqmi-glib5:armhf (1.35.6-1) ... 185s Setting up python3 (3.13.1-1~exp2) ... 185s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 185s for fn in glob1(directory, "%s.*" % fname): 185s Setting up linux-headers-generic (6.12.0-15.15+1) ... 185s Setting up binutils (2.44-1ubuntu1) ... 185s Setting up libnetplan1:armhf (1.1.2-2ubuntu1) ... 185s Setting up python3-newt:armhf (0.52.24-4ubuntu1) ... 186s Setting up libblockdev3:armhf (3.3.0-1) ... 186s Setting up fdisk (2.40.2-14ubuntu1) ... 186s Setting up dpkg-dev (1.22.11ubuntu4) ... 186s Setting up libjson-glib-1.0-0:armhf (1.10.6+ds-1) ... 186s Setting up libblockdev-part3:armhf (3.3.0-1) ... 186s Setting up dirmngr (2.4.4-2ubuntu22) ... 186s Setting up gir1.2-packagekitglib-1.0 (1.3.0-3build1) ... 186s Setting up dbus-user-session (1.16.0-1ubuntu1) ... 186s Setting up python3-jinja2 (3.1.5-2) ... 186s Setting up python3-pygments (2.18.0+dfsg-2) ... 188s Setting up python3-chardet (5.2.0+dfsg-2) ... 189s Setting up appstream (1.0.4-1) ... 191s ✔ Metadata cache was updated successfully. 191s Setting up python3-certifi (2025.1.31+ds-1) ... 192s Setting up gir1.2-girepository-2.0:armhf (1.82.0-4) ... 192s Setting up python3-gi (3.50.0-4) ... 192s Setting up python3-idna (3.10-1) ... 192s Setting up xfsprogs (6.12.0-1ubuntu1) ... 192s update-initramfs: deferring update (trigger activated) 193s Setting up keyboxd (2.4.4-2ubuntu22) ... 193s Setting up python3-urllib3 (2.3.0-1) ... 194s Setting up python3-json-pointer (2.4-3) ... 194s Setting up gnupg (2.4.4-2ubuntu22) ... 194s Setting up python3-netplan (1.1.2-2ubuntu1) ... 194s Setting up libpolkit-agent-1-0:armhf (126-2) ... 194s Setting up libgpgme11t64:armhf (1.24.2-1ubuntu1) ... 194s Setting up curl (8.12.0+git20250209.89ed161+ds-1ubuntu1) ... 194s Setting up libvolume-key1:armhf (0.3.12-9) ... 194s Setting up netplan-generator (1.1.2-2ubuntu1) ... 194s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 194s Setting up bind9-host (1:9.20.0-2ubuntu4) ... 194s Setting up python3-distro-info (1.13) ... 195s Setting up polkitd (126-2) ... 195s Setting up python3-more-itertools (10.6.0-1) ... 196s Setting up python3-attr (25.1.0-1) ... 196s Setting up gpg-wks-client (2.4.4-2ubuntu22) ... 196s Setting up libblockdev-crypto3:armhf (3.3.0-1) ... 196s Setting up python3-jwt (2.10.1-2) ... 196s Setting up python3-babel (2.17.0-1) ... 197s Setting up python3-rich (13.9.4-1) ... 198s Setting up python3-gdbm:armhf (3.13.1-1) ... 198s Setting up python3-problem-report (2.31.0-0ubuntu5) ... 198s Setting up python3-apt (2.9.8) ... 198s Setting up python3-jsonpatch (1.32-5) ... 198s Setting up python3-bcrypt (4.2.0-2.1) ... 199s Setting up libqmi-proxy (1.35.6-1) ... 199s Setting up libfwupd3:armhf (2.0.5-1) ... 199s Setting up ufw (0.36.2-9) ... 200s Setting up python3-lazr.uri (1.0.6-5) ... 200s Setting up netplan.io (1.1.2-2ubuntu1) ... 200s Setting up unattended-upgrades (2.12ubuntu2) ... 201s Replacing config file /etc/apt/apt.conf.d/50unattended-upgrades with new version 201s Setting up pollinate (4.33-4ubuntu2) ... 202s Setting up python3-cryptography (43.0.0-1) ... 203s Setting up python3-wadllib (2.0.0-2) ... 203s Setting up bind9-dnsutils (1:9.20.0-2ubuntu4) ... 203s Setting up fwupd (2.0.5-1) ... 203s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 203s fwupd.service is a disabled or a static unit not running, not starting it. 204s Setting up python3-referencing (0.35.1-2ubuntu1) ... 204s Setting up python3-pkg-resources (75.6.0-1) ... 204s Setting up udisks2 (2.10.1-11ubuntu2) ... 204s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 204s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 204s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 204s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 204s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 204s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 204s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 204s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 204s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 204s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 204s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 204s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 204s loop8: Failed to write 'change' to '/sys/devices/virtual/block/loop8/uevent': Permission denied 205s Setting up python3-setuptools (75.6.0-1) ... 208s Setting up ubuntu-minimal (1.547) ... 208s Setting up python3-openssl (25.0.0-1) ... 208s Setting up python3-launchpadlib (2.1.0-1) ... 208s Setting up ubuntu-standard (1.547) ... 208s Setting up python3-apport (2.31.0-0ubuntu5) ... 209s Setting up python3-oauthlib (3.2.2-3) ... 209s Setting up python3-software-properties (0.108) ... 209s Setting up python3-jsonschema (4.19.2-6ubuntu1) ... 210s Setting up cloud-init-base (25.1~3geb1965a4-0ubuntu1) ... 210s Installing new version of config file /etc/cloud/templates/sources.list.debian.deb822.tmpl ... 210s Installing new version of config file /etc/cloud/templates/sources.list.ubuntu.deb822.tmpl ... 213s Setting up cloud-init (25.1~3geb1965a4-0ubuntu1) ... 213s Setting up apport-core-dump-handler (2.31.0-0ubuntu5) ... 214s Setting up apport (2.31.0-0ubuntu5) ... 215s apport-autoreport.service is a disabled or a static unit not running, not starting it. 215s Processing triggers for shared-mime-info (2.4-5) ... 215s Warning: program compiled against libxml 212 using older 209 215s Processing triggers for sgml-base (1.31) ... 215s Processing triggers for debianutils (5.21) ... 215s Processing triggers for install-info (7.1.1-1) ... 215s Processing triggers for libc-bin (2.40-4ubuntu1) ... 215s Processing triggers for systemd (257.2-3ubuntu1) ... 216s Processing triggers for man-db (2.13.0-1) ... 217s Setting up packagekit (1.3.0-3build1) ... 218s Setting up packagekit-tools (1.3.0-3build1) ... 218s Setting up software-properties-common (0.108) ... 218s Processing triggers for ca-certificates (20241223) ... 218s Updating certificates in /etc/ssl/certs... 219s 0 added, 0 removed; done. 219s Running hooks in /etc/ca-certificates/update.d... 219s done. 219s Processing triggers for initramfs-tools (0.145ubuntu2) ... 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 224s Starting pkgProblemResolver with broken count: 0 224s Starting 2 pkgProblemResolver with broken count: 0 224s Done 225s The following packages will be REMOVED: 225s libassuan0* libicu74* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 225s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 225s python3.12* python3.12-minimal* 225s 0 upgraded, 0 newly installed, 10 to remove and 0 not upgraded. 225s After this operation, 151 MB disk space will be freed. 225s (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 ... 92763 files and directories currently installed.) 225s Removing libassuan0:armhf (2.5.6-1build1) ... 225s Removing libicu74:armhf (74.2-1ubuntu6) ... 226s Removing python3.12 (3.12.9-1) ... 226s Removing libpython3.12-stdlib:armhf (3.12.9-1) ... 226s Removing libnsl2:armhf (1.3.0-3build3) ... 226s Removing python3.12-minimal (3.12.9-1) ... 226s /usr/bin/py3clean:125: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 226s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 228s Removing libpython3.12-minimal:armhf (3.12.9-1) ... 228s Removing libunwind8:armhf (1.6.2-3.1) ... 228s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 228s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 229s Processing triggers for systemd (257.2-3ubuntu1) ... 230s Processing triggers for man-db (2.13.0-1) ... 230s Processing triggers for libc-bin (2.40-4ubuntu1) ... 230s (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 ... 60307 files and directories currently installed.) 230s Purging configuration files for python3.12-minimal (3.12.9-1) ... 230s Purging configuration files for libpython3.12-minimal:armhf (3.12.9-1) ... 233s autopkgtest [13:32:47]: rebooting testbed after setup commands that affected boot 278s autopkgtest [13:33:32]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 307s autopkgtest [13:34:01]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 325s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (dsc) [2291 B] 325s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (tar) [22.3 MB] 325s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (diff) [9600 B] 325s gpgv: Signature made Wed Jan 29 22:42:44 2025 UTC 325s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 325s gpgv: Can't check signature: No public key 325s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build1.dsc: no acceptable signature found 325s autopkgtest [13:34:19]: testing package tombo version 1.5.1-7build1 328s autopkgtest [13:34:22]: build not needed 332s autopkgtest [13:34:26]: test run-unit-test: preparing testbed 334s Reading package lists... 334s Building dependency tree... 334s Reading state information... 335s Starting pkgProblemResolver with broken count: 0 335s Starting 2 pkgProblemResolver with broken count: 0 335s Done 336s The following NEW packages will be installed: 336s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 336s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 336s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 336s python3-h5py python3-h5py-serial python3-mappy python3-numpy 336s python3-packaging python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 336s tombo-doc 336s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 336s Need to get 64.3 MB of archives. 336s After this operation, 222 MB of additional disk space will be used. 336s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 337s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 337s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 337s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 337s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 337s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250213-1ubuntu1 [330 kB] 337s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 337s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-310 armhf 1.14.5+repack-3 [1410 kB] 338s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [58.8 kB] 338s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 338s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 338s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 338s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 338s Get:14 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 338s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 338s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 338s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-13 [3978 kB] 338s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.12.1-1 [1489 kB] 338s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.12.1-1 [7970 B] 338s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mappy armhf 2.27+dfsg-1build1 [189 kB] 338s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.2-1 [51.5 kB] 338s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.1-2 [92.5 kB] 338s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 338s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu1 [19.5 MB] 339s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo armhf 1.5.1-7build1 [516 kB] 339s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 340s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo-doc all 1.5.1-7build1 [21.7 MB] 341s Fetched 64.3 MB in 5s (13.3 MB/s) 341s Selecting previously unselected package fonts-lato. 341s (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 ... 60305 files and directories currently installed.) 341s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 341s Unpacking fonts-lato (2.015-1) ... 341s Selecting previously unselected package fonts-font-awesome. 341s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 341s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 341s Selecting previously unselected package fonts-mathjax. 342s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 342s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 342s Selecting previously unselected package libaec0:armhf. 342s Preparing to unpack .../03-libaec0_1.1.3-1_armhf.deb ... 342s Unpacking libaec0:armhf (1.1.3-1) ... 342s Selecting previously unselected package libblas3:armhf. 342s Preparing to unpack .../04-libblas3_3.12.1-2_armhf.deb ... 342s Unpacking libblas3:armhf (3.12.1-2) ... 342s Selecting previously unselected package libgfortran5:armhf. 342s Preparing to unpack .../05-libgfortran5_15-20250213-1ubuntu1_armhf.deb ... 342s Unpacking libgfortran5:armhf (15-20250213-1ubuntu1) ... 342s Selecting previously unselected package libsz2:armhf. 342s Preparing to unpack .../06-libsz2_1.1.3-1_armhf.deb ... 342s Unpacking libsz2:armhf (1.1.3-1) ... 342s Selecting previously unselected package libhdf5-310:armhf. 342s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_armhf.deb ... 342s Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... 342s Selecting previously unselected package libhdf5-hl-310:armhf. 342s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_armhf.deb ... 342s Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3) ... 342s Selecting previously unselected package libjs-jquery. 342s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 342s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 342s Selecting previously unselected package libjs-underscore. 342s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 342s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 342s Selecting previously unselected package libjs-sphinxdoc. 342s Preparing to unpack .../11-libjs-sphinxdoc_8.1.3-5_all.deb ... 342s Unpacking libjs-sphinxdoc (8.1.3-5) ... 342s Selecting previously unselected package liblapack3:armhf. 342s Preparing to unpack .../12-liblapack3_3.12.1-2_armhf.deb ... 342s Unpacking liblapack3:armhf (3.12.1-2) ... 342s Selecting previously unselected package liblbfgsb0:armhf. 342s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 342s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 342s Selecting previously unselected package liblzf1:armhf. 342s Preparing to unpack .../14-liblzf1_3.6-4_armhf.deb ... 342s Unpacking liblzf1:armhf (3.6-4) ... 342s Selecting previously unselected package python3-decorator. 342s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 342s Unpacking python3-decorator (5.1.1-5) ... 342s Selecting previously unselected package python3-numpy. 342s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-13_armhf.deb ... 342s Unpacking python3-numpy (1:1.26.4+ds-13) ... 343s Selecting previously unselected package python3-h5py-serial. 343s Preparing to unpack .../17-python3-h5py-serial_3.12.1-1_armhf.deb ... 343s Unpacking python3-h5py-serial (3.12.1-1) ... 343s Selecting previously unselected package python3-h5py. 343s Preparing to unpack .../18-python3-h5py_3.12.1-1_all.deb ... 343s Unpacking python3-h5py (3.12.1-1) ... 343s Selecting previously unselected package python3-mappy. 343s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1build1_armhf.deb ... 343s Unpacking python3-mappy (2.27+dfsg-1build1) ... 343s Selecting previously unselected package python3-packaging. 343s Preparing to unpack .../20-python3-packaging_24.2-1_all.deb ... 343s Unpacking python3-packaging (24.2-1) ... 343s Selecting previously unselected package python3-tqdm. 343s Preparing to unpack .../21-python3-tqdm_4.67.1-2_all.deb ... 343s Unpacking python3-tqdm (4.67.1-2) ... 343s Selecting previously unselected package sphinx-rtd-theme-common. 343s Preparing to unpack .../22-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 343s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 343s Selecting previously unselected package python3-scipy. 343s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_armhf.deb ... 343s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 344s Selecting previously unselected package tombo. 344s Preparing to unpack .../24-tombo_1.5.1-7build1_armhf.deb ... 344s Unpacking tombo (1.5.1-7build1) ... 344s Selecting previously unselected package libjs-mathjax. 344s Preparing to unpack .../25-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 344s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 345s Selecting previously unselected package tombo-doc. 345s Preparing to unpack .../26-tombo-doc_1.5.1-7build1_all.deb ... 345s Unpacking tombo-doc (1.5.1-7build1) ... 345s Setting up fonts-lato (2.015-1) ... 345s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 345s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 345s Setting up python3-tqdm (4.67.1-2) ... 345s Setting up python3-mappy (2.27+dfsg-1build1) ... 345s Setting up libaec0:armhf (1.1.3-1) ... 345s Setting up python3-decorator (5.1.1-5) ... 345s Setting up libblas3:armhf (3.12.1-2) ... 345s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 345s Setting up python3-packaging (24.2-1) ... 346s Setting up liblzf1:armhf (3.6-4) ... 346s Setting up libgfortran5:armhf (15-20250213-1ubuntu1) ... 346s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 346s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 346s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 346s Setting up libsz2:armhf (1.1.3-1) ... 346s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 346s Setting up liblapack3:armhf (3.12.1-2) ... 346s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 346s Setting up python3-numpy (1:1.26.4+ds-13) ... 348s Setting up libjs-sphinxdoc (8.1.3-5) ... 348s Setting up tombo-doc (1.5.1-7build1) ... 348s Setting up libhdf5-310:armhf (1.14.5+repack-3) ... 348s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 348s Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... 348s Setting up python3-scipy (1.14.1-4ubuntu1) ... 352s Setting up python3-h5py-serial (3.12.1-1) ... 352s Setting up python3-h5py (3.12.1-1) ... 352s Setting up tombo (1.5.1-7build1) ... 353s Processing triggers for man-db (2.13.0-1) ... 353s Processing triggers for libc-bin (2.40-4ubuntu1) ... 365s autopkgtest [13:34:59]: test run-unit-test: [----------------------- 367s ********* Testing help commands ********** 367s usage: tombo [-h] [-v] 367s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 367s 367s ********** Tombo ********* 367s 367s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 367s 367s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 367s 367s Tombo command groups (additional help available within each command group): 367s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 367s preprocess Pre-process nanopore reads for Tombo processing. 367s filter Apply filter to Tombo index file for specified criterion. 367s detect_modifications Perform statistical testing to detect non-standard nucleotides. 367s text_output Output Tombo results in text files. 367s build_model Create canonical and alternative base Tombo models. 367s plot Save plots to visualize raw nanopore signal or testing results. 367s 367s options: 367s -h, --help show this help message and exit 367s -v, --version show Tombo version and exit. 367s usage: tombo resquiggle [--dna] [--rna] 367s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 367s [--q-score Q_SCORE] 367s [--signal-matching-score SIGNAL_MATCHING_SCORE] 367s [--processes PROCESSES] 367s [--corrected-group CORRECTED_GROUP] 367s [--basecall-group BASECALL_GROUP] 367s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 367s [--overwrite] 367s [--failed-reads-filename FAILED_READS_FILENAME] 367s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 367s [--print-advanced-arguments] [--quiet] [--help] 367s fast5s_basedir reference 367s 367s Required Arguments: 367s fast5s_basedir Directory containing fast5 files. All files ending in 367s "fast5" found recursively within this base directory 367s will be processed. 367s reference Reference genome/transcriptome FASTA file or minimap2 367s index (with "map-ont" preset) for mapping. 367s 367s Model Parameters: 367s --dna Explicitly select canonical DNA model. Default: 367s Automatically determine from FAST5s 367s --rna Explicitly select canonical RNA model. Default: 367s Automatically determine from FAST5s 367s 367s Read Filtering Argument: 367s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 367s Filter reads based on observations per base percentile 367s thresholds. Format thresholds as "percentile:thresh 367s [pctl2:thresh2 ...]". For example to filter reads with 367s 99th pctl > 200 obs/base or max > 5k obs/base use 367s "99:200 100:5000". 367s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 367s Default: 0.000000 367s --signal-matching-score SIGNAL_MATCHING_SCORE 367s Observed to expected signal matching score (higher 367s score indicates poor matching). Sample type defaults: 367s RNA : 2 || DNA : 1.1 367s 367s Multiprocessing Arguments: 367s --processes PROCESSES 367s Number of processes. Default: 1 367s 367s FAST5 Data Arguments: 367s --corrected-group CORRECTED_GROUP 367s FAST5 group created by resquiggle command. Default: 367s RawGenomeCorrected_000 367s --basecall-group BASECALL_GROUP 367s FAST5 group obtain original basecalls (under Analyses 367s group). Default: Basecall_1D_000 367s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 367s FAST5 subgroup(s) (under /Analyses/[--basecall- 367s group]/) containing basecalls and created within 367s [--corrected-group] containing re-squiggle results. 367s Default: ['BaseCalled_template'] 367s --overwrite Overwrite previous corrected group in FAST5 files. 367s Note: only effects --corrected-group or --new- 367s corrected-group. 367s 367s Input/Output Arguments: 367s --failed-reads-filename FAILED_READS_FILENAME 367s Output failed read filenames with assoicated error. 367s Default: Do not store failed reads. 367s --num-most-common-errors NUM_MOST_COMMON_ERRORS 367s Dynamically show this many most common errors so far 367s through run. Default: 0; Just show progress 367s 367s Advanced Arguments: 367s --print-advanced-arguments 367s Print advanced re-squiggle arguments and exit. 367s 367s Miscellaneous Arguments: 367s --quiet, -q Don't print status information. 367s --help, -h Print this help message and exit 368s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 368s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 368s [--basecall-group BASECALL_GROUP] 368s [--basecall-subgroup BASECALL_SUBGROUP] 368s [--overwrite] 368s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 368s [--processes PROCESSES] 368s [--quiet] [--help] 368s 368s Required Arguments: 368s --fast5-basedir FAST5_BASEDIR 368s Directory containing fast5 files. 368s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 368s FASTQ filenames containing basecalls to be added to 368s raw FAST5 files. 368s 368s FAST5 Data Arguments: 368s --basecall-group BASECALL_GROUP 368s FAST5 group obtain original basecalls (under Analyses 368s group). Default: Basecall_1D_000 368s --basecall-subgroup BASECALL_SUBGROUP 368s FAST5 subgroup (under /Analyses/[--basecall-group]/) 368s under which to store basecalls from FASTQs. Default: 368s BaseCalled_template 368s --overwrite Overwrite previous corrected group in FAST5 files. 368s Note: only effects --corrected-group or --new- 368s corrected-group. 368s 368s Sequencing Summary Argument: 368s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 368s Sequencing summary filenames produced by albacore. 368s These can make annotation of raw FAST5 files with 368s FASTQ sequence much faster. 368s 368s Multiprocessing Argument: 368s --processes PROCESSES 368s Number of processes. Default: 1 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo filter clear_filters 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s [--corrected-group CORRECTED_GROUP] 368s [--quiet] [--help] 368s 368s Required Argument: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s 368s FAST5 Data Argument: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 368s [--corrected-group CORRECTED_GROUP] [--quiet] 368s [--help] 368s 368s Required Argument: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s 368s Read Filtering Argument: 368s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 368s Filter reads based on observations per base percentile 368s thresholds. Format thresholds as "percentile:thresh 368s [pctl2:thresh2 ...]". For example to filter reads with 368s 99th pctl > 200 obs/base or max > 5k obs/base use 368s "99:200 100:5000". 368s 368s FAST5 Data Argument: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo filter level_coverage 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s [--percent-to-filter PERCENT_TO_FILTER] 368s [--corrected-group CORRECTED_GROUP] 368s [--quiet] [--help] 368s 368s Required Arguments: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s 368s Read Filtering Argument: 368s --percent-to-filter PERCENT_TO_FILTER 368s Percentage of all reads to filter. Reads are randomly 368s selected weighted according to the approximate 368s coverage at the mapped genomic location. This can be 368s useful in modeling and testing. Default: 10.000000 368s 368s FAST5 Data Arguments: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo filter q_score 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s [--q-score Q_SCORE] 368s [--corrected-group CORRECTED_GROUP] 368s [--basecall-group BASECALL_GROUP] [--quiet] 368s [--help] 368s 368s Required Arguments: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s 368s Read Filtering Argument: 368s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 368s Default: 7.000000 368s 368s FAST5 Data Arguments: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s --basecall-group BASECALL_GROUP 368s FAST5 group obtain original basecalls (under Analyses 368s group). Default: Basecall_1D_000 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo filter raw_signal_matching 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s --signal-matching-score SIGNAL_MATCHING_SCORE 368s [--corrected-group CORRECTED_GROUP] 368s [--quiet] [--help] 368s 368s Required Arguments: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s --signal-matching-score SIGNAL_MATCHING_SCORE 368s Observed to expected signal matching score (higher 368s score indicates poor matching). Sample type defaults: 368s RNA : 2 || DNA : 1.1 368s 368s FAST5 Data Arguments: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo filter genome_locations 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 368s [--include-partial-overlap] 368s [--corrected-group CORRECTED_GROUP] 368s [--quiet] [--help] 368s 368s Required Arguments: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 368s Filter out reads not falling completely within include 368s regions. Omit start and end coordinates to include an 368s entire chromosome/sequence record. Format regions as 368s "chrm[:start-end] [chrm2[:start2-end2] ...]". 368s 368s Filter Argument: 368s --include-partial-overlap 368s Include reads that partially overlap the specified 368s region. Default: Only include reads completely 368s contained in a specified region 368s 368s FAST5 Data Argument: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo detect_modifications de_novo 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s --statistics-file-basename STATISTICS_FILE_BASENAME 368s [--dna] [--rna] 368s [--fishers-method-context FISHERS_METHOD_CONTEXT] 368s [--minimum-test-reads MINIMUM_TEST_READS] 368s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 368s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 368s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 368s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 368s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 368s [--processes PROCESSES] 368s [--corrected-group CORRECTED_GROUP] 368s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 368s [--quiet] [--help] 368s 368s Required Argument: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s --statistics-file-basename STATISTICS_FILE_BASENAME 368s File base name to save base by base statistics from 368s testing. Filenames will be [--statistics-file- 368s basename].[--alternate-bases]?.tombo.stats 368s 368s Comparison Model Arguments: 368s --dna Explicitly select canonical DNA model. Default: 368s Automatically determine from FAST5s 368s --rna Explicitly select canonical RNA model. Default: 368s Automatically determine from FAST5s 368s 368s Significance Test Arguments: 368s --fishers-method-context FISHERS_METHOD_CONTEXT 368s Number of context bases up and downstream over which 368s to compute Fisher's method combined p-values. Note: 368s Not applicable for alternative model likelihood ratio 368s tests. Default: 1. 368s --minimum-test-reads MINIMUM_TEST_READS 368s Number of reads required at a position to perform 368s significance testing or contribute to model 368s estimation. Default: 1 368s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 368s P-value threshold when computing fraction of 368s significant reads at each genomic position. If two 368s values are provided, statistics between these values 368s are not considered. Default thresholds: DNA:0.15-0.5 , 368s RNA:0.05-0.4 368s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 368s Dampen fraction modified estimates for low coverage 368s sites. Two parameters are unmodified and modified 368s pseudo read counts. This is equivalent to a beta prior 368s on the fraction estimate. Set to "0 0" to disable 368s dampened fraction estimation. Default: [2, 0] 368s 368s Output Argument: 368s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 368s Base for binary files containing per-read statistics 368s from statistical testing. Filenames will be [--per- 368s read-statistics-basename].[--alternate- 368s bases]?.tombo.per_read_stats 368s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 368s Number of the most significant sites to store for 368s faster access. If a longer list of most significant 368s sites is required the list must be re-computed from 368s all batches. Very large values can increase RAM usage. 368s Default: 100000 368s 368s Multiprocessing Arguments: 368s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 368s Size of regions over which to multiprocesses statistic 368s computation. For very deep samples a smaller value is 368s recommmended in order to control memory consumption. 368s Default: 10000 368s --processes PROCESSES 368s Number of processes. Default: 1 368s 368s FAST5 Data Arguments: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 368s FAST5 subgroup(s) (under /Analyses/[--basecall- 368s group]/) containing basecalls and created within 368s [--corrected-group] containing re-squiggle results. 368s Default: ['BaseCalled_template'] 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 368s usage: tombo detect_modifications alternative_model 368s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 368s [--statistics-file-basename STATISTICS_FILE_BASENAME] 368s [--alternate-bases {CpG,5mC,dcm,6mA,dam} [{CpG,5mC,dcm,6mA,dam} ...]] 368s [--print-available-models] 368s [--dna] [--rna] 368s [--minimum-test-reads MINIMUM_TEST_READS] 368s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 368s [--standard-log-likelihood-ratio] 368s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 368s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 368s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 368s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 368s [--processes PROCESSES] 368s [--corrected-group CORRECTED_GROUP] 368s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 368s [--quiet] [--help] 368s 368s Required Argument: 368s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 368s Directories containing fast5 files. 368s --statistics-file-basename STATISTICS_FILE_BASENAME 368s File base name to save base by base statistics from 368s testing. Filenames will be [--statistics-file- 368s basename].[--alternate-bases]?.tombo.stats 368s --alternate-bases {CpG,5mC,dcm,6mA,dam} [{CpG,5mC,dcm,6mA,dam} ...] 368s Default non-standard base model for testing (not 368s required if user created --alternate-model-filenames 368s is provided). 368s 368s Comparison Arguments: 368s --print-available-models 368s Print available alternative models and exit. 368s --dna Explicitly select canonical DNA model. Default: 368s Automatically determine from FAST5s 368s --rna Explicitly select canonical RNA model. Default: 368s Automatically determine from FAST5s 368s 368s Significance Test Arguments: 368s --minimum-test-reads MINIMUM_TEST_READS 368s Number of reads required at a position to perform 368s significance testing or contribute to model 368s estimation. Default: 1 368s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 368s Log likelihood ratio threshold when computing fraction 368s of significant reads at each genomic position. If two 368s values are provided, statistics between these values 368s are not considered. Default thresholds: DNA:-1.5-2.5 , 368s RNA:-2.5-2.5 368s --standard-log-likelihood-ratio 368s Use a standard log likelihood ratio (LLR) statistic. 368s Default is to use an outlier-robust LLR-like 368s statistic. Detail in full online documentation. 368s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 368s Dampen fraction modified estimates for low coverage 368s sites. Two parameters are unmodified and modified 368s pseudo read counts. This is equivalent to a beta prior 368s on the fraction estimate. Set to "0 0" to disable 368s dampened fraction estimation. Default: [2, 0] 368s 368s Output Argument: 368s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 368s Base for binary files containing per-read statistics 368s from statistical testing. Filenames will be [--per- 368s read-statistics-basename].[--alternate- 368s bases]?.tombo.per_read_stats 368s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 368s Number of the most significant sites to store for 368s faster access. If a longer list of most significant 368s sites is required the list must be re-computed from 368s all batches. Very large values can increase RAM usage. 368s Default: 100000 368s 368s Multiprocessing Arguments: 368s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 368s Size of regions over which to multiprocesses statistic 368s computation. For very deep samples a smaller value is 368s recommmended in order to control memory consumption. 368s Default: 10000 368s --processes PROCESSES 368s Number of processes. Default: 1 368s 368s FAST5 Data Arguments: 368s --corrected-group CORRECTED_GROUP 368s FAST5 group created by resquiggle command. Default: 368s RawGenomeCorrected_000 368s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 368s FAST5 subgroup(s) (under /Analyses/[--basecall- 368s group]/) containing basecalls and created within 368s [--corrected-group] containing re-squiggle results. 368s Default: ['BaseCalled_template'] 368s 368s Miscellaneous Arguments: 368s --quiet, -q Don't print status information. 368s --help, -h Print this help message and exit 369s usage: tombo detect_modifications model_sample_compare 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s --statistics-file-basename STATISTICS_FILE_BASENAME 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s [--sample-only-estimates] 369s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 369s [--dna] [--rna] 369s [--fishers-method-context FISHERS_METHOD_CONTEXT] 369s [--minimum-test-reads MINIMUM_TEST_READS] 369s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 369s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 369s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 369s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 369s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 369s [--processes PROCESSES] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Argument: 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s --statistics-file-basename STATISTICS_FILE_BASENAME 369s File base name to save base by base statistics from 369s testing. Filenames will be [--statistics-file- 369s basename].[--alternate-bases]?.tombo.stats 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s Set of directories containing fast5 files for control 369s reads, containing only canonical nucleotides. 369s 369s Model Prior Arguments: 369s --sample-only-estimates 369s Only use canonical sample to estimate expected signal 369s level and spread. Default: Use canonical model to 369s improve estimtates (esp. for low coverage regions) 369s using baysian posterior estimates. 369s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 369s Prior weights (one each for mean and spread) applied 369s to canonical base model for estimating posterior model 369s parameters for sample comparison. Default: [5, 40] 369s --dna Explicitly select canonical DNA model. Default: 369s Automatically determine from FAST5s 369s --rna Explicitly select canonical RNA model. Default: 369s Automatically determine from FAST5s 369s 369s Significance Test Arguments: 369s --fishers-method-context FISHERS_METHOD_CONTEXT 369s Number of context bases up and downstream over which 369s to compute Fisher's method combined p-values. Note: 369s Not applicable for alternative model likelihood ratio 369s tests. Default: 1. 369s --minimum-test-reads MINIMUM_TEST_READS 369s Number of reads required at a position to perform 369s significance testing or contribute to model 369s estimation. Default: 1 369s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 369s P-value threshold when computing fraction of 369s significant reads at each genomic position. If two 369s values are provided, statistics between these values 369s are not considered. Default thresholds: DNA:0.15-0.5 , 369s RNA:0.05-0.4 369s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 369s Dampen fraction modified estimates for low coverage 369s sites. Two parameters are unmodified and modified 369s pseudo read counts. This is equivalent to a beta prior 369s on the fraction estimate. Set to "0 0" to disable 369s dampened fraction estimation. Default: [2, 0] 369s 369s Output Argument: 369s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 369s Base for binary files containing per-read statistics 369s from statistical testing. Filenames will be [--per- 369s read-statistics-basename].[--alternate- 369s bases]?.tombo.per_read_stats 369s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 369s Number of the most significant sites to store for 369s faster access. If a longer list of most significant 369s sites is required the list must be re-computed from 369s all batches. Very large values can increase RAM usage. 369s Default: 100000 369s 369s Multiprocessing Arguments: 369s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 369s Size of regions over which to multiprocesses statistic 369s computation. For very deep samples a smaller value is 369s recommmended in order to control memory consumption. 369s Default: 10000 369s --processes PROCESSES 369s Number of processes. Default: 1 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo detect_modifications level_sample_compare 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s --statistics-file-basename STATISTICS_FILE_BASENAME 369s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 369s [--fishers-method-context FISHERS_METHOD_CONTEXT] 369s [--minimum-test-reads MINIMUM_TEST_READS] 369s [--statistic-type {ks,u,t}] 369s [--store-p-value] 369s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 369s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 369s [--processes PROCESSES] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Argument: 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s --statistics-file-basename STATISTICS_FILE_BASENAME 369s File base name to save base by base statistics from 369s testing. Filenames will be [--statistics-file- 369s basename].[--alternate-bases]?.tombo.stats 369s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 369s Set of directories containing fast5 files for 369s alternate set of reads. 369s 369s Significance Test Arguments: 369s --fishers-method-context FISHERS_METHOD_CONTEXT 369s Number of context bases up and downstream over which 369s to compute Fisher's method combined p-values. Note: 369s Not applicable for alternative model likelihood ratio 369s tests. Default: 1. 369s --minimum-test-reads MINIMUM_TEST_READS 369s Number of reads required at a position to perform 369s significance testing or contribute to model 369s estimation. Default: 50 369s --statistic-type {ks,u,t} 369s Type of statistical test to apply. Default: "ks" 369s --store-p-value Store p-value instead of effect-size statistic. 369s Statistics are D-statistic (KS-test), deviation from 369s even common language effect size (u-test), and Cohen's 369s D (t-test). 369s 369s Output Argument: 369s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 369s Number of the most significant sites to store for 369s faster access. If a longer list of most significant 369s sites is required the list must be re-computed from 369s all batches. Very large values can increase RAM usage. 369s Default: 100000 369s 369s Multiprocessing Arguments: 369s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 369s Size of regions over which to multiprocesses statistic 369s computation. For very deep samples a smaller value is 369s recommmended in order to control memory consumption. 369s Default: 10000 369s --processes PROCESSES 369s Number of processes. Default: 1 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo detect_modifications aggregate_per_read_stats 369s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 369s --statistics-filename STATISTICS_FILENAME 369s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 369s [--minimum-test-reads MINIMUM_TEST_READS] 369s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 369s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 369s [--processes PROCESSES] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Argument: 369s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 369s Binary file containing per-read statistics from 369s statistical testing. 369s --statistics-filename STATISTICS_FILENAME 369s File to save/load genomic base anchored statistics. 369s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 369s P-value or log likelihood ratio threshold when 369s computing fraction of significant reads at each 369s genomic position. If two values are provided, 369s statistics between these values are not considered. 369s 369s Significance Test Arguments: 369s --minimum-test-reads MINIMUM_TEST_READS 369s Number of reads required at a position to perform 369s significance testing or contribute to model 369s estimation. Default: 1 369s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 369s Dampen fraction modified estimates for low coverage 369s sites. Two parameters are unmodified and modified 369s pseudo read counts. This is equivalent to a beta prior 369s on the fraction estimate. Set to "0 0" to disable 369s dampened fraction estimation. Default: [2, 0] 369s 369s Output Argument: 369s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 369s Number of the most significant sites to store for 369s faster access. If a longer list of most significant 369s sites is required the list must be re-computed from 369s all batches. Very large values can increase RAM usage. 369s Default: 100000 369s 369s Multiprocessing Arguments: 369s --processes PROCESSES 369s Number of processes. Default: 1 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo text_output browser_files 369s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 369s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 369s [--statistics-filename STATISTICS_FILENAME] 369s [--genome-fasta GENOME_FASTA] 369s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 369s [--browser-file-basename BROWSER_FILE_BASENAME] 369s [--file-types {coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} [{coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} ...]] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Data Arguments: 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s Set of directories containing fast5 files for control 369s reads, containing only canonical nucleotides. 369s --statistics-filename STATISTICS_FILENAME 369s File to save/load genomic base anchored statistics. 369s 369s Statistic Motif Filter Arguments: 369s --genome-fasta GENOME_FASTA 369s FASTA file used to re-squiggle. For faster sequence 369s access. 369s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 369s Ground truth, motif centered, modified base 369s descriptions for output filtering. Format descriptions 369s as: "motif:mod_pos:name". The mod_pos indicates the 369s modified base within the motif (1-based index). 369s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 369s output for identification of E. coli dam and dcm 369s methylation. 369s 369s Output Arguments: 369s --browser-file-basename BROWSER_FILE_BASENAME 369s Basename for output browser files. Two files (plus and 369s minus strand) will be produced for each --file-types 369s supplied. Filenames formatted as "[browser-file- 369s basename].[file- 369s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 369s Default: tombo_results 369s --file-types {coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} [{coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} ...] 369s Data types of genome browser files to produce. 369s Produced coverage files are in bedGraph format, while 369s all other file types will be in wiggle format 369s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 369s Default: "coverage" 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo text_output signif_sequence_context 369s --statistics-filename STATISTICS_FILENAME 369s [--genome-fasta GENOME_FASTA] 369s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 369s [--num-regions NUM_REGIONS] 369s [--num-bases NUM_BASES] 369s [--sequences-filename SEQUENCES_FILENAME] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Argument: 369s --statistics-filename STATISTICS_FILENAME 369s File to save/load genomic base anchored statistics. 369s 369s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 369s --genome-fasta GENOME_FASTA 369s FASTA file used to re-squiggle. For faster sequence 369s access. 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s 369s Region Selection Arguments: 369s --num-regions NUM_REGIONS 369s Number of regions to plot. Default: 100 369s --num-bases NUM_BASES 369s Number of bases to plot/output. Default: 15 369s 369s Output Arguments: 369s --sequences-filename SEQUENCES_FILENAME 369s File for sequences from selected regions. Sequences 369s will be stored in FASTA format. Default: 369s tombo_results.significant_regions.fasta. 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo plot max_coverage 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 369s [--plot-standard-model] 369s [--plot-alternate-model {dam,CpG,dcm,5mC,6mA}] 369s [--overplot-threshold OVERPLOT_THRESHOLD] 369s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 369s [--num-regions NUM_REGIONS] 369s [--num-bases NUM_BASES] 369s [--pdf-filename PDF_FILENAME] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Argument: 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s 369s Comparison Arguments: 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s Set of directories containing fast5 files for control 369s reads, containing only canonical nucleotides. 369s --plot-standard-model 369s Add default standard model distribution to the plot. 369s --plot-alternate-model {dam,CpG,dcm,5mC,6mA} 369s Add alternative model distribution to the plot. 369s 369s Overplotting Arguments: 369s --overplot-threshold OVERPLOT_THRESHOLD 369s Coverage level to trigger alternative plot type 369s instead of raw signal. Default: 50 369s --overplot-type {Downsample,Boxplot,Quantile,Density} 369s Plot type for regions with higher coverage. Default: 369s Downsample 369s 369s Plotting Region Arguments: 369s --num-regions NUM_REGIONS 369s Number of regions to plot. Default: 10 369s --num-bases NUM_BASES 369s Number of bases to plot/output. Default: 21 369s 369s Output Argument: 369s --pdf-filename PDF_FILENAME 369s PDF filename to store plot(s). Default: 369s tombo_results.max_coverage.pdf 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo plot genome_locations 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 369s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 369s [--plot-standard-model] 369s [--plot-alternate-model {dam,6mA,5mC,CpG,dcm}] 369s [--overplot-threshold OVERPLOT_THRESHOLD] 369s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 369s [--num-bases NUM_BASES] 369s [--pdf-filename PDF_FILENAME] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Arguments: 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 369s Genomic locations at which to plot signal. Format 369s locations as "chrm:position[:strand] 369s [chrm2:position2[:strand2] ...]" (strand not 369s applicable for all applications) 369s 369s Comparison Arguments: 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s Set of directories containing fast5 files for control 369s reads, containing only canonical nucleotides. 369s --plot-standard-model 369s Add default standard model distribution to the plot. 369s --plot-alternate-model {dam,6mA,5mC,CpG,dcm} 369s Add alternative model distribution to the plot. 369s 369s Overplotting Arguments: 369s --overplot-threshold OVERPLOT_THRESHOLD 369s Coverage level to trigger alternative plot type 369s instead of raw signal. Default: 50 369s --overplot-type {Downsample,Boxplot,Quantile,Density} 369s Plot type for regions with higher coverage. Default: 369s Downsample 369s 369s Plotting Region Argument: 369s --num-bases NUM_BASES 369s Number of bases to plot/output. Default: 21 369s 369s Output Argument: 369s --pdf-filename PDF_FILENAME 369s PDF filename to store plot(s). Default: 369s tombo_results.genome_locations.pdf 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo plot motif_centered 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s --motif MOTIF --genome-fasta GENOME_FASTA 369s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 369s [--plot-standard-model] 369s [--plot-alternate-model {dcm,6mA,dam,CpG,5mC}] 369s [--overplot-threshold OVERPLOT_THRESHOLD] 369s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 369s [--num-regions NUM_REGIONS] 369s [--num-bases NUM_BASES] [--deepest-coverage] 369s [--pdf-filename PDF_FILENAME] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Arguments: 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s --motif MOTIF Motif of interest at which to plot signal and 369s statsitics. Supports IUPAC single letter codes (use T 369s for RNA). 369s --genome-fasta GENOME_FASTA 369s FASTA file used to re-squiggle. For faster sequence 369s access. 369s 369s Comparison Arguments: 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s Set of directories containing fast5 files for control 369s reads, containing only canonical nucleotides. 369s --plot-standard-model 369s Add default standard model distribution to the plot. 369s --plot-alternate-model {dcm,6mA,dam,CpG,5mC} 369s Add alternative model distribution to the plot. 369s 369s Overplotting Arguments: 369s --overplot-threshold OVERPLOT_THRESHOLD 369s Coverage level to trigger alternative plot type 369s instead of raw signal. Default: 50 369s --overplot-type {Downsample,Boxplot,Quantile,Density} 369s Plot type for regions with higher coverage. Default: 369s Downsample 369s 369s Plotting Region Arguments: 369s --num-regions NUM_REGIONS 369s Number of regions to plot. Default: 10 369s --num-bases NUM_BASES 369s Number of bases to plot/output. Default: 21 369s --deepest-coverage Plot the deepest coverage regions. 369s 369s Output Argument: 369s --pdf-filename PDF_FILENAME 369s PDF filename to store plot(s). Default: 369s tombo_results.motif_centered.pdf 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 369s usage: tombo plot max_difference 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s [--overplot-threshold OVERPLOT_THRESHOLD] 369s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 369s [--num-regions NUM_REGIONS] 369s [--num-bases NUM_BASES] 369s [--pdf-filename PDF_FILENAME] 369s [--sequences-filename SEQUENCES_FILENAME] 369s [--corrected-group CORRECTED_GROUP] 369s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 369s [--quiet] [--help] 369s 369s Required Arguments: 369s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 369s Directories containing fast5 files. 369s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 369s Set of directories containing fast5 files for control 369s reads, containing only canonical nucleotides. 369s 369s Overplotting Arguments: 369s --overplot-threshold OVERPLOT_THRESHOLD 369s Coverage level to trigger alternative plot type 369s instead of raw signal. Default: 50 369s --overplot-type {Downsample,Boxplot,Quantile,Density} 369s Plot type for regions with higher coverage. Default: 369s Downsample 369s 369s Plotting Region Arguments: 369s --num-regions NUM_REGIONS 369s Number of regions to plot. Default: 10 369s --num-bases NUM_BASES 369s Number of bases to plot/output. Default: 21 369s 369s Output Arguments: 369s --pdf-filename PDF_FILENAME 369s PDF filename to store plot(s). Default: 369s tombo_results.max_difference.pdf 369s --sequences-filename SEQUENCES_FILENAME 369s File for sequences from selected regions. Sequences 369s will be stored in FASTA format. Default: None. 369s 369s FAST5 Data Arguments: 369s --corrected-group CORRECTED_GROUP 369s FAST5 group created by resquiggle command. Default: 369s RawGenomeCorrected_000 369s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 369s FAST5 subgroup(s) (under /Analyses/[--basecall- 369s group]/) containing basecalls and created within 369s [--corrected-group] containing re-squiggle results. 369s Default: ['BaseCalled_template'] 369s 369s Miscellaneous Arguments: 369s --quiet, -q Don't print status information. 369s --help, -h Print this help message and exit 370s usage: tombo plot most_significant 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s --statistics-filename STATISTICS_FILENAME 370s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 370s [--plot-standard-model] 370s [--plot-alternate-model {6mA,CpG,dcm,dam,5mC}] 370s [--overplot-threshold OVERPLOT_THRESHOLD] 370s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 370s [--num-regions NUM_REGIONS] 370s [--num-bases NUM_BASES] 370s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 370s [--pdf-filename PDF_FILENAME] 370s [--sequences-filename SEQUENCES_FILENAME] 370s [--corrected-group CORRECTED_GROUP] 370s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 370s [--quiet] [--help] 370s 370s Required Arguments: 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s Directories containing fast5 files. 370s --statistics-filename STATISTICS_FILENAME 370s File to save/load genomic base anchored statistics. 370s 370s Comparison Arguments: 370s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 370s Set of directories containing fast5 files for control 370s reads, containing only canonical nucleotides. 370s --plot-standard-model 370s Add default standard model distribution to the plot. 370s --plot-alternate-model {6mA,CpG,dcm,dam,5mC} 370s Add alternative model distribution to the plot. 370s 370s Overplotting Arguments: 370s --overplot-threshold OVERPLOT_THRESHOLD 370s Coverage level to trigger alternative plot type 370s instead of raw signal. Default: 50 370s --overplot-type {Downsample,Boxplot,Quantile,Density} 370s Plot type for regions with higher coverage. Default: 370s Downsample 370s 370s Plotting Region Arguments: 370s --num-regions NUM_REGIONS 370s Number of regions to plot. Default: 10 370s --num-bases NUM_BASES 370s Number of bases to plot/output. Default: 21 370s 370s Statistical Argument: 370s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 370s Dampen fraction modified estimates for low coverage 370s sites. Two parameters are unmodified and modified 370s pseudo read counts. This is equivalent to a beta prior 370s on the fraction estimate. Set to "0 0" to disable 370s dampened fraction estimation. Default: [2, 0] 370s 370s Output Arguments: 370s --pdf-filename PDF_FILENAME 370s PDF filename to store plot(s). Default: 370s tombo_results.significant_difference.pdf 370s --sequences-filename SEQUENCES_FILENAME 370s File for sequences from selected regions. Sequences 370s will be stored in FASTA format. Default: None. 370s 370s FAST5 Data Arguments: 370s --corrected-group CORRECTED_GROUP 370s FAST5 group created by resquiggle command. Default: 370s RawGenomeCorrected_000 370s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 370s FAST5 subgroup(s) (under /Analyses/[--basecall- 370s group]/) containing basecalls and created within 370s [--corrected-group] containing re-squiggle results. 370s Default: ['BaseCalled_template'] 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 370s usage: tombo plot motif_with_stats 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s --motif MOTIF 370s --statistics-filename STATISTICS_FILENAME 370s --genome-fasta GENOME_FASTA 370s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 370s [--plot-standard-model] 370s [--plot-alternate-model {dam,dcm,CpG,6mA,5mC}] 370s [--overplot-threshold OVERPLOT_THRESHOLD] 370s [--num-regions NUM_REGIONS] 370s [--num-context NUM_CONTEXT] 370s [--num-statistics NUM_STATISTICS] 370s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 370s [--pdf-filename PDF_FILENAME] 370s [--corrected-group CORRECTED_GROUP] 370s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 370s [--quiet] [--help] 370s 370s Required Arguments: 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s Directories containing fast5 files. 370s --motif MOTIF Motif of interest at which to plot signal and 370s statsitics. Supports IUPAC single letter codes (use T 370s for RNA). 370s --statistics-filename STATISTICS_FILENAME 370s File to save/load genomic base anchored statistics. 370s --genome-fasta GENOME_FASTA 370s FASTA file used to re-squiggle. For faster sequence 370s access. 370s 370s Comparison Arguments: 370s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 370s Set of directories containing fast5 files for control 370s reads, containing only canonical nucleotides. 370s --plot-standard-model 370s Add default standard model distribution to the plot. 370s --plot-alternate-model {dam,dcm,CpG,6mA,5mC} 370s Add alternative model distribution to the plot. 370s 370s Overplotting Argument: 370s --overplot-threshold OVERPLOT_THRESHOLD 370s Coverage level to trigger alternative plot type 370s instead of raw signal. Default: 50 370s 370s Plotting Region Arguments: 370s --num-regions NUM_REGIONS 370s Number of regions to plot. Default: 3 370s --num-context NUM_CONTEXT 370s Number of context bases around motif. Default: 5 370s --num-statistics NUM_STATISTICS 370s Number of motif centered regions to include in 370s statistic distributions. Default: 200 370s 370s Statistical Argument: 370s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 370s Dampen fraction modified estimates for low coverage 370s sites. Two parameters are unmodified and modified 370s pseudo read counts. This is equivalent to a beta prior 370s on the fraction estimate. Set to "0 0" to disable 370s dampened fraction estimation. Default: [2, 0] 370s 370s Output Argument: 370s --pdf-filename PDF_FILENAME 370s PDF filename to store plot(s). Default: 370s tombo_results.motif_statistics.pdf 370s 370s FAST5 Data Arguments: 370s --corrected-group CORRECTED_GROUP 370s FAST5 group created by resquiggle command. Default: 370s RawGenomeCorrected_000 370s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 370s FAST5 subgroup(s) (under /Analyses/[--basecall- 370s group]/) containing basecalls and created within 370s [--corrected-group] containing re-squiggle results. 370s Default: ['BaseCalled_template'] 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 370s usage: tombo plot per_read 370s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 370s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 370s [--genome-fasta GENOME_FASTA] 370s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 370s [--num-reads NUM_READS] [--num-bases NUM_BASES] 370s [--box-center] [--pdf-filename PDF_FILENAME] 370s [--corrected-group CORRECTED_GROUP] 370s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 370s [--quiet] [--help] 370s 370s Required Arguments: 370s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 370s Genomic locations at which to plot signal. Format 370s locations as "chrm:position[:strand] 370s [chrm2:position2[:strand2] ...]" (strand not 370s applicable for all applications) 370s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 370s Binary file containing per-read statistics from 370s statistical testing. 370s 370s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 370s --genome-fasta GENOME_FASTA 370s FASTA file used to re-squiggle. For faster sequence 370s access. 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s Directories containing fast5 files. 370s 370s Plotting Region Arguments: 370s --num-reads NUM_READS 370s Number of reads to plot. Default: 100 370s --num-bases NUM_BASES 370s Number of bases to plot/output. Default: 51 370s --box-center Plot a box around the central base. 370s 370s Output Argument: 370s --pdf-filename PDF_FILENAME 370s PDF filename to store plot(s). Default: 370s tombo_results.per_read_stats.pdf 370s 370s FAST5 Data Arguments: 370s --corrected-group CORRECTED_GROUP 370s FAST5 group created by resquiggle command. Default: 370s RawGenomeCorrected_000 370s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 370s FAST5 subgroup(s) (under /Analyses/[--basecall- 370s group]/) containing basecalls and created within 370s [--corrected-group] containing re-squiggle results. 370s Default: ['BaseCalled_template'] 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 370s usage: tombo plot roc 370s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 370s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 370s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 370s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 370s [--genome-fasta GENOME_FASTA] 370s [--pdf-filename PDF_FILENAME] 370s [--statistics-per-block STATISTICS_PER_BLOCK] 370s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 370s [--quiet] [--help] 370s 370s Required Argument: 370s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 370s Files to load genomic base anchored statistics. 370s 370s Ground Truth Arguments (provide bed files or motifs): 370s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 370s Modification description and bed format files 370s containing single base locations of ground truth 370s modified sites. Bed files should contain 6 fields 370s including strand. Format descriptions as 370s "mod_name:locs.bed". Example: "CpG 370s bisulfite":bisulfite_locs.bed 370s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 370s Bed format files containing single base locations of 370s ground truth unmodified sites. Bed files should 370s contain 6 fields including strand. 370s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 370s Ground truth, motif centered, modified base 370s descriptions for computing ROC and PR curves. Each 370s statistics file is associated with a set of motif 370s descriptions. Format descriptions as: 370s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 370s mod_pos indicates the alternate-base within the motif 370s (1-based index). Example: CCWGG:2:"dcm 370s 5mC"::GATC:2:"dam 6mA" would assess the performance of 370s a single Tombo statistics file for identification of 370s E. coli dam and dcm methylation. 370s --genome-fasta GENOME_FASTA 370s FASTA file used to re-squiggle. For faster sequence 370s access. 370s 370s Output Arguments: 370s --pdf-filename PDF_FILENAME 370s PDF filename to store plot(s). Default: 370s tombo_results.roc.pdf 370s 370s Down-sampling Arguments: 370s --statistics-per-block STATISTICS_PER_BLOCK 370s Number of randomly selected per-read, per-base 370s statistics to extract from each genomic block for 370s plotting. Default: Include all stats 370s --total-statistics-limit TOTAL_STATISTICS_LIMIT 370s Total per-read statistics to be extracted for 370s plotting. Avoids memory overflow for large runs. 370s Default: 5000000 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 370s usage: tombo plot per_read_roc 370s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 370s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 370s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 370s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 370s [--genome-fasta GENOME_FASTA] 370s [--statistics-per-block STATISTICS_PER_BLOCK] 370s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 370s [--pdf-filename PDF_FILENAME] [--quiet] 370s [--help] 370s 370s Required Argument: 370s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 370s Binary files containing per-read statistics from 370s statistical testing. 370s 370s Ground Truth Arguments (provide bed files or motifs): 370s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 370s Modification description and bed format files 370s containing single base locations of ground truth 370s modified sites. Bed files should contain 6 fields 370s including strand. Format descriptions as 370s "mod_name:locs.bed". Example: "CpG 370s bisulfite":bisulfite_locs.bed 370s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 370s Bed format files containing single base locations of 370s ground truth unmodified sites. Bed files should 370s contain 6 fields including strand. 370s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 370s Ground truth, motif centered, modified base 370s descriptions for computing ROC and PR curves. Each 370s statistics file is associated with a set of motif 370s descriptions. Format descriptions as: 370s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 370s mod_pos indicates the alternate-base within the motif 370s (1-based index). Example: CCWGG:2:"dcm 370s 5mC"::GATC:2:"dam 6mA" would assess the performance of 370s a single Tombo statistics file for identification of 370s E. coli dam and dcm methylation. 370s --genome-fasta GENOME_FASTA 370s FASTA file used to re-squiggle. For faster sequence 370s access. 370s 370s Down-sampling Arguments: 370s --statistics-per-block STATISTICS_PER_BLOCK 370s Number of randomly selected per-read, per-base 370s statistics to extract from each genomic block for 370s plotting. Default: 100000 370s --total-statistics-limit TOTAL_STATISTICS_LIMIT 370s Total per-read statistics to be extracted for 370s plotting. Avoids memory overflow for large runs. 370s Default: 5000000 370s 370s Output Arguments: 370s --pdf-filename PDF_FILENAME 370s PDF filename to store plot(s). Default: 370s tombo_results.per_reads_roc.pdf 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 370s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s [--upstream-bases {0,1,2,3,4}] 370s [--downstream-bases {0,1,2,3,4}] [--read-mean] 370s [--num-kmer-threshold NUM_KMER_THRESHOLD] 370s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 370s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 370s [--corrected-group CORRECTED_GROUP] 370s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 370s [--quiet] [--help] 370s 370s Required Argument: 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s Directories containing fast5 files. 370s 370s Data Processing Arguments: 370s --upstream-bases {0,1,2,3,4} 370s Upstream bases in k-mer. Default: 1 370s --downstream-bases {0,1,2,3,4} 370s Downstream bases in k-mer. Default: 2 370s --read-mean Plot k-mer means across whole reads as opposed to 370s individual k-mer event levels. 370s --num-kmer-threshold NUM_KMER_THRESHOLD 370s Observations of each k-mer required to include a read 370s in read level averages. Default: 1 370s 370s Plotting Region Arguments: 370s --num-reads NUM_READS 370s Number of reads to plot. Default: 100 370s 370s Output Arguments: 370s --pdf-filename PDF_FILENAME 370s PDF filename to store plot(s). Default: 370s tombo_results.kmer_distribution.pdf 370s --r-data-filename R_DATA_FILENAME 370s Filename to save R data structure. Default: Don't save 370s --dont-plot Don't plot result. Useful to produce only R data file. 370s 370s FAST5 Data Arguments: 370s --corrected-group CORRECTED_GROUP 370s FAST5 group created by resquiggle command. Default: 370s RawGenomeCorrected_000 370s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 370s FAST5 subgroup(s) (under /Analyses/[--basecall- 370s group]/) containing basecalls and created within 370s [--corrected-group] containing re-squiggle results. 370s Default: ['BaseCalled_template'] 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 370s usage: tombo plot cluster_most_significant 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 370s --statistics-filename STATISTICS_FILENAME 370s [--genome-fasta GENOME_FASTA] 370s [--processes PROCESSES] 370s [--num-regions NUM_REGIONS] 370s [--num-bases NUM_BASES] 370s [--slide-span SLIDE_SPAN] 370s [--pdf-filename PDF_FILENAME] 370s [--r-data-filename R_DATA_FILENAME] 370s [--corrected-group CORRECTED_GROUP] 370s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 370s [--quiet] [--help] 370s 370s Required Arguments: 370s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 370s Directories containing fast5 files. 370s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 370s Set of directories containing fast5 files for control 370s reads, containing only canonical nucleotides. 370s --statistics-filename STATISTICS_FILENAME 370s File to save/load genomic base anchored statistics. 370s 370s FASTA Sequence Argument: 370s --genome-fasta GENOME_FASTA 370s FASTA file used to re-squiggle. For faster sequence 370s access. 370s 370s Multiprocessing Argument: 370s --processes PROCESSES 370s Number of processes. Default: 1 370s 370s Plotting Region Arguments: 370s --num-regions NUM_REGIONS 370s Number of regions to plot. Default: 10 370s --num-bases NUM_BASES 370s Number of bases to plot/output. Default: 21 370s --slide-span SLIDE_SPAN 370s Number of bases offset over which to search when 370s computing distances for signal cluster plotting. 370s Default: 0 (exact position) 370s 370s Output Arguments: 370s --pdf-filename PDF_FILENAME 370s PDF filename to store plot(s). Default: 370s tombo_results.signal_clusters.pdf 370s --r-data-filename R_DATA_FILENAME 370s Filename to save R data structure. Default: Don't save 370s 370s FAST5 Data Arguments: 370s --corrected-group CORRECTED_GROUP 370s FAST5 group created by resquiggle command. Default: 370s RawGenomeCorrected_000 370s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 370s FAST5 subgroup(s) (under /Analyses/[--basecall- 370s group]/) containing basecalls and created within 370s [--corrected-group] containing re-squiggle results. 370s Default: ['BaseCalled_template'] 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 370s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 370s 370s Required Arguments: 370s fast5s_basedir Directory containing fast5 files. All files ending in 370s "fast5" found recursively within this base directory will be 370s processed. 370s 370s Miscellaneous Arguments: 370s --quiet, -q Don't print status information. 370s --help, -h Print this help message and exit 371s usage: tombo build_model event_resquiggle 371s [--minimap2-executable MINIMAP2_EXECUTABLE] 371s [--minimap2-index MINIMAP2_INDEX] 371s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 371s [--graphmap-executable GRAPHMAP_EXECUTABLE] 371s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 371s [--normalization-type {median,pA,pA_raw,none}] 371s [--pore-model-filename PORE_MODEL_FILENAME] 371s [--outlier-threshold OUTLIER_THRESHOLD] 371s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 371s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 371s [--timeout TIMEOUT] 371s [--cpts-limit CPTS_LIMIT] 371s [--skip-index] [--overwrite] 371s [--failed-reads-filename FAILED_READS_FILENAME] 371s [--include-event-stdev] 371s [--corrected-group CORRECTED_GROUP] 371s [--basecall-group BASECALL_GROUP] 371s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 371s [--processes PROCESSES] 371s [--align-processes ALIGN_PROCESSES] 371s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 371s [--resquiggle-processes RESQUIGGLE_PROCESSES] 371s [--quiet] [--help] 371s fast5s_basedir reference_fasta 371s 371s Required Arguments: 371s fast5s_basedir Directory containing fast5 files. All files ending in 371s "fast5" found recursively within this base directory 371s will be processed. 371s reference_fasta Reference genome/transcriptome FASTA file for mapping. 371s 371s Mapper Arguments (One mapper is required): 371s --minimap2-executable MINIMAP2_EXECUTABLE 371s Path to minimap2 executable. 371s --minimap2-index MINIMAP2_INDEX 371s Path to minimap2 index (with map-ont preset) file 371s corresponding to the [genome_fasta] provided. 371s --bwa-mem-executable BWA_MEM_EXECUTABLE 371s Path to bwa-mem executable. 371s --graphmap-executable GRAPHMAP_EXECUTABLE 371s Path to graphmap executable. 371s --alignment-batch-size ALIGNMENT_BATCH_SIZE 371s Number of reads included in each alignment call. Note: 371s A new system mapping call is made for each batch 371s (including loading of the genome), so it is advised to 371s use larger values for larger genomes. Default: 1000 371s 371s Signal Processing Arguments: 371s --normalization-type {median,pA,pA_raw,none} 371s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 371s as in the ONT events (using offset, range and 371s digitization), "pA": k-mer-based correction for pA 371s drift as in nanopolish (requires [--pore-model- 371s filename]), "median": median and MAD from raw signal. 371s Default: median 371s --pore-model-filename PORE_MODEL_FILENAME 371s File containing kmer model parameters (level_mean and 371s level_stdv) used in order to compute kmer-based 371s corrected pA values. E.g. https://github.com/jts/nanop 371s olish/blob/master/etc/r9- 371s models/template_median68pA.5mers.model 371s --outlier-threshold OUTLIER_THRESHOLD 371s Windosrize the signal at this number of scale values. 371s Negative value disables outlier clipping. Default: 371s 5.000000 371s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 371s Specify the 2 parameters for segmentation 1) running 371s neighboring windows width 2) minimum raw observations 371s per genomic base. Sample type defaults: RNA : 12 6 || 371s DNA : 5 3 371s 371s Read Filtering Arguments: 371s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 371s Filter reads based on observations per base percentile 371s thresholds. Format thresholds as "percentile:thresh 371s [pctl2:thresh2 ...]". For example to filter reads with 371s 99th pctl > 200 obs/base or max > 5k obs/base use 371s "99:200 100:5000". 371s --timeout TIMEOUT Timeout in seconds for processing a single read. 371s Default: No timeout. 371s --cpts-limit CPTS_LIMIT 371s Maximum number of changepoints to find within a single 371s indel group. Default: No limit. 371s 371s Input/Output Arguments: 371s --skip-index Skip creation of tombo index. This drastically slows 371s downstream tombo commands. Default stores tombo index 371s named ".[--fast5-basedir].[--corrected- 371s group].tombo.index" to be loaded automatically for 371s downstream commands. 371s --overwrite Overwrite previous corrected group in FAST5 files. 371s Note: only effects --corrected-group or --new- 371s corrected-group. 371s --failed-reads-filename FAILED_READS_FILENAME 371s Output failed read filenames with assoicated error. 371s Default: Do not store failed reads. 371s --include-event-stdev 371s Include corrected event standard deviation in output 371s FAST5 data. 371s 371s FAST5 Data Arguments: 371s --corrected-group CORRECTED_GROUP 371s FAST5 group created by resquiggle command. Default: 371s RawGenomeCorrected_000 371s --basecall-group BASECALL_GROUP 371s FAST5 group obtain original basecalls (under Analyses 371s group). Default: Basecall_1D_000 371s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 371s FAST5 subgroup(s) (under /Analyses/[--basecall- 371s group]/) containing basecalls and created within 371s [--corrected-group] containing re-squiggle results. 371s Default: ['BaseCalled_template'] 371s 371s Multiprocessing Arguments: 371s --processes PROCESSES 371s Number of processes. Default: 2 371s --align-processes ALIGN_PROCESSES 371s Number of processes to use for parsing and aligning 371s original basecalls. Each process will independently 371s load the genome into memory, so use caution with 371s larger genomes (e.g. human). Default: 1 371s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 371s Number of threads to use for aligner system call. 371s Default: [--processes] / (2 * [--align-processes)] 371s --resquiggle-processes RESQUIGGLE_PROCESSES 371s Number of processes to use for resquiggle algorithm. 371s Default: [--processes] / 2 371s 371s Miscellaneous Arguments: 371s --quiet, -q Don't print status information. 371s --help, -h Print this help message and exit 371s usage: tombo build_model estimate_reference 371s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 371s --tombo-model-filename TOMBO_MODEL_FILENAME 371s [--estimate-mean] 371s [--kmer-specific-sd] 371s [--upstream-bases {0,1,2,3,4}] 371s [--downstream-bases {0,1,2,3,4}] 371s [--minimum-test-reads MINIMUM_TEST_READS] 371s [--coverage-threshold COVERAGE_THRESHOLD] 371s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 371s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 371s [--processes PROCESSES] 371s [--corrected-group CORRECTED_GROUP] 371s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 371s [--quiet] [--help] 371s 371s Required Arguments: 371s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 371s Directories containing fast5 files. 371s --tombo-model-filename TOMBO_MODEL_FILENAME 371s Filename to save Tombo model. 371s 371s Modeling Arguments: 371s --estimate-mean Use the mean instead of median for model level 371s estimation. Note: This can cause poor fits due to 371s outliers 371s --kmer-specific-sd Estimate standard deviation for each k-mers 371s individually. 371s --upstream-bases {0,1,2,3,4} 371s Upstream bases in k-mer. Default: 1 371s --downstream-bases {0,1,2,3,4} 371s Downstream bases in k-mer. Default: 2 371s 371s Filtering Arguments: 371s --minimum-test-reads MINIMUM_TEST_READS 371s Number of reads required at a position to perform 371s significance testing or contribute to model 371s estimation. Default: 10 371s --coverage-threshold COVERAGE_THRESHOLD 371s Maximum mean coverage per region when estimating k-mer 371s model (limits compute time for deep samples). Default: 371s 100 371s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 371s Number of each k-mer observations required in order to 371s produce a reference (genomic locations for standard 371s reference and per-read for alternative reference). 371s Default: 5 371s 371s Multiprocessing Arguments: 371s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 371s Size of regions over which to multiprocesses statistic 371s computation. For very deep samples a smaller value is 371s recommmended in order to control memory consumption. 371s Default: 10000 371s --processes PROCESSES 371s Number of processes. Default: 1 371s 371s FAST5 Data Arguments: 371s --corrected-group CORRECTED_GROUP 371s FAST5 group created by resquiggle command. Default: 371s RawGenomeCorrected_000 371s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 371s FAST5 subgroup(s) (under /Analyses/[--basecall- 371s group]/) containing basecalls and created within 371s [--corrected-group] containing re-squiggle results. 371s Default: ['BaseCalled_template'] 371s 371s Miscellaneous Arguments: 371s --quiet, -q Don't print status information. 371s --help, -h Print this help message and exit 371s usage: tombo build_model estimate_alt_reference 371s --alternate-model-filename ALTERNATE_MODEL_FILENAME 371s --alternate-model-name ALTERNATE_MODEL_NAME 371s --alternate-model-base {A,C,G,T} 371s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 371s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 371s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 371s [--control-density-filename CONTROL_DENSITY_FILENAME] 371s [--dna] [--rna] 371s [--tombo-model-filename TOMBO_MODEL_FILENAME] 371s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 371s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 371s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 371s [--save-density-basename SAVE_DENSITY_BASENAME] 371s [--processes PROCESSES] 371s [--corrected-group CORRECTED_GROUP] 371s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 371s [--quiet] [--help] 371s 371s Required Arguments: 371s --alternate-model-filename ALTERNATE_MODEL_FILENAME 371s Tombo model for alternative likelihood ratio 371s significance testing. 371s --alternate-model-name ALTERNATE_MODEL_NAME 371s A short name to associate with this alternate model 371s (e.g. 5mC, 6mA, etc.). This text will be included in 371s output filenames when this model is used for testing. 371s --alternate-model-base {A,C,G,T} 371s Non-standard base is an alternative to this base. 371s 371s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 371s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 371s Directories containing fast5 files. 371s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 371s Set of directories containing fast5 files for control 371s reads, containing only canonical nucleotides. 371s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 371s File containing k-mer level kernel density estimates 371s for the alternative sample saved using --save-density- 371s basename. 371s --control-density-filename CONTROL_DENSITY_FILENAME 371s File containing k-mer level kernel density estimates 371s for the control sample saved using --save-density- 371s basename. 371s 371s Standard Model Arguments: 371s --dna Explicitly select canonical DNA model. Default: 371s Automatically determine from FAST5s 371s --rna Explicitly select canonical RNA model. Default: 371s Automatically determine from FAST5s 371s --tombo-model-filename TOMBO_MODEL_FILENAME 371s Tombo model filename. If no file is provided, the 371s default DNA or RNA Tombo model will be used. 371s 371s Model Fitting Arguments: 371s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 371s When esitmating the alternative base incorporation 371s rate, this percent of k-mers are assumed to have 371s significantly shifted signal so the alternative 371s distribution minimally overlaps the standard base 371s distribution. Default: 5.000000 371s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 371s Bandwidth applied when performing Gaussian kernal 371s density esitmation on standard and alternative base 371s signal distributions. Default: 0.050000 371s 371s Filtering Argument: 371s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 371s Number of each k-mer observations required in order to 371s produce a reference (genomic locations for standard 371s reference and per-read for alternative reference). 371s Default: 1000 371s 371s Output Argument: 371s --save-density-basename SAVE_DENSITY_BASENAME 371s Basename to save alternative model estimation density 371s estimation information. See scripts/debug_est_alt.R 371s for info use example. Default: Don't save. 371s 371s Multiprocessing Arguments: 371s --processes PROCESSES 371s Number of processes. Default: 1 371s 371s FAST5 Data Arguments: 371s --corrected-group CORRECTED_GROUP 371s FAST5 group created by resquiggle command. Default: 371s RawGenomeCorrected_000 371s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 371s FAST5 subgroup(s) (under /Analyses/[--basecall- 371s group]/) containing basecalls and created within 371s [--corrected-group] containing re-squiggle results. 371s Default: ['BaseCalled_template'] 371s 371s Miscellaneous Arguments: 371s --quiet, -q Don't print status information. 371s --help, -h Print this help message and exit 371s This test only tests the help system 371s There is an extensive test in 371s 371s tombo/tests/shell_tests.sh 371s 371s but this requires to download larger data 371s sets which is not done for the moment. 371s autopkgtest [13:35:05]: test run-unit-test: -----------------------] 376s autopkgtest [13:35:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 376s run-unit-test PASS 380s autopkgtest [13:35:14]: @@@@@@@@@@@@@@@@@@@@ summary 380s run-unit-test PASS