1s autopkgtest [13:21:15]: starting date and time: 2024-03-22 13:21:15+0000 1s autopkgtest [13:21:15]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 1s autopkgtest [13:21:15]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m88abq0f/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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- lxd -r lxd-armhf-10.145.243.59 lxd-armhf-10.145.243.59:autopkgtest/ubuntu/noble/armhf 29s autopkgtest [13:21:43]: testbed dpkg architecture: armhf 30s autopkgtest [13:21:44]: testbed apt version: 2.7.12 30s autopkgtest [13:21:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 38s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 38s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 39s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 39s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [54.0 kB] 39s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3771 kB] 39s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [636 kB] 39s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 39s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 39s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3883 kB] 39s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 39s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [46.6 kB] 39s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 42s Fetched 9022 kB in 2s (4345 kB/s) 42s Reading package lists... 51s tee: /proc/self/fd/2: Permission denied 77s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 77s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 80s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Calculating upgrade... 82s The following packages were automatically installed and are no longer required: 82s linux-headers-6.8.0-11 python3-lib2to3 82s Use 'apt autoremove' to remove them. 82s The following packages will be REMOVED: 82s libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1 82s libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11 82s libhogweed6 libmagic1 libnetplan0 libnettle8 libnpth0 libnvme1 libparted2 82s libpcap0.8 libperl5.38 libpng16-16 libpsl5 libreadline8 libreiserfscore0 82s libssl3 libtirpc3 libuv1 linux-headers-6.8.0-11-generic python3-distutils 82s The following NEW packages will be installed: 82s libapt-pkg6.0t64 libarchive13t64 libatm1t64 libcurl3t64-gnutls libcurl4t64 82s libdb5.3t64 libelf1t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 82s libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 libmagic1t64 82s libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64 82s libpcap0.8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 82s libreiserfscore0t64 libssl3t64 libtirpc3t64 libuv1t64 linux-headers-6.8.0-20 82s linux-headers-6.8.0-20-generic xdg-user-dirs 82s The following packages have been kept back: 82s multipath-tools 82s The following packages will be upgraded: 82s apparmor apt apt-utils bind9-dnsutils bind9-host bind9-libs binutils 82s binutils-arm-linux-gnueabihf binutils-common bolt bsdextrautils bsdutils 82s btrfs-progs coreutils cryptsetup-bin curl dbus dbus-bin dbus-daemon 82s dbus-session-bus-common dbus-system-bus-common dbus-user-session dhcpcd-base 82s dirmngr dmsetup dpkg dpkg-dev e2fsprogs e2fsprogs-l10n eject fdisk file ftp 82s fwupd gawk gcc-13-base gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0 82s gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv 82s groff-base ibverbs-providers inetutils-telnet info initramfs-tools 82s initramfs-tools-bin initramfs-tools-core install-info iproute2 jq keyboxd 82s kmod kpartx krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils 82s libblkid1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 82s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 82s libblockdev-utils3 libblockdev3 libbpf1 libbrotli1 libbsd0 libc-bin libc6 82s libcap-ng0 libcom-err2 libcryptsetup12 libctf-nobfd0 libctf0 libdbus-1-3 82s libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libevent-core-2.1-7 82s libexpat1 libfdisk1 libfido2-1 libftdi1-2 libfwupd2 libgcc-s1 82s libgirepository-1.0-1 libglib2.0-data libgssapi-krb5-2 libgudev-1.0-0 82s libgusb2 libibverbs1 libjcat1 libjq1 libjson-glib-1.0-0 82s libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 82s libldap-common libldap2 liblocale-gettext-perl liblzma5 libmagic-mgc 82s libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 libnsl2 82s libnss-systemd libpam-modules libpam-modules-bin libpam-runtime 82s libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0 82s libpolkit-gobject-1-0 libpython3-stdlib libpython3.11-minimal 82s libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libqmi-glib5 82s libqmi-proxy libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules 82s libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 82s libsframe1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssh-4 libstdc++6 82s libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl 82s libtirpc-common libudev1 libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1 82s libxml2 libxmlb2 libxmuu1 linux-headers-generic locales logsave lshw lsof 82s man-db mount mtr-tiny netplan-generator netplan.io openssh-client 82s openssh-server openssh-sftp-server openssl parted perl perl-base 82s perl-modules-5.38 pinentry-curses plymouth plymouth-theme-ubuntu-text psmisc 82s python-apt-common python3 python3-apt python3-cryptography python3-dbus 82s python3-gdbm python3-gi python3-lib2to3 python3-minimal python3-netplan 82s python3-pkg-resources python3-pyrsistent python3-setuptools 82s python3-typing-extensions python3-yaml python3.11 python3.11-minimal 82s python3.12 python3.12-minimal readline-common rsync shared-mime-info sudo 82s systemd systemd-dev systemd-resolved systemd-sysv systemd-timesyncd tcpdump 82s telnet tnftp ubuntu-pro-client ubuntu-pro-client-l10n udev udisks2 usb.ids 82s util-linux uuid-runtime vim-common vim-tiny wget xxd xz-utils zlib1g 82s 233 upgraded, 32 newly installed, 31 to remove and 1 not upgraded. 82s Need to get 106 MB of archives. 82s After this operation, 84.4 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu2 [102 kB] 82s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB] 82s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB] 82s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB] 82s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu6 [2827 kB] 83s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB] 83s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-5.1ubuntu1 [119 kB] 83s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-5.1ubuntu1 [321 kB] 83s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-5.1ubuntu1 [31.4 kB] 83s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-5.1ubuntu1 [78.6 kB] 83s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 83s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu1 [49.2 kB] 83s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build6 [51.3 kB] 83s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udisks2 armhf 2.10.1-6 [276 kB] 83s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudisks2-0 armhf 2.10.1-6 [143 kB] 83s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu2 [160 kB] 83s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.0-0.2 [117 kB] 83s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kmod armhf 31+20240202-2ubuntu4 [91.8 kB] 83s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu4 [44.9 kB] 83s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu5 [103 kB] 83s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-timesyncd armhf 255.4-1ubuntu5 [36.0 kB] 83s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB] 83s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B] 83s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build1 [13.5 kB] 83s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1 [44.3 kB] 83s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu3 [62.0 kB] 83s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2ubuntu1 [70.9 kB] 83s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4t64 armhf 8.5.0-2ubuntu7 [296 kB] 83s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf curl armhf 8.5.0-2ubuntu7 [219 kB] 83s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.7 kB] 83s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf wget armhf 1.21.4-1ubuntu2 [317 kB] 83s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tnftp armhf 20230507-2build1 [98.6 kB] 83s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcap0.8t64 armhf 1.10.4-4.1ubuntu1 [137 kB] 83s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tcpdump armhf 4.99.4-3ubuntu2 [425 kB] 83s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB] 83s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-resolved armhf 255.4-1ubuntu5 [289 kB] 83s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sudo armhf 1.9.15p5-3ubuntu3 [936 kB] 83s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsync armhf 3.2.7-1build1 [413 kB] 83s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cryptography armhf 41.0.7-4build2 [788 kB] 83s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu2 [975 kB] 83s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu11 [35.5 kB] 83s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-client armhf 1:9.6p1-3ubuntu11 [890 kB] 83s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-server armhf 1:9.6p1-3ubuntu11 [503 kB] 83s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB] 83s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20-generic armhf 6.8.0-20.20 [1287 kB] 83s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-generic armhf 6.8.0-20.20+1 [9610 B] 83s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu2 [1558 kB] 83s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnss-systemd armhf 255.4-1ubuntu5 [148 kB] 83s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB] 83s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB] 84s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udev armhf 255.4-1ubuntu5 [1852 kB] 84s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB] 84s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-systemd armhf 255.4-1ubuntu5 [216 kB] 84s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB] 84s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu3 [47.0 kB] 84s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu3 [261 kB] 84s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] 84s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-user-session armhf 1.14.10-4ubuntu2 [9962 B] 84s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu2 [45.0 kB] 84s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1 armhf 2.6.1-2 [65.9 kB] 84s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB] 84s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-bin armhf 1.14.10-4ubuntu2 [37.1 kB] 84s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus armhf 1.14.10-4ubuntu2 [28.1 kB] 84s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-daemon armhf 1.14.10-4ubuntu2 [109 kB] 84s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu2 [190 kB] 84s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu2 [171 kB] 84s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu2 [49.5 kB] 84s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu2 [135 kB] 84s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu2 [34.4 kB] 84s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu2 [238 kB] 84s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu2 [196 kB] 84s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu2 [134 kB] 84s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-utils3 armhf 3.1.0-1build1 [16.9 kB] 84s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libvolume-key1 armhf 0.3.12-7build1 [38.4 kB] 84s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjcat1 armhf 0.2.0-2build2 [30.4 kB] 84s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf parted armhf 3.6-3.1build2 [39.4 kB] 84s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libparted2t64 armhf 3.6-3.1build2 [143 kB] 84s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12 armhf 3.12.2-4build3 [645 kB] 84s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-minimal armhf 3.12.2-4build3 [1942 kB] 84s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-stdlib armhf 3.12.2-4build3 [1906 kB] 84s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-minimal armhf 3.12.2-4build3 [816 kB] 84s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-5ubuntu1 [19.0 kB] 84s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11 armhf 3.11.8-1build4 [589 kB] 84s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11-minimal armhf 3.11.8-1build4 [1795 kB] 84s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-stdlib armhf 3.11.8-1build4 [1810 kB] 84s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-minimal armhf 3.11.8-1build4 [826 kB] 84s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu1 [599 kB] 84s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build2 [12.7 kB] 84s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build2 [8962 B] 84s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 84s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6 [661 kB] 84s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gdbm armhf 3.12.2-3ubuntu2 [17.1 kB] 84s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-3build4 [1196 kB] 84s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1 [30.3 kB] 84s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1 [6208 B] 84s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2 [4101 kB] 84s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2 [231 kB] 84s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2 [1671 kB] 84s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu3 [15.0 kB] 84s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2 [187 kB] 84s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2 [187 kB] 84s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu2 [1046 kB] 85s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB] 85s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu7 [290 kB] 85s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf shared-mime-info armhf 2.4-1build1 [470 kB] 85s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-girepository-2.0 armhf 1.79.1-1ubuntu6 [24.8 kB] 85s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-glib-2.0 armhf 2.79.3-3ubuntu5 [182 kB] 85s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgirepository-1.0-1 armhf 1.79.1-1ubuntu6 [106 kB] 85s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gi armhf 3.47.0-3build1 [219 kB] 85s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dbus armhf 1.3.2-5build2 [94.7 kB] 85s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnetplan1 armhf 1.0-1 [113 kB] 85s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-netplan armhf 1.0-1 [22.5 kB] 85s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan-generator armhf 1.0-1 [58.7 kB] 85s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-bin armhf 0.142ubuntu23 [20.3 kB] 85s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-core all 0.142ubuntu23 [50.1 kB] 85s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools all 0.142ubuntu23 [9058 B] 85s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan.io armhf 1.0-1 [64.3 kB] 85s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmlb2 armhf 0.3.15-1build1 [57.0 kB] 85s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqrtr-glib0 armhf 1.2.2-1ubuntu3 [15.4 kB] 85s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-glib5 armhf 1.35.2-0ubuntu1 [908 kB] 85s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-proxy armhf 1.35.2-0ubuntu1 [5732 B] 85s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-agent-1-0 armhf 124-1ubuntu1 [15.3 kB] 85s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-gobject-1-0 armhf 124-1ubuntu1 [44.1 kB] 85s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0t64 armhf 2.79.3-3ubuntu5 [1414 kB] 85s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfwupd2 armhf 1.9.15-1 [123 kB] 85s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libarchive13t64 armhf 3.7.2-1.1ubuntu2 [330 kB] 85s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fwupd armhf 1.9.15-1 [4349 kB] 86s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.13ubuntu1 [210 kB] 86s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.13ubuntu1 [986 kB] 86s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.13ubuntu1 [1367 kB] 86s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client-l10n armhf 31.2 [19.4 kB] 86s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client armhf 31.2 [216 kB] 86s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf keyboxd armhf 2.4.4-2ubuntu15 [111 kB] 86s Get:134 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1 [6940 B] 86s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu15 [224 kB] 86s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu15 [524 kB] 86s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-wks-client armhf 2.4.4-2ubuntu15 [87.4 kB] 86s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-utils armhf 2.4.4-2ubuntu15 [158 kB] 86s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu15 [235 kB] 86s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgsm armhf 2.4.4-2ubuntu15 [241 kB] 86s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-3.1 [129 kB] 86s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gawk armhf 1:5.2.1-2build2 [415 kB] 86s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fdisk armhf 2.39.3-9ubuntu2 [135 kB] 86s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu15 [115 kB] 86s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dirmngr armhf 2.4.4-2ubuntu15 [346 kB] 86s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg all 2.4.4-2ubuntu15 [359 kB] 86s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-apt armhf 2.7.6build1 [162 kB] 86s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB] 86s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-yaml armhf 6.0.1-2build1 [117 kB] 86s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python-apt-common all 2.7.6build1 [19.8 kB] 86s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 86s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] 86s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu4 [1229 kB] 86s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.12.2-0ubuntu1 [27.1 kB] 86s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.12.2-0ubuntu1 [24.1 kB] 86s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.12.2-0ubuntu1 [9802 B] 86s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu2 [117 kB] 86s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu2 [78.7 kB] 86s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build1 [946 kB] 86s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-3.1 [56.4 kB] 86s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpgme11t64 armhf 1.18.0-4.1ubuntu3 [120 kB] 86s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-crypto3 armhf 3.1.0-1build1 [20.3 kB] 86s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B] 86s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 86s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dhcpcd-base armhf 1:10.0.6-1ubuntu2 [186 kB] 86s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-fs3 armhf 3.1.0-1build1 [34.4 kB] 86s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreiserfscore0t64 armhf 1:3.6.27-7.1 [66.2 kB] 86s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main armhf btrfs-progs armhf 6.6.3-1.1build1 [852 kB] 86s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu2 [201 kB] 86s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu2 [571 kB] 86s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-loop3 armhf 3.1.0-1build1 [6502 B] 86s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-mdraid3 armhf 3.1.0-1build1 [13.3 kB] 87s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-nvme3 armhf 3.1.0-1build1 [17.5 kB] 87s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnvme1t64 armhf 1.8-3 [67.5 kB] 87s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-part3 armhf 3.1.0-1build1 [16.4 kB] 87s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-swap3 armhf 3.1.0-1build1 [8894 B] 87s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev3 armhf 3.1.0-1build1 [42.9 kB] 87s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgudev-1.0-0 armhf 1:238-3ubuntu2 [13.6 kB] 87s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu2 [595 kB] 87s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbpf1 armhf 1:1.3.0-2build1 [146 kB] 87s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf iproute2 armhf 6.1.0-1ubuntu5 [1060 kB] 87s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build2 [49.9 kB] 87s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B] 87s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lsof armhf 4.95.0-1build2 [248 kB] 87s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build2 [36.5 kB] 87s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1 [73.2 kB] 87s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-proxy armhf 1.31.2-0ubuntu2 [5748 B] 87s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-glib4 armhf 1.31.2-0ubuntu2 [216 kB] 87s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-common all 1.8.0-2build1 [4210 B] 87s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-0 armhf 1.8.0-2build1 [61.2 kB] 87s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build1 [68.1 kB] 87s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB] 87s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libusb-1.0-0 armhf 2:1.0.27-1 [48.7 kB] 87s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgusb2 armhf 0.4.8-1build1 [34.6 kB] 87s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmm-glib0 armhf 1.23.4-0ubuntu1 [214 kB] 87s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-5ubuntu1 [49.7 kB] 87s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libibverbs1 armhf 50.0-2build1 [57.9 kB] 87s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfido2-1 armhf 1.14.0-1build1 [75.8 kB] 87s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu3 [1280 kB] 87s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu2 [1216 kB] 87s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu6 [530 kB] 87s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3 [21.1 kB] 87s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3 [307 kB] 87s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3 [81.4 kB] 87s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libplymouth5 armhf 24.004.60-1ubuntu6 [140 kB] 87s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-3 [166 kB] 88s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-host armhf 1:9.18.24-0ubuntu3 [47.4 kB] 88s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu3 [149 kB] 88s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-libs armhf 1:9.18.24-0ubuntu3 [1148 kB] 88s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuv1t64 armhf 1.48.0-1.1 [82.9 kB] 88s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu2 [41.7 kB] 88s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu2 [10.8 kB] 88s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build4 [10.1 kB] 88s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB] 88s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main armhf install-info armhf 7.1-3build1 [60.5 kB] 88s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-19ubuntu1 [47.7 kB] 88s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu2 [14.7 kB] 88s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dmsetup armhf 2:1.02.185-3ubuntu2 [81.1 kB] 88s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf eject armhf 2.39.3-9ubuntu2 [43.2 kB] 88s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-5.1ubuntu1 [13.9 kB] 88s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbsd0 armhf 0.12.1-1 [36.6 kB] 88s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 88s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libslang2 armhf 2.3.3-3build1 [478 kB] 88s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main armhf locales all 2.39-0ubuntu6 [4232 kB] 88s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-tiny armhf 2:9.1.0016-1ubuntu5 [665 kB] 88s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-common all 2:9.1.0016-1ubuntu5 [385 kB] 88s Get:227 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB] 88s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xxd armhf 2:9.1.0016-1ubuntu5 [62.4 kB] 88s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apparmor armhf 4.0.0-beta3-0ubuntu2 [562 kB] 88s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ftp all 20230507-2build1 [4724 B] 88s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main armhf inetutils-telnet armhf 2:2.5-3ubuntu3 [90.7 kB] 88s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main armhf info armhf 7.1-3build1 [127 kB] 88s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmuu1 armhf 2:1.1.3-3build1 [8004 B] 88s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2build2 [310 kB] 88s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mtr-tiny armhf 0.95-1.1build1 [51.7 kB] 88s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu6 [9818 B] 88s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth armhf 24.004.60-1ubuntu6 [142 kB] 88s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1 [176 kB] 88s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main armhf telnet all 0.17+2.5-3ubuntu3 [3682 B] 88s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main armhf usb.ids all 2024.03.18-1 [223 kB] 88s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.0-0.2 [271 kB] 88s Get:242 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf0 armhf 2.42-4ubuntu1 [87.7 kB] 88s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf-nobfd0 armhf 2.42-4ubuntu1 [88.0 kB] 88s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu1 [2925 kB] 88s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbinutils armhf 2.42-4ubuntu1 [464 kB] 88s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils armhf 2.42-4ubuntu1 [3078 B] 88s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-common armhf 2.42-4ubuntu1 [217 kB] 88s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsframe1 armhf 2.42-4ubuntu1 [13.1 kB] 88s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bolt armhf 0.9.6-2build1 [138 kB] 88s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu2 [214 kB] 88s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu4 [1074 kB] 88s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu4 [268 kB] 89s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB] 89s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ibverbs-providers armhf 50.0-2build1 [27.4 kB] 89s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf jq armhf 1.7.1-3 [65.2 kB] 89s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjq1 armhf 1.7.1-3 [156 kB] 89s Get:257 http://ftpmaster.internal/ubuntu noble/main armhf libatm1t64 armhf 1:2.5.1-5.1 [20.0 kB] 89s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 89s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libftdi1-2 armhf 1.5-6build4 [25.7 kB] 89s Get:260 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB] 89s Get:261 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules armhf 2.1.28+dfsg1-5ubuntu1 [61.3 kB] 89s Get:262 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lib2to3 all 3.12.2-3ubuntu2 [79.3 kB] 89s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyrsistent armhf 0.20.0-1build1 [53.0 kB] 89s Get:264 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-typing-extensions all 4.10.0-1 [60.7 kB] 89s Get:265 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kpartx armhf 0.9.4-5ubuntu5 [31.4 kB] 90s Preconfiguring packages ... 91s Fetched 106 MB in 7s (15.4 MB/s) 91s (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 ... 58619 files and directories currently installed.) 91s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_armhf.deb ... 91s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ... 91s Setting up bsdutils (1:2.39.3-9ubuntu2) ... 91s (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 ... 58619 files and directories currently installed.) 91s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ... 91s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 91s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ... 91s (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 ... 58619 files and directories currently installed.) 91s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ... 91s Unpacking libgcc-s1:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 92s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ... 92s (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 ... 58619 files and directories currently installed.) 92s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ... 92s Unpacking libstdc++6:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 92s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ... 92s (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 ... 58619 files and directories currently installed.) 92s Preparing to unpack .../libc6_2.39-0ubuntu6_armhf.deb ... 92s Unpacking libc6:armhf (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 93s Setting up libc6:armhf (2.39-0ubuntu6) ... 94s (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 ... 58619 files and directories currently installed.) 94s Preparing to unpack .../0-libbrotli1_1.1.0-2build1_armhf.deb ... 94s Unpacking libbrotli1:armhf (1.1.0-2build1) over (1.1.0-2) ... 94s Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-5.1ubuntu1_armhf.deb ... 94s Unpacking libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 94s Preparing to unpack .../2-libkrb5-3_1.20.1-5.1ubuntu1_armhf.deb ... 94s Unpacking libkrb5-3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 95s Preparing to unpack .../3-libkrb5support0_1.20.1-5.1ubuntu1_armhf.deb ... 95s Unpacking libkrb5support0:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 95s Preparing to unpack .../4-libk5crypto3_1.20.1-5.1ubuntu1_armhf.deb ... 95s Unpacking libk5crypto3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 95s Preparing to unpack .../5-libcom-err2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 95s Unpacking libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 95s Preparing to unpack .../6-zlib1g_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ... 95s Unpacking zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 95s Setting up zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) ... 96s (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 ... 58619 files and directories currently installed.) 96s Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2build6_armhf.deb ... 96s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ... 96s Preparing to unpack .../udisks2_2.10.1-6_armhf.deb ... 96s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ... 97s Preparing to unpack .../libudisks2-0_2.10.1-6_armhf.deb ... 97s Unpacking libudisks2-0:armhf (2.10.1-6) over (2.10.1-1ubuntu2) ... 97s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_armhf.deb ... 97s Unpacking libblkid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 98s Setting up libblkid1:armhf (2.39.3-9ubuntu2) ... 98s (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 ... 58619 files and directories currently installed.) 98s Preparing to unpack .../liblzma5_5.6.0-0.2_armhf.deb ... 98s Unpacking liblzma5:armhf (5.6.0-0.2) over (5.4.5-0.3) ... 98s Setting up liblzma5:armhf (5.6.0-0.2) ... 99s (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 ... 58619 files and directories currently installed.) 99s Preparing to unpack .../0-kmod_31+20240202-2ubuntu4_armhf.deb ... 99s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 99s dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty 99s Preparing to unpack .../1-libkmod2_31+20240202-2ubuntu4_armhf.deb ... 99s Unpacking libkmod2:armhf (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 99s Preparing to unpack .../2-systemd-dev_255.4-1ubuntu5_all.deb ... 99s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 99s Preparing to unpack .../3-systemd-timesyncd_255.4-1ubuntu5_armhf.deb ... 99s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 100s Preparing to unpack .../4-dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ... 100s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 100s Preparing to unpack .../5-libaudit-common_1%3a3.1.2-2.1_all.deb ... 100s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ... 100s Setting up libaudit-common (1:3.1.2-2.1) ... 100s (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 ... 58618 files and directories currently installed.) 100s Preparing to unpack .../libcap-ng0_0.8.4-2build1_armhf.deb ... 100s Unpacking libcap-ng0:armhf (0.8.4-2build1) over (0.8.4-2) ... 101s Setting up libcap-ng0:armhf (0.8.4-2build1) ... 101s (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 ... 58618 files and directories currently installed.) 101s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_armhf.deb ... 101s Unpacking libaudit1:armhf (1:3.1.2-2.1) over (1:3.1.2-2) ... 101s Setting up libaudit1:armhf (1:3.1.2-2.1) ... 101s (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 ... 58618 files and directories currently installed.) 101s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_armhf.deb ... 101s Unpacking libpam0g:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 101s Setting up libpam0g:armhf (1.5.3-5ubuntu3) ... 101s (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 ... 58618 files and directories currently installed.) 101s Preparing to unpack .../libselinux1_3.5-2ubuntu1_armhf.deb ... 101s Unpacking libselinux1:armhf (3.5-2ubuntu1) over (3.5-2build1) ... 101s Setting up libselinux1:armhf (3.5-2ubuntu1) ... 101s dpkg: libcurl4:armhf: dependency problems, but removing anyway as you requested: 101s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 101s 101s (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 ... 58618 files and directories currently installed.) 101s Removing libcurl4:armhf (8.5.0-2ubuntu2) ... 101s Selecting previously unselected package libcurl4t64:armhf. 101s (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 ... 58613 files and directories currently installed.) 101s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_armhf.deb ... 101s Unpacking libcurl4t64:armhf (8.5.0-2ubuntu7) ... 101s Preparing to unpack .../curl_8.5.0-2ubuntu7_armhf.deb ... 101s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 102s dpkg: libpsl5:armhf: dependency problems, but removing anyway as you requested: 102s wget depends on libpsl5 (>= 0.16.0). 102s libcurl3-gnutls:armhf depends on libpsl5 (>= 0.16.0). 102s 102s (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 ... 58619 files and directories currently installed.) 102s Removing libpsl5:armhf (0.21.2-1build1) ... 102s Selecting previously unselected package libpsl5t64:armhf. 102s (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 ... 58614 files and directories currently installed.) 102s Preparing to unpack .../libpsl5t64_0.21.2-1.1_armhf.deb ... 102s Unpacking libpsl5t64:armhf (0.21.2-1.1) ... 102s Preparing to unpack .../wget_1.21.4-1ubuntu2_armhf.deb ... 102s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 102s Preparing to unpack .../tnftp_20230507-2build1_armhf.deb ... 102s Unpacking tnftp (20230507-2build1) over (20230507-2) ... 102s dpkg: libpcap0.8:armhf: dependency problems, but removing anyway as you requested: 102s tcpdump depends on libpcap0.8 (>= 1.9.1). 102s 103s (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 ... 58620 files and directories currently installed.) 103s Removing libpcap0.8:armhf (1.10.4-4ubuntu3) ... 103s Selecting previously unselected package libpcap0.8t64:armhf. 103s (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 ... 58609 files and directories currently installed.) 103s Preparing to unpack .../00-libpcap0.8t64_1.10.4-4.1ubuntu1_armhf.deb ... 103s Unpacking libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 103s Preparing to unpack .../01-tcpdump_4.99.4-3ubuntu2_armhf.deb ... 103s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ... 103s Preparing to unpack .../02-libsystemd-shared_255.4-1ubuntu5_armhf.deb ... 103s Unpacking libsystemd-shared:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 103s Preparing to unpack .../03-systemd-resolved_255.4-1ubuntu5_armhf.deb ... 103s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 103s Preparing to unpack .../04-sudo_1.9.15p5-3ubuntu3_armhf.deb ... 103s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ... 104s Preparing to unpack .../05-rsync_3.2.7-1build1_armhf.deb ... 104s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ... 104s Preparing to unpack .../06-python3-cryptography_41.0.7-4build2_armhf.deb ... 104s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ... 104s Preparing to unpack .../07-openssl_3.0.13-0ubuntu2_armhf.deb ... 104s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 105s Preparing to unpack .../08-openssh-sftp-server_1%3a9.6p1-3ubuntu11_armhf.deb ... 105s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 105s Preparing to unpack .../09-openssh-client_1%3a9.6p1-3ubuntu11_armhf.deb ... 105s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 105s Preparing to unpack .../10-openssh-server_1%3a9.6p1-3ubuntu11_armhf.deb ... 105s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 105s Selecting previously unselected package linux-headers-6.8.0-20. 105s Preparing to unpack .../11-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ... 105s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ... 109s Selecting previously unselected package linux-headers-6.8.0-20-generic. 109s Preparing to unpack .../12-linux-headers-6.8.0-20-generic_6.8.0-20.20_armhf.deb ... 109s Unpacking linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 111s Preparing to unpack .../13-linux-headers-generic_6.8.0-20.20+1_armhf.deb ... 111s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 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 ... 89772 files and directories currently installed.) 112s Removing linux-headers-6.8.0-11-generic (6.8.0-11.11) ... 112s dpkg: libssl3:armhf: dependency problems, but removing anyway as you requested: 112s systemd depends on libssl3 (>= 3.0.0). 112s libssh-4:armhf depends on libssl3 (>= 3.0.0). 112s libsasl2-modules:armhf depends on libssl3 (>= 3.0.0). 112s libsasl2-2:armhf depends on libssl3 (>= 3.0.0). 112s libpython3.12-minimal:armhf depends on libssl3 (>= 3.0.0). 112s libpython3.11-minimal:armhf depends on libssl3 (>= 3.0.0). 112s libnvme1 depends on libssl3 (>= 3.0.0). 112s libfido2-1:armhf depends on libssl3 (>= 3.0.0). 112s libcryptsetup12:armhf depends on libssl3 (>= 3.0.0). 112s dhcpcd-base depends on libssl3 (>= 3.0.0). 112s bind9-libs:armhf depends on libssl3 (>= 3.0.0). 112s 112s Removing libssl3:armhf (3.0.10-1ubuntu4) ... 112s Selecting previously unselected package libssl3t64:armhf. 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 ... 78622 files and directories currently installed.) 113s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_armhf.deb ... 113s Unpacking libssl3t64:armhf (3.0.13-0ubuntu2) ... 113s Setting up libssl3t64:armhf (3.0.13-0ubuntu2) ... 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 ... 78635 files and directories currently installed.) 113s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_armhf.deb ... 113s Unpacking libnss-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 113s Preparing to unpack .../libudev1_255.4-1ubuntu5_armhf.deb ... 113s Unpacking libudev1:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 113s Setting up libudev1:armhf (255.4-1ubuntu5) ... 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 ... 78635 files and directories currently installed.) 114s Preparing to unpack .../systemd_255.4-1ubuntu5_armhf.deb ... 114s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 114s Preparing to unpack .../udev_255.4-1ubuntu5_armhf.deb ... 114s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 114s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_armhf.deb ... 114s Unpacking libsystemd0:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 115s Setting up libsystemd0:armhf (255.4-1ubuntu5) ... 115s Setting up libkmod2:armhf (31+20240202-2ubuntu4) ... 115s Setting up libsystemd-shared:armhf (255.4-1ubuntu5) ... 115s Setting up systemd-dev (255.4-1ubuntu5) ... 115s Setting up systemd (255.4-1ubuntu5) ... 116s (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 ... 78635 files and directories currently installed.) 116s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_armhf.deb ... 116s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 116s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_armhf.deb ... 116s Unpacking libpam-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 117s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_armhf.deb ... 117s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 117s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ... 117s pam_namespace.service is a disabled or a static unit not running, not starting it. 117s (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 ... 78635 files and directories currently installed.) 117s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_armhf.deb ... 118s Unpacking libpam-modules:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 118s Setting up libpam-modules:armhf (1.5.3-5ubuntu3) ... 118s Installing new version of config file /etc/security/namespace.init ... 118s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 118s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu3_all.deb ... 118s Unpacking libpam-runtime (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 118s Setting up libpam-runtime (1.5.3-5ubuntu3) ... 118s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 118s Preparing to unpack .../0-dbus-user-session_1.14.10-4ubuntu2_armhf.deb ... 118s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 118s Preparing to unpack .../1-libapparmor1_4.0.0-beta3-0ubuntu2_armhf.deb ... 118s Unpacking libapparmor1:armhf (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 118s Preparing to unpack .../2-libexpat1_2.6.1-2_armhf.deb ... 118s Unpacking libexpat1:armhf (2.6.1-2) over (2.6.0-1) ... 119s Preparing to unpack .../3-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ... 119s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 119s Preparing to unpack .../4-dbus-bin_1.14.10-4ubuntu2_armhf.deb ... 119s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 119s Preparing to unpack .../5-dbus_1.14.10-4ubuntu2_armhf.deb ... 119s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 119s Preparing to unpack .../6-dbus-daemon_1.14.10-4ubuntu2_armhf.deb ... 119s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 119s Preparing to unpack .../7-libdbus-1-3_1.14.10-4ubuntu2_armhf.deb ... 119s Unpacking libdbus-1-3:armhf (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 119s Preparing to unpack .../8-libmount1_2.39.3-9ubuntu2_armhf.deb ... 119s Unpacking libmount1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 119s Setting up libmount1:armhf (2.39.3-9ubuntu2) ... 119s (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 ... 78633 files and directories currently installed.) 119s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu2_armhf.deb ... 119s Unpacking libseccomp2:armhf (2.5.5-1ubuntu2) over (2.5.5-1ubuntu1) ... 119s Setting up libseccomp2:armhf (2.5.5-1ubuntu2) ... 120s (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 ... 78633 files and directories currently installed.) 120s Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_armhf.deb ... 120s Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 120s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_armhf.deb ... 120s Unpacking libuuid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 120s Setting up libuuid1:armhf (2.39.3-9ubuntu2) ... 120s (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 ... 78633 files and directories currently installed.) 120s Preparing to unpack .../0-libcryptsetup12_2%3a2.7.0-1ubuntu2_armhf.deb ... 120s Unpacking libcryptsetup12:armhf (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 120s Preparing to unpack .../1-libfdisk1_2.39.3-9ubuntu2_armhf.deb ... 120s Unpacking libfdisk1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 120s Preparing to unpack .../2-mount_2.39.3-9ubuntu2_armhf.deb ... 120s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 120s Preparing to unpack .../3-libblockdev-utils3_3.1.0-1build1_armhf.deb ... 120s Unpacking libblockdev-utils3:armhf (3.1.0-1build1) over (3.1.0-1) ... 120s Preparing to unpack .../4-libvolume-key1_0.3.12-7build1_armhf.deb ... 120s Unpacking libvolume-key1:armhf (0.3.12-7build1) over (0.3.12-5build2) ... 121s Preparing to unpack .../5-libjcat1_0.2.0-2build2_armhf.deb ... 121s Unpacking libjcat1:armhf (0.2.0-2build2) over (0.2.0-2) ... 121s (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 ... 78633 files and directories currently installed.) 121s Removing libgpgme11:armhf (1.18.0-4ubuntu1) ... 121s (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 ... 78627 files and directories currently installed.) 121s Preparing to unpack .../parted_3.6-3.1build2_armhf.deb ... 121s Unpacking parted (3.6-3.1build2) over (3.6-3) ... 121s (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 ... 78627 files and directories currently installed.) 121s Removing libparted2:armhf (3.6-3) ... 121s Selecting previously unselected package libparted2t64:armhf. 121s (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 ... 78621 files and directories currently installed.) 121s Preparing to unpack .../00-libparted2t64_3.6-3.1build2_armhf.deb ... 121s Unpacking libparted2t64:armhf (3.6-3.1build2) ... 123s Preparing to unpack .../01-python3.12_3.12.2-4build3_armhf.deb ... 123s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ... 126s Preparing to unpack .../02-python3.12-minimal_3.12.2-4build3_armhf.deb ... 126s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ... 128s Preparing to unpack .../03-libpython3.12-stdlib_3.12.2-4build3_armhf.deb ... 129s Unpacking libpython3.12-stdlib:armhf (3.12.2-4build3) over (3.12.2-1) ... 129s Preparing to unpack .../04-libpython3.12-minimal_3.12.2-4build3_armhf.deb ... 129s Unpacking libpython3.12-minimal:armhf (3.12.2-4build3) over (3.12.2-1) ... 129s Preparing to unpack .../05-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 129s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 129s Preparing to unpack .../06-python3.11_3.11.8-1build4_armhf.deb ... 129s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ... 130s Preparing to unpack .../07-python3.11-minimal_3.11.8-1build4_armhf.deb ... 130s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ... 130s Preparing to unpack .../08-libpython3.11-stdlib_3.11.8-1build4_armhf.deb ... 130s Unpacking libpython3.11-stdlib:armhf (3.11.8-1build4) over (3.11.8-1) ... 130s Preparing to unpack .../09-libpython3.11-minimal_3.11.8-1build4_armhf.deb ... 130s Unpacking libpython3.11-minimal:armhf (3.11.8-1build4) over (3.11.8-1) ... 131s Preparing to unpack .../10-libsqlite3-0_3.45.1-1ubuntu1_armhf.deb ... 131s Unpacking libsqlite3-0:armhf (3.45.1-1ubuntu1) over (3.45.1-1) ... 131s Preparing to unpack .../11-libtext-iconv-perl_1.7-8build2_armhf.deb ... 131s Unpacking libtext-iconv-perl:armhf (1.7-8build2) over (1.7-8build1) ... 131s Preparing to unpack .../12-libtext-charwidth-perl_0.04-11build2_armhf.deb ... 131s Unpacking libtext-charwidth-perl:armhf (0.04-11build2) over (0.04-11build1) ... 131s Preparing to unpack .../13-perl-modules-5.38_5.38.2-3.2_all.deb ... 131s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 132s dpkg: libperl5.38:armhf: dependency problems, but removing anyway as you requested: 132s perl depends on libperl5.38 (= 5.38.2-3). 132s 132s (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 ... 78624 files and directories currently installed.) 132s Removing libperl5.38:armhf (5.38.2-3) ... 132s dpkg: libdb5.3:armhf: dependency problems, but removing anyway as you requested: 132s iproute2 depends on libdb5.3. 132s apt-utils depends on libdb5.3. 132s 132s Removing libdb5.3:armhf (5.3.28+dfsg2-4) ... 132s Selecting previously unselected package libdb5.3t64:armhf. 132s (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 ... 78099 files and directories currently installed.) 132s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_armhf.deb ... 132s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-6) ... 132s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu2_armhf.deb ... 132s Unpacking python3-gdbm:armhf (3.12.2-3ubuntu2) over (3.11.5-1) ... 132s Preparing to unpack .../man-db_2.12.0-3build4_armhf.deb ... 132s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ... 132s (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 ... 78105 files and directories currently installed.) 132s Removing libgdbm-compat4:armhf (1.23-5) ... 132s Removing libgdbm6:armhf (1.23-5) ... 132s Selecting previously unselected package libgdbm6t64:armhf. 132s (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 ... 78095 files and directories currently installed.) 132s Preparing to unpack .../libgdbm6t64_1.23-5.1_armhf.deb ... 132s Unpacking libgdbm6t64:armhf (1.23-5.1) ... 132s Selecting previously unselected package libgdbm-compat4t64:armhf. 133s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_armhf.deb ... 133s Unpacking libgdbm-compat4t64:armhf (1.23-5.1) ... 133s Selecting previously unselected package libperl5.38t64:armhf. 133s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_armhf.deb ... 133s Unpacking libperl5.38t64:armhf (5.38.2-3.2) ... 133s Preparing to unpack .../perl_5.38.2-3.2_armhf.deb ... 133s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ... 133s Preparing to unpack .../perl-base_5.38.2-3.2_armhf.deb ... 133s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 133s Setting up perl-base (5.38.2-3.2) ... 133s (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 ... 78626 files and directories currently installed.) 133s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu3_armhf.deb ... 133s Unpacking liblocale-gettext-perl (1.07-6ubuntu3) over (1.07-6build1) ... 133s dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested: 133s libhogweed6:armhf depends on libnettle8. 133s libgnutls30:armhf depends on libnettle8 (>= 3.9~). 133s libcurl3-gnutls:armhf depends on libnettle8. 133s libarchive13:armhf depends on libnettle8. 133s 133s (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 ... 78626 files and directories currently installed.) 133s Removing libnettle8:armhf (3.9.1-2) ... 133s Selecting previously unselected package libnettle8t64:armhf. 133s (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 ... 78619 files and directories currently installed.) 133s Preparing to unpack .../libnettle8t64_3.9.1-2.2_armhf.deb ... 133s Unpacking libnettle8t64:armhf (3.9.1-2.2) ... 133s Setting up libnettle8t64:armhf (3.9.1-2.2) ... 134s dpkg: libhogweed6:armhf: dependency problems, but removing anyway as you requested: 134s libgnutls30:armhf depends on libhogweed6 (>= 3.6). 134s 134s (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 ... 78627 files and directories currently installed.) 134s Removing libhogweed6:armhf (3.9.1-2) ... 134s Selecting previously unselected package libhogweed6t64:armhf. 134s (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 ... 78622 files and directories currently installed.) 134s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_armhf.deb ... 134s Unpacking libhogweed6t64:armhf (3.9.1-2.2) ... 134s Setting up libhogweed6t64:armhf (3.9.1-2.2) ... 134s dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested: 134s libldap2:armhf depends on libgnutls30 (>= 3.8.2). 134s libcurl3-gnutls:armhf depends on libgnutls30 (>= 3.8.2). 134s fwupd depends on libgnutls30 (>= 3.7.3). 134s dirmngr depends on libgnutls30 (>= 3.8.1). 134s apt depends on libgnutls30 (>= 3.8.1). 134s 134s (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 ... 78628 files and directories currently installed.) 134s Removing libgnutls30:armhf (3.8.3-1ubuntu1) ... 134s Selecting previously unselected package libgnutls30t64:armhf. 134s (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 ... 78619 files and directories currently installed.) 134s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_armhf.deb ... 134s Unpacking libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 134s Setting up libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 134s (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 ... 78647 files and directories currently installed.) 134s Preparing to unpack .../libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ... 134s Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 134s dpkg: libcurl3-gnutls:armhf: dependency problems, but removing anyway as you requested: 134s libfwupd2:armhf depends on libcurl3-gnutls (>= 7.63.0). 134s fwupd depends on libcurl3-gnutls (>= 7.63.0). 134s 134s (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 ... 78647 files and directories currently installed.) 134s Removing libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ... 134s Selecting previously unselected package libcurl3t64-gnutls:armhf. 134s (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 ... 78640 files and directories currently installed.) 134s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu7_armhf.deb ... 134s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 134s Preparing to unpack .../01-shared-mime-info_2.4-1build1_armhf.deb ... 134s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ... 134s Preparing to unpack .../02-gir1.2-girepository-2.0_1.79.1-1ubuntu6_armhf.deb ... 134s Unpacking gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 134s Preparing to unpack .../03-gir1.2-glib-2.0_2.79.3-3ubuntu5_armhf.deb ... 134s Unpacking gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 134s Preparing to unpack .../04-libgirepository-1.0-1_1.79.1-1ubuntu6_armhf.deb ... 134s Unpacking libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 134s Preparing to unpack .../05-python3-gi_3.47.0-3build1_armhf.deb ... 135s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ... 135s Preparing to unpack .../06-python3-dbus_1.3.2-5build2_armhf.deb ... 135s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ... 135s Selecting previously unselected package libnetplan1:armhf. 135s Preparing to unpack .../07-libnetplan1_1.0-1_armhf.deb ... 135s Unpacking libnetplan1:armhf (1.0-1) ... 135s Preparing to unpack .../08-python3-netplan_1.0-1_armhf.deb ... 135s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ... 135s Preparing to unpack .../09-netplan-generator_1.0-1_armhf.deb ... 135s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 135s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ... 135s Preparing to unpack .../10-initramfs-tools-bin_0.142ubuntu23_armhf.deb ... 135s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ... 135s Preparing to unpack .../11-initramfs-tools-core_0.142ubuntu23_all.deb ... 135s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ... 135s Preparing to unpack .../12-initramfs-tools_0.142ubuntu23_all.deb ... 135s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ... 135s Preparing to unpack .../13-netplan.io_1.0-1_armhf.deb ... 135s Unpacking netplan.io (1.0-1) over (0.107.1-3) ... 136s Preparing to unpack .../14-libxmlb2_0.3.15-1build1_armhf.deb ... 136s Unpacking libxmlb2:armhf (0.3.15-1build1) over (0.3.15-1) ... 136s Preparing to unpack .../15-libqrtr-glib0_1.2.2-1ubuntu3_armhf.deb ... 136s Unpacking libqrtr-glib0:armhf (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ... 136s Preparing to unpack .../16-libqmi-glib5_1.35.2-0ubuntu1_armhf.deb ... 136s Unpacking libqmi-glib5:armhf (1.35.2-0ubuntu1) over (1.34.0-2) ... 136s Preparing to unpack .../17-libqmi-proxy_1.35.2-0ubuntu1_armhf.deb ... 136s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ... 136s Preparing to unpack .../18-libpolkit-agent-1-0_124-1ubuntu1_armhf.deb ... 136s Unpacking libpolkit-agent-1-0:armhf (124-1ubuntu1) over (124-1) ... 136s Preparing to unpack .../19-libpolkit-gobject-1-0_124-1ubuntu1_armhf.deb ... 136s Unpacking libpolkit-gobject-1-0:armhf (124-1ubuntu1) over (124-1) ... 136s (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 ... 78651 files and directories currently installed.) 136s Removing libnetplan0:armhf (0.107.1-3) ... 136s dpkg: libglib2.0-0:armhf: dependency problems, but removing anyway as you requested: 136s libmm-glib0:armhf depends on libglib2.0-0 (>= 2.62.0). 136s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 136s libmbim-glib4:armhf depends on libglib2.0-0 (>= 2.56). 136s libjson-glib-1.0-0:armhf depends on libglib2.0-0 (>= 2.75.3). 136s libgusb2:armhf depends on libglib2.0-0 (>= 2.75.3). 136s libgudev-1.0-0:armhf depends on libglib2.0-0 (>= 2.38.0). 136s libfwupd2:armhf depends on libglib2.0-0 (>= 2.79.0). 136s libblockdev3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s libblockdev-swap3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s libblockdev-part3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s libblockdev-nvme3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s libblockdev-mdraid3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s libblockdev-loop3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s libblockdev-fs3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s libblockdev-crypto3:armhf depends on libglib2.0-0 (>= 2.42.2). 136s fwupd depends on libglib2.0-0 (>= 2.79.0). 136s bolt depends on libglib2.0-0 (>= 2.56.0). 136s 136s Removing libglib2.0-0:armhf (2.79.2-1~ubuntu1) ... 136s Selecting previously unselected package libglib2.0-0t64:armhf. 136s (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 ... 78622 files and directories currently installed.) 136s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_armhf.deb ... 136s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:armhf.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 136s removed '/var/lib/dpkg/info/libglib2.0-0:armhf.postrm' 136s Unpacking libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 136s Preparing to unpack .../libfwupd2_1.9.15-1_armhf.deb ... 136s Unpacking libfwupd2:armhf (1.9.15-1) over (1.9.14-1) ... 136s dpkg: libarchive13:armhf: dependency problems, but removing anyway as you requested: 136s fwupd depends on libarchive13 (>= 3.2.1). 136s 136s (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 ... 78647 files and directories currently installed.) 136s Removing libarchive13:armhf (3.7.2-1ubuntu2) ... 136s Selecting previously unselected package libarchive13t64:armhf. 136s (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 ... 78641 files and directories currently installed.) 136s Preparing to unpack .../libarchive13t64_3.7.2-1.1ubuntu2_armhf.deb ... 136s Unpacking libarchive13t64:armhf (3.7.2-1.1ubuntu2) ... 136s Preparing to unpack .../fwupd_1.9.15-1_armhf.deb ... 137s Unpacking fwupd (1.9.15-1) over (1.9.14-1) ... 137s Preparing to unpack .../apt-utils_2.7.13ubuntu1_armhf.deb ... 137s Unpacking apt-utils (2.7.13ubuntu1) over (2.7.12) ... 137s dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested: 137s ubuntu-pro-client depends on libapt-pkg6.0 (>= 1.9~). 137s python3-apt depends on libapt-pkg6.0 (>= 2.7.11). 137s apt depends on libapt-pkg6.0 (>= 2.7.12). 137s 137s (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 ... 78648 files and directories currently installed.) 137s Removing libapt-pkg6.0:armhf (2.7.12) ... 137s Selecting previously unselected package libapt-pkg6.0t64:armhf. 137s (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 ... 78599 files and directories currently installed.) 137s Preparing to unpack .../libapt-pkg6.0t64_2.7.13ubuntu1_armhf.deb ... 137s Unpacking libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ... 137s Setting up libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ... 137s (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 ... 78649 files and directories currently installed.) 137s Preparing to unpack .../apt_2.7.13ubuntu1_armhf.deb ... 137s Unpacking apt (2.7.13ubuntu1) over (2.7.12) ... 137s Setting up apt (2.7.13ubuntu1) ... 138s (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 ... 78649 files and directories currently installed.) 138s Preparing to unpack .../ubuntu-pro-client-l10n_31.2_armhf.deb ... 138s Unpacking ubuntu-pro-client-l10n (31.2) over (31.1) ... 138s Preparing to unpack .../ubuntu-pro-client_31.2_armhf.deb ... 138s Unpacking ubuntu-pro-client (31.2) over (31.1) ... 138s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_armhf.deb ... 138s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 138s dpkg: libnpth0:armhf: dependency problems, but removing anyway as you requested: 138s gpgv depends on libnpth0 (>= 0.90). 138s gpgsm depends on libnpth0 (>= 0.90). 138s gpg-agent depends on libnpth0 (>= 0.90). 138s gpg depends on libnpth0 (>= 0.90). 138s dirmngr depends on libnpth0 (>= 0.90). 138s 138s (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 ... 78649 files and directories currently installed.) 138s Removing libnpth0:armhf (1.6-3build2) ... 139s Selecting previously unselected package libnpth0t64:armhf. 139s (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 ... 78644 files and directories currently installed.) 139s Preparing to unpack .../libnpth0t64_1.6-3.1_armhf.deb ... 139s Unpacking libnpth0t64:armhf (1.6-3.1) ... 139s Setting up libnpth0t64:armhf (1.6-3.1) ... 139s (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 ... 78650 files and directories currently installed.) 139s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_armhf.deb ... 139s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 139s Setting up gpgv (2.4.4-2ubuntu15) ... 139s (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 ... 78650 files and directories currently installed.) 139s Preparing to unpack .../gpg_2.4.4-2ubuntu15_armhf.deb ... 139s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 139s Preparing to unpack .../gpg-wks-client_2.4.4-2ubuntu15_armhf.deb ... 139s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 139s Preparing to unpack .../gnupg-utils_2.4.4-2ubuntu15_armhf.deb ... 139s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 139s Preparing to unpack .../gpg-agent_2.4.4-2ubuntu15_armhf.deb ... 139s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 139s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_armhf.deb ... 139s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 139s dpkg: libreadline8:armhf: dependency problems, but removing anyway as you requested: 139s gpgconf depends on libreadline8 (>= 6.0). 139s gawk depends on libreadline8 (>= 6.0). 139s fdisk depends on libreadline8 (>= 6.0). 139s 139s (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 ... 78650 files and directories currently installed.) 139s Removing libreadline8:armhf (8.2-3) ... 139s Selecting previously unselected package libreadline8t64:armhf. 139s (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 ... 78638 files and directories currently installed.) 139s Preparing to unpack .../libreadline8t64_8.2-3.1_armhf.deb ... 139s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' 139s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' 139s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' 139s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' 139s Unpacking libreadline8t64:armhf (8.2-3.1) ... 139s Setting up libreadline8t64:armhf (8.2-3.1) ... 139s (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 ... 78658 files and directories currently installed.) 139s Preparing to unpack .../00-gawk_1%3a5.2.1-2build2_armhf.deb ... 139s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ... 140s Preparing to unpack .../01-fdisk_2.39.3-9ubuntu2_armhf.deb ... 140s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 140s Preparing to unpack .../02-gpgconf_2.4.4-2ubuntu15_armhf.deb ... 140s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 140s Preparing to unpack .../03-dirmngr_2.4.4-2ubuntu15_armhf.deb ... 140s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 140s Preparing to unpack .../04-gnupg_2.4.4-2ubuntu15_all.deb ... 140s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 140s Preparing to unpack .../05-python3-apt_2.7.6build1_armhf.deb ... 140s Unpacking python3-apt (2.7.6build1) over (2.7.6) ... 140s Preparing to unpack .../06-pinentry-curses_1.2.1-3ubuntu4_armhf.deb ... 140s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ... 140s Preparing to unpack .../07-python3-yaml_6.0.1-2build1_armhf.deb ... 140s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ... 140s Preparing to unpack .../08-python-apt-common_2.7.6build1_all.deb ... 140s Unpacking python-apt-common (2.7.6build1) over (2.7.6) ... 140s Preparing to unpack .../09-python3-setuptools_68.1.2-2ubuntu1_all.deb ... 141s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ... 141s Preparing to unpack .../10-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ... 141s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ... 141s Preparing to unpack .../11-dpkg_1.22.6ubuntu4_armhf.deb ... 141s Unpacking dpkg (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 141s Setting up dpkg (1.22.6ubuntu4) ... 141s Setting up libpython3.12-minimal:armhf (3.12.2-4build3) ... 141s Setting up libexpat1:armhf (2.6.1-2) ... 141s Setting up python3.12-minimal (3.12.2-4build3) ... 143s (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 ... 78655 files and directories currently installed.) 143s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_armhf.deb ... 143s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 143s Setting up python3-minimal (3.12.2-0ubuntu1) ... 143s (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 ... 78655 files and directories currently installed.) 143s Preparing to unpack .../python3_3.12.2-0ubuntu1_armhf.deb ... 143s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 143s Preparing to unpack .../libpython3-stdlib_3.12.2-0ubuntu1_armhf.deb ... 143s Unpacking libpython3-stdlib:armhf (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 143s Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu2_armhf.deb ... 143s Unpacking libsmartcols1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 143s Setting up libsmartcols1:armhf (2.39.3-9ubuntu2) ... 143s (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 ... 78655 files and directories currently installed.) 143s Preparing to unpack .../0-bsdextrautils_2.39.3-9ubuntu2_armhf.deb ... 143s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 143s Preparing to unpack .../1-groff-base_1.23.0-3build1_armhf.deb ... 143s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ... 143s Preparing to unpack .../2-readline-common_8.2-3.1_all.deb ... 143s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 143s Selecting previously unselected package libgpgme11t64:armhf. 143s Preparing to unpack .../3-libgpgme11t64_1.18.0-4.1ubuntu3_armhf.deb ... 143s Unpacking libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 144s Preparing to unpack .../4-libblockdev-crypto3_3.1.0-1build1_armhf.deb ... 144s Unpacking libblockdev-crypto3:armhf (3.1.0-1build1) over (3.1.0-1) ... 144s Preparing to unpack .../5-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ... 144s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 144s Preparing to unpack .../6-logsave_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 144s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 144s Preparing to unpack .../7-dhcpcd-base_1%3a10.0.6-1ubuntu2_armhf.deb ... 144s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ... 144s Preparing to unpack .../8-libblockdev-fs3_3.1.0-1build1_armhf.deb ... 144s Unpacking libblockdev-fs3:armhf (3.1.0-1build1) over (3.1.0-1) ... 144s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested: 144s btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27). 144s 144s (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 ... 78662 files and directories currently installed.) 144s Removing libreiserfscore0 (1:3.6.27-7) ... 144s Selecting previously unselected package libreiserfscore0t64. 144s (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 ... 78657 files and directories currently installed.) 144s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_armhf.deb ... 144s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ... 144s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_armhf.deb ... 144s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ... 144s dpkg: libext2fs2:armhf: dependency problems, but removing anyway as you requested: 144s e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). 144s 144s (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 ... 78663 files and directories currently installed.) 144s Removing libext2fs2:armhf (1.47.0-2ubuntu1) ... 144s Selecting previously unselected package libext2fs2t64:armhf. 144s (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 ... 78656 files and directories currently installed.) 144s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 144s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' 144s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 144s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' 144s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 144s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 144s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) ... 144s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 144s (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 ... 78672 files and directories currently installed.) 144s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 144s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 144s Preparing to unpack .../libblockdev-loop3_3.1.0-1build1_armhf.deb ... 144s Unpacking libblockdev-loop3:armhf (3.1.0-1build1) over (3.1.0-1) ... 144s Preparing to unpack .../libblockdev-mdraid3_3.1.0-1build1_armhf.deb ... 144s Unpacking libblockdev-mdraid3:armhf (3.1.0-1build1) over (3.1.0-1) ... 145s Preparing to unpack .../libblockdev-nvme3_3.1.0-1build1_armhf.deb ... 145s Unpacking libblockdev-nvme3:armhf (3.1.0-1build1) over (3.1.0-1) ... 145s (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 ... 78672 files and directories currently installed.) 145s Removing libnvme1 (1.8-2) ... 145s Selecting previously unselected package libnvme1t64. 145s (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 ... 78665 files and directories currently installed.) 145s Preparing to unpack .../0-libnvme1t64_1.8-3_armhf.deb ... 145s Unpacking libnvme1t64 (1.8-3) ... 145s Preparing to unpack .../1-libblockdev-part3_3.1.0-1build1_armhf.deb ... 145s Unpacking libblockdev-part3:armhf (3.1.0-1build1) over (3.1.0-1) ... 145s Preparing to unpack .../2-libblockdev-swap3_3.1.0-1build1_armhf.deb ... 145s Unpacking libblockdev-swap3:armhf (3.1.0-1build1) over (3.1.0-1) ... 145s Preparing to unpack .../3-libblockdev3_3.1.0-1build1_armhf.deb ... 145s Unpacking libblockdev3:armhf (3.1.0-1build1) over (3.1.0-1) ... 145s Preparing to unpack .../4-libgudev-1.0-0_1%3a238-3ubuntu2_armhf.deb ... 145s Unpacking libgudev-1.0-0:armhf (1:238-3ubuntu2) over (1:238-3) ... 145s Preparing to unpack .../5-libxml2_2.9.14+dfsg-1.3ubuntu2_armhf.deb ... 145s Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ... 145s Preparing to unpack .../6-libbpf1_1%3a1.3.0-2build1_armhf.deb ... 145s Unpacking libbpf1:armhf (1:1.3.0-2build1) over (1:1.3.0-2) ... 145s Preparing to unpack .../7-iproute2_6.1.0-1ubuntu5_armhf.deb ... 145s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ... 145s (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 ... 78673 files and directories currently installed.) 145s Removing libelf1:armhf (0.190-1) ... 145s Selecting previously unselected package libelf1t64:armhf. 145s (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 ... 78668 files and directories currently installed.) 145s Preparing to unpack .../libelf1t64_0.190-1.1build2_armhf.deb ... 145s Unpacking libelf1t64:armhf (0.190-1.1build2) ... 145s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 145s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 146s Preparing to unpack .../lsof_4.95.0-1build2_armhf.deb ... 146s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ... 146s Preparing to unpack .../libnsl2_1.3.0-3build2_armhf.deb ... 146s Unpacking libnsl2:armhf (1.3.0-3build2) over (1.3.0-3) ... 146s (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 ... 78673 files and directories currently installed.) 146s Removing libtirpc3:armhf (1.3.4+ds-1build1) ... 146s Selecting previously unselected package libtirpc3t64:armhf. 146s (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 ... 78667 files and directories currently installed.) 146s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_armhf.deb ... 146s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' 146s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 146s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1) ... 146s Preparing to unpack .../01-libmbim-proxy_1.31.2-0ubuntu2_armhf.deb ... 146s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ... 146s Preparing to unpack .../02-libmbim-glib4_1.31.2-0ubuntu2_armhf.deb ... 146s Unpacking libmbim-glib4:armhf (1.31.2-0ubuntu2) over (1.30.0-1) ... 146s Preparing to unpack .../03-libjson-glib-1.0-common_1.8.0-2build1_all.deb ... 146s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ... 146s Preparing to unpack .../04-libjson-glib-1.0-0_1.8.0-2build1_armhf.deb ... 146s Unpacking libjson-glib-1.0-0:armhf (1.8.0-2build1) over (1.8.0-2) ... 146s Preparing to unpack .../05-libnghttp2-14_1.59.0-1build1_armhf.deb ... 146s Unpacking libnghttp2-14:armhf (1.59.0-1build1) over (1.59.0-1) ... 146s Preparing to unpack .../06-libssh-4_0.10.6-2build1_armhf.deb ... 146s Unpacking libssh-4:armhf (0.10.6-2build1) over (0.10.6-2) ... 147s Preparing to unpack .../07-libusb-1.0-0_2%3a1.0.27-1_armhf.deb ... 147s Unpacking libusb-1.0-0:armhf (2:1.0.27-1) over (2:1.0.26-1) ... 147s Preparing to unpack .../08-libgusb2_0.4.8-1build1_armhf.deb ... 147s Unpacking libgusb2:armhf (0.4.8-1build1) over (0.4.8-1) ... 147s Preparing to unpack .../09-libmm-glib0_1.23.4-0ubuntu1_armhf.deb ... 147s Unpacking libmm-glib0:armhf (1.23.4-0ubuntu1) over (1.22.0-3) ... 147s Preparing to unpack .../10-libsasl2-2_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 147s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 147s Preparing to unpack .../11-libibverbs1_50.0-2build1_armhf.deb ... 147s Unpacking libibverbs1:armhf (50.0-2build1) over (50.0-2) ... 147s Preparing to unpack .../12-libfido2-1_1.14.0-1build1_armhf.deb ... 147s Unpacking libfido2-1:armhf (1.14.0-1build1) over (1.14.0-1) ... 147s Preparing to unpack .../13-coreutils_9.4-3ubuntu3_armhf.deb ... 147s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ... 147s Setting up coreutils (9.4-3ubuntu3) ... 147s (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 ... 78678 files and directories currently installed.) 147s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_armhf.deb ... 147s Unpacking util-linux (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 148s Setting up util-linux (2.39.3-9ubuntu2) ... 148s fstrim.service is a disabled or a static unit not running, not starting it. 148s (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 ... 78678 files and directories currently installed.) 148s Preparing to unpack .../libc-bin_2.39-0ubuntu6_armhf.deb ... 148s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 148s Setting up libc-bin (2.39-0ubuntu6) ... 149s (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 ... 78678 files and directories currently installed.) 149s Removing libatm1:armhf (1:2.5.1-5) ... 149s (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 ... 78673 files and directories currently installed.) 149s Preparing to unpack .../file_1%3a5.45-3_armhf.deb ... 149s Unpacking file (1:5.45-3) over (1:5.45-2) ... 149s (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 ... 78673 files and directories currently installed.) 149s Removing libmagic1:armhf (1:5.45-2) ... 149s (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 ... 78663 files and directories currently installed.) 149s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_armhf.deb ... 149s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ... 149s Selecting previously unselected package libmagic1t64:armhf. 149s Preparing to unpack .../libmagic1t64_1%3a5.45-3_armhf.deb ... 149s Unpacking libmagic1t64:armhf (1:5.45-3) ... 149s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu6_armhf.deb ... 149s Unpacking libplymouth5:armhf (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 149s (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 ... 78674 files and directories currently installed.) 149s Removing libpng16-16:armhf (1.6.43-1) ... 149s Selecting previously unselected package libpng16-16t64:armhf. 149s (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 ... 78664 files and directories currently installed.) 149s Preparing to unpack .../libpng16-16t64_1.6.43-3_armhf.deb ... 149s Unpacking libpng16-16t64:armhf (1.6.43-3) ... 149s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_armhf.deb ... 149s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 150s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_armhf.deb ... 150s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 150s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_armhf.deb ... 150s Unpacking bind9-libs:armhf (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 150s (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 ... 78675 files and directories currently installed.) 150s Removing libuv1:armhf (1.48.0-1) ... 150s Selecting previously unselected package libuv1t64:armhf. 150s (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 ... 78670 files and directories currently installed.) 150s Preparing to unpack .../libuv1t64_1.48.0-1.1_armhf.deb ... 150s Unpacking libuv1t64:armhf (1.48.0-1.1) ... 150s (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 ... 78676 files and directories currently installed.) 150s Removing python3-distutils (3.11.5-1) ... 150s (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 ... 78621 files and directories currently installed.) 150s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_armhf.deb ... 150s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 150s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_armhf.deb ... 150s Unpacking libdebconfclient0:armhf (0.271ubuntu2) over (0.271ubuntu1) ... 150s Setting up libdebconfclient0:armhf (0.271ubuntu2) ... 150s (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 ... 78621 files and directories currently installed.) 150s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ... 150s Unpacking libsemanage-common (3.5-1build4) over (3.5-1build2) ... 150s Setting up libsemanage-common (3.5-1build4) ... 150s (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 ... 78621 files and directories currently installed.) 150s Preparing to unpack .../libsemanage2_3.5-1build4_armhf.deb ... 150s Unpacking libsemanage2:armhf (3.5-1build4) over (3.5-1build2) ... 150s Setting up libsemanage2:armhf (3.5-1build4) ... 150s (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 ... 78621 files and directories currently installed.) 150s Preparing to unpack .../install-info_7.1-3build1_armhf.deb ... 150s Unpacking install-info (7.1-3build1) over (7.1-3) ... 150s Setting up install-info (7.1-3build1) ... 151s (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 ... 78621 files and directories currently installed.) 151s Preparing to unpack .../00-gcc-13-base_13.2.0-19ubuntu1_armhf.deb ... 151s Unpacking gcc-13-base:armhf (13.2.0-19ubuntu1) over (13.2.0-17ubuntu2) ... 151s Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 151s Unpacking libss2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 151s Preparing to unpack .../02-dmsetup_2%3a1.02.185-3ubuntu2_armhf.deb ... 151s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 151s Preparing to unpack .../03-eject_2.39.3-9ubuntu2_armhf.deb ... 151s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 151s Preparing to unpack .../04-krb5-locales_1.20.1-5.1ubuntu1_all.deb ... 151s Unpacking krb5-locales (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 151s Preparing to unpack .../05-libbsd0_0.12.1-1_armhf.deb ... 151s Unpacking libbsd0:armhf (0.12.1-1) over (0.11.8-1) ... 151s Preparing to unpack .../06-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 151s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 151s Preparing to unpack .../07-libslang2_2.3.3-3build1_armhf.deb ... 151s Unpacking libslang2:armhf (2.3.3-3build1) over (2.3.3-3) ... 151s Preparing to unpack .../08-locales_2.39-0ubuntu6_all.deb ... 151s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 152s Preparing to unpack .../09-vim-tiny_2%3a9.1.0016-1ubuntu5_armhf.deb ... 152s Unpacking vim-tiny (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 152s Preparing to unpack .../10-vim-common_2%3a9.1.0016-1ubuntu5_all.deb ... 152s Unpacking vim-common (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 152s Selecting previously unselected package xdg-user-dirs. 152s Preparing to unpack .../11-xdg-user-dirs_0.18-1_armhf.deb ... 152s Unpacking xdg-user-dirs (0.18-1) ... 152s Preparing to unpack .../12-xxd_2%3a9.1.0016-1ubuntu5_armhf.deb ... 152s Unpacking xxd (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 152s Preparing to unpack .../13-apparmor_4.0.0-beta3-0ubuntu2_armhf.deb ... 153s Unpacking apparmor (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 153s Preparing to unpack .../14-ftp_20230507-2build1_all.deb ... 153s Unpacking ftp (20230507-2build1) over (20230507-2) ... 153s Preparing to unpack .../15-inetutils-telnet_2%3a2.5-3ubuntu3_armhf.deb ... 153s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ... 153s Preparing to unpack .../16-info_7.1-3build1_armhf.deb ... 153s Unpacking info (7.1-3build1) over (7.1-3) ... 153s Preparing to unpack .../17-libxmuu1_2%3a1.1.3-3build1_armhf.deb ... 153s Unpacking libxmuu1:armhf (2:1.1.3-3build1) over (2:1.1.3-3) ... 153s Preparing to unpack .../18-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_armhf.deb ... 153s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ... 154s Preparing to unpack .../19-mtr-tiny_0.95-1.1build1_armhf.deb ... 154s Unpacking mtr-tiny (0.95-1.1build1) over (0.95-1.1) ... 154s Preparing to unpack .../20-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_armhf.deb ... 154s Unpacking plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 154s Preparing to unpack .../21-plymouth_24.004.60-1ubuntu6_armhf.deb ... 154s Unpacking plymouth (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 154s Preparing to unpack .../22-psmisc_23.7-1_armhf.deb ... 154s Unpacking psmisc (23.7-1) over (23.6-2) ... 154s Preparing to unpack .../23-telnet_0.17+2.5-3ubuntu3_all.deb ... 154s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ... 154s Preparing to unpack .../24-usb.ids_2024.03.18-1_all.deb ... 154s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ... 154s Preparing to unpack .../25-xz-utils_5.6.0-0.2_armhf.deb ... 154s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... 154s Preparing to unpack .../26-libctf0_2.42-4ubuntu1_armhf.deb ... 154s Unpacking libctf0:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 154s Preparing to unpack .../27-libctf-nobfd0_2.42-4ubuntu1_armhf.deb ... 154s Unpacking libctf-nobfd0:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 154s Preparing to unpack .../28-binutils-arm-linux-gnueabihf_2.42-4ubuntu1_armhf.deb ... 154s Unpacking binutils-arm-linux-gnueabihf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 155s Preparing to unpack .../29-libbinutils_2.42-4ubuntu1_armhf.deb ... 155s Unpacking libbinutils:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 155s Preparing to unpack .../30-binutils_2.42-4ubuntu1_armhf.deb ... 155s Unpacking binutils (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 155s Preparing to unpack .../31-binutils-common_2.42-4ubuntu1_armhf.deb ... 155s Unpacking binutils-common:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 155s Preparing to unpack .../32-libsframe1_2.42-4ubuntu1_armhf.deb ... 155s Unpacking libsframe1:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 155s Preparing to unpack .../33-bolt_0.9.6-2build1_armhf.deb ... 155s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ... 155s Preparing to unpack .../34-cryptsetup-bin_2%3a2.7.0-1ubuntu2_armhf.deb ... 155s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 155s Preparing to unpack .../35-dpkg-dev_1.22.6ubuntu4_all.deb ... 155s Unpacking dpkg-dev (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 155s Preparing to unpack .../36-libdpkg-perl_1.22.6ubuntu4_all.deb ... 155s Unpacking libdpkg-perl (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 156s Preparing to unpack .../37-gnupg-l10n_2.4.4-2ubuntu15_all.deb ... 156s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 156s Preparing to unpack .../38-ibverbs-providers_50.0-2build1_armhf.deb ... 156s Unpacking ibverbs-providers:armhf (50.0-2build1) over (50.0-2) ... 156s Preparing to unpack .../39-jq_1.7.1-3_armhf.deb ... 156s Unpacking jq (1.7.1-3) over (1.7.1-2) ... 156s Preparing to unpack .../40-libjq1_1.7.1-3_armhf.deb ... 156s Unpacking libjq1:armhf (1.7.1-3) over (1.7.1-2) ... 156s Selecting previously unselected package libatm1t64:armhf. 156s Preparing to unpack .../41-libatm1t64_1%3a2.5.1-5.1_armhf.deb ... 156s Unpacking libatm1t64:armhf (1:2.5.1-5.1) ... 156s Preparing to unpack .../42-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 156s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 156s Preparing to unpack .../43-libftdi1-2_1.5-6build4_armhf.deb ... 156s Unpacking libftdi1-2:armhf (1.5-6build4) over (1.5-6build3) ... 156s Preparing to unpack .../44-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ... 156s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 156s Preparing to unpack .../45-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 156s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 156s Preparing to unpack .../46-python3-lib2to3_3.12.2-3ubuntu2_all.deb ... 156s Unpacking python3-lib2to3 (3.12.2-3ubuntu2) over (3.11.5-1) ... 156s Preparing to unpack .../47-python3-pyrsistent_0.20.0-1build1_armhf.deb ... 156s Unpacking python3-pyrsistent:armhf (0.20.0-1build1) over (0.20.0-1) ... 156s Preparing to unpack .../48-python3-typing-extensions_4.10.0-1_all.deb ... 156s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ... 156s Preparing to unpack .../49-kpartx_0.9.4-5ubuntu5_armhf.deb ... 156s Unpacking kpartx (0.9.4-5ubuntu5) over (0.9.4-5ubuntu3) ... 156s Setting up pinentry-curses (1.2.1-3ubuntu4) ... 156s Setting up libtext-iconv-perl:armhf (1.7-8build2) ... 156s Setting up libtext-charwidth-perl:armhf (0.04-11build2) ... 156s Setting up libibverbs1:armhf (50.0-2build1) ... 156s Setting up systemd-sysv (255.4-1ubuntu5) ... 156s Setting up libapparmor1:armhf (4.0.0-beta3-0ubuntu2) ... 156s Setting up libatm1t64:armhf (1:2.5.1-5.1) ... 156s Setting up libgdbm6t64:armhf (1.23-5.1) ... 156s Setting up bsdextrautils (2.39.3-9ubuntu2) ... 156s Setting up libgdbm-compat4t64:armhf (1.23-5.1) ... 156s Setting up xdg-user-dirs (0.18-1) ... 156s Setting up ibverbs-providers:armhf (50.0-2build1) ... 156s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ... 156s Setting up libmagic-mgc (1:5.45-3) ... 156s Setting up gawk (1:5.2.1-2build2) ... 156s Setting up psmisc (23.7-1) ... 156s Setting up libjq1:armhf (1.7.1-3) ... 156s Setting up libtirpc-common (1.3.4+ds-1.1) ... 156s Setting up libbrotli1:armhf (1.1.0-2build1) ... 156s Setting up libsqlite3-0:armhf (3.45.1-1ubuntu1) ... 156s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) ... 156s Setting up libuv1t64:armhf (1.48.0-1.1) ... 156s Setting up libmagic1t64:armhf (1:5.45-3) ... 156s Setting up binutils-common:armhf (2.42-4ubuntu1) ... 156s Setting up libpsl5t64:armhf (0.21.2-1.1) ... 156s Setting up libnghttp2-14:armhf (1.59.0-1build1) ... 156s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ... 156s Setting up libctf-nobfd0:armhf (2.42-4ubuntu1) ... 156s Setting up libnss-systemd:armhf (255.4-1ubuntu5) ... 156s Setting up krb5-locales (1.20.1-5.1ubuntu1) ... 156s Setting up file (1:5.45-3) ... 156s Setting up kmod (31+20240202-2ubuntu4) ... 157s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ... 157s Setting up locales (2.39-0ubuntu6) ... 157s Generating locales (this might take a while)... 159s en_US.UTF-8... done 159s Generation complete. 160s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ... 160s Setting up xxd (2:9.1.0016-1ubuntu5) ... 160s Setting up libsframe1:armhf (2.42-4ubuntu1) ... 160s Setting up libelf1t64:armhf (0.190-1.1build2) ... 160s Setting up libkrb5support0:armhf (1.20.1-5.1ubuntu1) ... 160s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 160s Setting up eject (2.39.3-9ubuntu2) ... 160s Setting up apparmor (4.0.0-beta3-0ubuntu2) ... 160s Installing new version of config file /etc/apparmor.d/abstractions/authentication ... 160s Installing new version of config file /etc/apparmor.d/abstractions/crypto ... 160s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ... 160s Installing new version of config file /etc/apparmor.d/abstractions/openssl ... 160s Installing new version of config file /etc/apparmor.d/code ... 160s Installing new version of config file /etc/apparmor.d/firefox ... 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 sysctl: cannot stat /proc/sys/kernel/apparmor_restrict_unprivileged_userns: No such file or directory 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 "brave". /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 "buildah". /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 "chrome". /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: 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 "vscode". /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 "evolution". /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 "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /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: 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 "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: Access denied. You need policy admin privileges to manage profiles. 161s 161s /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: 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 "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 "kchmviewer". /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 "libcamerify". /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 "linux-sandbox". /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-execute". /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-usernsexec". /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 "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 "mmdebstrap". /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 "obsidian". /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 "qcam". /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: Unable to replace "privacybrowser". /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 "qmapshack". /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: 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 "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /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: 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: Unable to replace "sbuild". /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 "opam". /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-apt". /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: Access denied. You need policy admin privileges to manage profiles. 161s 161s /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: 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-destroychroot". /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: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /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: 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-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /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 "sbuild-update". /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 "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s /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 "slirp4netns". /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 "surfshark". /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: Access denied. You need policy admin privileges to manage profiles. 161s 161s /sbin/apparmor_parser: Unable to replace "thunderbird". /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: 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 "stress-ng". /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 "trinity". /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 "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 "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 "wpcom". /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 "lsb_release". /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 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 "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 161s 161s Error: At least one profile failed to load 161s Setting up libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 161s No schema files found: doing nothing. 161s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 161s Setting up vim-common (2:9.1.0016-1ubuntu5) ... 161s Setting up gcc-13-base:armhf (13.2.0-19ubuntu1) ... 161s Setting up libqrtr-glib0:armhf (1.2.2-1ubuntu3) ... 161s Setting up libslang2:armhf (2.3.3-3build1) ... 161s Setting up libnvme1t64 (1.8-3) ... 161s Setting up mtr-tiny (0.95-1.1build1) ... 161s Setting up gnupg-l10n (2.4.4-2ubuntu15) ... 161s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) ... 161s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu2) ... 161s Setting up xz-utils (5.6.0-0.2) ... 161s Setting up perl-modules-5.38 (5.38.2-3.2) ... 161s Setting up libblockdev-utils3:armhf (3.1.0-1build1) ... 161s Setting up libpng16-16t64:armhf (1.6.43-3) ... 161s Setting up systemd-timesyncd (255.4-1ubuntu5) ... 161s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 161s Setting up udev (255.4-1ubuntu5) ... 162s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu2) ... 162s Setting up usb.ids (2024.03.18-1) ... 162s Setting up sudo (1.9.15p5-3ubuntu3) ... 162s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ... 162s Setting up gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) ... 162s Setting up libk5crypto3:armhf (1.20.1-5.1ubuntu1) ... 162s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ... 162s Setting up libfdisk1:armhf (2.39.3-9ubuntu2) ... 162s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-6) ... 162s Setting up libblockdev-nvme3:armhf (3.1.0-1build1) ... 162s Setting up libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) ... 162s Setting up libblockdev-fs3:armhf (3.1.0-1build1) ... 162s Setting up python-apt-common (2.7.6build1) ... 162s Setting up mount (2.39.3-9ubuntu2) ... 162s Setting up dmsetup (2:1.02.185-3ubuntu2) ... 162s Setting up uuid-runtime (2.39.3-9ubuntu2) ... 163s uuidd.service is a disabled or a static unit not running, not starting it. 163s Setting up libmm-glib0:armhf (1.23.4-0ubuntu1) ... 163s Setting up groff-base (1.23.0-3build1) ... 163s Setting up libplymouth5:armhf (24.004.60-1ubuntu6) ... 163s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ... 163s Setting up kpartx (0.9.4-5ubuntu5) ... 163s Setting up jq (1.7.1-3) ... 163s Setting up gpgconf (2.4.4-2ubuntu15) ... 163s Setting up libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 163s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu2) ... 163s Setting up libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) ... 163s Setting up libjson-glib-1.0-common (1.8.0-2build1) ... 163s Setting up libkrb5-3:armhf (1.20.1-5.1ubuntu1) ... 163s Setting up libpython3.11-minimal:armhf (3.11.8-1build4) ... 163s Setting up libusb-1.0-0:armhf (2:1.0.27-1) ... 163s Setting up libperl5.38t64:armhf (5.38.2-3.2) ... 163s Setting up tnftp (20230507-2build1) ... 163s Setting up libbinutils:armhf (2.42-4ubuntu1) ... 163s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ... 163s Setting up libfido2-1:armhf (1.14.0-1build1) ... 163s Setting up openssl (3.0.13-0ubuntu2) ... 163s Setting up libbsd0:armhf (0.12.1-1) ... 163s Setting up readline-common (8.2-3.1) ... 163s Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) ... 163s Setting up libxmuu1:armhf (2:1.1.3-3build1) ... 163s Setting up dbus-bin (1.14.10-4ubuntu2) ... 163s Setting up info (7.1-3build1) ... 163s Setting up liblocale-gettext-perl (1.07-6ubuntu3) ... 163s Setting up gpg (2.4.4-2ubuntu15) ... 163s Setting up libgudev-1.0-0:armhf (1:238-3ubuntu2) ... 163s Setting up libpolkit-gobject-1-0:armhf (124-1ubuntu1) ... 163s Setting up libbpf1:armhf (1:1.3.0-2build1) ... 163s Setting up libmbim-glib4:armhf (1.31.2-0ubuntu2) ... 163s Setting up rsync (3.2.7-1build1) ... 164s rsync.service is a disabled or a static unit not running, not starting it. 164s Setting up libudisks2-0:armhf (2.10.1-6) ... 164s Setting up bolt (0.9.6-2build1) ... 165s bolt.service is a disabled or a static unit not running, not starting it. 165s Setting up gnupg-utils (2.4.4-2ubuntu15) ... 165s Setting up initramfs-tools-bin (0.142ubuntu23) ... 165s Setting up libctf0:armhf (2.42-4ubuntu1) ... 165s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ... 165s Setting up python3.11-minimal (3.11.8-1build4) ... 166s Setting up tcpdump (4.99.4-3ubuntu2) ... 166s apparmor_parser: Unable to replace "tcpdump". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 166s 166s Setting up apt-utils (2.7.13ubuntu1) ... 166s Setting up gpg-agent (2.4.4-2ubuntu15) ... 167s Setting up libpython3.12-stdlib:armhf (3.12.2-4build3) ... 167s Setting up libblockdev-mdraid3:armhf (3.1.0-1build1) ... 167s Setting up wget (1.21.4-1ubuntu2) ... 167s Setting up libblockdev-swap3:armhf (3.1.0-1build1) ... 167s Setting up plymouth (24.004.60-1ubuntu6) ... 167s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 167s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 168s Setting up libxmlb2:armhf (0.3.15-1build1) ... 168s Setting up btrfs-progs (6.6.3-1.1build1) ... 168s Setting up libpython3.11-stdlib:armhf (3.11.8-1build4) ... 168s Setting up python3.12 (3.12.2-4build3) ... 169s Setting up libblockdev-loop3:armhf (3.1.0-1build1) ... 169s Setting up gpgsm (2.4.4-2ubuntu15) ... 169s Setting up inetutils-telnet (2:2.5-3ubuntu3) ... 169s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ... 169s update-initramfs: deferring update (trigger activated) 169s e2scrub_all.service is a disabled or a static unit not running, not starting it. 169s Setting up libparted2t64:armhf (3.6-3.1build2) ... 169s Setting up linux-headers-generic (6.8.0-20.20+1) ... 169s Setting up dbus-daemon (1.14.10-4ubuntu2) ... 169s Setting up libmbim-proxy (1.31.2-0ubuntu2) ... 169s Setting up vim-tiny (2:9.1.0016-1ubuntu5) ... 169s Setting up libnetplan1:armhf (1.0-1) ... 169s Setting up man-db (2.12.0-3build4) ... 170s Updating database of manual pages ... 171s apparmor_parser: Unable to replace "/usr/bin/man". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 171s 171s man-db.service is a disabled or a static unit not running, not starting it. 171s Setting up libblockdev3:armhf (3.1.0-1build1) ... 171s Setting up fdisk (2.39.3-9ubuntu2) ... 171s Setting up libjson-glib-1.0-0:armhf (1.8.0-2build1) ... 171s Setting up libblockdev-part3:armhf (3.1.0-1build1) ... 171s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) ... 171s Setting up libftdi1-2:armhf (1.5-6build4) ... 171s Setting up perl (5.38.2-3.2) ... 172s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ... 172s update-initramfs: deferring update (trigger activated) 172s Setting up gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) ... 172s Setting up dbus (1.14.10-4ubuntu2) ... 172s A reboot is required to replace the running dbus-daemon. 172s Please reboot the system when convenient. 172s Setting up shared-mime-info (2.4-1build1) ... 172s Setting up libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) ... 172s Setting up ftp (20230507-2build1) ... 172s Setting up keyboxd (2.4.4-2ubuntu15) ... 173s Setting up libdpkg-perl (1.22.6ubuntu4) ... 173s Setting up libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) ... 173s Setting up libssh-4:armhf (0.10.6-2build1) ... 173s Setting up libpam-systemd:armhf (255.4-1ubuntu5) ... 173s Setting up libpolkit-agent-1-0:armhf (124-1ubuntu1) ... 173s Setting up libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 173s Setting up netplan-generator (1.0-1) ... 173s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 173s Setting up initramfs-tools-core (0.142ubuntu23) ... 173s Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu1) ... 173s Setting up libarchive13t64:armhf (3.7.2-1.1ubuntu2) ... 173s Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ... 173s Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu1) ... 173s Setting up systemd-resolved (255.4-1ubuntu5) ... 174s Setting up python3.11 (3.11.8-1build4) ... 175s Setting up telnet (0.17+2.5-3ubuntu3) ... 175s Setting up initramfs-tools (0.142ubuntu23) ... 175s update-initramfs: deferring update (trigger activated) 175s Setting up libcurl4t64:armhf (8.5.0-2ubuntu7) ... 175s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu3) ... 175s Setting up libtirpc3t64:armhf (1.3.4+ds-1.1) ... 175s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ... 175s Setting up iproute2 (6.1.0-1ubuntu5) ... 175s Setting up openssh-client (1:9.6p1-3ubuntu11) ... 175s Setting up libgusb2:armhf (0.4.8-1build1) ... 175s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 175s Setting up parted (3.6-3.1build2) ... 175s Setting up libqmi-glib5:armhf (1.35.2-0ubuntu1) ... 175s Setting up python3 (3.12.2-0ubuntu1) ... 175s Setting up binutils (2.42-4ubuntu1) ... 175s Setting up libjcat1:armhf (0.2.0-2build2) ... 175s Setting up dpkg-dev (1.22.6ubuntu4) ... 175s Setting up dirmngr (2.4.4-2ubuntu15) ... 176s Setting up dbus-user-session (1.14.10-4ubuntu2) ... 176s Setting up python3-cryptography (41.0.7-4build2) ... 176s Setting up python3-gi (3.47.0-3build1) ... 176s Setting up python3-typing-extensions (4.10.0-1) ... 176s Setting up lsof (4.95.0-1build2) ... 176s Setting up python3-pyrsistent:armhf (0.20.0-1build1) ... 177s Setting up libnsl2:armhf (1.3.0-3build2) ... 177s Setting up gnupg (2.4.4-2ubuntu15) ... 177s Setting up python3-netplan (1.0-1) ... 177s Setting up curl (8.5.0-2ubuntu7) ... 177s Setting up libvolume-key1:armhf (0.3.12-7build1) ... 177s Setting up bind9-host (1:9.18.24-0ubuntu3) ... 177s Setting up python3-lib2to3 (3.12.2-3ubuntu2) ... 177s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... 177s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ... 177s Setting up python3-dbus (1.3.2-5build2) ... 178s Setting up python3-setuptools (68.1.2-2ubuntu1) ... 178s Setting up gpg-wks-client (2.4.4-2ubuntu15) ... 178s Setting up openssh-server (1:9.6p1-3ubuntu11) ... 178s Replacing config file /etc/ssh/sshd_config with new version 180s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket. 182s Setting up libblockdev-crypto3:armhf (3.1.0-1build1) ... 182s Setting up python3-gdbm:armhf (3.12.2-3ubuntu2) ... 182s Setting up python3-apt (2.7.6build1) ... 182s Setting up libfwupd2:armhf (1.9.15-1) ... 182s Setting up python3-yaml (6.0.1-2build1) ... 182s Setting up libqmi-proxy (1.35.2-0ubuntu1) ... 182s Setting up netplan.io (1.0-1) ... 182s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ... 182s Setting up ubuntu-pro-client (31.2) ... 182s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 182s 184s Setting up fwupd (1.9.15-1) ... 184s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 184s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 184s fwupd.service is a disabled or a static unit not running, not starting it. 184s Setting up ubuntu-pro-client-l10n (31.2) ... 184s Setting up udisks2 (2.10.1-6) ... 184s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 184s 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 184s 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 184s 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 184s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 184s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 184s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 184s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 184s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 184s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 184s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 184s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 185s Processing triggers for ufw (0.36.2-5) ... 185s Processing triggers for systemd (255.4-1ubuntu5) ... 185s Processing triggers for install-info (7.1-3build1) ... 185s Processing triggers for libc-bin (2.39-0ubuntu6) ... 185s Processing triggers for initramfs-tools (0.142ubuntu23) ... 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s The following packages will be REMOVED: 188s linux-headers-6.8.0-11* python3-lib2to3* 188s 0 upgraded, 0 newly installed, 2 to remove and 1 not upgraded. 188s After this operation, 85.8 MB disk space will be freed. 188s (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 ... 78592 files and directories currently installed.) 188s Removing linux-headers-6.8.0-11 (6.8.0-11.11) ... 189s Removing python3-lib2to3 (3.12.2-3ubuntu2) ... 191s autopkgtest [13:24:25]: rebooting testbed after setup commands that affected boot 230s autopkgtest [13:25:04]: testbed running kernel: Linux 5.15.0-101-generic #111-Ubuntu SMP Wed Mar 6 18:01:01 UTC 2024 256s autopkgtest [13:25:30]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 273s Get:1 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 273s Get:2 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 273s Get:3 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 274s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 274s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 274s gpgv: Can't check signature: No public key 274s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 275s autopkgtest [13:25:49]: testing package pdb2pqr version 3.6.1+dfsg-1 276s autopkgtest [13:25:50]: build not needed 279s autopkgtest [13:25:53]: test installation-test: preparing testbed 289s Reading package lists... 289s Building dependency tree... 289s Reading state information... 290s Starting pkgProblemResolver with broken count: 0 290s Starting 2 pkgProblemResolver with broken count: 0 290s Done 291s The following additional packages will be installed: 291s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 291s python3-numpy python3-pdb2pqr python3-pdbx python3-propka python3-roman 291s sgml-base xml-core 291s Suggested packages: 291s apbs docutils-doc fonts-linuxlibertine | ttf-linux-libertine 291s texlive-lang-french texlive-latex-base texlive-latex-recommended gcc 291s gfortran python3-dev python3-pytest python-pdbx-doc python-propka-doc 291s sgml-base-doc debhelper 291s Recommended packages: 291s libpaper-utils python3-pil 291s The following NEW packages will be installed: 291s autopkgtest-satdep docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr 291s python3-docutils python3-numpy python3-pdb2pqr python3-pdbx python3-propka 291s python3-roman sgml-base xml-core 291s 0 upgraded, 14 newly installed, 0 to remove and 1 not upgraded. 291s Need to get 6953 kB/6954 kB of archives. 291s After this operation, 26.9 MB of additional disk space will be used. 291s Get:1 /tmp/autopkgtest.QQILMZ/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 291s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf sgml-base all 1.31 [11.4 kB] 291s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf xml-core all 0.19 [20.3 kB] 291s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf docutils-common all 0.20.1+dfsg-3 [132 kB] 291s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.12.0-3 [123 kB] 291s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgfortran5 armhf 14-20240315-1ubuntu1 [312 kB] 291s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3 [2085 kB] 291s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-numpy armhf 1:1.24.2-3ubuntu1 [3610 kB] 292s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf python3-roman all 3.3-3 [9632 B] 292s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf python3-docutils all 0.20.1+dfsg-3 [393 kB] 292s Get:11 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pdbx all 2.0.1-2 [16.5 kB] 292s Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf python3-propka all 3.5.1-1 [85.5 kB] 292s Get:13 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 292s Get:14 http://ftpmaster.internal/ubuntu noble/universe armhf pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 292s Fetched 6953 kB in 1s (9137 kB/s) 292s Selecting previously unselected package sgml-base. 292s (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 ... 58435 files and directories currently installed.) 292s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 292s Unpacking sgml-base (1.31) ... 292s Selecting previously unselected package xml-core. 292s Preparing to unpack .../01-xml-core_0.19_all.deb ... 292s Unpacking xml-core (0.19) ... 292s Selecting previously unselected package docutils-common. 292s Preparing to unpack .../02-docutils-common_0.20.1+dfsg-3_all.deb ... 292s Unpacking docutils-common (0.20.1+dfsg-3) ... 292s Selecting previously unselected package libblas3:armhf. 292s Preparing to unpack .../03-libblas3_3.12.0-3_armhf.deb ... 292s Unpacking libblas3:armhf (3.12.0-3) ... 292s Selecting previously unselected package libgfortran5:armhf. 292s Preparing to unpack .../04-libgfortran5_14-20240315-1ubuntu1_armhf.deb ... 292s Unpacking libgfortran5:armhf (14-20240315-1ubuntu1) ... 292s Selecting previously unselected package liblapack3:armhf. 292s Preparing to unpack .../05-liblapack3_3.12.0-3_armhf.deb ... 292s Unpacking liblapack3:armhf (3.12.0-3) ... 292s Selecting previously unselected package python3-numpy. 292s Preparing to unpack .../06-python3-numpy_1%3a1.24.2-3ubuntu1_armhf.deb ... 292s Unpacking python3-numpy (1:1.24.2-3ubuntu1) ... 293s Selecting previously unselected package python3-roman. 293s Preparing to unpack .../07-python3-roman_3.3-3_all.deb ... 293s Unpacking python3-roman (3.3-3) ... 293s Selecting previously unselected package python3-docutils. 293s Preparing to unpack .../08-python3-docutils_0.20.1+dfsg-3_all.deb ... 293s Unpacking python3-docutils (0.20.1+dfsg-3) ... 293s Selecting previously unselected package python3-pdbx. 293s Preparing to unpack .../09-python3-pdbx_2.0.1-2_all.deb ... 293s Unpacking python3-pdbx (2.0.1-2) ... 293s Selecting previously unselected package python3-propka. 293s Preparing to unpack .../10-python3-propka_3.5.1-1_all.deb ... 293s Unpacking python3-propka (3.5.1-1) ... 293s Selecting previously unselected package python3-pdb2pqr. 293s Preparing to unpack .../11-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 293s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 293s Selecting previously unselected package pdb2pqr. 293s Preparing to unpack .../12-pdb2pqr_3.6.1+dfsg-1_all.deb ... 293s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 293s Selecting previously unselected package autopkgtest-satdep. 293s Preparing to unpack .../13-1-autopkgtest-satdep.deb ... 293s Unpacking autopkgtest-satdep (0) ... 293s Setting up python3-propka (3.5.1-1) ... 293s Setting up python3-pdbx (2.0.1-2) ... 293s Setting up python3-roman (3.3-3) ... 293s Setting up libblas3:armhf (3.12.0-3) ... 293s 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 293s Setting up libgfortran5:armhf (14-20240315-1ubuntu1) ... 293s Setting up sgml-base (1.31) ... 293s Setting up liblapack3:armhf (3.12.0-3) ... 293s 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 293s Setting up python3-numpy (1:1.24.2-3ubuntu1) ... 296s Setting up xml-core (0.19) ... 296s Processing triggers for libc-bin (2.39-0ubuntu6) ... 296s Processing triggers for man-db (2.12.0-3build4) ... 297s Processing triggers for sgml-base (1.31) ... 297s Setting up docutils-common (0.20.1+dfsg-3) ... 297s Processing triggers for sgml-base (1.31) ... 297s Setting up python3-docutils (0.20.1+dfsg-3) ... 298s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 298s Setting up pdb2pqr (3.6.1+dfsg-1) ... 298s Setting up autopkgtest-satdep (0) ... 309s (Reading database ... 59917 files and directories currently installed.) 309s Removing autopkgtest-satdep (0) ... 315s autopkgtest [13:26:29]: test installation-test: [----------------------- 316s Run pdb2pqr... 317s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 317s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 317s INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 317s INFO:Checking and transforming input arguments. 317s INFO:Loading topology files. 317s INFO:Loading molecule: examples/1a1p/1a1p.pdb 317s INFO:Setting up molecule. 317s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 317s INFO:Created biomolecule object with 14 residues and 208 atoms. 317s INFO:Setting termini states for biomolecule chains. 317s INFO:Loading forcefield. 317s INFO:Loading hydrogen topology definitions. 317s INFO:This biomolecule is clean. No repair needed. 317s INFO:Updating disulfide bridges. 317s INFO:Debumping biomolecule. 317s INFO:Adding hydrogens to biomolecule. 317s INFO:Debumping biomolecule (again). 317s INFO:Optimizing hydrogen bonds 317s INFO:Applying force field to biomolecule states. 317s INFO:Regenerating headers. 317s INFO:Regenerating PDB lines. 317s WARNING:Ignoring 852 header lines in output. 317s WARNING:Ignoring 3 missing lines in output. 317s autopkgtest [13:26:31]: test installation-test: -----------------------] 321s autopkgtest [13:26:35]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 321s installation-test PASS 324s autopkgtest [13:26:38]: test pdb2pka-test: preparing testbed 334s Reading package lists... 335s Building dependency tree... 335s Reading state information... 335s Starting pkgProblemResolver with broken count: 0 335s Starting 2 pkgProblemResolver with broken count: 0 335s Done 335s The following additional packages will be installed: 335s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 335s pdb2pqr-doc sphinx-rtd-theme-common 335s Recommended packages: 335s javascript-common 335s The following NEW packages will be installed: 335s autopkgtest-satdep fonts-font-awesome fonts-lato libjs-jquery 335s libjs-sphinxdoc libjs-underscore pdb2pqr-doc sphinx-rtd-theme-common 335s 0 upgraded, 8 newly installed, 0 to remove and 1 not upgraded. 335s Need to get 5162 kB/5162 kB of archives. 335s After this operation, 20.1 MB of additional disk space will be used. 335s Get:1 /tmp/autopkgtest.QQILMZ/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 336s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf fonts-lato all 2.015-1 [2781 kB] 336s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 336s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 336s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 336s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjs-sphinxdoc all 7.2.6-6 [149 kB] 336s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 336s Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 337s Fetched 5162 kB in 1s (6849 kB/s) 337s Selecting previously unselected package fonts-lato. 337s (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 ... 59917 files and directories currently installed.) 337s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 337s Unpacking fonts-lato (2.015-1) ... 337s Selecting previously unselected package fonts-font-awesome. 337s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 337s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 337s Selecting previously unselected package libjs-jquery. 337s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 337s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 337s Selecting previously unselected package libjs-underscore. 337s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 337s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 337s Selecting previously unselected package libjs-sphinxdoc. 337s Preparing to unpack .../4-libjs-sphinxdoc_7.2.6-6_all.deb ... 337s Unpacking libjs-sphinxdoc (7.2.6-6) ... 337s Selecting previously unselected package sphinx-rtd-theme-common. 337s Preparing to unpack .../5-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 337s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 337s Selecting previously unselected package pdb2pqr-doc. 337s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 337s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 337s Selecting previously unselected package autopkgtest-satdep. 337s Preparing to unpack .../7-2-autopkgtest-satdep.deb ... 337s Unpacking autopkgtest-satdep (0) ... 337s Setting up fonts-lato (2.015-1) ... 337s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 337s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 337s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 337s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 337s Setting up libjs-sphinxdoc (7.2.6-6) ... 337s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 337s Setting up autopkgtest-satdep (0) ... 353s (Reading database ... 60251 files and directories currently installed.) 353s Removing autopkgtest-satdep (0) ... 359s autopkgtest [13:27:13]: test pdb2pka-test: [----------------------- 360s Run pdb2pqr... 361s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 361s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 361s INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 361s INFO:Checking and transforming input arguments. 361s INFO:Loading topology files. 361s INFO:Loading molecule: 1a1p/1a1p.pdb 361s INFO:Setting up molecule. 361s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 361s INFO:Created biomolecule object with 14 residues and 208 atoms. 361s INFO:Setting termini states for biomolecule chains. 361s INFO:Loading forcefield. 361s INFO:Loading hydrogen topology definitions. 361s INFO:This biomolecule is clean. No repair needed. 361s INFO:Updating disulfide bridges. 361s INFO:Debumping biomolecule. 361s INFO:Adding hydrogens to biomolecule. 361s INFO:Debumping biomolecule (again). 361s INFO:Optimizing hydrogen bonds 361s INFO:Applying force field to biomolecule states. 361s INFO:Regenerating headers. 361s INFO:Regenerating PDB lines. 361s WARNING:Ignoring 852 header lines in output. 361s WARNING:Ignoring 3 missing lines in output. 361s autopkgtest [13:27:15]: test pdb2pka-test: -----------------------] 365s autopkgtest [13:27:19]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 365s pdb2pka-test PASS 368s autopkgtest [13:27:22]: test command1: preparing testbed 379s Reading package lists... 380s Building dependency tree... 380s Reading state information... 380s Starting pkgProblemResolver with broken count: 0 380s Starting 2 pkgProblemResolver with broken count: 0 380s Done 381s The following additional packages will be installed: 381s python3-dateutil python3-iniconfig python3-packaging python3-pandas 381s python3-pandas-lib python3-pluggy python3-pytest python3-testfixtures 381s Suggested packages: 381s python-pandas-doc python3-statsmodels python-testfixtures-doc 381s Recommended packages: 381s python3-scipy python3-matplotlib python3-bottleneck python3-numexpr 381s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 381s python3-tables 381s The following NEW packages will be installed: 381s autopkgtest-satdep python3-dateutil python3-iniconfig python3-packaging 381s python3-pandas python3-pandas-lib python3-pluggy python3-pytest 381s python3-testfixtures 381s 0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded. 381s Need to get 11.7 MB/11.7 MB of archives. 381s After this operation, 51.0 MB of additional disk space will be used. 381s Get:1 /tmp/autopkgtest.QQILMZ/3-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [740 B] 382s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf python3-dateutil all 2.8.2-3 [79.2 kB] 382s Get:3 http://ftpmaster.internal/ubuntu noble/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 382s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf python3-packaging all 23.2-1 [40.6 kB] 382s Get:5 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pandas-lib armhf 2.1.4+dfsg-4ubuntu2 [8219 kB] 382s Get:6 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 382s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pluggy all 1.4.0-1 [20.4 kB] 382s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-pytest all 8.0.2-1 [248 kB] 382s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf python3-testfixtures all 8.1.0-1 [73.5 kB] 383s Fetched 11.7 MB in 1s (13.0 MB/s) 383s Selecting previously unselected package python3-dateutil. 383s (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 ... 60251 files and directories currently installed.) 383s Preparing to unpack .../0-python3-dateutil_2.8.2-3_all.deb ... 383s Unpacking python3-dateutil (2.8.2-3) ... 383s Selecting previously unselected package python3-iniconfig. 383s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 383s Unpacking python3-iniconfig (1.1.1-2) ... 383s Selecting previously unselected package python3-packaging. 383s Preparing to unpack .../2-python3-packaging_23.2-1_all.deb ... 383s Unpacking python3-packaging (23.2-1) ... 383s Selecting previously unselected package python3-pandas-lib:armhf. 383s Preparing to unpack .../3-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_armhf.deb ... 383s Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-4ubuntu2) ... 383s Selecting previously unselected package python3-pandas. 383s Preparing to unpack .../4-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 383s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 384s Selecting previously unselected package python3-pluggy. 384s Preparing to unpack .../5-python3-pluggy_1.4.0-1_all.deb ... 384s Unpacking python3-pluggy (1.4.0-1) ... 384s Selecting previously unselected package python3-pytest. 384s Preparing to unpack .../6-python3-pytest_8.0.2-1_all.deb ... 384s Unpacking python3-pytest (8.0.2-1) ... 384s Selecting previously unselected package python3-testfixtures. 384s Preparing to unpack .../7-python3-testfixtures_8.1.0-1_all.deb ... 384s Unpacking python3-testfixtures (8.1.0-1) ... 384s Selecting previously unselected package autopkgtest-satdep. 384s Preparing to unpack .../8-3-autopkgtest-satdep.deb ... 384s Unpacking autopkgtest-satdep (0) ... 384s Setting up python3-iniconfig (1.1.1-2) ... 384s Setting up python3-pandas-lib:armhf (2.1.4+dfsg-4ubuntu2) ... 384s Setting up python3-testfixtures (8.1.0-1) ... 385s Setting up python3-packaging (23.2-1) ... 385s Setting up python3-pluggy (1.4.0-1) ... 385s Setting up python3-dateutil (2.8.2-3) ... 385s Setting up python3-pytest (8.0.2-1) ... 386s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 392s Setting up autopkgtest-satdep (0) ... 392s Processing triggers for man-db (2.12.0-3build4) ... 408s (Reading database ... 62265 files and directories currently installed.) 408s Removing autopkgtest-satdep (0) ... 414s autopkgtest [13:28:08]: test command1: pytest-3 414s autopkgtest [13:28:08]: test command1: [----------------------- 416s ============================= test session starts ============================== 416s platform linux -- Python 3.12.2, pytest-8.0.2, pluggy-1.4.0 416s rootdir: /tmp/autopkgtest.QQILMZ/build.MbH/src 416s configfile: pytest.ini 416s 416s ----------------------------- live log collection ------------------------------ 416s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.QQILMZ/build.MbH/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 416s @pytest.mark.long_test 416s 416s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 416s collected 316 items 416s 416s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 0%] 416s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 0%] 416s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 0%] 416s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 1%] 416s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 1%] 416s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 1%] 416s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 2%] 416s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) 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[ 65%] 417s tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 65%] 417s tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 65%] 417s tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 66%] 417s tests/core_test.py::test_broken_backbone[1EJG] 417s -------------------------------- live log call --------------------------------- 417s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 417s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 417s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 417s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 417s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 417s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 417s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 417s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 417s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 417s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 417s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 417s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 417s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 417s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 417s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 417s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 417s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 417s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 417s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 405 CG SER 22 4.661 14.854 -4.058 0.0000 0.0000 417s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 418s XFAIL [ 66%] 418s tests/core_test.py::test_broken_backbone[3U7T] 418s -------------------------------- live log call --------------------------------- 418s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 418s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 418s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 418s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 418s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 418s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 418s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 418s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 418s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 418s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 418s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 418s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 418s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 418s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 418s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 418s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 418s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 418s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 418s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 313 OG PRO 22 -13.108 -5.696 -15.739 0.0000 0.0000 418s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 419s XFAIL [ 66%] 419s tests/core_test.py::test_broken_backbone[4MGP] 419s -------------------------------- live log call --------------------------------- 419s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 419s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 419s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 419s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 419s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 419s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 419s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 419s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 419s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 419s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 419s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 419s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 419s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 419s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 419s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 419s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 419s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 419s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 419s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 419s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 419s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 419s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 419s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 419s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 419s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 419s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 419s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 419s CRITICAL PDB2PQR3.6.1:main.py:800 Too few atoms present to reconstruct or cap residue SER A 23 in structure! This error is generally caused by missing backbone atoms in this biomolecule; you must use an external program to complete gaps in the biomolecule backbone. Heavy atoms missing from SER A 23: C O CB OG OXT CA 419s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 419s XFAIL [ 67%] 419s tests/core_test.py::test_broken_backbone[2V75] 419s -------------------------------- live log call --------------------------------- 419s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 419s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 419s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 419s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 419s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 419s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 419s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 420s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 420s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 420s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 420s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 420s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 420s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 420s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 420s CRITICAL PDB2PQR3.6.1:main.py:800 Too few atoms present to reconstruct or cap residue ASN A 95 in structure! This error is generally caused by missing backbone atoms in this biomolecule; you must use an external program to complete gaps in the biomolecule backbone. Heavy atoms missing from ASN A 95: C O CB CG OD1 ND2 OXT CA 420s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 420s XFAIL [ 67%] 420s tests/core_test.py::test_protonated_terminals[C-terminal HID] 420s -------------------------------- live log call --------------------------------- 420s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 420s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 420s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 420s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 420s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 420s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 420s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 420s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 420s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 420s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 420s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 420s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 420s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 420s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 420s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 420s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 420s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 420s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 420s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 420s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 420s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 420s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 420s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 420s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 420s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 420s INFO common:common.py:198 0 atoms have position differences > 0 420s INFO common:common.py:198 0 atoms have position differences > 0.01 420s INFO common:common.py:198 0 atoms have charge differences > 0 420s INFO common:common.py:198 0 atoms have charge differences > 0.01 420s INFO common:common.py:198 0 atoms have radius differences > 0 420s INFO common:common.py:198 0 atoms have radius differences > 0.01 420s PASSED [ 67%] 420s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 420s -------------------------------- live log call --------------------------------- 420s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 420s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 420s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 420s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 420s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 420s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 420s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 420s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 420s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 420s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 420s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 421s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 421s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 421s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 421s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 421s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 421s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 421s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 421s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 421s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 421s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 421s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 421s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 421s INFO common:common.py:198 0 atoms have position differences > 0 421s INFO common:common.py:198 0 atoms have position differences > 0.01 421s INFO common:common.py:198 0 atoms have charge differences > 0 421s INFO common:common.py:198 0 atoms have charge differences > 0.01 421s INFO common:common.py:198 0 atoms have radius differences > 0 421s INFO common:common.py:198 0 atoms have radius differences > 0.01 421s PASSED [ 68%] 421s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 68%] 421s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 68%] 421s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] 421s tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 69%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 69%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 69%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 70%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 70%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 71%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 71%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 72%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 72%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 73%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 73%] 421s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] 421s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 74%] 421s tests/io_test.py::test_read_qcd PASSED [ 74%] 421s tests/io_test.py::test_dx2cube 421s -------------------------------- live log call --------------------------------- 421s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 421s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 422s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 423s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 423s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 424s INFO io_test:io_test.py:68 No differences found in output 424s PASSED [ 74%] 424s tests/ligand_test.py::test_peoe_charges 424s -------------------------------- live log call --------------------------------- 424s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 424s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 424s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 424s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 424s PASSED [ 75%] 425s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 425s -------------------------------- live log call --------------------------------- 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 425s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 425s PASSED [ 75%] 426s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 426s -------------------------------- live log call --------------------------------- 426s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 426s PASSED [ 75%] 426s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 426s -------------------------------- live log call --------------------------------- 426s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 426s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 426s PASSED [ 75%] 426s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 426s PASSED [ 76%] 426s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 426s PASSED [ 76%] 426s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 426s -------------------------------- live log call --------------------------------- 426s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 426s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 426s PASSED [ 76%] 426s tests/ligand_test.py::test_assign_parameters[adp.mol2] 426s -------------------------------- live log call --------------------------------- 426s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 426s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 426s PASSED [ 77%] 426s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 426s PASSED [ 77%] 426s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 426s PASSED [ 77%] 426s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 426s PASSED [ 78%] 426s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 426s PASSED [ 78%] 426s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 426s PASSED [ 78%] 426s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 426s PASSED [ 79%] 426s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 426s -------------------------------- live log call --------------------------------- 426s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 426s PASSED [ 79%] 426s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 426s -------------------------------- live log call --------------------------------- 426s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 426s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 426s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 426s PASSED [ 79%] 427s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 427s -------------------------------- live log call --------------------------------- 427s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 427s PASSED [ 80%] 427s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 427s -------------------------------- live log call --------------------------------- 427s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 427s PASSED [ 80%] 427s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 427s -------------------------------- live log call --------------------------------- 427s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 427s PASSED [ 80%] 427s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 427s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 427s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 427s -------------------------------- live log call --------------------------------- 427s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 427s PASSED [ 81%] 427s tests/ligand_test.py::test_formal_charge[adp.mol2] 427s -------------------------------- live log call --------------------------------- 427s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 427s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 427s PASSED [ 81%] 427s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 427s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 427s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 427s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 427s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 427s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 427s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 427s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 427s -------------------------------- live log call --------------------------------- 427s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 427s PASSED [ 84%] 427s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 427s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 427s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 427s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 427s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 427s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 428s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 429s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 429s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 429s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 429s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 429s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 429s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 429s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 429s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 429s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 429s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 429s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 429s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 429s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 429s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 429s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 429s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 429s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 429s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 429s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 429s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 429s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 429s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 429s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 429s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 429s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 429s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 429s tests/regression_test.py::test_basic[1AFS basic local] 429s -------------------------------- live log call --------------------------------- 429s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 429s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 429s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 429s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 429s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 429s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 429s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 429s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 429s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 429s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 429s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 429s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 429s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 429s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 429s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 429s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 429s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 430s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 430s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 430s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 430s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 430s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 430s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 430s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 431s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 432s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 432s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 435s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 435s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 435s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 435s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 435s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 435s WARNING common:common.py:186 6 atoms have position differences > 0 435s INFO common:common.py:198 0 atoms have position differences > 0.01 435s INFO common:common.py:198 0 atoms have charge differences > 0 435s INFO common:common.py:198 0 atoms have charge differences > 0.01 435s INFO common:common.py:198 0 atoms have radius differences > 0 435s INFO common:common.py:198 0 atoms have radius differences > 0.01 435s PASSED [ 95%] 435s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 435s -------------------------------- live log call --------------------------------- 435s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 435s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 435s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 435s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 435s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 435s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 435s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 435s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 435s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 435s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 435s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 435s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 435s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 435s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 435s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 435s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 435s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 435s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 435s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 435s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 435s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 435s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 435s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 435s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 435s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 435s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 435s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 435s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 436s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 437s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 440s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 440s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 440s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 440s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 440s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 441s WARNING common:common.py:186 6 atoms have position differences > 0 441s INFO common:common.py:198 0 atoms have position differences > 0.01 441s INFO common:common.py:198 0 atoms have charge differences > 0 441s INFO common:common.py:198 0 atoms have charge differences > 0.01 441s INFO common:common.py:198 0 atoms have radius differences > 0 441s INFO common:common.py:198 0 atoms have radius differences > 0.01 441s PASSED [ 95%] 441s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 441s -------------------------------- live log call --------------------------------- 441s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 441s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 441s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 441s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 441s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 441s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 441s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 441s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 441s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 441s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 441s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 441s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 441s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 441s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 441s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 441s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 441s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 441s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 441s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 441s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 441s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 441s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 441s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 441s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 441s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 442s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 443s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 446s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 446s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 446s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 446s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 446s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 446s WARNING common:common.py:186 5 atoms have position differences > 0 446s INFO common:common.py:198 0 atoms have position differences > 0.01 446s INFO common:common.py:198 0 atoms have charge differences > 0 446s INFO common:common.py:198 0 atoms have charge differences > 0.01 446s INFO common:common.py:198 0 atoms have radius differences > 0 446s INFO common:common.py:198 0 atoms have radius differences > 0.01 446s PASSED [ 95%] 446s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 446s -------------------------------- live log call --------------------------------- 446s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 446s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 446s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 446s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 446s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 446s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 446s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 446s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 446s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 446s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 446s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 446s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 446s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 446s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 447s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 447s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 447s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 447s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 447s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 447s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 447s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 447s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 447s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 447s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 447s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 448s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 452s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 452s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 452s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 452s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 452s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 452s WARNING common:common.py:186 6 atoms have position differences > 0 452s INFO common:common.py:198 0 atoms have position differences > 0.01 452s INFO common:common.py:198 0 atoms have charge differences > 0 452s INFO common:common.py:198 0 atoms have charge differences > 0.01 452s INFO common:common.py:198 0 atoms have radius differences > 0 452s INFO common:common.py:198 0 atoms have radius differences > 0.01 452s PASSED [ 96%] 452s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 452s -------------------------------- live log call --------------------------------- 452s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 452s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 452s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 452s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 452s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 452s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 452s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 452s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 452s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 452s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 452s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 452s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 452s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 452s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 452s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 452s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 452s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 452s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 452s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 452s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 452s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 452s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 452s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 452s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 453s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 454s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 457s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 457s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 457s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 457s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 457s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 458s WARNING common:common.py:186 6 atoms have position differences > 0 458s INFO common:common.py:198 0 atoms have position differences > 0.01 458s INFO common:common.py:198 0 atoms have charge differences > 0 458s INFO common:common.py:198 0 atoms have charge differences > 0.01 458s INFO common:common.py:198 0 atoms have radius differences > 0 458s INFO common:common.py:198 0 atoms have radius differences > 0.01 458s PASSED [ 96%] 458s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 458s -------------------------------- live log call --------------------------------- 458s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 458s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 458s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 458s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 458s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 458s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 458s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 458s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 458s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 458s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 458s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 458s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 458s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 458s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 458s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 458s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 458s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 458s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 458s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 458s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 458s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 458s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 458s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 458s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 459s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 460s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 463s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 463s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 463s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 463s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 463s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 463s WARNING common:common.py:186 6 atoms have position differences > 0 463s INFO common:common.py:198 0 atoms have position differences > 0.01 463s INFO common:common.py:198 0 atoms have charge differences > 0 463s INFO common:common.py:198 0 atoms have charge differences > 0.01 463s INFO common:common.py:198 0 atoms have radius differences > 0 463s INFO common:common.py:198 0 atoms have radius differences > 0.01 463s PASSED [ 96%] 463s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 463s -------------------------------- live log call --------------------------------- 463s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 463s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 463s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 463s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 463s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 463s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 464s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 464s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 464s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 464s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 464s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 464s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 464s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 464s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 464s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 464s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 464s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 464s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 464s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 464s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 464s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 464s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 464s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 464s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 464s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 465s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 469s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 469s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 469s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 469s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 469s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 469s WARNING common:common.py:186 6 atoms have position differences > 0 469s INFO common:common.py:198 0 atoms have position differences > 0.01 469s INFO common:common.py:198 0 atoms have charge differences > 0 469s INFO common:common.py:198 0 atoms have charge differences > 0.01 469s INFO common:common.py:198 0 atoms have radius differences > 0 469s INFO common:common.py:198 0 atoms have radius differences > 0.01 469s PASSED [ 97%] 469s tests/regression_test.py::test_other_options[1AFS whitespace clean] 469s -------------------------------- live log call --------------------------------- 469s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 469s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 469s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 469s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 469s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 469s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 469s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 469s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 469s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 469s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 469s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 470s INFO common:common.py:198 0 atoms have position differences > 0 470s INFO common:common.py:198 0 atoms have position differences > 0.01 470s INFO common:common.py:198 0 atoms have charge differences > 0 470s INFO common:common.py:198 0 atoms have charge differences > 0.01 470s INFO common:common.py:198 0 atoms have radius differences > 0 470s INFO common:common.py:198 0 atoms have radius differences > 0.01 470s PASSED [ 97%] 470s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 470s -------------------------------- live log call --------------------------------- 470s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 470s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 470s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 470s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 470s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 470s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 470s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 470s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 470s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 470s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 470s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 470s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 470s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 470s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 470s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 470s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 470s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 470s INFO common:common.py:198 0 atoms have position differences > 0 470s INFO common:common.py:198 0 atoms have position differences > 0.01 470s INFO common:common.py:198 0 atoms have charge differences > 0 470s INFO common:common.py:198 0 atoms have charge differences > 0.01 470s INFO common:common.py:198 0 atoms have radius differences > 0 470s INFO common:common.py:198 0 atoms have radius differences > 0.01 470s PASSED [ 97%] 470s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 470s -------------------------------- live log call --------------------------------- 470s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 470s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 470s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 470s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 470s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 470s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 470s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 470s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 470s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 470s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 470s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 470s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 470s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 470s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 470s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 470s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 470s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 470s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 470s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 470s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 470s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 470s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 470s INFO common:common.py:198 0 atoms have position differences > 0 470s INFO common:common.py:198 0 atoms have position differences > 0.01 470s INFO common:common.py:198 0 atoms have charge differences > 0 470s INFO common:common.py:198 0 atoms have charge differences > 0.01 470s INFO common:common.py:198 0 atoms have radius differences > 0 470s INFO common:common.py:198 0 atoms have radius differences > 0.01 470s PASSED [ 98%] 470s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 470s -------------------------------- live log call --------------------------------- 470s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 470s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 470s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 470s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 470s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 470s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 470s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 470s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 470s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 470s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 470s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 470s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 470s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 470s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 470s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 470s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 470s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 470s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 470s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 470s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 470s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 470s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 470s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 470s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 471s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 472s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 475s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 475s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 475s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 475s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 475s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 476s WARNING common:common.py:186 6 atoms have position differences > 0 476s INFO common:common.py:198 0 atoms have position differences > 0.01 476s INFO common:common.py:198 0 atoms have charge differences > 0 476s INFO common:common.py:198 0 atoms have charge differences > 0.01 476s INFO common:common.py:198 0 atoms have radius differences > 0 476s INFO common:common.py:198 0 atoms have radius differences > 0.01 476s PASSED [ 98%] 476s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 476s -------------------------------- live log call --------------------------------- 476s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 476s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 476s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 476s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 476s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 476s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 476s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 476s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 476s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 476s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 476s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 476s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 476s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 476s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 476s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 476s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 476s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 476s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 476s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 476s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 476s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 476s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 476s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 476s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 477s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 478s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 481s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 481s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 481s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 481s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 481s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 481s WARNING common:common.py:186 6 atoms have position differences > 0 481s INFO common:common.py:198 0 atoms have position differences > 0.01 481s INFO common:common.py:198 0 atoms have charge differences > 0 481s INFO common:common.py:198 0 atoms have charge differences > 0.01 481s INFO common:common.py:198 0 atoms have radius differences > 0 481s INFO common:common.py:198 0 atoms have radius differences > 0.01 481s PASSED [ 98%] 481s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 481s -------------------------------- live log call --------------------------------- 481s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 481s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 481s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 481s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 481s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 481s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 481s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 481s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 481s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 481s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 481s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 482s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 482s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 482s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 482s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 482s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 482s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 482s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 482s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 482s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 482s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 482s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 482s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 482s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 482s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 482s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 483s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 485s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 485s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 485s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 486s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 486s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 486s WARNING common:common.py:186 6 atoms have position differences > 0 486s INFO common:common.py:198 0 atoms have position differences > 0.01 486s INFO common:common.py:198 0 atoms have charge differences > 0 486s INFO common:common.py:198 0 atoms have charge differences > 0.01 486s INFO common:common.py:198 0 atoms have radius differences > 0 486s INFO common:common.py:198 0 atoms have radius differences > 0.01 486s PASSED [ 99%] 486s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 486s -------------------------------- live log call --------------------------------- 486s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 486s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 486s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 486s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 486s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 486s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 486s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 486s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 486s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 486s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 486s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 486s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 486s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 486s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 486s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 486s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 486s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 486s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 486s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 486s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 486s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 486s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 486s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 486s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 487s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 488s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 491s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 491s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 491s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 491s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 491s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 491s WARNING common:common.py:186 6 atoms have position differences > 0 491s INFO common:common.py:198 0 atoms have position differences > 0.01 491s INFO common:common.py:198 0 atoms have charge differences > 0 491s INFO common:common.py:198 0 atoms have charge differences > 0.01 491s INFO common:common.py:198 0 atoms have radius differences > 0 491s INFO common:common.py:198 0 atoms have radius differences > 0.01 491s PASSED [ 99%] 491s tests/test_version.py::test_version_exists PASSED [ 99%] 491s tests/test_version.py::test_version PASSED [100%] 491s 491s =============================== warnings summary =============================== 491s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 491s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 491s EPOCH = datetime.datetime.utcfromtimestamp(0) 491s 491s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 491s ======= 92 passed, 220 skipped, 4 xfailed, 1 warning in 75.78s (0:01:15) ======= 492s autopkgtest [13:29:26]: test command1: -----------------------] 496s command1 PASS 496s autopkgtest [13:29:30]: test command1: - - - - - - - - - - results - - - - - - - - - - 499s autopkgtest [13:29:33]: @@@@@@@@@@@@@@@@@@@@ summary 499s installation-test PASS 499s pdb2pka-test PASS 499s command1 PASS